diff --git a/Examples/2-res-Annotate-prodigal/Genes/EXAM.1216.00002.gen b/Examples/2-res-Annotate-prodigal/Genes/EXAM.1216.00002.gen
deleted file mode 100644
index 81773f56dd99243e2da5b018480c6f36f4668672..0000000000000000000000000000000000000000
--- a/Examples/2-res-Annotate-prodigal/Genes/EXAM.1216.00002.gen
+++ /dev/null
@@ -1,141 +0,0 @@
->EXAM.1216.00002.0001b_00001 831 NA | NA | NA |  ID=1_1;partial=10;start_type=Edge;rbs_motif=None;rbs_spacer=None;gc_cont=0.578 | NA
-ATGAGAGCGCTACTGTGGCTGGTGGGTCTTGCGTTGCTGTTAACAGGCTGCGCGAGCGAAAAAGGAATTA
-TCGATGAAGAGGGATATCAGCTTGATACCCGACATCGGGCGCAGGCGGCCTATCCGCGCATTAAAGTCCT
-GGTGATTCACTATACGGCGGAAAACTTTGACGTTTCGCTGGCGACGTTAACGGGCCGCAACGTCAGTTCG
-CATTACCTGATTCCCGCAACCCCGCCATTATATGGCGGTAAACCGCGCATCTGGCAACTGGTGCCGGAAC
-AGGATCAGGCCTGGCATGCGGGCGTCAGTTTCTGGCGAGGCGCCACGCGTCTCAATGATACGTCTATTGG
-CATTGAGCTGGAAAATCGCGGCTGGCGAATGTCCGGCGGGGTGAAATCTTTCGCGCCGTTTGAATCCGCG
-CAAATTCAGGCATTGATTCCGTTAGCGAAGGACATTATCGCGCGCTATGACATCAAACCGCAGAATGTGG
-TGGCCCATGCGGATATCGCGCCGCAGCGTAAAGACGATCCCGGCCCGCGCTTCCCGTGGCGCGAGCTGGC
-GGCACAGGGGATTGGCGCCTGGCCTGACGCCCAGCGTGTGGCGTTTTATCTGGCTGGACGCGCGCCGTAT
-ACGCCAGTCGATACCGCAACGGTGCTTGCGTTACTCTCGCGCTATGGCTATGAAGTCAAAGCCGATATGA
-CGGCGCGCGAGCAACAGCGGGTGATTATGGCGTTCCAGATGCACTTCCGTCCGGCGCAATGGAACGGTAT
-CGCAGATGCCGAAACGCAGGCGATTGCCGAAGCATTACTGGAGAAGTACGGCCAGGATTAA
->EXAM.1216.00002.0001i_00002 831 NA | NA | NA |  ID=1_2;partial=00;start_type=ATG;rbs_motif=AGGAG/GGAGG;rbs_spacer=11-12bp;gc_cont=0.578 | NA
-ATGAGAGCGCTACTGTGGCTGGTGGGTCTTGCGTTGCTGTTAACAGGCTGCGCGAGCGAAAAAGGAATTA
-TCGATGAAGAGGGATATCAGCTTGATACCCGACATCGGGCGCAGGCGGCCTATCCGCGCATTAAAGTCCT
-GGTGATTCACTATACGGCGGAAAACTTTGACGTTTCGCTGGCGACGTTAACGGGCCGCAACGTCAGTTCG
-CATTACCTGATTCCCGCAACCCCGCCATTATATGGCGGTAAACCGCGCATCTGGCAACTGGTGCCGGAAC
-AGGATCAGGCCTGGCATGCGGGCGTCAGTTTCTGGCGAGGCGCCACGCGTCTCAATGATACGTCTATTGG
-CATTGAGCTGGAAAATCGCGGCTGGCGAATGTCCGGCGGGGTGAAATCTTTCGCGCCGTTTGAATCCGCG
-CAAATTCAGGCATTGATTCCGTTAGCGAAGGACATTATCGCGCGCTATGACATCAAACCGCAGAATGTGG
-TGGCCCATGCGGATATCGCGCCGCAGCGTAAAGACGATCCCGGCCCGCGCTTCCCGTGGCGCGAGCTGGC
-GGCACAGGGGATTGGCGCCTGGCCTGACGCCCAGCGTGTGGCGTTTTATCTGGCTGGACGCGCGCCGTAT
-ACGCCAGTCGATACCGCAACGGTGCTTGCGTTACTCTCGCGCTATGGCTATGAAGTCAAAGCCGATATGA
-CGGCGCGCGAGCAACAGCGGGTGATTATGGCGTTCCAGATGCACTTCCGTCCGGCGCAATGGAACGGTAT
-CGCAGATGCCGAAACGCAGGCGATTGCCGAAGCATTACTGGAGAAGTACGGCCAGGATTAA
->EXAM.1216.00002.0001i_00003 474 NA | NA | NA |  ID=1_3;partial=00;start_type=ATG;rbs_motif=GGA/GAG/AGG;rbs_spacer=11-12bp;gc_cont=0.544 | NA
-ATGCCGAAACGCAGGCGATTGCCGAAGCATTACTGGAGAAGTACGGCCAGGATTAACAGGGCGCGGTATC
-GCGAGGACTCTCTCTTCGAGGACATGCCGCACTTTATTGCTGAATGTACTGAAAATATTCGCGAGCAGGC
-TGATTTACCCGGCCTGTTCAGCAAGGTAAACGAGGCGCTGGCCGCCAGCGGGATTTTCCCCATCGGCGGT
-ATCCGCAGTCGCGCCCACTGGCTGGATACCTGGCAGATGGCTGACGGTAAGCATGATTACGCGTTTGTGC
-ATATGACGCTGAAAATCGGCGCCGGGCGCAGCCTGGAGAGCCGTCAGGAAGTCGGCGAAATGCTGTTCGG
-GCTGATTAAAGCCCACTTCGCCGACCTGATGGAGAACCGCTATCTGGCGCTGTCGTTTGAGATTGCCGAG
-TTACATCCAACGCTCAATTACAAACAAAACAACGTACACGCGTTATTTAAATAG
->EXAM.1216.00002.0001i_00004 225 NA | NA | NA |  ID=1_4;partial=00;start_type=ATG;rbs_motif=GGA/GAG/AGG;rbs_spacer=11-12bp;gc_cont=0.542 | NA
-ATGAGCGCGCTATTTCTGGCCATCCCGTTAACCATTTTTGTGTTGTTTGTGTTACCGATTTGGCTGTGGC
-TGCATTACAGCAACCGCGCCGGTCGGGGAGAACTGTCGCAAAGCGAGCAGCAACGCTTACTGCAACTCAC
-AGACGACGCGCAACGTATGCGCGAGCGCATTCAGGCGCTGGAAGACATTCTTGATGCAGAGCATCCGAAC
-TGGAGAGAGCGCTAA
->EXAM.1216.00002.0001i_00005 1404 NA | NA | NA |  ID=1_5;partial=00;start_type=ATG;rbs_motif=AGGAG/GGAGG;rbs_spacer=11-12bp;gc_cont=0.513 | NA
-ATGCCCGCGACTAAATTCTCCCGACGTACCCTCCTGACGGCAGGTTCTGCGCTTGCTGTTCTTCCTTTCC
-TGCGCGCCTTGCCGGTACAGGCGCGTGAACCTCGCGAGACCGTCGATATTAAGGATTATCCGGCGGATGA
-CGGTATCGCCTCGTTCAAACAGGCCTTCGCCGACGGACAGACCGTGGTCGTACCGCCAGGATGGGTGTGT
-GAAAATATCAATGCGGCGATAACGATTCCGGCGGGAAAAACGCTGCGGGTACAGGGCGCGGTGCGTGGGA
-ATGGCCGGGGACGGTTTATTTTGCAGGACGGGTGTCAGGTGGTGGGGGAGCAGGGCGGCAGTCTGCACAA
-TGTGACGCTGGATGTTCGCGGGTCGGACTGTGTGATTAAAGGCGTGGCGATGAGCGGCTTTGGCCCCGTC
-GCGCAAATTTTCATCGGTGGTAAGGAACCGCAGGTGATGCGTAATCTCATTATCGATGACATCACCGTTA
-CCCACGCCAACTACGCCATTCTCCGCCAGGGATTTCATAACCAAATGGACGGCGCGAGGATTACGCATAG
-CCGCTTTAGCGATTTACAGGGGGACGCCATTGAGTGGAATGTCGCGATTCACGACCGCGATATCCTGATT
-TCCGATCATGTCATCGAACGCATTGATTGTACCAATGGCAAAATCAACTGGGGGATCGGCATCGGGCTGG
-CGGGTAGCACCTATGACAACAGTTATCCTGAAGACCAGGCAGTAAAAAACTTTGTGGTGGCCAATATTAC
-CGGATCTGATTGCCGACAGCTTGTGCACGTAGAAAATGGCAAACATTTCGTCATTCGCAATGTCAAAGCC
-AAAAACATCACGCCCGATTTCAGTAAAAATGCGGGTATTGATAACGCAACGATCGCAATTTATGGCTGTG
-ATAATTTCGTCATTGATAATATTGATATGACGAATAGTGCCGGGATGCTCATCGGCTATGGCGTCGTTAA
-AGGAAAATACCTGTCAATTCCGCAAAACTTTAAATTAAACGCTATTCGGTTGGATAATCGCCAGGTTGCT
-TATAAATTACGCGGCATTCAAATTTCCTCCGGCAACACCCCCTCTTTTGTCGCCATCACCAATGTACGGA
-TGACGCGTGCTACGCTGGAACTGCATAATCAACCGCAGCACCTCTTCCTGCGTAATATCAACGTGATGCA
-AACTTCAGCGATTGGCCCGGCGTTAAAAATGCATTTCGATTTGCGTAAAGATGTCCGTGGTCAATTTATG
-GCCCGCCAGGACACGCTGCTTTCCCTCGCTAATGTTCATGCCATCAATGAAAACGGGCAGAGTTCCGTGG
-ATATCGACAGGATTAATCACCAAACCGTGAATGTCGAAGCAGTGAATTTTTCGCTGCCGAAGCGGGGAGG
-GTAA
->EXAM.1216.00002.0001i_00006 774 NA | NA | NA |  ID=1_6;partial=00;start_type=ATG;rbs_motif=GGAG/GAGG;rbs_spacer=5-10bp;gc_cont=0.527 | NA
-ATGTCAGAAAATAAATTACACGTTATCGATTTGCACAAACGCTACGGCGGTCATGAAGTGCTGAAAGGGG
-TATCGCTGCAGGCCCGCGCCGGAGATGTGATTAGCATCATCGGCTCGTCCGGCTCCGGTAAAAGCACTTT
-TTTGCGCTGTATTAACTTCCTCGAAAAACCGAGCGAAGACGCGATTATCGTGAACGGTCAGAACATTAAT
-CTGGTGCGCGACAAAGACGGGCAGCTCAAAGTGGCGGATAAAAATCAGCTACGCTTGTTGCGTACCCGCC
-TGACGATGGTGTTTCAGCACTTTAACCTCTGGAGCCACATGACGGTGCTGGAAAATGTGATGGAAGCGCC
-GATTCAGGTACTGGGATTAAGCAAGCACGACGCGCGCGAGCGGGCGTTGAAATATCTGGCGAAGGTGGGG
-ATTGATGAGCGCGCTCAGGGCAAATATCCCGTTCATCTCTCCGGTGGCCAACAGCAGCGCGTTTCTATTG
-CGCGCGCGCTGGCGATGGAACCTGACGTTTTACTGTTCGATGAACCCACTTCGGCGCTCGATCCTGAACT
-GGTCGGCGAAGTGTTGCGCATCATGCAACAACTGGCGGAAGAAGGCAAAACGATGGTGGTGGTCACGCAT
-GAAATGGGCTTCGTTCGCCATGTCTCTTCGCACGTTATTTTTCTGCATCAGGGGAAAATTGAAGAAGAGG
-GCGATCCGGAGCAGGTGTTCGGCAATCCGCAAAGCCCGCGTTTACAGCAATTCCTGAAAGGCTCGCTGAA
-ATAA
->EXAM.1216.00002.0001i_00007 792 NA | NA | NA |  ID=1_7;partial=00;start_type=ATG;rbs_motif=None;rbs_spacer=None;gc_cont=0.537 | NA
-ATGCGCGCGATATATCGGCGATGCGTGTTTATTGGCATCGTTAGCCTGTTTCCTGAAATGTTCCGCGCAA
-TTACCGATTACGGGGTAACTGGCCGGGCAGTAAAAAATGGCCTGCTGAACATCCAAAGCTGGAGTCCTCG
-CGACTTCACGCATGACCGGCACCGTACCGTGGACGATCGTCCTTACGGCGGCGGACCAGGGATGTTAATG
-ATGGTGCAACCCTTGCGGGACGCCATTCACGCAGCAAAAGCCGCGGCAGGTGAAGGCGCTAAAGTGATTT
-ATCTGTCGCCTCAGGGACGCAAGCTTGATCAAGCGGGCGTTAGCGAGCTGGCCACGAATCAGAAGCTTAT
-TCTGGTGTGTGGTCGCTACGAAGGCGTAGATGAGCGCGTAATTCAGACCGAAATTGACGAAGAATGGTCA
-ATTGGCGATTACGTTCTCAGCGGTGGCGAACTACCGGCAATGACGCTGATTGACTCCGTCGCCCGGTTTA
-TACCGGGAGTTCTGGGGCATGAAGCATCAGCAATCGAAGATTCGTTTGCTGATGGGTTGCTGGATTGTCC
-GCACTATACGCGCCCTGAAGTGTTAGAGGGGATGGAAGTACCGCCAGTATTGCTGTCGGGAAACCATGCT
-GAGATACGTCGCTGGCGTTTGAAACAGTCGCTGGGCCGAACCTGGCTTAGAAGACCTGAACTTCTGGAAA
-ACCTGGCTCTGACTGAAGAGCAAGCAAGGTTGCTGGCGGAGTTCAAAACAGAACACGCACAACAGCAGCA
-TAAACATGATGGGATGGCATAG
->EXAM.1216.00002.0001b_00008 288 NA | NA | NA |  ID=1_8;partial=00;start_type=ATG;rbs_motif=AGGAG;rbs_spacer=5-10bp;gc_cont=0.469 | NA
-ATGAATAATCATTTTGGGAAAGGGTTAATGGCCGGGTTGCACGCGCCATATGCATATAGCGCGCATCATG
-CGGTGAATTTCTGTTCTGAGTATAAACGTGGCTTTGTATTGGGTTTTACACACCGTATGTTCGAAAAGAC
-CGGCGATCGTCAACTTAGCGCGTGGGAGGCTGGAATTCTGACGCGTCGCTATGGTCTGGATAAAGAAATG
-GTGATGGATTTCTTTAAAGAGAATCATTCCGGGATGGCGGTTCGCTTCTTTATGGCCGGTTATCGACTCG
-AAGGTTGA
->EXAM.1216.00002.0002b_00009 582 NA | NA | NA |  ID=2_1;partial=10;start_type=Edge;rbs_motif=None;rbs_spacer=None;gc_cont=0.546 | NA
-ATGTCTACGCTTCTCTATTTGCACGGATTCAACAGTTCCCCTCGCTCGGCAAAAGCGTGCCAGCTAAAAA
-ACTGGCTGGCGGAGCGTCATCCGCATGTTGAGATGATCGTCCCTCAACTACCGCCGTATCCTGCCGATGC
-GGCGGAGTTGCTGGAGTCTCTCGTGCTTGAGCATGGCGGTGCGCCATTAGGGCTGGTAGGATCGTCGCTG
-GGTGGTTATTACGCCACCTGGCTGTCGCAATGTTTTATGCTGCCGGCTGTGGTGGTGAATCCCGCCGTGC
-GGCCCTTTGAATTACTGACCGACTATCTCGGTCAGAACGAGAACCCCTACACCGGGCAGCAATATGTGCT
-AGAGTCTCGCCATATTTATGATCTTAAAGTCATGCAGATTGACCCGCTGGAAGCGCCGGACCTGATCTGG
-CTACTGCAACAGACGGGCGATGAAGTGCTGGATTACCGCCAGGCGGTGGCATATTACGCCTCCTGCCGTC
-AGACAGTGACCGAGGGTGGTAATCACGCATTCACGGGCTTCGAAGATTATTTCAACCAGATTGTCGATTT
-TCTTGGACTGCACAGTTGCTGA
->EXAM.1216.00002.0002b_00010 1308 NA | NA | NA |  ID=2_2;partial=00;start_type=ATG;rbs_motif=None;rbs_spacer=None;gc_cont=0.520 | NA
-ATGATTGACCCTATTTTTGCGTCCTGTACGCTAATTGCCGTCTTTGTTGTTTTACTGGCCATGGGCGCGC
-CTATCGGGATCTGCATCGTTATCGCCTCTTTCAGCACCATGATGCTGGTACTGCCTTTCGATATTTCGAT
-GTTCGCCACCGCGCAAAAAATGTTCTCCAGCCTGGACAGTTTTGCCTTGCTGGCCGTGCCGTTCTTCGTT
-TTGTCCGGGGTGATCATGAATAGCGGGGGAATTGCCGCCCGGCTGATCAATTTTGCCAAACTGTTTACTG
-GCAAACTGCCCGGTTCGCTCTCTTATACCAACATCGTCGGCAATATGATGTTCGGTGCAATTTCCGGATC
-GGCAATTGCCGCCTCAACCTCCATCGGCGGCGTGATGGTGCCGATGAGCGCGCGCGAAGGTTACGATCGC
-GGCTTTGCGGCCGCGGTGAATATCGCCTCCGCGCCGACGGGAATGTTAATTCCGCCCACCACGGCTTTTA
-TCCTTTATGCGCTGGCAAGCGGGGGAACATCGATTGCCGCTCTGTTCGCCGGCGGTCTGGTCGCGGGAGT
-GCTGTGGGGCGTTGGCTGTATGCTGGTCACGCTGGTAGTCGCTAAGCGTCGAAATTATCGGGTTTTCTTC
-ACCGTCCAAAAAGGCATGGCGCTAAAAGTTGCCGTTGAGGCCATTCCCAGCCTGTTACTGATCGTGATTA
-TCGTCGGCGGCATTGTGCAGGGGATTTTCACCGCCATTGAAGCCTCCGCGATTGCCGTGGTGTATACGTT
-ATTGCTGACGATGGTGTTTTACCGCACGCTGAAAATTAAGGATTTGCCTTCGATTTTGCTCCAGACAGTG
-GTAATGACCGGGGTCATCATGTTCCTGCTGGCAACCTCTTCGGCGATGTCCTTCTCAATGTCGATCACCA
-ATATTCCTGCGGCGCTGAGCGATATGATCCTCGGTATTTCCGCCAATAAACTGGTTATCCTGTTAGTCAT
-TACCGTCTTTTTGTTGATTATCGGCGCATTTATGGATATCGGTCCGGCCATTCTGATTTTTACCCCGATT
-CTGCTGCCGATCATGGCTAAACTGGGCGTCGATCCGGTGCATTTGGGCATTATCATGATCTATAACCTGG
-CGATTGGCACCATTACGCCGCCAGTTGGCAGTGGTTTATATGTCGGGGCGAGCGTCGGTAAGGTCAAAGT
-TGAGGAAGTGATTAAACCGTTGCTGCCTTTTTACGGCGCGATTATCGGCGTTCTGTTATTAATTACCTAC
-ATTCCGGAAATCATACTGTTCTTACCCCGTCTACTGGGCATCATGTAA
->EXAM.1216.00002.0003b_00011 279 NA | NA | NA |  ID=3_1;partial=10;start_type=Edge;rbs_motif=None;rbs_spacer=None;gc_cont=0.355 | NA
-ACAGGGCTTAGAGGCGCTATGGCAATGATAATTAATGGGAAATTAATTAAAGCAAAAGACTTAGCTAAGG
-CTGCAGGTGTATCTCGTTCAACAGTGATTAAATATTACGGCATTAGCCGTGAGAATTACGAAAGGGTAGC
-AACTGAAAGAAGGAAGCTTGCTTTTGAACTAAGAGCATCAGGTTTAAAATGGAAAGAAGTTGCTGAAAAA
-ATGAACACGACAAAATATAGCGCAATTGCATATTATAGACGATATTTAGCATTAGAGAAAAACAAATAA
->EXAM.1216.00002.0003b_00012 780 NA | NA | NA |  ID=3_2;partial=00;start_type=ATG;rbs_motif=None;rbs_spacer=None;gc_cont=0.559 | NA
-ATGGTCGAACTGCAACATCAACGGCTGATGGTGCTTGCCGAACAGCTCCAGCTGGACAGTCTTATCGGCG
-CAGCGCCGGCGCTGTCGCAACAGGCGGTGGATCAGGAATGGAGCTACATGGACTTCCTGGAGCACCTGTT
-ACATGAGGAGAAACTGGCCCGGCATCAGCGTAAACAGGCGATGTACACGCGGATGGCAGCCTTCCCGGCG
-GTAAAGACGTTCGAGGAGTACGACTTCACCTTCGCCACCGGCGCTCCTCAGAAGCAAATCCAGTCGCTGC
-GATCCCTGAGCTTCATAGAGCGTAACGAAAACATCGTGTTGCTGGGGCCATCGGGCGTGGGAAAAACGCA
-TCTGGCGATAGCCATGGGCTACGAAGCAGTACGGGCGGGCATCAAGGTTCGCTTCACAACAGCAGCGGAC
-CTGCTGCTACAGCTGTCCACTTCACAGCGTCAGGGCCGTTACAAAACGACTCTCAATCGTGGTGTCATGG
-CCCCGAAGCTGCTTATCATCGATGAAATAGGTTATCTGCCGTTCAGTCAGGAGGAAGCCAAGCTGTTCTT
-CCAGGTCATCGCCAAACGTTACGAGAAGAGCGCGATGATCCTGACCTCCAACCTGCCGTTCGGGCAGTGG
-GATCAGACGTTCGCCGGTGATGCAGCGCTGACATCGGCGATGCTGGACCGGATCTTACATCACTCACACG
-TCGTGCAAATAAAAGGGGAAAGCTATCGACTGAAGCAGAAACGAAAGGCCGGGGTTATAGCTGAAGCTAA
-TCCTGAGTAA
diff --git a/Examples/2-res-Annotate-prodigal/Genes/EXAM.1219.00001.gen b/Examples/2-res-Annotate-prodigal/Genes/EXAM.1219.00001.gen
deleted file mode 100644
index 599ce47397e67c0148d1210135847c17c01ae0df..0000000000000000000000000000000000000000
--- a/Examples/2-res-Annotate-prodigal/Genes/EXAM.1219.00001.gen
+++ /dev/null
@@ -1,148 +0,0 @@
->EXAM.1219.00001.0001b_00001 1668 NA | NA | NA |  ID=1_1;partial=00;start_type=ATG;rbs_motif=None;rbs_spacer=None;gc_cont=0.534 | NA
-ATGAGTGAGGCTGAAGCCCGCCCGACTAACTTTATTCGTCAGATTATTGATGAAGATCTGGCGAGTGGTA
-AACATACCACTGTCCATACCCGTTTTCCGCCGGAGCCGAATGGCTATCTGCATATCGGCCACGCGAAATC
-TATCTGCCTGAACTTTGGCATCGCGCAAGATTATCAGGGCCAGTGCAACCTGCGTTTCGATGACACCAAC
-CCGGTAAAAGAAGATATCGAGTACGTTGATTCGATCAAAAACGACGTCGAGTGGTTAGGCTTTCACTGGT
-CTGGCGATATTCGCTACTCCTCCGATTACTTTGACCAACTGCACGCCTATGCGGTCGAGCTAATCAATAA
-AGGCCTGGCCTATGTTGATGAGCTGACGCCGGAGCAGATCCGTGAATACCGCGGTACGCTGACCGCGCCG
-GGTAAAAACAGCCCGTTCCGCGATCGCAGCGTCGAAGAGAACCTCGCGCTATTTGAAAAAATGCGTACCG
-GCGGTTTTGAAGAGGGTAAAGCCTGTCTGCGCGCTAAAATCGACATGGCGTCGCCGTTTATCGTGATGCG
-CGATCCGGTGCTGTATCGCATTAAATTCGCCGAGCATCATCAGACTGGCAACAAGTGGTGCATCTATCCG
-ATGTACGACTTTACTCACTGCATCAGCGATGCGCTGGAAGGCATTACTCATTCTCTGTGTACGCTGGAGT
-TCCAGGATAACCGTCGTCTGTACGACTGGGTGCTGGACAACATCACCATTCCGGTTCACCCGCGCCAGTA
-CGAATTCTCGCGCCTGAATCTGGAATACACCGTGATGTCCAAGCGTAAGCTGAACCTGCTGGTGACCGAC
-AAACACGTCGAAGGTTGGGACGATCCGCGTATGCCGACTATTTCCGGTCTGCGCCGTCGCGGCTATACCG
-CGGCTTCTATTCGTGAGTTCTGCAAACGCATCGGCGTCACCAAGCAGGACAACACTATTGAGATGGCGTC
-GCTGGAATCCTGCATTCGCGAAGATCTGAACGAAAACGCGCCGCGCGCGATGGCGGTAATCGATCCGGTA
-AAACTGGTTATCGAAAATTACCCGCAGGGTGAGAGCGAAATGGTTACCATGCCTAACCATCCGAATAAAC
-CGGAGATGGGCAGCCGTGAAGTGCCGTTTAGCGGTGAGATCTGGATCGATCGCGCAGATTTCCGCGAAGA
-AGCGAACAAACAGTACAAACGTCTGGTGATGGGCAAAGAAGTGCGTCTGCGTAATGCCTACGTCATTAAA
-GCGGAGCGCGTAGAGAAGGATGCCGAAGGGAATATCACCACCATCTTCTGTACCTATGATGCTGATACGC
-TGAGTAAAGATCCGGCTGACGGGCGTAAAGTGAAAGGCGTAATCCACTGGGTTAGCGCAGCACATGCGCT
-GCCGATTGAAATTCGTCTCTACGACCGTCTGTTCAGCGTGCCGAATCCGGGCGCCGCGGAGGACTTCCTG
-TCTGTTATCAACCCCGAATCATTAGTGATTAAGCAGGGGTATGGCGAGCCGTCGCTGAAAGCGGCGGTAG
-CAGGAAAAGCTTTCCAGTTTGAACGTGAAGGCTACTTCTGCCTCGACAGCCGCTATGCAACGGCCGATAA
-GCTGGTCTTTAACCGCACCGTGGGCCTGCGTGATACCTGGGCGAAAGCGGGCGAGTAA
->EXAM.1219.00001.0001b_00002 831 NA | NA | NA |  ID=1_2;partial=00;start_type=ATG;rbs_motif=AGGAGG;rbs_spacer=5-10bp;gc_cont=0.570 | NA
-ATGAAAGCGCTACTGTGGCTGGTGGGTCTCGCGTTGCTGTTAACAGGCTGCGCGAGCGAAAAAGGAATTA
-TCGATAAAGAGGGATATCAGCTTGATACCCGACATCGGGCGCAGGCGGCCTATCCGCGCATTAAAGTCCT
-GGTGATTCACTATACGGCGGAAAACTTTGACGTTTCGCTGGCGACGTTAACGGGTCGCAACGTCAGTTCG
-CATTACCTGATTCCCGCAACCCCGCCATTATATGGCGGTAAACCGCGCATCTGGCAACTGGTGCCGGAAC
-AGGATCAGGCCTGGCATGCGGGCGTCAGTTTCTGGCGAGGCGCCACGCGTCTCAATGATACGTCTATTGG
-CATTGAGCTGGAAAATCGTGGTTGGCGAATGTCCGGCGGGGTGAAATCTTTCGCGCCGTTTGAATCCGCG
-CAAATTCAGGCATTGATTCCGTTAGCGAAGGATATTATCGCGCGCTATAACATCAAACCGCAGAATGTGG
-TGGCCCATGCGGATATCGCGCCGCAGCGTAAAGACGATCCCGGCCCGCGCTTCCCGTGGCGCGAGCTGGC
-GGCGCAGGGGATTAGCGCCTGGCCTGACGCCCAGCGTGTGGCGTTTTATCTGGCTGGACGCGCGCCGTAT
-ACGCCAGTCGATACCGCAACGGTGCTTGCGTTACTCTCGCGCTATGGCTATGAAGTCAAAGCCGATATGA
-CGGCACGCGAGCAGCAGCGGGTGATTATGGCGTTCCAGATGCACTTCCGTCCGGCGCAATGGAACGGTAT
-CGCAGATGCCGAAACGCAGGCGATTGCCGAAGCATTACTGGAGAAGTACGGCCAGGATTAA
->EXAM.1219.00001.0002b_00003 381 NA | NA | NA |  ID=2_1;partial=00;start_type=ATG;rbs_motif=None;rbs_spacer=None;gc_cont=0.538 | NA
-ATGCCGCACTTTATTGCTGAATGTACTGAAAATATTCGCGAGCAGGCTGATTTACCCGGCCTGTTCAGCA
-AGGTAAACGAGGCGCTGGCCGCCAGCGGGATTTTCCCCATCGGCGGTATCCGCAGTCGCGCCCACTGGCT
-GGATACCTGGCAGATGGCTGACGGTAAGCATGATTACGCGTTTGTGCATATGACGCTGAAAATCGGCGCC
-GGGCGCAGCCTGGAGAGCCGTCAGGAAGTTGGCGAAATGCTGTTTGGGCTGATTAAAGCCCACTTCGCCG
-ACCTGATGGAGAACCGCTATCTGGCGCTGTCGTTTGAGATTGCCGAGCTACATCCGACGCTCAATTACAA
-ACAAAACAACGTACACGCGTTATTTAAATAG
->EXAM.1219.00001.0002i_00004 1410 NA | NA | NA |  ID=2_2;partial=00;start_type=ATG;rbs_motif=GGA/GAG/AGG;rbs_spacer=5-10bp;gc_cont=0.512 | NA
-ATGAGCATGCCCGCGACTAAATTCTCCCGACGTACCCTCCTGACGGCAGGTTCTGCGCTTGCTGTTCTTC
-CTTTTCTGCGCGCCTTGCCGGTACAGGCGCGTGAACCTCGCGAGACCGTCGATATTAAGGATTATCCGGC
-GGATGACGGTATCGCCTCGTTCAAACAGGCCTTCGCCGACGGACAGACCGTGGTCGTACCGCCAGGATGG
-GTGTGTGAAAATATCAATGCGGCGATAACGATTCCGGCGGGAAAAACGCTGCGGGTACAGGGCGCGGTGC
-GTGGGAATGGCCGGGGACGGTTTATTTTGCAGGACGGGTGTCAGGTGGTGGGGGAGCAGGGCGGCAGTCT
-GCACAATGTGACGCTGGATGTTCGCGGGTCGGACTGTGTGATTAAAGGCGTGGCGATGAGCGGCTTTGGC
-CCCGTCGCGCAAATTTTCATCGGTGGTAAGGAACCGCAGGTGATGCGTAATCTCATTATCGATGACATCA
-CCGTTACCCACGCCAACTACGCCATTCTCCGCCAGGGATTTCATAACCAAATGGATGGCGCGCGGATTAC
-GCATAGCCGCTTTAGCGATTTACAGGGGGACGCCATTGAGTGGAATGTCGCGATTCACGACCGCGACATC
-CTGATTTCCGATCATGTCATCGAACGCATTAATTGTACCAATGGCAAAATCAACTGGGGGATCGGCATCG
-GGCTGGCGGGTAGCACCTATGACAACAGTTATCCTGAAGACCAGGCAGTAAAAAACTTTGTGGTGGCCAA
-TATTACCGGATCTGATTGCCGACAGCTTGTGCACGTAGAAAATGGCAAACATTTCGTCATTCGCAATGTC
-AAAGCCAAAAACATCACGCCCGGTTTCAGTAAAAATGCGGGTATTGATAACGCAACGATCGCAATTTATG
-GCTGTGATAATTTCGTCATTGATAATATTGATATGACGAATAGTGCCGGGATGCTCATCGGCTATGGCGT
-CGTTAAAGGAAAATACCTGTCAATTCCGCAAAACTTTAAATTAAACGCTATTCGGTTGGATAATCGCCAG
-GTTGCTTATAAATTACGCGGCATTCAAATTTCCTCCGGCAACACCCCCTCTTTTGTCGCCATCACCAATG
-TACGGATGACGCGTGCTACGCTGGAACTGCATAATCAACCGCAGCACCTCTTTCTGCGCAATATCAACGT
-GATGCAAACTTCAGCGATTGGCCCGGCGTTAAAAATGCATTTCGATTTGCGTAAAGATGTACGTGGTCAA
-TTTATGGCCCGCCAGGACACGCTGCTTTCCCTCGCTAATGTTCATGCCATCAATGAAAACGGGCAGAGTT
-CCGTGGATATCGACAGGATTAATCACCAAACCGTGAATGTCGAAGCAGTGAATTTTTCGCTGCCGAAGCG
-GGGAGGGTAA
->EXAM.1219.00001.0002i_00005 774 NA | NA | NA |  ID=2_3;partial=00;start_type=ATG;rbs_motif=None;rbs_spacer=None;gc_cont=0.531 | NA
-ATGTCAGAAAATAAATTACACGTTATCGATTTGCACAAACGCTACGGCGGTCATGAAGTGCTGAAAGGGG
-TATCGCTGCAGGCCCGCGCCGGAGATGTGATTAGCATCATCGGCTCGTCCGGCTCCGGTAAAAGCACTTT
-TTTGCGCTGTATTAACTTCCTCGAAAAACCGAGCGAAGGCGCGATTATCGTGAACGGTCAGAACATTAAT
-CTGGTGCGCGACAAAGATGGGCAGCTCAAAGTGGCGGATAAAAATCAGCTACGCTTGTTGCGTACCCGCC
-TGACGATGGTGTTTCAGCACTTCAACCTCTGGAGCCACATGACGGTGCTGGAAAATGTGATGGAAGCGCC
-GATTCAGGTACTGGGATTAAGCAAGCACGACGCGCGCGAGCGGGCGTTGAAATATCTGGCGAAGGTGGGG
-ATTGATGAGCGCGCTCAGGGCAAATATCCCGTCCATCTCTCCGGCGGCCAACAGCAGCGCGTTTCTATTG
-CGCGCGCGCTGGCGATGGAACCTGACGTTTTACTGTTCGATGAACCCACATCGGCGCTCGATCCTGAACT
-GGTCGGCGAAGTGTTGCGCATCATGCAACAACTGGCGGAAGAAGGCAAAACGATGGTGGTGGTCACGCAT
-GAAATGGGCTTCGCTCGCCATGTCTCTTCGCACGTTATTTTTCTGCATCAGGGGAAAATTGAAGAAGAGG
-GTGATCCGGAGCAGGTGTTCGGCAATCCGCAAAGCCCGCGTTTACAGCAATTCCTGAAAGGCTCGCTGAA
-ATAA
->EXAM.1219.00001.0002i_00006 735 NA | NA | NA |  ID=2_4;partial=00;start_type=ATG;rbs_motif=None;rbs_spacer=None;gc_cont=0.547 | NA
-ATGTTCCGCGCAATTACCGATTACGGGGTAACTGGCCGGGCAGTAAAAAAAGGCCTGCTGAACATCCAAA
-GCTGGAGTCCTCGCGACTTCGCGCATGACCGGCACCGTACCGTGGACGACCGTCCTTACGGCGGCGGACC
-GGGGATGTTAATGATGGTGCAACCCTTGCGGGACGCCATTCACGCAGCAAAAGCCGCGGCAGGTGAAGGC
-GCTAAAGTGATTTATCTGTCGCCTCAGGGACGCAAGCTTGATCAAGCGGGCGTTAGCGAGCTGGCCACGA
-ATCAGAAGCTTATTCTGGTGTGTGGTCGCTACGAAGGCGTAGATGAGCGCGTAATTCAGACCGAAATTGA
-CGAAGAATGGTCAATTGGCGATTACGTTCTCAGCGGTGGCGAACTACCGGCAATGACGCTGATTGACTCC
-GTCGCCCGGTTTATACCGGGGGTTCTGGGGCATGAGGCATCAGCAATCGAAGATTCGTTTGCTGATGGGT
-TGCTGGATTGTCCGCACTATACGCGCCCTGAAGTGTTAGAGGGGATGGAAGTACCGCCAGTATTGCTGTC
-GGGAAACCATGCTGAGATACGTCGCTGGCGTTTGAAACAGTCGCTGGGCCGAACCTGGCTTAGAAGACCT
-GAACTTCTGGAAAACCTGGCTCTGACTGAAGAGCAAGCAAGGTTGCTGGCGGAGTTCAAAACAGAACACG
-CACAACAGCAGCATAAACATGATGGGATGGCATAG
->EXAM.1219.00001.0002i_00007 828 NA | NA | NA |  ID=2_5;partial=00;start_type=ATG;rbs_motif=AGxAG;rbs_spacer=5-10bp;gc_cont=0.541 | NA
-ATGATGGGATGGCATAGCCGTCATATGGGCTCTCAGAGGAGACGCGCTAATGCGCAGTACGTGTTTATTG
-GCATAGTTAGCCTGTTTCCTGAAATGTTCCGCGCAATTACCGATTACGGGGTAACTGGCCGGGCAGTAAA
-AAAAGGCCTGCTGAACATCCAAAGCTGGAGTCCTCGCGACTTCGCGCATGACCGGCACCGTACCGTGGAC
-GACCGTCCTTACGGCGGCGGACCGGGGATGTTAATGATGGTGCAACCCTTGCGGGACGCCATTCACGCAG
-CAAAAGCCGCGGCAGGTGAAGGCGCTAAAGTGATTTATCTGTCGCCTCAGGGACGCAAGCTTGATCAAGC
-GGGCGTTAGCGAGCTGGCCACGAATCAGAAGCTTATTCTGGTGTGTGGTCGCTACGAAGGCGTAGATGAG
-CGCGTAATTCAGACCGAAATTGACGAAGAATGGTCAATTGGCGATTACGTTCTCAGCGGTGGCGAACTAC
-CGGCAATGACGCTGATTGACTCCGTCGCCCGGTTTATACCGGGGGTTCTGGGGCATGAGGCATCAGCAAT
-CGAAGATTCGTTTGCTGATGGGTTGCTGGATTGTCCGCACTATACGCGCCCTGAAGTGTTAGAGGGGATG
-GAAGTACCGCCAGTATTGCTGTCGGGAAACCATGCTGAGATACGTCGCTGGCGTTTGAAACAGTCGCTGG
-GCCGAACCTGGCTTAGAAGACCTGAACTTCTGGAAAACCTGGCTCTGACTGAAGAGCAAGCAAGGTTGCT
-GGCGGAGTTCAAAACAGAACACGCACAACAGCAGCATAAACATGATGGGATGGCATAG
->EXAM.1219.00001.0002i_00008 465 NA | NA | NA |  ID=2_6;partial=00;start_type=ATG;rbs_motif=AGGA/GGAG/GAGG;rbs_spacer=11-12bp;gc_cont=0.596 | NA
-ATGAAGTTTGTTGCGCCCGAACAGGCACCGGAACAGGCGGAGGTCATCAAAAATACGCCGTTCTGGCCTG
-ATGTGGACCTGTCGGAATTTCGCAGTGTGATGCGCACTGACGGCACGGTGACGCAGCCGCGTTTAAAGCA
-GGTCGTGCTGACGGCGATCTCTGAGGTTAACGCTGAGCTGTACGACTTCCGCAACCGTCAGCAGATGCTG
-GGCTGGCGGACACTTGCTGAGGTTCCCGCAGAAATGCTGGACGGTAAAAGCGAGCGTATCCGGCACTACC
-ACAACGCTGTTTTTTGCTGGGCGCGCGCTGTGCTTAATGAGCGTTATCAGGACTATGACGCCACGGCGTC
-AGGCGTGAAGCGAGGGGAGGAGCTGGCGGAGGCCAGCGGCGATCTGTGGCGTGATGCCCGCTGGGCCATC
-AGCCGGGTGCAGGATGTACCGCACTGTACGGTGGAGCTTATCTGA
->EXAM.1219.00001.0002i_00009 261 NA | NA | NA |  ID=2_7;partial=00;start_type=ATG;rbs_motif=GGA/GAG/AGG;rbs_spacer=5-10bp;gc_cont=0.487 | NA
-ATGGCCGGGTTGCACGCGCCATATGCATATAGCGCGCATCATGCGGTGAATTTCTGTTCTGAGTATAAAC
-GTGGCTTTGTATTGGGTTTTACACACCGTATGTTCGAAAAGACCGGCGATCGTCAACTTAGCGCGTGGGA
-GGCTGGAATTCTGACGCGTCGCTATGGTCTGGATAAAGAAATGGTGATGGATTTCTTTAAAGAGAATCAT
-TCCGGGATGGCGGTTCGCTTCTTTATGGCCGGTTATCGACTCGAAGGTTGA
->EXAM.1219.00001.0002i_00010 582 NA | NA | NA |  ID=2_8;partial=00;start_type=ATG;rbs_motif=None;rbs_spacer=None;gc_cont=0.546 | NA
-ATGTCTACGCTTCTCTATTTGCACGGATTCAACAGTTCCCCTCGCTCGGCAAAAGCGTGCCAGCTAAAAA
-ACTGGCTGGCGGAGCGTCATCCGCATGTTGAGATGATCGTCCCTCAGCTGCCGCCGTATCCTGCCGATGC
-GGCGGAGTTGCTGGAATCTCTCGTGCTTGAGCATGGCGGTGCGCCATTAGGGCTGGTAGGATCGTCGCTG
-GGTGGTTATTACGCCACCTGGCTGTCGCAATGTTTTATGCTGCCGGCTGTGGTGGTGAATCCCGCCGTGC
-GGCCCTTTGAATTACTGACCGACTATCTCGGTCAGAACGAGAACCCCTACACCGGGCAGCAATATGTGCT
-AGAGTCTCGCCATATTTATGATCTTAAAGTCATGCAGATTGACCCGCTGGAAGCGCCGGACCTGATCTGG
-CTACTGCAACAGACGGGCGATGAAGTGCTGTATTACCGCCAGGCGGTGGCATATTACGCCTCCTGCCGTC
-AGACAGTGACCGAGGGTGGTAATCACGCATTCACGGGCTTCGAAGATTATTTCAACCAGATTGTCGATTT
-TCTTGGACTGCACAGTTGCTGA
->EXAM.1219.00001.0002b_00011 1308 NA | NA | NA |  ID=2_9;partial=00;start_type=ATG;rbs_motif=None;rbs_spacer=None;gc_cont=0.524 | NA
-ATGATTGACCCTATTTTTGCGTCCTGTACGCTAATTGCCGTCTTTGTTGTTTTACTGGCCATGGGCGCGC
-CTATCGGGATCTGCATCGTTATCGCCTCTTTCAGCACCATGATGCTGGTACTGCCTTTCGATATTTCGAT
-GTTCGCCACCGCGCAAAAAATGTTCTCCAGCCTGGACAGTTTTGCCTTGCTGGCCGTGCCGTTCTTCGTT
-TTGTCCGGGGTGATCATGAATAGCGGGGGAATTGCCGCCCGGCTGGTCAATTTTGCCAAACTGTTTACTG
-GCAAACTGCCCGGCTCGCTCTCTTATACCAACATCGTCGGCAATATGATGTTCGGTGCAATTTCCGGATC
-GGCGATTGCCGCCTCAACCTCCATCGGCGGCGTGATGGTGCCGATGAGCGCGCGCGAAGGTTACGATCGC
-GGCTTTGCGGCCGCGGTGAATATCGCCTCCGCGCCGACGGGAATGTTAATTCCGCCCACCACGGCTTTTA
-TCCTTTACGCGCTGGCAAGCGGGGGAACATCGATTGCCGCTCTGTTCGCCGGCGGTCTGGTCGCGGGAGT
-GCTGTGGGGCGTTGGCTGTATGCTGGTCACGCTGGTGGTCGCTAAGCGTCGAAATTATCGGGTTTTCTTC
-ACCGTCCAAAAAGGTATGGCGCTAAAAGTTGCCGTTGAGGCCATTCCCAGCCTGCTGCTGATCGTGATTA
-TTGTCGGCGGCATTGTGCAGGGGATTTTCACCGCCATTGAAGCCTCCGCGATTGCCGTGGTGTATACGTT
-ATTGCTGACGATGGTGTTTTACCGCACGCTGAAAATTAAGGATTTGCCTTCGATTTTGCTCCAGACAGTG
-GTAATGACCGGGGTCATCATGTTCCTGCTGGCAACCTCTTCGGCGATGTCCTTCTCGATGTCGATCACCA
-ATATTCCTGCGGCGCTGAGCGATATGATCCTCGGTATTTCCGCCAATAAACTGGTTATCCTGTTAGTCAT
-TACCGTCTTTTTGTTGATTATCGGCGCATTTATGGATATTGGTCCGGCCATTCTGATTTTTACCCCGATT
-CTGCTGCCAATCATGGCTAAACTGGGCGTCGATCCGGTGCATTTCGGCATTATCATGATCTATAACCTGG
-CGATTGGCACCATTACGCCGCCAGTTGGCAGTGGTTTATATGTCGGGGCGAGCGTCGGTAAGGTCAAAGT
-TGAGGAAGTGATTAAACCGTTGCTGCCTTTTTACGGCGCGATTATCGGCGTTCTGTTATTAATTACCTAC
-ATTCCGGAAATCACACTGTTCTTACCCCGTCTACTGGGCATCATGTAA
diff --git a/Examples/2-res-Annotate-prodigal/Genes/GEN2.1219.00001.gen b/Examples/2-res-Annotate-prodigal/Genes/GEN2.1219.00001.gen
deleted file mode 100644
index 201a64b5c70fc26d74ef66dc27605c6d844b9a7b..0000000000000000000000000000000000000000
--- a/Examples/2-res-Annotate-prodigal/Genes/GEN2.1219.00001.gen
+++ /dev/null
@@ -1,163 +0,0 @@
->GEN2.1219.00001.0001b_00001 774 NA | NA | NA |  ID=1_1;partial=10;start_type=Edge;rbs_motif=None;rbs_spacer=None;gc_cont=0.530 | NA
-ATGTCAGAAAATAAATTACACGTTATCGATTTGCACAAACGCTACGGCGGTCATGAAGTGCTGAAAGGGG
-TATCGCTGCAGGCCCGCGCCGGAGATGTGATTAGCATTATCGGCTCGTCCGGTTCCGGTAAAAGCACTTT
-TTTGCGCTGCATTAACTTCCTCGAAAAATCGAGCGAAGGCGCGATTATCGTGAACGGTCAGAACATTAAT
-CTGGTGCGCGACAAAGACGGGCAGCTCAAAGTGGCGGATAAAAATCAGCTACGCTTGTTGCGTACCCGCC
-TGACGATGGTGTTTCAGCACTTTAACCTCTGGAACCACATGACGGTGCTGGAAAATGTGATGGAAGCGCC
-GATTCAGGTACTGGGATTAAGCAAGCACGACGCGCGCGAGCGGGCGTTGAAATATCTGGCGAAGGTGGGG
-ATTGATGAGCGCGCTCAGGGCAAATATCCCGTCCATCTCTCCGGCGGCCAACAGCAGCGCGTTTCTATTG
-CGCGCGCGCTGGCGATGGAACCTGACGTTTTACTGTTCGATGAACCCACATCGGCGCTCGATCCTGAACT
-GGTCGGCGAAGTGTTGCGCATCATGCAACAACTGGCGGAAGAAGGCAAAACGATGGTGGTGGTCACGCAT
-GAAATGGGCTTCGCCCGCCATGTCTCTTCGCACGTGATTTTTCTGCATCAGGGGAAAATTGAAGAAGAGG
-GCAATCCGGAGCAGGTGTTCGGCAATCCGCAAAGCCCGCGTTTACAGCAATTCCTGAAAGGCTCGCTGAA
-ATAA
->GEN2.1219.00001.0001b_00002 1404 NA | NA | NA |  ID=1_2;partial=00;start_type=ATG;rbs_motif=None;rbs_spacer=None;gc_cont=0.510 | NA
-ATGCCCGCGACTAAATTCTCCCGACGTACCCTCCTGACGGCAGGTTCCGCGCTTGCTGTTCTTCCTTTTC
-TGCGCGCCTTGCCGGTACAGGCGCGTGAACCTCGCCAGACCGTCGATATTAAGGATTATCCGGCGGATGA
-CGGTATCGCCTCGTTCAAACAGGCCTTCGCCGACGGGCAGACTGTGGTCGTGCCGTCAGGATGGGTGTGT
-GAAAATATCAATGCGGCGATAACGATTCCGGCGGGAAAAACGCTGCGGATACAGGGCGCGGTGCGTGGGA
-ATGGCCGGGGACGGTTTATTTTGCTGGACGGGTGTCAGGTGGTGGGGGAGCAGGGCGGCAGTCTGCACAA
-TGTGACGCTGGATGTTCGCGGGTCGGACTGTGTGATTAAAGGCGTGACGATGAGCGGCTTTGGCCCCGTC
-GCGCAAATTTTCATCGGCGGTAAGGAACCGCAGGTGATGCGTAATCTCATTATCGATGACATCACCGTTA
-CCCACGCCAACTACGCCATTCTCCGCCAGGGATTTCATAACCAAATGGACGGCGCGCGGATTACGCATAG
-TCGCTTTAGCGATTTGCAGGGGGACGCCATTGAGTGGAATGTCGCGATTCATGACCGCGACATCCTGATT
-TCCGATCATGTCATCGAACGCATTGATTGTACCAATGGCAAAATCAACTGGGGGATCGGCATCGGGCTGG
-CGGGTAGCGCCTATGACAATAGTTATCCTGAAGACCAGGCAGTAAAAAACTTTGTGGTGGCCAATATTAC
-CGGATCTGATTGCCGACAACTGGTACACGTAGAAAATGGCAAACATTTCGTCATTCGCAATGTCAAAGCC
-AAAAACATCACGCCCGATTTCAGTAAAAATGCGGGTATTGATAACGCAACGATCGCCATTTATGGCTGTG
-ATAATTTCGTCATTGATAATATTGATATGACGAATAGTGCCGGGATGCTCATCGGCTATGGCGTCGTTAA
-AGGAAAATACCTGTCAATTCCGCAAAACTTTAAATTAAACGCTATTCGGTTGGATAATCGCCAGGTTGCT
-TATAAATTACGCGGCATTCAAATTTCCTCCGGTAACGCCCCCTCATTTGTTGCCATCACCAATGTACGGA
-TGACGCGTGCTACGCTGGAACTGCATAATCAACCGCAGCACCTCTTTTTGCGTAATATCAACGTGATGCA
-AACTTCAGCGATTGGCCCGGCGTTAAAAATGCATTTTGATTTGCGTAAAGATGTCCGTGGTCAATTTATG
-GCCCGCCAGGACACGCTGCTTTCCCTCGCTAATGTTCATGCCATCAATGAAAACGGGCAGAGTTCCGTGG
-ATATCGACAGGATTAATCACCAAACCGTGAATGTCGAAGCAGTGAATTTTTCGCTGCCGAAGCGGGGAGG
-GTAA
->GEN2.1219.00001.0002b_00003 252 NA | NA | NA |  ID=2_1;partial=10;start_type=Edge;rbs_motif=None;rbs_spacer=None;gc_cont=0.540 | NA
-CGCGATAATATAGCGCGCGCTCATAGCATGAGCGCGCTATTTCTGGCCATCCCGTTAACCATTTTTGTGT
-TGTTTGTGTTACCGATTTGGCTGTGGCTGCATTACAGCAACCGCGCCGGTCGGGGAGAACTGTCGCAAAG
-CGAGCAGCAACGCTTACTGCAACTCACAGACGACGCGCAACGTATGCGCGAGCGCATTCAGGCGCTGGAA
-GATATTCTTGATGCAGAGCATCCGAACTGGAGAGAGCGCTAA
->GEN2.1219.00001.0002i_00004 381 NA | NA | NA |  ID=2_2;partial=00;start_type=ATG;rbs_motif=None;rbs_spacer=None;gc_cont=0.530 | NA
-ATGCCGCACTTTATTGCTGAATGTACTGAAAATATTCGCGAGCAGGCTGATTTACCAAGCCTGTTCAGCA
-AGGTAAACGAGGCGCTGGCCGCCACCGGGATTTTCCCCATCGGCGGTATCCGCAGTCGCGCCCACTGGCT
-GGATACCTGGCAGATGGCTGACGGTAAGCATGATTACGCGTTTGTGCATATGACGCTGAAAATCGGCGCC
-GGGCGCAGCCTGGAGAGCCGTCAGGAAGTCGGCGAAATGCTGTTTGGGCTGATTAAAGCCCACTTCGCCG
-ACCTGATGGAGAACCGCTATCTGGCGCTGTCGTTTGAGATTGCCGAGTTACATCCAACGCTCAATTACAA
-ACAAAACAACGTACACGCGTTATTTAAATAG
->GEN2.1219.00001.0002i_00005 834 NA | NA | NA |  ID=2_3;partial=00;start_type=ATG;rbs_motif=None;rbs_spacer=None;gc_cont=0.573 | NA
-ATGATGAAAGCGCTACTGTGGCTGGTTGGTCTCGCGTTGCTGTTAACAGGCTGCGCGAGCGAAAAAGGAA
-TTATCGATAAAGAGGGATATCAGCTTGATACCCGACATCGGGCGCAGGCGGCCTATCCGCGCATTAAAGT
-CCTGGTGATTCACTATACGGCGGAAAACTTTGACGTTTCGCTGGCGACGTTAACGGGTCGCAACGTCAGT
-TCGCATTACCTGATTCCCGCAACCCCGCCATTATATGGCGGTAAACCGCGCATCTGGCAACTGGTGCCGG
-AACAGGATCAGGCTTGGCATGCGGGCGTCAGTTTCTGGCGAGGCGCCACGCGTCTCAATGATACGTCTAT
-TGGCATTGAGCTGGAAAATCGCGGCTGGCGAATGTCCGGCGGGGTGAAATCTTTCGCGCCGTTTGAATCC
-GCGCAAATTCAGGCATTGATCCCGTTAGCGAAGGACATTATCGCGCGCTATGACATCAAACCGCAGAATG
-TGGTGGCCCATGCGGATATCGCGCCGCAGCGTAAAGACGATCCCGGCCCGCGCTTCCCGTGGCGCGAGCT
-GGCGGCACAGGGGATTGGCGCCTGGCCTGACGCCCAGCGTGTGGCGTTTTATCTGGCTGGACGCGCGCCG
-TATACGCCAGTCGATACCGCAACGGTGCTTGCGTTACTCTCGCGCTATGGCTATGAAGTCAAAGCCGATA
-TGACGGCGCGCGAGCAACAGCGGGTGATTATGGCGTTCCAGATGCACTTCCGTCCGGCGCAATGGAACGG
-TATCGCAGATGCCGAAACGCAGGCGATTGCCGAAGCATTACTGGAGAAGTACGGCCAGGATTAA
->GEN2.1219.00001.0002b_00006 1668 NA | NA | NA |  ID=2_4;partial=00;start_type=ATG;rbs_motif=GGA/GAG/AGG;rbs_spacer=5-10bp;gc_cont=0.537 | NA
-ATGAGTGAGGCTGAAGCCCGCCCGACTAACTTTATTCGTCAGATTATTGATGAAGATCTGGCGAGTGGTA
-AACATACCACTGTCCATACCCGTTTTCCGCCGGAGCCGAATGGCTATCTGCACATCGGCCACGCGAAATC
-TATCTGCCTGAACTTTGGCATCGCGCAAGATTATCAGGGCCAGTGCAACCTGCGTTTCGATGACACCAAC
-CCGGTAAAAGAAGATATCGAGTACGTTGATTCGATCAAAAACGACGTCGAGTGGTTAGGCTTTCACTGGT
-CTGGCGATATTCGCTACTCCTCCGATTACTTTGACCAACTGCACGCCTATGCGGTCGAGCTCATCAATAA
-AGGCCTGGCCTACGTTGATGAGCTGACGCCGGAGCAGATCCGCGAATACCGTGGTACGCTGACCGCGCCG
-GGTAAAAACAGCCCGTTCCGCGATCGCAGCGTGGAAGAAAACCTCGCGCTATTTGAAAAAATGCGTACCG
-GCGGTTTTGAAGAGGGTAAAGCCTGTCTGCGCGCTAAAATCGACATGGCGTCGCCGTTTATCGTGATGCG
-CGATCCGGTGCTGTATCGCATTAAATTCGCCGAGCATCATCAGACCGGCACGAAGTGGTGCATCTATCCG
-ATGTACGACTTTACTCACTGCATCAGCGATGCGCTGGAAGGCATTACTCATTCTCTGTGTACGCTGGAGT
-TCCAGGACAACCGTCGTCTGTACGACTGGGTGCTGGACAACATCACCATTCCGGTTCACCCGCGCCAGTA
-CGAATTCTCGCGCCTGAATCTGGAATACACCGTGATGTCCAAGCGTAAGCTGAACCTGCTGGTGACCGAC
-AAACACGTCGAAGGTTGGGATGATCCGCGTATGCCGACTATTTCCGGTCTGCGCCGTCGCGGCTATACCG
-CGGCTTCTATTCGTGAGTTCTGCAAACGCATCGGCGTCACCAAGCAGGACAACACTATTGAGATGGCGTC
-GCTGGAATCCTGCATTCGCGAAGATCTGAACGAAAACGCGCCGCGCGCGATGGCGGTAATCGATCCGGTA
-AAACTGGTTATCGAAAACTACCCGCAGGGCGAGAGCGAAATGGTTACCATGCCTAACCATCCGAATAAAC
-CGGAGATGGGCAGCCGTGAAGTGCCGTTTAGCGGTGAGATCTGGATCGATCGCGCGGATTTCCGCGAAGA
-AGCGAACAAACAGTACAAACGTCTGGTGATGGGCAAAGAAGTGCGTCTGCGTAATGCCTACGTCATTAAA
-GCGGAGCGCGTAGAGAAGGATGCCGAAGGGAATATCACCACCATCTTCTGTACCTATGATGCTGATACGC
-TGAGTAAAGATCCGGCTGACGGGCGTAAAGTGAAAGGCGTAATCCACTGGGTTAGCGTAGCACATGCGCT
-GCCGATTGAAATTCGTCTCTACGACCGTCTGTTCAGCGTGCCGAACCCGGGCGCCGCGGAGGACTTCCTG
-TCTGTTATCAACCCCGAATCATTAGTGATTAAGCAGGGGTATGGCGAGCCGTCGCTGAAAGCGGCGGTAG
-CAGGGAAAGCTTTCCAGTTTGAACGTGAAGGTTACTTCTGCCTTGACAGCCGCTATGCAACGGCCGATAA
-GCTGGTCTTTAACCGCACCGTGGGCCTGCGTGATACCTGGGCGAAAGCGGGCGAATAA
->GEN2.1219.00001.0003b_00007 768 NA | NA | NA |  ID=3_1;partial=00;start_type=GTG;rbs_motif=GGA/GAG/AGG;rbs_spacer=5-10bp;gc_cont=0.540 | NA
-GTGTTTATTGGCATCGTTAGCCTGTTTCCTGAAATGTTCCGCGCAATTACCGATTACGGGGTAACTGGCC
-GGGCAGTAAAAAAAGGCCTGCTGAACATCCAAAGCTGGAGTCCTCGCGACTTCGCGCATGACCGGCACCG
-TACCGTGGACGACCGTCCTTACGGCGGCGGACCGGGGATGTTAATGATGGTGCAACCCTTGCGGGACGCC
-ATTCATGCAGCAAAAGCCGCGGCAGGTGAAGGCGCTAAAGTGATTTATCTGTCGCCTCAGGGACGCAAGC
-TTGATCAAGCGGGCGTTAGCGAGCTGGCCACGAATCAGAAACTCATTCTGGTGTGTGGTCGCTACGAAGG
-CGTAGATGAGCGCGTAATTCAGGCCGAAATTGACGAAGAATGGTCAATTGGCGATTACGTTCTCAGCGGT
-GGCGAACTACCGGCAATGACGCTGATTGACTCCGTCGCCCGGTTTATACCGGGGGTTCTGGGGCATGAGG
-CATCAGCAATCGAAGATTCGTTTGCTGATGGGTTGCTGGATTGTCCGCACTATACGCGCCCTGAAGTGTT
-AGAGGGGATGGAAGTACCGCCAGTATTGCTGTCGGGAAACCATGCTGAGATACGTCGCTGGCGTTTGAAA
-CAGTCACTGGGCCGAACCTGGCTTAGAAGACCTGAACTTCTGGAAAACCTGGCTCTGACTGAAGAGCAAG
-CAAGGTTGCTGGCGGAGTTCAAAACAGAACACGCACAACAGCAGCATAAACATGATGGGATGGCATAG
->GEN2.1219.00001.0003i_00008 261 NA | NA | NA |  ID=3_2;partial=00;start_type=ATG;rbs_motif=GGA/GAG/AGG;rbs_spacer=5-10bp;gc_cont=0.487 | NA
-ATGGCCGGGTTGCACGCGCCATATGCATATAGCGCGCATCATGCGGTGAATTTCTGTTCTGAGTATAAAC
-GTGGCTTTGTATTGGGTTTTACACACCGTATGTTCGAAAAGACCGGCGATCGTCAACTTAGCGCGTGGGA
-GGCCGGAATTCTGACGCGTCGCTATGGTCTGGATAAAGAAATGGTGATGGATTTCTTTAAAGAGAATCAT
-TCCGGGATGGCGGTTCGCTTCTTTATGGCTGGTTATCGACTCGAAGGTTGA
->GEN2.1219.00001.0003i_00009 582 NA | NA | NA |  ID=3_3;partial=00;start_type=ATG;rbs_motif=None;rbs_spacer=None;gc_cont=0.546 | NA
-ATGTCTACGCTTCTCTATTTGCACGGATTCAACAGTTCCCCTCGCTCGGCAAAAGCGTGCCAGCTAAAAA
-ACTGGCTGGCGGAGCGTCATCCGCATGTTGAGATGATCGTCCCTCAACTGCCGCCGTATCCTGCCGATGC
-GGCGGAGTTGCTGGAATCTCTCGTACTTGAGCATGGCGGTGCGCCATTAGGGCTGGTAGGATCGTCGCTG
-GGTGGTTATTACGCCACCTGGCTGTCGCAATGTTTTATGCTGCCGGCTGTGGTGGTGAATCCCGCCGTGC
-GGCCCTTTGAATTACTGACCGACTATCTCGGTCAGAACGAGAACCCCTACACCGGGCAGCAATATGTGCT
-AGAGTCTCGCCATATTTATGATCTTAAAGTCATGCAGATTGACCCGCTGGAAGCGCCGGACCTGATCTGG
-CTACTGCAACAGACGGGCGATGAAGTGCTGGATTACCGCCAGGCGGTGGCATATTACGCCTCCTGCCGTC
-AGACAGTGACCGAGGGGGGTAATCACGCATTCACGGGCTTCGAAGATTATTTCAACCAGATTGTCGATTT
-TCTTGGACTGCACAGTTGCTGA
->GEN2.1219.00001.0003b_00010 369 NA | NA | NA |  ID=3_4;partial=00;start_type=ATG;rbs_motif=GGAG/GAGG;rbs_spacer=5-10bp;gc_cont=0.599 | NA
-ATGATGCGCACTGATGGCACGGTGACGCAGCCGCGTTTAAAGCAGGTTGCGCTGTCGGCAATTTCGGAGG
-TCAACGCAGAGCTGTATGAGTTTCGCAGACGCCAGCAGATGCTGGGGTATGCCTCGCTGGCAGAAGTCCC
-GGCGGAACAACTGGACGGCAAAAGCGAGCGCATTCAGCACTATTTCAACGCGGTTTACTGCTGGGCACGC
-GCCATGCTCAACGAACGTTACCAGGACTATGACGCCACGGCATCCGGTGTGAAGCGGGGCGAAGAACTGG
-CAGAAGCCAGCGGTGATTTGTGGCGTGACGCCCGCTGGGCCATCAGCCGGGTGCAGGATGCGCCGCACTG
-CACAGTGGAGCTTATCTGA
->GEN2.1219.00001.0004b_00011 1308 NA | NA | NA |  ID=4_1;partial=10;start_type=Edge;rbs_motif=None;rbs_spacer=None;gc_cont=0.519 | NA
-ATGATTGACCCTATTTTTGCGTCCTGTACGCTAATTGCCGTCTTTGTTGTTTTACTGGCCATGGGCGCGC
-CTATCGGGATCTGCATCGTTATCGCCTCTTTCAGCACCATGATGCTGGTACTGCCTTTCGATATTTCGAT
-GTTCGCCACCGCGCAAAAAATGTTCTCCAGCCTGGACAGTTTTGCCTTGCTGGCCGTGCCGTTCTTCGTT
-TTGTCCGGGGTGATCATGAATAGCGGGGGAATTGCCGCCCGACTGGTCAATTTTGCCAAACTGTTTACTG
-GCAAACTGCCCGGCTCGCTCTCTTACACCAACATCGTCGGCAATATGATGTTCGGTGCAATTTCCGGATC
-GGCGATTGCCGCCTCAACCTCTATCGGCGGCGTGATGGTGCCGATGAGCGCGCGCGAAGGTTACGATCGC
-GGTTTTGCGGCCGCGGTGAATATCGCCTCCGCGCCGACGGGAATGTTAATTCCGCCCACCACGGCTTTTA
-TCCTTTATGCGCTGGCAAGCGGGGGAACATCGATTGCCGCTCTGTTCGCCGGCGGTCTGGTCGCGGGAGT
-GCTGTGGGGCGTTGGCTGTATGCTGGTCACGCTGGTGGTCGCTAAGCGTCGAAATTATCGGGTTTTCTTC
-ACCGTCCAAAAAGGCATGGCGCTAAAAGTTGCCGTTGAGGCCATTCCCAGCCTGTTACTGATCGTGATTA
-TTGTCGGCGGCATTGTGCAGGGGATTTTCACCGCCATTGAAGCCTCCGCGATTGCCGTGGTGTATACGTT
-ATTGCTGACGATAGTGTTTTACCGCACGCTGAAAATTAAGGATTTGCCTTCGATTTTGCTCCAGACAGTG
-GTAATGACCGGGGTCATCATGTTCCTGCTGGCAACCTCTTCGGCGATGTCCTTCTCGATGTCGATCACCA
-ATATTCCTGCGGCGCTGAGCGATATGATCCTCGGTATTTCCGCCAATAAACTGGTTATCCTGTTAGTCAT
-TACCGTCTTTTTGTTGATTATCGGCGCATTTATGGATATCGGTCCGGCCATTCTGATTTTTACCCCGATT
-CTGCTGCCGATTATGACTAAACTGGGCGTCGATCCGGTGCATTTCGGCATTATCATGATCTATAACCTGG
-CGATAGGCACCATTACGCCGCCAGTTGGCAGTGGTTTATATGTCGGGGCGAGCGTCGGTAAGGTCAAAGT
-TGAGGACGTTATCAAACCGTTGATGCCTTTTTACGGCGCGATTATCGGCGTTCTGTTATTAATTACCTAC
-ATTCCGGAAATCACACTGTTTTTACCCCGTCTACTGGGCATCATGTAA
->GEN2.1219.00001.0004i_00012 465 NA | NA | NA |  ID=4_2;partial=00;start_type=ATG;rbs_motif=None;rbs_spacer=None;gc_cont=0.594 | NA
-ATGAAGTTTGTTGCGCCAGAACAGGCACCGGAACAGGCGGAGGTCATCAAAAATACGCCGTTCTGGCCTG
-ATGTGAACCTGTCGGAATTTCGCAGTGTGATGCGCACTGACGGCACGGTGACGCAGCCGCGTTTAAAGCA
-GGTCGTGCTGACGGCGATCTCTGAGGTTAACGCTGAGCTGTACGACTTCCGCAACCGTCAGCAGATGCTG
-GGCTGGCGGACACTTGCTGAGGTTCCCGCAGAAATGCTGGACGGTAAAAGCGAGCGTATCCGGCACTACC
-ACAACGCTGTTTTTTGCTGGGCGCGCGCTGTGCTTAATGAGCGTTATCAGGACTATGACGCCACGGCGTC
-AGGCGTGAAGCGAGGGGAGGAGCTGGCGGAGGCCAGCGGCGATCTGTGGCGTGATGCCCGCTGGGCCATC
-AGCCGGGTGCAGGATGCACCGCACTGTACGGTGGAGCTTATCTGA
->GEN2.1219.00001.0004b_00013 1014 NA | NA | NA |  ID=4_3;partial=00;start_type=ATG;rbs_motif=None;rbs_spacer=None;gc_cont=0.456 | NA
-ATGGAAACAAATATTACCTGGCAACAATTGATAGATGAATATTTCTTCGCAAAACCTCTGCGCTCAGCAT
-CTGAATGGAGTTACACCAAAGTCTTCAAATCATTTGTACATTATATGGGGCCGTTAAGCTGCCCTAATGA
-TGTGACATATCACAAAGTGCTTGCCTGGCGCCGTTTTCTTTTAAAAGAGAAAAAGCTGTCCGGACGTACC
-TGGAATAACAAGGTGGCGCATATGCGGGCCATCTTTAACTACGGAATACAGCGAGGGTTACTGCACTATG
-ACGAAAATCCGTTTAACAATTCGGTAGTTAAACCGGACAAGAAGAGAAAGAAAACGCTCACTCAGGCACA
-GATTGAGTATGCCTATCAGATCATGGAGCAGTATGAAAATCAGGAGAATACAGGGCTGGGACTGAAATAT
-TCCCGCTGCGCCTTATTTCCTGCATGGTTCTGGCTCACTGTCCTGGATACGCTCTATTACACAGGGATAC
-GTCAGAACCAGTTATTACATATTCGGCTGAATGATGTTGATTTGAGAGAAGGGCAGATTCGGCTGATTAC
-GGAGGGGTGTAAAAATCACAAAGAACACTATGTGCCGGTGATCAGTTTTCTGCGTCCACGGCTGACCTGT
-TTAATGGAGAAAGCGCAGAGCGAAGGATTGAAAGGTAATGACCGCCTGTTCAATATTGCACTTTTTACCG
-GCAAAGATCCCGCCATTGGCGATGACATGGATTCTCCTCAGGTAAGAGCATTCTTCCGTCGTCTGTCCAA
-GGAGTGTCAGTTTGCGATCAGTCCTCATCGTTTCAGACACACGCTGGCCACGGAGATGATGAAAATGCCG
-GAACAGAATCTGCATATGGCGCAAAGTGTGCTGGGTCATTCAAACATGAAATCCACGCTGGAGTATGTGG
-AGAATGATATTGCAGTGATGGGGAGGGCTCTGGAAGCGCAGTTTATGCAGATTAAGGCAGCACATGCCCG
-AAGCATTTACAGTGGGTTGACAAAGAATAGATAA
diff --git a/Examples/2-res-Annotate-prodigal/Genes/GEN4.1111.00001.gen b/Examples/2-res-Annotate-prodigal/Genes/GEN4.1111.00001.gen
deleted file mode 100644
index 7415130219cc63e3e7ca7f9e0300da146f9bd0c4..0000000000000000000000000000000000000000
--- a/Examples/2-res-Annotate-prodigal/Genes/GEN4.1111.00001.gen
+++ /dev/null
@@ -1,112 +0,0 @@
->GEN4.1111.00001.0001b_00001 831 NA | NA | NA |  ID=1_1;partial=10;start_type=Edge;rbs_motif=None;rbs_spacer=None;gc_cont=0.579 | NA
-ATGAAAGCGCTACTGTGGCTGGTGGGTCTCGCGTTGCTGTTAACAGGCTGCGCGAGCGAAAAAGGAATTA
-TCGATAAAGAGGGATATCAGCTTGATACCCGACATCGGGCGCAGGCGGCCTATCCGCGCATTAAAGTCCT
-GGTGATTCACTATACGGCGGAAAACTTTGACGTTTCGCTGGCGACGTTAACGGGCCGCAACGTCAGTTCG
-CATTACCTGATTCCCGCAACCCCGCCATTATATGGCGGTAAACCGCGCATCTGGCAACTGGTGCCGGAAC
-AGGATCAGGCCTGGCATGCGGGCGTCAGTTTCTGGCGAGGCGCCACGCGTCTCAATGATACGTCTATTGG
-CATTGAGCTGGAAAATCGCGGCTGGCGAATGTCCGGCGGGGTGAAATCTTTCGCGCCGTTTGAATCCGCG
-CAAATTCAGGCATTGATTCCGTTAGCGAAGGACATTATCGCGCGCTATGACATCAAACCGCAGAATGTGG
-TGGCCCATGCGGATATCGCGCCGCAGCGTAAAGACGATCCCGGCCCGCGCTTCCCGTGGCGCGAGCTGGC
-GGCGCAGGGGATTGGCGCCTGGCCTGACGCCCAGCGTGTGGCGTTTTATCTGGCTGGACGCGCGCCGTAT
-ACGCCAGTCGATACCGCAACGGTGCTTGCGTTACTCTCGCGCTATGGCTATGAAGTCAAAGCCGATATGA
-CGGCGCGCGAGCAGCAGCGGGTGATTATGGCGTTCCAGATGCACTTCCGTCCGGCGCAATGGAACGGTAT
-CGCAGATGCCGAAACGCAGGCGATTGCCGAAGCATTACTGGAGAAGTACGGCCAGGATTAA
->GEN4.1111.00001.0001i_00002 381 NA | NA | NA |  ID=1_2;partial=00;start_type=ATG;rbs_motif=None;rbs_spacer=None;gc_cont=0.533 | NA
-ATGCCGCACTTTATTGCTGAATGTACTGAAAATATTCGCGAGCAGGCTGATTTACCCGGCCTGTTCAGCA
-AGGTAAACGAGGCGCTGGCCGCCAGCGGGATTTTCCCCATCGGCGGTATCCGCAGTCGCGCCCACTGGCT
-GGATACCTGGCAGATGGCTGACGGTAAGCATGATTATGCGTTTGTGCATATGACGCTGAAAATCGGTACC
-GGGCGCAGCCTGGAGAGCCGTCAGGAAGTCGGCGAAATGCTGTTTGGGCTGATTAAAGCCCACTTCGCCG
-ACCTGATGGAGAACCGCTATCTGGCGCTGTCGTTTGAGATTGCCGAGCTACATCCGACGCTCAATTACAA
-ACAAAACAACGTACACGCGTTATTTAAATAG
->GEN4.1111.00001.0001i_00003 804 NA | NA | NA |  ID=1_3;partial=00;start_type=ATG;rbs_motif=AGGAG;rbs_spacer=5-10bp;gc_cont=0.591 | NA
-ATGCTCGATAAACAGACCCATACCCTGATCGCCCAGCGACTTAATCAGGCTGAAAAACAGCGTGAACAAA
-TTCGCGCAGTGTCGCTGGATTATCCCAACATCACTATTGAAGATGCCTATGCCGTACAGCGTGAATGGGT
-CAATATCAAGATCGCCGAAGGGCGCACGCTCAAAGGCCACAAAATCGGCCTGACCTCAAAAGCGATGCAG
-GCCAGCTCGCAAATCAGCGAACCGGATTACGGCGCGCTGCTTGACGATATGTTCTTCCATGACGGCGGCG
-ATATCCCCACCGACCGTTTTATCGTCCCGCGTATTGAAGTGGAGCTGGCGTTCGTGCTGGCGAAACCGCT
-GCGCGGCCCTCACTGCACGCTGTTCGACGTCTACAACGCCACGGATTATGTGATTCCGGCGCTGGAACTG
-ATTGACGCCCGCAGCCACAACATCGACCCGGAAACCCAGCGCCCGCGCAAAGTGTTCGACACCATTTCCG
-ACAACGCCGCCAACGCCGGGGTGATCCTCGGTGGTCGCCCCATCAAACCAGACGAGCTGGATCTGCGCTG
-GATCTCCGCGCTGCTCTATCGCAACGGCGTGATCGAAGAAACCGGCGTCGCCGCAGGCGTGCTGAATCAT
-CCGGCCAACGGCGTGGCGTGGCTGGCGAACAAGCTTGCCCCCTACGATGTCCAGCTTGAAGCCGGGCAGA
-TCATCCTCGGCGGCTCGTTCACCCGCCCGGTGCCGGCGAGCAAGGGCGACACCTTCCATGTCGATTACGG
-CAACATGGGCGCGATCAGTTGCCGGTTTGTGTAA
->GEN4.1111.00001.0001i_00004 1404 NA | NA | NA |  ID=1_4;partial=00;start_type=ATG;rbs_motif=None;rbs_spacer=None;gc_cont=0.512 | NA
-ATGCCCGTGAATAAGTTCTCCCGACGTACCCTCCTGACGGCAGGTTCCGCGCTTGCTGTTCTTCCTTTTC
-TGCGCGCCTTGCCGGTACAGGCGCGTGAACCTCGCGAGACCGTCGATATTAAGGATTATCCGGCGGATGA
-CGGTATCGCCTCGTTCAAACAGGCCTTCGCCGACGGACAGACCGTGGTCTTACCGCCAGGATGGGTGTGT
-GAAAATATCAATGCGGCGATAACGATTCCGGCGGGAAAAACGCTGCGGGTACAGGGCGCGGTGCGTGGGA
-ATGGCCGGGGACGGTTTATTTTGCAGGACGGGTGTCAGGTGGTGGGGGAGCAGGGCGGCAGTCTGCACAA
-TGTGACGCTGGATGTTCGCGGGTCGGACTGTGTGATTAAAGGCGTGACGATGAGCGGCTTTGGCCCCGTC
-GCGCAAATTTTCATCGGCGGTAAGGAACCGCAGGTGATGCGTAATCTCATTATCGATGACATCACCGTTA
-CCCACGCCAACTACGCCATTCTCCGCCAGGGATTTCATAACCAAATGGACGGCGCGCGGATTACGCATAG
-CCGCTTTAGCGATTTGCAGGGGGACGCCATTGAGTGGAATGTCGCGATTCACGACCGCGACATCCTGATT
-TCCGATCATGTCATCGAACGCATTGATTGTACCAATGGCAAAATCAACTGGGGGATCGGCATCGGGCTGG
-CGGGTAGCACCTATGACAACAGTTATCCTGAAGATCAGGCAGTAAAAAACTTTGTGGTGGCCAATATTAC
-CGGATCTGATTGCCGACAGCTGGTGCACGTAGAAAATGGCAAACATTTCGTCATTCGCAATGTCAAAGCC
-AAAAACATCACGCCCGATTTCAGTAAAAATGCGGGTATTGATAACGCAACGATCGCCATTTATGGCTGTG
-ATAATTTCGTCATTGATAATATTGATATGACGAATAGTGCTGGGATGCTCATCGGCTATGGCGTCGTTAA
-AGGAAAATACCTGTCAATTCCGCAAAACTTTAAATTAAACGCTATTCGGTTGGATAATCGCCAGGTTGCT
-TATAAATTACGCGGCATTCAAATTTCCTCCGGCAACATCCCCTCTTTTGTCGCCATCACCAATGTACGGA
-TGACGCGTGCTACGCTGGAACTGCATAATCAACCGCAGCACCTCTTTCTGCGTAATATCAACGTGATGCA
-AACTTCAGCGATTGGCCCGGCGTTAAAAATGCATTTCGATTTGCGTAAAGATGTCCGTGGTCAATTTATG
-GCCCGCCAGGACACGCTGCTTTCCCTCGCTAATGTTCATGCCATCAATGAAAACGGGCAGAGTTCCGTGG
-ATATCGACAGGATTAATCACCAAACCGTGAATGTCGAAGCAGTGAATTTTTCGCTGCCGAAGCGGGGAGG
-GTAA
->GEN4.1111.00001.0001i_00005 774 NA | NA | NA |  ID=1_5;partial=00;start_type=ATG;rbs_motif=3Base/5BMM;rbs_spacer=13-15bp;gc_cont=0.532 | NA
-ATGTCAGAAAATAAATTACACGTTATCGATTTGCACAAACGCTACGGCGGTCATGAAGTGCTGAAAGGGG
-TATCGTTGCAGGCCCGCGCCGGAGATGTGATTAGCATCATCGGCTCGTCCGGCTCCGGTAAAAGCACTTT
-TTTGCGCTGTATTAACTTCCTCGAAAAACCGAGCGAAGGCGCGATTATCGTGAACGGTCAGAACATTAAT
-CTGGTGCGCGACAAAGACGGGCAGCTCAAAGTGGCGGATAAAAATCAGCTACGCTTGTTGCGTACCCGCC
-TGACGATGGTGTTTCAGCACTTTAACCTCTGGAGCCACATGACGGTGCTGGAAAATGTGATGGAAGCGCC
-GATTCAGGTACTGGGATTAAGCAAGCACGACGCGCGCGAGCGGGCGTTGAAATATCTGGCGAAGGTGGGG
-ATTGATGAGCGCGCTCAGGGCAAATATCCCGTCCATCTCTCCGGCGGCCAACAGCAGCGCGTTTCTATTG
-CGCGCGCGCTGGCGATGGAACCTGACGTTTTACTGTTCGATGAACCCACATCGGCGCTCGATCCTGAACT
-GGTCGGCGAAGTGTTGCGCATCATGCAACAACTGGCGGAAGAAGGCAAAACGATGGTGGTGGTCACGCAT
-GAAATGGGCTTCGCCCGCCATGTCTCTTCGCACGTTATTTTTCTGCATCAGGGGAAAATTGAAGAAGAGG
-GCGATCCGGAGCAGGTGTTCGGCAATCCGCAAAGCCCGCGTTTACAGCAATTCCTGAAAGGCTCGCTGAA
-ATAA
->GEN4.1111.00001.0001i_00006 768 NA | NA | NA |  ID=1_6;partial=00;start_type=GTG;rbs_motif=None;rbs_spacer=None;gc_cont=0.544 | NA
-GTGTTTATTGGCATCGTTAGCCTGTTTCCTGAAATGTTCCGCGCAATTACCGATTACGGGGTAACTGGCC
-GGGCAGTAAAAAAAGGCCTGCTGAACATCCAAAGCTGGAGTCCTCGCGACTTCGCGCATGACCGGCACCG
-TACCGTGGACGACCGTCCTTACGGCGGCGGACCGGGGATGTTAATGATGGTGCAACCCTTGCGGGACGCC
-ATTCACGCAGCAAAAGCCGCGGCAGGTGAAGGCGCTAAAGTGATTTATCTGTCGCCTCAGGGACGCAAGC
-TTGATCAAGCGGGCGTTAGCGAGCTGGCCACGAATCAGAAGCTTATTCTGGTGTGTGGTCGCTACGAAGG
-CGTAGATGAGCGCGTAATTCAGACCGAAATTGACGAAGAATGGTCAATTGGCGATTACGTTCTCAGCGGT
-GGCGAACTACCGGCAATGACGCTGATTGACTCCGTCGCCCGGTTTATACCGGGGGTTCTGGGGCATGAGG
-CATCAGCAATCGAAGATTCGTTTGCTGATGGGTTGCTGGATTGTCCGCACTATACGCGCCCTGAAGTGTT
-AGAGGGGATGGAAGTACCGCCAGTATTGCTGTCGGGAAACCATGCCGAGATACGTCGCTGGCGCTTGAAA
-CAGTCGCTGGGCCGAACCTGGCTTAGAAGACCTGAACTTCTGGAAAACCTGGCTCTGACTGAAGAGCAAG
-CAAGGTTGCTGGCGGAGTTCAAAACAGAACACGCACAACAGCAGCATAAACATGATGGGATGGCATAG
->GEN4.1111.00001.0001i_00007 261 NA | NA | NA |  ID=1_7;partial=00;start_type=ATG;rbs_motif=GGA/GAG/AGG;rbs_spacer=5-10bp;gc_cont=0.483 | NA
-ATGGCTGGGTTGCACGCGCCATATGCATATAGCGCGCATCATGCGGTGAATTTCTGTTCTGAGTATAAAC
-GTGGCTTTGTATTGGGTTTTACACACCGTATGTTCGAAAAGACCGGCGATCGTCAACTTAGCGCGTGGGA
-GGCCGGAATTCTGACGCGTCGCTATGGTCTGGATAAAGAAATGGTGATGGATTTCTTTAAAGAGAATCAT
-TCCGGGATGGCGGTTCGCTTCTTTATGGTCGGTTATCGACTCGAAGGTTGA
->GEN4.1111.00001.0001i_00008 582 NA | NA | NA |  ID=1_8;partial=00;start_type=ATG;rbs_motif=None;rbs_spacer=None;gc_cont=0.546 | NA
-ATGTCTACGCTTCTCTATTTGCACGGATTCAACAGTTCCCCTCGCTCGGCAAAAGCGTGCCAGCTAAAAA
-ACTGGCTGGCGGAGCGTCATCCGCATGTCGAGATGATCGTCCCTCAACTACCGCCGTATCCTGCCGATGC
-GGCGGAGTTGCTGGAATCTCTCGTGCTTGAGCATGGCGGTGCGCCATTAGGGCTGGTAGGATCGTCGCTG
-GGTGGTTATTACGCCACCTGGCTGTCGCAATGTTTTATGCTGCCGGCTGTGGTGGTGAATCCCGCCGTGC
-GGCCCTTTGAATTACTGACCGACTATCTCGGTCAGAACGAGAACCCCTACACCGGGCAGCAATATGTGCT
-AGAGTCTCGCCATATTTATGATCTTAAAGTCATGCAGATTGACCCGCTGGAAGCGCCGGACCTGATCTGG
-CTACTGCAACAGACGGGCGATGAAGTGCTGGATTACCGCCAGGCGGTGGCATATTACGCCTCCTGCCGTC
-AGACAGTGACCGAGGGTGGTAATCACGCATTCACGGGCTTCGAAGATTATTTCAACCAGATTGTCGATTT
-TCTTGGACTGCACAGTTGCTGA
->GEN4.1111.00001.0001b_00009 1083 NA | NA | NA |  ID=1_9;partial=00;start_type=ATG;rbs_motif=None;rbs_spacer=None;gc_cont=0.525 | NA
-ATGAATAGCGGGGGAATTGCCGCCCGGCTGGTCAATTTTGCCAAACTGTTTACTGGCAAACTGCCCGGCT
-CGCTCTCTTATACCAACATCGTCGGCAATATGATGTTCGGTGCAATTTCCGGATCGGCAATTGCCGCCTC
-AACCTCCATCGGCGGCGTGATGGTGCCGATGAGCGCGCGCGAAGGTTACGATCGCGGCTTTGCGGCCGCG
-GTGAATATCGCCTCCGCGCCGACGGGAATGTTAATTCCGCCCACCACGGCTTTTATCCTTTATGCGCTGG
-CAAGCGGGGGAACATCGATTGCCGCTCTGTTCGCCGGCGGTCTGGTCGCGGGAGTGCTGTGGGGCGTTGG
-CTGTATGCTGGTCACGCTGGTGGTCGCTAAGCGTCGAAATTATCGGGTTTTCTTCACCGTCCAAAAAGGC
-ATGGCGCTAAAAGTTGCCGTTGAGGCCATTCCCAGCCTGCTGCTGATCGTGATTATCGTCGGCGGCATTG
-TGCAGGGGATTTTCACCGCCATTGAAGCCTCCGCGATTGCCGTGGTGTATACATTATTGTTGACGATGGT
-GTTTTACCGCACGCTGAAAATTAAGGATTTGCCTTCGATTTTGCTCCAGACAGTGGTAATGACCGGGGTC
-ATCATGTTCCTGCTGGCAACCTCTTCGGCGATGTCCTTCTCGATGTCGATCACCAATATTCCTGCGGCGC
-TGAGCGATATGATCCTCGGTATTTCCGCCAATAAACTGGTTATCCTGTTAGTCATTACCGTCTTTTTGTT
-GATTATCGGCGCATTTATGGATATCGGTCCGGCCATTCTGATTTTTACCCCGATTCTGCTGCCGATCATG
-GCTAAACTGGGCGTCGATCCGGTGCATTTTGGCATTATCATGATCTATAACCTGGCGATTGGCACCATTA
-CGCCGCCAGTTGGCAGTGGTTTATATGTCGGGGCGAGCGTCGGTAAGGTCAAAGTTGAGGAAGTGATTAA
-ACCGTTGCTGCCTTTTTACGGCGCGATTATCGGCGTTCTGTTATTAATTACCTACATTCCGGAAATCACA
-CTGTTCTTACCCCGTCTACTGGGCATCATGTAA
diff --git a/Examples/2-res-Annotate-prodigal/LSTINFO-list_genomes.lst b/Examples/2-res-Annotate-prodigal/LSTINFO-list_genomes.lst
deleted file mode 100644
index df32874a03f9905aa558e17a39f8f4227a43e203..0000000000000000000000000000000000000000
--- a/Examples/2-res-Annotate-prodigal/LSTINFO-list_genomes.lst
+++ /dev/null
@@ -1,5 +0,0 @@
-gembase_name	orig_name	to_annotate	gsize	nb_conts	L90
-EXAM.1219.00001	genome1.fst	genome1.fst_prodigal-split5N.fna	9808	2	2
-EXAM.1216.00002	genome3-chromo.fst-all.fna	genome3-chromo.fst-all.fna_prodigal-split5N.fna	8817	3	3
-GEN2.1219.00001	genome2.fst	genome2.fst_prodigal-split5N.fna	10717	5	4
-GEN4.1111.00001	genome4.fst	genome4.fst_prodigal-split5N.fna	7134	1	1
diff --git a/Examples/2-res-Annotate-prodigal/LSTINFO/EXAM.1216.00002.lst b/Examples/2-res-Annotate-prodigal/LSTINFO/EXAM.1216.00002.lst
deleted file mode 100644
index be3646543ed0b3b21b12f5d3c90a9d3191548bf5..0000000000000000000000000000000000000000
--- a/Examples/2-res-Annotate-prodigal/LSTINFO/EXAM.1216.00002.lst
+++ /dev/null
@@ -1,12 +0,0 @@
- 1 	 831 	D	CDS	EXAM.1216.00002.0001b_00001	NA	| NA | NA |  ID=1_1;partial=10;start_type=Edge;rbs_motif=None;rbs_spacer=None;gc_cont=0.578 | NA
- 880 	 1710 	D	CDS	EXAM.1216.00002.0001i_00002	NA	| NA | NA |  ID=1_2;partial=00;start_type=ATG;rbs_motif=AGGAG/GGAGG;rbs_spacer=11-12bp;gc_cont=0.578 | NA
- 1655 	 2128 	D	CDS	EXAM.1216.00002.0001i_00003	NA	| NA | NA |  ID=1_3;partial=00;start_type=ATG;rbs_motif=GGA/GAG/AGG;rbs_spacer=11-12bp;gc_cont=0.544 | NA
- 2172 	 2396 	D	CDS	EXAM.1216.00002.0001i_00004	NA	| NA | NA |  ID=1_4;partial=00;start_type=ATG;rbs_motif=GGA/GAG/AGG;rbs_spacer=11-12bp;gc_cont=0.542 | NA
- 2425 	 3828 	D	CDS	EXAM.1216.00002.0001i_00005	NA	| NA | NA |  ID=1_5;partial=00;start_type=ATG;rbs_motif=AGGAG/GGAGG;rbs_spacer=11-12bp;gc_cont=0.513 | NA
- 3863 	 4636 	D	CDS	EXAM.1216.00002.0001i_00006	NA	| NA | NA |  ID=1_6;partial=00;start_type=ATG;rbs_motif=GGAG/GAGG;rbs_spacer=5-10bp;gc_cont=0.527 | NA
- 4641 	 5432 	D	CDS	EXAM.1216.00002.0001i_00007	NA	| NA | NA |  ID=1_7;partial=00;start_type=ATG;rbs_motif=None;rbs_spacer=None;gc_cont=0.537 | NA
- 5460 	 5747 	D	CDS	EXAM.1216.00002.0001b_00008	NA	| NA | NA |  ID=1_8;partial=00;start_type=ATG;rbs_motif=AGGAG;rbs_spacer=5-10bp;gc_cont=0.469 | NA
- 1 	 582 	D	CDS	EXAM.1216.00002.0002b_00009	NA	| NA | NA |  ID=2_1;partial=10;start_type=Edge;rbs_motif=None;rbs_spacer=None;gc_cont=0.546 | NA
- 629 	 1936 	D	CDS	EXAM.1216.00002.0002b_00010	NA	| NA | NA |  ID=2_2;partial=00;start_type=ATG;rbs_motif=None;rbs_spacer=None;gc_cont=0.520 | NA
- 2 	 280 	D	CDS	EXAM.1216.00002.0003b_00011	NA	| NA | NA |  ID=3_1;partial=10;start_type=Edge;rbs_motif=None;rbs_spacer=None;gc_cont=0.355 | NA
- 323 	 1102 	D	CDS	EXAM.1216.00002.0003b_00012	NA	| NA | NA |  ID=3_2;partial=00;start_type=ATG;rbs_motif=None;rbs_spacer=None;gc_cont=0.559 | NA
diff --git a/Examples/2-res-Annotate-prodigal/LSTINFO/EXAM.1219.00001.lst b/Examples/2-res-Annotate-prodigal/LSTINFO/EXAM.1219.00001.lst
deleted file mode 100644
index 3c361e9234b6585a0b1cbf1742a3bfaa604037ff..0000000000000000000000000000000000000000
--- a/Examples/2-res-Annotate-prodigal/LSTINFO/EXAM.1219.00001.lst
+++ /dev/null
@@ -1,11 +0,0 @@
- 213 	 1880 	D	CDS	EXAM.1219.00001.0001b_00001	NA	| NA | NA |  ID=1_1;partial=00;start_type=ATG;rbs_motif=None;rbs_spacer=None;gc_cont=0.534 | NA
- 1916 	 2746 	D	CDS	EXAM.1219.00001.0001b_00002	NA	| NA | NA |  ID=1_2;partial=00;start_type=ATG;rbs_motif=AGGAGG;rbs_spacer=5-10bp;gc_cont=0.570 | NA
- 16 	 396 	D	CDS	EXAM.1219.00001.0002b_00003	NA	| NA | NA |  ID=2_1;partial=00;start_type=ATG;rbs_motif=None;rbs_spacer=None;gc_cont=0.538 | NA
- 428 	 1837 	D	CDS	EXAM.1219.00001.0002i_00004	NA	| NA | NA |  ID=2_2;partial=00;start_type=ATG;rbs_motif=GGA/GAG/AGG;rbs_spacer=5-10bp;gc_cont=0.512 | NA
- 1869 	 2642 	D	CDS	EXAM.1219.00001.0002i_00005	NA	| NA | NA |  ID=2_3;partial=00;start_type=ATG;rbs_motif=None;rbs_spacer=None;gc_cont=0.531 | NA
- 2709 	 3443 	D	CDS	EXAM.1219.00001.0002i_00006	NA	| NA | NA |  ID=2_4;partial=00;start_type=ATG;rbs_motif=None;rbs_spacer=None;gc_cont=0.547 | NA
- 3427 	 4254 	D	CDS	EXAM.1219.00001.0002i_00007	NA	| NA | NA |  ID=2_5;partial=00;start_type=ATG;rbs_motif=AGxAG;rbs_spacer=5-10bp;gc_cont=0.541 | NA
- 4299 	 4763 	D	CDS	EXAM.1219.00001.0002i_00008	NA	| NA | NA |  ID=2_6;partial=00;start_type=ATG;rbs_motif=AGGA/GGAG/GAGG;rbs_spacer=11-12bp;gc_cont=0.596 | NA
- 4818 	 5078 	D	CDS	EXAM.1219.00001.0002i_00009	NA	| NA | NA |  ID=2_7;partial=00;start_type=ATG;rbs_motif=GGA/GAG/AGG;rbs_spacer=5-10bp;gc_cont=0.487 | NA
- 5117 	 5698 	D	CDS	EXAM.1219.00001.0002i_00010	NA	| NA | NA |  ID=2_8;partial=00;start_type=ATG;rbs_motif=None;rbs_spacer=None;gc_cont=0.546 | NA
- 5717 	 7024 	D	CDS	EXAM.1219.00001.0002b_00011	NA	| NA | NA |  ID=2_9;partial=00;start_type=ATG;rbs_motif=None;rbs_spacer=None;gc_cont=0.524 | NA
diff --git a/Examples/2-res-Annotate-prodigal/LSTINFO/GEN2.1219.00001.lst b/Examples/2-res-Annotate-prodigal/LSTINFO/GEN2.1219.00001.lst
deleted file mode 100644
index a0410fdf534750495fe465ad754726a7d13c65e3..0000000000000000000000000000000000000000
--- a/Examples/2-res-Annotate-prodigal/LSTINFO/GEN2.1219.00001.lst
+++ /dev/null
@@ -1,13 +0,0 @@
- 1 	 774 	D	CDS	GEN2.1219.00001.0001b_00001	NA	| NA | NA |  ID=1_1;partial=10;start_type=Edge;rbs_motif=None;rbs_spacer=None;gc_cont=0.530 | NA
- 857 	 2260 	D	CDS	GEN2.1219.00001.0001b_00002	NA	| NA | NA |  ID=1_2;partial=00;start_type=ATG;rbs_motif=None;rbs_spacer=None;gc_cont=0.510 | NA
- 1 	 252 	D	CDS	GEN2.1219.00001.0002b_00003	NA	| NA | NA |  ID=2_1;partial=10;start_type=Edge;rbs_motif=None;rbs_spacer=None;gc_cont=0.540 | NA
- 301 	 681 	D	CDS	GEN2.1219.00001.0002i_00004	NA	| NA | NA |  ID=2_2;partial=00;start_type=ATG;rbs_motif=None;rbs_spacer=None;gc_cont=0.530 | NA
- 764 	 1597 	D	CDS	GEN2.1219.00001.0002i_00005	NA	| NA | NA |  ID=2_3;partial=00;start_type=ATG;rbs_motif=None;rbs_spacer=None;gc_cont=0.573 | NA
- 1628 	 3295 	D	CDS	GEN2.1219.00001.0002b_00006	NA	| NA | NA |  ID=2_4;partial=00;start_type=ATG;rbs_motif=GGA/GAG/AGG;rbs_spacer=5-10bp;gc_cont=0.537 | NA
- 30 	 797 	D	CDS	GEN2.1219.00001.0003b_00007	NA	| NA | NA |  ID=3_1;partial=00;start_type=GTG;rbs_motif=GGA/GAG/AGG;rbs_spacer=5-10bp;gc_cont=0.540 | NA
- 862 	 1122 	D	CDS	GEN2.1219.00001.0003i_00008	NA	| NA | NA |  ID=3_2;partial=00;start_type=ATG;rbs_motif=GGA/GAG/AGG;rbs_spacer=5-10bp;gc_cont=0.487 | NA
- 1170 	 1751 	D	CDS	GEN2.1219.00001.0003i_00009	NA	| NA | NA |  ID=3_3;partial=00;start_type=ATG;rbs_motif=None;rbs_spacer=None;gc_cont=0.546 | NA
- 1895 	 2263 	D	CDS	GEN2.1219.00001.0003b_00010	NA	| NA | NA |  ID=3_4;partial=00;start_type=ATG;rbs_motif=GGAG/GAGG;rbs_spacer=5-10bp;gc_cont=0.599 | NA
- 1 	 1308 	D	CDS	GEN2.1219.00001.0004b_00011	NA	| NA | NA |  ID=4_1;partial=10;start_type=Edge;rbs_motif=None;rbs_spacer=None;gc_cont=0.519 | NA
- 1340 	 1804 	D	CDS	GEN2.1219.00001.0004i_00012	NA	| NA | NA |  ID=4_2;partial=00;start_type=ATG;rbs_motif=None;rbs_spacer=None;gc_cont=0.594 | NA
- 1832 	 2845 	D	CDS	GEN2.1219.00001.0004b_00013	NA	| NA | NA |  ID=4_3;partial=00;start_type=ATG;rbs_motif=None;rbs_spacer=None;gc_cont=0.456 | NA
diff --git a/Examples/2-res-Annotate-prodigal/LSTINFO/GEN4.1111.00001.lst b/Examples/2-res-Annotate-prodigal/LSTINFO/GEN4.1111.00001.lst
deleted file mode 100644
index c77d5936658fdbc155eb5be5a048c008db78c2fd..0000000000000000000000000000000000000000
--- a/Examples/2-res-Annotate-prodigal/LSTINFO/GEN4.1111.00001.lst
+++ /dev/null
@@ -1,9 +0,0 @@
- 1 	 831 	D	CDS	GEN4.1111.00001.0001b_00001	NA	| NA | NA |  ID=1_1;partial=10;start_type=Edge;rbs_motif=None;rbs_spacer=None;gc_cont=0.579 | NA
- 861 	 1241 	D	CDS	GEN4.1111.00001.0001i_00002	NA	| NA | NA |  ID=1_2;partial=00;start_type=ATG;rbs_motif=None;rbs_spacer=None;gc_cont=0.533 | NA
- 1271 	 2074 	D	CDS	GEN4.1111.00001.0001i_00003	NA	| NA | NA |  ID=1_3;partial=00;start_type=ATG;rbs_motif=AGGAG;rbs_spacer=5-10bp;gc_cont=0.591 | NA
- 2111 	 3514 	D	CDS	GEN4.1111.00001.0001i_00004	NA	| NA | NA |  ID=1_4;partial=00;start_type=ATG;rbs_motif=None;rbs_spacer=None;gc_cont=0.512 | NA
- 3535 	 4308 	D	CDS	GEN4.1111.00001.0001i_00005	NA	| NA | NA |  ID=1_5;partial=00;start_type=ATG;rbs_motif=3Base/5BMM;rbs_spacer=13-15bp;gc_cont=0.532 | NA
- 4327 	 5094 	D	CDS	GEN4.1111.00001.0001i_00006	NA	| NA | NA |  ID=1_6;partial=00;start_type=GTG;rbs_motif=None;rbs_spacer=None;gc_cont=0.544 | NA
- 5138 	 5398 	D	CDS	GEN4.1111.00001.0001i_00007	NA	| NA | NA |  ID=1_7;partial=00;start_type=ATG;rbs_motif=GGA/GAG/AGG;rbs_spacer=5-10bp;gc_cont=0.483 | NA
- 5413 	 5994 	D	CDS	GEN4.1111.00001.0001i_00008	NA	| NA | NA |  ID=1_8;partial=00;start_type=ATG;rbs_motif=None;rbs_spacer=None;gc_cont=0.546 | NA
- 6052 	 7134 	D	CDS	GEN4.1111.00001.0001b_00009	NA	| NA | NA |  ID=1_9;partial=00;start_type=ATG;rbs_motif=None;rbs_spacer=None;gc_cont=0.525 | NA
diff --git a/Examples/2-res-Annotate-prodigal/PanACoTA-annotate_list_genomes.log b/Examples/2-res-Annotate-prodigal/PanACoTA-annotate_list_genomes.log
deleted file mode 100644
index b400656a1a303e3213b4783d558cc1d89d813097..0000000000000000000000000000000000000000
--- a/Examples/2-res-Annotate-prodigal/PanACoTA-annotate_list_genomes.log
+++ /dev/null
@@ -1,12 +0,0 @@
-[2019-12-05 10:00:47] :: INFO :: PanACoTA version 20190425
-[2019-12-05 10:00:47] :: INFO :: Command used
- 	 > PanACoTA annotate -d Examples/genomes_init -l Examples/input_files/list_genomes.lst -n EXAM -r Examples/1-res-Annotate-prodigal2 --prodigal --small
-[2019-12-05 10:00:47] :: INFO :: Let's start!
-[2019-12-05 10:00:47] :: INFO :: Cutting genomes at each stretch of at least 5 'N', and then, calculating genome size, number of contigs and L90.
-[2019-12-05 10:00:47] :: INFO :: Generating distribution of L90 and #contigs graphs.
-[2019-12-05 10:00:48] :: INFO :: -> Original sequences folder ('orig_name' column): Examples/genomes_init 
-[2019-12-05 10:00:48] :: INFO :: 	-> If original sequence not found in Examples/genomes_init, look for it in Examples/1-res-Annotate-prodigal2/tmp_files, as it must be a concatenation of several input sequence files.
-[2019-12-05 10:00:48] :: INFO :: -> Folder with sequence files that will be used for annotation ('to_annotate' column): Examples/1-res-Annotate-prodigal2/tmp_files
-[2019-12-05 10:00:48] :: INFO :: Renaming kept genomes according to their quality.
-[2019-12-05 10:00:48] :: INFO :: Annotating all genomes with prodigal
-[2019-12-05 10:00:49] :: INFO :: Annotation step done.
diff --git a/Examples/2-res-Annotate-prodigal/PanACoTA-annotate_list_genomes.log.details b/Examples/2-res-Annotate-prodigal/PanACoTA-annotate_list_genomes.log.details
deleted file mode 100644
index b400656a1a303e3213b4783d558cc1d89d813097..0000000000000000000000000000000000000000
--- a/Examples/2-res-Annotate-prodigal/PanACoTA-annotate_list_genomes.log.details
+++ /dev/null
@@ -1,12 +0,0 @@
-[2019-12-05 10:00:47] :: INFO :: PanACoTA version 20190425
-[2019-12-05 10:00:47] :: INFO :: Command used
- 	 > PanACoTA annotate -d Examples/genomes_init -l Examples/input_files/list_genomes.lst -n EXAM -r Examples/1-res-Annotate-prodigal2 --prodigal --small
-[2019-12-05 10:00:47] :: INFO :: Let's start!
-[2019-12-05 10:00:47] :: INFO :: Cutting genomes at each stretch of at least 5 'N', and then, calculating genome size, number of contigs and L90.
-[2019-12-05 10:00:47] :: INFO :: Generating distribution of L90 and #contigs graphs.
-[2019-12-05 10:00:48] :: INFO :: -> Original sequences folder ('orig_name' column): Examples/genomes_init 
-[2019-12-05 10:00:48] :: INFO :: 	-> If original sequence not found in Examples/genomes_init, look for it in Examples/1-res-Annotate-prodigal2/tmp_files, as it must be a concatenation of several input sequence files.
-[2019-12-05 10:00:48] :: INFO :: -> Folder with sequence files that will be used for annotation ('to_annotate' column): Examples/1-res-Annotate-prodigal2/tmp_files
-[2019-12-05 10:00:48] :: INFO :: Renaming kept genomes according to their quality.
-[2019-12-05 10:00:48] :: INFO :: Annotating all genomes with prodigal
-[2019-12-05 10:00:49] :: INFO :: Annotation step done.
diff --git a/Examples/2-res-Annotate-prodigal/PanACoTA-annotate_list_genomes.log.err b/Examples/2-res-Annotate-prodigal/PanACoTA-annotate_list_genomes.log.err
deleted file mode 100644
index e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
diff --git a/Examples/2-res-Annotate-prodigal/Proteins/EXAM.1216.00002.prt b/Examples/2-res-Annotate-prodigal/Proteins/EXAM.1216.00002.prt
deleted file mode 100644
index e068a04de2cd5f3d9df04a61c0e58d6b10384fd3..0000000000000000000000000000000000000000
--- a/Examples/2-res-Annotate-prodigal/Proteins/EXAM.1216.00002.prt
+++ /dev/null
@@ -1,66 +0,0 @@
->EXAM.1216.00002.0001b_00001 831 NA | NA | NA |  ID=1_1;partial=10;start_type=Edge;rbs_motif=None;rbs_spacer=None;gc_cont=0.578 | NA
-MRALLWLVGLALLLTGCASEKGIIDEEGYQLDTRHRAQAAYPRIKVLVIHYTAENFDVSL
-ATLTGRNVSSHYLIPATPPLYGGKPRIWQLVPEQDQAWHAGVSFWRGATRLNDTSIGIEL
-ENRGWRMSGGVKSFAPFESAQIQALIPLAKDIIARYDIKPQNVVAHADIAPQRKDDPGPR
-FPWRELAAQGIGAWPDAQRVAFYLAGRAPYTPVDTATVLALLSRYGYEVKADMTAREQQR
-VIMAFQMHFRPAQWNGIADAETQAIAEALLEKYGQD*
->EXAM.1216.00002.0001i_00002 831 NA | NA | NA |  ID=1_2;partial=00;start_type=ATG;rbs_motif=AGGAG/GGAGG;rbs_spacer=11-12bp;gc_cont=0.578 | NA
-MRALLWLVGLALLLTGCASEKGIIDEEGYQLDTRHRAQAAYPRIKVLVIHYTAENFDVSL
-ATLTGRNVSSHYLIPATPPLYGGKPRIWQLVPEQDQAWHAGVSFWRGATRLNDTSIGIEL
-ENRGWRMSGGVKSFAPFESAQIQALIPLAKDIIARYDIKPQNVVAHADIAPQRKDDPGPR
-FPWRELAAQGIGAWPDAQRVAFYLAGRAPYTPVDTATVLALLSRYGYEVKADMTAREQQR
-VIMAFQMHFRPAQWNGIADAETQAIAEALLEKYGQD*
->EXAM.1216.00002.0001i_00003 474 NA | NA | NA |  ID=1_3;partial=00;start_type=ATG;rbs_motif=GGA/GAG/AGG;rbs_spacer=11-12bp;gc_cont=0.544 | NA
-MPKRRRLPKHYWRSTARINRARYREDSLFEDMPHFIAECTENIREQADLPGLFSKVNEAL
-AASGIFPIGGIRSRAHWLDTWQMADGKHDYAFVHMTLKIGAGRSLESRQEVGEMLFGLIK
-AHFADLMENRYLALSFEIAELHPTLNYKQNNVHALFK*
->EXAM.1216.00002.0001i_00004 225 NA | NA | NA |  ID=1_4;partial=00;start_type=ATG;rbs_motif=GGA/GAG/AGG;rbs_spacer=11-12bp;gc_cont=0.542 | NA
-MSALFLAIPLTIFVLFVLPIWLWLHYSNRAGRGELSQSEQQRLLQLTDDAQRMRERIQAL
-EDILDAEHPNWRER*
->EXAM.1216.00002.0001i_00005 1404 NA | NA | NA |  ID=1_5;partial=00;start_type=ATG;rbs_motif=AGGAG/GGAGG;rbs_spacer=11-12bp;gc_cont=0.513 | NA
-MPATKFSRRTLLTAGSALAVLPFLRALPVQAREPRETVDIKDYPADDGIASFKQAFADGQ
-TVVVPPGWVCENINAAITIPAGKTLRVQGAVRGNGRGRFILQDGCQVVGEQGGSLHNVTL
-DVRGSDCVIKGVAMSGFGPVAQIFIGGKEPQVMRNLIIDDITVTHANYAILRQGFHNQMD
-GARITHSRFSDLQGDAIEWNVAIHDRDILISDHVIERIDCTNGKINWGIGIGLAGSTYDN
-SYPEDQAVKNFVVANITGSDCRQLVHVENGKHFVIRNVKAKNITPDFSKNAGIDNATIAI
-YGCDNFVIDNIDMTNSAGMLIGYGVVKGKYLSIPQNFKLNAIRLDNRQVAYKLRGIQISS
-GNTPSFVAITNVRMTRATLELHNQPQHLFLRNINVMQTSAIGPALKMHFDLRKDVRGQFM
-ARQDTLLSLANVHAINENGQSSVDIDRINHQTVNVEAVNFSLPKRGG*
->EXAM.1216.00002.0001i_00006 774 NA | NA | NA |  ID=1_6;partial=00;start_type=ATG;rbs_motif=GGAG/GAGG;rbs_spacer=5-10bp;gc_cont=0.527 | NA
-MSENKLHVIDLHKRYGGHEVLKGVSLQARAGDVISIIGSSGSGKSTFLRCINFLEKPSED
-AIIVNGQNINLVRDKDGQLKVADKNQLRLLRTRLTMVFQHFNLWSHMTVLENVMEAPIQV
-LGLSKHDARERALKYLAKVGIDERAQGKYPVHLSGGQQQRVSIARALAMEPDVLLFDEPT
-SALDPELVGEVLRIMQQLAEEGKTMVVVTHEMGFVRHVSSHVIFLHQGKIEEEGDPEQVF
-GNPQSPRLQQFLKGSLK*
->EXAM.1216.00002.0001i_00007 792 NA | NA | NA |  ID=1_7;partial=00;start_type=ATG;rbs_motif=None;rbs_spacer=None;gc_cont=0.537 | NA
-MRAIYRRCVFIGIVSLFPEMFRAITDYGVTGRAVKNGLLNIQSWSPRDFTHDRHRTVDDR
-PYGGGPGMLMMVQPLRDAIHAAKAAAGEGAKVIYLSPQGRKLDQAGVSELATNQKLILVC
-GRYEGVDERVIQTEIDEEWSIGDYVLSGGELPAMTLIDSVARFIPGVLGHEASAIEDSFA
-DGLLDCPHYTRPEVLEGMEVPPVLLSGNHAEIRRWRLKQSLGRTWLRRPELLENLALTEE
-QARLLAEFKTEHAQQQHKHDGMA*
->EXAM.1216.00002.0001b_00008 288 NA | NA | NA |  ID=1_8;partial=00;start_type=ATG;rbs_motif=AGGAG;rbs_spacer=5-10bp;gc_cont=0.469 | NA
-MNNHFGKGLMAGLHAPYAYSAHHAVNFCSEYKRGFVLGFTHRMFEKTGDRQLSAWEAGIL
-TRRYGLDKEMVMDFFKENHSGMAVRFFMAGYRLEG*
->EXAM.1216.00002.0002b_00009 582 NA | NA | NA |  ID=2_1;partial=10;start_type=Edge;rbs_motif=None;rbs_spacer=None;gc_cont=0.546 | NA
-MSTLLYLHGFNSSPRSAKACQLKNWLAERHPHVEMIVPQLPPYPADAAELLESLVLEHGG
-APLGLVGSSLGGYYATWLSQCFMLPAVVVNPAVRPFELLTDYLGQNENPYTGQQYVLESR
-HIYDLKVMQIDPLEAPDLIWLLQQTGDEVLDYRQAVAYYASCRQTVTEGGNHAFTGFEDY
-FNQIVDFLGLHSC*
->EXAM.1216.00002.0002b_00010 1308 NA | NA | NA |  ID=2_2;partial=00;start_type=ATG;rbs_motif=None;rbs_spacer=None;gc_cont=0.520 | NA
-MIDPIFASCTLIAVFVVLLAMGAPIGICIVIASFSTMMLVLPFDISMFATAQKMFSSLDS
-FALLAVPFFVLSGVIMNSGGIAARLINFAKLFTGKLPGSLSYTNIVGNMMFGAISGSAIA
-ASTSIGGVMVPMSAREGYDRGFAAAVNIASAPTGMLIPPTTAFILYALASGGTSIAALFA
-GGLVAGVLWGVGCMLVTLVVAKRRNYRVFFTVQKGMALKVAVEAIPSLLLIVIIVGGIVQ
-GIFTAIEASAIAVVYTLLLTMVFYRTLKIKDLPSILLQTVVMTGVIMFLLATSSAMSFSM
-SITNIPAALSDMILGISANKLVILLVITVFLLIIGAFMDIGPAILIFTPILLPIMAKLGV
-DPVHLGIIMIYNLAIGTITPPVGSGLYVGASVGKVKVEEVIKPLLPFYGAIIGVLLLITY
-IPEIILFLPRLLGIM*
->EXAM.1216.00002.0003b_00011 279 NA | NA | NA |  ID=3_1;partial=10;start_type=Edge;rbs_motif=None;rbs_spacer=None;gc_cont=0.355 | NA
-TGLRGAMAMIINGKLIKAKDLAKAAGVSRSTVIKYYGISRENYERVATERRKLAFELRAS
-GLKWKEVAEKMNTTKYSAIAYYRRYLALEKNK*
->EXAM.1216.00002.0003b_00012 780 NA | NA | NA |  ID=3_2;partial=00;start_type=ATG;rbs_motif=None;rbs_spacer=None;gc_cont=0.559 | NA
-MVELQHQRLMVLAEQLQLDSLIGAAPALSQQAVDQEWSYMDFLEHLLHEEKLARHQRKQA
-MYTRMAAFPAVKTFEEYDFTFATGAPQKQIQSLRSLSFIERNENIVLLGPSGVGKTHLAI
-AMGYEAVRAGIKVRFTTAADLLLQLSTSQRQGRYKTTLNRGVMAPKLLIIDEIGYLPFSQ
-EEAKLFFQVIAKRYEKSAMILTSNLPFGQWDQTFAGDAALTSAMLDRILHHSHVVQIKGE
-SYRLKQKRKAGVIAEANPE*
diff --git a/Examples/2-res-Annotate-prodigal/Proteins/EXAM.1219.00001.prt b/Examples/2-res-Annotate-prodigal/Proteins/EXAM.1219.00001.prt
deleted file mode 100644
index 8814964e31f7170f8990718ecd57207b2322a54b..0000000000000000000000000000000000000000
--- a/Examples/2-res-Annotate-prodigal/Proteins/EXAM.1219.00001.prt
+++ /dev/null
@@ -1,69 +0,0 @@
->EXAM.1219.00001.0001b_00001 1668 NA | NA | NA |  ID=1_1;partial=00;start_type=ATG;rbs_motif=None;rbs_spacer=None;gc_cont=0.534 | NA
-MSEAEARPTNFIRQIIDEDLASGKHTTVHTRFPPEPNGYLHIGHAKSICLNFGIAQDYQG
-QCNLRFDDTNPVKEDIEYVDSIKNDVEWLGFHWSGDIRYSSDYFDQLHAYAVELINKGLA
-YVDELTPEQIREYRGTLTAPGKNSPFRDRSVEENLALFEKMRTGGFEEGKACLRAKIDMA
-SPFIVMRDPVLYRIKFAEHHQTGNKWCIYPMYDFTHCISDALEGITHSLCTLEFQDNRRL
-YDWVLDNITIPVHPRQYEFSRLNLEYTVMSKRKLNLLVTDKHVEGWDDPRMPTISGLRRR
-GYTAASIREFCKRIGVTKQDNTIEMASLESCIREDLNENAPRAMAVIDPVKLVIENYPQG
-ESEMVTMPNHPNKPEMGSREVPFSGEIWIDRADFREEANKQYKRLVMGKEVRLRNAYVIK
-AERVEKDAEGNITTIFCTYDADTLSKDPADGRKVKGVIHWVSAAHALPIEIRLYDRLFSV
-PNPGAAEDFLSVINPESLVIKQGYGEPSLKAAVAGKAFQFEREGYFCLDSRYATADKLVF
-NRTVGLRDTWAKAGE*
->EXAM.1219.00001.0001b_00002 831 NA | NA | NA |  ID=1_2;partial=00;start_type=ATG;rbs_motif=AGGAGG;rbs_spacer=5-10bp;gc_cont=0.570 | NA
-MKALLWLVGLALLLTGCASEKGIIDKEGYQLDTRHRAQAAYPRIKVLVIHYTAENFDVSL
-ATLTGRNVSSHYLIPATPPLYGGKPRIWQLVPEQDQAWHAGVSFWRGATRLNDTSIGIEL
-ENRGWRMSGGVKSFAPFESAQIQALIPLAKDIIARYNIKPQNVVAHADIAPQRKDDPGPR
-FPWRELAAQGISAWPDAQRVAFYLAGRAPYTPVDTATVLALLSRYGYEVKADMTAREQQR
-VIMAFQMHFRPAQWNGIADAETQAIAEALLEKYGQD*
->EXAM.1219.00001.0002b_00003 381 NA | NA | NA |  ID=2_1;partial=00;start_type=ATG;rbs_motif=None;rbs_spacer=None;gc_cont=0.538 | NA
-MPHFIAECTENIREQADLPGLFSKVNEALAASGIFPIGGIRSRAHWLDTWQMADGKHDYA
-FVHMTLKIGAGRSLESRQEVGEMLFGLIKAHFADLMENRYLALSFEIAELHPTLNYKQNN
-VHALFK*
->EXAM.1219.00001.0002i_00004 1410 NA | NA | NA |  ID=2_2;partial=00;start_type=ATG;rbs_motif=GGA/GAG/AGG;rbs_spacer=5-10bp;gc_cont=0.512 | NA
-MSMPATKFSRRTLLTAGSALAVLPFLRALPVQAREPRETVDIKDYPADDGIASFKQAFAD
-GQTVVVPPGWVCENINAAITIPAGKTLRVQGAVRGNGRGRFILQDGCQVVGEQGGSLHNV
-TLDVRGSDCVIKGVAMSGFGPVAQIFIGGKEPQVMRNLIIDDITVTHANYAILRQGFHNQ
-MDGARITHSRFSDLQGDAIEWNVAIHDRDILISDHVIERINCTNGKINWGIGIGLAGSTY
-DNSYPEDQAVKNFVVANITGSDCRQLVHVENGKHFVIRNVKAKNITPGFSKNAGIDNATI
-AIYGCDNFVIDNIDMTNSAGMLIGYGVVKGKYLSIPQNFKLNAIRLDNRQVAYKLRGIQI
-SSGNTPSFVAITNVRMTRATLELHNQPQHLFLRNINVMQTSAIGPALKMHFDLRKDVRGQ
-FMARQDTLLSLANVHAINENGQSSVDIDRINHQTVNVEAVNFSLPKRGG*
->EXAM.1219.00001.0002i_00005 774 NA | NA | NA |  ID=2_3;partial=00;start_type=ATG;rbs_motif=None;rbs_spacer=None;gc_cont=0.531 | NA
-MSENKLHVIDLHKRYGGHEVLKGVSLQARAGDVISIIGSSGSGKSTFLRCINFLEKPSEG
-AIIVNGQNINLVRDKDGQLKVADKNQLRLLRTRLTMVFQHFNLWSHMTVLENVMEAPIQV
-LGLSKHDARERALKYLAKVGIDERAQGKYPVHLSGGQQQRVSIARALAMEPDVLLFDEPT
-SALDPELVGEVLRIMQQLAEEGKTMVVVTHEMGFARHVSSHVIFLHQGKIEEEGDPEQVF
-GNPQSPRLQQFLKGSLK*
->EXAM.1219.00001.0002i_00006 735 NA | NA | NA |  ID=2_4;partial=00;start_type=ATG;rbs_motif=None;rbs_spacer=None;gc_cont=0.547 | NA
-MFRAITDYGVTGRAVKKGLLNIQSWSPRDFAHDRHRTVDDRPYGGGPGMLMMVQPLRDAI
-HAAKAAAGEGAKVIYLSPQGRKLDQAGVSELATNQKLILVCGRYEGVDERVIQTEIDEEW
-SIGDYVLSGGELPAMTLIDSVARFIPGVLGHEASAIEDSFADGLLDCPHYTRPEVLEGME
-VPPVLLSGNHAEIRRWRLKQSLGRTWLRRPELLENLALTEEQARLLAEFKTEHAQQQHKH
-DGMA*
->EXAM.1219.00001.0002i_00007 828 NA | NA | NA |  ID=2_5;partial=00;start_type=ATG;rbs_motif=AGxAG;rbs_spacer=5-10bp;gc_cont=0.541 | NA
-MMGWHSRHMGSQRRRANAQYVFIGIVSLFPEMFRAITDYGVTGRAVKKGLLNIQSWSPRD
-FAHDRHRTVDDRPYGGGPGMLMMVQPLRDAIHAAKAAAGEGAKVIYLSPQGRKLDQAGVS
-ELATNQKLILVCGRYEGVDERVIQTEIDEEWSIGDYVLSGGELPAMTLIDSVARFIPGVL
-GHEASAIEDSFADGLLDCPHYTRPEVLEGMEVPPVLLSGNHAEIRRWRLKQSLGRTWLRR
-PELLENLALTEEQARLLAEFKTEHAQQQHKHDGMA*
->EXAM.1219.00001.0002i_00008 465 NA | NA | NA |  ID=2_6;partial=00;start_type=ATG;rbs_motif=AGGA/GGAG/GAGG;rbs_spacer=11-12bp;gc_cont=0.596 | NA
-MKFVAPEQAPEQAEVIKNTPFWPDVDLSEFRSVMRTDGTVTQPRLKQVVLTAISEVNAEL
-YDFRNRQQMLGWRTLAEVPAEMLDGKSERIRHYHNAVFCWARAVLNERYQDYDATASGVK
-RGEELAEASGDLWRDARWAISRVQDVPHCTVELI*
->EXAM.1219.00001.0002i_00009 261 NA | NA | NA |  ID=2_7;partial=00;start_type=ATG;rbs_motif=GGA/GAG/AGG;rbs_spacer=5-10bp;gc_cont=0.487 | NA
-MAGLHAPYAYSAHHAVNFCSEYKRGFVLGFTHRMFEKTGDRQLSAWEAGILTRRYGLDKE
-MVMDFFKENHSGMAVRFFMAGYRLEG*
->EXAM.1219.00001.0002i_00010 582 NA | NA | NA |  ID=2_8;partial=00;start_type=ATG;rbs_motif=None;rbs_spacer=None;gc_cont=0.546 | NA
-MSTLLYLHGFNSSPRSAKACQLKNWLAERHPHVEMIVPQLPPYPADAAELLESLVLEHGG
-APLGLVGSSLGGYYATWLSQCFMLPAVVVNPAVRPFELLTDYLGQNENPYTGQQYVLESR
-HIYDLKVMQIDPLEAPDLIWLLQQTGDEVLYYRQAVAYYASCRQTVTEGGNHAFTGFEDY
-FNQIVDFLGLHSC*
->EXAM.1219.00001.0002b_00011 1308 NA | NA | NA |  ID=2_9;partial=00;start_type=ATG;rbs_motif=None;rbs_spacer=None;gc_cont=0.524 | NA
-MIDPIFASCTLIAVFVVLLAMGAPIGICIVIASFSTMMLVLPFDISMFATAQKMFSSLDS
-FALLAVPFFVLSGVIMNSGGIAARLVNFAKLFTGKLPGSLSYTNIVGNMMFGAISGSAIA
-ASTSIGGVMVPMSAREGYDRGFAAAVNIASAPTGMLIPPTTAFILYALASGGTSIAALFA
-GGLVAGVLWGVGCMLVTLVVAKRRNYRVFFTVQKGMALKVAVEAIPSLLLIVIIVGGIVQ
-GIFTAIEASAIAVVYTLLLTMVFYRTLKIKDLPSILLQTVVMTGVIMFLLATSSAMSFSM
-SITNIPAALSDMILGISANKLVILLVITVFLLIIGAFMDIGPAILIFTPILLPIMAKLGV
-DPVHFGIIMIYNLAIGTITPPVGSGLYVGASVGKVKVEEVIKPLLPFYGAIIGVLLLITY
-IPEITLFLPRLLGIM*
diff --git a/Examples/2-res-Annotate-prodigal/Proteins/GEN2.1219.00001.prt b/Examples/2-res-Annotate-prodigal/Proteins/GEN2.1219.00001.prt
deleted file mode 100644
index 59773c48cecdc678e34d28c4936b15083ca4d282..0000000000000000000000000000000000000000
--- a/Examples/2-res-Annotate-prodigal/Proteins/GEN2.1219.00001.prt
+++ /dev/null
@@ -1,77 +0,0 @@
->GEN2.1219.00001.0001b_00001 774 NA | NA | NA |  ID=1_1;partial=10;start_type=Edge;rbs_motif=None;rbs_spacer=None;gc_cont=0.530 | NA
-MSENKLHVIDLHKRYGGHEVLKGVSLQARAGDVISIIGSSGSGKSTFLRCINFLEKSSEG
-AIIVNGQNINLVRDKDGQLKVADKNQLRLLRTRLTMVFQHFNLWNHMTVLENVMEAPIQV
-LGLSKHDARERALKYLAKVGIDERAQGKYPVHLSGGQQQRVSIARALAMEPDVLLFDEPT
-SALDPELVGEVLRIMQQLAEEGKTMVVVTHEMGFARHVSSHVIFLHQGKIEEEGNPEQVF
-GNPQSPRLQQFLKGSLK*
->GEN2.1219.00001.0001b_00002 1404 NA | NA | NA |  ID=1_2;partial=00;start_type=ATG;rbs_motif=None;rbs_spacer=None;gc_cont=0.510 | NA
-MPATKFSRRTLLTAGSALAVLPFLRALPVQAREPRQTVDIKDYPADDGIASFKQAFADGQ
-TVVVPSGWVCENINAAITIPAGKTLRIQGAVRGNGRGRFILLDGCQVVGEQGGSLHNVTL
-DVRGSDCVIKGVTMSGFGPVAQIFIGGKEPQVMRNLIIDDITVTHANYAILRQGFHNQMD
-GARITHSRFSDLQGDAIEWNVAIHDRDILISDHVIERIDCTNGKINWGIGIGLAGSAYDN
-SYPEDQAVKNFVVANITGSDCRQLVHVENGKHFVIRNVKAKNITPDFSKNAGIDNATIAI
-YGCDNFVIDNIDMTNSAGMLIGYGVVKGKYLSIPQNFKLNAIRLDNRQVAYKLRGIQISS
-GNAPSFVAITNVRMTRATLELHNQPQHLFLRNINVMQTSAIGPALKMHFDLRKDVRGQFM
-ARQDTLLSLANVHAINENGQSSVDIDRINHQTVNVEAVNFSLPKRGG*
->GEN2.1219.00001.0002b_00003 252 NA | NA | NA |  ID=2_1;partial=10;start_type=Edge;rbs_motif=None;rbs_spacer=None;gc_cont=0.540 | NA
-RDNIARAHSMSALFLAIPLTIFVLFVLPIWLWLHYSNRAGRGELSQSEQQRLLQLTDDAQ
-RMRERIQALEDILDAEHPNWRER*
->GEN2.1219.00001.0002i_00004 381 NA | NA | NA |  ID=2_2;partial=00;start_type=ATG;rbs_motif=None;rbs_spacer=None;gc_cont=0.530 | NA
-MPHFIAECTENIREQADLPSLFSKVNEALAATGIFPIGGIRSRAHWLDTWQMADGKHDYA
-FVHMTLKIGAGRSLESRQEVGEMLFGLIKAHFADLMENRYLALSFEIAELHPTLNYKQNN
-VHALFK*
->GEN2.1219.00001.0002i_00005 834 NA | NA | NA |  ID=2_3;partial=00;start_type=ATG;rbs_motif=None;rbs_spacer=None;gc_cont=0.573 | NA
-MMKALLWLVGLALLLTGCASEKGIIDKEGYQLDTRHRAQAAYPRIKVLVIHYTAENFDVS
-LATLTGRNVSSHYLIPATPPLYGGKPRIWQLVPEQDQAWHAGVSFWRGATRLNDTSIGIE
-LENRGWRMSGGVKSFAPFESAQIQALIPLAKDIIARYDIKPQNVVAHADIAPQRKDDPGP
-RFPWRELAAQGIGAWPDAQRVAFYLAGRAPYTPVDTATVLALLSRYGYEVKADMTAREQQ
-RVIMAFQMHFRPAQWNGIADAETQAIAEALLEKYGQD*
->GEN2.1219.00001.0002b_00006 1668 NA | NA | NA |  ID=2_4;partial=00;start_type=ATG;rbs_motif=GGA/GAG/AGG;rbs_spacer=5-10bp;gc_cont=0.537 | NA
-MSEAEARPTNFIRQIIDEDLASGKHTTVHTRFPPEPNGYLHIGHAKSICLNFGIAQDYQG
-QCNLRFDDTNPVKEDIEYVDSIKNDVEWLGFHWSGDIRYSSDYFDQLHAYAVELINKGLA
-YVDELTPEQIREYRGTLTAPGKNSPFRDRSVEENLALFEKMRTGGFEEGKACLRAKIDMA
-SPFIVMRDPVLYRIKFAEHHQTGTKWCIYPMYDFTHCISDALEGITHSLCTLEFQDNRRL
-YDWVLDNITIPVHPRQYEFSRLNLEYTVMSKRKLNLLVTDKHVEGWDDPRMPTISGLRRR
-GYTAASIREFCKRIGVTKQDNTIEMASLESCIREDLNENAPRAMAVIDPVKLVIENYPQG
-ESEMVTMPNHPNKPEMGSREVPFSGEIWIDRADFREEANKQYKRLVMGKEVRLRNAYVIK
-AERVEKDAEGNITTIFCTYDADTLSKDPADGRKVKGVIHWVSVAHALPIEIRLYDRLFSV
-PNPGAAEDFLSVINPESLVIKQGYGEPSLKAAVAGKAFQFEREGYFCLDSRYATADKLVF
-NRTVGLRDTWAKAGE*
->GEN2.1219.00001.0003b_00007 768 NA | NA | NA |  ID=3_1;partial=00;start_type=GTG;rbs_motif=GGA/GAG/AGG;rbs_spacer=5-10bp;gc_cont=0.540 | NA
-MFIGIVSLFPEMFRAITDYGVTGRAVKKGLLNIQSWSPRDFAHDRHRTVDDRPYGGGPGM
-LMMVQPLRDAIHAAKAAAGEGAKVIYLSPQGRKLDQAGVSELATNQKLILVCGRYEGVDE
-RVIQAEIDEEWSIGDYVLSGGELPAMTLIDSVARFIPGVLGHEASAIEDSFADGLLDCPH
-YTRPEVLEGMEVPPVLLSGNHAEIRRWRLKQSLGRTWLRRPELLENLALTEEQARLLAEF
-KTEHAQQQHKHDGMA*
->GEN2.1219.00001.0003i_00008 261 NA | NA | NA |  ID=3_2;partial=00;start_type=ATG;rbs_motif=GGA/GAG/AGG;rbs_spacer=5-10bp;gc_cont=0.487 | NA
-MAGLHAPYAYSAHHAVNFCSEYKRGFVLGFTHRMFEKTGDRQLSAWEAGILTRRYGLDKE
-MVMDFFKENHSGMAVRFFMAGYRLEG*
->GEN2.1219.00001.0003i_00009 582 NA | NA | NA |  ID=3_3;partial=00;start_type=ATG;rbs_motif=None;rbs_spacer=None;gc_cont=0.546 | NA
-MSTLLYLHGFNSSPRSAKACQLKNWLAERHPHVEMIVPQLPPYPADAAELLESLVLEHGG
-APLGLVGSSLGGYYATWLSQCFMLPAVVVNPAVRPFELLTDYLGQNENPYTGQQYVLESR
-HIYDLKVMQIDPLEAPDLIWLLQQTGDEVLDYRQAVAYYASCRQTVTEGGNHAFTGFEDY
-FNQIVDFLGLHSC*
->GEN2.1219.00001.0003b_00010 369 NA | NA | NA |  ID=3_4;partial=00;start_type=ATG;rbs_motif=GGAG/GAGG;rbs_spacer=5-10bp;gc_cont=0.599 | NA
-MMRTDGTVTQPRLKQVALSAISEVNAELYEFRRRQQMLGYASLAEVPAEQLDGKSERIQH
-YFNAVYCWARAMLNERYQDYDATASGVKRGEELAEASGDLWRDARWAISRVQDAPHCTVE
-LI*
->GEN2.1219.00001.0004b_00011 1308 NA | NA | NA |  ID=4_1;partial=10;start_type=Edge;rbs_motif=None;rbs_spacer=None;gc_cont=0.519 | NA
-MIDPIFASCTLIAVFVVLLAMGAPIGICIVIASFSTMMLVLPFDISMFATAQKMFSSLDS
-FALLAVPFFVLSGVIMNSGGIAARLVNFAKLFTGKLPGSLSYTNIVGNMMFGAISGSAIA
-ASTSIGGVMVPMSAREGYDRGFAAAVNIASAPTGMLIPPTTAFILYALASGGTSIAALFA
-GGLVAGVLWGVGCMLVTLVVAKRRNYRVFFTVQKGMALKVAVEAIPSLLLIVIIVGGIVQ
-GIFTAIEASAIAVVYTLLLTIVFYRTLKIKDLPSILLQTVVMTGVIMFLLATSSAMSFSM
-SITNIPAALSDMILGISANKLVILLVITVFLLIIGAFMDIGPAILIFTPILLPIMTKLGV
-DPVHFGIIMIYNLAIGTITPPVGSGLYVGASVGKVKVEDVIKPLMPFYGAIIGVLLLITY
-IPEITLFLPRLLGIM*
->GEN2.1219.00001.0004i_00012 465 NA | NA | NA |  ID=4_2;partial=00;start_type=ATG;rbs_motif=None;rbs_spacer=None;gc_cont=0.594 | NA
-MKFVAPEQAPEQAEVIKNTPFWPDVNLSEFRSVMRTDGTVTQPRLKQVVLTAISEVNAEL
-YDFRNRQQMLGWRTLAEVPAEMLDGKSERIRHYHNAVFCWARAVLNERYQDYDATASGVK
-RGEELAEASGDLWRDARWAISRVQDAPHCTVELI*
->GEN2.1219.00001.0004b_00013 1014 NA | NA | NA |  ID=4_3;partial=00;start_type=ATG;rbs_motif=None;rbs_spacer=None;gc_cont=0.456 | NA
-METNITWQQLIDEYFFAKPLRSASEWSYTKVFKSFVHYMGPLSCPNDVTYHKVLAWRRFL
-LKEKKLSGRTWNNKVAHMRAIFNYGIQRGLLHYDENPFNNSVVKPDKKRKKTLTQAQIEY
-AYQIMEQYENQENTGLGLKYSRCALFPAWFWLTVLDTLYYTGIRQNQLLHIRLNDVDLRE
-GQIRLITEGCKNHKEHYVPVISFLRPRLTCLMEKAQSEGLKGNDRLFNIALFTGKDPAIG
-DDMDSPQVRAFFRRLSKECQFAISPHRFRHTLATEMMKMPEQNLHMAQSVLGHSNMKSTL
-EYVENDIAVMGRALEAQFMQIKAAHARSIYSGLTKNR*
diff --git a/Examples/2-res-Annotate-prodigal/Proteins/GEN4.1111.00001.prt b/Examples/2-res-Annotate-prodigal/Proteins/GEN4.1111.00001.prt
deleted file mode 100644
index 50fff31770d30deb9bd4735e236d3fdb0087eb90..0000000000000000000000000000000000000000
--- a/Examples/2-res-Annotate-prodigal/Proteins/GEN4.1111.00001.prt
+++ /dev/null
@@ -1,53 +0,0 @@
->GEN4.1111.00001.0001b_00001 831 NA | NA | NA |  ID=1_1;partial=10;start_type=Edge;rbs_motif=None;rbs_spacer=None;gc_cont=0.579 | NA
-MKALLWLVGLALLLTGCASEKGIIDKEGYQLDTRHRAQAAYPRIKVLVIHYTAENFDVSL
-ATLTGRNVSSHYLIPATPPLYGGKPRIWQLVPEQDQAWHAGVSFWRGATRLNDTSIGIEL
-ENRGWRMSGGVKSFAPFESAQIQALIPLAKDIIARYDIKPQNVVAHADIAPQRKDDPGPR
-FPWRELAAQGIGAWPDAQRVAFYLAGRAPYTPVDTATVLALLSRYGYEVKADMTAREQQR
-VIMAFQMHFRPAQWNGIADAETQAIAEALLEKYGQD*
->GEN4.1111.00001.0001i_00002 381 NA | NA | NA |  ID=1_2;partial=00;start_type=ATG;rbs_motif=None;rbs_spacer=None;gc_cont=0.533 | NA
-MPHFIAECTENIREQADLPGLFSKVNEALAASGIFPIGGIRSRAHWLDTWQMADGKHDYA
-FVHMTLKIGTGRSLESRQEVGEMLFGLIKAHFADLMENRYLALSFEIAELHPTLNYKQNN
-VHALFK*
->GEN4.1111.00001.0001i_00003 804 NA | NA | NA |  ID=1_3;partial=00;start_type=ATG;rbs_motif=AGGAG;rbs_spacer=5-10bp;gc_cont=0.591 | NA
-MLDKQTHTLIAQRLNQAEKQREQIRAVSLDYPNITIEDAYAVQREWVNIKIAEGRTLKGH
-KIGLTSKAMQASSQISEPDYGALLDDMFFHDGGDIPTDRFIVPRIEVELAFVLAKPLRGP
-HCTLFDVYNATDYVIPALELIDARSHNIDPETQRPRKVFDTISDNAANAGVILGGRPIKP
-DELDLRWISALLYRNGVIEETGVAAGVLNHPANGVAWLANKLAPYDVQLEAGQIILGGSF
-TRPVPASKGDTFHVDYGNMGAISCRFV*
->GEN4.1111.00001.0001i_00004 1404 NA | NA | NA |  ID=1_4;partial=00;start_type=ATG;rbs_motif=None;rbs_spacer=None;gc_cont=0.512 | NA
-MPVNKFSRRTLLTAGSALAVLPFLRALPVQAREPRETVDIKDYPADDGIASFKQAFADGQ
-TVVLPPGWVCENINAAITIPAGKTLRVQGAVRGNGRGRFILQDGCQVVGEQGGSLHNVTL
-DVRGSDCVIKGVTMSGFGPVAQIFIGGKEPQVMRNLIIDDITVTHANYAILRQGFHNQMD
-GARITHSRFSDLQGDAIEWNVAIHDRDILISDHVIERIDCTNGKINWGIGIGLAGSTYDN
-SYPEDQAVKNFVVANITGSDCRQLVHVENGKHFVIRNVKAKNITPDFSKNAGIDNATIAI
-YGCDNFVIDNIDMTNSAGMLIGYGVVKGKYLSIPQNFKLNAIRLDNRQVAYKLRGIQISS
-GNIPSFVAITNVRMTRATLELHNQPQHLFLRNINVMQTSAIGPALKMHFDLRKDVRGQFM
-ARQDTLLSLANVHAINENGQSSVDIDRINHQTVNVEAVNFSLPKRGG*
->GEN4.1111.00001.0001i_00005 774 NA | NA | NA |  ID=1_5;partial=00;start_type=ATG;rbs_motif=3Base/5BMM;rbs_spacer=13-15bp;gc_cont=0.532 | NA
-MSENKLHVIDLHKRYGGHEVLKGVSLQARAGDVISIIGSSGSGKSTFLRCINFLEKPSEG
-AIIVNGQNINLVRDKDGQLKVADKNQLRLLRTRLTMVFQHFNLWSHMTVLENVMEAPIQV
-LGLSKHDARERALKYLAKVGIDERAQGKYPVHLSGGQQQRVSIARALAMEPDVLLFDEPT
-SALDPELVGEVLRIMQQLAEEGKTMVVVTHEMGFARHVSSHVIFLHQGKIEEEGDPEQVF
-GNPQSPRLQQFLKGSLK*
->GEN4.1111.00001.0001i_00006 768 NA | NA | NA |  ID=1_6;partial=00;start_type=GTG;rbs_motif=None;rbs_spacer=None;gc_cont=0.544 | NA
-MFIGIVSLFPEMFRAITDYGVTGRAVKKGLLNIQSWSPRDFAHDRHRTVDDRPYGGGPGM
-LMMVQPLRDAIHAAKAAAGEGAKVIYLSPQGRKLDQAGVSELATNQKLILVCGRYEGVDE
-RVIQTEIDEEWSIGDYVLSGGELPAMTLIDSVARFIPGVLGHEASAIEDSFADGLLDCPH
-YTRPEVLEGMEVPPVLLSGNHAEIRRWRLKQSLGRTWLRRPELLENLALTEEQARLLAEF
-KTEHAQQQHKHDGMA*
->GEN4.1111.00001.0001i_00007 261 NA | NA | NA |  ID=1_7;partial=00;start_type=ATG;rbs_motif=GGA/GAG/AGG;rbs_spacer=5-10bp;gc_cont=0.483 | NA
-MAGLHAPYAYSAHHAVNFCSEYKRGFVLGFTHRMFEKTGDRQLSAWEAGILTRRYGLDKE
-MVMDFFKENHSGMAVRFFMVGYRLEG*
->GEN4.1111.00001.0001i_00008 582 NA | NA | NA |  ID=1_8;partial=00;start_type=ATG;rbs_motif=None;rbs_spacer=None;gc_cont=0.546 | NA
-MSTLLYLHGFNSSPRSAKACQLKNWLAERHPHVEMIVPQLPPYPADAAELLESLVLEHGG
-APLGLVGSSLGGYYATWLSQCFMLPAVVVNPAVRPFELLTDYLGQNENPYTGQQYVLESR
-HIYDLKVMQIDPLEAPDLIWLLQQTGDEVLDYRQAVAYYASCRQTVTEGGNHAFTGFEDY
-FNQIVDFLGLHSC*
->GEN4.1111.00001.0001b_00009 1083 NA | NA | NA |  ID=1_9;partial=00;start_type=ATG;rbs_motif=None;rbs_spacer=None;gc_cont=0.525 | NA
-MNSGGIAARLVNFAKLFTGKLPGSLSYTNIVGNMMFGAISGSAIAASTSIGGVMVPMSAR
-EGYDRGFAAAVNIASAPTGMLIPPTTAFILYALASGGTSIAALFAGGLVAGVLWGVGCML
-VTLVVAKRRNYRVFFTVQKGMALKVAVEAIPSLLLIVIIVGGIVQGIFTAIEASAIAVVY
-TLLLTMVFYRTLKIKDLPSILLQTVVMTGVIMFLLATSSAMSFSMSITNIPAALSDMILG
-ISANKLVILLVITVFLLIIGAFMDIGPAILIFTPILLPIMAKLGVDPVHFGIIMIYNLAI
-GTITPPVGSGLYVGASVGKVKVEEVIKPLLPFYGAIIGVLLLITYIPEITLFLPRLLGIM
-*
diff --git a/Examples/2-res-Annotate-prodigal/QC_L90-list_genomes.png b/Examples/2-res-Annotate-prodigal/QC_L90-list_genomes.png
deleted file mode 100644
index 98988190f52b4fc64da18473ed96bc3bf3751f04..0000000000000000000000000000000000000000
Binary files a/Examples/2-res-Annotate-prodigal/QC_L90-list_genomes.png and /dev/null differ
diff --git a/Examples/2-res-Annotate-prodigal/QC_nb-contigs-list_genomes.png b/Examples/2-res-Annotate-prodigal/QC_nb-contigs-list_genomes.png
deleted file mode 100644
index 25433444de0c917cb715f8f4a67f9836a6e2afde..0000000000000000000000000000000000000000
Binary files a/Examples/2-res-Annotate-prodigal/QC_nb-contigs-list_genomes.png and /dev/null differ
diff --git a/Examples/2-res-Annotate-prodigal/Replicons/EXAM.1216.00002.fna b/Examples/2-res-Annotate-prodigal/Replicons/EXAM.1216.00002.fna
deleted file mode 100644
index bd0e1394f21b9f26a5a6dbf61eb728bc620e97f1..0000000000000000000000000000000000000000
--- a/Examples/2-res-Annotate-prodigal/Replicons/EXAM.1216.00002.fna
+++ /dev/null
@@ -1,6 +0,0 @@
->EXAM.1216.00002.0001	5747
-ATGAGAGCGCTACTGTGGCTGGTGGGTCTTGCGTTGCTGTTAACAGGCTGCGCGAGCGAAAAAGGAATTATCGATGAAGAGGGATATCAGCTTGATACCCGACATCGGGCGCAGGCGGCCTATCCGCGCATTAAAGTCCTGGTGATTCACTATACGGCGGAAAACTTTGACGTTTCGCTGGCGACGTTAACGGGCCGCAACGTCAGTTCGCATTACCTGATTCCCGCAACCCCGCCATTATATGGCGGTAAACCGCGCATCTGGCAACTGGTGCCGGAACAGGATCAGGCCTGGCATGCGGGCGTCAGTTTCTGGCGAGGCGCCACGCGTCTCAATGATACGTCTATTGGCATTGAGCTGGAAAATCGCGGCTGGCGAATGTCCGGCGGGGTGAAATCTTTCGCGCCGTTTGAATCCGCGCAAATTCAGGCATTGATTCCGTTAGCGAAGGACATTATCGCGCGCTATGACATCAAACCGCAGAATGTGGTGGCCCATGCGGATATCGCGCCGCAGCGTAAAGACGATCCCGGCCCGCGCTTCCCGTGGCGCGAGCTGGCGGCACAGGGGATTGGCGCCTGGCCTGACGCCCAGCGTGTGGCGTTTTATCTGGCTGGACGCGCGCCGTATACGCCAGTCGATACCGCAACGGTGCTTGCGTTACTCTCGCGCTATGGCTATGAAGTCAAAGCCGATATGACGGCGCGCGAGCAACAGCGGGTGATTATGGCGTTCCAGATGCACTTCCGTCCGGCGCAATGGAACGGTATCGCAGATGCCGAAACGCAGGCGATTGCCGAAGCATTACTGGAGAAGTACGGCCAGGATTAACGAGTCCGGGAGCGGCGAGATTCCGGGCAGAGGAGGCGGCTATAGCGGATGAGAGCGCTACTGTGGCTGGTGGGTCTTGCGTTGCTGTTAACAGGCTGCGCGAGCGAAAAAGGAATTATCGATGAAGAGGGATATCAGCTTGATACCCGACATCGGGCGCAGGCGGCCTATCCGCGCATTAAAGTCCTGGTGATTCACTATACGGCGGAAAACTTTGACGTTTCGCTGGCGACGTTAACGGGCCGCAACGTCAGTTCGCATTACCTGATTCCCGCAACCCCGCCATTATATGGCGGTAAACCGCGCATCTGGCAACTGGTGCCGGAACAGGATCAGGCCTGGCATGCGGGCGTCAGTTTCTGGCGAGGCGCCACGCGTCTCAATGATACGTCTATTGGCATTGAGCTGGAAAATCGCGGCTGGCGAATGTCCGGCGGGGTGAAATCTTTCGCGCCGTTTGAATCCGCGCAAATTCAGGCATTGATTCCGTTAGCGAAGGACATTATCGCGCGCTATGACATCAAACCGCAGAATGTGGTGGCCCATGCGGATATCGCGCCGCAGCGTAAAGACGATCCCGGCCCGCGCTTCCCGTGGCGCGAGCTGGCGGCACAGGGGATTGGCGCCTGGCCTGACGCCCAGCGTGTGGCGTTTTATCTGGCTGGACGCGCGCCGTATACGCCAGTCGATACCGCAACGGTGCTTGCGTTACTCTCGCGCTATGGCTATGAAGTCAAAGCCGATATGACGGCGCGCGAGCAACAGCGGGTGATTATGGCGTTCCAGATGCACTTCCGTCCGGCGCAATGGAACGGTATCGCAGATGCCGAAACGCAGGCGATTGCCGAAGCATTACTGGAGAAGTACGGCCAGGATTAACAGGGCGCGGTATCGCGAGGACTCTCTCTTCGAGGACATGCCGCACTTTATTGCTGAATGTACTGAAAATATTCGCGAGCAGGCTGATTTACCCGGCCTGTTCAGCAAGGTAAACGAGGCGCTGGCCGCCAGCGGGATTTTCCCCATCGGCGGTATCCGCAGTCGCGCCCACTGGCTGGATACCTGGCAGATGGCTGACGGTAAGCATGATTACGCGTTTGTGCATATGACGCTGAAAATCGGCGCCGGGCGCAGCCTGGAGAGCCGTCAGGAAGTCGGCGAAATGCTGTTCGGGCTGATTAAAGCCCACTTCGCCGACCTGATGGAGAACCGCTATCTGGCGCTGTCGTTTGAGATTGCCGAGTTACATCCAACGCTCAATTACAAACAAAACAACGTACACGCGTTATTTAAATAGCCCGAGTATTAGCGCGCGGCGGCGCTATAGGCGCGCTATAGGCATGAGCGCGCTATTTCTGGCCATCCCGTTAACCATTTTTGTGTTGTTTGTGTTACCGATTTGGCTGTGGCTGCATTACAGCAACCGCGCCGGTCGGGGAGAACTGTCGCAAAGCGAGCAGCAACGCTTACTGCAACTCACAGACGACGCGCAACGTATGCGCGAGCGCATTCAGGCGCTGGAAGACATTCTTGATGCAGAGCATCCGAACTGGAGAGAGCGCTAACGAGAGTCTCGGAGGAGCGGCGCTCTGGATGCCCGCGACTAAATTCTCCCGACGTACCCTCCTGACGGCAGGTTCTGCGCTTGCTGTTCTTCCTTTCCTGCGCGCCTTGCCGGTACAGGCGCGTGAACCTCGCGAGACCGTCGATATTAAGGATTATCCGGCGGATGACGGTATCGCCTCGTTCAAACAGGCCTTCGCCGACGGACAGACCGTGGTCGTACCGCCAGGATGGGTGTGTGAAAATATCAATGCGGCGATAACGATTCCGGCGGGAAAAACGCTGCGGGTACAGGGCGCGGTGCGTGGGAATGGCCGGGGACGGTTTATTTTGCAGGACGGGTGTCAGGTGGTGGGGGAGCAGGGCGGCAGTCTGCACAATGTGACGCTGGATGTTCGCGGGTCGGACTGTGTGATTAAAGGCGTGGCGATGAGCGGCTTTGGCCCCGTCGCGCAAATTTTCATCGGTGGTAAGGAACCGCAGGTGATGCGTAATCTCATTATCGATGACATCACCGTTACCCACGCCAACTACGCCATTCTCCGCCAGGGATTTCATAACCAAATGGACGGCGCGAGGATTACGCATAGCCGCTTTAGCGATTTACAGGGGGACGCCATTGAGTGGAATGTCGCGATTCACGACCGCGATATCCTGATTTCCGATCATGTCATCGAACGCATTGATTGTACCAATGGCAAAATCAACTGGGGGATCGGCATCGGGCTGGCGGGTAGCACCTATGACAACAGTTATCCTGAAGACCAGGCAGTAAAAAACTTTGTGGTGGCCAATATTACCGGATCTGATTGCCGACAGCTTGTGCACGTAGAAAATGGCAAACATTTCGTCATTCGCAATGTCAAAGCCAAAAACATCACGCCCGATTTCAGTAAAAATGCGGGTATTGATAACGCAACGATCGCAATTTATGGCTGTGATAATTTCGTCATTGATAATATTGATATGACGAATAGTGCCGGGATGCTCATCGGCTATGGCGTCGTTAAAGGAAAATACCTGTCAATTCCGCAAAACTTTAAATTAAACGCTATTCGGTTGGATAATCGCCAGGTTGCTTATAAATTACGCGGCATTCAAATTTCCTCCGGCAACACCCCCTCTTTTGTCGCCATCACCAATGTACGGATGACGCGTGCTACGCTGGAACTGCATAATCAACCGCAGCACCTCTTCCTGCGTAATATCAACGTGATGCAAACTTCAGCGATTGGCCCGGCGTTAAAAATGCATTTCGATTTGCGTAAAGATGTCCGTGGTCAATTTATGGCCCGCCAGGACACGCTGCTTTCCCTCGCTAATGTTCATGCCATCAATGAAAACGGGCAGAGTTCCGTGGATATCGACAGGATTAATCACCAAACCGTGAATGTCGAAGCAGTGAATTTTTCGCTGCCGAAGCGGGGAGGGTAACGCGTCTGCGCGCGCGGAGAGAGGCTCTCAGGACATGTCAGAAAATAAATTACACGTTATCGATTTGCACAAACGCTACGGCGGTCATGAAGTGCTGAAAGGGGTATCGCTGCAGGCCCGCGCCGGAGATGTGATTAGCATCATCGGCTCGTCCGGCTCCGGTAAAAGCACTTTTTTGCGCTGTATTAACTTCCTCGAAAAACCGAGCGAAGACGCGATTATCGTGAACGGTCAGAACATTAATCTGGTGCGCGACAAAGACGGGCAGCTCAAAGTGGCGGATAAAAATCAGCTACGCTTGTTGCGTACCCGCCTGACGATGGTGTTTCAGCACTTTAACCTCTGGAGCCACATGACGGTGCTGGAAAATGTGATGGAAGCGCCGATTCAGGTACTGGGATTAAGCAAGCACGACGCGCGCGAGCGGGCGTTGAAATATCTGGCGAAGGTGGGGATTGATGAGCGCGCTCAGGGCAAATATCCCGTTCATCTCTCCGGTGGCCAACAGCAGCGCGTTTCTATTGCGCGCGCGCTGGCGATGGAACCTGACGTTTTACTGTTCGATGAACCCACTTCGGCGCTCGATCCTGAACTGGTCGGCGAAGTGTTGCGCATCATGCAACAACTGGCGGAAGAAGGCAAAACGATGGTGGTGGTCACGCATGAAATGGGCTTCGTTCGCCATGTCTCTTCGCACGTTATTTTTCTGCATCAGGGGAAAATTGAAGAAGAGGGCGATCCGGAGCAGGTGTTCGGCAATCCGCAAAGCCCGCGTTTACAGCAATTCCTGAAAGGCTCGCTGAAATAACCGGATGCGCGCGATATATCGGCGATGCGTGTTTATTGGCATCGTTAGCCTGTTTCCTGAAATGTTCCGCGCAATTACCGATTACGGGGTAACTGGCCGGGCAGTAAAAAATGGCCTGCTGAACATCCAAAGCTGGAGTCCTCGCGACTTCACGCATGACCGGCACCGTACCGTGGACGATCGTCCTTACGGCGGCGGACCAGGGATGTTAATGATGGTGCAACCCTTGCGGGACGCCATTCACGCAGCAAAAGCCGCGGCAGGTGAAGGCGCTAAAGTGATTTATCTGTCGCCTCAGGGACGCAAGCTTGATCAAGCGGGCGTTAGCGAGCTGGCCACGAATCAGAAGCTTATTCTGGTGTGTGGTCGCTACGAAGGCGTAGATGAGCGCGTAATTCAGACCGAAATTGACGAAGAATGGTCAATTGGCGATTACGTTCTCAGCGGTGGCGAACTACCGGCAATGACGCTGATTGACTCCGTCGCCCGGTTTATACCGGGAGTTCTGGGGCATGAAGCATCAGCAATCGAAGATTCGTTTGCTGATGGGTTGCTGGATTGTCCGCACTATACGCGCCCTGAAGTGTTAGAGGGGATGGAAGTACCGCCAGTATTGCTGTCGGGAAACCATGCTGAGATACGTCGCTGGCGTTTGAAACAGTCGCTGGGCCGAACCTGGCTTAGAAGACCTGAACTTCTGGAAAACCTGGCTCTGACTGAAGAGCAAGCAAGGTTGCTGGCGGAGTTCAAAACAGAACACGCACAACAGCAGCATAAACATGATGGGATGGCATAGCCGGCTCTGCGAGAGAGGAGCGCTCGCATGAATAATCATTTTGGGAAAGGGTTAATGGCCGGGTTGCACGCGCCATATGCATATAGCGCGCATCATGCGGTGAATTTCTGTTCTGAGTATAAACGTGGCTTTGTATTGGGTTTTACACACCGTATGTTCGAAAAGACCGGCGATCGTCAACTTAGCGCGTGGGAGGCTGGAATTCTGACGCGTCGCTATGGTCTGGATAAAGAAATGGTGATGGATTTCTTTAAAGAGAATCATTCCGGGATGGCGGTTCGCTTCTTTATGGCCGGTTATCGACTCGAAGGTTGA
->EXAM.1216.00002.0002	1968
-ATGTCTACGCTTCTCTATTTGCACGGATTCAACAGTTCCCCTCGCTCGGCAAAAGCGTGCCAGCTAAAAAACTGGCTGGCGGAGCGTCATCCGCATGTTGAGATGATCGTCCCTCAACTACCGCCGTATCCTGCCGATGCGGCGGAGTTGCTGGAGTCTCTCGTGCTTGAGCATGGCGGTGCGCCATTAGGGCTGGTAGGATCGTCGCTGGGTGGTTATTACGCCACCTGGCTGTCGCAATGTTTTATGCTGCCGGCTGTGGTGGTGAATCCCGCCGTGCGGCCCTTTGAATTACTGACCGACTATCTCGGTCAGAACGAGAACCCCTACACCGGGCAGCAATATGTGCTAGAGTCTCGCCATATTTATGATCTTAAAGTCATGCAGATTGACCCGCTGGAAGCGCCGGACCTGATCTGGCTACTGCAACAGACGGGCGATGAAGTGCTGGATTACCGCCAGGCGGTGGCATATTACGCCTCCTGCCGTCAGACAGTGACCGAGGGTGGTAATCACGCATTCACGGGCTTCGAAGATTATTTCAACCAGATTGTCGATTTTCTTGGACTGCACAGTTGCTGACGCGTAGCGGCCGGAATCTTCTCGGAGAGGCGCTTCTCTCTCGGAGATGATTGACCCTATTTTTGCGTCCTGTACGCTAATTGCCGTCTTTGTTGTTTTACTGGCCATGGGCGCGCCTATCGGGATCTGCATCGTTATCGCCTCTTTCAGCACCATGATGCTGGTACTGCCTTTCGATATTTCGATGTTCGCCACCGCGCAAAAAATGTTCTCCAGCCTGGACAGTTTTGCCTTGCTGGCCGTGCCGTTCTTCGTTTTGTCCGGGGTGATCATGAATAGCGGGGGAATTGCCGCCCGGCTGATCAATTTTGCCAAACTGTTTACTGGCAAACTGCCCGGTTCGCTCTCTTATACCAACATCGTCGGCAATATGATGTTCGGTGCAATTTCCGGATCGGCAATTGCCGCCTCAACCTCCATCGGCGGCGTGATGGTGCCGATGAGCGCGCGCGAAGGTTACGATCGCGGCTTTGCGGCCGCGGTGAATATCGCCTCCGCGCCGACGGGAATGTTAATTCCGCCCACCACGGCTTTTATCCTTTATGCGCTGGCAAGCGGGGGAACATCGATTGCCGCTCTGTTCGCCGGCGGTCTGGTCGCGGGAGTGCTGTGGGGCGTTGGCTGTATGCTGGTCACGCTGGTAGTCGCTAAGCGTCGAAATTATCGGGTTTTCTTCACCGTCCAAAAAGGCATGGCGCTAAAAGTTGCCGTTGAGGCCATTCCCAGCCTGTTACTGATCGTGATTATCGTCGGCGGCATTGTGCAGGGGATTTTCACCGCCATTGAAGCCTCCGCGATTGCCGTGGTGTATACGTTATTGCTGACGATGGTGTTTTACCGCACGCTGAAAATTAAGGATTTGCCTTCGATTTTGCTCCAGACAGTGGTAATGACCGGGGTCATCATGTTCCTGCTGGCAACCTCTTCGGCGATGTCCTTCTCAATGTCGATCACCAATATTCCTGCGGCGCTGAGCGATATGATCCTCGGTATTTCCGCCAATAAACTGGTTATCCTGTTAGTCATTACCGTCTTTTTGTTGATTATCGGCGCATTTATGGATATCGGTCCGGCCATTCTGATTTTTACCCCGATTCTGCTGCCGATCATGGCTAAACTGGGCGTCGATCCGGTGCATTTGGGCATTATCATGATCTATAACCTGGCGATTGGCACCATTACGCCGCCAGTTGGCAGTGGTTTATATGTCGGGGCGAGCGTCGGTAAGGTCAAAGTTGAGGAAGTGATTAAACCGTTGCTGCCTTTTTACGGCGCGATTATCGGCGTTCTGTTATTAATTACCTACATTCCGGAAATCATACTGTTCTTACCCCGTCTACTGGGCATCATGTAAACCCGATGGCGCGCAGAGGCGCGAGTTCTGGA
->EXAM.1216.00002.0003	1102
-CACAGGGCTTAGAGGCGCTATGGCAATGATAATTAATGGGAAATTAATTAAAGCAAAAGACTTAGCTAAGGCTGCAGGTGTATCTCGTTCAACAGTGATTAAATATTACGGCATTAGCCGTGAGAATTACGAAAGGGTAGCAACTGAAAGAAGGAAGCTTGCTTTTGAACTAAGAGCATCAGGTTTAAAATGGAAAGAAGTTGCTGAAAAAATGAACACGACAAAATATAGCGCAATTGCATATTATAGACGATATTTAGCATTAGAGAAAAACAAATAACAGGCGCTAAGGCGGCGATCCTAGCGCGCGATCGCGCATGCGATGGTCGAACTGCAACATCAACGGCTGATGGTGCTTGCCGAACAGCTCCAGCTGGACAGTCTTATCGGCGCAGCGCCGGCGCTGTCGCAACAGGCGGTGGATCAGGAATGGAGCTACATGGACTTCCTGGAGCACCTGTTACATGAGGAGAAACTGGCCCGGCATCAGCGTAAACAGGCGATGTACACGCGGATGGCAGCCTTCCCGGCGGTAAAGACGTTCGAGGAGTACGACTTCACCTTCGCCACCGGCGCTCCTCAGAAGCAAATCCAGTCGCTGCGATCCCTGAGCTTCATAGAGCGTAACGAAAACATCGTGTTGCTGGGGCCATCGGGCGTGGGAAAAACGCATCTGGCGATAGCCATGGGCTACGAAGCAGTACGGGCGGGCATCAAGGTTCGCTTCACAACAGCAGCGGACCTGCTGCTACAGCTGTCCACTTCACAGCGTCAGGGCCGTTACAAAACGACTCTCAATCGTGGTGTCATGGCCCCGAAGCTGCTTATCATCGATGAAATAGGTTATCTGCCGTTCAGTCAGGAGGAAGCCAAGCTGTTCTTCCAGGTCATCGCCAAACGTTACGAGAAGAGCGCGATGATCCTGACCTCCAACCTGCCGTTCGGGCAGTGGGATCAGACGTTCGCCGGTGATGCAGCGCTGACATCGGCGATGCTGGACCGGATCTTACATCACTCACACGTCGTGCAAATAAAAGGGGAAAGCTATCGACTGAAGCAGAAACGAAAGGCCGGGGTTATAGCTGAAGCTAATCCTGAGTAA
diff --git a/Examples/2-res-Annotate-prodigal/Replicons/EXAM.1219.00001.fna b/Examples/2-res-Annotate-prodigal/Replicons/EXAM.1219.00001.fna
deleted file mode 100644
index 8245cff51e58bd17ae799d8507ae99b28b3e9fdd..0000000000000000000000000000000000000000
--- a/Examples/2-res-Annotate-prodigal/Replicons/EXAM.1219.00001.fna
+++ /dev/null
@@ -1,4 +0,0 @@
->EXAM.1219.00001.0001	2784
-ATGTGTAAAAGCCGGAGGGGTTATCTTTTCCCGGCTTTTTATTATCAATTACTCATTAACTCCTGTTCCGTTCTTTTGCGTTTAATCACCGGAATATCTCCGGTATTGTTCAGCGCCCCGGAAATGTTTTTAACCACTGTTCTGCACTCCGTTTATTAAACGCGCTCAGCGCGCGCTCATATATCGCGCGCGCGCGCGCGCATATATATATAATGAGTGAGGCTGAAGCCCGCCCGACTAACTTTATTCGTCAGATTATTGATGAAGATCTGGCGAGTGGTAAACATACCACTGTCCATACCCGTTTTCCGCCGGAGCCGAATGGCTATCTGCATATCGGCCACGCGAAATCTATCTGCCTGAACTTTGGCATCGCGCAAGATTATCAGGGCCAGTGCAACCTGCGTTTCGATGACACCAACCCGGTAAAAGAAGATATCGAGTACGTTGATTCGATCAAAAACGACGTCGAGTGGTTAGGCTTTCACTGGTCTGGCGATATTCGCTACTCCTCCGATTACTTTGACCAACTGCACGCCTATGCGGTCGAGCTAATCAATAAAGGCCTGGCCTATGTTGATGAGCTGACGCCGGAGCAGATCCGTGAATACCGCGGTACGCTGACCGCGCCGGGTAAAAACAGCCCGTTCCGCGATCGCAGCGTCGAAGAGAACCTCGCGCTATTTGAAAAAATGCGTACCGGCGGTTTTGAAGAGGGTAAAGCCTGTCTGCGCGCTAAAATCGACATGGCGTCGCCGTTTATCGTGATGCGCGATCCGGTGCTGTATCGCATTAAATTCGCCGAGCATCATCAGACTGGCAACAAGTGGTGCATCTATCCGATGTACGACTTTACTCACTGCATCAGCGATGCGCTGGAAGGCATTACTCATTCTCTGTGTACGCTGGAGTTCCAGGATAACCGTCGTCTGTACGACTGGGTGCTGGACAACATCACCATTCCGGTTCACCCGCGCCAGTACGAATTCTCGCGCCTGAATCTGGAATACACCGTGATGTCCAAGCGTAAGCTGAACCTGCTGGTGACCGACAAACACGTCGAAGGTTGGGACGATCCGCGTATGCCGACTATTTCCGGTCTGCGCCGTCGCGGCTATACCGCGGCTTCTATTCGTGAGTTCTGCAAACGCATCGGCGTCACCAAGCAGGACAACACTATTGAGATGGCGTCGCTGGAATCCTGCATTCGCGAAGATCTGAACGAAAACGCGCCGCGCGCGATGGCGGTAATCGATCCGGTAAAACTGGTTATCGAAAATTACCCGCAGGGTGAGAGCGAAATGGTTACCATGCCTAACCATCCGAATAAACCGGAGATGGGCAGCCGTGAAGTGCCGTTTAGCGGTGAGATCTGGATCGATCGCGCAGATTTCCGCGAAGAAGCGAACAAACAGTACAAACGTCTGGTGATGGGCAAAGAAGTGCGTCTGCGTAATGCCTACGTCATTAAAGCGGAGCGCGTAGAGAAGGATGCCGAAGGGAATATCACCACCATCTTCTGTACCTATGATGCTGATACGCTGAGTAAAGATCCGGCTGACGGGCGTAAAGTGAAAGGCGTAATCCACTGGGTTAGCGCAGCACATGCGCTGCCGATTGAAATTCGTCTCTACGACCGTCTGTTCAGCGTGCCGAATCCGGGCGCCGCGGAGGACTTCCTGTCTGTTATCAACCCCGAATCATTAGTGATTAAGCAGGGGTATGGCGAGCCGTCGCTGAAAGCGGCGGTAGCAGGAAAAGCTTTCCAGTTTGAACGTGAAGGCTACTTCTGCCTCGACAGCCGCTATGCAACGGCCGATAAGCTGGTCTTTAACCGCACCGTGGGCCTGCGTGATACCTGGGCGAAAGCGGGCGAGTAACGCGCATAGGCGGCCTTCAAGGAGGCGCTAGGCGAATGAAAGCGCTACTGTGGCTGGTGGGTCTCGCGTTGCTGTTAACAGGCTGCGCGAGCGAAAAAGGAATTATCGATAAAGAGGGATATCAGCTTGATACCCGACATCGGGCGCAGGCGGCCTATCCGCGCATTAAAGTCCTGGTGATTCACTATACGGCGGAAAACTTTGACGTTTCGCTGGCGACGTTAACGGGTCGCAACGTCAGTTCGCATTACCTGATTCCCGCAACCCCGCCATTATATGGCGGTAAACCGCGCATCTGGCAACTGGTGCCGGAACAGGATCAGGCCTGGCATGCGGGCGTCAGTTTCTGGCGAGGCGCCACGCGTCTCAATGATACGTCTATTGGCATTGAGCTGGAAAATCGTGGTTGGCGAATGTCCGGCGGGGTGAAATCTTTCGCGCCGTTTGAATCCGCGCAAATTCAGGCATTGATTCCGTTAGCGAAGGATATTATCGCGCGCTATAACATCAAACCGCAGAATGTGGTGGCCCATGCGGATATCGCGCCGCAGCGTAAAGACGATCCCGGCCCGCGCTTCCCGTGGCGCGAGCTGGCGGCGCAGGGGATTAGCGCCTGGCCTGACGCCCAGCGTGTGGCGTTTTATCTGGCTGGACGCGCGCCGTATACGCCAGTCGATACCGCAACGGTGCTTGCGTTACTCTCGCGCTATGGCTATGAAGTCAAAGCCGATATGACGGCACGCGAGCAGCAGCGGGTGATTATGGCGTTCCAGATGCACTTCCGTCCGGCGCAATGGAACGGTATCGCAGATGCCGAAACGCAGGCGATTGCCGAAGCATTACTGGAGAAGTACGGCCAGGATTAACGCGATAGGCGCGCGAGATTACGCGCGCAGTATCGCGC
->EXAM.1219.00001.0002	7024
-CGCGCATAGCGCGCAATGCCGCACTTTATTGCTGAATGTACTGAAAATATTCGCGAGCAGGCTGATTTACCCGGCCTGTTCAGCAAGGTAAACGAGGCGCTGGCCGCCAGCGGGATTTTCCCCATCGGCGGTATCCGCAGTCGCGCCCACTGGCTGGATACCTGGCAGATGGCTGACGGTAAGCATGATTACGCGTTTGTGCATATGACGCTGAAAATCGGCGCCGGGCGCAGCCTGGAGAGCCGTCAGGAAGTTGGCGAAATGCTGTTTGGGCTGATTAAAGCCCACTTCGCCGACCTGATGGAGAACCGCTATCTGGCGCTGTCGTTTGAGATTGCCGAGCTACATCCGACGCTCAATTACAAACAAAACAACGTACACGCGTTATTTAAATAGCCGATATGAGGCGCGGCGCTATAAGGCGCTCATGAGCATGCCCGCGACTAAATTCTCCCGACGTACCCTCCTGACGGCAGGTTCTGCGCTTGCTGTTCTTCCTTTTCTGCGCGCCTTGCCGGTACAGGCGCGTGAACCTCGCGAGACCGTCGATATTAAGGATTATCCGGCGGATGACGGTATCGCCTCGTTCAAACAGGCCTTCGCCGACGGACAGACCGTGGTCGTACCGCCAGGATGGGTGTGTGAAAATATCAATGCGGCGATAACGATTCCGGCGGGAAAAACGCTGCGGGTACAGGGCGCGGTGCGTGGGAATGGCCGGGGACGGTTTATTTTGCAGGACGGGTGTCAGGTGGTGGGGGAGCAGGGCGGCAGTCTGCACAATGTGACGCTGGATGTTCGCGGGTCGGACTGTGTGATTAAAGGCGTGGCGATGAGCGGCTTTGGCCCCGTCGCGCAAATTTTCATCGGTGGTAAGGAACCGCAGGTGATGCGTAATCTCATTATCGATGACATCACCGTTACCCACGCCAACTACGCCATTCTCCGCCAGGGATTTCATAACCAAATGGATGGCGCGCGGATTACGCATAGCCGCTTTAGCGATTTACAGGGGGACGCCATTGAGTGGAATGTCGCGATTCACGACCGCGACATCCTGATTTCCGATCATGTCATCGAACGCATTAATTGTACCAATGGCAAAATCAACTGGGGGATCGGCATCGGGCTGGCGGGTAGCACCTATGACAACAGTTATCCTGAAGACCAGGCAGTAAAAAACTTTGTGGTGGCCAATATTACCGGATCTGATTGCCGACAGCTTGTGCACGTAGAAAATGGCAAACATTTCGTCATTCGCAATGTCAAAGCCAAAAACATCACGCCCGGTTTCAGTAAAAATGCGGGTATTGATAACGCAACGATCGCAATTTATGGCTGTGATAATTTCGTCATTGATAATATTGATATGACGAATAGTGCCGGGATGCTCATCGGCTATGGCGTCGTTAAAGGAAAATACCTGTCAATTCCGCAAAACTTTAAATTAAACGCTATTCGGTTGGATAATCGCCAGGTTGCTTATAAATTACGCGGCATTCAAATTTCCTCCGGCAACACCCCCTCTTTTGTCGCCATCACCAATGTACGGATGACGCGTGCTACGCTGGAACTGCATAATCAACCGCAGCACCTCTTTCTGCGCAATATCAACGTGATGCAAACTTCAGCGATTGGCCCGGCGTTAAAAATGCATTTCGATTTGCGTAAAGATGTACGTGGTCAATTTATGGCCCGCCAGGACACGCTGCTTTCCCTCGCTAATGTTCATGCCATCAATGAAAACGGGCAGAGTTCCGTGGATATCGACAGGATTAATCACCAAACCGTGAATGTCGAAGCAGTGAATTTTTCGCTGCCGAAGCGGGGAGGGTAACGAATTCCGCGGCATATAGCGGCGCGATAGCATGTCAGAAAATAAATTACACGTTATCGATTTGCACAAACGCTACGGCGGTCATGAAGTGCTGAAAGGGGTATCGCTGCAGGCCCGCGCCGGAGATGTGATTAGCATCATCGGCTCGTCCGGCTCCGGTAAAAGCACTTTTTTGCGCTGTATTAACTTCCTCGAAAAACCGAGCGAAGGCGCGATTATCGTGAACGGTCAGAACATTAATCTGGTGCGCGACAAAGATGGGCAGCTCAAAGTGGCGGATAAAAATCAGCTACGCTTGTTGCGTACCCGCCTGACGATGGTGTTTCAGCACTTCAACCTCTGGAGCCACATGACGGTGCTGGAAAATGTGATGGAAGCGCCGATTCAGGTACTGGGATTAAGCAAGCACGACGCGCGCGAGCGGGCGTTGAAATATCTGGCGAAGGTGGGGATTGATGAGCGCGCTCAGGGCAAATATCCCGTCCATCTCTCCGGCGGCCAACAGCAGCGCGTTTCTATTGCGCGCGCGCTGGCGATGGAACCTGACGTTTTACTGTTCGATGAACCCACATCGGCGCTCGATCCTGAACTGGTCGGCGAAGTGTTGCGCATCATGCAACAACTGGCGGAAGAAGGCAAAACGATGGTGGTGGTCACGCATGAAATGGGCTTCGCTCGCCATGTCTCTTCGCACGTTATTTTTCTGCATCAGGGGAAAATTGAAGAAGAGGGTGATCCGGAGCAGGTGTTCGGCAATCCGCAAAGCCCGCGTTTACAGCAATTCCTGAAAGGCTCGCTGAAATAACGCTCAGAGGCGCGCGCGCGCTATATACGCGCAGTGTTTATTGGCATAGTTAGCCTGTTTCCTGAAATGTTCCGCGCAATTACCGATTACGGGGTAACTGGCCGGGCAGTAAAAAAAGGCCTGCTGAACATCCAAAGCTGGAGTCCTCGCGACTTCGCGCATGACCGGCACCGTACCGTGGACGACCGTCCTTACGGCGGCGGACCGGGGATGTTAATGATGGTGCAACCCTTGCGGGACGCCATTCACGCAGCAAAAGCCGCGGCAGGTGAAGGCGCTAAAGTGATTTATCTGTCGCCTCAGGGACGCAAGCTTGATCAAGCGGGCGTTAGCGAGCTGGCCACGAATCAGAAGCTTATTCTGGTGTGTGGTCGCTACGAAGGCGTAGATGAGCGCGTAATTCAGACCGAAATTGACGAAGAATGGTCAATTGGCGATTACGTTCTCAGCGGTGGCGAACTACCGGCAATGACGCTGATTGACTCCGTCGCCCGGTTTATACCGGGGGTTCTGGGGCATGAGGCATCAGCAATCGAAGATTCGTTTGCTGATGGGTTGCTGGATTGTCCGCACTATACGCGCCCTGAAGTGTTAGAGGGGATGGAAGTACCGCCAGTATTGCTGTCGGGAAACCATGCTGAGATACGTCGCTGGCGTTTGAAACAGTCGCTGGGCCGAACCTGGCTTAGAAGACCTGAACTTCTGGAAAACCTGGCTCTGACTGAAGAGCAAGCAAGGTTGCTGGCGGAGTTCAAAACAGAACACGCACAACAGCAGCATAAACATGATGGGATGGCATAGCCGTCATATGGGCTCTCAGAGGAGACGCGCTAATGCGCAGTACGTGTTTATTGGCATAGTTAGCCTGTTTCCTGAAATGTTCCGCGCAATTACCGATTACGGGGTAACTGGCCGGGCAGTAAAAAAAGGCCTGCTGAACATCCAAAGCTGGAGTCCTCGCGACTTCGCGCATGACCGGCACCGTACCGTGGACGACCGTCCTTACGGCGGCGGACCGGGGATGTTAATGATGGTGCAACCCTTGCGGGACGCCATTCACGCAGCAAAAGCCGCGGCAGGTGAAGGCGCTAAAGTGATTTATCTGTCGCCTCAGGGACGCAAGCTTGATCAAGCGGGCGTTAGCGAGCTGGCCACGAATCAGAAGCTTATTCTGGTGTGTGGTCGCTACGAAGGCGTAGATGAGCGCGTAATTCAGACCGAAATTGACGAAGAATGGTCAATTGGCGATTACGTTCTCAGCGGTGGCGAACTACCGGCAATGACGCTGATTGACTCCGTCGCCCGGTTTATACCGGGGGTTCTGGGGCATGAGGCATCAGCAATCGAAGATTCGTTTGCTGATGGGTTGCTGGATTGTCCGCACTATACGCGCCCTGAAGTGTTAGAGGGGATGGAAGTACCGCCAGTATTGCTGTCGGGAAACCATGCTGAGATACGTCGCTGGCGTTTGAAACAGTCGCTGGGCCGAACCTGGCTTAGAAGACCTGAACTTCTGGAAAACCTGGCTCTGACTGAAGAGCAAGCAAGGTTGCTGGCGGAGTTCAAAACAGAACACGCACAACAGCAGCATAAACATGATGGGATGGCATAGCGCATACGCGCGCGATATATATTCGCGCAGAGGCGCGCATAGCGATGAAGTTTGTTGCGCCCGAACAGGCACCGGAACAGGCGGAGGTCATCAAAAATACGCCGTTCTGGCCTGATGTGGACCTGTCGGAATTTCGCAGTGTGATGCGCACTGACGGCACGGTGACGCAGCCGCGTTTAAAGCAGGTCGTGCTGACGGCGATCTCTGAGGTTAACGCTGAGCTGTACGACTTCCGCAACCGTCAGCAGATGCTGGGCTGGCGGACACTTGCTGAGGTTCCCGCAGAAATGCTGGACGGTAAAAGCGAGCGTATCCGGCACTACCACAACGCTGTTTTTTGCTGGGCGCGCGCTGTGCTTAATGAGCGTTATCAGGACTATGACGCCACGGCGTCAGGCGTGAAGCGAGGGGAGGAGCTGGCGGAGGCCAGCGGCGATCTGTGGCGTGATGCCCGCTGGGCCATCAGCCGGGTGCAGGATGTACCGCACTGTACGGTGGAGCTTATCTGAACGGCTAGCGCGTAGCGGCAGTCTCGGATGAATAATCATTTTGGGAAAGGGTTAATGGCCGGGTTGCACGCGCCATATGCATATAGCGCGCATCATGCGGTGAATTTCTGTTCTGAGTATAAACGTGGCTTTGTATTGGGTTTTACACACCGTATGTTCGAAAAGACCGGCGATCGTCAACTTAGCGCGTGGGAGGCTGGAATTCTGACGCGTCGCTATGGTCTGGATAAAGAAATGGTGATGGATTTCTTTAAAGAGAATCATTCCGGGATGGCGGTTCGCTTCTTTATGGCCGGTTATCGACTCGAAGGTTGACGATCGCGCGCAGGAGGAGAGCTCTCTTCTTCTAGAGCATGTCTACGCTTCTCTATTTGCACGGATTCAACAGTTCCCCTCGCTCGGCAAAAGCGTGCCAGCTAAAAAACTGGCTGGCGGAGCGTCATCCGCATGTTGAGATGATCGTCCCTCAGCTGCCGCCGTATCCTGCCGATGCGGCGGAGTTGCTGGAATCTCTCGTGCTTGAGCATGGCGGTGCGCCATTAGGGCTGGTAGGATCGTCGCTGGGTGGTTATTACGCCACCTGGCTGTCGCAATGTTTTATGCTGCCGGCTGTGGTGGTGAATCCCGCCGTGCGGCCCTTTGAATTACTGACCGACTATCTCGGTCAGAACGAGAACCCCTACACCGGGCAGCAATATGTGCTAGAGTCTCGCCATATTTATGATCTTAAAGTCATGCAGATTGACCCGCTGGAAGCGCCGGACCTGATCTGGCTACTGCAACAGACGGGCGATGAAGTGCTGTATTACCGCCAGGCGGTGGCATATTACGCCTCCTGCCGTCAGACAGTGACCGAGGGTGGTAATCACGCATTCACGGGCTTCGAAGATTATTTCAACCAGATTGTCGATTTTCTTGGACTGCACAGTTGCTGACGGCTATGCGCGCGCTCGATGATTGACCCTATTTTTGCGTCCTGTACGCTAATTGCCGTCTTTGTTGTTTTACTGGCCATGGGCGCGCCTATCGGGATCTGCATCGTTATCGCCTCTTTCAGCACCATGATGCTGGTACTGCCTTTCGATATTTCGATGTTCGCCACCGCGCAAAAAATGTTCTCCAGCCTGGACAGTTTTGCCTTGCTGGCCGTGCCGTTCTTCGTTTTGTCCGGGGTGATCATGAATAGCGGGGGAATTGCCGCCCGGCTGGTCAATTTTGCCAAACTGTTTACTGGCAAACTGCCCGGCTCGCTCTCTTATACCAACATCGTCGGCAATATGATGTTCGGTGCAATTTCCGGATCGGCGATTGCCGCCTCAACCTCCATCGGCGGCGTGATGGTGCCGATGAGCGCGCGCGAAGGTTACGATCGCGGCTTTGCGGCCGCGGTGAATATCGCCTCCGCGCCGACGGGAATGTTAATTCCGCCCACCACGGCTTTTATCCTTTACGCGCTGGCAAGCGGGGGAACATCGATTGCCGCTCTGTTCGCCGGCGGTCTGGTCGCGGGAGTGCTGTGGGGCGTTGGCTGTATGCTGGTCACGCTGGTGGTCGCTAAGCGTCGAAATTATCGGGTTTTCTTCACCGTCCAAAAAGGTATGGCGCTAAAAGTTGCCGTTGAGGCCATTCCCAGCCTGCTGCTGATCGTGATTATTGTCGGCGGCATTGTGCAGGGGATTTTCACCGCCATTGAAGCCTCCGCGATTGCCGTGGTGTATACGTTATTGCTGACGATGGTGTTTTACCGCACGCTGAAAATTAAGGATTTGCCTTCGATTTTGCTCCAGACAGTGGTAATGACCGGGGTCATCATGTTCCTGCTGGCAACCTCTTCGGCGATGTCCTTCTCGATGTCGATCACCAATATTCCTGCGGCGCTGAGCGATATGATCCTCGGTATTTCCGCCAATAAACTGGTTATCCTGTTAGTCATTACCGTCTTTTTGTTGATTATCGGCGCATTTATGGATATTGGTCCGGCCATTCTGATTTTTACCCCGATTCTGCTGCCAATCATGGCTAAACTGGGCGTCGATCCGGTGCATTTCGGCATTATCATGATCTATAACCTGGCGATTGGCACCATTACGCCGCCAGTTGGCAGTGGTTTATATGTCGGGGCGAGCGTCGGTAAGGTCAAAGTTGAGGAAGTGATTAAACCGTTGCTGCCTTTTTACGGCGCGATTATCGGCGTTCTGTTATTAATTACCTACATTCCGGAAATCACACTGTTCTTACCCCGTCTACTGGGCATCATGTAA
diff --git a/Examples/2-res-Annotate-prodigal/Replicons/GEN2.1219.00001.fna b/Examples/2-res-Annotate-prodigal/Replicons/GEN2.1219.00001.fna
deleted file mode 100644
index 8fe856eefd3b0b8ab18cac65ebb213940f127894..0000000000000000000000000000000000000000
--- a/Examples/2-res-Annotate-prodigal/Replicons/GEN2.1219.00001.fna
+++ /dev/null
@@ -1,10 +0,0 @@
->GEN2.1219.00001.0001	2308
-ATGTCAGAAAATAAATTACACGTTATCGATTTGCACAAACGCTACGGCGGTCATGAAGTGCTGAAAGGGGTATCGCTGCAGGCCCGCGCCGGAGATGTGATTAGCATTATCGGCTCGTCCGGTTCCGGTAAAAGCACTTTTTTGCGCTGCATTAACTTCCTCGAAAAATCGAGCGAAGGCGCGATTATCGTGAACGGTCAGAACATTAATCTGGTGCGCGACAAAGACGGGCAGCTCAAAGTGGCGGATAAAAATCAGCTACGCTTGTTGCGTACCCGCCTGACGATGGTGTTTCAGCACTTTAACCTCTGGAACCACATGACGGTGCTGGAAAATGTGATGGAAGCGCCGATTCAGGTACTGGGATTAAGCAAGCACGACGCGCGCGAGCGGGCGTTGAAATATCTGGCGAAGGTGGGGATTGATGAGCGCGCTCAGGGCAAATATCCCGTCCATCTCTCCGGCGGCCAACAGCAGCGCGTTTCTATTGCGCGCGCGCTGGCGATGGAACCTGACGTTTTACTGTTCGATGAACCCACATCGGCGCTCGATCCTGAACTGGTCGGCGAAGTGTTGCGCATCATGCAACAACTGGCGGAAGAAGGCAAAACGATGGTGGTGGTCACGCATGAAATGGGCTTCGCCCGCCATGTCTCTTCGCACGTGATTTTTCTGCATCAGGGGAAAATTGAAGAAGAGGGCAATCCGGAGCAGGTGTTCGGCAATCCGCAAAGCCCGCGTTTACAGCAATTCCTGAAAGGCTCGCTGAAATAAACGCTAGAGGACGCGCCTCTCAGAGAGCGCGCTCTCTCAGAGAGGCGCGCGCCTCTTTCGCAGAGACCNNCGCTCATGAGCGATGCCCGCGACTAAATTCTCCCGACGTACCCTCCTGACGGCAGGTTCCGCGCTTGCTGTTCTTCCTTTTCTGCGCGCCTTGCCGGTACAGGCGCGTGAACCTCGCCAGACCGTCGATATTAAGGATTATCCGGCGGATGACGGTATCGCCTCGTTCAAACAGGCCTTCGCCGACGGGCAGACTGTGGTCGTGCCGTCAGGATGGGTGTGTGAAAATATCAATGCGGCGATAACGATTCCGGCGGGAAAAACGCTGCGGATACAGGGCGCGGTGCGTGGGAATGGCCGGGGACGGTTTATTTTGCTGGACGGGTGTCAGGTGGTGGGGGAGCAGGGCGGCAGTCTGCACAATGTGACGCTGGATGTTCGCGGGTCGGACTGTGTGATTAAAGGCGTGACGATGAGCGGCTTTGGCCCCGTCGCGCAAATTTTCATCGGCGGTAAGGAACCGCAGGTGATGCGTAATCTCATTATCGATGACATCACCGTTACCCACGCCAACTACGCCATTCTCCGCCAGGGATTTCATAACCAAATGGACGGCGCGCGGATTACGCATAGTCGCTTTAGCGATTTGCAGGGGGACGCCATTGAGTGGAATGTCGCGATTCATGACCGCGACATCCTGATTTCCGATCATGTCATCGAACGCATTGATTGTACCAATGGCAAAATCAACTGGGGGATCGGCATCGGGCTGGCGGGTAGCGCCTATGACAATAGTTATCCTGAAGACCAGGCAGTAAAAAACTTTGTGGTGGCCAATATTACCGGATCTGATTGCCGACAACTGGTACACGTAGAAAATGGCAAACATTTCGTCATTCGCAATGTCAAAGCCAAAAACATCACGCCCGATTTCAGTAAAAATGCGGGTATTGATAACGCAACGATCGCCATTTATGGCTGTGATAATTTCGTCATTGATAATATTGATATGACGAATAGTGCCGGGATGCTCATCGGCTATGGCGTCGTTAAAGGAAAATACCTGTCAATTCCGCAAAACTTTAAATTAAACGCTATTCGGTTGGATAATCGCCAGGTTGCTTATAAATTACGCGGCATTCAAATTTCCTCCGGTAACGCCCCCTCATTTGTTGCCATCACCAATGTACGGATGACGCGTGCTACGCTGGAACTGCATAATCAACCGCAGCACCTCTTTTTGCGTAATATCAACGTGATGCAAACTTCAGCGATTGGCCCGGCGTTAAAAATGCATTTTGATTTGCGTAAAGATGTCCGTGGTCAATTTATGGCCCGCCAGGACACGCTGCTTTCCCTCGCTAATGTTCATGCCATCAATGAAAACGGGCAGAGTTCCGTGGATATCGACAGGATTAATCACCAAACCGTGAATGTCGAAGCAGTGAATTTTTCGCTGCCGAAGCGGGGAGGGTAACACTCGCGCATAGAGAGCTCTCAGAGGAGCGCGCGCGCTATAGCGCGC
->GEN2.1219.00001.0002	3295
-CGCGATAATATAGCGCGCGCTCATAGCATGAGCGCGCTATTTCTGGCCATCCCGTTAACCATTTTTGTGTTGTTTGTGTTACCGATTTGGCTGTGGCTGCATTACAGCAACCGCGCCGGTCGGGGAGAACTGTCGCAAAGCGAGCAGCAACGCTTACTGCAACTCACAGACGACGCGCAACGTATGCGCGAGCGCATTCAGGCGCTGGAAGATATTCTTGATGCAGAGCATCCGAACTGGAGAGAGCGCTAACGCCATATTATAGCGCGCCTCATAAGAGCGGCCTATAGCGCGCTANNNATGCCGCACTTTATTGCTGAATGTACTGAAAATATTCGCGAGCAGGCTGATTTACCAAGCCTGTTCAGCAAGGTAAACGAGGCGCTGGCCGCCACCGGGATTTTCCCCATCGGCGGTATCCGCAGTCGCGCCCACTGGCTGGATACCTGGCAGATGGCTGACGGTAAGCATGATTACGCGTTTGTGCATATGACGCTGAAAATCGGCGCCGGGCGCAGCCTGGAGAGCCGTCAGGAAGTCGGCGAAATGCTGTTTGGGCTGATTAAAGCCCACTTCGCCGACCTGATGGAGAACCGCTATCTGGCGCTGTCGTTTGAGATTGCCGAGTTACATCCAACGCTCAATTACAAACAAAACAACGTACACGCGTTATTTAAATAGCCAGAGATTCGCGCGTTCAGAGAGGAGCTCTCTCATAGACGCGCGCATATGCGCTCTAGAGAGGCGCGCCTAATGGCGCGCTATGATGAAAGCGCTACTGTGGCTGGTTGGTCTCGCGTTGCTGTTAACAGGCTGCGCGAGCGAAAAAGGAATTATCGATAAAGAGGGATATCAGCTTGATACCCGACATCGGGCGCAGGCGGCCTATCCGCGCATTAAAGTCCTGGTGATTCACTATACGGCGGAAAACTTTGACGTTTCGCTGGCGACGTTAACGGGTCGCAACGTCAGTTCGCATTACCTGATTCCCGCAACCCCGCCATTATATGGCGGTAAACCGCGCATCTGGCAACTGGTGCCGGAACAGGATCAGGCTTGGCATGCGGGCGTCAGTTTCTGGCGAGGCGCCACGCGTCTCAATGATACGTCTATTGGCATTGAGCTGGAAAATCGCGGCTGGCGAATGTCCGGCGGGGTGAAATCTTTCGCGCCGTTTGAATCCGCGCAAATTCAGGCATTGATCCCGTTAGCGAAGGACATTATCGCGCGCTATGACATCAAACCGCAGAATGTGGTGGCCCATGCGGATATCGCGCCGCAGCGTAAAGACGATCCCGGCCCGCGCTTCCCGTGGCGCGAGCTGGCGGCACAGGGGATTGGCGCCTGGCCTGACGCCCAGCGTGTGGCGTTTTATCTGGCTGGACGCGCGCCGTATACGCCAGTCGATACCGCAACGGTGCTTGCGTTACTCTCGCGCTATGGCTATGAAGTCAAAGCCGATATGACGGCGCGCGAGCAACAGCGGGTGATTATGGCGTTCCAGATGCACTTCCGTCCGGCGCAATGGAACGGTATCGCAGATGCCGAAACGCAGGCGATTGCCGAAGCATTACTGGAGAAGTACGGCCAGGATTAACAAAGCGCTCTCAGAGAGAGCGCTCTGCAGATGAGTGAGGCTGAAGCCCGCCCGACTAACTTTATTCGTCAGATTATTGATGAAGATCTGGCGAGTGGTAAACATACCACTGTCCATACCCGTTTTCCGCCGGAGCCGAATGGCTATCTGCACATCGGCCACGCGAAATCTATCTGCCTGAACTTTGGCATCGCGCAAGATTATCAGGGCCAGTGCAACCTGCGTTTCGATGACACCAACCCGGTAAAAGAAGATATCGAGTACGTTGATTCGATCAAAAACGACGTCGAGTGGTTAGGCTTTCACTGGTCTGGCGATATTCGCTACTCCTCCGATTACTTTGACCAACTGCACGCCTATGCGGTCGAGCTCATCAATAAAGGCCTGGCCTACGTTGATGAGCTGACGCCGGAGCAGATCCGCGAATACCGTGGTACGCTGACCGCGCCGGGTAAAAACAGCCCGTTCCGCGATCGCAGCGTGGAAGAAAACCTCGCGCTATTTGAAAAAATGCGTACCGGCGGTTTTGAAGAGGGTAAAGCCTGTCTGCGCGCTAAAATCGACATGGCGTCGCCGTTTATCGTGATGCGCGATCCGGTGCTGTATCGCATTAAATTCGCCGAGCATCATCAGACCGGCACGAAGTGGTGCATCTATCCGATGTACGACTTTACTCACTGCATCAGCGATGCGCTGGAAGGCATTACTCATTCTCTGTGTACGCTGGAGTTCCAGGACAACCGTCGTCTGTACGACTGGGTGCTGGACAACATCACCATTCCGGTTCACCCGCGCCAGTACGAATTCTCGCGCCTGAATCTGGAATACACCGTGATGTCCAAGCGTAAGCTGAACCTGCTGGTGACCGACAAACACGTCGAAGGTTGGGATGATCCGCGTATGCCGACTATTTCCGGTCTGCGCCGTCGCGGCTATACCGCGGCTTCTATTCGTGAGTTCTGCAAACGCATCGGCGTCACCAAGCAGGACAACACTATTGAGATGGCGTCGCTGGAATCCTGCATTCGCGAAGATCTGAACGAAAACGCGCCGCGCGCGATGGCGGTAATCGATCCGGTAAAACTGGTTATCGAAAACTACCCGCAGGGCGAGAGCGAAATGGTTACCATGCCTAACCATCCGAATAAACCGGAGATGGGCAGCCGTGAAGTGCCGTTTAGCGGTGAGATCTGGATCGATCGCGCGGATTTCCGCGAAGAAGCGAACAAACAGTACAAACGTCTGGTGATGGGCAAAGAAGTGCGTCTGCGTAATGCCTACGTCATTAAAGCGGAGCGCGTAGAGAAGGATGCCGAAGGGAATATCACCACCATCTTCTGTACCTATGATGCTGATACGCTGAGTAAAGATCCGGCTGACGGGCGTAAAGTGAAAGGCGTAATCCACTGGGTTAGCGTAGCACATGCGCTGCCGATTGAAATTCGTCTCTACGACCGTCTGTTCAGCGTGCCGAACCCGGGCGCCGCGGAGGACTTCCTGTCTGTTATCAACCCCGAATCATTAGTGATTAAGCAGGGGTATGGCGAGCCGTCGCTGAAAGCGGCGGTAGCAGGGAAAGCTTTCCAGTTTGAACGTGAAGGTTACTTCTGCCTTGACAGCCGCTATGCAACGGCCGATAAGCTGGTCTTTAACCGCACCGTGGGCCTGCGTGATACCTGGGCGAAAGCGGGCGAATAA
->GEN2.1219.00001.0003	2263
-ACGCGCTATAGGGCTCTCAGAGAGTCTCAGTGTTTATTGGCATCGTTAGCCTGTTTCCTGAAATGTTCCGCGCAATTACCGATTACGGGGTAACTGGCCGGGCAGTAAAAAAAGGCCTGCTGAACATCCAAAGCTGGAGTCCTCGCGACTTCGCGCATGACCGGCACCGTACCGTGGACGACCGTCCTTACGGCGGCGGACCGGGGATGTTAATGATGGTGCAACCCTTGCGGGACGCCATTCATGCAGCAAAAGCCGCGGCAGGTGAAGGCGCTAAAGTGATTTATCTGTCGCCTCAGGGACGCAAGCTTGATCAAGCGGGCGTTAGCGAGCTGGCCACGAATCAGAAACTCATTCTGGTGTGTGGTCGCTACGAAGGCGTAGATGAGCGCGTAATTCAGGCCGAAATTGACGAAGAATGGTCAATTGGCGATTACGTTCTCAGCGGTGGCGAACTACCGGCAATGACGCTGATTGACTCCGTCGCCCGGTTTATACCGGGGGTTCTGGGGCATGAGGCATCAGCAATCGAAGATTCGTTTGCTGATGGGTTGCTGGATTGTCCGCACTATACGCGCCCTGAAGTGTTAGAGGGGATGGAAGTACCGCCAGTATTGCTGTCGGGAAACCATGCTGAGATACGTCGCTGGCGTTTGAAACAGTCACTGGGCCGAACCTGGCTTAGAAGACCTGAACTTCTGGAAAACCTGGCTCTGACTGAAGAGCAAGCAAGGTTGCTGGCGGAGTTCAAAACAGAACACGCACAACAGCAGCATAAACATGATGGGATGGCATAGCGAGATCGCGCATAGCGCGCGGCGAGATCCGCGAGACATGAATAATCATTTTGGGAAAGGGTTAATGGCCGGGTTGCACGCGCCATATGCATATAGCGCGCATCATGCGGTGAATTTCTGTTCTGAGTATAAACGTGGCTTTGTATTGGGTTTTACACACCGTATGTTCGAAAAGACCGGCGATCGTCAACTTAGCGCGTGGGAGGCCGGAATTCTGACGCGTCGCTATGGTCTGGATAAAGAAATGGTGATGGATTTCTTTAAAGAGAATCATTCCGGGATGGCGGTTCGCTTCTTTATGGCTGGTTATCGACTCGAAGGTTGAACGCCTCTAGAGCGCTAGAGGCGCGCGCGATATACGCGGCGCGAGACATGTCTACGCTTCTCTATTTGCACGGATTCAACAGTTCCCCTCGCTCGGCAAAAGCGTGCCAGCTAAAAAACTGGCTGGCGGAGCGTCATCCGCATGTTGAGATGATCGTCCCTCAACTGCCGCCGTATCCTGCCGATGCGGCGGAGTTGCTGGAATCTCTCGTACTTGAGCATGGCGGTGCGCCATTAGGGCTGGTAGGATCGTCGCTGGGTGGTTATTACGCCACCTGGCTGTCGCAATGTTTTATGCTGCCGGCTGTGGTGGTGAATCCCGCCGTGCGGCCCTTTGAATTACTGACCGACTATCTCGGTCAGAACGAGAACCCCTACACCGGGCAGCAATATGTGCTAGAGTCTCGCCATATTTATGATCTTAAAGTCATGCAGATTGACCCGCTGGAAGCGCCGGACCTGATCTGGCTACTGCAACAGACGGGCGATGAAGTGCTGGATTACCGCCAGGCGGTGGCATATTACGCCTCCTGCCGTCAGACAGTGACCGAGGGGGGTAATCACGCATTCACGGGCTTCGAAGATTATTTCAACCAGATTGTCGATTTTCTTGGACTGCACAGTTGCTGACCGGATATACGCGCGCGCGCTATATAGCGCGCGCGGCGATATAGCGCATGAAGTTTGTTGCGCCAGAACAGGCACCGGAACAGGCGGAAATCATCAGAAATACGCCGTTCTGGCCTGATGTGGACCTGTCGGAGTTTCGCAGCATGATGCGCACTGATGGCACGGTGACGCAGCCGCGTTTAAAGCAGGTTGCGCTGTCGGCAATTTCGGAGGTCAACGCAGAGCTGTATGAGTTTCGCAGACGCCAGCAGATGCTGGGGTATGCCTCGCTGGCAGAAGTCCCGGCGGAACAACTGGACGGCAAAAGCGAGCGCATTCAGCACTATTTCAACGCGGTTTACTGCTGGGCACGCGCCATGCTCAACGAACGTTACCAGGACTATGACGCCACGGCATCCGGTGTGAAGCGGGGCGAAGAACTGGCAGAAGCCAGCGGTGATTTGTGGCGTGACGCCCGCTGGGCCATCAGCCGGGTGCAGGATGCGCCGCACTGCACAGTGGAGCTTATCTGA
->GEN2.1219.00001.0004	2845
-ATGATTGACCCTATTTTTGCGTCCTGTACGCTAATTGCCGTCTTTGTTGTTTTACTGGCCATGGGCGCGCCTATCGGGATCTGCATCGTTATCGCCTCTTTCAGCACCATGATGCTGGTACTGCCTTTCGATATTTCGATGTTCGCCACCGCGCAAAAAATGTTCTCCAGCCTGGACAGTTTTGCCTTGCTGGCCGTGCCGTTCTTCGTTTTGTCCGGGGTGATCATGAATAGCGGGGGAATTGCCGCCCGACTGGTCAATTTTGCCAAACTGTTTACTGGCAAACTGCCCGGCTCGCTCTCTTACACCAACATCGTCGGCAATATGATGTTCGGTGCAATTTCCGGATCGGCGATTGCCGCCTCAACCTCTATCGGCGGCGTGATGGTGCCGATGAGCGCGCGCGAAGGTTACGATCGCGGTTTTGCGGCCGCGGTGAATATCGCCTCCGCGCCGACGGGAATGTTAATTCCGCCCACCACGGCTTTTATCCTTTATGCGCTGGCAAGCGGGGGAACATCGATTGCCGCTCTGTTCGCCGGCGGTCTGGTCGCGGGAGTGCTGTGGGGCGTTGGCTGTATGCTGGTCACGCTGGTGGTCGCTAAGCGTCGAAATTATCGGGTTTTCTTCACCGTCCAAAAAGGCATGGCGCTAAAAGTTGCCGTTGAGGCCATTCCCAGCCTGTTACTGATCGTGATTATTGTCGGCGGCATTGTGCAGGGGATTTTCACCGCCATTGAAGCCTCCGCGATTGCCGTGGTGTATACGTTATTGCTGACGATAGTGTTTTACCGCACGCTGAAAATTAAGGATTTGCCTTCGATTTTGCTCCAGACAGTGGTAATGACCGGGGTCATCATGTTCCTGCTGGCAACCTCTTCGGCGATGTCCTTCTCGATGTCGATCACCAATATTCCTGCGGCGCTGAGCGATATGATCCTCGGTATTTCCGCCAATAAACTGGTTATCCTGTTAGTCATTACCGTCTTTTTGTTGATTATCGGCGCATTTATGGATATCGGTCCGGCCATTCTGATTTTTACCCCGATTCTGCTGCCGATTATGACTAAACTGGGCGTCGATCCGGTGCATTTCGGCATTATCATGATCTATAACCTGGCGATAGGCACCATTACGCCGCCAGTTGGCAGTGGTTTATATGTCGGGGCGAGCGTCGGTAAGGTCAAAGTTGAGGACGTTATCAAACCGTTGATGCCTTTTTACGGCGCGATTATCGGCGTTCTGTTATTAATTACCTACATTCCGGAAATCACACTGTTTTTACCCCGTCTACTGGGCATCATGTAAACGCTCATAGGCGGCGCGCGCGCTCTCAGGAATGAAGTTTGTTGCGCCAGAACAGGCACCGGAACAGGCGGAGGTCATCAAAAATACGCCGTTCTGGCCTGATGTGAACCTGTCGGAATTTCGCAGTGTGATGCGCACTGACGGCACGGTGACGCAGCCGCGTTTAAAGCAGGTCGTGCTGACGGCGATCTCTGAGGTTAACGCTGAGCTGTACGACTTCCGCAACCGTCAGCAGATGCTGGGCTGGCGGACACTTGCTGAGGTTCCCGCAGAAATGCTGGACGGTAAAAGCGAGCGTATCCGGCACTACCACAACGCTGTTTTTTGCTGGGCGCGCGCTGTGCTTAATGAGCGTTATCAGGACTATGACGCCACGGCGTCAGGCGTGAAGCGAGGGGAGGAGCTGGCGGAGGCCAGCGGCGATCTGTGGCGTGATGCCCGCTGGGCCATCAGCCGGGTGCAGGATGCACCGCACTGTACGGTGGAGCTTATCTGACGCTCATAGGCGCGCGCTCATAGCGCGATGGAAACAAATATTACCTGGCAACAATTGATAGATGAATATTTCTTCGCAAAACCTCTGCGCTCAGCATCTGAATGGAGTTACACCAAAGTCTTCAAATCATTTGTACATTATATGGGGCCGTTAAGCTGCCCTAATGATGTGACATATCACAAAGTGCTTGCCTGGCGCCGTTTTCTTTTAAAAGAGAAAAAGCTGTCCGGACGTACCTGGAATAACAAGGTGGCGCATATGCGGGCCATCTTTAACTACGGAATACAGCGAGGGTTACTGCACTATGACGAAAATCCGTTTAACAATTCGGTAGTTAAACCGGACAAGAAGAGAAAGAAAACGCTCACTCAGGCACAGATTGAGTATGCCTATCAGATCATGGAGCAGTATGAAAATCAGGAGAATACAGGGCTGGGACTGAAATATTCCCGCTGCGCCTTATTTCCTGCATGGTTCTGGCTCACTGTCCTGGATACGCTCTATTACACAGGGATACGTCAGAACCAGTTATTACATATTCGGCTGAATGATGTTGATTTGAGAGAAGGGCAGATTCGGCTGATTACGGAGGGGTGTAAAAATCACAAAGAACACTATGTGCCGGTGATCAGTTTTCTGCGTCCACGGCTGACCTGTTTAATGGAGAAAGCGCAGAGCGAAGGATTGAAAGGTAATGACCGCCTGTTCAATATTGCACTTTTTACCGGCAAAGATCCCGCCATTGGCGATGACATGGATTCTCCTCAGGTAAGAGCATTCTTCCGTCGTCTGTCCAAGGAGTGTCAGTTTGCGATCAGTCCTCATCGTTTCAGACACACGCTGGCCACGGAGATGATGAAAATGCCGGAACAGAATCTGCATATGGCGCAAAGTGTGCTGGGTCATTCAAACATGAAATCCACGCTGGAGTATGTGGAGAATGATATTGCAGTGATGGGGAGGGCTCTGGAAGCGCAGTTTATGCAGATTAAGGCAGCACATGCCCGAAGCATTTACAGTGGGTTGACAAAGAATAGATAA
->GEN2.1219.00001.0005	6
-GATACA
diff --git a/Examples/2-res-Annotate-prodigal/Replicons/GEN4.1111.00001.fna b/Examples/2-res-Annotate-prodigal/Replicons/GEN4.1111.00001.fna
deleted file mode 100644
index 5bd3953cedaf5748f1d63155735c530cc8487f01..0000000000000000000000000000000000000000
--- a/Examples/2-res-Annotate-prodigal/Replicons/GEN4.1111.00001.fna
+++ /dev/null
@@ -1,2 +0,0 @@
->GEN4.1111.00001.0001	7134
-ATGAAAGCGCTACTGTGGCTGGTGGGTCTCGCGTTGCTGTTAACAGGCTGCGCGAGCGAAAAAGGAATTATCGATAAAGAGGGATATCAGCTTGATACCCGACATCGGGCGCAGGCGGCCTATCCGCGCATTAAAGTCCTGGTGATTCACTATACGGCGGAAAACTTTGACGTTTCGCTGGCGACGTTAACGGGCCGCAACGTCAGTTCGCATTACCTGATTCCCGCAACCCCGCCATTATATGGCGGTAAACCGCGCATCTGGCAACTGGTGCCGGAACAGGATCAGGCCTGGCATGCGGGCGTCAGTTTCTGGCGAGGCGCCACGCGTCTCAATGATACGTCTATTGGCATTGAGCTGGAAAATCGCGGCTGGCGAATGTCCGGCGGGGTGAAATCTTTCGCGCCGTTTGAATCCGCGCAAATTCAGGCATTGATTCCGTTAGCGAAGGACATTATCGCGCGCTATGACATCAAACCGCAGAATGTGGTGGCCCATGCGGATATCGCGCCGCAGCGTAAAGACGATCCCGGCCCGCGCTTCCCGTGGCGCGAGCTGGCGGCGCAGGGGATTGGCGCCTGGCCTGACGCCCAGCGTGTGGCGTTTTATCTGGCTGGACGCGCGCCGTATACGCCAGTCGATACCGCAACGGTGCTTGCGTTACTCTCGCGCTATGGCTATGAAGTCAAAGCCGATATGACGGCGCGCGAGCAGCAGCGGGTGATTATGGCGTTCCAGATGCACTTCCGTCCGGCGCAATGGAACGGTATCGCAGATGCCGAAACGCAGGCGATTGCCGAAGCATTACTGGAGAAGTACGGCCAGGATTAACGCGATCGCGCGCATATCGCGCGCGATAGATGCCGCACTTTATTGCTGAATGTACTGAAAATATTCGCGAGCAGGCTGATTTACCCGGCCTGTTCAGCAAGGTAAACGAGGCGCTGGCCGCCAGCGGGATTTTCCCCATCGGCGGTATCCGCAGTCGCGCCCACTGGCTGGATACCTGGCAGATGGCTGACGGTAAGCATGATTATGCGTTTGTGCATATGACGCTGAAAATCGGTACCGGGCGCAGCCTGGAGAGCCGTCAGGAAGTCGGCGAAATGCTGTTTGGGCTGATTAAAGCCCACTTCGCCGACCTGATGGAGAACCGCTATCTGGCGCTGTCGTTTGAGATTGCCGAGCTACATCCGACGCTCAATTACAAACAAAACAACGTACACGCGTTATTTAAATAGCCGCATATGCGGCGCTCAGGAGCGCTAGCATGCTCGATAAACAGACCCATACCCTGATCGCCCAGCGACTTAATCAGGCTGAAAAACAGCGTGAACAAATTCGCGCAGTGTCGCTGGATTATCCCAACATCACTATTGAAGATGCCTATGCCGTACAGCGTGAATGGGTCAATATCAAGATCGCCGAAGGGCGCACGCTCAAAGGCCACAAAATCGGCCTGACCTCAAAAGCGATGCAGGCCAGCTCGCAAATCAGCGAACCGGATTACGGCGCGCTGCTTGACGATATGTTCTTCCATGACGGCGGCGATATCCCCACCGACCGTTTTATCGTCCCGCGTATTGAAGTGGAGCTGGCGTTCGTGCTGGCGAAACCGCTGCGCGGCCCTCACTGCACGCTGTTCGACGTCTACAACGCCACGGATTATGTGATTCCGGCGCTGGAACTGATTGACGCCCGCAGCCACAACATCGACCCGGAAACCCAGCGCCCGCGCAAAGTGTTCGACACCATTTCCGACAACGCCGCCAACGCCGGGGTGATCCTCGGTGGTCGCCCCATCAAACCAGACGAGCTGGATCTGCGCTGGATCTCCGCGCTGCTCTATCGCAACGGCGTGATCGAAGAAACCGGCGTCGCCGCAGGCGTGCTGAATCATCCGGCCAACGGCGTGGCGTGGCTGGCGAACAAGCTTGCCCCCTACGATGTCCAGCTTGAAGCCGGGCAGATCATCCTCGGCGGCTCGTTCACCCGCCCGGTGCCGGCGAGCAAGGGCGACACCTTCCATGTCGATTACGGCAACATGGGCGCGATCAGTTGCCGGTTTGTGTAACCAGATCCGCGCGCGCATATATATCGCGCGCATACGATGCCCGTGAATAAGTTCTCCCGACGTACCCTCCTGACGGCAGGTTCCGCGCTTGCTGTTCTTCCTTTTCTGCGCGCCTTGCCGGTACAGGCGCGTGAACCTCGCGAGACCGTCGATATTAAGGATTATCCGGCGGATGACGGTATCGCCTCGTTCAAACAGGCCTTCGCCGACGGACAGACCGTGGTCTTACCGCCAGGATGGGTGTGTGAAAATATCAATGCGGCGATAACGATTCCGGCGGGAAAAACGCTGCGGGTACAGGGCGCGGTGCGTGGGAATGGCCGGGGACGGTTTATTTTGCAGGACGGGTGTCAGGTGGTGGGGGAGCAGGGCGGCAGTCTGCACAATGTGACGCTGGATGTTCGCGGGTCGGACTGTGTGATTAAAGGCGTGACGATGAGCGGCTTTGGCCCCGTCGCGCAAATTTTCATCGGCGGTAAGGAACCGCAGGTGATGCGTAATCTCATTATCGATGACATCACCGTTACCCACGCCAACTACGCCATTCTCCGCCAGGGATTTCATAACCAAATGGACGGCGCGCGGATTACGCATAGCCGCTTTAGCGATTTGCAGGGGGACGCCATTGAGTGGAATGTCGCGATTCACGACCGCGACATCCTGATTTCCGATCATGTCATCGAACGCATTGATTGTACCAATGGCAAAATCAACTGGGGGATCGGCATCGGGCTGGCGGGTAGCACCTATGACAACAGTTATCCTGAAGATCAGGCAGTAAAAAACTTTGTGGTGGCCAATATTACCGGATCTGATTGCCGACAGCTGGTGCACGTAGAAAATGGCAAACATTTCGTCATTCGCAATGTCAAAGCCAAAAACATCACGCCCGATTTCAGTAAAAATGCGGGTATTGATAACGCAACGATCGCCATTTATGGCTGTGATAATTTCGTCATTGATAATATTGATATGACGAATAGTGCTGGGATGCTCATCGGCTATGGCGTCGTTAAAGGAAAATACCTGTCAATTCCGCAAAACTTTAAATTAAACGCTATTCGGTTGGATAATCGCCAGGTTGCTTATAAATTACGCGGCATTCAAATTTCCTCCGGCAACATCCCCTCTTTTGTCGCCATCACCAATGTACGGATGACGCGTGCTACGCTGGAACTGCATAATCAACCGCAGCACCTCTTTCTGCGTAATATCAACGTGATGCAAACTTCAGCGATTGGCCCGGCGTTAAAAATGCATTTCGATTTGCGTAAAGATGTCCGTGGTCAATTTATGGCCCGCCAGGACACGCTGCTTTCCCTCGCTAATGTTCATGCCATCAATGAAAACGGGCAGAGTTCCGTGGATATCGACAGGATTAATCACCAAACCGTGAATGTCGAAGCAGTGAATTTTTCGCTGCCGAAGCGGGGAGGGTAACAGAGCTCGCGCGATCGCGAATGTCAGAAAATAAATTACACGTTATCGATTTGCACAAACGCTACGGCGGTCATGAAGTGCTGAAAGGGGTATCGTTGCAGGCCCGCGCCGGAGATGTGATTAGCATCATCGGCTCGTCCGGCTCCGGTAAAAGCACTTTTTTGCGCTGTATTAACTTCCTCGAAAAACCGAGCGAAGGCGCGATTATCGTGAACGGTCAGAACATTAATCTGGTGCGCGACAAAGACGGGCAGCTCAAAGTGGCGGATAAAAATCAGCTACGCTTGTTGCGTACCCGCCTGACGATGGTGTTTCAGCACTTTAACCTCTGGAGCCACATGACGGTGCTGGAAAATGTGATGGAAGCGCCGATTCAGGTACTGGGATTAAGCAAGCACGACGCGCGCGAGCGGGCGTTGAAATATCTGGCGAAGGTGGGGATTGATGAGCGCGCTCAGGGCAAATATCCCGTCCATCTCTCCGGCGGCCAACAGCAGCGCGTTTCTATTGCGCGCGCGCTGGCGATGGAACCTGACGTTTTACTGTTCGATGAACCCACATCGGCGCTCGATCCTGAACTGGTCGGCGAAGTGTTGCGCATCATGCAACAACTGGCGGAAGAAGGCAAAACGATGGTGGTGGTCACGCATGAAATGGGCTTCGCCCGCCATGTCTCTTCGCACGTTATTTTTCTGCATCAGGGGAAAATTGAAGAAGAGGGCGATCCGGAGCAGGTGTTCGGCAATCCGCAAAGCCCGCGTTTACAGCAATTCCTGAAAGGCTCGCTGAAATAACAGATACGCGCATGGCGAGTGTTTATTGGCATCGTTAGCCTGTTTCCTGAAATGTTCCGCGCAATTACCGATTACGGGGTAACTGGCCGGGCAGTAAAAAAAGGCCTGCTGAACATCCAAAGCTGGAGTCCTCGCGACTTCGCGCATGACCGGCACCGTACCGTGGACGACCGTCCTTACGGCGGCGGACCGGGGATGTTAATGATGGTGCAACCCTTGCGGGACGCCATTCACGCAGCAAAAGCCGCGGCAGGTGAAGGCGCTAAAGTGATTTATCTGTCGCCTCAGGGACGCAAGCTTGATCAAGCGGGCGTTAGCGAGCTGGCCACGAATCAGAAGCTTATTCTGGTGTGTGGTCGCTACGAAGGCGTAGATGAGCGCGTAATTCAGACCGAAATTGACGAAGAATGGTCAATTGGCGATTACGTTCTCAGCGGTGGCGAACTACCGGCAATGACGCTGATTGACTCCGTCGCCCGGTTTATACCGGGGGTTCTGGGGCATGAGGCATCAGCAATCGAAGATTCGTTTGCTGATGGGTTGCTGGATTGTCCGCACTATACGCGCCCTGAAGTGTTAGAGGGGATGGAAGTACCGCCAGTATTGCTGTCGGGAAACCATGCCGAGATACGTCGCTGGCGCTTGAAACAGTCGCTGGGCCGAACCTGGCTTAGAAGACCTGAACTTCTGGAAAACCTGGCTCTGACTGAAGAGCAAGCAAGGTTGCTGGCGGAGTTCAAAACAGAACACGCACAACAGCAGCATAAACATGATGGGATGGCATAGCGATAGCGCTAGAGCGATGAATAATCATTTTGGGAAAGGGTTAATGGCTGGGTTGCACGCGCCATATGCATATAGCGCGCATCATGCGGTGAATTTCTGTTCTGAGTATAAACGTGGCTTTGTATTGGGTTTTACACACCGTATGTTCGAAAAGACCGGCGATCGTCAACTTAGCGCGTGGGAGGCCGGAATTCTGACGCGTCGCTATGGTCTGGATAAAGAAATGGTGATGGATTTCTTTAAAGAGAATCATTCCGGGATGGCGGTTCGCTTCTTTATGGTCGGTTATCGACTCGAAGGTTGACAGATGCGCGATCGATGTCTACGCTTCTCTATTTGCACGGATTCAACAGTTCCCCTCGCTCGGCAAAAGCGTGCCAGCTAAAAAACTGGCTGGCGGAGCGTCATCCGCATGTCGAGATGATCGTCCCTCAACTACCGCCGTATCCTGCCGATGCGGCGGAGTTGCTGGAATCTCTCGTGCTTGAGCATGGCGGTGCGCCATTAGGGCTGGTAGGATCGTCGCTGGGTGGTTATTACGCCACCTGGCTGTCGCAATGTTTTATGCTGCCGGCTGTGGTGGTGAATCCCGCCGTGCGGCCCTTTGAATTACTGACCGACTATCTCGGTCAGAACGAGAACCCCTACACCGGGCAGCAATATGTGCTAGAGTCTCGCCATATTTATGATCTTAAAGTCATGCAGATTGACCCGCTGGAAGCGCCGGACCTGATCTGGCTACTGCAACAGACGGGCGATGAAGTGCTGGATTACCGCCAGGCGGTGGCATATTACGCCTCCTGCCGTCAGACAGTGACCGAGGGTGGTAATCACGCATTCACGGGCTTCGAAGATTATTTCAACCAGATTGTCGATTTTCTTGGACTGCACAGTTGCTGACACGGATGCGCCATCGGCTTGCTGGCCGTGCCGTTCTTCGTTTTGTCCGGGGTGATCATGAATAGCGGGGGAATTGCCGCCCGGCTGGTCAATTTTGCCAAACTGTTTACTGGCAAACTGCCCGGCTCGCTCTCTTATACCAACATCGTCGGCAATATGATGTTCGGTGCAATTTCCGGATCGGCAATTGCCGCCTCAACCTCCATCGGCGGCGTGATGGTGCCGATGAGCGCGCGCGAAGGTTACGATCGCGGCTTTGCGGCCGCGGTGAATATCGCCTCCGCGCCGACGGGAATGTTAATTCCGCCCACCACGGCTTTTATCCTTTATGCGCTGGCAAGCGGGGGAACATCGATTGCCGCTCTGTTCGCCGGCGGTCTGGTCGCGGGAGTGCTGTGGGGCGTTGGCTGTATGCTGGTCACGCTGGTGGTCGCTAAGCGTCGAAATTATCGGGTTTTCTTCACCGTCCAAAAAGGCATGGCGCTAAAAGTTGCCGTTGAGGCCATTCCCAGCCTGCTGCTGATCGTGATTATCGTCGGCGGCATTGTGCAGGGGATTTTCACCGCCATTGAAGCCTCCGCGATTGCCGTGGTGTATACATTATTGTTGACGATGGTGTTTTACCGCACGCTGAAAATTAAGGATTTGCCTTCGATTTTGCTCCAGACAGTGGTAATGACCGGGGTCATCATGTTCCTGCTGGCAACCTCTTCGGCGATGTCCTTCTCGATGTCGATCACCAATATTCCTGCGGCGCTGAGCGATATGATCCTCGGTATTTCCGCCAATAAACTGGTTATCCTGTTAGTCATTACCGTCTTTTTGTTGATTATCGGCGCATTTATGGATATCGGTCCGGCCATTCTGATTTTTACCCCGATTCTGCTGCCGATCATGGCTAAACTGGGCGTCGATCCGGTGCATTTTGGCATTATCATGATCTATAACCTGGCGATTGGCACCATTACGCCGCCAGTTGGCAGTGGTTTATATGTCGGGGCGAGCGTCGGTAAGGTCAAAGTTGAGGAAGTGATTAAACCGTTGCTGCCTTTTTACGGCGCGATTATCGGCGTTCTGTTATTAATTACCTACATTCCGGAAATCACACTGTTCTTACCCCGTCTACTGGGCATCATGTAA
diff --git a/Examples/2-res-Annotate-prodigal/discarded-list_genomes.lst b/Examples/2-res-Annotate-prodigal/discarded-list_genomes.lst
deleted file mode 100644
index 16c2d0c0909dd12b783df1afa25997442caf0d99..0000000000000000000000000000000000000000
--- a/Examples/2-res-Annotate-prodigal/discarded-list_genomes.lst
+++ /dev/null
@@ -1 +0,0 @@
-orig_name	to_annotate	gsize	nb_conts	L90
diff --git a/Examples/2-res-Annotate-prodigal/gff3/EXAM.1216.00002.gff b/Examples/2-res-Annotate-prodigal/gff3/EXAM.1216.00002.gff
deleted file mode 100644
index ab479b2600c38c43251a704ab51200ced15122e5..0000000000000000000000000000000000000000
--- a/Examples/2-res-Annotate-prodigal/gff3/EXAM.1216.00002.gff
+++ /dev/null
@@ -1,16 +0,0 @@
-##gff-version  3
-##sequence-region	EXAM.1216.00002.0001	1	>header_genome3_chromo_1
-##sequence-region	EXAM.1216.00002.0002	1	>genome3_plasmid_2
-##sequence-region	EXAM.1216.00002.0003	1	>genome3_plasmid_3
-EXAM.1216.00002.0001	Prodigal_v2.6.3	CDS	1	831	104.1	+	0	ID=EXAM.1216.00002.0001b_00001;partial=10;start_type=Edge;rbs_motif=None;rbs_spacer=None;gc_cont=0.578;conf=100.00;score=104.13;cscore=100.92;sscore=3.22;rscore=0.00;uscore=0.00;tscore=3.22;
-EXAM.1216.00002.0001	Prodigal_v2.6.3	CDS	880	1710	106.5	+	0	ID=EXAM.1216.00002.0001i_00002;partial=00;start_type=ATG;rbs_motif=AGGAG/GGAGG;rbs_spacer=11-12bp;gc_cont=0.578;conf=100.00;score=107.29;cscore=100.92;sscore=6.38;rscore=7.06;uscore=-5.38;tscore=3.95;
-EXAM.1216.00002.0001	Prodigal_v2.6.3	CDS	1655	2128	40.8	+	0	ID=EXAM.1216.00002.0001i_00003;partial=00;start_type=ATG;rbs_motif=GGA/GAG/AGG;rbs_spacer=11-12bp;gc_cont=0.544;conf=99.99;score=40.80;cscore=40.20;sscore=0.60;rscore=-1.74;uscore=-1.61;tscore=3.95;
-EXAM.1216.00002.0001	Prodigal_v2.6.3	CDS	2172	2396	19.5	+	0	ID=EXAM.1216.00002.0001i_00004;partial=00;start_type=ATG;rbs_motif=GGA/GAG/AGG;rbs_spacer=11-12bp;gc_cont=0.542;conf=99.08;score=20.33;cscore=21.30;sscore=-0.97;rscore=-1.96;uscore=-3.32;tscore=3.51;
-EXAM.1216.00002.0001	Prodigal_v2.6.3	CDS	2425	3828	146.8	+	0	ID=EXAM.1216.00002.0001i_00005;partial=00;start_type=ATG;rbs_motif=AGGAG/GGAGG;rbs_spacer=11-12bp;gc_cont=0.513;conf=100.00;score=147.74;cscore=139.37;sscore=8.37;rscore=7.06;uscore=-3.60;tscore=3.95;
-EXAM.1216.00002.0001	Prodigal_v2.6.3	CDS	3863	4636	118.2	+	0	ID=EXAM.1216.00002.0001i_00006;partial=00;start_type=ATG;rbs_motif=GGAG/GAGG;rbs_spacer=5-10bp;gc_cont=0.527;conf=100.00;score=119.07;cscore=106.36;sscore=12.71;rscore=11.19;uscore=-3.33;tscore=3.95;
-EXAM.1216.00002.0001	Prodigal_v2.6.3	CDS	4641	5432	48.3	+	0	ID=EXAM.1216.00002.0001i_00007;partial=00;start_type=ATG;rbs_motif=None;rbs_spacer=None;gc_cont=0.537;conf=100.00;score=49.55;cscore=55.53;sscore=-5.99;rscore=-8.50;uscore=-2.67;tscore=3.95;
-EXAM.1216.00002.0001	Prodigal_v2.6.3	CDS	5460	5747	35.4	+	0	ID=EXAM.1216.00002.0001b_00008;partial=00;start_type=ATG;rbs_motif=AGGAG;rbs_spacer=5-10bp;gc_cont=0.469;conf=99.98;score=36.42;cscore=19.87;sscore=16.55;rscore=14.84;uscore=-3.22;tscore=3.95;
-EXAM.1216.00002.0002	Prodigal_v2.6.3	CDS	1	582	63.1	+	0	ID=EXAM.1216.00002.0002b_00009;partial=10;start_type=Edge;rbs_motif=None;rbs_spacer=None;gc_cont=0.546;conf=100.00;score=63.13;cscore=59.91;sscore=3.22;rscore=0.00;uscore=0.00;tscore=3.22;
-EXAM.1216.00002.0002	Prodigal_v2.6.3	CDS	629	1936	156.9	+	0	ID=EXAM.1216.00002.0002b_00010;partial=00;start_type=ATG;rbs_motif=None;rbs_spacer=None;gc_cont=0.520;conf=100.00;score=157.65;cscore=165.52;sscore=-7.87;rscore=-8.50;uscore=-4.09;tscore=3.95;
-EXAM.1216.00002.0003	Prodigal_v2.6.3	CDS	2	280	8.3	+	0	ID=EXAM.1216.00002.0003b_00011;partial=10;start_type=Edge;rbs_motif=None;rbs_spacer=None;gc_cont=0.355;conf=87.21;score=8.35;cscore=5.13;sscore=3.22;rscore=0.00;uscore=0.00;tscore=3.22;
-EXAM.1216.00002.0003	Prodigal_v2.6.3	CDS	323	1102	58.2	+	0	ID=EXAM.1216.00002.0003b_00012;partial=00;start_type=ATG;rbs_motif=None;rbs_spacer=None;gc_cont=0.559;conf=100.00;score=59.02;cscore=60.68;sscore=-1.66;rscore=-0.28;uscore=-5.50;tscore=3.30;
diff --git a/Examples/2-res-Annotate-prodigal/gff3/EXAM.1219.00001.gff b/Examples/2-res-Annotate-prodigal/gff3/EXAM.1219.00001.gff
deleted file mode 100644
index f359c95539609c0f25083c69aeda16179968b236..0000000000000000000000000000000000000000
--- a/Examples/2-res-Annotate-prodigal/gff3/EXAM.1219.00001.gff
+++ /dev/null
@@ -1,14 +0,0 @@
-##gff-version  3
-##sequence-region	EXAM.1219.00001.0001	1	>genome1_1
-##sequence-region	EXAM.1219.00001.0002	1	>genome1_2
-EXAM.1219.00001.0001	Prodigal_v2.6.3	CDS	213	1880	260.0	+	0	ID=EXAM.1219.00001.0001b_00001;partial=00;start_type=ATG;rbs_motif=None;rbs_spacer=None;gc_cont=0.534;conf=99.99;score=259.99;cscore=268.89;sscore=-8.89;rscore=-8.50;uscore=-4.34;tscore=3.95;
-EXAM.1219.00001.0001	Prodigal_v2.6.3	CDS	1916	2746	117.8	+	0	ID=EXAM.1219.00001.0001b_00002;partial=00;start_type=ATG;rbs_motif=AGGAGG;rbs_spacer=5-10bp;gc_cont=0.570;conf=100.00;score=118.71;cscore=102.01;sscore=16.70;rscore=14.38;uscore=-2.52;tscore=3.95;
-EXAM.1219.00001.0002	Prodigal_v2.6.3	CDS	16	396	43.9	+	0	ID=EXAM.1219.00001.0002b_00003;partial=00;start_type=ATG;rbs_motif=None;rbs_spacer=None;gc_cont=0.538;conf=100.00;score=43.95;cscore=48.77;sscore=-4.82;rscore=-8.50;uscore=-0.27;tscore=3.95;
-EXAM.1219.00001.0002	Prodigal_v2.6.3	CDS	428	1837	146.3	+	0	ID=EXAM.1219.00001.0002i_00004;partial=00;start_type=ATG;rbs_motif=GGA/GAG/AGG;rbs_spacer=5-10bp;gc_cont=0.512;conf=100.00;score=147.28;cscore=140.86;sscore=6.42;rscore=2.79;uscore=-1.25;tscore=3.95;
-EXAM.1219.00001.0002	Prodigal_v2.6.3	CDS	1869	2642	98.1	+	0	ID=EXAM.1219.00001.0002i_00005;partial=00;start_type=ATG;rbs_motif=None;rbs_spacer=None;gc_cont=0.531;conf=100.00;score=99.06;cscore=104.90;sscore=-5.84;rscore=-8.50;uscore=-2.23;tscore=3.95;
-EXAM.1219.00001.0002	Prodigal_v2.6.3	CDS	2709	3443	50.8	+	0	ID=EXAM.1219.00001.0002i_00006;partial=00;start_type=ATG;rbs_motif=None;rbs_spacer=None;gc_cont=0.547;conf=100.00;score=50.78;cscore=54.23;sscore=-3.45;rscore=-8.50;uscore=1.10;tscore=3.95;
-EXAM.1219.00001.0002	Prodigal_v2.6.3	CDS	3427	4254	66.1	+	0	ID=EXAM.1219.00001.0002i_00007;partial=00;start_type=ATG;rbs_motif=AGxAG;rbs_spacer=5-10bp;gc_cont=0.541;conf=100.00;score=67.21;cscore=64.98;sscore=2.23;rscore=-2.56;uscore=-0.31;tscore=3.95;
-EXAM.1219.00001.0002	Prodigal_v2.6.3	CDS	4299	4763	48.2	+	0	ID=EXAM.1219.00001.0002i_00008;partial=00;start_type=ATG;rbs_motif=AGGA/GGAG/GAGG;rbs_spacer=11-12bp;gc_cont=0.596;conf=100.00;score=48.97;cscore=42.02;sscore=6.96;rscore=4.46;uscore=-2.24;tscore=3.95;
-EXAM.1219.00001.0002	Prodigal_v2.6.3	CDS	4818	5078	23.5	+	0	ID=EXAM.1219.00001.0002i_00009;partial=00;start_type=ATG;rbs_motif=GGA/GAG/AGG;rbs_spacer=5-10bp;gc_cont=0.487;conf=99.62;score=24.19;cscore=15.16;sscore=9.03;rscore=2.79;uscore=1.60;tscore=3.95;
-EXAM.1219.00001.0002	Prodigal_v2.6.3	CDS	5117	5698	52.3	+	0	ID=EXAM.1219.00001.0002i_00010;partial=00;start_type=ATG;rbs_motif=None;rbs_spacer=None;gc_cont=0.546;conf=100.00;score=53.17;cscore=61.65;sscore=-8.48;rscore=-8.50;uscore=-4.79;tscore=3.95;
-EXAM.1219.00001.0002	Prodigal_v2.6.3	CDS	5717	7024	164.7	+	0	ID=EXAM.1219.00001.0002b_00011;partial=00;start_type=ATG;rbs_motif=None;rbs_spacer=None;gc_cont=0.524;conf=100.00;score=165.75;cscore=171.22;sscore=-5.47;rscore=-8.50;uscore=-1.99;tscore=3.95;
diff --git a/Examples/2-res-Annotate-prodigal/gff3/GEN2.1219.00001.gff b/Examples/2-res-Annotate-prodigal/gff3/GEN2.1219.00001.gff
deleted file mode 100644
index 63c842a82c115fd2a928974e942d375ae8515f34..0000000000000000000000000000000000000000
--- a/Examples/2-res-Annotate-prodigal/gff3/GEN2.1219.00001.gff
+++ /dev/null
@@ -1,19 +0,0 @@
-##gff-version  3
-##sequence-region	GEN2.1219.00001.0001	1	>this_is_genome2_contig_number1_1
-##sequence-region	GEN2.1219.00001.0002	1	>this_is_genome2_contig_number1_2
-##sequence-region	GEN2.1219.00001.0003	1	>this_is_genome2_contig_number2_3
-##sequence-region	GEN2.1219.00001.0004	1	>this_is_genome2_contig_number3_4
-##sequence-region	GEN2.1219.00001.0005	1	>genome2_small_5
-GEN2.1219.00001.0001	Prodigal_v2.6.3	CDS	1	774	109.1	+	0	ID=GEN2.1219.00001.0001b_00001;partial=10;start_type=Edge;rbs_motif=None;rbs_spacer=None;gc_cont=0.530;conf=100.00;score=109.07;cscore=105.85;sscore=3.22;rscore=0.00;uscore=0.00;tscore=3.22;
-GEN2.1219.00001.0001	Prodigal_v2.6.3	CDS	857	2260	130.8	+	0	ID=GEN2.1219.00001.0001b_00002;partial=00;start_type=ATG;rbs_motif=None;rbs_spacer=None;gc_cont=0.510;conf=100.00;score=130.80;cscore=138.51;sscore=-7.71;rscore=-8.50;uscore=-3.16;tscore=3.95;
-GEN2.1219.00001.0002	Prodigal_v2.6.3	CDS	1	252	25.2	+	0	ID=GEN2.1219.00001.0002b_00003;partial=10;start_type=Edge;rbs_motif=None;rbs_spacer=None;gc_cont=0.540;conf=99.70;score=25.25;cscore=22.03;sscore=3.22;rscore=0.00;uscore=0.00;tscore=3.22;
-GEN2.1219.00001.0002	Prodigal_v2.6.3	CDS	301	681	42.0	+	0	ID=GEN2.1219.00001.0002i_00004;partial=00;start_type=ATG;rbs_motif=None;rbs_spacer=None;gc_cont=0.530;conf=99.99;score=42.75;cscore=48.52;sscore=-5.77;rscore=-8.50;uscore=-1.97;tscore=3.95;
-GEN2.1219.00001.0002	Prodigal_v2.6.3	CDS	764	1597	93.2	+	0	ID=GEN2.1219.00001.0002i_00005;partial=00;start_type=ATG;rbs_motif=None;rbs_spacer=None;gc_cont=0.573;conf=100.00;score=93.20;cscore=101.05;sscore=-7.85;rscore=-8.50;uscore=-3.30;tscore=3.95;
-GEN2.1219.00001.0002	Prodigal_v2.6.3	CDS	1628	3295	276.3	+	0	ID=GEN2.1219.00001.0002b_00006;partial=00;start_type=ATG;rbs_motif=GGA/GAG/AGG;rbs_spacer=5-10bp;gc_cont=0.537;conf=99.99;score=277.27;cscore=270.94;sscore=6.32;rscore=2.79;uscore=-1.36;tscore=3.95;
-GEN2.1219.00001.0003	Prodigal_v2.6.3	CDS	30	797	58.3	+	0	ID=GEN2.1219.00001.0003b_00007;partial=00;start_type=GTG;rbs_motif=GGA/GAG/AGG;rbs_spacer=5-10bp;gc_cont=0.540;conf=100.00;score=58.32;cscore=63.52;sscore=-5.21;rscore=2.79;uscore=-1.37;tscore=-6.63;
-GEN2.1219.00001.0003	Prodigal_v2.6.3	CDS	862	1122	22.1	+	0	ID=GEN2.1219.00001.0003i_00008;partial=00;start_type=ATG;rbs_motif=GGA/GAG/AGG;rbs_spacer=5-10bp;gc_cont=0.487;conf=99.38;score=22.10;cscore=13.73;sscore=8.37;rscore=2.79;uscore=1.62;tscore=3.95;
-GEN2.1219.00001.0003	Prodigal_v2.6.3	CDS	1170	1751	51.0	+	0	ID=GEN2.1219.00001.0003i_00009;partial=00;start_type=ATG;rbs_motif=None;rbs_spacer=None;gc_cont=0.546;conf=100.00;score=51.73;cscore=58.14;sscore=-6.42;rscore=-8.50;uscore=-2.63;tscore=3.95;
-GEN2.1219.00001.0003	Prodigal_v2.6.3	CDS	1895	2263	34.8	+	0	ID=GEN2.1219.00001.0003b_00010;partial=00;start_type=ATG;rbs_motif=GGAG/GAGG;rbs_spacer=5-10bp;gc_cont=0.599;conf=99.97;score=34.83;cscore=22.60;sscore=12.23;rscore=11.19;uscore=-2.91;tscore=3.95;
-GEN2.1219.00001.0004	Prodigal_v2.6.3	CDS	1	1308	169.7	+	0	ID=GEN2.1219.00001.0004b_00011;partial=10;start_type=Edge;rbs_motif=None;rbs_spacer=None;gc_cont=0.519;conf=100.00;score=169.75;cscore=166.53;sscore=3.22;rscore=0.00;uscore=0.00;tscore=3.22;
-GEN2.1219.00001.0004	Prodigal_v2.6.3	CDS	1340	1804	33.2	+	0	ID=GEN2.1219.00001.0004i_00012;partial=00;start_type=ATG;rbs_motif=None;rbs_spacer=None;gc_cont=0.594;conf=99.96;score=34.14;cscore=41.34;sscore=-7.21;rscore=-8.50;uscore=-3.59;tscore=3.95;
-GEN2.1219.00001.0004	Prodigal_v2.6.3	CDS	1832	2845	78.4	+	0	ID=GEN2.1219.00001.0004b_00013;partial=00;start_type=ATG;rbs_motif=None;rbs_spacer=None;gc_cont=0.456;conf=100.00;score=79.42;cscore=85.62;sscore=-6.20;rscore=-8.50;uscore=-2.63;tscore=3.95;
diff --git a/Examples/2-res-Annotate-prodigal/gff3/GEN4.1111.00001.gff b/Examples/2-res-Annotate-prodigal/gff3/GEN4.1111.00001.gff
deleted file mode 100644
index e451e36e4cfc52ab3777a19c5ccd7005a946d55d..0000000000000000000000000000000000000000
--- a/Examples/2-res-Annotate-prodigal/gff3/GEN4.1111.00001.gff
+++ /dev/null
@@ -1,11 +0,0 @@
-##gff-version  3
-##sequence-region	GEN4.1111.00001.0001	1	>g4_1
-GEN4.1111.00001.0001	Prodigal_v2.6.3	CDS	1	831	106.7	+	0	ID=GEN4.1111.00001.0001b_00001;partial=10;start_type=Edge;rbs_motif=None;rbs_spacer=None;gc_cont=0.579;conf=100.00;score=106.71;cscore=103.49;sscore=3.22;rscore=0.00;uscore=0.00;tscore=3.22;
-GEN4.1111.00001.0001	Prodigal_v2.6.3	CDS	861	1241	42.3	+	0	ID=GEN4.1111.00001.0001i_00002;partial=00;start_type=ATG;rbs_motif=None;rbs_spacer=None;gc_cont=0.533;conf=100.00;score=43.30;cscore=49.63;sscore=-6.33;rscore=-8.50;uscore=-2.74;tscore=3.95;
-GEN4.1111.00001.0001	Prodigal_v2.6.3	CDS	1271	2074	143.6	+	0	ID=GEN4.1111.00001.0001i_00003;partial=00;start_type=ATG;rbs_motif=AGGAG;rbs_spacer=5-10bp;gc_cont=0.591;conf=100.00;score=144.59;cscore=127.77;sscore=16.82;rscore=14.84;uscore=-2.92;tscore=3.95;
-GEN4.1111.00001.0001	Prodigal_v2.6.3	CDS	2111	3514	138.1	+	0	ID=GEN4.1111.00001.0001i_00004;partial=00;start_type=ATG;rbs_motif=None;rbs_spacer=None;gc_cont=0.512;conf=100.00;score=138.96;cscore=143.16;sscore=-4.20;rscore=-8.50;uscore=-0.53;tscore=3.95;
-GEN4.1111.00001.0001	Prodigal_v2.6.3	CDS	3535	4308	99.1	+	0	ID=GEN4.1111.00001.0001i_00005;partial=00;start_type=ATG;rbs_motif=3Base/5BMM;rbs_spacer=13-15bp;gc_cont=0.532;conf=100.00;score=100.11;cscore=105.95;sscore=-5.84;rscore=-6.58;uscore=-4.27;tscore=3.95;
-GEN4.1111.00001.0001	Prodigal_v2.6.3	CDS	4327	5094	50.2	+	0	ID=GEN4.1111.00001.0001i_00006;partial=00;start_type=GTG;rbs_motif=None;rbs_spacer=None;gc_cont=0.544;conf=100.00;score=51.24;cscore=64.63;sscore=-13.39;rscore=-8.50;uscore=0.66;tscore=-6.63;
-GEN4.1111.00001.0001	Prodigal_v2.6.3	CDS	5138	5398	23.6	+	0	ID=GEN4.1111.00001.0001i_00007;partial=00;start_type=ATG;rbs_motif=GGA/GAG/AGG;rbs_spacer=5-10bp;gc_cont=0.483;conf=99.64;score=24.44;cscore=15.14;sscore=9.29;rscore=2.79;uscore=1.75;tscore=3.95;
-GEN4.1111.00001.0001	Prodigal_v2.6.3	CDS	5413	5994	54.9	+	0	ID=GEN4.1111.00001.0001i_00008;partial=00;start_type=ATG;rbs_motif=None;rbs_spacer=None;gc_cont=0.546;conf=100.00;score=56.05;cscore=59.63;sscore=-3.58;rscore=-8.50;uscore=-0.15;tscore=3.95;
-GEN4.1111.00001.0001	Prodigal_v2.6.3	CDS	6052	7134	135.9	+	0	ID=GEN4.1111.00001.0001b_00009;partial=00;start_type=ATG;rbs_motif=None;rbs_spacer=None;gc_cont=0.525;conf=100.00;score=136.58;cscore=141.36;sscore=-4.77;rscore=-8.50;uscore=-0.88;tscore=3.95;
diff --git a/Examples/2-res-Annotate-prodigal/tmp_files/genome1.fst_prodigal-split5N.fna b/Examples/2-res-Annotate-prodigal/tmp_files/genome1.fst_prodigal-split5N.fna
deleted file mode 100644
index 11feaae3628ca13667c0d695bbcacd5a2139310d..0000000000000000000000000000000000000000
--- a/Examples/2-res-Annotate-prodigal/tmp_files/genome1.fst_prodigal-split5N.fna
+++ /dev/null
@@ -1,4 +0,0 @@
->genome1_1
-ATGTGTAAAAGCCGGAGGGGTTATCTTTTCCCGGCTTTTTATTATCAATTACTCATTAACTCCTGTTCCGTTCTTTTGCGTTTAATCACCGGAATATCTCCGGTATTGTTCAGCGCCCCGGAAATGTTTTTAACCACTGTTCTGCACTCCGTTTATTAAACGCGCTCAGCGCGCGCTCATATATCGCGCGCGCGCGCGCGCATATATATATAATGAGTGAGGCTGAAGCCCGCCCGACTAACTTTATTCGTCAGATTATTGATGAAGATCTGGCGAGTGGTAAACATACCACTGTCCATACCCGTTTTCCGCCGGAGCCGAATGGCTATCTGCATATCGGCCACGCGAAATCTATCTGCCTGAACTTTGGCATCGCGCAAGATTATCAGGGCCAGTGCAACCTGCGTTTCGATGACACCAACCCGGTAAAAGAAGATATCGAGTACGTTGATTCGATCAAAAACGACGTCGAGTGGTTAGGCTTTCACTGGTCTGGCGATATTCGCTACTCCTCCGATTACTTTGACCAACTGCACGCCTATGCGGTCGAGCTAATCAATAAAGGCCTGGCCTATGTTGATGAGCTGACGCCGGAGCAGATCCGTGAATACCGCGGTACGCTGACCGCGCCGGGTAAAAACAGCCCGTTCCGCGATCGCAGCGTCGAAGAGAACCTCGCGCTATTTGAAAAAATGCGTACCGGCGGTTTTGAAGAGGGTAAAGCCTGTCTGCGCGCTAAAATCGACATGGCGTCGCCGTTTATCGTGATGCGCGATCCGGTGCTGTATCGCATTAAATTCGCCGAGCATCATCAGACTGGCAACAAGTGGTGCATCTATCCGATGTACGACTTTACTCACTGCATCAGCGATGCGCTGGAAGGCATTACTCATTCTCTGTGTACGCTGGAGTTCCAGGATAACCGTCGTCTGTACGACTGGGTGCTGGACAACATCACCATTCCGGTTCACCCGCGCCAGTACGAATTCTCGCGCCTGAATCTGGAATACACCGTGATGTCCAAGCGTAAGCTGAACCTGCTGGTGACCGACAAACACGTCGAAGGTTGGGACGATCCGCGTATGCCGACTATTTCCGGTCTGCGCCGTCGCGGCTATACCGCGGCTTCTATTCGTGAGTTCTGCAAACGCATCGGCGTCACCAAGCAGGACAACACTATTGAGATGGCGTCGCTGGAATCCTGCATTCGCGAAGATCTGAACGAAAACGCGCCGCGCGCGATGGCGGTAATCGATCCGGTAAAACTGGTTATCGAAAATTACCCGCAGGGTGAGAGCGAAATGGTTACCATGCCTAACCATCCGAATAAACCGGAGATGGGCAGCCGTGAAGTGCCGTTTAGCGGTGAGATCTGGATCGATCGCGCAGATTTCCGCGAAGAAGCGAACAAACAGTACAAACGTCTGGTGATGGGCAAAGAAGTGCGTCTGCGTAATGCCTACGTCATTAAAGCGGAGCGCGTAGAGAAGGATGCCGAAGGGAATATCACCACCATCTTCTGTACCTATGATGCTGATACGCTGAGTAAAGATCCGGCTGACGGGCGTAAAGTGAAAGGCGTAATCCACTGGGTTAGCGCAGCACATGCGCTGCCGATTGAAATTCGTCTCTACGACCGTCTGTTCAGCGTGCCGAATCCGGGCGCCGCGGAGGACTTCCTGTCTGTTATCAACCCCGAATCATTAGTGATTAAGCAGGGGTATGGCGAGCCGTCGCTGAAAGCGGCGGTAGCAGGAAAAGCTTTCCAGTTTGAACGTGAAGGCTACTTCTGCCTCGACAGCCGCTATGCAACGGCCGATAAGCTGGTCTTTAACCGCACCGTGGGCCTGCGTGATACCTGGGCGAAAGCGGGCGAGTAACGCGCATAGGCGGCCTTCAAGGAGGCGCTAGGCGAATGAAAGCGCTACTGTGGCTGGTGGGTCTCGCGTTGCTGTTAACAGGCTGCGCGAGCGAAAAAGGAATTATCGATAAAGAGGGATATCAGCTTGATACCCGACATCGGGCGCAGGCGGCCTATCCGCGCATTAAAGTCCTGGTGATTCACTATACGGCGGAAAACTTTGACGTTTCGCTGGCGACGTTAACGGGTCGCAACGTCAGTTCGCATTACCTGATTCCCGCAACCCCGCCATTATATGGCGGTAAACCGCGCATCTGGCAACTGGTGCCGGAACAGGATCAGGCCTGGCATGCGGGCGTCAGTTTCTGGCGAGGCGCCACGCGTCTCAATGATACGTCTATTGGCATTGAGCTGGAAAATCGTGGTTGGCGAATGTCCGGCGGGGTGAAATCTTTCGCGCCGTTTGAATCCGCGCAAATTCAGGCATTGATTCCGTTAGCGAAGGATATTATCGCGCGCTATAACATCAAACCGCAGAATGTGGTGGCCCATGCGGATATCGCGCCGCAGCGTAAAGACGATCCCGGCCCGCGCTTCCCGTGGCGCGAGCTGGCGGCGCAGGGGATTAGCGCCTGGCCTGACGCCCAGCGTGTGGCGTTTTATCTGGCTGGACGCGCGCCGTATACGCCAGTCGATACCGCAACGGTGCTTGCGTTACTCTCGCGCTATGGCTATGAAGTCAAAGCCGATATGACGGCACGCGAGCAGCAGCGGGTGATTATGGCGTTCCAGATGCACTTCCGTCCGGCGCAATGGAACGGTATCGCAGATGCCGAAACGCAGGCGATTGCCGAAGCATTACTGGAGAAGTACGGCCAGGATTAACGCGATAGGCGCGCGAGATTACGCGCGCAGTATCGCGC
->genome1_2
-CGCGCATAGCGCGCAATGCCGCACTTTATTGCTGAATGTACTGAAAATATTCGCGAGCAGGCTGATTTACCCGGCCTGTTCAGCAAGGTAAACGAGGCGCTGGCCGCCAGCGGGATTTTCCCCATCGGCGGTATCCGCAGTCGCGCCCACTGGCTGGATACCTGGCAGATGGCTGACGGTAAGCATGATTACGCGTTTGTGCATATGACGCTGAAAATCGGCGCCGGGCGCAGCCTGGAGAGCCGTCAGGAAGTTGGCGAAATGCTGTTTGGGCTGATTAAAGCCCACTTCGCCGACCTGATGGAGAACCGCTATCTGGCGCTGTCGTTTGAGATTGCCGAGCTACATCCGACGCTCAATTACAAACAAAACAACGTACACGCGTTATTTAAATAGCCGATATGAGGCGCGGCGCTATAAGGCGCTCATGAGCATGCCCGCGACTAAATTCTCCCGACGTACCCTCCTGACGGCAGGTTCTGCGCTTGCTGTTCTTCCTTTTCTGCGCGCCTTGCCGGTACAGGCGCGTGAACCTCGCGAGACCGTCGATATTAAGGATTATCCGGCGGATGACGGTATCGCCTCGTTCAAACAGGCCTTCGCCGACGGACAGACCGTGGTCGTACCGCCAGGATGGGTGTGTGAAAATATCAATGCGGCGATAACGATTCCGGCGGGAAAAACGCTGCGGGTACAGGGCGCGGTGCGTGGGAATGGCCGGGGACGGTTTATTTTGCAGGACGGGTGTCAGGTGGTGGGGGAGCAGGGCGGCAGTCTGCACAATGTGACGCTGGATGTTCGCGGGTCGGACTGTGTGATTAAAGGCGTGGCGATGAGCGGCTTTGGCCCCGTCGCGCAAATTTTCATCGGTGGTAAGGAACCGCAGGTGATGCGTAATCTCATTATCGATGACATCACCGTTACCCACGCCAACTACGCCATTCTCCGCCAGGGATTTCATAACCAAATGGATGGCGCGCGGATTACGCATAGCCGCTTTAGCGATTTACAGGGGGACGCCATTGAGTGGAATGTCGCGATTCACGACCGCGACATCCTGATTTCCGATCATGTCATCGAACGCATTAATTGTACCAATGGCAAAATCAACTGGGGGATCGGCATCGGGCTGGCGGGTAGCACCTATGACAACAGTTATCCTGAAGACCAGGCAGTAAAAAACTTTGTGGTGGCCAATATTACCGGATCTGATTGCCGACAGCTTGTGCACGTAGAAAATGGCAAACATTTCGTCATTCGCAATGTCAAAGCCAAAAACATCACGCCCGGTTTCAGTAAAAATGCGGGTATTGATAACGCAACGATCGCAATTTATGGCTGTGATAATTTCGTCATTGATAATATTGATATGACGAATAGTGCCGGGATGCTCATCGGCTATGGCGTCGTTAAAGGAAAATACCTGTCAATTCCGCAAAACTTTAAATTAAACGCTATTCGGTTGGATAATCGCCAGGTTGCTTATAAATTACGCGGCATTCAAATTTCCTCCGGCAACACCCCCTCTTTTGTCGCCATCACCAATGTACGGATGACGCGTGCTACGCTGGAACTGCATAATCAACCGCAGCACCTCTTTCTGCGCAATATCAACGTGATGCAAACTTCAGCGATTGGCCCGGCGTTAAAAATGCATTTCGATTTGCGTAAAGATGTACGTGGTCAATTTATGGCCCGCCAGGACACGCTGCTTTCCCTCGCTAATGTTCATGCCATCAATGAAAACGGGCAGAGTTCCGTGGATATCGACAGGATTAATCACCAAACCGTGAATGTCGAAGCAGTGAATTTTTCGCTGCCGAAGCGGGGAGGGTAACGAATTCCGCGGCATATAGCGGCGCGATAGCATGTCAGAAAATAAATTACACGTTATCGATTTGCACAAACGCTACGGCGGTCATGAAGTGCTGAAAGGGGTATCGCTGCAGGCCCGCGCCGGAGATGTGATTAGCATCATCGGCTCGTCCGGCTCCGGTAAAAGCACTTTTTTGCGCTGTATTAACTTCCTCGAAAAACCGAGCGAAGGCGCGATTATCGTGAACGGTCAGAACATTAATCTGGTGCGCGACAAAGATGGGCAGCTCAAAGTGGCGGATAAAAATCAGCTACGCTTGTTGCGTACCCGCCTGACGATGGTGTTTCAGCACTTCAACCTCTGGAGCCACATGACGGTGCTGGAAAATGTGATGGAAGCGCCGATTCAGGTACTGGGATTAAGCAAGCACGACGCGCGCGAGCGGGCGTTGAAATATCTGGCGAAGGTGGGGATTGATGAGCGCGCTCAGGGCAAATATCCCGTCCATCTCTCCGGCGGCCAACAGCAGCGCGTTTCTATTGCGCGCGCGCTGGCGATGGAACCTGACGTTTTACTGTTCGATGAACCCACATCGGCGCTCGATCCTGAACTGGTCGGCGAAGTGTTGCGCATCATGCAACAACTGGCGGAAGAAGGCAAAACGATGGTGGTGGTCACGCATGAAATGGGCTTCGCTCGCCATGTCTCTTCGCACGTTATTTTTCTGCATCAGGGGAAAATTGAAGAAGAGGGTGATCCGGAGCAGGTGTTCGGCAATCCGCAAAGCCCGCGTTTACAGCAATTCCTGAAAGGCTCGCTGAAATAACGCTCAGAGGCGCGCGCGCGCTATATACGCGCAGTGTTTATTGGCATAGTTAGCCTGTTTCCTGAAATGTTCCGCGCAATTACCGATTACGGGGTAACTGGCCGGGCAGTAAAAAAAGGCCTGCTGAACATCCAAAGCTGGAGTCCTCGCGACTTCGCGCATGACCGGCACCGTACCGTGGACGACCGTCCTTACGGCGGCGGACCGGGGATGTTAATGATGGTGCAACCCTTGCGGGACGCCATTCACGCAGCAAAAGCCGCGGCAGGTGAAGGCGCTAAAGTGATTTATCTGTCGCCTCAGGGACGCAAGCTTGATCAAGCGGGCGTTAGCGAGCTGGCCACGAATCAGAAGCTTATTCTGGTGTGTGGTCGCTACGAAGGCGTAGATGAGCGCGTAATTCAGACCGAAATTGACGAAGAATGGTCAATTGGCGATTACGTTCTCAGCGGTGGCGAACTACCGGCAATGACGCTGATTGACTCCGTCGCCCGGTTTATACCGGGGGTTCTGGGGCATGAGGCATCAGCAATCGAAGATTCGTTTGCTGATGGGTTGCTGGATTGTCCGCACTATACGCGCCCTGAAGTGTTAGAGGGGATGGAAGTACCGCCAGTATTGCTGTCGGGAAACCATGCTGAGATACGTCGCTGGCGTTTGAAACAGTCGCTGGGCCGAACCTGGCTTAGAAGACCTGAACTTCTGGAAAACCTGGCTCTGACTGAAGAGCAAGCAAGGTTGCTGGCGGAGTTCAAAACAGAACACGCACAACAGCAGCATAAACATGATGGGATGGCATAGCCGTCATATGGGCTCTCAGAGGAGACGCGCTAATGCGCAGTACGTGTTTATTGGCATAGTTAGCCTGTTTCCTGAAATGTTCCGCGCAATTACCGATTACGGGGTAACTGGCCGGGCAGTAAAAAAAGGCCTGCTGAACATCCAAAGCTGGAGTCCTCGCGACTTCGCGCATGACCGGCACCGTACCGTGGACGACCGTCCTTACGGCGGCGGACCGGGGATGTTAATGATGGTGCAACCCTTGCGGGACGCCATTCACGCAGCAAAAGCCGCGGCAGGTGAAGGCGCTAAAGTGATTTATCTGTCGCCTCAGGGACGCAAGCTTGATCAAGCGGGCGTTAGCGAGCTGGCCACGAATCAGAAGCTTATTCTGGTGTGTGGTCGCTACGAAGGCGTAGATGAGCGCGTAATTCAGACCGAAATTGACGAAGAATGGTCAATTGGCGATTACGTTCTCAGCGGTGGCGAACTACCGGCAATGACGCTGATTGACTCCGTCGCCCGGTTTATACCGGGGGTTCTGGGGCATGAGGCATCAGCAATCGAAGATTCGTTTGCTGATGGGTTGCTGGATTGTCCGCACTATACGCGCCCTGAAGTGTTAGAGGGGATGGAAGTACCGCCAGTATTGCTGTCGGGAAACCATGCTGAGATACGTCGCTGGCGTTTGAAACAGTCGCTGGGCCGAACCTGGCTTAGAAGACCTGAACTTCTGGAAAACCTGGCTCTGACTGAAGAGCAAGCAAGGTTGCTGGCGGAGTTCAAAACAGAACACGCACAACAGCAGCATAAACATGATGGGATGGCATAGCGCATACGCGCGCGATATATATTCGCGCAGAGGCGCGCATAGCGATGAAGTTTGTTGCGCCCGAACAGGCACCGGAACAGGCGGAGGTCATCAAAAATACGCCGTTCTGGCCTGATGTGGACCTGTCGGAATTTCGCAGTGTGATGCGCACTGACGGCACGGTGACGCAGCCGCGTTTAAAGCAGGTCGTGCTGACGGCGATCTCTGAGGTTAACGCTGAGCTGTACGACTTCCGCAACCGTCAGCAGATGCTGGGCTGGCGGACACTTGCTGAGGTTCCCGCAGAAATGCTGGACGGTAAAAGCGAGCGTATCCGGCACTACCACAACGCTGTTTTTTGCTGGGCGCGCGCTGTGCTTAATGAGCGTTATCAGGACTATGACGCCACGGCGTCAGGCGTGAAGCGAGGGGAGGAGCTGGCGGAGGCCAGCGGCGATCTGTGGCGTGATGCCCGCTGGGCCATCAGCCGGGTGCAGGATGTACCGCACTGTACGGTGGAGCTTATCTGAACGGCTAGCGCGTAGCGGCAGTCTCGGATGAATAATCATTTTGGGAAAGGGTTAATGGCCGGGTTGCACGCGCCATATGCATATAGCGCGCATCATGCGGTGAATTTCTGTTCTGAGTATAAACGTGGCTTTGTATTGGGTTTTACACACCGTATGTTCGAAAAGACCGGCGATCGTCAACTTAGCGCGTGGGAGGCTGGAATTCTGACGCGTCGCTATGGTCTGGATAAAGAAATGGTGATGGATTTCTTTAAAGAGAATCATTCCGGGATGGCGGTTCGCTTCTTTATGGCCGGTTATCGACTCGAAGGTTGACGATCGCGCGCAGGAGGAGAGCTCTCTTCTTCTAGAGCATGTCTACGCTTCTCTATTTGCACGGATTCAACAGTTCCCCTCGCTCGGCAAAAGCGTGCCAGCTAAAAAACTGGCTGGCGGAGCGTCATCCGCATGTTGAGATGATCGTCCCTCAGCTGCCGCCGTATCCTGCCGATGCGGCGGAGTTGCTGGAATCTCTCGTGCTTGAGCATGGCGGTGCGCCATTAGGGCTGGTAGGATCGTCGCTGGGTGGTTATTACGCCACCTGGCTGTCGCAATGTTTTATGCTGCCGGCTGTGGTGGTGAATCCCGCCGTGCGGCCCTTTGAATTACTGACCGACTATCTCGGTCAGAACGAGAACCCCTACACCGGGCAGCAATATGTGCTAGAGTCTCGCCATATTTATGATCTTAAAGTCATGCAGATTGACCCGCTGGAAGCGCCGGACCTGATCTGGCTACTGCAACAGACGGGCGATGAAGTGCTGTATTACCGCCAGGCGGTGGCATATTACGCCTCCTGCCGTCAGACAGTGACCGAGGGTGGTAATCACGCATTCACGGGCTTCGAAGATTATTTCAACCAGATTGTCGATTTTCTTGGACTGCACAGTTGCTGACGGCTATGCGCGCGCTCGATGATTGACCCTATTTTTGCGTCCTGTACGCTAATTGCCGTCTTTGTTGTTTTACTGGCCATGGGCGCGCCTATCGGGATCTGCATCGTTATCGCCTCTTTCAGCACCATGATGCTGGTACTGCCTTTCGATATTTCGATGTTCGCCACCGCGCAAAAAATGTTCTCCAGCCTGGACAGTTTTGCCTTGCTGGCCGTGCCGTTCTTCGTTTTGTCCGGGGTGATCATGAATAGCGGGGGAATTGCCGCCCGGCTGGTCAATTTTGCCAAACTGTTTACTGGCAAACTGCCCGGCTCGCTCTCTTATACCAACATCGTCGGCAATATGATGTTCGGTGCAATTTCCGGATCGGCGATTGCCGCCTCAACCTCCATCGGCGGCGTGATGGTGCCGATGAGCGCGCGCGAAGGTTACGATCGCGGCTTTGCGGCCGCGGTGAATATCGCCTCCGCGCCGACGGGAATGTTAATTCCGCCCACCACGGCTTTTATCCTTTACGCGCTGGCAAGCGGGGGAACATCGATTGCCGCTCTGTTCGCCGGCGGTCTGGTCGCGGGAGTGCTGTGGGGCGTTGGCTGTATGCTGGTCACGCTGGTGGTCGCTAAGCGTCGAAATTATCGGGTTTTCTTCACCGTCCAAAAAGGTATGGCGCTAAAAGTTGCCGTTGAGGCCATTCCCAGCCTGCTGCTGATCGTGATTATTGTCGGCGGCATTGTGCAGGGGATTTTCACCGCCATTGAAGCCTCCGCGATTGCCGTGGTGTATACGTTATTGCTGACGATGGTGTTTTACCGCACGCTGAAAATTAAGGATTTGCCTTCGATTTTGCTCCAGACAGTGGTAATGACCGGGGTCATCATGTTCCTGCTGGCAACCTCTTCGGCGATGTCCTTCTCGATGTCGATCACCAATATTCCTGCGGCGCTGAGCGATATGATCCTCGGTATTTCCGCCAATAAACTGGTTATCCTGTTAGTCATTACCGTCTTTTTGTTGATTATCGGCGCATTTATGGATATTGGTCCGGCCATTCTGATTTTTACCCCGATTCTGCTGCCAATCATGGCTAAACTGGGCGTCGATCCGGTGCATTTCGGCATTATCATGATCTATAACCTGGCGATTGGCACCATTACGCCGCCAGTTGGCAGTGGTTTATATGTCGGGGCGAGCGTCGGTAAGGTCAAAGTTGAGGAAGTGATTAAACCGTTGCTGCCTTTTTACGGCGCGATTATCGGCGTTCTGTTATTAATTACCTACATTCCGGAAATCACACTGTTCTTACCCCGTCTACTGGGCATCATGTAA
diff --git a/Examples/2-res-Annotate-prodigal/tmp_files/genome1.fst_prodigal-split5N.fna-prodigal.log b/Examples/2-res-Annotate-prodigal/tmp_files/genome1.fst_prodigal-split5N.fna-prodigal.log
deleted file mode 100644
index e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
diff --git a/Examples/2-res-Annotate-prodigal/tmp_files/genome1.fst_prodigal-split5N.fna-prodigal.log.err b/Examples/2-res-Annotate-prodigal/tmp_files/genome1.fst_prodigal-split5N.fna-prodigal.log.err
deleted file mode 100644
index e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
diff --git a/Examples/2-res-Annotate-prodigal/tmp_files/genome1.fst_prodigal-split5N.fna-prodigalRes/EXAM.1219.00001.faa b/Examples/2-res-Annotate-prodigal/tmp_files/genome1.fst_prodigal-split5N.fna-prodigalRes/EXAM.1219.00001.faa
deleted file mode 100644
index 5e3bdf1a1053c15daf2b10b3df81e24c6f80b4ce..0000000000000000000000000000000000000000
--- a/Examples/2-res-Annotate-prodigal/tmp_files/genome1.fst_prodigal-split5N.fna-prodigalRes/EXAM.1219.00001.faa
+++ /dev/null
@@ -1,69 +0,0 @@
->genome1_1_1 # 213 # 1880 # 1 # ID=1_1;partial=00;start_type=ATG;rbs_motif=None;rbs_spacer=None;gc_cont=0.534
-MSEAEARPTNFIRQIIDEDLASGKHTTVHTRFPPEPNGYLHIGHAKSICLNFGIAQDYQG
-QCNLRFDDTNPVKEDIEYVDSIKNDVEWLGFHWSGDIRYSSDYFDQLHAYAVELINKGLA
-YVDELTPEQIREYRGTLTAPGKNSPFRDRSVEENLALFEKMRTGGFEEGKACLRAKIDMA
-SPFIVMRDPVLYRIKFAEHHQTGNKWCIYPMYDFTHCISDALEGITHSLCTLEFQDNRRL
-YDWVLDNITIPVHPRQYEFSRLNLEYTVMSKRKLNLLVTDKHVEGWDDPRMPTISGLRRR
-GYTAASIREFCKRIGVTKQDNTIEMASLESCIREDLNENAPRAMAVIDPVKLVIENYPQG
-ESEMVTMPNHPNKPEMGSREVPFSGEIWIDRADFREEANKQYKRLVMGKEVRLRNAYVIK
-AERVEKDAEGNITTIFCTYDADTLSKDPADGRKVKGVIHWVSAAHALPIEIRLYDRLFSV
-PNPGAAEDFLSVINPESLVIKQGYGEPSLKAAVAGKAFQFEREGYFCLDSRYATADKLVF
-NRTVGLRDTWAKAGE*
->genome1_1_2 # 1916 # 2746 # 1 # ID=1_2;partial=00;start_type=ATG;rbs_motif=AGGAGG;rbs_spacer=5-10bp;gc_cont=0.570
-MKALLWLVGLALLLTGCASEKGIIDKEGYQLDTRHRAQAAYPRIKVLVIHYTAENFDVSL
-ATLTGRNVSSHYLIPATPPLYGGKPRIWQLVPEQDQAWHAGVSFWRGATRLNDTSIGIEL
-ENRGWRMSGGVKSFAPFESAQIQALIPLAKDIIARYNIKPQNVVAHADIAPQRKDDPGPR
-FPWRELAAQGISAWPDAQRVAFYLAGRAPYTPVDTATVLALLSRYGYEVKADMTAREQQR
-VIMAFQMHFRPAQWNGIADAETQAIAEALLEKYGQD*
->genome1_2_1 # 16 # 396 # 1 # ID=2_1;partial=00;start_type=ATG;rbs_motif=None;rbs_spacer=None;gc_cont=0.538
-MPHFIAECTENIREQADLPGLFSKVNEALAASGIFPIGGIRSRAHWLDTWQMADGKHDYA
-FVHMTLKIGAGRSLESRQEVGEMLFGLIKAHFADLMENRYLALSFEIAELHPTLNYKQNN
-VHALFK*
->genome1_2_2 # 428 # 1837 # 1 # ID=2_2;partial=00;start_type=ATG;rbs_motif=GGA/GAG/AGG;rbs_spacer=5-10bp;gc_cont=0.512
-MSMPATKFSRRTLLTAGSALAVLPFLRALPVQAREPRETVDIKDYPADDGIASFKQAFAD
-GQTVVVPPGWVCENINAAITIPAGKTLRVQGAVRGNGRGRFILQDGCQVVGEQGGSLHNV
-TLDVRGSDCVIKGVAMSGFGPVAQIFIGGKEPQVMRNLIIDDITVTHANYAILRQGFHNQ
-MDGARITHSRFSDLQGDAIEWNVAIHDRDILISDHVIERINCTNGKINWGIGIGLAGSTY
-DNSYPEDQAVKNFVVANITGSDCRQLVHVENGKHFVIRNVKAKNITPGFSKNAGIDNATI
-AIYGCDNFVIDNIDMTNSAGMLIGYGVVKGKYLSIPQNFKLNAIRLDNRQVAYKLRGIQI
-SSGNTPSFVAITNVRMTRATLELHNQPQHLFLRNINVMQTSAIGPALKMHFDLRKDVRGQ
-FMARQDTLLSLANVHAINENGQSSVDIDRINHQTVNVEAVNFSLPKRGG*
->genome1_2_3 # 1869 # 2642 # 1 # ID=2_3;partial=00;start_type=ATG;rbs_motif=None;rbs_spacer=None;gc_cont=0.531
-MSENKLHVIDLHKRYGGHEVLKGVSLQARAGDVISIIGSSGSGKSTFLRCINFLEKPSEG
-AIIVNGQNINLVRDKDGQLKVADKNQLRLLRTRLTMVFQHFNLWSHMTVLENVMEAPIQV
-LGLSKHDARERALKYLAKVGIDERAQGKYPVHLSGGQQQRVSIARALAMEPDVLLFDEPT
-SALDPELVGEVLRIMQQLAEEGKTMVVVTHEMGFARHVSSHVIFLHQGKIEEEGDPEQVF
-GNPQSPRLQQFLKGSLK*
->genome1_2_4 # 2709 # 3443 # 1 # ID=2_4;partial=00;start_type=ATG;rbs_motif=None;rbs_spacer=None;gc_cont=0.547
-MFRAITDYGVTGRAVKKGLLNIQSWSPRDFAHDRHRTVDDRPYGGGPGMLMMVQPLRDAI
-HAAKAAAGEGAKVIYLSPQGRKLDQAGVSELATNQKLILVCGRYEGVDERVIQTEIDEEW
-SIGDYVLSGGELPAMTLIDSVARFIPGVLGHEASAIEDSFADGLLDCPHYTRPEVLEGME
-VPPVLLSGNHAEIRRWRLKQSLGRTWLRRPELLENLALTEEQARLLAEFKTEHAQQQHKH
-DGMA*
->genome1_2_5 # 3427 # 4254 # 1 # ID=2_5;partial=00;start_type=ATG;rbs_motif=AGxAG;rbs_spacer=5-10bp;gc_cont=0.541
-MMGWHSRHMGSQRRRANAQYVFIGIVSLFPEMFRAITDYGVTGRAVKKGLLNIQSWSPRD
-FAHDRHRTVDDRPYGGGPGMLMMVQPLRDAIHAAKAAAGEGAKVIYLSPQGRKLDQAGVS
-ELATNQKLILVCGRYEGVDERVIQTEIDEEWSIGDYVLSGGELPAMTLIDSVARFIPGVL
-GHEASAIEDSFADGLLDCPHYTRPEVLEGMEVPPVLLSGNHAEIRRWRLKQSLGRTWLRR
-PELLENLALTEEQARLLAEFKTEHAQQQHKHDGMA*
->genome1_2_6 # 4299 # 4763 # 1 # ID=2_6;partial=00;start_type=ATG;rbs_motif=AGGA/GGAG/GAGG;rbs_spacer=11-12bp;gc_cont=0.596
-MKFVAPEQAPEQAEVIKNTPFWPDVDLSEFRSVMRTDGTVTQPRLKQVVLTAISEVNAEL
-YDFRNRQQMLGWRTLAEVPAEMLDGKSERIRHYHNAVFCWARAVLNERYQDYDATASGVK
-RGEELAEASGDLWRDARWAISRVQDVPHCTVELI*
->genome1_2_7 # 4818 # 5078 # 1 # ID=2_7;partial=00;start_type=ATG;rbs_motif=GGA/GAG/AGG;rbs_spacer=5-10bp;gc_cont=0.487
-MAGLHAPYAYSAHHAVNFCSEYKRGFVLGFTHRMFEKTGDRQLSAWEAGILTRRYGLDKE
-MVMDFFKENHSGMAVRFFMAGYRLEG*
->genome1_2_8 # 5117 # 5698 # 1 # ID=2_8;partial=00;start_type=ATG;rbs_motif=None;rbs_spacer=None;gc_cont=0.546
-MSTLLYLHGFNSSPRSAKACQLKNWLAERHPHVEMIVPQLPPYPADAAELLESLVLEHGG
-APLGLVGSSLGGYYATWLSQCFMLPAVVVNPAVRPFELLTDYLGQNENPYTGQQYVLESR
-HIYDLKVMQIDPLEAPDLIWLLQQTGDEVLYYRQAVAYYASCRQTVTEGGNHAFTGFEDY
-FNQIVDFLGLHSC*
->genome1_2_9 # 5717 # 7024 # 1 # ID=2_9;partial=00;start_type=ATG;rbs_motif=None;rbs_spacer=None;gc_cont=0.524
-MIDPIFASCTLIAVFVVLLAMGAPIGICIVIASFSTMMLVLPFDISMFATAQKMFSSLDS
-FALLAVPFFVLSGVIMNSGGIAARLVNFAKLFTGKLPGSLSYTNIVGNMMFGAISGSAIA
-ASTSIGGVMVPMSAREGYDRGFAAAVNIASAPTGMLIPPTTAFILYALASGGTSIAALFA
-GGLVAGVLWGVGCMLVTLVVAKRRNYRVFFTVQKGMALKVAVEAIPSLLLIVIIVGGIVQ
-GIFTAIEASAIAVVYTLLLTMVFYRTLKIKDLPSILLQTVVMTGVIMFLLATSSAMSFSM
-SITNIPAALSDMILGISANKLVILLVITVFLLIIGAFMDIGPAILIFTPILLPIMAKLGV
-DPVHFGIIMIYNLAIGTITPPVGSGLYVGASVGKVKVEEVIKPLLPFYGAIIGVLLLITY
-IPEITLFLPRLLGIM*
diff --git a/Examples/2-res-Annotate-prodigal/tmp_files/genome1.fst_prodigal-split5N.fna-prodigalRes/EXAM.1219.00001.ffn b/Examples/2-res-Annotate-prodigal/tmp_files/genome1.fst_prodigal-split5N.fna-prodigalRes/EXAM.1219.00001.ffn
deleted file mode 100644
index 558bebfb7a1994c89ea122280798186c7c1c541d..0000000000000000000000000000000000000000
--- a/Examples/2-res-Annotate-prodigal/tmp_files/genome1.fst_prodigal-split5N.fna-prodigalRes/EXAM.1219.00001.ffn
+++ /dev/null
@@ -1,148 +0,0 @@
->genome1_1_1 # 213 # 1880 # 1 # ID=1_1;partial=00;start_type=ATG;rbs_motif=None;rbs_spacer=None;gc_cont=0.534
-ATGAGTGAGGCTGAAGCCCGCCCGACTAACTTTATTCGTCAGATTATTGATGAAGATCTGGCGAGTGGTA
-AACATACCACTGTCCATACCCGTTTTCCGCCGGAGCCGAATGGCTATCTGCATATCGGCCACGCGAAATC
-TATCTGCCTGAACTTTGGCATCGCGCAAGATTATCAGGGCCAGTGCAACCTGCGTTTCGATGACACCAAC
-CCGGTAAAAGAAGATATCGAGTACGTTGATTCGATCAAAAACGACGTCGAGTGGTTAGGCTTTCACTGGT
-CTGGCGATATTCGCTACTCCTCCGATTACTTTGACCAACTGCACGCCTATGCGGTCGAGCTAATCAATAA
-AGGCCTGGCCTATGTTGATGAGCTGACGCCGGAGCAGATCCGTGAATACCGCGGTACGCTGACCGCGCCG
-GGTAAAAACAGCCCGTTCCGCGATCGCAGCGTCGAAGAGAACCTCGCGCTATTTGAAAAAATGCGTACCG
-GCGGTTTTGAAGAGGGTAAAGCCTGTCTGCGCGCTAAAATCGACATGGCGTCGCCGTTTATCGTGATGCG
-CGATCCGGTGCTGTATCGCATTAAATTCGCCGAGCATCATCAGACTGGCAACAAGTGGTGCATCTATCCG
-ATGTACGACTTTACTCACTGCATCAGCGATGCGCTGGAAGGCATTACTCATTCTCTGTGTACGCTGGAGT
-TCCAGGATAACCGTCGTCTGTACGACTGGGTGCTGGACAACATCACCATTCCGGTTCACCCGCGCCAGTA
-CGAATTCTCGCGCCTGAATCTGGAATACACCGTGATGTCCAAGCGTAAGCTGAACCTGCTGGTGACCGAC
-AAACACGTCGAAGGTTGGGACGATCCGCGTATGCCGACTATTTCCGGTCTGCGCCGTCGCGGCTATACCG
-CGGCTTCTATTCGTGAGTTCTGCAAACGCATCGGCGTCACCAAGCAGGACAACACTATTGAGATGGCGTC
-GCTGGAATCCTGCATTCGCGAAGATCTGAACGAAAACGCGCCGCGCGCGATGGCGGTAATCGATCCGGTA
-AAACTGGTTATCGAAAATTACCCGCAGGGTGAGAGCGAAATGGTTACCATGCCTAACCATCCGAATAAAC
-CGGAGATGGGCAGCCGTGAAGTGCCGTTTAGCGGTGAGATCTGGATCGATCGCGCAGATTTCCGCGAAGA
-AGCGAACAAACAGTACAAACGTCTGGTGATGGGCAAAGAAGTGCGTCTGCGTAATGCCTACGTCATTAAA
-GCGGAGCGCGTAGAGAAGGATGCCGAAGGGAATATCACCACCATCTTCTGTACCTATGATGCTGATACGC
-TGAGTAAAGATCCGGCTGACGGGCGTAAAGTGAAAGGCGTAATCCACTGGGTTAGCGCAGCACATGCGCT
-GCCGATTGAAATTCGTCTCTACGACCGTCTGTTCAGCGTGCCGAATCCGGGCGCCGCGGAGGACTTCCTG
-TCTGTTATCAACCCCGAATCATTAGTGATTAAGCAGGGGTATGGCGAGCCGTCGCTGAAAGCGGCGGTAG
-CAGGAAAAGCTTTCCAGTTTGAACGTGAAGGCTACTTCTGCCTCGACAGCCGCTATGCAACGGCCGATAA
-GCTGGTCTTTAACCGCACCGTGGGCCTGCGTGATACCTGGGCGAAAGCGGGCGAGTAA
->genome1_1_2 # 1916 # 2746 # 1 # ID=1_2;partial=00;start_type=ATG;rbs_motif=AGGAGG;rbs_spacer=5-10bp;gc_cont=0.570
-ATGAAAGCGCTACTGTGGCTGGTGGGTCTCGCGTTGCTGTTAACAGGCTGCGCGAGCGAAAAAGGAATTA
-TCGATAAAGAGGGATATCAGCTTGATACCCGACATCGGGCGCAGGCGGCCTATCCGCGCATTAAAGTCCT
-GGTGATTCACTATACGGCGGAAAACTTTGACGTTTCGCTGGCGACGTTAACGGGTCGCAACGTCAGTTCG
-CATTACCTGATTCCCGCAACCCCGCCATTATATGGCGGTAAACCGCGCATCTGGCAACTGGTGCCGGAAC
-AGGATCAGGCCTGGCATGCGGGCGTCAGTTTCTGGCGAGGCGCCACGCGTCTCAATGATACGTCTATTGG
-CATTGAGCTGGAAAATCGTGGTTGGCGAATGTCCGGCGGGGTGAAATCTTTCGCGCCGTTTGAATCCGCG
-CAAATTCAGGCATTGATTCCGTTAGCGAAGGATATTATCGCGCGCTATAACATCAAACCGCAGAATGTGG
-TGGCCCATGCGGATATCGCGCCGCAGCGTAAAGACGATCCCGGCCCGCGCTTCCCGTGGCGCGAGCTGGC
-GGCGCAGGGGATTAGCGCCTGGCCTGACGCCCAGCGTGTGGCGTTTTATCTGGCTGGACGCGCGCCGTAT
-ACGCCAGTCGATACCGCAACGGTGCTTGCGTTACTCTCGCGCTATGGCTATGAAGTCAAAGCCGATATGA
-CGGCACGCGAGCAGCAGCGGGTGATTATGGCGTTCCAGATGCACTTCCGTCCGGCGCAATGGAACGGTAT
-CGCAGATGCCGAAACGCAGGCGATTGCCGAAGCATTACTGGAGAAGTACGGCCAGGATTAA
->genome1_2_1 # 16 # 396 # 1 # ID=2_1;partial=00;start_type=ATG;rbs_motif=None;rbs_spacer=None;gc_cont=0.538
-ATGCCGCACTTTATTGCTGAATGTACTGAAAATATTCGCGAGCAGGCTGATTTACCCGGCCTGTTCAGCA
-AGGTAAACGAGGCGCTGGCCGCCAGCGGGATTTTCCCCATCGGCGGTATCCGCAGTCGCGCCCACTGGCT
-GGATACCTGGCAGATGGCTGACGGTAAGCATGATTACGCGTTTGTGCATATGACGCTGAAAATCGGCGCC
-GGGCGCAGCCTGGAGAGCCGTCAGGAAGTTGGCGAAATGCTGTTTGGGCTGATTAAAGCCCACTTCGCCG
-ACCTGATGGAGAACCGCTATCTGGCGCTGTCGTTTGAGATTGCCGAGCTACATCCGACGCTCAATTACAA
-ACAAAACAACGTACACGCGTTATTTAAATAG
->genome1_2_2 # 428 # 1837 # 1 # ID=2_2;partial=00;start_type=ATG;rbs_motif=GGA/GAG/AGG;rbs_spacer=5-10bp;gc_cont=0.512
-ATGAGCATGCCCGCGACTAAATTCTCCCGACGTACCCTCCTGACGGCAGGTTCTGCGCTTGCTGTTCTTC
-CTTTTCTGCGCGCCTTGCCGGTACAGGCGCGTGAACCTCGCGAGACCGTCGATATTAAGGATTATCCGGC
-GGATGACGGTATCGCCTCGTTCAAACAGGCCTTCGCCGACGGACAGACCGTGGTCGTACCGCCAGGATGG
-GTGTGTGAAAATATCAATGCGGCGATAACGATTCCGGCGGGAAAAACGCTGCGGGTACAGGGCGCGGTGC
-GTGGGAATGGCCGGGGACGGTTTATTTTGCAGGACGGGTGTCAGGTGGTGGGGGAGCAGGGCGGCAGTCT
-GCACAATGTGACGCTGGATGTTCGCGGGTCGGACTGTGTGATTAAAGGCGTGGCGATGAGCGGCTTTGGC
-CCCGTCGCGCAAATTTTCATCGGTGGTAAGGAACCGCAGGTGATGCGTAATCTCATTATCGATGACATCA
-CCGTTACCCACGCCAACTACGCCATTCTCCGCCAGGGATTTCATAACCAAATGGATGGCGCGCGGATTAC
-GCATAGCCGCTTTAGCGATTTACAGGGGGACGCCATTGAGTGGAATGTCGCGATTCACGACCGCGACATC
-CTGATTTCCGATCATGTCATCGAACGCATTAATTGTACCAATGGCAAAATCAACTGGGGGATCGGCATCG
-GGCTGGCGGGTAGCACCTATGACAACAGTTATCCTGAAGACCAGGCAGTAAAAAACTTTGTGGTGGCCAA
-TATTACCGGATCTGATTGCCGACAGCTTGTGCACGTAGAAAATGGCAAACATTTCGTCATTCGCAATGTC
-AAAGCCAAAAACATCACGCCCGGTTTCAGTAAAAATGCGGGTATTGATAACGCAACGATCGCAATTTATG
-GCTGTGATAATTTCGTCATTGATAATATTGATATGACGAATAGTGCCGGGATGCTCATCGGCTATGGCGT
-CGTTAAAGGAAAATACCTGTCAATTCCGCAAAACTTTAAATTAAACGCTATTCGGTTGGATAATCGCCAG
-GTTGCTTATAAATTACGCGGCATTCAAATTTCCTCCGGCAACACCCCCTCTTTTGTCGCCATCACCAATG
-TACGGATGACGCGTGCTACGCTGGAACTGCATAATCAACCGCAGCACCTCTTTCTGCGCAATATCAACGT
-GATGCAAACTTCAGCGATTGGCCCGGCGTTAAAAATGCATTTCGATTTGCGTAAAGATGTACGTGGTCAA
-TTTATGGCCCGCCAGGACACGCTGCTTTCCCTCGCTAATGTTCATGCCATCAATGAAAACGGGCAGAGTT
-CCGTGGATATCGACAGGATTAATCACCAAACCGTGAATGTCGAAGCAGTGAATTTTTCGCTGCCGAAGCG
-GGGAGGGTAA
->genome1_2_3 # 1869 # 2642 # 1 # ID=2_3;partial=00;start_type=ATG;rbs_motif=None;rbs_spacer=None;gc_cont=0.531
-ATGTCAGAAAATAAATTACACGTTATCGATTTGCACAAACGCTACGGCGGTCATGAAGTGCTGAAAGGGG
-TATCGCTGCAGGCCCGCGCCGGAGATGTGATTAGCATCATCGGCTCGTCCGGCTCCGGTAAAAGCACTTT
-TTTGCGCTGTATTAACTTCCTCGAAAAACCGAGCGAAGGCGCGATTATCGTGAACGGTCAGAACATTAAT
-CTGGTGCGCGACAAAGATGGGCAGCTCAAAGTGGCGGATAAAAATCAGCTACGCTTGTTGCGTACCCGCC
-TGACGATGGTGTTTCAGCACTTCAACCTCTGGAGCCACATGACGGTGCTGGAAAATGTGATGGAAGCGCC
-GATTCAGGTACTGGGATTAAGCAAGCACGACGCGCGCGAGCGGGCGTTGAAATATCTGGCGAAGGTGGGG
-ATTGATGAGCGCGCTCAGGGCAAATATCCCGTCCATCTCTCCGGCGGCCAACAGCAGCGCGTTTCTATTG
-CGCGCGCGCTGGCGATGGAACCTGACGTTTTACTGTTCGATGAACCCACATCGGCGCTCGATCCTGAACT
-GGTCGGCGAAGTGTTGCGCATCATGCAACAACTGGCGGAAGAAGGCAAAACGATGGTGGTGGTCACGCAT
-GAAATGGGCTTCGCTCGCCATGTCTCTTCGCACGTTATTTTTCTGCATCAGGGGAAAATTGAAGAAGAGG
-GTGATCCGGAGCAGGTGTTCGGCAATCCGCAAAGCCCGCGTTTACAGCAATTCCTGAAAGGCTCGCTGAA
-ATAA
->genome1_2_4 # 2709 # 3443 # 1 # ID=2_4;partial=00;start_type=ATG;rbs_motif=None;rbs_spacer=None;gc_cont=0.547
-ATGTTCCGCGCAATTACCGATTACGGGGTAACTGGCCGGGCAGTAAAAAAAGGCCTGCTGAACATCCAAA
-GCTGGAGTCCTCGCGACTTCGCGCATGACCGGCACCGTACCGTGGACGACCGTCCTTACGGCGGCGGACC
-GGGGATGTTAATGATGGTGCAACCCTTGCGGGACGCCATTCACGCAGCAAAAGCCGCGGCAGGTGAAGGC
-GCTAAAGTGATTTATCTGTCGCCTCAGGGACGCAAGCTTGATCAAGCGGGCGTTAGCGAGCTGGCCACGA
-ATCAGAAGCTTATTCTGGTGTGTGGTCGCTACGAAGGCGTAGATGAGCGCGTAATTCAGACCGAAATTGA
-CGAAGAATGGTCAATTGGCGATTACGTTCTCAGCGGTGGCGAACTACCGGCAATGACGCTGATTGACTCC
-GTCGCCCGGTTTATACCGGGGGTTCTGGGGCATGAGGCATCAGCAATCGAAGATTCGTTTGCTGATGGGT
-TGCTGGATTGTCCGCACTATACGCGCCCTGAAGTGTTAGAGGGGATGGAAGTACCGCCAGTATTGCTGTC
-GGGAAACCATGCTGAGATACGTCGCTGGCGTTTGAAACAGTCGCTGGGCCGAACCTGGCTTAGAAGACCT
-GAACTTCTGGAAAACCTGGCTCTGACTGAAGAGCAAGCAAGGTTGCTGGCGGAGTTCAAAACAGAACACG
-CACAACAGCAGCATAAACATGATGGGATGGCATAG
->genome1_2_5 # 3427 # 4254 # 1 # ID=2_5;partial=00;start_type=ATG;rbs_motif=AGxAG;rbs_spacer=5-10bp;gc_cont=0.541
-ATGATGGGATGGCATAGCCGTCATATGGGCTCTCAGAGGAGACGCGCTAATGCGCAGTACGTGTTTATTG
-GCATAGTTAGCCTGTTTCCTGAAATGTTCCGCGCAATTACCGATTACGGGGTAACTGGCCGGGCAGTAAA
-AAAAGGCCTGCTGAACATCCAAAGCTGGAGTCCTCGCGACTTCGCGCATGACCGGCACCGTACCGTGGAC
-GACCGTCCTTACGGCGGCGGACCGGGGATGTTAATGATGGTGCAACCCTTGCGGGACGCCATTCACGCAG
-CAAAAGCCGCGGCAGGTGAAGGCGCTAAAGTGATTTATCTGTCGCCTCAGGGACGCAAGCTTGATCAAGC
-GGGCGTTAGCGAGCTGGCCACGAATCAGAAGCTTATTCTGGTGTGTGGTCGCTACGAAGGCGTAGATGAG
-CGCGTAATTCAGACCGAAATTGACGAAGAATGGTCAATTGGCGATTACGTTCTCAGCGGTGGCGAACTAC
-CGGCAATGACGCTGATTGACTCCGTCGCCCGGTTTATACCGGGGGTTCTGGGGCATGAGGCATCAGCAAT
-CGAAGATTCGTTTGCTGATGGGTTGCTGGATTGTCCGCACTATACGCGCCCTGAAGTGTTAGAGGGGATG
-GAAGTACCGCCAGTATTGCTGTCGGGAAACCATGCTGAGATACGTCGCTGGCGTTTGAAACAGTCGCTGG
-GCCGAACCTGGCTTAGAAGACCTGAACTTCTGGAAAACCTGGCTCTGACTGAAGAGCAAGCAAGGTTGCT
-GGCGGAGTTCAAAACAGAACACGCACAACAGCAGCATAAACATGATGGGATGGCATAG
->genome1_2_6 # 4299 # 4763 # 1 # ID=2_6;partial=00;start_type=ATG;rbs_motif=AGGA/GGAG/GAGG;rbs_spacer=11-12bp;gc_cont=0.596
-ATGAAGTTTGTTGCGCCCGAACAGGCACCGGAACAGGCGGAGGTCATCAAAAATACGCCGTTCTGGCCTG
-ATGTGGACCTGTCGGAATTTCGCAGTGTGATGCGCACTGACGGCACGGTGACGCAGCCGCGTTTAAAGCA
-GGTCGTGCTGACGGCGATCTCTGAGGTTAACGCTGAGCTGTACGACTTCCGCAACCGTCAGCAGATGCTG
-GGCTGGCGGACACTTGCTGAGGTTCCCGCAGAAATGCTGGACGGTAAAAGCGAGCGTATCCGGCACTACC
-ACAACGCTGTTTTTTGCTGGGCGCGCGCTGTGCTTAATGAGCGTTATCAGGACTATGACGCCACGGCGTC
-AGGCGTGAAGCGAGGGGAGGAGCTGGCGGAGGCCAGCGGCGATCTGTGGCGTGATGCCCGCTGGGCCATC
-AGCCGGGTGCAGGATGTACCGCACTGTACGGTGGAGCTTATCTGA
->genome1_2_7 # 4818 # 5078 # 1 # ID=2_7;partial=00;start_type=ATG;rbs_motif=GGA/GAG/AGG;rbs_spacer=5-10bp;gc_cont=0.487
-ATGGCCGGGTTGCACGCGCCATATGCATATAGCGCGCATCATGCGGTGAATTTCTGTTCTGAGTATAAAC
-GTGGCTTTGTATTGGGTTTTACACACCGTATGTTCGAAAAGACCGGCGATCGTCAACTTAGCGCGTGGGA
-GGCTGGAATTCTGACGCGTCGCTATGGTCTGGATAAAGAAATGGTGATGGATTTCTTTAAAGAGAATCAT
-TCCGGGATGGCGGTTCGCTTCTTTATGGCCGGTTATCGACTCGAAGGTTGA
->genome1_2_8 # 5117 # 5698 # 1 # ID=2_8;partial=00;start_type=ATG;rbs_motif=None;rbs_spacer=None;gc_cont=0.546
-ATGTCTACGCTTCTCTATTTGCACGGATTCAACAGTTCCCCTCGCTCGGCAAAAGCGTGCCAGCTAAAAA
-ACTGGCTGGCGGAGCGTCATCCGCATGTTGAGATGATCGTCCCTCAGCTGCCGCCGTATCCTGCCGATGC
-GGCGGAGTTGCTGGAATCTCTCGTGCTTGAGCATGGCGGTGCGCCATTAGGGCTGGTAGGATCGTCGCTG
-GGTGGTTATTACGCCACCTGGCTGTCGCAATGTTTTATGCTGCCGGCTGTGGTGGTGAATCCCGCCGTGC
-GGCCCTTTGAATTACTGACCGACTATCTCGGTCAGAACGAGAACCCCTACACCGGGCAGCAATATGTGCT
-AGAGTCTCGCCATATTTATGATCTTAAAGTCATGCAGATTGACCCGCTGGAAGCGCCGGACCTGATCTGG
-CTACTGCAACAGACGGGCGATGAAGTGCTGTATTACCGCCAGGCGGTGGCATATTACGCCTCCTGCCGTC
-AGACAGTGACCGAGGGTGGTAATCACGCATTCACGGGCTTCGAAGATTATTTCAACCAGATTGTCGATTT
-TCTTGGACTGCACAGTTGCTGA
->genome1_2_9 # 5717 # 7024 # 1 # ID=2_9;partial=00;start_type=ATG;rbs_motif=None;rbs_spacer=None;gc_cont=0.524
-ATGATTGACCCTATTTTTGCGTCCTGTACGCTAATTGCCGTCTTTGTTGTTTTACTGGCCATGGGCGCGC
-CTATCGGGATCTGCATCGTTATCGCCTCTTTCAGCACCATGATGCTGGTACTGCCTTTCGATATTTCGAT
-GTTCGCCACCGCGCAAAAAATGTTCTCCAGCCTGGACAGTTTTGCCTTGCTGGCCGTGCCGTTCTTCGTT
-TTGTCCGGGGTGATCATGAATAGCGGGGGAATTGCCGCCCGGCTGGTCAATTTTGCCAAACTGTTTACTG
-GCAAACTGCCCGGCTCGCTCTCTTATACCAACATCGTCGGCAATATGATGTTCGGTGCAATTTCCGGATC
-GGCGATTGCCGCCTCAACCTCCATCGGCGGCGTGATGGTGCCGATGAGCGCGCGCGAAGGTTACGATCGC
-GGCTTTGCGGCCGCGGTGAATATCGCCTCCGCGCCGACGGGAATGTTAATTCCGCCCACCACGGCTTTTA
-TCCTTTACGCGCTGGCAAGCGGGGGAACATCGATTGCCGCTCTGTTCGCCGGCGGTCTGGTCGCGGGAGT
-GCTGTGGGGCGTTGGCTGTATGCTGGTCACGCTGGTGGTCGCTAAGCGTCGAAATTATCGGGTTTTCTTC
-ACCGTCCAAAAAGGTATGGCGCTAAAAGTTGCCGTTGAGGCCATTCCCAGCCTGCTGCTGATCGTGATTA
-TTGTCGGCGGCATTGTGCAGGGGATTTTCACCGCCATTGAAGCCTCCGCGATTGCCGTGGTGTATACGTT
-ATTGCTGACGATGGTGTTTTACCGCACGCTGAAAATTAAGGATTTGCCTTCGATTTTGCTCCAGACAGTG
-GTAATGACCGGGGTCATCATGTTCCTGCTGGCAACCTCTTCGGCGATGTCCTTCTCGATGTCGATCACCA
-ATATTCCTGCGGCGCTGAGCGATATGATCCTCGGTATTTCCGCCAATAAACTGGTTATCCTGTTAGTCAT
-TACCGTCTTTTTGTTGATTATCGGCGCATTTATGGATATTGGTCCGGCCATTCTGATTTTTACCCCGATT
-CTGCTGCCAATCATGGCTAAACTGGGCGTCGATCCGGTGCATTTCGGCATTATCATGATCTATAACCTGG
-CGATTGGCACCATTACGCCGCCAGTTGGCAGTGGTTTATATGTCGGGGCGAGCGTCGGTAAGGTCAAAGT
-TGAGGAAGTGATTAAACCGTTGCTGCCTTTTTACGGCGCGATTATCGGCGTTCTGTTATTAATTACCTAC
-ATTCCGGAAATCACACTGTTCTTACCCCGTCTACTGGGCATCATGTAA
diff --git a/Examples/2-res-Annotate-prodigal/tmp_files/genome1.fst_prodigal-split5N.fna-prodigalRes/EXAM.1219.00001.gff b/Examples/2-res-Annotate-prodigal/tmp_files/genome1.fst_prodigal-split5N.fna-prodigalRes/EXAM.1219.00001.gff
deleted file mode 100644
index 44815edf64a8b83d3e6ce4163e7dc66bf5805000..0000000000000000000000000000000000000000
--- a/Examples/2-res-Annotate-prodigal/tmp_files/genome1.fst_prodigal-split5N.fna-prodigalRes/EXAM.1219.00001.gff
+++ /dev/null
@@ -1,16 +0,0 @@
-##gff-version  3
-# Sequence Data: seqnum=1;seqlen=2784;seqhdr="genome1_1"
-# Model Data: version=Prodigal.v2.6.3;run_type=Metagenomic;model="20|Escherichia_coli_UMN026|B|50.7|11|1";gc_cont=50.70;transl_table=11;uses_sd=1
-genome1_1	Prodigal_v2.6.3	CDS	213	1880	260.0	+	0	ID=1_1;partial=00;start_type=ATG;rbs_motif=None;rbs_spacer=None;gc_cont=0.534;conf=99.99;score=259.99;cscore=268.89;sscore=-8.89;rscore=-8.50;uscore=-4.34;tscore=3.95;
-genome1_1	Prodigal_v2.6.3	CDS	1916	2746	117.8	+	0	ID=1_2;partial=00;start_type=ATG;rbs_motif=AGGAGG;rbs_spacer=5-10bp;gc_cont=0.570;conf=100.00;score=118.71;cscore=102.01;sscore=16.70;rscore=14.38;uscore=-2.52;tscore=3.95;
-# Sequence Data: seqnum=2;seqlen=7024;seqhdr="genome1_2"
-# Model Data: version=Prodigal.v2.6.3;run_type=Metagenomic;model="20|Escherichia_coli_UMN026|B|50.7|11|1";gc_cont=50.70;transl_table=11;uses_sd=1
-genome1_2	Prodigal_v2.6.3	CDS	16	396	43.9	+	0	ID=2_1;partial=00;start_type=ATG;rbs_motif=None;rbs_spacer=None;gc_cont=0.538;conf=100.00;score=43.95;cscore=48.77;sscore=-4.82;rscore=-8.50;uscore=-0.27;tscore=3.95;
-genome1_2	Prodigal_v2.6.3	CDS	428	1837	146.3	+	0	ID=2_2;partial=00;start_type=ATG;rbs_motif=GGA/GAG/AGG;rbs_spacer=5-10bp;gc_cont=0.512;conf=100.00;score=147.28;cscore=140.86;sscore=6.42;rscore=2.79;uscore=-1.25;tscore=3.95;
-genome1_2	Prodigal_v2.6.3	CDS	1869	2642	98.1	+	0	ID=2_3;partial=00;start_type=ATG;rbs_motif=None;rbs_spacer=None;gc_cont=0.531;conf=100.00;score=99.06;cscore=104.90;sscore=-5.84;rscore=-8.50;uscore=-2.23;tscore=3.95;
-genome1_2	Prodigal_v2.6.3	CDS	2709	3443	50.8	+	0	ID=2_4;partial=00;start_type=ATG;rbs_motif=None;rbs_spacer=None;gc_cont=0.547;conf=100.00;score=50.78;cscore=54.23;sscore=-3.45;rscore=-8.50;uscore=1.10;tscore=3.95;
-genome1_2	Prodigal_v2.6.3	CDS	3427	4254	66.1	+	0	ID=2_5;partial=00;start_type=ATG;rbs_motif=AGxAG;rbs_spacer=5-10bp;gc_cont=0.541;conf=100.00;score=67.21;cscore=64.98;sscore=2.23;rscore=-2.56;uscore=-0.31;tscore=3.95;
-genome1_2	Prodigal_v2.6.3	CDS	4299	4763	48.2	+	0	ID=2_6;partial=00;start_type=ATG;rbs_motif=AGGA/GGAG/GAGG;rbs_spacer=11-12bp;gc_cont=0.596;conf=100.00;score=48.97;cscore=42.02;sscore=6.96;rscore=4.46;uscore=-2.24;tscore=3.95;
-genome1_2	Prodigal_v2.6.3	CDS	4818	5078	23.5	+	0	ID=2_7;partial=00;start_type=ATG;rbs_motif=GGA/GAG/AGG;rbs_spacer=5-10bp;gc_cont=0.487;conf=99.62;score=24.19;cscore=15.16;sscore=9.03;rscore=2.79;uscore=1.60;tscore=3.95;
-genome1_2	Prodigal_v2.6.3	CDS	5117	5698	52.3	+	0	ID=2_8;partial=00;start_type=ATG;rbs_motif=None;rbs_spacer=None;gc_cont=0.546;conf=100.00;score=53.17;cscore=61.65;sscore=-8.48;rscore=-8.50;uscore=-4.79;tscore=3.95;
-genome1_2	Prodigal_v2.6.3	CDS	5717	7024	164.7	+	0	ID=2_9;partial=00;start_type=ATG;rbs_motif=None;rbs_spacer=None;gc_cont=0.524;conf=100.00;score=165.75;cscore=171.22;sscore=-5.47;rscore=-8.50;uscore=-1.99;tscore=3.95;
diff --git a/Examples/2-res-Annotate-prodigal/tmp_files/genome2.fst_prodigal-split5N.fna b/Examples/2-res-Annotate-prodigal/tmp_files/genome2.fst_prodigal-split5N.fna
deleted file mode 100644
index 7862d06ecb76fa125d92cc6fced535fcea2850c9..0000000000000000000000000000000000000000
--- a/Examples/2-res-Annotate-prodigal/tmp_files/genome2.fst_prodigal-split5N.fna
+++ /dev/null
@@ -1,10 +0,0 @@
->this_is_genome2_contig_number1_1
-ATGTCAGAAAATAAATTACACGTTATCGATTTGCACAAACGCTACGGCGGTCATGAAGTGCTGAAAGGGGTATCGCTGCAGGCCCGCGCCGGAGATGTGATTAGCATTATCGGCTCGTCCGGTTCCGGTAAAAGCACTTTTTTGCGCTGCATTAACTTCCTCGAAAAATCGAGCGAAGGCGCGATTATCGTGAACGGTCAGAACATTAATCTGGTGCGCGACAAAGACGGGCAGCTCAAAGTGGCGGATAAAAATCAGCTACGCTTGTTGCGTACCCGCCTGACGATGGTGTTTCAGCACTTTAACCTCTGGAACCACATGACGGTGCTGGAAAATGTGATGGAAGCGCCGATTCAGGTACTGGGATTAAGCAAGCACGACGCGCGCGAGCGGGCGTTGAAATATCTGGCGAAGGTGGGGATTGATGAGCGCGCTCAGGGCAAATATCCCGTCCATCTCTCCGGCGGCCAACAGCAGCGCGTTTCTATTGCGCGCGCGCTGGCGATGGAACCTGACGTTTTACTGTTCGATGAACCCACATCGGCGCTCGATCCTGAACTGGTCGGCGAAGTGTTGCGCATCATGCAACAACTGGCGGAAGAAGGCAAAACGATGGTGGTGGTCACGCATGAAATGGGCTTCGCCCGCCATGTCTCTTCGCACGTGATTTTTCTGCATCAGGGGAAAATTGAAGAAGAGGGCAATCCGGAGCAGGTGTTCGGCAATCCGCAAAGCCCGCGTTTACAGCAATTCCTGAAAGGCTCGCTGAAATAAACGCTAGAGGACGCGCCTCTCAGAGAGCGCGCTCTCTCAGAGAGGCGCGCGCCTCTTTCGCAGAGACCNNCGCTCATGAGCGATGCCCGCGACTAAATTCTCCCGACGTACCCTCCTGACGGCAGGTTCCGCGCTTGCTGTTCTTCCTTTTCTGCGCGCCTTGCCGGTACAGGCGCGTGAACCTCGCCAGACCGTCGATATTAAGGATTATCCGGCGGATGACGGTATCGCCTCGTTCAAACAGGCCTTCGCCGACGGGCAGACTGTGGTCGTGCCGTCAGGATGGGTGTGTGAAAATATCAATGCGGCGATAACGATTCCGGCGGGAAAAACGCTGCGGATACAGGGCGCGGTGCGTGGGAATGGCCGGGGACGGTTTATTTTGCTGGACGGGTGTCAGGTGGTGGGGGAGCAGGGCGGCAGTCTGCACAATGTGACGCTGGATGTTCGCGGGTCGGACTGTGTGATTAAAGGCGTGACGATGAGCGGCTTTGGCCCCGTCGCGCAAATTTTCATCGGCGGTAAGGAACCGCAGGTGATGCGTAATCTCATTATCGATGACATCACCGTTACCCACGCCAACTACGCCATTCTCCGCCAGGGATTTCATAACCAAATGGACGGCGCGCGGATTACGCATAGTCGCTTTAGCGATTTGCAGGGGGACGCCATTGAGTGGAATGTCGCGATTCATGACCGCGACATCCTGATTTCCGATCATGTCATCGAACGCATTGATTGTACCAATGGCAAAATCAACTGGGGGATCGGCATCGGGCTGGCGGGTAGCGCCTATGACAATAGTTATCCTGAAGACCAGGCAGTAAAAAACTTTGTGGTGGCCAATATTACCGGATCTGATTGCCGACAACTGGTACACGTAGAAAATGGCAAACATTTCGTCATTCGCAATGTCAAAGCCAAAAACATCACGCCCGATTTCAGTAAAAATGCGGGTATTGATAACGCAACGATCGCCATTTATGGCTGTGATAATTTCGTCATTGATAATATTGATATGACGAATAGTGCCGGGATGCTCATCGGCTATGGCGTCGTTAAAGGAAAATACCTGTCAATTCCGCAAAACTTTAAATTAAACGCTATTCGGTTGGATAATCGCCAGGTTGCTTATAAATTACGCGGCATTCAAATTTCCTCCGGTAACGCCCCCTCATTTGTTGCCATCACCAATGTACGGATGACGCGTGCTACGCTGGAACTGCATAATCAACCGCAGCACCTCTTTTTGCGTAATATCAACGTGATGCAAACTTCAGCGATTGGCCCGGCGTTAAAAATGCATTTTGATTTGCGTAAAGATGTCCGTGGTCAATTTATGGCCCGCCAGGACACGCTGCTTTCCCTCGCTAATGTTCATGCCATCAATGAAAACGGGCAGAGTTCCGTGGATATCGACAGGATTAATCACCAAACCGTGAATGTCGAAGCAGTGAATTTTTCGCTGCCGAAGCGGGGAGGGTAACACTCGCGCATAGAGAGCTCTCAGAGGAGCGCGCGCGCTATAGCGCGC
->this_is_genome2_contig_number1_2
-CGCGATAATATAGCGCGCGCTCATAGCATGAGCGCGCTATTTCTGGCCATCCCGTTAACCATTTTTGTGTTGTTTGTGTTACCGATTTGGCTGTGGCTGCATTACAGCAACCGCGCCGGTCGGGGAGAACTGTCGCAAAGCGAGCAGCAACGCTTACTGCAACTCACAGACGACGCGCAACGTATGCGCGAGCGCATTCAGGCGCTGGAAGATATTCTTGATGCAGAGCATCCGAACTGGAGAGAGCGCTAACGCCATATTATAGCGCGCCTCATAAGAGCGGCCTATAGCGCGCTANNNATGCCGCACTTTATTGCTGAATGTACTGAAAATATTCGCGAGCAGGCTGATTTACCAAGCCTGTTCAGCAAGGTAAACGAGGCGCTGGCCGCCACCGGGATTTTCCCCATCGGCGGTATCCGCAGTCGCGCCCACTGGCTGGATACCTGGCAGATGGCTGACGGTAAGCATGATTACGCGTTTGTGCATATGACGCTGAAAATCGGCGCCGGGCGCAGCCTGGAGAGCCGTCAGGAAGTCGGCGAAATGCTGTTTGGGCTGATTAAAGCCCACTTCGCCGACCTGATGGAGAACCGCTATCTGGCGCTGTCGTTTGAGATTGCCGAGTTACATCCAACGCTCAATTACAAACAAAACAACGTACACGCGTTATTTAAATAGCCAGAGATTCGCGCGTTCAGAGAGGAGCTCTCTCATAGACGCGCGCATATGCGCTCTAGAGAGGCGCGCCTAATGGCGCGCTATGATGAAAGCGCTACTGTGGCTGGTTGGTCTCGCGTTGCTGTTAACAGGCTGCGCGAGCGAAAAAGGAATTATCGATAAAGAGGGATATCAGCTTGATACCCGACATCGGGCGCAGGCGGCCTATCCGCGCATTAAAGTCCTGGTGATTCACTATACGGCGGAAAACTTTGACGTTTCGCTGGCGACGTTAACGGGTCGCAACGTCAGTTCGCATTACCTGATTCCCGCAACCCCGCCATTATATGGCGGTAAACCGCGCATCTGGCAACTGGTGCCGGAACAGGATCAGGCTTGGCATGCGGGCGTCAGTTTCTGGCGAGGCGCCACGCGTCTCAATGATACGTCTATTGGCATTGAGCTGGAAAATCGCGGCTGGCGAATGTCCGGCGGGGTGAAATCTTTCGCGCCGTTTGAATCCGCGCAAATTCAGGCATTGATCCCGTTAGCGAAGGACATTATCGCGCGCTATGACATCAAACCGCAGAATGTGGTGGCCCATGCGGATATCGCGCCGCAGCGTAAAGACGATCCCGGCCCGCGCTTCCCGTGGCGCGAGCTGGCGGCACAGGGGATTGGCGCCTGGCCTGACGCCCAGCGTGTGGCGTTTTATCTGGCTGGACGCGCGCCGTATACGCCAGTCGATACCGCAACGGTGCTTGCGTTACTCTCGCGCTATGGCTATGAAGTCAAAGCCGATATGACGGCGCGCGAGCAACAGCGGGTGATTATGGCGTTCCAGATGCACTTCCGTCCGGCGCAATGGAACGGTATCGCAGATGCCGAAACGCAGGCGATTGCCGAAGCATTACTGGAGAAGTACGGCCAGGATTAACAAAGCGCTCTCAGAGAGAGCGCTCTGCAGATGAGTGAGGCTGAAGCCCGCCCGACTAACTTTATTCGTCAGATTATTGATGAAGATCTGGCGAGTGGTAAACATACCACTGTCCATACCCGTTTTCCGCCGGAGCCGAATGGCTATCTGCACATCGGCCACGCGAAATCTATCTGCCTGAACTTTGGCATCGCGCAAGATTATCAGGGCCAGTGCAACCTGCGTTTCGATGACACCAACCCGGTAAAAGAAGATATCGAGTACGTTGATTCGATCAAAAACGACGTCGAGTGGTTAGGCTTTCACTGGTCTGGCGATATTCGCTACTCCTCCGATTACTTTGACCAACTGCACGCCTATGCGGTCGAGCTCATCAATAAAGGCCTGGCCTACGTTGATGAGCTGACGCCGGAGCAGATCCGCGAATACCGTGGTACGCTGACCGCGCCGGGTAAAAACAGCCCGTTCCGCGATCGCAGCGTGGAAGAAAACCTCGCGCTATTTGAAAAAATGCGTACCGGCGGTTTTGAAGAGGGTAAAGCCTGTCTGCGCGCTAAAATCGACATGGCGTCGCCGTTTATCGTGATGCGCGATCCGGTGCTGTATCGCATTAAATTCGCCGAGCATCATCAGACCGGCACGAAGTGGTGCATCTATCCGATGTACGACTTTACTCACTGCATCAGCGATGCGCTGGAAGGCATTACTCATTCTCTGTGTACGCTGGAGTTCCAGGACAACCGTCGTCTGTACGACTGGGTGCTGGACAACATCACCATTCCGGTTCACCCGCGCCAGTACGAATTCTCGCGCCTGAATCTGGAATACACCGTGATGTCCAAGCGTAAGCTGAACCTGCTGGTGACCGACAAACACGTCGAAGGTTGGGATGATCCGCGTATGCCGACTATTTCCGGTCTGCGCCGTCGCGGCTATACCGCGGCTTCTATTCGTGAGTTCTGCAAACGCATCGGCGTCACCAAGCAGGACAACACTATTGAGATGGCGTCGCTGGAATCCTGCATTCGCGAAGATCTGAACGAAAACGCGCCGCGCGCGATGGCGGTAATCGATCCGGTAAAACTGGTTATCGAAAACTACCCGCAGGGCGAGAGCGAAATGGTTACCATGCCTAACCATCCGAATAAACCGGAGATGGGCAGCCGTGAAGTGCCGTTTAGCGGTGAGATCTGGATCGATCGCGCGGATTTCCGCGAAGAAGCGAACAAACAGTACAAACGTCTGGTGATGGGCAAAGAAGTGCGTCTGCGTAATGCCTACGTCATTAAAGCGGAGCGCGTAGAGAAGGATGCCGAAGGGAATATCACCACCATCTTCTGTACCTATGATGCTGATACGCTGAGTAAAGATCCGGCTGACGGGCGTAAAGTGAAAGGCGTAATCCACTGGGTTAGCGTAGCACATGCGCTGCCGATTGAAATTCGTCTCTACGACCGTCTGTTCAGCGTGCCGAACCCGGGCGCCGCGGAGGACTTCCTGTCTGTTATCAACCCCGAATCATTAGTGATTAAGCAGGGGTATGGCGAGCCGTCGCTGAAAGCGGCGGTAGCAGGGAAAGCTTTCCAGTTTGAACGTGAAGGTTACTTCTGCCTTGACAGCCGCTATGCAACGGCCGATAAGCTGGTCTTTAACCGCACCGTGGGCCTGCGTGATACCTGGGCGAAAGCGGGCGAATAA
->this_is_genome2_contig_number2_3
-ACGCGCTATAGGGCTCTCAGAGAGTCTCAGTGTTTATTGGCATCGTTAGCCTGTTTCCTGAAATGTTCCGCGCAATTACCGATTACGGGGTAACTGGCCGGGCAGTAAAAAAAGGCCTGCTGAACATCCAAAGCTGGAGTCCTCGCGACTTCGCGCATGACCGGCACCGTACCGTGGACGACCGTCCTTACGGCGGCGGACCGGGGATGTTAATGATGGTGCAACCCTTGCGGGACGCCATTCATGCAGCAAAAGCCGCGGCAGGTGAAGGCGCTAAAGTGATTTATCTGTCGCCTCAGGGACGCAAGCTTGATCAAGCGGGCGTTAGCGAGCTGGCCACGAATCAGAAACTCATTCTGGTGTGTGGTCGCTACGAAGGCGTAGATGAGCGCGTAATTCAGGCCGAAATTGACGAAGAATGGTCAATTGGCGATTACGTTCTCAGCGGTGGCGAACTACCGGCAATGACGCTGATTGACTCCGTCGCCCGGTTTATACCGGGGGTTCTGGGGCATGAGGCATCAGCAATCGAAGATTCGTTTGCTGATGGGTTGCTGGATTGTCCGCACTATACGCGCCCTGAAGTGTTAGAGGGGATGGAAGTACCGCCAGTATTGCTGTCGGGAAACCATGCTGAGATACGTCGCTGGCGTTTGAAACAGTCACTGGGCCGAACCTGGCTTAGAAGACCTGAACTTCTGGAAAACCTGGCTCTGACTGAAGAGCAAGCAAGGTTGCTGGCGGAGTTCAAAACAGAACACGCACAACAGCAGCATAAACATGATGGGATGGCATAGCGAGATCGCGCATAGCGCGCGGCGAGATCCGCGAGACATGAATAATCATTTTGGGAAAGGGTTAATGGCCGGGTTGCACGCGCCATATGCATATAGCGCGCATCATGCGGTGAATTTCTGTTCTGAGTATAAACGTGGCTTTGTATTGGGTTTTACACACCGTATGTTCGAAAAGACCGGCGATCGTCAACTTAGCGCGTGGGAGGCCGGAATTCTGACGCGTCGCTATGGTCTGGATAAAGAAATGGTGATGGATTTCTTTAAAGAGAATCATTCCGGGATGGCGGTTCGCTTCTTTATGGCTGGTTATCGACTCGAAGGTTGAACGCCTCTAGAGCGCTAGAGGCGCGCGCGATATACGCGGCGCGAGACATGTCTACGCTTCTCTATTTGCACGGATTCAACAGTTCCCCTCGCTCGGCAAAAGCGTGCCAGCTAAAAAACTGGCTGGCGGAGCGTCATCCGCATGTTGAGATGATCGTCCCTCAACTGCCGCCGTATCCTGCCGATGCGGCGGAGTTGCTGGAATCTCTCGTACTTGAGCATGGCGGTGCGCCATTAGGGCTGGTAGGATCGTCGCTGGGTGGTTATTACGCCACCTGGCTGTCGCAATGTTTTATGCTGCCGGCTGTGGTGGTGAATCCCGCCGTGCGGCCCTTTGAATTACTGACCGACTATCTCGGTCAGAACGAGAACCCCTACACCGGGCAGCAATATGTGCTAGAGTCTCGCCATATTTATGATCTTAAAGTCATGCAGATTGACCCGCTGGAAGCGCCGGACCTGATCTGGCTACTGCAACAGACGGGCGATGAAGTGCTGGATTACCGCCAGGCGGTGGCATATTACGCCTCCTGCCGTCAGACAGTGACCGAGGGGGGTAATCACGCATTCACGGGCTTCGAAGATTATTTCAACCAGATTGTCGATTTTCTTGGACTGCACAGTTGCTGACCGGATATACGCGCGCGCGCTATATAGCGCGCGCGGCGATATAGCGCATGAAGTTTGTTGCGCCAGAACAGGCACCGGAACAGGCGGAAATCATCAGAAATACGCCGTTCTGGCCTGATGTGGACCTGTCGGAGTTTCGCAGCATGATGCGCACTGATGGCACGGTGACGCAGCCGCGTTTAAAGCAGGTTGCGCTGTCGGCAATTTCGGAGGTCAACGCAGAGCTGTATGAGTTTCGCAGACGCCAGCAGATGCTGGGGTATGCCTCGCTGGCAGAAGTCCCGGCGGAACAACTGGACGGCAAAAGCGAGCGCATTCAGCACTATTTCAACGCGGTTTACTGCTGGGCACGCGCCATGCTCAACGAACGTTACCAGGACTATGACGCCACGGCATCCGGTGTGAAGCGGGGCGAAGAACTGGCAGAAGCCAGCGGTGATTTGTGGCGTGACGCCCGCTGGGCCATCAGCCGGGTGCAGGATGCGCCGCACTGCACAGTGGAGCTTATCTGA
->this_is_genome2_contig_number3_4
-ATGATTGACCCTATTTTTGCGTCCTGTACGCTAATTGCCGTCTTTGTTGTTTTACTGGCCATGGGCGCGCCTATCGGGATCTGCATCGTTATCGCCTCTTTCAGCACCATGATGCTGGTACTGCCTTTCGATATTTCGATGTTCGCCACCGCGCAAAAAATGTTCTCCAGCCTGGACAGTTTTGCCTTGCTGGCCGTGCCGTTCTTCGTTTTGTCCGGGGTGATCATGAATAGCGGGGGAATTGCCGCCCGACTGGTCAATTTTGCCAAACTGTTTACTGGCAAACTGCCCGGCTCGCTCTCTTACACCAACATCGTCGGCAATATGATGTTCGGTGCAATTTCCGGATCGGCGATTGCCGCCTCAACCTCTATCGGCGGCGTGATGGTGCCGATGAGCGCGCGCGAAGGTTACGATCGCGGTTTTGCGGCCGCGGTGAATATCGCCTCCGCGCCGACGGGAATGTTAATTCCGCCCACCACGGCTTTTATCCTTTATGCGCTGGCAAGCGGGGGAACATCGATTGCCGCTCTGTTCGCCGGCGGTCTGGTCGCGGGAGTGCTGTGGGGCGTTGGCTGTATGCTGGTCACGCTGGTGGTCGCTAAGCGTCGAAATTATCGGGTTTTCTTCACCGTCCAAAAAGGCATGGCGCTAAAAGTTGCCGTTGAGGCCATTCCCAGCCTGTTACTGATCGTGATTATTGTCGGCGGCATTGTGCAGGGGATTTTCACCGCCATTGAAGCCTCCGCGATTGCCGTGGTGTATACGTTATTGCTGACGATAGTGTTTTACCGCACGCTGAAAATTAAGGATTTGCCTTCGATTTTGCTCCAGACAGTGGTAATGACCGGGGTCATCATGTTCCTGCTGGCAACCTCTTCGGCGATGTCCTTCTCGATGTCGATCACCAATATTCCTGCGGCGCTGAGCGATATGATCCTCGGTATTTCCGCCAATAAACTGGTTATCCTGTTAGTCATTACCGTCTTTTTGTTGATTATCGGCGCATTTATGGATATCGGTCCGGCCATTCTGATTTTTACCCCGATTCTGCTGCCGATTATGACTAAACTGGGCGTCGATCCGGTGCATTTCGGCATTATCATGATCTATAACCTGGCGATAGGCACCATTACGCCGCCAGTTGGCAGTGGTTTATATGTCGGGGCGAGCGTCGGTAAGGTCAAAGTTGAGGACGTTATCAAACCGTTGATGCCTTTTTACGGCGCGATTATCGGCGTTCTGTTATTAATTACCTACATTCCGGAAATCACACTGTTTTTACCCCGTCTACTGGGCATCATGTAAACGCTCATAGGCGGCGCGCGCGCTCTCAGGAATGAAGTTTGTTGCGCCAGAACAGGCACCGGAACAGGCGGAGGTCATCAAAAATACGCCGTTCTGGCCTGATGTGAACCTGTCGGAATTTCGCAGTGTGATGCGCACTGACGGCACGGTGACGCAGCCGCGTTTAAAGCAGGTCGTGCTGACGGCGATCTCTGAGGTTAACGCTGAGCTGTACGACTTCCGCAACCGTCAGCAGATGCTGGGCTGGCGGACACTTGCTGAGGTTCCCGCAGAAATGCTGGACGGTAAAAGCGAGCGTATCCGGCACTACCACAACGCTGTTTTTTGCTGGGCGCGCGCTGTGCTTAATGAGCGTTATCAGGACTATGACGCCACGGCGTCAGGCGTGAAGCGAGGGGAGGAGCTGGCGGAGGCCAGCGGCGATCTGTGGCGTGATGCCCGCTGGGCCATCAGCCGGGTGCAGGATGCACCGCACTGTACGGTGGAGCTTATCTGACGCTCATAGGCGCGCGCTCATAGCGCGATGGAAACAAATATTACCTGGCAACAATTGATAGATGAATATTTCTTCGCAAAACCTCTGCGCTCAGCATCTGAATGGAGTTACACCAAAGTCTTCAAATCATTTGTACATTATATGGGGCCGTTAAGCTGCCCTAATGATGTGACATATCACAAAGTGCTTGCCTGGCGCCGTTTTCTTTTAAAAGAGAAAAAGCTGTCCGGACGTACCTGGAATAACAAGGTGGCGCATATGCGGGCCATCTTTAACTACGGAATACAGCGAGGGTTACTGCACTATGACGAAAATCCGTTTAACAATTCGGTAGTTAAACCGGACAAGAAGAGAAAGAAAACGCTCACTCAGGCACAGATTGAGTATGCCTATCAGATCATGGAGCAGTATGAAAATCAGGAGAATACAGGGCTGGGACTGAAATATTCCCGCTGCGCCTTATTTCCTGCATGGTTCTGGCTCACTGTCCTGGATACGCTCTATTACACAGGGATACGTCAGAACCAGTTATTACATATTCGGCTGAATGATGTTGATTTGAGAGAAGGGCAGATTCGGCTGATTACGGAGGGGTGTAAAAATCACAAAGAACACTATGTGCCGGTGATCAGTTTTCTGCGTCCACGGCTGACCTGTTTAATGGAGAAAGCGCAGAGCGAAGGATTGAAAGGTAATGACCGCCTGTTCAATATTGCACTTTTTACCGGCAAAGATCCCGCCATTGGCGATGACATGGATTCTCCTCAGGTAAGAGCATTCTTCCGTCGTCTGTCCAAGGAGTGTCAGTTTGCGATCAGTCCTCATCGTTTCAGACACACGCTGGCCACGGAGATGATGAAAATGCCGGAACAGAATCTGCATATGGCGCAAAGTGTGCTGGGTCATTCAAACATGAAATCCACGCTGGAGTATGTGGAGAATGATATTGCAGTGATGGGGAGGGCTCTGGAAGCGCAGTTTATGCAGATTAAGGCAGCACATGCCCGAAGCATTTACAGTGGGTTGACAAAGAATAGATAA
->genome2_small_5
-GATACA
diff --git a/Examples/2-res-Annotate-prodigal/tmp_files/genome2.fst_prodigal-split5N.fna-prodigal.log b/Examples/2-res-Annotate-prodigal/tmp_files/genome2.fst_prodigal-split5N.fna-prodigal.log
deleted file mode 100644
index e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
diff --git a/Examples/2-res-Annotate-prodigal/tmp_files/genome2.fst_prodigal-split5N.fna-prodigal.log.err b/Examples/2-res-Annotate-prodigal/tmp_files/genome2.fst_prodigal-split5N.fna-prodigal.log.err
deleted file mode 100644
index e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
diff --git a/Examples/2-res-Annotate-prodigal/tmp_files/genome2.fst_prodigal-split5N.fna-prodigalRes/GEN2.1219.00001.faa b/Examples/2-res-Annotate-prodigal/tmp_files/genome2.fst_prodigal-split5N.fna-prodigalRes/GEN2.1219.00001.faa
deleted file mode 100644
index f5ff7e0e528954746d365c382a0d8fbb1e99fb55..0000000000000000000000000000000000000000
--- a/Examples/2-res-Annotate-prodigal/tmp_files/genome2.fst_prodigal-split5N.fna-prodigalRes/GEN2.1219.00001.faa
+++ /dev/null
@@ -1,77 +0,0 @@
->this_is_genome2_contig_number1_1_1 # 1 # 774 # 1 # ID=1_1;partial=10;start_type=Edge;rbs_motif=None;rbs_spacer=None;gc_cont=0.530
-MSENKLHVIDLHKRYGGHEVLKGVSLQARAGDVISIIGSSGSGKSTFLRCINFLEKSSEG
-AIIVNGQNINLVRDKDGQLKVADKNQLRLLRTRLTMVFQHFNLWNHMTVLENVMEAPIQV
-LGLSKHDARERALKYLAKVGIDERAQGKYPVHLSGGQQQRVSIARALAMEPDVLLFDEPT
-SALDPELVGEVLRIMQQLAEEGKTMVVVTHEMGFARHVSSHVIFLHQGKIEEEGNPEQVF
-GNPQSPRLQQFLKGSLK*
->this_is_genome2_contig_number1_1_2 # 857 # 2260 # 1 # ID=1_2;partial=00;start_type=ATG;rbs_motif=None;rbs_spacer=None;gc_cont=0.510
-MPATKFSRRTLLTAGSALAVLPFLRALPVQAREPRQTVDIKDYPADDGIASFKQAFADGQ
-TVVVPSGWVCENINAAITIPAGKTLRIQGAVRGNGRGRFILLDGCQVVGEQGGSLHNVTL
-DVRGSDCVIKGVTMSGFGPVAQIFIGGKEPQVMRNLIIDDITVTHANYAILRQGFHNQMD
-GARITHSRFSDLQGDAIEWNVAIHDRDILISDHVIERIDCTNGKINWGIGIGLAGSAYDN
-SYPEDQAVKNFVVANITGSDCRQLVHVENGKHFVIRNVKAKNITPDFSKNAGIDNATIAI
-YGCDNFVIDNIDMTNSAGMLIGYGVVKGKYLSIPQNFKLNAIRLDNRQVAYKLRGIQISS
-GNAPSFVAITNVRMTRATLELHNQPQHLFLRNINVMQTSAIGPALKMHFDLRKDVRGQFM
-ARQDTLLSLANVHAINENGQSSVDIDRINHQTVNVEAVNFSLPKRGG*
->this_is_genome2_contig_number1_2_1 # 1 # 252 # 1 # ID=2_1;partial=10;start_type=Edge;rbs_motif=None;rbs_spacer=None;gc_cont=0.540
-RDNIARAHSMSALFLAIPLTIFVLFVLPIWLWLHYSNRAGRGELSQSEQQRLLQLTDDAQ
-RMRERIQALEDILDAEHPNWRER*
->this_is_genome2_contig_number1_2_2 # 301 # 681 # 1 # ID=2_2;partial=00;start_type=ATG;rbs_motif=None;rbs_spacer=None;gc_cont=0.530
-MPHFIAECTENIREQADLPSLFSKVNEALAATGIFPIGGIRSRAHWLDTWQMADGKHDYA
-FVHMTLKIGAGRSLESRQEVGEMLFGLIKAHFADLMENRYLALSFEIAELHPTLNYKQNN
-VHALFK*
->this_is_genome2_contig_number1_2_3 # 764 # 1597 # 1 # ID=2_3;partial=00;start_type=ATG;rbs_motif=None;rbs_spacer=None;gc_cont=0.573
-MMKALLWLVGLALLLTGCASEKGIIDKEGYQLDTRHRAQAAYPRIKVLVIHYTAENFDVS
-LATLTGRNVSSHYLIPATPPLYGGKPRIWQLVPEQDQAWHAGVSFWRGATRLNDTSIGIE
-LENRGWRMSGGVKSFAPFESAQIQALIPLAKDIIARYDIKPQNVVAHADIAPQRKDDPGP
-RFPWRELAAQGIGAWPDAQRVAFYLAGRAPYTPVDTATVLALLSRYGYEVKADMTAREQQ
-RVIMAFQMHFRPAQWNGIADAETQAIAEALLEKYGQD*
->this_is_genome2_contig_number1_2_4 # 1628 # 3295 # 1 # ID=2_4;partial=00;start_type=ATG;rbs_motif=GGA/GAG/AGG;rbs_spacer=5-10bp;gc_cont=0.537
-MSEAEARPTNFIRQIIDEDLASGKHTTVHTRFPPEPNGYLHIGHAKSICLNFGIAQDYQG
-QCNLRFDDTNPVKEDIEYVDSIKNDVEWLGFHWSGDIRYSSDYFDQLHAYAVELINKGLA
-YVDELTPEQIREYRGTLTAPGKNSPFRDRSVEENLALFEKMRTGGFEEGKACLRAKIDMA
-SPFIVMRDPVLYRIKFAEHHQTGTKWCIYPMYDFTHCISDALEGITHSLCTLEFQDNRRL
-YDWVLDNITIPVHPRQYEFSRLNLEYTVMSKRKLNLLVTDKHVEGWDDPRMPTISGLRRR
-GYTAASIREFCKRIGVTKQDNTIEMASLESCIREDLNENAPRAMAVIDPVKLVIENYPQG
-ESEMVTMPNHPNKPEMGSREVPFSGEIWIDRADFREEANKQYKRLVMGKEVRLRNAYVIK
-AERVEKDAEGNITTIFCTYDADTLSKDPADGRKVKGVIHWVSVAHALPIEIRLYDRLFSV
-PNPGAAEDFLSVINPESLVIKQGYGEPSLKAAVAGKAFQFEREGYFCLDSRYATADKLVF
-NRTVGLRDTWAKAGE*
->this_is_genome2_contig_number2_3_1 # 30 # 797 # 1 # ID=3_1;partial=00;start_type=GTG;rbs_motif=GGA/GAG/AGG;rbs_spacer=5-10bp;gc_cont=0.540
-MFIGIVSLFPEMFRAITDYGVTGRAVKKGLLNIQSWSPRDFAHDRHRTVDDRPYGGGPGM
-LMMVQPLRDAIHAAKAAAGEGAKVIYLSPQGRKLDQAGVSELATNQKLILVCGRYEGVDE
-RVIQAEIDEEWSIGDYVLSGGELPAMTLIDSVARFIPGVLGHEASAIEDSFADGLLDCPH
-YTRPEVLEGMEVPPVLLSGNHAEIRRWRLKQSLGRTWLRRPELLENLALTEEQARLLAEF
-KTEHAQQQHKHDGMA*
->this_is_genome2_contig_number2_3_2 # 862 # 1122 # 1 # ID=3_2;partial=00;start_type=ATG;rbs_motif=GGA/GAG/AGG;rbs_spacer=5-10bp;gc_cont=0.487
-MAGLHAPYAYSAHHAVNFCSEYKRGFVLGFTHRMFEKTGDRQLSAWEAGILTRRYGLDKE
-MVMDFFKENHSGMAVRFFMAGYRLEG*
->this_is_genome2_contig_number2_3_3 # 1170 # 1751 # 1 # ID=3_3;partial=00;start_type=ATG;rbs_motif=None;rbs_spacer=None;gc_cont=0.546
-MSTLLYLHGFNSSPRSAKACQLKNWLAERHPHVEMIVPQLPPYPADAAELLESLVLEHGG
-APLGLVGSSLGGYYATWLSQCFMLPAVVVNPAVRPFELLTDYLGQNENPYTGQQYVLESR
-HIYDLKVMQIDPLEAPDLIWLLQQTGDEVLDYRQAVAYYASCRQTVTEGGNHAFTGFEDY
-FNQIVDFLGLHSC*
->this_is_genome2_contig_number2_3_4 # 1895 # 2263 # 1 # ID=3_4;partial=00;start_type=ATG;rbs_motif=GGAG/GAGG;rbs_spacer=5-10bp;gc_cont=0.599
-MMRTDGTVTQPRLKQVALSAISEVNAELYEFRRRQQMLGYASLAEVPAEQLDGKSERIQH
-YFNAVYCWARAMLNERYQDYDATASGVKRGEELAEASGDLWRDARWAISRVQDAPHCTVE
-LI*
->this_is_genome2_contig_number3_4_1 # 1 # 1308 # 1 # ID=4_1;partial=10;start_type=Edge;rbs_motif=None;rbs_spacer=None;gc_cont=0.519
-MIDPIFASCTLIAVFVVLLAMGAPIGICIVIASFSTMMLVLPFDISMFATAQKMFSSLDS
-FALLAVPFFVLSGVIMNSGGIAARLVNFAKLFTGKLPGSLSYTNIVGNMMFGAISGSAIA
-ASTSIGGVMVPMSAREGYDRGFAAAVNIASAPTGMLIPPTTAFILYALASGGTSIAALFA
-GGLVAGVLWGVGCMLVTLVVAKRRNYRVFFTVQKGMALKVAVEAIPSLLLIVIIVGGIVQ
-GIFTAIEASAIAVVYTLLLTIVFYRTLKIKDLPSILLQTVVMTGVIMFLLATSSAMSFSM
-SITNIPAALSDMILGISANKLVILLVITVFLLIIGAFMDIGPAILIFTPILLPIMTKLGV
-DPVHFGIIMIYNLAIGTITPPVGSGLYVGASVGKVKVEDVIKPLMPFYGAIIGVLLLITY
-IPEITLFLPRLLGIM*
->this_is_genome2_contig_number3_4_2 # 1340 # 1804 # 1 # ID=4_2;partial=00;start_type=ATG;rbs_motif=None;rbs_spacer=None;gc_cont=0.594
-MKFVAPEQAPEQAEVIKNTPFWPDVNLSEFRSVMRTDGTVTQPRLKQVVLTAISEVNAEL
-YDFRNRQQMLGWRTLAEVPAEMLDGKSERIRHYHNAVFCWARAVLNERYQDYDATASGVK
-RGEELAEASGDLWRDARWAISRVQDAPHCTVELI*
->this_is_genome2_contig_number3_4_3 # 1832 # 2845 # 1 # ID=4_3;partial=00;start_type=ATG;rbs_motif=None;rbs_spacer=None;gc_cont=0.456
-METNITWQQLIDEYFFAKPLRSASEWSYTKVFKSFVHYMGPLSCPNDVTYHKVLAWRRFL
-LKEKKLSGRTWNNKVAHMRAIFNYGIQRGLLHYDENPFNNSVVKPDKKRKKTLTQAQIEY
-AYQIMEQYENQENTGLGLKYSRCALFPAWFWLTVLDTLYYTGIRQNQLLHIRLNDVDLRE
-GQIRLITEGCKNHKEHYVPVISFLRPRLTCLMEKAQSEGLKGNDRLFNIALFTGKDPAIG
-DDMDSPQVRAFFRRLSKECQFAISPHRFRHTLATEMMKMPEQNLHMAQSVLGHSNMKSTL
-EYVENDIAVMGRALEAQFMQIKAAHARSIYSGLTKNR*
diff --git a/Examples/2-res-Annotate-prodigal/tmp_files/genome2.fst_prodigal-split5N.fna-prodigalRes/GEN2.1219.00001.ffn b/Examples/2-res-Annotate-prodigal/tmp_files/genome2.fst_prodigal-split5N.fna-prodigalRes/GEN2.1219.00001.ffn
deleted file mode 100644
index 0d9892453b27c6c446126a486e510be4983499a1..0000000000000000000000000000000000000000
--- a/Examples/2-res-Annotate-prodigal/tmp_files/genome2.fst_prodigal-split5N.fna-prodigalRes/GEN2.1219.00001.ffn
+++ /dev/null
@@ -1,163 +0,0 @@
->this_is_genome2_contig_number1_1_1 # 1 # 774 # 1 # ID=1_1;partial=10;start_type=Edge;rbs_motif=None;rbs_spacer=None;gc_cont=0.530
-ATGTCAGAAAATAAATTACACGTTATCGATTTGCACAAACGCTACGGCGGTCATGAAGTGCTGAAAGGGG
-TATCGCTGCAGGCCCGCGCCGGAGATGTGATTAGCATTATCGGCTCGTCCGGTTCCGGTAAAAGCACTTT
-TTTGCGCTGCATTAACTTCCTCGAAAAATCGAGCGAAGGCGCGATTATCGTGAACGGTCAGAACATTAAT
-CTGGTGCGCGACAAAGACGGGCAGCTCAAAGTGGCGGATAAAAATCAGCTACGCTTGTTGCGTACCCGCC
-TGACGATGGTGTTTCAGCACTTTAACCTCTGGAACCACATGACGGTGCTGGAAAATGTGATGGAAGCGCC
-GATTCAGGTACTGGGATTAAGCAAGCACGACGCGCGCGAGCGGGCGTTGAAATATCTGGCGAAGGTGGGG
-ATTGATGAGCGCGCTCAGGGCAAATATCCCGTCCATCTCTCCGGCGGCCAACAGCAGCGCGTTTCTATTG
-CGCGCGCGCTGGCGATGGAACCTGACGTTTTACTGTTCGATGAACCCACATCGGCGCTCGATCCTGAACT
-GGTCGGCGAAGTGTTGCGCATCATGCAACAACTGGCGGAAGAAGGCAAAACGATGGTGGTGGTCACGCAT
-GAAATGGGCTTCGCCCGCCATGTCTCTTCGCACGTGATTTTTCTGCATCAGGGGAAAATTGAAGAAGAGG
-GCAATCCGGAGCAGGTGTTCGGCAATCCGCAAAGCCCGCGTTTACAGCAATTCCTGAAAGGCTCGCTGAA
-ATAA
->this_is_genome2_contig_number1_1_2 # 857 # 2260 # 1 # ID=1_2;partial=00;start_type=ATG;rbs_motif=None;rbs_spacer=None;gc_cont=0.510
-ATGCCCGCGACTAAATTCTCCCGACGTACCCTCCTGACGGCAGGTTCCGCGCTTGCTGTTCTTCCTTTTC
-TGCGCGCCTTGCCGGTACAGGCGCGTGAACCTCGCCAGACCGTCGATATTAAGGATTATCCGGCGGATGA
-CGGTATCGCCTCGTTCAAACAGGCCTTCGCCGACGGGCAGACTGTGGTCGTGCCGTCAGGATGGGTGTGT
-GAAAATATCAATGCGGCGATAACGATTCCGGCGGGAAAAACGCTGCGGATACAGGGCGCGGTGCGTGGGA
-ATGGCCGGGGACGGTTTATTTTGCTGGACGGGTGTCAGGTGGTGGGGGAGCAGGGCGGCAGTCTGCACAA
-TGTGACGCTGGATGTTCGCGGGTCGGACTGTGTGATTAAAGGCGTGACGATGAGCGGCTTTGGCCCCGTC
-GCGCAAATTTTCATCGGCGGTAAGGAACCGCAGGTGATGCGTAATCTCATTATCGATGACATCACCGTTA
-CCCACGCCAACTACGCCATTCTCCGCCAGGGATTTCATAACCAAATGGACGGCGCGCGGATTACGCATAG
-TCGCTTTAGCGATTTGCAGGGGGACGCCATTGAGTGGAATGTCGCGATTCATGACCGCGACATCCTGATT
-TCCGATCATGTCATCGAACGCATTGATTGTACCAATGGCAAAATCAACTGGGGGATCGGCATCGGGCTGG
-CGGGTAGCGCCTATGACAATAGTTATCCTGAAGACCAGGCAGTAAAAAACTTTGTGGTGGCCAATATTAC
-CGGATCTGATTGCCGACAACTGGTACACGTAGAAAATGGCAAACATTTCGTCATTCGCAATGTCAAAGCC
-AAAAACATCACGCCCGATTTCAGTAAAAATGCGGGTATTGATAACGCAACGATCGCCATTTATGGCTGTG
-ATAATTTCGTCATTGATAATATTGATATGACGAATAGTGCCGGGATGCTCATCGGCTATGGCGTCGTTAA
-AGGAAAATACCTGTCAATTCCGCAAAACTTTAAATTAAACGCTATTCGGTTGGATAATCGCCAGGTTGCT
-TATAAATTACGCGGCATTCAAATTTCCTCCGGTAACGCCCCCTCATTTGTTGCCATCACCAATGTACGGA
-TGACGCGTGCTACGCTGGAACTGCATAATCAACCGCAGCACCTCTTTTTGCGTAATATCAACGTGATGCA
-AACTTCAGCGATTGGCCCGGCGTTAAAAATGCATTTTGATTTGCGTAAAGATGTCCGTGGTCAATTTATG
-GCCCGCCAGGACACGCTGCTTTCCCTCGCTAATGTTCATGCCATCAATGAAAACGGGCAGAGTTCCGTGG
-ATATCGACAGGATTAATCACCAAACCGTGAATGTCGAAGCAGTGAATTTTTCGCTGCCGAAGCGGGGAGG
-GTAA
->this_is_genome2_contig_number1_2_1 # 1 # 252 # 1 # ID=2_1;partial=10;start_type=Edge;rbs_motif=None;rbs_spacer=None;gc_cont=0.540
-CGCGATAATATAGCGCGCGCTCATAGCATGAGCGCGCTATTTCTGGCCATCCCGTTAACCATTTTTGTGT
-TGTTTGTGTTACCGATTTGGCTGTGGCTGCATTACAGCAACCGCGCCGGTCGGGGAGAACTGTCGCAAAG
-CGAGCAGCAACGCTTACTGCAACTCACAGACGACGCGCAACGTATGCGCGAGCGCATTCAGGCGCTGGAA
-GATATTCTTGATGCAGAGCATCCGAACTGGAGAGAGCGCTAA
->this_is_genome2_contig_number1_2_2 # 301 # 681 # 1 # ID=2_2;partial=00;start_type=ATG;rbs_motif=None;rbs_spacer=None;gc_cont=0.530
-ATGCCGCACTTTATTGCTGAATGTACTGAAAATATTCGCGAGCAGGCTGATTTACCAAGCCTGTTCAGCA
-AGGTAAACGAGGCGCTGGCCGCCACCGGGATTTTCCCCATCGGCGGTATCCGCAGTCGCGCCCACTGGCT
-GGATACCTGGCAGATGGCTGACGGTAAGCATGATTACGCGTTTGTGCATATGACGCTGAAAATCGGCGCC
-GGGCGCAGCCTGGAGAGCCGTCAGGAAGTCGGCGAAATGCTGTTTGGGCTGATTAAAGCCCACTTCGCCG
-ACCTGATGGAGAACCGCTATCTGGCGCTGTCGTTTGAGATTGCCGAGTTACATCCAACGCTCAATTACAA
-ACAAAACAACGTACACGCGTTATTTAAATAG
->this_is_genome2_contig_number1_2_3 # 764 # 1597 # 1 # ID=2_3;partial=00;start_type=ATG;rbs_motif=None;rbs_spacer=None;gc_cont=0.573
-ATGATGAAAGCGCTACTGTGGCTGGTTGGTCTCGCGTTGCTGTTAACAGGCTGCGCGAGCGAAAAAGGAA
-TTATCGATAAAGAGGGATATCAGCTTGATACCCGACATCGGGCGCAGGCGGCCTATCCGCGCATTAAAGT
-CCTGGTGATTCACTATACGGCGGAAAACTTTGACGTTTCGCTGGCGACGTTAACGGGTCGCAACGTCAGT
-TCGCATTACCTGATTCCCGCAACCCCGCCATTATATGGCGGTAAACCGCGCATCTGGCAACTGGTGCCGG
-AACAGGATCAGGCTTGGCATGCGGGCGTCAGTTTCTGGCGAGGCGCCACGCGTCTCAATGATACGTCTAT
-TGGCATTGAGCTGGAAAATCGCGGCTGGCGAATGTCCGGCGGGGTGAAATCTTTCGCGCCGTTTGAATCC
-GCGCAAATTCAGGCATTGATCCCGTTAGCGAAGGACATTATCGCGCGCTATGACATCAAACCGCAGAATG
-TGGTGGCCCATGCGGATATCGCGCCGCAGCGTAAAGACGATCCCGGCCCGCGCTTCCCGTGGCGCGAGCT
-GGCGGCACAGGGGATTGGCGCCTGGCCTGACGCCCAGCGTGTGGCGTTTTATCTGGCTGGACGCGCGCCG
-TATACGCCAGTCGATACCGCAACGGTGCTTGCGTTACTCTCGCGCTATGGCTATGAAGTCAAAGCCGATA
-TGACGGCGCGCGAGCAACAGCGGGTGATTATGGCGTTCCAGATGCACTTCCGTCCGGCGCAATGGAACGG
-TATCGCAGATGCCGAAACGCAGGCGATTGCCGAAGCATTACTGGAGAAGTACGGCCAGGATTAA
->this_is_genome2_contig_number1_2_4 # 1628 # 3295 # 1 # ID=2_4;partial=00;start_type=ATG;rbs_motif=GGA/GAG/AGG;rbs_spacer=5-10bp;gc_cont=0.537
-ATGAGTGAGGCTGAAGCCCGCCCGACTAACTTTATTCGTCAGATTATTGATGAAGATCTGGCGAGTGGTA
-AACATACCACTGTCCATACCCGTTTTCCGCCGGAGCCGAATGGCTATCTGCACATCGGCCACGCGAAATC
-TATCTGCCTGAACTTTGGCATCGCGCAAGATTATCAGGGCCAGTGCAACCTGCGTTTCGATGACACCAAC
-CCGGTAAAAGAAGATATCGAGTACGTTGATTCGATCAAAAACGACGTCGAGTGGTTAGGCTTTCACTGGT
-CTGGCGATATTCGCTACTCCTCCGATTACTTTGACCAACTGCACGCCTATGCGGTCGAGCTCATCAATAA
-AGGCCTGGCCTACGTTGATGAGCTGACGCCGGAGCAGATCCGCGAATACCGTGGTACGCTGACCGCGCCG
-GGTAAAAACAGCCCGTTCCGCGATCGCAGCGTGGAAGAAAACCTCGCGCTATTTGAAAAAATGCGTACCG
-GCGGTTTTGAAGAGGGTAAAGCCTGTCTGCGCGCTAAAATCGACATGGCGTCGCCGTTTATCGTGATGCG
-CGATCCGGTGCTGTATCGCATTAAATTCGCCGAGCATCATCAGACCGGCACGAAGTGGTGCATCTATCCG
-ATGTACGACTTTACTCACTGCATCAGCGATGCGCTGGAAGGCATTACTCATTCTCTGTGTACGCTGGAGT
-TCCAGGACAACCGTCGTCTGTACGACTGGGTGCTGGACAACATCACCATTCCGGTTCACCCGCGCCAGTA
-CGAATTCTCGCGCCTGAATCTGGAATACACCGTGATGTCCAAGCGTAAGCTGAACCTGCTGGTGACCGAC
-AAACACGTCGAAGGTTGGGATGATCCGCGTATGCCGACTATTTCCGGTCTGCGCCGTCGCGGCTATACCG
-CGGCTTCTATTCGTGAGTTCTGCAAACGCATCGGCGTCACCAAGCAGGACAACACTATTGAGATGGCGTC
-GCTGGAATCCTGCATTCGCGAAGATCTGAACGAAAACGCGCCGCGCGCGATGGCGGTAATCGATCCGGTA
-AAACTGGTTATCGAAAACTACCCGCAGGGCGAGAGCGAAATGGTTACCATGCCTAACCATCCGAATAAAC
-CGGAGATGGGCAGCCGTGAAGTGCCGTTTAGCGGTGAGATCTGGATCGATCGCGCGGATTTCCGCGAAGA
-AGCGAACAAACAGTACAAACGTCTGGTGATGGGCAAAGAAGTGCGTCTGCGTAATGCCTACGTCATTAAA
-GCGGAGCGCGTAGAGAAGGATGCCGAAGGGAATATCACCACCATCTTCTGTACCTATGATGCTGATACGC
-TGAGTAAAGATCCGGCTGACGGGCGTAAAGTGAAAGGCGTAATCCACTGGGTTAGCGTAGCACATGCGCT
-GCCGATTGAAATTCGTCTCTACGACCGTCTGTTCAGCGTGCCGAACCCGGGCGCCGCGGAGGACTTCCTG
-TCTGTTATCAACCCCGAATCATTAGTGATTAAGCAGGGGTATGGCGAGCCGTCGCTGAAAGCGGCGGTAG
-CAGGGAAAGCTTTCCAGTTTGAACGTGAAGGTTACTTCTGCCTTGACAGCCGCTATGCAACGGCCGATAA
-GCTGGTCTTTAACCGCACCGTGGGCCTGCGTGATACCTGGGCGAAAGCGGGCGAATAA
->this_is_genome2_contig_number2_3_1 # 30 # 797 # 1 # ID=3_1;partial=00;start_type=GTG;rbs_motif=GGA/GAG/AGG;rbs_spacer=5-10bp;gc_cont=0.540
-GTGTTTATTGGCATCGTTAGCCTGTTTCCTGAAATGTTCCGCGCAATTACCGATTACGGGGTAACTGGCC
-GGGCAGTAAAAAAAGGCCTGCTGAACATCCAAAGCTGGAGTCCTCGCGACTTCGCGCATGACCGGCACCG
-TACCGTGGACGACCGTCCTTACGGCGGCGGACCGGGGATGTTAATGATGGTGCAACCCTTGCGGGACGCC
-ATTCATGCAGCAAAAGCCGCGGCAGGTGAAGGCGCTAAAGTGATTTATCTGTCGCCTCAGGGACGCAAGC
-TTGATCAAGCGGGCGTTAGCGAGCTGGCCACGAATCAGAAACTCATTCTGGTGTGTGGTCGCTACGAAGG
-CGTAGATGAGCGCGTAATTCAGGCCGAAATTGACGAAGAATGGTCAATTGGCGATTACGTTCTCAGCGGT
-GGCGAACTACCGGCAATGACGCTGATTGACTCCGTCGCCCGGTTTATACCGGGGGTTCTGGGGCATGAGG
-CATCAGCAATCGAAGATTCGTTTGCTGATGGGTTGCTGGATTGTCCGCACTATACGCGCCCTGAAGTGTT
-AGAGGGGATGGAAGTACCGCCAGTATTGCTGTCGGGAAACCATGCTGAGATACGTCGCTGGCGTTTGAAA
-CAGTCACTGGGCCGAACCTGGCTTAGAAGACCTGAACTTCTGGAAAACCTGGCTCTGACTGAAGAGCAAG
-CAAGGTTGCTGGCGGAGTTCAAAACAGAACACGCACAACAGCAGCATAAACATGATGGGATGGCATAG
->this_is_genome2_contig_number2_3_2 # 862 # 1122 # 1 # ID=3_2;partial=00;start_type=ATG;rbs_motif=GGA/GAG/AGG;rbs_spacer=5-10bp;gc_cont=0.487
-ATGGCCGGGTTGCACGCGCCATATGCATATAGCGCGCATCATGCGGTGAATTTCTGTTCTGAGTATAAAC
-GTGGCTTTGTATTGGGTTTTACACACCGTATGTTCGAAAAGACCGGCGATCGTCAACTTAGCGCGTGGGA
-GGCCGGAATTCTGACGCGTCGCTATGGTCTGGATAAAGAAATGGTGATGGATTTCTTTAAAGAGAATCAT
-TCCGGGATGGCGGTTCGCTTCTTTATGGCTGGTTATCGACTCGAAGGTTGA
->this_is_genome2_contig_number2_3_3 # 1170 # 1751 # 1 # ID=3_3;partial=00;start_type=ATG;rbs_motif=None;rbs_spacer=None;gc_cont=0.546
-ATGTCTACGCTTCTCTATTTGCACGGATTCAACAGTTCCCCTCGCTCGGCAAAAGCGTGCCAGCTAAAAA
-ACTGGCTGGCGGAGCGTCATCCGCATGTTGAGATGATCGTCCCTCAACTGCCGCCGTATCCTGCCGATGC
-GGCGGAGTTGCTGGAATCTCTCGTACTTGAGCATGGCGGTGCGCCATTAGGGCTGGTAGGATCGTCGCTG
-GGTGGTTATTACGCCACCTGGCTGTCGCAATGTTTTATGCTGCCGGCTGTGGTGGTGAATCCCGCCGTGC
-GGCCCTTTGAATTACTGACCGACTATCTCGGTCAGAACGAGAACCCCTACACCGGGCAGCAATATGTGCT
-AGAGTCTCGCCATATTTATGATCTTAAAGTCATGCAGATTGACCCGCTGGAAGCGCCGGACCTGATCTGG
-CTACTGCAACAGACGGGCGATGAAGTGCTGGATTACCGCCAGGCGGTGGCATATTACGCCTCCTGCCGTC
-AGACAGTGACCGAGGGGGGTAATCACGCATTCACGGGCTTCGAAGATTATTTCAACCAGATTGTCGATTT
-TCTTGGACTGCACAGTTGCTGA
->this_is_genome2_contig_number2_3_4 # 1895 # 2263 # 1 # ID=3_4;partial=00;start_type=ATG;rbs_motif=GGAG/GAGG;rbs_spacer=5-10bp;gc_cont=0.599
-ATGATGCGCACTGATGGCACGGTGACGCAGCCGCGTTTAAAGCAGGTTGCGCTGTCGGCAATTTCGGAGG
-TCAACGCAGAGCTGTATGAGTTTCGCAGACGCCAGCAGATGCTGGGGTATGCCTCGCTGGCAGAAGTCCC
-GGCGGAACAACTGGACGGCAAAAGCGAGCGCATTCAGCACTATTTCAACGCGGTTTACTGCTGGGCACGC
-GCCATGCTCAACGAACGTTACCAGGACTATGACGCCACGGCATCCGGTGTGAAGCGGGGCGAAGAACTGG
-CAGAAGCCAGCGGTGATTTGTGGCGTGACGCCCGCTGGGCCATCAGCCGGGTGCAGGATGCGCCGCACTG
-CACAGTGGAGCTTATCTGA
->this_is_genome2_contig_number3_4_1 # 1 # 1308 # 1 # ID=4_1;partial=10;start_type=Edge;rbs_motif=None;rbs_spacer=None;gc_cont=0.519
-ATGATTGACCCTATTTTTGCGTCCTGTACGCTAATTGCCGTCTTTGTTGTTTTACTGGCCATGGGCGCGC
-CTATCGGGATCTGCATCGTTATCGCCTCTTTCAGCACCATGATGCTGGTACTGCCTTTCGATATTTCGAT
-GTTCGCCACCGCGCAAAAAATGTTCTCCAGCCTGGACAGTTTTGCCTTGCTGGCCGTGCCGTTCTTCGTT
-TTGTCCGGGGTGATCATGAATAGCGGGGGAATTGCCGCCCGACTGGTCAATTTTGCCAAACTGTTTACTG
-GCAAACTGCCCGGCTCGCTCTCTTACACCAACATCGTCGGCAATATGATGTTCGGTGCAATTTCCGGATC
-GGCGATTGCCGCCTCAACCTCTATCGGCGGCGTGATGGTGCCGATGAGCGCGCGCGAAGGTTACGATCGC
-GGTTTTGCGGCCGCGGTGAATATCGCCTCCGCGCCGACGGGAATGTTAATTCCGCCCACCACGGCTTTTA
-TCCTTTATGCGCTGGCAAGCGGGGGAACATCGATTGCCGCTCTGTTCGCCGGCGGTCTGGTCGCGGGAGT
-GCTGTGGGGCGTTGGCTGTATGCTGGTCACGCTGGTGGTCGCTAAGCGTCGAAATTATCGGGTTTTCTTC
-ACCGTCCAAAAAGGCATGGCGCTAAAAGTTGCCGTTGAGGCCATTCCCAGCCTGTTACTGATCGTGATTA
-TTGTCGGCGGCATTGTGCAGGGGATTTTCACCGCCATTGAAGCCTCCGCGATTGCCGTGGTGTATACGTT
-ATTGCTGACGATAGTGTTTTACCGCACGCTGAAAATTAAGGATTTGCCTTCGATTTTGCTCCAGACAGTG
-GTAATGACCGGGGTCATCATGTTCCTGCTGGCAACCTCTTCGGCGATGTCCTTCTCGATGTCGATCACCA
-ATATTCCTGCGGCGCTGAGCGATATGATCCTCGGTATTTCCGCCAATAAACTGGTTATCCTGTTAGTCAT
-TACCGTCTTTTTGTTGATTATCGGCGCATTTATGGATATCGGTCCGGCCATTCTGATTTTTACCCCGATT
-CTGCTGCCGATTATGACTAAACTGGGCGTCGATCCGGTGCATTTCGGCATTATCATGATCTATAACCTGG
-CGATAGGCACCATTACGCCGCCAGTTGGCAGTGGTTTATATGTCGGGGCGAGCGTCGGTAAGGTCAAAGT
-TGAGGACGTTATCAAACCGTTGATGCCTTTTTACGGCGCGATTATCGGCGTTCTGTTATTAATTACCTAC
-ATTCCGGAAATCACACTGTTTTTACCCCGTCTACTGGGCATCATGTAA
->this_is_genome2_contig_number3_4_2 # 1340 # 1804 # 1 # ID=4_2;partial=00;start_type=ATG;rbs_motif=None;rbs_spacer=None;gc_cont=0.594
-ATGAAGTTTGTTGCGCCAGAACAGGCACCGGAACAGGCGGAGGTCATCAAAAATACGCCGTTCTGGCCTG
-ATGTGAACCTGTCGGAATTTCGCAGTGTGATGCGCACTGACGGCACGGTGACGCAGCCGCGTTTAAAGCA
-GGTCGTGCTGACGGCGATCTCTGAGGTTAACGCTGAGCTGTACGACTTCCGCAACCGTCAGCAGATGCTG
-GGCTGGCGGACACTTGCTGAGGTTCCCGCAGAAATGCTGGACGGTAAAAGCGAGCGTATCCGGCACTACC
-ACAACGCTGTTTTTTGCTGGGCGCGCGCTGTGCTTAATGAGCGTTATCAGGACTATGACGCCACGGCGTC
-AGGCGTGAAGCGAGGGGAGGAGCTGGCGGAGGCCAGCGGCGATCTGTGGCGTGATGCCCGCTGGGCCATC
-AGCCGGGTGCAGGATGCACCGCACTGTACGGTGGAGCTTATCTGA
->this_is_genome2_contig_number3_4_3 # 1832 # 2845 # 1 # ID=4_3;partial=00;start_type=ATG;rbs_motif=None;rbs_spacer=None;gc_cont=0.456
-ATGGAAACAAATATTACCTGGCAACAATTGATAGATGAATATTTCTTCGCAAAACCTCTGCGCTCAGCAT
-CTGAATGGAGTTACACCAAAGTCTTCAAATCATTTGTACATTATATGGGGCCGTTAAGCTGCCCTAATGA
-TGTGACATATCACAAAGTGCTTGCCTGGCGCCGTTTTCTTTTAAAAGAGAAAAAGCTGTCCGGACGTACC
-TGGAATAACAAGGTGGCGCATATGCGGGCCATCTTTAACTACGGAATACAGCGAGGGTTACTGCACTATG
-ACGAAAATCCGTTTAACAATTCGGTAGTTAAACCGGACAAGAAGAGAAAGAAAACGCTCACTCAGGCACA
-GATTGAGTATGCCTATCAGATCATGGAGCAGTATGAAAATCAGGAGAATACAGGGCTGGGACTGAAATAT
-TCCCGCTGCGCCTTATTTCCTGCATGGTTCTGGCTCACTGTCCTGGATACGCTCTATTACACAGGGATAC
-GTCAGAACCAGTTATTACATATTCGGCTGAATGATGTTGATTTGAGAGAAGGGCAGATTCGGCTGATTAC
-GGAGGGGTGTAAAAATCACAAAGAACACTATGTGCCGGTGATCAGTTTTCTGCGTCCACGGCTGACCTGT
-TTAATGGAGAAAGCGCAGAGCGAAGGATTGAAAGGTAATGACCGCCTGTTCAATATTGCACTTTTTACCG
-GCAAAGATCCCGCCATTGGCGATGACATGGATTCTCCTCAGGTAAGAGCATTCTTCCGTCGTCTGTCCAA
-GGAGTGTCAGTTTGCGATCAGTCCTCATCGTTTCAGACACACGCTGGCCACGGAGATGATGAAAATGCCG
-GAACAGAATCTGCATATGGCGCAAAGTGTGCTGGGTCATTCAAACATGAAATCCACGCTGGAGTATGTGG
-AGAATGATATTGCAGTGATGGGGAGGGCTCTGGAAGCGCAGTTTATGCAGATTAAGGCAGCACATGCCCG
-AAGCATTTACAGTGGGTTGACAAAGAATAGATAA
diff --git a/Examples/2-res-Annotate-prodigal/tmp_files/genome2.fst_prodigal-split5N.fna-prodigalRes/GEN2.1219.00001.gff b/Examples/2-res-Annotate-prodigal/tmp_files/genome2.fst_prodigal-split5N.fna-prodigalRes/GEN2.1219.00001.gff
deleted file mode 100644
index 3edb3f0f8cfce01ecc761edbb2278a5d786b4110..0000000000000000000000000000000000000000
--- a/Examples/2-res-Annotate-prodigal/tmp_files/genome2.fst_prodigal-split5N.fna-prodigalRes/GEN2.1219.00001.gff
+++ /dev/null
@@ -1,24 +0,0 @@
-##gff-version  3
-# Sequence Data: seqnum=1;seqlen=2308;seqhdr="this_is_genome2_contig_number1_1"
-# Model Data: version=Prodigal.v2.6.3;run_type=Metagenomic;model="20|Escherichia_coli_UMN026|B|50.7|11|1";gc_cont=50.70;transl_table=11;uses_sd=1
-this_is_genome2_contig_number1_1	Prodigal_v2.6.3	CDS	1	774	109.1	+	0	ID=1_1;partial=10;start_type=Edge;rbs_motif=None;rbs_spacer=None;gc_cont=0.530;conf=100.00;score=109.07;cscore=105.85;sscore=3.22;rscore=0.00;uscore=0.00;tscore=3.22;
-this_is_genome2_contig_number1_1	Prodigal_v2.6.3	CDS	857	2260	130.8	+	0	ID=1_2;partial=00;start_type=ATG;rbs_motif=None;rbs_spacer=None;gc_cont=0.510;conf=100.00;score=130.80;cscore=138.51;sscore=-7.71;rscore=-8.50;uscore=-3.16;tscore=3.95;
-# Sequence Data: seqnum=2;seqlen=3295;seqhdr="this_is_genome2_contig_number1_2"
-# Model Data: version=Prodigal.v2.6.3;run_type=Metagenomic;model="20|Escherichia_coli_UMN026|B|50.7|11|1";gc_cont=50.70;transl_table=11;uses_sd=1
-this_is_genome2_contig_number1_2	Prodigal_v2.6.3	CDS	1	252	25.2	+	0	ID=2_1;partial=10;start_type=Edge;rbs_motif=None;rbs_spacer=None;gc_cont=0.540;conf=99.70;score=25.25;cscore=22.03;sscore=3.22;rscore=0.00;uscore=0.00;tscore=3.22;
-this_is_genome2_contig_number1_2	Prodigal_v2.6.3	CDS	301	681	42.0	+	0	ID=2_2;partial=00;start_type=ATG;rbs_motif=None;rbs_spacer=None;gc_cont=0.530;conf=99.99;score=42.75;cscore=48.52;sscore=-5.77;rscore=-8.50;uscore=-1.97;tscore=3.95;
-this_is_genome2_contig_number1_2	Prodigal_v2.6.3	CDS	764	1597	93.2	+	0	ID=2_3;partial=00;start_type=ATG;rbs_motif=None;rbs_spacer=None;gc_cont=0.573;conf=100.00;score=93.20;cscore=101.05;sscore=-7.85;rscore=-8.50;uscore=-3.30;tscore=3.95;
-this_is_genome2_contig_number1_2	Prodigal_v2.6.3	CDS	1628	3295	276.3	+	0	ID=2_4;partial=00;start_type=ATG;rbs_motif=GGA/GAG/AGG;rbs_spacer=5-10bp;gc_cont=0.537;conf=99.99;score=277.27;cscore=270.94;sscore=6.32;rscore=2.79;uscore=-1.36;tscore=3.95;
-# Sequence Data: seqnum=3;seqlen=2263;seqhdr="this_is_genome2_contig_number2_3"
-# Model Data: version=Prodigal.v2.6.3;run_type=Metagenomic;model="20|Escherichia_coli_UMN026|B|50.7|11|1";gc_cont=50.70;transl_table=11;uses_sd=1
-this_is_genome2_contig_number2_3	Prodigal_v2.6.3	CDS	30	797	58.3	+	0	ID=3_1;partial=00;start_type=GTG;rbs_motif=GGA/GAG/AGG;rbs_spacer=5-10bp;gc_cont=0.540;conf=100.00;score=58.32;cscore=63.52;sscore=-5.21;rscore=2.79;uscore=-1.37;tscore=-6.63;
-this_is_genome2_contig_number2_3	Prodigal_v2.6.3	CDS	862	1122	22.1	+	0	ID=3_2;partial=00;start_type=ATG;rbs_motif=GGA/GAG/AGG;rbs_spacer=5-10bp;gc_cont=0.487;conf=99.38;score=22.10;cscore=13.73;sscore=8.37;rscore=2.79;uscore=1.62;tscore=3.95;
-this_is_genome2_contig_number2_3	Prodigal_v2.6.3	CDS	1170	1751	51.0	+	0	ID=3_3;partial=00;start_type=ATG;rbs_motif=None;rbs_spacer=None;gc_cont=0.546;conf=100.00;score=51.73;cscore=58.14;sscore=-6.42;rscore=-8.50;uscore=-2.63;tscore=3.95;
-this_is_genome2_contig_number2_3	Prodigal_v2.6.3	CDS	1895	2263	34.8	+	0	ID=3_4;partial=00;start_type=ATG;rbs_motif=GGAG/GAGG;rbs_spacer=5-10bp;gc_cont=0.599;conf=99.97;score=34.83;cscore=22.60;sscore=12.23;rscore=11.19;uscore=-2.91;tscore=3.95;
-# Sequence Data: seqnum=4;seqlen=2845;seqhdr="this_is_genome2_contig_number3_4"
-# Model Data: version=Prodigal.v2.6.3;run_type=Metagenomic;model="20|Escherichia_coli_UMN026|B|50.7|11|1";gc_cont=50.70;transl_table=11;uses_sd=1
-this_is_genome2_contig_number3_4	Prodigal_v2.6.3	CDS	1	1308	169.7	+	0	ID=4_1;partial=10;start_type=Edge;rbs_motif=None;rbs_spacer=None;gc_cont=0.519;conf=100.00;score=169.75;cscore=166.53;sscore=3.22;rscore=0.00;uscore=0.00;tscore=3.22;
-this_is_genome2_contig_number3_4	Prodigal_v2.6.3	CDS	1340	1804	33.2	+	0	ID=4_2;partial=00;start_type=ATG;rbs_motif=None;rbs_spacer=None;gc_cont=0.594;conf=99.96;score=34.14;cscore=41.34;sscore=-7.21;rscore=-8.50;uscore=-3.59;tscore=3.95;
-this_is_genome2_contig_number3_4	Prodigal_v2.6.3	CDS	1832	2845	78.4	+	0	ID=4_3;partial=00;start_type=ATG;rbs_motif=None;rbs_spacer=None;gc_cont=0.456;conf=100.00;score=79.42;cscore=85.62;sscore=-6.20;rscore=-8.50;uscore=-2.63;tscore=3.95;
-# Sequence Data: seqnum=5;seqlen=6;seqhdr="genome2_small_5"
-# Model Data: version=Prodigal.v2.6.3;run_type=Metagenomic;model="0|Mycoplasma_bovis_PG45|B|29.3|4|1";gc_cont=29.30;transl_table=4;uses_sd=1
diff --git a/Examples/2-res-Annotate-prodigal/tmp_files/genome3-chromo.fst-all.fna b/Examples/2-res-Annotate-prodigal/tmp_files/genome3-chromo.fst-all.fna
deleted file mode 100644
index 35d4e193748f3c3fa8abcaa61bc65ae4cae8054f..0000000000000000000000000000000000000000
--- a/Examples/2-res-Annotate-prodigal/tmp_files/genome3-chromo.fst-all.fna
+++ /dev/null
@@ -1,25 +0,0 @@
->header_genome3_chromo
-ATGAGAGCGCTACTGTGGCTGGTGGGTCTTGCGTTGCTGTTAACAGGCTGCGCGAGCGAAAAAGGAATTATCGATGAAGAGGGATATCAGCTTGATACCCGACATCGGGCGCAGGCGGCCTATCCGCGCATTAAAGTCCTGGTGATTCACTATACGGCGGAAAACTTTGACGTTTCGCTGGCGACGTTAACGGGCCGCAACGTCAGTTCGCATTACCTGATTCCCGCAACCCCGCCATTATATGGCGGTAAACCGCGCATCTGGCAACTGGTGCCGGAACAGGATCAGGCCTGGCATGCGGGCGTCAGTTTCTGGCGAGGCGCCACGCGTCTCAATGATACGTCTATTGGCATTGAGCTGGAAAATCGCGGCTGGCGAATGTCCGGCGGGGTGAAATCTTTCGCGCCGTTTGAATCCGCGCAAATTCAGGCATTGATTCCGTTAGCGAAGGACATTATCGCGCGCTATGACATCAAACCGCAGAATGTGGTGGCCCATGCGGATATCGCGCCGCAGCGTAAAGACGATCCCGGCCCGCGCTTCCCGTGGCGCGAGCTGGCGGCACAGGGGATTGGCGCCTGGCCTGACGCCCAGCGTGTGGCGTTTTATCTGGCTGGACGCGCGCCGTATACGCCAGTCGATACCGCAACGGTGCTTGCGTTACTCTCGCGCTATGGCTATGAAGTCAAAGCCGATATGACGGCGCGCGAGCAACAGCGGGTGATTATGGCGTTCCAGATGCACTTCCGTCCGGCGCAATGGAACGGTATCGCAGATGCCGAAACGCAGGCGATTGCCGAAGCATTACTGGAGAAGTACGGCCAGGATTAA
-CGAGTCCGGGAGCGGCGAGATTCCGGGCAGAGGAGGCGGCTATAGCGG
-ATGAGAGCGCTACTGTGGCTGGTGGGTCTTGCGTTGCTGTTAACAGGCTGCGCGAGCGAAAAAGGAATTATCGATGAAGAGGGATATCAGCTTGATACCCGACATCGGGCGCAGGCGGCCTATCCGCGCATTAAAGTCCTGGTGATTCACTATACGGCGGAAAACTTTGACGTTTCGCTGGCGACGTTAACGGGCCGCAACGTCAGTTCGCATTACCTGATTCCCGCAACCCCGCCATTATATGGCGGTAAACCGCGCATCTGGCAACTGGTGCCGGAACAGGATCAGGCCTGGCATGCGGGCGTCAGTTTCTGGCGAGGCGCCACGCGTCTCAATGATACGTCTATTGGCATTGAGCTGGAAAATCGCGGCTGGCGAATGTCCGGCGGGGTGAAATCTTTCGCGCCGTTTGAATCCGCGCAAATTCAGGCATTGATTCCGTTAGCGAAGGACATTATCGCGCGCTATGACATCAAACCGCAGAATGTGGTGGCCCATGCGGATATCGCGCCGCAGCGTAAAGACGATCCCGGCCCGCGCTTCCCGTGGCGCGAGCTGGCGGCACAGGGGATTGGCGCCTGGCCTGACGCCCAGCGTGTGGCGTTTTATCTGGCTGGACGCGCGCCGTATACGCCAGTCGATACCGCAACGGTGCTTGCGTTACTCTCGCGCTATGGCTATGAAGTCAAAGCCGATATGACGGCGCGCGAGCAACAGCGGGTGATTATGGCGTTCCAGATGCACTTCCGTCCGGCGCAATGGAACGGTATCGCAGATGCCGAAACGCAGGCGATTGCCGAAGCATTACTGGAGAAGTACGGCCAGGATTAA
-CAGGGCGCGGTATCGCGAGGACTCTCTCTTCGAGGAC
-ATGCCGCACTTTATTGCTGAATGTACTGAAAATATTCGCGAGCAGGCTGATTTACCCGGCCTGTTCAGCAAGGTAAACGAGGCGCTGGCCGCCAGCGGGATTTTCCCCATCGGCGGTATCCGCAGTCGCGCCCACTGGCTGGATACCTGGCAGATGGCTGACGGTAAGCATGATTACGCGTTTGTGCATATGACGCTGAAAATCGGCGCCGGGCGCAGCCTGGAGAGCCGTCAGGAAGTCGGCGAAATGCTGTTCGGGCTGATTAAAGCCCACTTCGCCGACCTGATGGAGAACCGCTATCTGGCGCTGTCGTTTGAGATTGCCGAGTTACATCCAACGCTCAATTACAAACAAAACAACGTACACGCGTTATTTAAATAG
-CCCGAGTATTAGCGCGCGGCGGCGCTATAGGCGCGCTATAGGC
-ATGAGCGCGCTATTTCTGGCCATCCCGTTAACCATTTTTGTGTTGTTTGTGTTACCGATTTGGCTGTGGCTGCATTACAGCAACCGCGCCGGTCGGGGAGAACTGTCGCAAAGCGAGCAGCAACGCTTACTGCAACTCACAGACGACGCGCAACGTATGCGCGAGCGCATTCAGGCGCTGGAAGACATTCTTGATGCAGAGCATCCGAACTGGAGAGAGCGCTAA
-CGAGAGTCTCGGAGGAGCGGCGCTCTGg
-ATGCCCGCGACTAAATTCTCCCGACGTACCCTCCTGACGGCAGGTTCTGCGCTTGCTGTTCTTCCTTTCCTGCGCGCCTTGCCGGTACAGGCGCGTGAACCTCGCGAGACCGTCGATATTAAGGATTATCCGGCGGATGACGGTATCGCCTCGTTCAAACAGGCCTTCGCCGACGGACAGACCGTGGTCGTACCGCCAGGATGGGTGTGTGAAAATATCAATGCGGCGATAACGATTCCGGCGGGAAAAACGCTGCGGGTACAGGGCGCGGTGCGTGGGAATGGCCGGGGACGGTTTATTTTGCAGGACGGGTGTCAGGTGGTGGGGGAGCAGGGCGGCAGTCTGCACAATGTGACGCTGGATGTTCGCGGGTCGGACTGTGTGATTAAAGGCGTGGCGATGAGCGGCTTTGGCCCCGTCGCGCAAATTTTCATCGGTGGTAAGGAACCGCAGGTGATGCGTAATCTCATTATCGATGACATCACCGTTACCCACGCCAACTACGCCATTCTCCGCCAGGGATTTCATAACCAAATGGACGGCGCGAGGATTACGCATAGCCGCTTTAGCGATTTACAGGGGGACGCCATTGAGTGGAATGTCGCGATTCACGACCGCGATATCCTGATTTCCGATCATGTCATCGAACGCATTGATTGTACCAATGGCAAAATCAACTGGGGGATCGGCATCGGGCTGGCGGGTAGCACCTATGACAACAGTTATCCTGAAGACCAGGCAGTAAAAAACTTTGTGGTGGCCAATATTACCGGATCTGATTGCCGACAGCTTGTGCACGTAGAAAATGGCAAACATTTCGTCATTCGCAATGTCAAAGCCAAAAACATCACGCCCGATTTCAGTAAAAATGCGGGTATTGATAACGCAACGATCGCAATTTATGGCTGTGATAATTTCGTCATTGATAATATTGATATGACGAATAGTGCCGGGATGCTCATCGGCTATGGCGTCGTTAAAGGAAAATACCTGTCAATTCCGCAAAACTTTAAATTAAACGCTATTCGGTTGGATAATCGCCAGGTTGCTTATAAATTACGCGGCATTCAAATTTCCTCCGGCAACACCCCCTCTTTTGTCGCCATCACCAATGTACGGATGACGCGTGCTACGCTGGAACTGCATAATCAACCGCAGCACCTCTTCCTGCGTAATATCAACGTGATGCAAACTTCAGCGATTGGCCCGGCGTTAAAAATGCATTTCGATTTGCGTAAAGATGTCCGTGGTCAATTTATGGCCCGCCAGGACACGCTGCTTTCCCTCGCTAATGTTCATGCCATCAATGAAAACGGGCAGAGTTCCGTGGATATCGACAGGATTAATCACCAAACCGTGAATGTCGAAGCAGTGAATTTTTCGCTGCCGAAGCGGGGAGGGTAA
-CGCGTCTGCGCGCGCGGAGAGAGGCTCTCAGGAC
-ATGTCAGAAAATAAATTACACGTTATCGATTTGCACAAACGCTACGGCGGTCATGAAGTGCTGAAAGGGGTATCGCTGCAGGCCCGCGCCGGAGATGTGATTAGCATCATCGGCTCGTCCGGCTCCGGTAAAAGCACTTTTTTGCGCTGTATTAACTTCCTCGAAAAACCGAGCGAAGACGCGATTATCGTGAACGGTCAGAACATTAATCTGGTGCGCGACAAAGACGGGCAGCTCAAAGTGGCGGATAAAAATCAGCTACGCTTGTTGCGTACCCGCCTGACGATGGTGTTTCAGCACTTTAACCTCTGGAGCCACATGACGGTGCTGGAAAATGTGATGGAAGCGCCGATTCAGGTACTGGGATTAAGCAAGCACGACGCGCGCGAGCGGGCGTTGAAATATCTGGCGAAGGTGGGGATTGATGAGCGCGCTCAGGGCAAATATCCCGTTCATCTCTCCGGTGGCCAACAGCAGCGCGTTTCTATTGCGCGCGCGCTGGCGATGGAACCTGACGTTTTACTGTTCGATGAACCCACTTCGGCGCTCGATCCTGAACTGGTCGGCGAAGTGTTGCGCATCATGCAACAACTGGCGGAAGAAGGCAAAACGATGGTGGTGGTCACGCATGAAATGGGCTTCGTTCGCCATGTCTCTTCGCACGTTATTTTTCTGCATCAGGGGAAAATTGAAGAAGAGGGCGATCCGGAGCAGGTGTTCGGCAATCCGCAAAGCCCGCGTTTACAGCAATTCCTGAAAGGCTCGCTGAAATAA
-CCGGATGCGCGCGATATATCGGCGATGC
-GTGTTTATTGGCATCGTTAGCCTGTTTCCTGAAATGTTCCGCGCAATTACCGATTACGGGGTAACTGGCCGGGCAGTAAAAAATGGCCTGCTGAACATCCAAAGCTGGAGTCCTCGCGACTTCACGCATGACCGGCACCGTACCGTGGACGATCGTCCTTACGGCGGCGGACCAGGGATGTTAATGATGGTGCAACCCTTGCGGGACGCCATTCACGCAGCAAAAGCCGCGGCAGGTGAAGGCGCTAAAGTGATTTATCTGTCGCCTCAGGGACGCAAGCTTGATCAAGCGGGCGTTAGCGAGCTGGCCACGAATCAGAAGCTTATTCTGGTGTGTGGTCGCTACGAAGGCGTAGATGAGCGCGTAATTCAGACCGAAATTGACGAAGAATGGTCAATTGGCGATTACGTTCTCAGCGGTGGCGAACTACCGGCAATGACGCTGATTGACTCCGTCGCCCGGTTTATACCGGGAGTTCTGGGGCATGAAGCATCAGCAATCGAAGATTCGTTTGCTGATGGGTTGCTGGATTGTCCGCACTATACGCGCCCTGAAGTGTTAGAGGGGATGGAAGTACCGCCAGTATTGCTGTCGGGAAACCATGCTGAGATACGTCGCTGGCGTTTGAAACAGTCGCTGGGCCGAACCTGGCTTAGAAGACCTGAACTTCTGGAAAACCTGGCTCTGACTGAAGAGCAAGCAAGGTTGCTGGCGGAGTTCAAAACAGAACACGCACAACAGCAGCATAAACATGATGGGATGGCATAG
-CCGGCTCTGCGAGAGAGGAGCGCTCGC
-ATGAATAATCATTTTGGGAAAGGGTTAATGGCCGGGTTGCACGCGCCATATGCATATAGCGCGCATCATGCGGTGAATTTCTGTTCTGAGTATAAACGTGGCTTTGTATTGGGTTTTACACACCGTATGTTCGAAAAGACCGGCGATCGTCAACTTAGCGCGTGGGAGGCTGGAATTCTGACGCGTCGCTATGGTCTGGATAAAGAAATGGTGATGGATTTCTTTAAAGAGAATCATTCCGGGATGGCGGTTCGCTTCTTTATGGCCGGTTATCGACTCGAAGGTTGA
-
->genome3_plasmid
-ATGTCTACGCTTCTCTATTTGCACGGATTCAACAGTTCCCCTCGCTCGGCAAAAGCGTGCCAGCTAAAAAACTGGCTGGCGGAGCGTCATCCGCATGTTGAGATGATCGTCCCTCAACTACCGCCGTATCCTGCCGATGCGGCGGAGTTGCTGGAGTCTCTCGTGCTTGAGCATGGCGGTGCGCCATTAGGGCTGGTAGGATCGTCGCTGGGTGGTTATTACGCCACCTGGCTGTCGCAATGTTTTATGCTGCCGGCTGTGGTGGTGAATCCCGCCGTGCGGCCCTTTGAATTACTGACCGACTATCTCGGTCAGAACGAGAACCCCTACACCGGGCAGCAATATGTGCTAGAGTCTCGCCATATTTATGATCTTAAAGTCATGCAGATTGACCCGCTGGAAGCGCCGGACCTGATCTGGCTACTGCAACAGACGGGCGATGAAGTGCTGGATTACCGCCAGGCGGTGGCATATTACGCCTCCTGCCGTCAGACAGTGACCGAGGGTGGTAATCACGCATTCACGGGCTTCGAAGATTATTTCAACCAGATTGTCGATTTTCTTGGACTGCACAGTTGCTGA
-CGCGTAGCGGCCGGAATCTTCTCGGAGAGGCGCTTCTCTCTCGGAG
-ATGATTGACCCTATTTTTGCGTCCTGTACGCTAATTGCCGTCTTTGTTGTTTTACTGGCCATGGGCGCGCCTATCGGGATCTGCATCGTTATCGCCTCTTTCAGCACCATGATGCTGGTACTGCCTTTCGATATTTCGATGTTCGCCACCGCGCAAAAAATGTTCTCCAGCCTGGACAGTTTTGCCTTGCTGGCCGTGCCGTTCTTCGTTTTGTCCGGGGTGATCATGAATAGCGGGGGAATTGCCGCCCGGCTGATCAATTTTGCCAAACTGTTTACTGGCAAACTGCCCGGTTCGCTCTCTTATACCAACATCGTCGGCAATATGATGTTCGGTGCAATTTCCGGATCGGCAATTGCCGCCTCAACCTCCATCGGCGGCGTGATGGTGCCGATGAGCGCGCGCGAAGGTTACGATCGCGGCTTTGCGGCCGCGGTGAATATCGCCTCCGCGCCGACGGGAATGTTAATTCCGCCCACCACGGCTTTTATCCTTTATGCGCTGGCAAGCGGGGGAACATCGATTGCCGCTCTGTTCGCCGGCGGTCTGGTCGCGGGAGTGCTGTGGGGCGTTGGCTGTATGCTGGTCACGCTGGTAGTCGCTAAGCGTCGAAATTATCGGGTTTTCTTCACCGTCCAAAAAGGCATGGCGCTAAAAGTTGCCGTTGAGGCCATTCCCAGCCTGTTACTGATCGTGATTATCGTCGGCGGCATTGTGCAGGGGATTTTCACCGCCATTGAAGCCTCCGCGATTGCCGTGGTGTATACGTTATTGCTGACGATGGTGTTTTACCGCACGCTGAAAATTAAGGATTTGCCTTCGATTTTGCTCCAGACAGTGGTAATGACCGGGGTCATCATGTTCCTGCTGGCAACCTCTTCGGCGATGTCCTTCTCAATGTCGATCACCAATATTCCTGCGGCGCTGAGCGATATGATCCTCGGTATTTCCGCCAATAAACTGGTTATCCTGTTAGTCATTACCGTCTTTTTGTTGATTATCGGCGCATTTATGGATATCGGTCCGGCCATTCTGATTTTTACCCCGATTCTGCTGCCGATCATGGCTAAACTGGGCGTCGATCCGGTGCATTTGGGCATTATCATGATCTATAACCTGGCGATTGGCACCATTACGCCGCCAGTTGGCAGTGGTTTATATGTCGGGGCGAGCGTCGGTAAGGTCAAAGTTGAGGAAGTGATTAAACCGTTGCTGCCTTTTTACGGCGCGATTATCGGCGTTCTGTTATTAATTACCTACATTCCGGAAATCATACTGTTCTTACCCCGTCTACTGGGCATCATGTAA
-ACCCGATGGCGCGCAGAGGCGCGAGTTCTGGANNNNNNCACAGGGCTTAGAGGCGCTATGGCA
-ATGATAATTAATGGGAAATTAATTAAAGCAAAAGACTTAGCTAAGGCTGCAGGTGTATCTCGTTCAACAGTGATTAAATATTACGGCATTAGCCGTGAGAATTACGAAAGGGTAGCAACTGAAAGAAGGAAGCTTGCTTTTGAACTAAGAGCATCAGGTTTAAAATGGAAAGAAGTTGCTGAAAAAATGAACACGACAAAATATAGCGCAATTGCATATTATAGACGATATTTAGCATTAGAGAAAAACAAATAA
-CAGGCGCTAAGGCGGCGATCCTAGCGCGCGATCGCGCATGCG
-ATGGTCGAACTGCAACATCAACGGCTGATGGTGCTTGCCGAACAGCTCCAGCTGGACAGTCTTATCGGCGCAGCGCCGGCGCTGTCGCAACAGGCGGTGGATCAGGAATGGAGCTACATGGACTTCCTGGAGCACCTGTTACATGAGGAGAAACTGGCCCGGCATCAGCGTAAACAGGCGATGTACACGCGGATGGCAGCCTTCCCGGCGGTAAAGACGTTCGAGGAGTACGACTTCACCTTCGCCACCGGCGCTCCTCAGAAGCAAATCCAGTCGCTGCGATCCCTGAGCTTCATAGAGCGTAACGAAAACATCGTGTTGCTGGGGCCATCGGGCGTGGGAAAAACGCATCTGGCGATAGCCATGGGCTACGAAGCAGTACGGGCGGGCATCAAGGTTCGCTTCACAACAGCAGCGGACCTGCTGCTACAGCTGTCCACTTCACAGCGTCAGGGCCGTTACAAAACGACTCTCAATCGTGGTGTCATGGCCCCGAAGCTGCTTATCATCGATGAAATAGGTTATCTGCCGTTCAGTCAGGAGGAAGCCAAGCTGTTCTTCCAGGTCATCGCCAAACGTTACGAGAAGAGCGCGATGATCCTGACCTCCAACCTGCCGTTCGGGCAGTGGGATCAGACGTTCGCCGGTGATGCAGCGCTGACATCGGCGATGCTGGACCGGATCTTACATCACTCACACGTCGTGCAAATAAAAGGGGAAAGCTATCGACTGAAGCAGAAACGAAAGGCCGGGGTTATAGCTGAAGCTAATCCTGAGTAA
\ No newline at end of file
diff --git a/Examples/2-res-Annotate-prodigal/tmp_files/genome3-chromo.fst-all.fna_prodigal-split5N.fna b/Examples/2-res-Annotate-prodigal/tmp_files/genome3-chromo.fst-all.fna_prodigal-split5N.fna
deleted file mode 100644
index 18c8b375f71dc4149f4fd9de41b6a6a6fe03ef86..0000000000000000000000000000000000000000
--- a/Examples/2-res-Annotate-prodigal/tmp_files/genome3-chromo.fst-all.fna_prodigal-split5N.fna
+++ /dev/null
@@ -1,6 +0,0 @@
->header_genome3_chromo_1
-ATGAGAGCGCTACTGTGGCTGGTGGGTCTTGCGTTGCTGTTAACAGGCTGCGCGAGCGAAAAAGGAATTATCGATGAAGAGGGATATCAGCTTGATACCCGACATCGGGCGCAGGCGGCCTATCCGCGCATTAAAGTCCTGGTGATTCACTATACGGCGGAAAACTTTGACGTTTCGCTGGCGACGTTAACGGGCCGCAACGTCAGTTCGCATTACCTGATTCCCGCAACCCCGCCATTATATGGCGGTAAACCGCGCATCTGGCAACTGGTGCCGGAACAGGATCAGGCCTGGCATGCGGGCGTCAGTTTCTGGCGAGGCGCCACGCGTCTCAATGATACGTCTATTGGCATTGAGCTGGAAAATCGCGGCTGGCGAATGTCCGGCGGGGTGAAATCTTTCGCGCCGTTTGAATCCGCGCAAATTCAGGCATTGATTCCGTTAGCGAAGGACATTATCGCGCGCTATGACATCAAACCGCAGAATGTGGTGGCCCATGCGGATATCGCGCCGCAGCGTAAAGACGATCCCGGCCCGCGCTTCCCGTGGCGCGAGCTGGCGGCACAGGGGATTGGCGCCTGGCCTGACGCCCAGCGTGTGGCGTTTTATCTGGCTGGACGCGCGCCGTATACGCCAGTCGATACCGCAACGGTGCTTGCGTTACTCTCGCGCTATGGCTATGAAGTCAAAGCCGATATGACGGCGCGCGAGCAACAGCGGGTGATTATGGCGTTCCAGATGCACTTCCGTCCGGCGCAATGGAACGGTATCGCAGATGCCGAAACGCAGGCGATTGCCGAAGCATTACTGGAGAAGTACGGCCAGGATTAACGAGTCCGGGAGCGGCGAGATTCCGGGCAGAGGAGGCGGCTATAGCGGATGAGAGCGCTACTGTGGCTGGTGGGTCTTGCGTTGCTGTTAACAGGCTGCGCGAGCGAAAAAGGAATTATCGATGAAGAGGGATATCAGCTTGATACCCGACATCGGGCGCAGGCGGCCTATCCGCGCATTAAAGTCCTGGTGATTCACTATACGGCGGAAAACTTTGACGTTTCGCTGGCGACGTTAACGGGCCGCAACGTCAGTTCGCATTACCTGATTCCCGCAACCCCGCCATTATATGGCGGTAAACCGCGCATCTGGCAACTGGTGCCGGAACAGGATCAGGCCTGGCATGCGGGCGTCAGTTTCTGGCGAGGCGCCACGCGTCTCAATGATACGTCTATTGGCATTGAGCTGGAAAATCGCGGCTGGCGAATGTCCGGCGGGGTGAAATCTTTCGCGCCGTTTGAATCCGCGCAAATTCAGGCATTGATTCCGTTAGCGAAGGACATTATCGCGCGCTATGACATCAAACCGCAGAATGTGGTGGCCCATGCGGATATCGCGCCGCAGCGTAAAGACGATCCCGGCCCGCGCTTCCCGTGGCGCGAGCTGGCGGCACAGGGGATTGGCGCCTGGCCTGACGCCCAGCGTGTGGCGTTTTATCTGGCTGGACGCGCGCCGTATACGCCAGTCGATACCGCAACGGTGCTTGCGTTACTCTCGCGCTATGGCTATGAAGTCAAAGCCGATATGACGGCGCGCGAGCAACAGCGGGTGATTATGGCGTTCCAGATGCACTTCCGTCCGGCGCAATGGAACGGTATCGCAGATGCCGAAACGCAGGCGATTGCCGAAGCATTACTGGAGAAGTACGGCCAGGATTAACAGGGCGCGGTATCGCGAGGACTCTCTCTTCGAGGACATGCCGCACTTTATTGCTGAATGTACTGAAAATATTCGCGAGCAGGCTGATTTACCCGGCCTGTTCAGCAAGGTAAACGAGGCGCTGGCCGCCAGCGGGATTTTCCCCATCGGCGGTATCCGCAGTCGCGCCCACTGGCTGGATACCTGGCAGATGGCTGACGGTAAGCATGATTACGCGTTTGTGCATATGACGCTGAAAATCGGCGCCGGGCGCAGCCTGGAGAGCCGTCAGGAAGTCGGCGAAATGCTGTTCGGGCTGATTAAAGCCCACTTCGCCGACCTGATGGAGAACCGCTATCTGGCGCTGTCGTTTGAGATTGCCGAGTTACATCCAACGCTCAATTACAAACAAAACAACGTACACGCGTTATTTAAATAGCCCGAGTATTAGCGCGCGGCGGCGCTATAGGCGCGCTATAGGCATGAGCGCGCTATTTCTGGCCATCCCGTTAACCATTTTTGTGTTGTTTGTGTTACCGATTTGGCTGTGGCTGCATTACAGCAACCGCGCCGGTCGGGGAGAACTGTCGCAAAGCGAGCAGCAACGCTTACTGCAACTCACAGACGACGCGCAACGTATGCGCGAGCGCATTCAGGCGCTGGAAGACATTCTTGATGCAGAGCATCCGAACTGGAGAGAGCGCTAACGAGAGTCTCGGAGGAGCGGCGCTCTGGATGCCCGCGACTAAATTCTCCCGACGTACCCTCCTGACGGCAGGTTCTGCGCTTGCTGTTCTTCCTTTCCTGCGCGCCTTGCCGGTACAGGCGCGTGAACCTCGCGAGACCGTCGATATTAAGGATTATCCGGCGGATGACGGTATCGCCTCGTTCAAACAGGCCTTCGCCGACGGACAGACCGTGGTCGTACCGCCAGGATGGGTGTGTGAAAATATCAATGCGGCGATAACGATTCCGGCGGGAAAAACGCTGCGGGTACAGGGCGCGGTGCGTGGGAATGGCCGGGGACGGTTTATTTTGCAGGACGGGTGTCAGGTGGTGGGGGAGCAGGGCGGCAGTCTGCACAATGTGACGCTGGATGTTCGCGGGTCGGACTGTGTGATTAAAGGCGTGGCGATGAGCGGCTTTGGCCCCGTCGCGCAAATTTTCATCGGTGGTAAGGAACCGCAGGTGATGCGTAATCTCATTATCGATGACATCACCGTTACCCACGCCAACTACGCCATTCTCCGCCAGGGATTTCATAACCAAATGGACGGCGCGAGGATTACGCATAGCCGCTTTAGCGATTTACAGGGGGACGCCATTGAGTGGAATGTCGCGATTCACGACCGCGATATCCTGATTTCCGATCATGTCATCGAACGCATTGATTGTACCAATGGCAAAATCAACTGGGGGATCGGCATCGGGCTGGCGGGTAGCACCTATGACAACAGTTATCCTGAAGACCAGGCAGTAAAAAACTTTGTGGTGGCCAATATTACCGGATCTGATTGCCGACAGCTTGTGCACGTAGAAAATGGCAAACATTTCGTCATTCGCAATGTCAAAGCCAAAAACATCACGCCCGATTTCAGTAAAAATGCGGGTATTGATAACGCAACGATCGCAATTTATGGCTGTGATAATTTCGTCATTGATAATATTGATATGACGAATAGTGCCGGGATGCTCATCGGCTATGGCGTCGTTAAAGGAAAATACCTGTCAATTCCGCAAAACTTTAAATTAAACGCTATTCGGTTGGATAATCGCCAGGTTGCTTATAAATTACGCGGCATTCAAATTTCCTCCGGCAACACCCCCTCTTTTGTCGCCATCACCAATGTACGGATGACGCGTGCTACGCTGGAACTGCATAATCAACCGCAGCACCTCTTCCTGCGTAATATCAACGTGATGCAAACTTCAGCGATTGGCCCGGCGTTAAAAATGCATTTCGATTTGCGTAAAGATGTCCGTGGTCAATTTATGGCCCGCCAGGACACGCTGCTTTCCCTCGCTAATGTTCATGCCATCAATGAAAACGGGCAGAGTTCCGTGGATATCGACAGGATTAATCACCAAACCGTGAATGTCGAAGCAGTGAATTTTTCGCTGCCGAAGCGGGGAGGGTAACGCGTCTGCGCGCGCGGAGAGAGGCTCTCAGGACATGTCAGAAAATAAATTACACGTTATCGATTTGCACAAACGCTACGGCGGTCATGAAGTGCTGAAAGGGGTATCGCTGCAGGCCCGCGCCGGAGATGTGATTAGCATCATCGGCTCGTCCGGCTCCGGTAAAAGCACTTTTTTGCGCTGTATTAACTTCCTCGAAAAACCGAGCGAAGACGCGATTATCGTGAACGGTCAGAACATTAATCTGGTGCGCGACAAAGACGGGCAGCTCAAAGTGGCGGATAAAAATCAGCTACGCTTGTTGCGTACCCGCCTGACGATGGTGTTTCAGCACTTTAACCTCTGGAGCCACATGACGGTGCTGGAAAATGTGATGGAAGCGCCGATTCAGGTACTGGGATTAAGCAAGCACGACGCGCGCGAGCGGGCGTTGAAATATCTGGCGAAGGTGGGGATTGATGAGCGCGCTCAGGGCAAATATCCCGTTCATCTCTCCGGTGGCCAACAGCAGCGCGTTTCTATTGCGCGCGCGCTGGCGATGGAACCTGACGTTTTACTGTTCGATGAACCCACTTCGGCGCTCGATCCTGAACTGGTCGGCGAAGTGTTGCGCATCATGCAACAACTGGCGGAAGAAGGCAAAACGATGGTGGTGGTCACGCATGAAATGGGCTTCGTTCGCCATGTCTCTTCGCACGTTATTTTTCTGCATCAGGGGAAAATTGAAGAAGAGGGCGATCCGGAGCAGGTGTTCGGCAATCCGCAAAGCCCGCGTTTACAGCAATTCCTGAAAGGCTCGCTGAAATAACCGGATGCGCGCGATATATCGGCGATGCGTGTTTATTGGCATCGTTAGCCTGTTTCCTGAAATGTTCCGCGCAATTACCGATTACGGGGTAACTGGCCGGGCAGTAAAAAATGGCCTGCTGAACATCCAAAGCTGGAGTCCTCGCGACTTCACGCATGACCGGCACCGTACCGTGGACGATCGTCCTTACGGCGGCGGACCAGGGATGTTAATGATGGTGCAACCCTTGCGGGACGCCATTCACGCAGCAAAAGCCGCGGCAGGTGAAGGCGCTAAAGTGATTTATCTGTCGCCTCAGGGACGCAAGCTTGATCAAGCGGGCGTTAGCGAGCTGGCCACGAATCAGAAGCTTATTCTGGTGTGTGGTCGCTACGAAGGCGTAGATGAGCGCGTAATTCAGACCGAAATTGACGAAGAATGGTCAATTGGCGATTACGTTCTCAGCGGTGGCGAACTACCGGCAATGACGCTGATTGACTCCGTCGCCCGGTTTATACCGGGAGTTCTGGGGCATGAAGCATCAGCAATCGAAGATTCGTTTGCTGATGGGTTGCTGGATTGTCCGCACTATACGCGCCCTGAAGTGTTAGAGGGGATGGAAGTACCGCCAGTATTGCTGTCGGGAAACCATGCTGAGATACGTCGCTGGCGTTTGAAACAGTCGCTGGGCCGAACCTGGCTTAGAAGACCTGAACTTCTGGAAAACCTGGCTCTGACTGAAGAGCAAGCAAGGTTGCTGGCGGAGTTCAAAACAGAACACGCACAACAGCAGCATAAACATGATGGGATGGCATAGCCGGCTCTGCGAGAGAGGAGCGCTCGCATGAATAATCATTTTGGGAAAGGGTTAATGGCCGGGTTGCACGCGCCATATGCATATAGCGCGCATCATGCGGTGAATTTCTGTTCTGAGTATAAACGTGGCTTTGTATTGGGTTTTACACACCGTATGTTCGAAAAGACCGGCGATCGTCAACTTAGCGCGTGGGAGGCTGGAATTCTGACGCGTCGCTATGGTCTGGATAAAGAAATGGTGATGGATTTCTTTAAAGAGAATCATTCCGGGATGGCGGTTCGCTTCTTTATGGCCGGTTATCGACTCGAAGGTTGA
->genome3_plasmid_2
-ATGTCTACGCTTCTCTATTTGCACGGATTCAACAGTTCCCCTCGCTCGGCAAAAGCGTGCCAGCTAAAAAACTGGCTGGCGGAGCGTCATCCGCATGTTGAGATGATCGTCCCTCAACTACCGCCGTATCCTGCCGATGCGGCGGAGTTGCTGGAGTCTCTCGTGCTTGAGCATGGCGGTGCGCCATTAGGGCTGGTAGGATCGTCGCTGGGTGGTTATTACGCCACCTGGCTGTCGCAATGTTTTATGCTGCCGGCTGTGGTGGTGAATCCCGCCGTGCGGCCCTTTGAATTACTGACCGACTATCTCGGTCAGAACGAGAACCCCTACACCGGGCAGCAATATGTGCTAGAGTCTCGCCATATTTATGATCTTAAAGTCATGCAGATTGACCCGCTGGAAGCGCCGGACCTGATCTGGCTACTGCAACAGACGGGCGATGAAGTGCTGGATTACCGCCAGGCGGTGGCATATTACGCCTCCTGCCGTCAGACAGTGACCGAGGGTGGTAATCACGCATTCACGGGCTTCGAAGATTATTTCAACCAGATTGTCGATTTTCTTGGACTGCACAGTTGCTGACGCGTAGCGGCCGGAATCTTCTCGGAGAGGCGCTTCTCTCTCGGAGATGATTGACCCTATTTTTGCGTCCTGTACGCTAATTGCCGTCTTTGTTGTTTTACTGGCCATGGGCGCGCCTATCGGGATCTGCATCGTTATCGCCTCTTTCAGCACCATGATGCTGGTACTGCCTTTCGATATTTCGATGTTCGCCACCGCGCAAAAAATGTTCTCCAGCCTGGACAGTTTTGCCTTGCTGGCCGTGCCGTTCTTCGTTTTGTCCGGGGTGATCATGAATAGCGGGGGAATTGCCGCCCGGCTGATCAATTTTGCCAAACTGTTTACTGGCAAACTGCCCGGTTCGCTCTCTTATACCAACATCGTCGGCAATATGATGTTCGGTGCAATTTCCGGATCGGCAATTGCCGCCTCAACCTCCATCGGCGGCGTGATGGTGCCGATGAGCGCGCGCGAAGGTTACGATCGCGGCTTTGCGGCCGCGGTGAATATCGCCTCCGCGCCGACGGGAATGTTAATTCCGCCCACCACGGCTTTTATCCTTTATGCGCTGGCAAGCGGGGGAACATCGATTGCCGCTCTGTTCGCCGGCGGTCTGGTCGCGGGAGTGCTGTGGGGCGTTGGCTGTATGCTGGTCACGCTGGTAGTCGCTAAGCGTCGAAATTATCGGGTTTTCTTCACCGTCCAAAAAGGCATGGCGCTAAAAGTTGCCGTTGAGGCCATTCCCAGCCTGTTACTGATCGTGATTATCGTCGGCGGCATTGTGCAGGGGATTTTCACCGCCATTGAAGCCTCCGCGATTGCCGTGGTGTATACGTTATTGCTGACGATGGTGTTTTACCGCACGCTGAAAATTAAGGATTTGCCTTCGATTTTGCTCCAGACAGTGGTAATGACCGGGGTCATCATGTTCCTGCTGGCAACCTCTTCGGCGATGTCCTTCTCAATGTCGATCACCAATATTCCTGCGGCGCTGAGCGATATGATCCTCGGTATTTCCGCCAATAAACTGGTTATCCTGTTAGTCATTACCGTCTTTTTGTTGATTATCGGCGCATTTATGGATATCGGTCCGGCCATTCTGATTTTTACCCCGATTCTGCTGCCGATCATGGCTAAACTGGGCGTCGATCCGGTGCATTTGGGCATTATCATGATCTATAACCTGGCGATTGGCACCATTACGCCGCCAGTTGGCAGTGGTTTATATGTCGGGGCGAGCGTCGGTAAGGTCAAAGTTGAGGAAGTGATTAAACCGTTGCTGCCTTTTTACGGCGCGATTATCGGCGTTCTGTTATTAATTACCTACATTCCGGAAATCATACTGTTCTTACCCCGTCTACTGGGCATCATGTAAACCCGATGGCGCGCAGAGGCGCGAGTTCTGGA
->genome3_plasmid_3
-CACAGGGCTTAGAGGCGCTATGGCAATGATAATTAATGGGAAATTAATTAAAGCAAAAGACTTAGCTAAGGCTGCAGGTGTATCTCGTTCAACAGTGATTAAATATTACGGCATTAGCCGTGAGAATTACGAAAGGGTAGCAACTGAAAGAAGGAAGCTTGCTTTTGAACTAAGAGCATCAGGTTTAAAATGGAAAGAAGTTGCTGAAAAAATGAACACGACAAAATATAGCGCAATTGCATATTATAGACGATATTTAGCATTAGAGAAAAACAAATAACAGGCGCTAAGGCGGCGATCCTAGCGCGCGATCGCGCATGCGATGGTCGAACTGCAACATCAACGGCTGATGGTGCTTGCCGAACAGCTCCAGCTGGACAGTCTTATCGGCGCAGCGCCGGCGCTGTCGCAACAGGCGGTGGATCAGGAATGGAGCTACATGGACTTCCTGGAGCACCTGTTACATGAGGAGAAACTGGCCCGGCATCAGCGTAAACAGGCGATGTACACGCGGATGGCAGCCTTCCCGGCGGTAAAGACGTTCGAGGAGTACGACTTCACCTTCGCCACCGGCGCTCCTCAGAAGCAAATCCAGTCGCTGCGATCCCTGAGCTTCATAGAGCGTAACGAAAACATCGTGTTGCTGGGGCCATCGGGCGTGGGAAAAACGCATCTGGCGATAGCCATGGGCTACGAAGCAGTACGGGCGGGCATCAAGGTTCGCTTCACAACAGCAGCGGACCTGCTGCTACAGCTGTCCACTTCACAGCGTCAGGGCCGTTACAAAACGACTCTCAATCGTGGTGTCATGGCCCCGAAGCTGCTTATCATCGATGAAATAGGTTATCTGCCGTTCAGTCAGGAGGAAGCCAAGCTGTTCTTCCAGGTCATCGCCAAACGTTACGAGAAGAGCGCGATGATCCTGACCTCCAACCTGCCGTTCGGGCAGTGGGATCAGACGTTCGCCGGTGATGCAGCGCTGACATCGGCGATGCTGGACCGGATCTTACATCACTCACACGTCGTGCAAATAAAAGGGGAAAGCTATCGACTGAAGCAGAAACGAAAGGCCGGGGTTATAGCTGAAGCTAATCCTGAGTAA
diff --git a/Examples/2-res-Annotate-prodigal/tmp_files/genome3-chromo.fst-all.fna_prodigal-split5N.fna-prodigal.log b/Examples/2-res-Annotate-prodigal/tmp_files/genome3-chromo.fst-all.fna_prodigal-split5N.fna-prodigal.log
deleted file mode 100644
index e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
diff --git a/Examples/2-res-Annotate-prodigal/tmp_files/genome3-chromo.fst-all.fna_prodigal-split5N.fna-prodigal.log.err b/Examples/2-res-Annotate-prodigal/tmp_files/genome3-chromo.fst-all.fna_prodigal-split5N.fna-prodigal.log.err
deleted file mode 100644
index e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
diff --git a/Examples/2-res-Annotate-prodigal/tmp_files/genome3-chromo.fst-all.fna_prodigal-split5N.fna-prodigalRes/EXAM.1216.00002.faa b/Examples/2-res-Annotate-prodigal/tmp_files/genome3-chromo.fst-all.fna_prodigal-split5N.fna-prodigalRes/EXAM.1216.00002.faa
deleted file mode 100644
index f037a2a7a2b4ae28c0de23baea7d7b6f4fd14cbc..0000000000000000000000000000000000000000
--- a/Examples/2-res-Annotate-prodigal/tmp_files/genome3-chromo.fst-all.fna_prodigal-split5N.fna-prodigalRes/EXAM.1216.00002.faa
+++ /dev/null
@@ -1,66 +0,0 @@
->header_genome3_chromo_1_1 # 1 # 831 # 1 # ID=1_1;partial=10;start_type=Edge;rbs_motif=None;rbs_spacer=None;gc_cont=0.578
-MRALLWLVGLALLLTGCASEKGIIDEEGYQLDTRHRAQAAYPRIKVLVIHYTAENFDVSL
-ATLTGRNVSSHYLIPATPPLYGGKPRIWQLVPEQDQAWHAGVSFWRGATRLNDTSIGIEL
-ENRGWRMSGGVKSFAPFESAQIQALIPLAKDIIARYDIKPQNVVAHADIAPQRKDDPGPR
-FPWRELAAQGIGAWPDAQRVAFYLAGRAPYTPVDTATVLALLSRYGYEVKADMTAREQQR
-VIMAFQMHFRPAQWNGIADAETQAIAEALLEKYGQD*
->header_genome3_chromo_1_2 # 880 # 1710 # 1 # ID=1_2;partial=00;start_type=ATG;rbs_motif=AGGAG/GGAGG;rbs_spacer=11-12bp;gc_cont=0.578
-MRALLWLVGLALLLTGCASEKGIIDEEGYQLDTRHRAQAAYPRIKVLVIHYTAENFDVSL
-ATLTGRNVSSHYLIPATPPLYGGKPRIWQLVPEQDQAWHAGVSFWRGATRLNDTSIGIEL
-ENRGWRMSGGVKSFAPFESAQIQALIPLAKDIIARYDIKPQNVVAHADIAPQRKDDPGPR
-FPWRELAAQGIGAWPDAQRVAFYLAGRAPYTPVDTATVLALLSRYGYEVKADMTAREQQR
-VIMAFQMHFRPAQWNGIADAETQAIAEALLEKYGQD*
->header_genome3_chromo_1_3 # 1655 # 2128 # 1 # ID=1_3;partial=00;start_type=ATG;rbs_motif=GGA/GAG/AGG;rbs_spacer=11-12bp;gc_cont=0.544
-MPKRRRLPKHYWRSTARINRARYREDSLFEDMPHFIAECTENIREQADLPGLFSKVNEAL
-AASGIFPIGGIRSRAHWLDTWQMADGKHDYAFVHMTLKIGAGRSLESRQEVGEMLFGLIK
-AHFADLMENRYLALSFEIAELHPTLNYKQNNVHALFK*
->header_genome3_chromo_1_4 # 2172 # 2396 # 1 # ID=1_4;partial=00;start_type=ATG;rbs_motif=GGA/GAG/AGG;rbs_spacer=11-12bp;gc_cont=0.542
-MSALFLAIPLTIFVLFVLPIWLWLHYSNRAGRGELSQSEQQRLLQLTDDAQRMRERIQAL
-EDILDAEHPNWRER*
->header_genome3_chromo_1_5 # 2425 # 3828 # 1 # ID=1_5;partial=00;start_type=ATG;rbs_motif=AGGAG/GGAGG;rbs_spacer=11-12bp;gc_cont=0.513
-MPATKFSRRTLLTAGSALAVLPFLRALPVQAREPRETVDIKDYPADDGIASFKQAFADGQ
-TVVVPPGWVCENINAAITIPAGKTLRVQGAVRGNGRGRFILQDGCQVVGEQGGSLHNVTL
-DVRGSDCVIKGVAMSGFGPVAQIFIGGKEPQVMRNLIIDDITVTHANYAILRQGFHNQMD
-GARITHSRFSDLQGDAIEWNVAIHDRDILISDHVIERIDCTNGKINWGIGIGLAGSTYDN
-SYPEDQAVKNFVVANITGSDCRQLVHVENGKHFVIRNVKAKNITPDFSKNAGIDNATIAI
-YGCDNFVIDNIDMTNSAGMLIGYGVVKGKYLSIPQNFKLNAIRLDNRQVAYKLRGIQISS
-GNTPSFVAITNVRMTRATLELHNQPQHLFLRNINVMQTSAIGPALKMHFDLRKDVRGQFM
-ARQDTLLSLANVHAINENGQSSVDIDRINHQTVNVEAVNFSLPKRGG*
->header_genome3_chromo_1_6 # 3863 # 4636 # 1 # ID=1_6;partial=00;start_type=ATG;rbs_motif=GGAG/GAGG;rbs_spacer=5-10bp;gc_cont=0.527
-MSENKLHVIDLHKRYGGHEVLKGVSLQARAGDVISIIGSSGSGKSTFLRCINFLEKPSED
-AIIVNGQNINLVRDKDGQLKVADKNQLRLLRTRLTMVFQHFNLWSHMTVLENVMEAPIQV
-LGLSKHDARERALKYLAKVGIDERAQGKYPVHLSGGQQQRVSIARALAMEPDVLLFDEPT
-SALDPELVGEVLRIMQQLAEEGKTMVVVTHEMGFVRHVSSHVIFLHQGKIEEEGDPEQVF
-GNPQSPRLQQFLKGSLK*
->header_genome3_chromo_1_7 # 4641 # 5432 # 1 # ID=1_7;partial=00;start_type=ATG;rbs_motif=None;rbs_spacer=None;gc_cont=0.537
-MRAIYRRCVFIGIVSLFPEMFRAITDYGVTGRAVKNGLLNIQSWSPRDFTHDRHRTVDDR
-PYGGGPGMLMMVQPLRDAIHAAKAAAGEGAKVIYLSPQGRKLDQAGVSELATNQKLILVC
-GRYEGVDERVIQTEIDEEWSIGDYVLSGGELPAMTLIDSVARFIPGVLGHEASAIEDSFA
-DGLLDCPHYTRPEVLEGMEVPPVLLSGNHAEIRRWRLKQSLGRTWLRRPELLENLALTEE
-QARLLAEFKTEHAQQQHKHDGMA*
->header_genome3_chromo_1_8 # 5460 # 5747 # 1 # ID=1_8;partial=00;start_type=ATG;rbs_motif=AGGAG;rbs_spacer=5-10bp;gc_cont=0.469
-MNNHFGKGLMAGLHAPYAYSAHHAVNFCSEYKRGFVLGFTHRMFEKTGDRQLSAWEAGIL
-TRRYGLDKEMVMDFFKENHSGMAVRFFMAGYRLEG*
->genome3_plasmid_2_1 # 1 # 582 # 1 # ID=2_1;partial=10;start_type=Edge;rbs_motif=None;rbs_spacer=None;gc_cont=0.546
-MSTLLYLHGFNSSPRSAKACQLKNWLAERHPHVEMIVPQLPPYPADAAELLESLVLEHGG
-APLGLVGSSLGGYYATWLSQCFMLPAVVVNPAVRPFELLTDYLGQNENPYTGQQYVLESR
-HIYDLKVMQIDPLEAPDLIWLLQQTGDEVLDYRQAVAYYASCRQTVTEGGNHAFTGFEDY
-FNQIVDFLGLHSC*
->genome3_plasmid_2_2 # 629 # 1936 # 1 # ID=2_2;partial=00;start_type=ATG;rbs_motif=None;rbs_spacer=None;gc_cont=0.520
-MIDPIFASCTLIAVFVVLLAMGAPIGICIVIASFSTMMLVLPFDISMFATAQKMFSSLDS
-FALLAVPFFVLSGVIMNSGGIAARLINFAKLFTGKLPGSLSYTNIVGNMMFGAISGSAIA
-ASTSIGGVMVPMSAREGYDRGFAAAVNIASAPTGMLIPPTTAFILYALASGGTSIAALFA
-GGLVAGVLWGVGCMLVTLVVAKRRNYRVFFTVQKGMALKVAVEAIPSLLLIVIIVGGIVQ
-GIFTAIEASAIAVVYTLLLTMVFYRTLKIKDLPSILLQTVVMTGVIMFLLATSSAMSFSM
-SITNIPAALSDMILGISANKLVILLVITVFLLIIGAFMDIGPAILIFTPILLPIMAKLGV
-DPVHLGIIMIYNLAIGTITPPVGSGLYVGASVGKVKVEEVIKPLLPFYGAIIGVLLLITY
-IPEIILFLPRLLGIM*
->genome3_plasmid_3_1 # 2 # 280 # 1 # ID=3_1;partial=10;start_type=Edge;rbs_motif=None;rbs_spacer=None;gc_cont=0.355
-TGLRGAMAMIINGKLIKAKDLAKAAGVSRSTVIKYYGISRENYERVATERRKLAFELRAS
-GLKWKEVAEKMNTTKYSAIAYYRRYLALEKNK*
->genome3_plasmid_3_2 # 323 # 1102 # 1 # ID=3_2;partial=00;start_type=ATG;rbs_motif=None;rbs_spacer=None;gc_cont=0.559
-MVELQHQRLMVLAEQLQLDSLIGAAPALSQQAVDQEWSYMDFLEHLLHEEKLARHQRKQA
-MYTRMAAFPAVKTFEEYDFTFATGAPQKQIQSLRSLSFIERNENIVLLGPSGVGKTHLAI
-AMGYEAVRAGIKVRFTTAADLLLQLSTSQRQGRYKTTLNRGVMAPKLLIIDEIGYLPFSQ
-EEAKLFFQVIAKRYEKSAMILTSNLPFGQWDQTFAGDAALTSAMLDRILHHSHVVQIKGE
-SYRLKQKRKAGVIAEANPE*
diff --git a/Examples/2-res-Annotate-prodigal/tmp_files/genome3-chromo.fst-all.fna_prodigal-split5N.fna-prodigalRes/EXAM.1216.00002.ffn b/Examples/2-res-Annotate-prodigal/tmp_files/genome3-chromo.fst-all.fna_prodigal-split5N.fna-prodigalRes/EXAM.1216.00002.ffn
deleted file mode 100644
index 527489f0e0e2b0b64344ed42bbfd2cdb018336e0..0000000000000000000000000000000000000000
--- a/Examples/2-res-Annotate-prodigal/tmp_files/genome3-chromo.fst-all.fna_prodigal-split5N.fna-prodigalRes/EXAM.1216.00002.ffn
+++ /dev/null
@@ -1,141 +0,0 @@
->header_genome3_chromo_1_1 # 1 # 831 # 1 # ID=1_1;partial=10;start_type=Edge;rbs_motif=None;rbs_spacer=None;gc_cont=0.578
-ATGAGAGCGCTACTGTGGCTGGTGGGTCTTGCGTTGCTGTTAACAGGCTGCGCGAGCGAAAAAGGAATTA
-TCGATGAAGAGGGATATCAGCTTGATACCCGACATCGGGCGCAGGCGGCCTATCCGCGCATTAAAGTCCT
-GGTGATTCACTATACGGCGGAAAACTTTGACGTTTCGCTGGCGACGTTAACGGGCCGCAACGTCAGTTCG
-CATTACCTGATTCCCGCAACCCCGCCATTATATGGCGGTAAACCGCGCATCTGGCAACTGGTGCCGGAAC
-AGGATCAGGCCTGGCATGCGGGCGTCAGTTTCTGGCGAGGCGCCACGCGTCTCAATGATACGTCTATTGG
-CATTGAGCTGGAAAATCGCGGCTGGCGAATGTCCGGCGGGGTGAAATCTTTCGCGCCGTTTGAATCCGCG
-CAAATTCAGGCATTGATTCCGTTAGCGAAGGACATTATCGCGCGCTATGACATCAAACCGCAGAATGTGG
-TGGCCCATGCGGATATCGCGCCGCAGCGTAAAGACGATCCCGGCCCGCGCTTCCCGTGGCGCGAGCTGGC
-GGCACAGGGGATTGGCGCCTGGCCTGACGCCCAGCGTGTGGCGTTTTATCTGGCTGGACGCGCGCCGTAT
-ACGCCAGTCGATACCGCAACGGTGCTTGCGTTACTCTCGCGCTATGGCTATGAAGTCAAAGCCGATATGA
-CGGCGCGCGAGCAACAGCGGGTGATTATGGCGTTCCAGATGCACTTCCGTCCGGCGCAATGGAACGGTAT
-CGCAGATGCCGAAACGCAGGCGATTGCCGAAGCATTACTGGAGAAGTACGGCCAGGATTAA
->header_genome3_chromo_1_2 # 880 # 1710 # 1 # ID=1_2;partial=00;start_type=ATG;rbs_motif=AGGAG/GGAGG;rbs_spacer=11-12bp;gc_cont=0.578
-ATGAGAGCGCTACTGTGGCTGGTGGGTCTTGCGTTGCTGTTAACAGGCTGCGCGAGCGAAAAAGGAATTA
-TCGATGAAGAGGGATATCAGCTTGATACCCGACATCGGGCGCAGGCGGCCTATCCGCGCATTAAAGTCCT
-GGTGATTCACTATACGGCGGAAAACTTTGACGTTTCGCTGGCGACGTTAACGGGCCGCAACGTCAGTTCG
-CATTACCTGATTCCCGCAACCCCGCCATTATATGGCGGTAAACCGCGCATCTGGCAACTGGTGCCGGAAC
-AGGATCAGGCCTGGCATGCGGGCGTCAGTTTCTGGCGAGGCGCCACGCGTCTCAATGATACGTCTATTGG
-CATTGAGCTGGAAAATCGCGGCTGGCGAATGTCCGGCGGGGTGAAATCTTTCGCGCCGTTTGAATCCGCG
-CAAATTCAGGCATTGATTCCGTTAGCGAAGGACATTATCGCGCGCTATGACATCAAACCGCAGAATGTGG
-TGGCCCATGCGGATATCGCGCCGCAGCGTAAAGACGATCCCGGCCCGCGCTTCCCGTGGCGCGAGCTGGC
-GGCACAGGGGATTGGCGCCTGGCCTGACGCCCAGCGTGTGGCGTTTTATCTGGCTGGACGCGCGCCGTAT
-ACGCCAGTCGATACCGCAACGGTGCTTGCGTTACTCTCGCGCTATGGCTATGAAGTCAAAGCCGATATGA
-CGGCGCGCGAGCAACAGCGGGTGATTATGGCGTTCCAGATGCACTTCCGTCCGGCGCAATGGAACGGTAT
-CGCAGATGCCGAAACGCAGGCGATTGCCGAAGCATTACTGGAGAAGTACGGCCAGGATTAA
->header_genome3_chromo_1_3 # 1655 # 2128 # 1 # ID=1_3;partial=00;start_type=ATG;rbs_motif=GGA/GAG/AGG;rbs_spacer=11-12bp;gc_cont=0.544
-ATGCCGAAACGCAGGCGATTGCCGAAGCATTACTGGAGAAGTACGGCCAGGATTAACAGGGCGCGGTATC
-GCGAGGACTCTCTCTTCGAGGACATGCCGCACTTTATTGCTGAATGTACTGAAAATATTCGCGAGCAGGC
-TGATTTACCCGGCCTGTTCAGCAAGGTAAACGAGGCGCTGGCCGCCAGCGGGATTTTCCCCATCGGCGGT
-ATCCGCAGTCGCGCCCACTGGCTGGATACCTGGCAGATGGCTGACGGTAAGCATGATTACGCGTTTGTGC
-ATATGACGCTGAAAATCGGCGCCGGGCGCAGCCTGGAGAGCCGTCAGGAAGTCGGCGAAATGCTGTTCGG
-GCTGATTAAAGCCCACTTCGCCGACCTGATGGAGAACCGCTATCTGGCGCTGTCGTTTGAGATTGCCGAG
-TTACATCCAACGCTCAATTACAAACAAAACAACGTACACGCGTTATTTAAATAG
->header_genome3_chromo_1_4 # 2172 # 2396 # 1 # ID=1_4;partial=00;start_type=ATG;rbs_motif=GGA/GAG/AGG;rbs_spacer=11-12bp;gc_cont=0.542
-ATGAGCGCGCTATTTCTGGCCATCCCGTTAACCATTTTTGTGTTGTTTGTGTTACCGATTTGGCTGTGGC
-TGCATTACAGCAACCGCGCCGGTCGGGGAGAACTGTCGCAAAGCGAGCAGCAACGCTTACTGCAACTCAC
-AGACGACGCGCAACGTATGCGCGAGCGCATTCAGGCGCTGGAAGACATTCTTGATGCAGAGCATCCGAAC
-TGGAGAGAGCGCTAA
->header_genome3_chromo_1_5 # 2425 # 3828 # 1 # ID=1_5;partial=00;start_type=ATG;rbs_motif=AGGAG/GGAGG;rbs_spacer=11-12bp;gc_cont=0.513
-ATGCCCGCGACTAAATTCTCCCGACGTACCCTCCTGACGGCAGGTTCTGCGCTTGCTGTTCTTCCTTTCC
-TGCGCGCCTTGCCGGTACAGGCGCGTGAACCTCGCGAGACCGTCGATATTAAGGATTATCCGGCGGATGA
-CGGTATCGCCTCGTTCAAACAGGCCTTCGCCGACGGACAGACCGTGGTCGTACCGCCAGGATGGGTGTGT
-GAAAATATCAATGCGGCGATAACGATTCCGGCGGGAAAAACGCTGCGGGTACAGGGCGCGGTGCGTGGGA
-ATGGCCGGGGACGGTTTATTTTGCAGGACGGGTGTCAGGTGGTGGGGGAGCAGGGCGGCAGTCTGCACAA
-TGTGACGCTGGATGTTCGCGGGTCGGACTGTGTGATTAAAGGCGTGGCGATGAGCGGCTTTGGCCCCGTC
-GCGCAAATTTTCATCGGTGGTAAGGAACCGCAGGTGATGCGTAATCTCATTATCGATGACATCACCGTTA
-CCCACGCCAACTACGCCATTCTCCGCCAGGGATTTCATAACCAAATGGACGGCGCGAGGATTACGCATAG
-CCGCTTTAGCGATTTACAGGGGGACGCCATTGAGTGGAATGTCGCGATTCACGACCGCGATATCCTGATT
-TCCGATCATGTCATCGAACGCATTGATTGTACCAATGGCAAAATCAACTGGGGGATCGGCATCGGGCTGG
-CGGGTAGCACCTATGACAACAGTTATCCTGAAGACCAGGCAGTAAAAAACTTTGTGGTGGCCAATATTAC
-CGGATCTGATTGCCGACAGCTTGTGCACGTAGAAAATGGCAAACATTTCGTCATTCGCAATGTCAAAGCC
-AAAAACATCACGCCCGATTTCAGTAAAAATGCGGGTATTGATAACGCAACGATCGCAATTTATGGCTGTG
-ATAATTTCGTCATTGATAATATTGATATGACGAATAGTGCCGGGATGCTCATCGGCTATGGCGTCGTTAA
-AGGAAAATACCTGTCAATTCCGCAAAACTTTAAATTAAACGCTATTCGGTTGGATAATCGCCAGGTTGCT
-TATAAATTACGCGGCATTCAAATTTCCTCCGGCAACACCCCCTCTTTTGTCGCCATCACCAATGTACGGA
-TGACGCGTGCTACGCTGGAACTGCATAATCAACCGCAGCACCTCTTCCTGCGTAATATCAACGTGATGCA
-AACTTCAGCGATTGGCCCGGCGTTAAAAATGCATTTCGATTTGCGTAAAGATGTCCGTGGTCAATTTATG
-GCCCGCCAGGACACGCTGCTTTCCCTCGCTAATGTTCATGCCATCAATGAAAACGGGCAGAGTTCCGTGG
-ATATCGACAGGATTAATCACCAAACCGTGAATGTCGAAGCAGTGAATTTTTCGCTGCCGAAGCGGGGAGG
-GTAA
->header_genome3_chromo_1_6 # 3863 # 4636 # 1 # ID=1_6;partial=00;start_type=ATG;rbs_motif=GGAG/GAGG;rbs_spacer=5-10bp;gc_cont=0.527
-ATGTCAGAAAATAAATTACACGTTATCGATTTGCACAAACGCTACGGCGGTCATGAAGTGCTGAAAGGGG
-TATCGCTGCAGGCCCGCGCCGGAGATGTGATTAGCATCATCGGCTCGTCCGGCTCCGGTAAAAGCACTTT
-TTTGCGCTGTATTAACTTCCTCGAAAAACCGAGCGAAGACGCGATTATCGTGAACGGTCAGAACATTAAT
-CTGGTGCGCGACAAAGACGGGCAGCTCAAAGTGGCGGATAAAAATCAGCTACGCTTGTTGCGTACCCGCC
-TGACGATGGTGTTTCAGCACTTTAACCTCTGGAGCCACATGACGGTGCTGGAAAATGTGATGGAAGCGCC
-GATTCAGGTACTGGGATTAAGCAAGCACGACGCGCGCGAGCGGGCGTTGAAATATCTGGCGAAGGTGGGG
-ATTGATGAGCGCGCTCAGGGCAAATATCCCGTTCATCTCTCCGGTGGCCAACAGCAGCGCGTTTCTATTG
-CGCGCGCGCTGGCGATGGAACCTGACGTTTTACTGTTCGATGAACCCACTTCGGCGCTCGATCCTGAACT
-GGTCGGCGAAGTGTTGCGCATCATGCAACAACTGGCGGAAGAAGGCAAAACGATGGTGGTGGTCACGCAT
-GAAATGGGCTTCGTTCGCCATGTCTCTTCGCACGTTATTTTTCTGCATCAGGGGAAAATTGAAGAAGAGG
-GCGATCCGGAGCAGGTGTTCGGCAATCCGCAAAGCCCGCGTTTACAGCAATTCCTGAAAGGCTCGCTGAA
-ATAA
->header_genome3_chromo_1_7 # 4641 # 5432 # 1 # ID=1_7;partial=00;start_type=ATG;rbs_motif=None;rbs_spacer=None;gc_cont=0.537
-ATGCGCGCGATATATCGGCGATGCGTGTTTATTGGCATCGTTAGCCTGTTTCCTGAAATGTTCCGCGCAA
-TTACCGATTACGGGGTAACTGGCCGGGCAGTAAAAAATGGCCTGCTGAACATCCAAAGCTGGAGTCCTCG
-CGACTTCACGCATGACCGGCACCGTACCGTGGACGATCGTCCTTACGGCGGCGGACCAGGGATGTTAATG
-ATGGTGCAACCCTTGCGGGACGCCATTCACGCAGCAAAAGCCGCGGCAGGTGAAGGCGCTAAAGTGATTT
-ATCTGTCGCCTCAGGGACGCAAGCTTGATCAAGCGGGCGTTAGCGAGCTGGCCACGAATCAGAAGCTTAT
-TCTGGTGTGTGGTCGCTACGAAGGCGTAGATGAGCGCGTAATTCAGACCGAAATTGACGAAGAATGGTCA
-ATTGGCGATTACGTTCTCAGCGGTGGCGAACTACCGGCAATGACGCTGATTGACTCCGTCGCCCGGTTTA
-TACCGGGAGTTCTGGGGCATGAAGCATCAGCAATCGAAGATTCGTTTGCTGATGGGTTGCTGGATTGTCC
-GCACTATACGCGCCCTGAAGTGTTAGAGGGGATGGAAGTACCGCCAGTATTGCTGTCGGGAAACCATGCT
-GAGATACGTCGCTGGCGTTTGAAACAGTCGCTGGGCCGAACCTGGCTTAGAAGACCTGAACTTCTGGAAA
-ACCTGGCTCTGACTGAAGAGCAAGCAAGGTTGCTGGCGGAGTTCAAAACAGAACACGCACAACAGCAGCA
-TAAACATGATGGGATGGCATAG
->header_genome3_chromo_1_8 # 5460 # 5747 # 1 # ID=1_8;partial=00;start_type=ATG;rbs_motif=AGGAG;rbs_spacer=5-10bp;gc_cont=0.469
-ATGAATAATCATTTTGGGAAAGGGTTAATGGCCGGGTTGCACGCGCCATATGCATATAGCGCGCATCATG
-CGGTGAATTTCTGTTCTGAGTATAAACGTGGCTTTGTATTGGGTTTTACACACCGTATGTTCGAAAAGAC
-CGGCGATCGTCAACTTAGCGCGTGGGAGGCTGGAATTCTGACGCGTCGCTATGGTCTGGATAAAGAAATG
-GTGATGGATTTCTTTAAAGAGAATCATTCCGGGATGGCGGTTCGCTTCTTTATGGCCGGTTATCGACTCG
-AAGGTTGA
->genome3_plasmid_2_1 # 1 # 582 # 1 # ID=2_1;partial=10;start_type=Edge;rbs_motif=None;rbs_spacer=None;gc_cont=0.546
-ATGTCTACGCTTCTCTATTTGCACGGATTCAACAGTTCCCCTCGCTCGGCAAAAGCGTGCCAGCTAAAAA
-ACTGGCTGGCGGAGCGTCATCCGCATGTTGAGATGATCGTCCCTCAACTACCGCCGTATCCTGCCGATGC
-GGCGGAGTTGCTGGAGTCTCTCGTGCTTGAGCATGGCGGTGCGCCATTAGGGCTGGTAGGATCGTCGCTG
-GGTGGTTATTACGCCACCTGGCTGTCGCAATGTTTTATGCTGCCGGCTGTGGTGGTGAATCCCGCCGTGC
-GGCCCTTTGAATTACTGACCGACTATCTCGGTCAGAACGAGAACCCCTACACCGGGCAGCAATATGTGCT
-AGAGTCTCGCCATATTTATGATCTTAAAGTCATGCAGATTGACCCGCTGGAAGCGCCGGACCTGATCTGG
-CTACTGCAACAGACGGGCGATGAAGTGCTGGATTACCGCCAGGCGGTGGCATATTACGCCTCCTGCCGTC
-AGACAGTGACCGAGGGTGGTAATCACGCATTCACGGGCTTCGAAGATTATTTCAACCAGATTGTCGATTT
-TCTTGGACTGCACAGTTGCTGA
->genome3_plasmid_2_2 # 629 # 1936 # 1 # ID=2_2;partial=00;start_type=ATG;rbs_motif=None;rbs_spacer=None;gc_cont=0.520
-ATGATTGACCCTATTTTTGCGTCCTGTACGCTAATTGCCGTCTTTGTTGTTTTACTGGCCATGGGCGCGC
-CTATCGGGATCTGCATCGTTATCGCCTCTTTCAGCACCATGATGCTGGTACTGCCTTTCGATATTTCGAT
-GTTCGCCACCGCGCAAAAAATGTTCTCCAGCCTGGACAGTTTTGCCTTGCTGGCCGTGCCGTTCTTCGTT
-TTGTCCGGGGTGATCATGAATAGCGGGGGAATTGCCGCCCGGCTGATCAATTTTGCCAAACTGTTTACTG
-GCAAACTGCCCGGTTCGCTCTCTTATACCAACATCGTCGGCAATATGATGTTCGGTGCAATTTCCGGATC
-GGCAATTGCCGCCTCAACCTCCATCGGCGGCGTGATGGTGCCGATGAGCGCGCGCGAAGGTTACGATCGC
-GGCTTTGCGGCCGCGGTGAATATCGCCTCCGCGCCGACGGGAATGTTAATTCCGCCCACCACGGCTTTTA
-TCCTTTATGCGCTGGCAAGCGGGGGAACATCGATTGCCGCTCTGTTCGCCGGCGGTCTGGTCGCGGGAGT
-GCTGTGGGGCGTTGGCTGTATGCTGGTCACGCTGGTAGTCGCTAAGCGTCGAAATTATCGGGTTTTCTTC
-ACCGTCCAAAAAGGCATGGCGCTAAAAGTTGCCGTTGAGGCCATTCCCAGCCTGTTACTGATCGTGATTA
-TCGTCGGCGGCATTGTGCAGGGGATTTTCACCGCCATTGAAGCCTCCGCGATTGCCGTGGTGTATACGTT
-ATTGCTGACGATGGTGTTTTACCGCACGCTGAAAATTAAGGATTTGCCTTCGATTTTGCTCCAGACAGTG
-GTAATGACCGGGGTCATCATGTTCCTGCTGGCAACCTCTTCGGCGATGTCCTTCTCAATGTCGATCACCA
-ATATTCCTGCGGCGCTGAGCGATATGATCCTCGGTATTTCCGCCAATAAACTGGTTATCCTGTTAGTCAT
-TACCGTCTTTTTGTTGATTATCGGCGCATTTATGGATATCGGTCCGGCCATTCTGATTTTTACCCCGATT
-CTGCTGCCGATCATGGCTAAACTGGGCGTCGATCCGGTGCATTTGGGCATTATCATGATCTATAACCTGG
-CGATTGGCACCATTACGCCGCCAGTTGGCAGTGGTTTATATGTCGGGGCGAGCGTCGGTAAGGTCAAAGT
-TGAGGAAGTGATTAAACCGTTGCTGCCTTTTTACGGCGCGATTATCGGCGTTCTGTTATTAATTACCTAC
-ATTCCGGAAATCATACTGTTCTTACCCCGTCTACTGGGCATCATGTAA
->genome3_plasmid_3_1 # 2 # 280 # 1 # ID=3_1;partial=10;start_type=Edge;rbs_motif=None;rbs_spacer=None;gc_cont=0.355
-ACAGGGCTTAGAGGCGCTATGGCAATGATAATTAATGGGAAATTAATTAAAGCAAAAGACTTAGCTAAGG
-CTGCAGGTGTATCTCGTTCAACAGTGATTAAATATTACGGCATTAGCCGTGAGAATTACGAAAGGGTAGC
-AACTGAAAGAAGGAAGCTTGCTTTTGAACTAAGAGCATCAGGTTTAAAATGGAAAGAAGTTGCTGAAAAA
-ATGAACACGACAAAATATAGCGCAATTGCATATTATAGACGATATTTAGCATTAGAGAAAAACAAATAA
->genome3_plasmid_3_2 # 323 # 1102 # 1 # ID=3_2;partial=00;start_type=ATG;rbs_motif=None;rbs_spacer=None;gc_cont=0.559
-ATGGTCGAACTGCAACATCAACGGCTGATGGTGCTTGCCGAACAGCTCCAGCTGGACAGTCTTATCGGCG
-CAGCGCCGGCGCTGTCGCAACAGGCGGTGGATCAGGAATGGAGCTACATGGACTTCCTGGAGCACCTGTT
-ACATGAGGAGAAACTGGCCCGGCATCAGCGTAAACAGGCGATGTACACGCGGATGGCAGCCTTCCCGGCG
-GTAAAGACGTTCGAGGAGTACGACTTCACCTTCGCCACCGGCGCTCCTCAGAAGCAAATCCAGTCGCTGC
-GATCCCTGAGCTTCATAGAGCGTAACGAAAACATCGTGTTGCTGGGGCCATCGGGCGTGGGAAAAACGCA
-TCTGGCGATAGCCATGGGCTACGAAGCAGTACGGGCGGGCATCAAGGTTCGCTTCACAACAGCAGCGGAC
-CTGCTGCTACAGCTGTCCACTTCACAGCGTCAGGGCCGTTACAAAACGACTCTCAATCGTGGTGTCATGG
-CCCCGAAGCTGCTTATCATCGATGAAATAGGTTATCTGCCGTTCAGTCAGGAGGAAGCCAAGCTGTTCTT
-CCAGGTCATCGCCAAACGTTACGAGAAGAGCGCGATGATCCTGACCTCCAACCTGCCGTTCGGGCAGTGG
-GATCAGACGTTCGCCGGTGATGCAGCGCTGACATCGGCGATGCTGGACCGGATCTTACATCACTCACACG
-TCGTGCAAATAAAAGGGGAAAGCTATCGACTGAAGCAGAAACGAAAGGCCGGGGTTATAGCTGAAGCTAA
-TCCTGAGTAA
diff --git a/Examples/2-res-Annotate-prodigal/tmp_files/genome3-chromo.fst-all.fna_prodigal-split5N.fna-prodigalRes/EXAM.1216.00002.gff b/Examples/2-res-Annotate-prodigal/tmp_files/genome3-chromo.fst-all.fna_prodigal-split5N.fna-prodigalRes/EXAM.1216.00002.gff
deleted file mode 100644
index 54202b410eb654831c46417941f6c96d8912bad7..0000000000000000000000000000000000000000
--- a/Examples/2-res-Annotate-prodigal/tmp_files/genome3-chromo.fst-all.fna_prodigal-split5N.fna-prodigalRes/EXAM.1216.00002.gff
+++ /dev/null
@@ -1,19 +0,0 @@
-##gff-version  3
-# Sequence Data: seqnum=1;seqlen=5747;seqhdr="header_genome3_chromo_1"
-# Model Data: version=Prodigal.v2.6.3;run_type=Metagenomic;model="20|Escherichia_coli_UMN026|B|50.7|11|1";gc_cont=50.70;transl_table=11;uses_sd=1
-header_genome3_chromo_1	Prodigal_v2.6.3	CDS	1	831	104.1	+	0	ID=1_1;partial=10;start_type=Edge;rbs_motif=None;rbs_spacer=None;gc_cont=0.578;conf=100.00;score=104.13;cscore=100.92;sscore=3.22;rscore=0.00;uscore=0.00;tscore=3.22;
-header_genome3_chromo_1	Prodigal_v2.6.3	CDS	880	1710	106.5	+	0	ID=1_2;partial=00;start_type=ATG;rbs_motif=AGGAG/GGAGG;rbs_spacer=11-12bp;gc_cont=0.578;conf=100.00;score=107.29;cscore=100.92;sscore=6.38;rscore=7.06;uscore=-5.38;tscore=3.95;
-header_genome3_chromo_1	Prodigal_v2.6.3	CDS	1655	2128	40.8	+	0	ID=1_3;partial=00;start_type=ATG;rbs_motif=GGA/GAG/AGG;rbs_spacer=11-12bp;gc_cont=0.544;conf=99.99;score=40.80;cscore=40.20;sscore=0.60;rscore=-1.74;uscore=-1.61;tscore=3.95;
-header_genome3_chromo_1	Prodigal_v2.6.3	CDS	2172	2396	19.5	+	0	ID=1_4;partial=00;start_type=ATG;rbs_motif=GGA/GAG/AGG;rbs_spacer=11-12bp;gc_cont=0.542;conf=99.08;score=20.33;cscore=21.30;sscore=-0.97;rscore=-1.96;uscore=-3.32;tscore=3.51;
-header_genome3_chromo_1	Prodigal_v2.6.3	CDS	2425	3828	146.8	+	0	ID=1_5;partial=00;start_type=ATG;rbs_motif=AGGAG/GGAGG;rbs_spacer=11-12bp;gc_cont=0.513;conf=100.00;score=147.74;cscore=139.37;sscore=8.37;rscore=7.06;uscore=-3.60;tscore=3.95;
-header_genome3_chromo_1	Prodigal_v2.6.3	CDS	3863	4636	118.2	+	0	ID=1_6;partial=00;start_type=ATG;rbs_motif=GGAG/GAGG;rbs_spacer=5-10bp;gc_cont=0.527;conf=100.00;score=119.07;cscore=106.36;sscore=12.71;rscore=11.19;uscore=-3.33;tscore=3.95;
-header_genome3_chromo_1	Prodigal_v2.6.3	CDS	4641	5432	48.3	+	0	ID=1_7;partial=00;start_type=ATG;rbs_motif=None;rbs_spacer=None;gc_cont=0.537;conf=100.00;score=49.55;cscore=55.53;sscore=-5.99;rscore=-8.50;uscore=-2.67;tscore=3.95;
-header_genome3_chromo_1	Prodigal_v2.6.3	CDS	5460	5747	35.4	+	0	ID=1_8;partial=00;start_type=ATG;rbs_motif=AGGAG;rbs_spacer=5-10bp;gc_cont=0.469;conf=99.98;score=36.42;cscore=19.87;sscore=16.55;rscore=14.84;uscore=-3.22;tscore=3.95;
-# Sequence Data: seqnum=2;seqlen=1968;seqhdr="genome3_plasmid_2"
-# Model Data: version=Prodigal.v2.6.3;run_type=Metagenomic;model="20|Escherichia_coli_UMN026|B|50.7|11|1";gc_cont=50.70;transl_table=11;uses_sd=1
-genome3_plasmid_2	Prodigal_v2.6.3	CDS	1	582	63.1	+	0	ID=2_1;partial=10;start_type=Edge;rbs_motif=None;rbs_spacer=None;gc_cont=0.546;conf=100.00;score=63.13;cscore=59.91;sscore=3.22;rscore=0.00;uscore=0.00;tscore=3.22;
-genome3_plasmid_2	Prodigal_v2.6.3	CDS	629	1936	156.9	+	0	ID=2_2;partial=00;start_type=ATG;rbs_motif=None;rbs_spacer=None;gc_cont=0.520;conf=100.00;score=157.65;cscore=165.52;sscore=-7.87;rscore=-8.50;uscore=-4.09;tscore=3.95;
-# Sequence Data: seqnum=3;seqlen=1102;seqhdr="genome3_plasmid_3"
-# Model Data: version=Prodigal.v2.6.3;run_type=Metagenomic;model="15|Chlorobium_phaeobacteroides_BS1|B|48.9|11|0";gc_cont=48.90;transl_table=11;uses_sd=0
-genome3_plasmid_3	Prodigal_v2.6.3	CDS	2	280	8.3	+	0	ID=3_1;partial=10;start_type=Edge;rbs_motif=None;rbs_spacer=None;gc_cont=0.355;conf=87.21;score=8.35;cscore=5.13;sscore=3.22;rscore=0.00;uscore=0.00;tscore=3.22;
-genome3_plasmid_3	Prodigal_v2.6.3	CDS	323	1102	58.2	+	0	ID=3_2;partial=00;start_type=ATG;rbs_motif=None;rbs_spacer=None;gc_cont=0.559;conf=100.00;score=59.02;cscore=60.68;sscore=-1.66;rscore=-0.28;uscore=-5.50;tscore=3.30;
diff --git a/Examples/2-res-Annotate-prodigal/tmp_files/genome4.fst_prodigal-split5N.fna b/Examples/2-res-Annotate-prodigal/tmp_files/genome4.fst_prodigal-split5N.fna
deleted file mode 100644
index 85013c024cf3d318b654b2e8b07613ef6052c0ae..0000000000000000000000000000000000000000
--- a/Examples/2-res-Annotate-prodigal/tmp_files/genome4.fst_prodigal-split5N.fna
+++ /dev/null
@@ -1,2 +0,0 @@
->g4_1
-ATGAAAGCGCTACTGTGGCTGGTGGGTCTCGCGTTGCTGTTAACAGGCTGCGCGAGCGAAAAAGGAATTATCGATAAAGAGGGATATCAGCTTGATACCCGACATCGGGCGCAGGCGGCCTATCCGCGCATTAAAGTCCTGGTGATTCACTATACGGCGGAAAACTTTGACGTTTCGCTGGCGACGTTAACGGGCCGCAACGTCAGTTCGCATTACCTGATTCCCGCAACCCCGCCATTATATGGCGGTAAACCGCGCATCTGGCAACTGGTGCCGGAACAGGATCAGGCCTGGCATGCGGGCGTCAGTTTCTGGCGAGGCGCCACGCGTCTCAATGATACGTCTATTGGCATTGAGCTGGAAAATCGCGGCTGGCGAATGTCCGGCGGGGTGAAATCTTTCGCGCCGTTTGAATCCGCGCAAATTCAGGCATTGATTCCGTTAGCGAAGGACATTATCGCGCGCTATGACATCAAACCGCAGAATGTGGTGGCCCATGCGGATATCGCGCCGCAGCGTAAAGACGATCCCGGCCCGCGCTTCCCGTGGCGCGAGCTGGCGGCGCAGGGGATTGGCGCCTGGCCTGACGCCCAGCGTGTGGCGTTTTATCTGGCTGGACGCGCGCCGTATACGCCAGTCGATACCGCAACGGTGCTTGCGTTACTCTCGCGCTATGGCTATGAAGTCAAAGCCGATATGACGGCGCGCGAGCAGCAGCGGGTGATTATGGCGTTCCAGATGCACTTCCGTCCGGCGCAATGGAACGGTATCGCAGATGCCGAAACGCAGGCGATTGCCGAAGCATTACTGGAGAAGTACGGCCAGGATTAACGCGATCGCGCGCATATCGCGCGCGATAGATGCCGCACTTTATTGCTGAATGTACTGAAAATATTCGCGAGCAGGCTGATTTACCCGGCCTGTTCAGCAAGGTAAACGAGGCGCTGGCCGCCAGCGGGATTTTCCCCATCGGCGGTATCCGCAGTCGCGCCCACTGGCTGGATACCTGGCAGATGGCTGACGGTAAGCATGATTATGCGTTTGTGCATATGACGCTGAAAATCGGTACCGGGCGCAGCCTGGAGAGCCGTCAGGAAGTCGGCGAAATGCTGTTTGGGCTGATTAAAGCCCACTTCGCCGACCTGATGGAGAACCGCTATCTGGCGCTGTCGTTTGAGATTGCCGAGCTACATCCGACGCTCAATTACAAACAAAACAACGTACACGCGTTATTTAAATAGCCGCATATGCGGCGCTCAGGAGCGCTAGCATGCTCGATAAACAGACCCATACCCTGATCGCCCAGCGACTTAATCAGGCTGAAAAACAGCGTGAACAAATTCGCGCAGTGTCGCTGGATTATCCCAACATCACTATTGAAGATGCCTATGCCGTACAGCGTGAATGGGTCAATATCAAGATCGCCGAAGGGCGCACGCTCAAAGGCCACAAAATCGGCCTGACCTCAAAAGCGATGCAGGCCAGCTCGCAAATCAGCGAACCGGATTACGGCGCGCTGCTTGACGATATGTTCTTCCATGACGGCGGCGATATCCCCACCGACCGTTTTATCGTCCCGCGTATTGAAGTGGAGCTGGCGTTCGTGCTGGCGAAACCGCTGCGCGGCCCTCACTGCACGCTGTTCGACGTCTACAACGCCACGGATTATGTGATTCCGGCGCTGGAACTGATTGACGCCCGCAGCCACAACATCGACCCGGAAACCCAGCGCCCGCGCAAAGTGTTCGACACCATTTCCGACAACGCCGCCAACGCCGGGGTGATCCTCGGTGGTCGCCCCATCAAACCAGACGAGCTGGATCTGCGCTGGATCTCCGCGCTGCTCTATCGCAACGGCGTGATCGAAGAAACCGGCGTCGCCGCAGGCGTGCTGAATCATCCGGCCAACGGCGTGGCGTGGCTGGCGAACAAGCTTGCCCCCTACGATGTCCAGCTTGAAGCCGGGCAGATCATCCTCGGCGGCTCGTTCACCCGCCCGGTGCCGGCGAGCAAGGGCGACACCTTCCATGTCGATTACGGCAACATGGGCGCGATCAGTTGCCGGTTTGTGTAACCAGATCCGCGCGCGCATATATATCGCGCGCATACGATGCCCGTGAATAAGTTCTCCCGACGTACCCTCCTGACGGCAGGTTCCGCGCTTGCTGTTCTTCCTTTTCTGCGCGCCTTGCCGGTACAGGCGCGTGAACCTCGCGAGACCGTCGATATTAAGGATTATCCGGCGGATGACGGTATCGCCTCGTTCAAACAGGCCTTCGCCGACGGACAGACCGTGGTCTTACCGCCAGGATGGGTGTGTGAAAATATCAATGCGGCGATAACGATTCCGGCGGGAAAAACGCTGCGGGTACAGGGCGCGGTGCGTGGGAATGGCCGGGGACGGTTTATTTTGCAGGACGGGTGTCAGGTGGTGGGGGAGCAGGGCGGCAGTCTGCACAATGTGACGCTGGATGTTCGCGGGTCGGACTGTGTGATTAAAGGCGTGACGATGAGCGGCTTTGGCCCCGTCGCGCAAATTTTCATCGGCGGTAAGGAACCGCAGGTGATGCGTAATCTCATTATCGATGACATCACCGTTACCCACGCCAACTACGCCATTCTCCGCCAGGGATTTCATAACCAAATGGACGGCGCGCGGATTACGCATAGCCGCTTTAGCGATTTGCAGGGGGACGCCATTGAGTGGAATGTCGCGATTCACGACCGCGACATCCTGATTTCCGATCATGTCATCGAACGCATTGATTGTACCAATGGCAAAATCAACTGGGGGATCGGCATCGGGCTGGCGGGTAGCACCTATGACAACAGTTATCCTGAAGATCAGGCAGTAAAAAACTTTGTGGTGGCCAATATTACCGGATCTGATTGCCGACAGCTGGTGCACGTAGAAAATGGCAAACATTTCGTCATTCGCAATGTCAAAGCCAAAAACATCACGCCCGATTTCAGTAAAAATGCGGGTATTGATAACGCAACGATCGCCATTTATGGCTGTGATAATTTCGTCATTGATAATATTGATATGACGAATAGTGCTGGGATGCTCATCGGCTATGGCGTCGTTAAAGGAAAATACCTGTCAATTCCGCAAAACTTTAAATTAAACGCTATTCGGTTGGATAATCGCCAGGTTGCTTATAAATTACGCGGCATTCAAATTTCCTCCGGCAACATCCCCTCTTTTGTCGCCATCACCAATGTACGGATGACGCGTGCTACGCTGGAACTGCATAATCAACCGCAGCACCTCTTTCTGCGTAATATCAACGTGATGCAAACTTCAGCGATTGGCCCGGCGTTAAAAATGCATTTCGATTTGCGTAAAGATGTCCGTGGTCAATTTATGGCCCGCCAGGACACGCTGCTTTCCCTCGCTAATGTTCATGCCATCAATGAAAACGGGCAGAGTTCCGTGGATATCGACAGGATTAATCACCAAACCGTGAATGTCGAAGCAGTGAATTTTTCGCTGCCGAAGCGGGGAGGGTAACAGAGCTCGCGCGATCGCGAATGTCAGAAAATAAATTACACGTTATCGATTTGCACAAACGCTACGGCGGTCATGAAGTGCTGAAAGGGGTATCGTTGCAGGCCCGCGCCGGAGATGTGATTAGCATCATCGGCTCGTCCGGCTCCGGTAAAAGCACTTTTTTGCGCTGTATTAACTTCCTCGAAAAACCGAGCGAAGGCGCGATTATCGTGAACGGTCAGAACATTAATCTGGTGCGCGACAAAGACGGGCAGCTCAAAGTGGCGGATAAAAATCAGCTACGCTTGTTGCGTACCCGCCTGACGATGGTGTTTCAGCACTTTAACCTCTGGAGCCACATGACGGTGCTGGAAAATGTGATGGAAGCGCCGATTCAGGTACTGGGATTAAGCAAGCACGACGCGCGCGAGCGGGCGTTGAAATATCTGGCGAAGGTGGGGATTGATGAGCGCGCTCAGGGCAAATATCCCGTCCATCTCTCCGGCGGCCAACAGCAGCGCGTTTCTATTGCGCGCGCGCTGGCGATGGAACCTGACGTTTTACTGTTCGATGAACCCACATCGGCGCTCGATCCTGAACTGGTCGGCGAAGTGTTGCGCATCATGCAACAACTGGCGGAAGAAGGCAAAACGATGGTGGTGGTCACGCATGAAATGGGCTTCGCCCGCCATGTCTCTTCGCACGTTATTTTTCTGCATCAGGGGAAAATTGAAGAAGAGGGCGATCCGGAGCAGGTGTTCGGCAATCCGCAAAGCCCGCGTTTACAGCAATTCCTGAAAGGCTCGCTGAAATAACAGATACGCGCATGGCGAGTGTTTATTGGCATCGTTAGCCTGTTTCCTGAAATGTTCCGCGCAATTACCGATTACGGGGTAACTGGCCGGGCAGTAAAAAAAGGCCTGCTGAACATCCAAAGCTGGAGTCCTCGCGACTTCGCGCATGACCGGCACCGTACCGTGGACGACCGTCCTTACGGCGGCGGACCGGGGATGTTAATGATGGTGCAACCCTTGCGGGACGCCATTCACGCAGCAAAAGCCGCGGCAGGTGAAGGCGCTAAAGTGATTTATCTGTCGCCTCAGGGACGCAAGCTTGATCAAGCGGGCGTTAGCGAGCTGGCCACGAATCAGAAGCTTATTCTGGTGTGTGGTCGCTACGAAGGCGTAGATGAGCGCGTAATTCAGACCGAAATTGACGAAGAATGGTCAATTGGCGATTACGTTCTCAGCGGTGGCGAACTACCGGCAATGACGCTGATTGACTCCGTCGCCCGGTTTATACCGGGGGTTCTGGGGCATGAGGCATCAGCAATCGAAGATTCGTTTGCTGATGGGTTGCTGGATTGTCCGCACTATACGCGCCCTGAAGTGTTAGAGGGGATGGAAGTACCGCCAGTATTGCTGTCGGGAAACCATGCCGAGATACGTCGCTGGCGCTTGAAACAGTCGCTGGGCCGAACCTGGCTTAGAAGACCTGAACTTCTGGAAAACCTGGCTCTGACTGAAGAGCAAGCAAGGTTGCTGGCGGAGTTCAAAACAGAACACGCACAACAGCAGCATAAACATGATGGGATGGCATAGCGATAGCGCTAGAGCGATGAATAATCATTTTGGGAAAGGGTTAATGGCTGGGTTGCACGCGCCATATGCATATAGCGCGCATCATGCGGTGAATTTCTGTTCTGAGTATAAACGTGGCTTTGTATTGGGTTTTACACACCGTATGTTCGAAAAGACCGGCGATCGTCAACTTAGCGCGTGGGAGGCCGGAATTCTGACGCGTCGCTATGGTCTGGATAAAGAAATGGTGATGGATTTCTTTAAAGAGAATCATTCCGGGATGGCGGTTCGCTTCTTTATGGTCGGTTATCGACTCGAAGGTTGACAGATGCGCGATCGATGTCTACGCTTCTCTATTTGCACGGATTCAACAGTTCCCCTCGCTCGGCAAAAGCGTGCCAGCTAAAAAACTGGCTGGCGGAGCGTCATCCGCATGTCGAGATGATCGTCCCTCAACTACCGCCGTATCCTGCCGATGCGGCGGAGTTGCTGGAATCTCTCGTGCTTGAGCATGGCGGTGCGCCATTAGGGCTGGTAGGATCGTCGCTGGGTGGTTATTACGCCACCTGGCTGTCGCAATGTTTTATGCTGCCGGCTGTGGTGGTGAATCCCGCCGTGCGGCCCTTTGAATTACTGACCGACTATCTCGGTCAGAACGAGAACCCCTACACCGGGCAGCAATATGTGCTAGAGTCTCGCCATATTTATGATCTTAAAGTCATGCAGATTGACCCGCTGGAAGCGCCGGACCTGATCTGGCTACTGCAACAGACGGGCGATGAAGTGCTGGATTACCGCCAGGCGGTGGCATATTACGCCTCCTGCCGTCAGACAGTGACCGAGGGTGGTAATCACGCATTCACGGGCTTCGAAGATTATTTCAACCAGATTGTCGATTTTCTTGGACTGCACAGTTGCTGACACGGATGCGCCATCGGCTTGCTGGCCGTGCCGTTCTTCGTTTTGTCCGGGGTGATCATGAATAGCGGGGGAATTGCCGCCCGGCTGGTCAATTTTGCCAAACTGTTTACTGGCAAACTGCCCGGCTCGCTCTCTTATACCAACATCGTCGGCAATATGATGTTCGGTGCAATTTCCGGATCGGCAATTGCCGCCTCAACCTCCATCGGCGGCGTGATGGTGCCGATGAGCGCGCGCGAAGGTTACGATCGCGGCTTTGCGGCCGCGGTGAATATCGCCTCCGCGCCGACGGGAATGTTAATTCCGCCCACCACGGCTTTTATCCTTTATGCGCTGGCAAGCGGGGGAACATCGATTGCCGCTCTGTTCGCCGGCGGTCTGGTCGCGGGAGTGCTGTGGGGCGTTGGCTGTATGCTGGTCACGCTGGTGGTCGCTAAGCGTCGAAATTATCGGGTTTTCTTCACCGTCCAAAAAGGCATGGCGCTAAAAGTTGCCGTTGAGGCCATTCCCAGCCTGCTGCTGATCGTGATTATCGTCGGCGGCATTGTGCAGGGGATTTTCACCGCCATTGAAGCCTCCGCGATTGCCGTGGTGTATACATTATTGTTGACGATGGTGTTTTACCGCACGCTGAAAATTAAGGATTTGCCTTCGATTTTGCTCCAGACAGTGGTAATGACCGGGGTCATCATGTTCCTGCTGGCAACCTCTTCGGCGATGTCCTTCTCGATGTCGATCACCAATATTCCTGCGGCGCTGAGCGATATGATCCTCGGTATTTCCGCCAATAAACTGGTTATCCTGTTAGTCATTACCGTCTTTTTGTTGATTATCGGCGCATTTATGGATATCGGTCCGGCCATTCTGATTTTTACCCCGATTCTGCTGCCGATCATGGCTAAACTGGGCGTCGATCCGGTGCATTTTGGCATTATCATGATCTATAACCTGGCGATTGGCACCATTACGCCGCCAGTTGGCAGTGGTTTATATGTCGGGGCGAGCGTCGGTAAGGTCAAAGTTGAGGAAGTGATTAAACCGTTGCTGCCTTTTTACGGCGCGATTATCGGCGTTCTGTTATTAATTACCTACATTCCGGAAATCACACTGTTCTTACCCCGTCTACTGGGCATCATGTAA
diff --git a/Examples/2-res-Annotate-prodigal/tmp_files/genome4.fst_prodigal-split5N.fna-prodigal.log b/Examples/2-res-Annotate-prodigal/tmp_files/genome4.fst_prodigal-split5N.fna-prodigal.log
deleted file mode 100644
index e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
diff --git a/Examples/2-res-Annotate-prodigal/tmp_files/genome4.fst_prodigal-split5N.fna-prodigal.log.err b/Examples/2-res-Annotate-prodigal/tmp_files/genome4.fst_prodigal-split5N.fna-prodigal.log.err
deleted file mode 100644
index e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
diff --git a/Examples/2-res-Annotate-prodigal/tmp_files/genome4.fst_prodigal-split5N.fna-prodigalRes/GEN4.1111.00001.faa b/Examples/2-res-Annotate-prodigal/tmp_files/genome4.fst_prodigal-split5N.fna-prodigalRes/GEN4.1111.00001.faa
deleted file mode 100644
index 813d2b889b7dea1d6984b8f9041ac831299d3c18..0000000000000000000000000000000000000000
--- a/Examples/2-res-Annotate-prodigal/tmp_files/genome4.fst_prodigal-split5N.fna-prodigalRes/GEN4.1111.00001.faa
+++ /dev/null
@@ -1,53 +0,0 @@
->g4_1_1 # 1 # 831 # 1 # ID=1_1;partial=10;start_type=Edge;rbs_motif=None;rbs_spacer=None;gc_cont=0.579
-MKALLWLVGLALLLTGCASEKGIIDKEGYQLDTRHRAQAAYPRIKVLVIHYTAENFDVSL
-ATLTGRNVSSHYLIPATPPLYGGKPRIWQLVPEQDQAWHAGVSFWRGATRLNDTSIGIEL
-ENRGWRMSGGVKSFAPFESAQIQALIPLAKDIIARYDIKPQNVVAHADIAPQRKDDPGPR
-FPWRELAAQGIGAWPDAQRVAFYLAGRAPYTPVDTATVLALLSRYGYEVKADMTAREQQR
-VIMAFQMHFRPAQWNGIADAETQAIAEALLEKYGQD*
->g4_1_2 # 861 # 1241 # 1 # ID=1_2;partial=00;start_type=ATG;rbs_motif=None;rbs_spacer=None;gc_cont=0.533
-MPHFIAECTENIREQADLPGLFSKVNEALAASGIFPIGGIRSRAHWLDTWQMADGKHDYA
-FVHMTLKIGTGRSLESRQEVGEMLFGLIKAHFADLMENRYLALSFEIAELHPTLNYKQNN
-VHALFK*
->g4_1_3 # 1271 # 2074 # 1 # ID=1_3;partial=00;start_type=ATG;rbs_motif=AGGAG;rbs_spacer=5-10bp;gc_cont=0.591
-MLDKQTHTLIAQRLNQAEKQREQIRAVSLDYPNITIEDAYAVQREWVNIKIAEGRTLKGH
-KIGLTSKAMQASSQISEPDYGALLDDMFFHDGGDIPTDRFIVPRIEVELAFVLAKPLRGP
-HCTLFDVYNATDYVIPALELIDARSHNIDPETQRPRKVFDTISDNAANAGVILGGRPIKP
-DELDLRWISALLYRNGVIEETGVAAGVLNHPANGVAWLANKLAPYDVQLEAGQIILGGSF
-TRPVPASKGDTFHVDYGNMGAISCRFV*
->g4_1_4 # 2111 # 3514 # 1 # ID=1_4;partial=00;start_type=ATG;rbs_motif=None;rbs_spacer=None;gc_cont=0.512
-MPVNKFSRRTLLTAGSALAVLPFLRALPVQAREPRETVDIKDYPADDGIASFKQAFADGQ
-TVVLPPGWVCENINAAITIPAGKTLRVQGAVRGNGRGRFILQDGCQVVGEQGGSLHNVTL
-DVRGSDCVIKGVTMSGFGPVAQIFIGGKEPQVMRNLIIDDITVTHANYAILRQGFHNQMD
-GARITHSRFSDLQGDAIEWNVAIHDRDILISDHVIERIDCTNGKINWGIGIGLAGSTYDN
-SYPEDQAVKNFVVANITGSDCRQLVHVENGKHFVIRNVKAKNITPDFSKNAGIDNATIAI
-YGCDNFVIDNIDMTNSAGMLIGYGVVKGKYLSIPQNFKLNAIRLDNRQVAYKLRGIQISS
-GNIPSFVAITNVRMTRATLELHNQPQHLFLRNINVMQTSAIGPALKMHFDLRKDVRGQFM
-ARQDTLLSLANVHAINENGQSSVDIDRINHQTVNVEAVNFSLPKRGG*
->g4_1_5 # 3535 # 4308 # 1 # ID=1_5;partial=00;start_type=ATG;rbs_motif=3Base/5BMM;rbs_spacer=13-15bp;gc_cont=0.532
-MSENKLHVIDLHKRYGGHEVLKGVSLQARAGDVISIIGSSGSGKSTFLRCINFLEKPSEG
-AIIVNGQNINLVRDKDGQLKVADKNQLRLLRTRLTMVFQHFNLWSHMTVLENVMEAPIQV
-LGLSKHDARERALKYLAKVGIDERAQGKYPVHLSGGQQQRVSIARALAMEPDVLLFDEPT
-SALDPELVGEVLRIMQQLAEEGKTMVVVTHEMGFARHVSSHVIFLHQGKIEEEGDPEQVF
-GNPQSPRLQQFLKGSLK*
->g4_1_6 # 4327 # 5094 # 1 # ID=1_6;partial=00;start_type=GTG;rbs_motif=None;rbs_spacer=None;gc_cont=0.544
-MFIGIVSLFPEMFRAITDYGVTGRAVKKGLLNIQSWSPRDFAHDRHRTVDDRPYGGGPGM
-LMMVQPLRDAIHAAKAAAGEGAKVIYLSPQGRKLDQAGVSELATNQKLILVCGRYEGVDE
-RVIQTEIDEEWSIGDYVLSGGELPAMTLIDSVARFIPGVLGHEASAIEDSFADGLLDCPH
-YTRPEVLEGMEVPPVLLSGNHAEIRRWRLKQSLGRTWLRRPELLENLALTEEQARLLAEF
-KTEHAQQQHKHDGMA*
->g4_1_7 # 5138 # 5398 # 1 # ID=1_7;partial=00;start_type=ATG;rbs_motif=GGA/GAG/AGG;rbs_spacer=5-10bp;gc_cont=0.483
-MAGLHAPYAYSAHHAVNFCSEYKRGFVLGFTHRMFEKTGDRQLSAWEAGILTRRYGLDKE
-MVMDFFKENHSGMAVRFFMVGYRLEG*
->g4_1_8 # 5413 # 5994 # 1 # ID=1_8;partial=00;start_type=ATG;rbs_motif=None;rbs_spacer=None;gc_cont=0.546
-MSTLLYLHGFNSSPRSAKACQLKNWLAERHPHVEMIVPQLPPYPADAAELLESLVLEHGG
-APLGLVGSSLGGYYATWLSQCFMLPAVVVNPAVRPFELLTDYLGQNENPYTGQQYVLESR
-HIYDLKVMQIDPLEAPDLIWLLQQTGDEVLDYRQAVAYYASCRQTVTEGGNHAFTGFEDY
-FNQIVDFLGLHSC*
->g4_1_9 # 6052 # 7134 # 1 # ID=1_9;partial=00;start_type=ATG;rbs_motif=None;rbs_spacer=None;gc_cont=0.525
-MNSGGIAARLVNFAKLFTGKLPGSLSYTNIVGNMMFGAISGSAIAASTSIGGVMVPMSAR
-EGYDRGFAAAVNIASAPTGMLIPPTTAFILYALASGGTSIAALFAGGLVAGVLWGVGCML
-VTLVVAKRRNYRVFFTVQKGMALKVAVEAIPSLLLIVIIVGGIVQGIFTAIEASAIAVVY
-TLLLTMVFYRTLKIKDLPSILLQTVVMTGVIMFLLATSSAMSFSMSITNIPAALSDMILG
-ISANKLVILLVITVFLLIIGAFMDIGPAILIFTPILLPIMAKLGVDPVHFGIIMIYNLAI
-GTITPPVGSGLYVGASVGKVKVEEVIKPLLPFYGAIIGVLLLITYIPEITLFLPRLLGIM
-*
diff --git a/Examples/2-res-Annotate-prodigal/tmp_files/genome4.fst_prodigal-split5N.fna-prodigalRes/GEN4.1111.00001.ffn b/Examples/2-res-Annotate-prodigal/tmp_files/genome4.fst_prodigal-split5N.fna-prodigalRes/GEN4.1111.00001.ffn
deleted file mode 100644
index f721fa1b5865712394432f2a2cb6c5165af1a5f0..0000000000000000000000000000000000000000
--- a/Examples/2-res-Annotate-prodigal/tmp_files/genome4.fst_prodigal-split5N.fna-prodigalRes/GEN4.1111.00001.ffn
+++ /dev/null
@@ -1,112 +0,0 @@
->g4_1_1 # 1 # 831 # 1 # ID=1_1;partial=10;start_type=Edge;rbs_motif=None;rbs_spacer=None;gc_cont=0.579
-ATGAAAGCGCTACTGTGGCTGGTGGGTCTCGCGTTGCTGTTAACAGGCTGCGCGAGCGAAAAAGGAATTA
-TCGATAAAGAGGGATATCAGCTTGATACCCGACATCGGGCGCAGGCGGCCTATCCGCGCATTAAAGTCCT
-GGTGATTCACTATACGGCGGAAAACTTTGACGTTTCGCTGGCGACGTTAACGGGCCGCAACGTCAGTTCG
-CATTACCTGATTCCCGCAACCCCGCCATTATATGGCGGTAAACCGCGCATCTGGCAACTGGTGCCGGAAC
-AGGATCAGGCCTGGCATGCGGGCGTCAGTTTCTGGCGAGGCGCCACGCGTCTCAATGATACGTCTATTGG
-CATTGAGCTGGAAAATCGCGGCTGGCGAATGTCCGGCGGGGTGAAATCTTTCGCGCCGTTTGAATCCGCG
-CAAATTCAGGCATTGATTCCGTTAGCGAAGGACATTATCGCGCGCTATGACATCAAACCGCAGAATGTGG
-TGGCCCATGCGGATATCGCGCCGCAGCGTAAAGACGATCCCGGCCCGCGCTTCCCGTGGCGCGAGCTGGC
-GGCGCAGGGGATTGGCGCCTGGCCTGACGCCCAGCGTGTGGCGTTTTATCTGGCTGGACGCGCGCCGTAT
-ACGCCAGTCGATACCGCAACGGTGCTTGCGTTACTCTCGCGCTATGGCTATGAAGTCAAAGCCGATATGA
-CGGCGCGCGAGCAGCAGCGGGTGATTATGGCGTTCCAGATGCACTTCCGTCCGGCGCAATGGAACGGTAT
-CGCAGATGCCGAAACGCAGGCGATTGCCGAAGCATTACTGGAGAAGTACGGCCAGGATTAA
->g4_1_2 # 861 # 1241 # 1 # ID=1_2;partial=00;start_type=ATG;rbs_motif=None;rbs_spacer=None;gc_cont=0.533
-ATGCCGCACTTTATTGCTGAATGTACTGAAAATATTCGCGAGCAGGCTGATTTACCCGGCCTGTTCAGCA
-AGGTAAACGAGGCGCTGGCCGCCAGCGGGATTTTCCCCATCGGCGGTATCCGCAGTCGCGCCCACTGGCT
-GGATACCTGGCAGATGGCTGACGGTAAGCATGATTATGCGTTTGTGCATATGACGCTGAAAATCGGTACC
-GGGCGCAGCCTGGAGAGCCGTCAGGAAGTCGGCGAAATGCTGTTTGGGCTGATTAAAGCCCACTTCGCCG
-ACCTGATGGAGAACCGCTATCTGGCGCTGTCGTTTGAGATTGCCGAGCTACATCCGACGCTCAATTACAA
-ACAAAACAACGTACACGCGTTATTTAAATAG
->g4_1_3 # 1271 # 2074 # 1 # ID=1_3;partial=00;start_type=ATG;rbs_motif=AGGAG;rbs_spacer=5-10bp;gc_cont=0.591
-ATGCTCGATAAACAGACCCATACCCTGATCGCCCAGCGACTTAATCAGGCTGAAAAACAGCGTGAACAAA
-TTCGCGCAGTGTCGCTGGATTATCCCAACATCACTATTGAAGATGCCTATGCCGTACAGCGTGAATGGGT
-CAATATCAAGATCGCCGAAGGGCGCACGCTCAAAGGCCACAAAATCGGCCTGACCTCAAAAGCGATGCAG
-GCCAGCTCGCAAATCAGCGAACCGGATTACGGCGCGCTGCTTGACGATATGTTCTTCCATGACGGCGGCG
-ATATCCCCACCGACCGTTTTATCGTCCCGCGTATTGAAGTGGAGCTGGCGTTCGTGCTGGCGAAACCGCT
-GCGCGGCCCTCACTGCACGCTGTTCGACGTCTACAACGCCACGGATTATGTGATTCCGGCGCTGGAACTG
-ATTGACGCCCGCAGCCACAACATCGACCCGGAAACCCAGCGCCCGCGCAAAGTGTTCGACACCATTTCCG
-ACAACGCCGCCAACGCCGGGGTGATCCTCGGTGGTCGCCCCATCAAACCAGACGAGCTGGATCTGCGCTG
-GATCTCCGCGCTGCTCTATCGCAACGGCGTGATCGAAGAAACCGGCGTCGCCGCAGGCGTGCTGAATCAT
-CCGGCCAACGGCGTGGCGTGGCTGGCGAACAAGCTTGCCCCCTACGATGTCCAGCTTGAAGCCGGGCAGA
-TCATCCTCGGCGGCTCGTTCACCCGCCCGGTGCCGGCGAGCAAGGGCGACACCTTCCATGTCGATTACGG
-CAACATGGGCGCGATCAGTTGCCGGTTTGTGTAA
->g4_1_4 # 2111 # 3514 # 1 # ID=1_4;partial=00;start_type=ATG;rbs_motif=None;rbs_spacer=None;gc_cont=0.512
-ATGCCCGTGAATAAGTTCTCCCGACGTACCCTCCTGACGGCAGGTTCCGCGCTTGCTGTTCTTCCTTTTC
-TGCGCGCCTTGCCGGTACAGGCGCGTGAACCTCGCGAGACCGTCGATATTAAGGATTATCCGGCGGATGA
-CGGTATCGCCTCGTTCAAACAGGCCTTCGCCGACGGACAGACCGTGGTCTTACCGCCAGGATGGGTGTGT
-GAAAATATCAATGCGGCGATAACGATTCCGGCGGGAAAAACGCTGCGGGTACAGGGCGCGGTGCGTGGGA
-ATGGCCGGGGACGGTTTATTTTGCAGGACGGGTGTCAGGTGGTGGGGGAGCAGGGCGGCAGTCTGCACAA
-TGTGACGCTGGATGTTCGCGGGTCGGACTGTGTGATTAAAGGCGTGACGATGAGCGGCTTTGGCCCCGTC
-GCGCAAATTTTCATCGGCGGTAAGGAACCGCAGGTGATGCGTAATCTCATTATCGATGACATCACCGTTA
-CCCACGCCAACTACGCCATTCTCCGCCAGGGATTTCATAACCAAATGGACGGCGCGCGGATTACGCATAG
-CCGCTTTAGCGATTTGCAGGGGGACGCCATTGAGTGGAATGTCGCGATTCACGACCGCGACATCCTGATT
-TCCGATCATGTCATCGAACGCATTGATTGTACCAATGGCAAAATCAACTGGGGGATCGGCATCGGGCTGG
-CGGGTAGCACCTATGACAACAGTTATCCTGAAGATCAGGCAGTAAAAAACTTTGTGGTGGCCAATATTAC
-CGGATCTGATTGCCGACAGCTGGTGCACGTAGAAAATGGCAAACATTTCGTCATTCGCAATGTCAAAGCC
-AAAAACATCACGCCCGATTTCAGTAAAAATGCGGGTATTGATAACGCAACGATCGCCATTTATGGCTGTG
-ATAATTTCGTCATTGATAATATTGATATGACGAATAGTGCTGGGATGCTCATCGGCTATGGCGTCGTTAA
-AGGAAAATACCTGTCAATTCCGCAAAACTTTAAATTAAACGCTATTCGGTTGGATAATCGCCAGGTTGCT
-TATAAATTACGCGGCATTCAAATTTCCTCCGGCAACATCCCCTCTTTTGTCGCCATCACCAATGTACGGA
-TGACGCGTGCTACGCTGGAACTGCATAATCAACCGCAGCACCTCTTTCTGCGTAATATCAACGTGATGCA
-AACTTCAGCGATTGGCCCGGCGTTAAAAATGCATTTCGATTTGCGTAAAGATGTCCGTGGTCAATTTATG
-GCCCGCCAGGACACGCTGCTTTCCCTCGCTAATGTTCATGCCATCAATGAAAACGGGCAGAGTTCCGTGG
-ATATCGACAGGATTAATCACCAAACCGTGAATGTCGAAGCAGTGAATTTTTCGCTGCCGAAGCGGGGAGG
-GTAA
->g4_1_5 # 3535 # 4308 # 1 # ID=1_5;partial=00;start_type=ATG;rbs_motif=3Base/5BMM;rbs_spacer=13-15bp;gc_cont=0.532
-ATGTCAGAAAATAAATTACACGTTATCGATTTGCACAAACGCTACGGCGGTCATGAAGTGCTGAAAGGGG
-TATCGTTGCAGGCCCGCGCCGGAGATGTGATTAGCATCATCGGCTCGTCCGGCTCCGGTAAAAGCACTTT
-TTTGCGCTGTATTAACTTCCTCGAAAAACCGAGCGAAGGCGCGATTATCGTGAACGGTCAGAACATTAAT
-CTGGTGCGCGACAAAGACGGGCAGCTCAAAGTGGCGGATAAAAATCAGCTACGCTTGTTGCGTACCCGCC
-TGACGATGGTGTTTCAGCACTTTAACCTCTGGAGCCACATGACGGTGCTGGAAAATGTGATGGAAGCGCC
-GATTCAGGTACTGGGATTAAGCAAGCACGACGCGCGCGAGCGGGCGTTGAAATATCTGGCGAAGGTGGGG
-ATTGATGAGCGCGCTCAGGGCAAATATCCCGTCCATCTCTCCGGCGGCCAACAGCAGCGCGTTTCTATTG
-CGCGCGCGCTGGCGATGGAACCTGACGTTTTACTGTTCGATGAACCCACATCGGCGCTCGATCCTGAACT
-GGTCGGCGAAGTGTTGCGCATCATGCAACAACTGGCGGAAGAAGGCAAAACGATGGTGGTGGTCACGCAT
-GAAATGGGCTTCGCCCGCCATGTCTCTTCGCACGTTATTTTTCTGCATCAGGGGAAAATTGAAGAAGAGG
-GCGATCCGGAGCAGGTGTTCGGCAATCCGCAAAGCCCGCGTTTACAGCAATTCCTGAAAGGCTCGCTGAA
-ATAA
->g4_1_6 # 4327 # 5094 # 1 # ID=1_6;partial=00;start_type=GTG;rbs_motif=None;rbs_spacer=None;gc_cont=0.544
-GTGTTTATTGGCATCGTTAGCCTGTTTCCTGAAATGTTCCGCGCAATTACCGATTACGGGGTAACTGGCC
-GGGCAGTAAAAAAAGGCCTGCTGAACATCCAAAGCTGGAGTCCTCGCGACTTCGCGCATGACCGGCACCG
-TACCGTGGACGACCGTCCTTACGGCGGCGGACCGGGGATGTTAATGATGGTGCAACCCTTGCGGGACGCC
-ATTCACGCAGCAAAAGCCGCGGCAGGTGAAGGCGCTAAAGTGATTTATCTGTCGCCTCAGGGACGCAAGC
-TTGATCAAGCGGGCGTTAGCGAGCTGGCCACGAATCAGAAGCTTATTCTGGTGTGTGGTCGCTACGAAGG
-CGTAGATGAGCGCGTAATTCAGACCGAAATTGACGAAGAATGGTCAATTGGCGATTACGTTCTCAGCGGT
-GGCGAACTACCGGCAATGACGCTGATTGACTCCGTCGCCCGGTTTATACCGGGGGTTCTGGGGCATGAGG
-CATCAGCAATCGAAGATTCGTTTGCTGATGGGTTGCTGGATTGTCCGCACTATACGCGCCCTGAAGTGTT
-AGAGGGGATGGAAGTACCGCCAGTATTGCTGTCGGGAAACCATGCCGAGATACGTCGCTGGCGCTTGAAA
-CAGTCGCTGGGCCGAACCTGGCTTAGAAGACCTGAACTTCTGGAAAACCTGGCTCTGACTGAAGAGCAAG
-CAAGGTTGCTGGCGGAGTTCAAAACAGAACACGCACAACAGCAGCATAAACATGATGGGATGGCATAG
->g4_1_7 # 5138 # 5398 # 1 # ID=1_7;partial=00;start_type=ATG;rbs_motif=GGA/GAG/AGG;rbs_spacer=5-10bp;gc_cont=0.483
-ATGGCTGGGTTGCACGCGCCATATGCATATAGCGCGCATCATGCGGTGAATTTCTGTTCTGAGTATAAAC
-GTGGCTTTGTATTGGGTTTTACACACCGTATGTTCGAAAAGACCGGCGATCGTCAACTTAGCGCGTGGGA
-GGCCGGAATTCTGACGCGTCGCTATGGTCTGGATAAAGAAATGGTGATGGATTTCTTTAAAGAGAATCAT
-TCCGGGATGGCGGTTCGCTTCTTTATGGTCGGTTATCGACTCGAAGGTTGA
->g4_1_8 # 5413 # 5994 # 1 # ID=1_8;partial=00;start_type=ATG;rbs_motif=None;rbs_spacer=None;gc_cont=0.546
-ATGTCTACGCTTCTCTATTTGCACGGATTCAACAGTTCCCCTCGCTCGGCAAAAGCGTGCCAGCTAAAAA
-ACTGGCTGGCGGAGCGTCATCCGCATGTCGAGATGATCGTCCCTCAACTACCGCCGTATCCTGCCGATGC
-GGCGGAGTTGCTGGAATCTCTCGTGCTTGAGCATGGCGGTGCGCCATTAGGGCTGGTAGGATCGTCGCTG
-GGTGGTTATTACGCCACCTGGCTGTCGCAATGTTTTATGCTGCCGGCTGTGGTGGTGAATCCCGCCGTGC
-GGCCCTTTGAATTACTGACCGACTATCTCGGTCAGAACGAGAACCCCTACACCGGGCAGCAATATGTGCT
-AGAGTCTCGCCATATTTATGATCTTAAAGTCATGCAGATTGACCCGCTGGAAGCGCCGGACCTGATCTGG
-CTACTGCAACAGACGGGCGATGAAGTGCTGGATTACCGCCAGGCGGTGGCATATTACGCCTCCTGCCGTC
-AGACAGTGACCGAGGGTGGTAATCACGCATTCACGGGCTTCGAAGATTATTTCAACCAGATTGTCGATTT
-TCTTGGACTGCACAGTTGCTGA
->g4_1_9 # 6052 # 7134 # 1 # ID=1_9;partial=00;start_type=ATG;rbs_motif=None;rbs_spacer=None;gc_cont=0.525
-ATGAATAGCGGGGGAATTGCCGCCCGGCTGGTCAATTTTGCCAAACTGTTTACTGGCAAACTGCCCGGCT
-CGCTCTCTTATACCAACATCGTCGGCAATATGATGTTCGGTGCAATTTCCGGATCGGCAATTGCCGCCTC
-AACCTCCATCGGCGGCGTGATGGTGCCGATGAGCGCGCGCGAAGGTTACGATCGCGGCTTTGCGGCCGCG
-GTGAATATCGCCTCCGCGCCGACGGGAATGTTAATTCCGCCCACCACGGCTTTTATCCTTTATGCGCTGG
-CAAGCGGGGGAACATCGATTGCCGCTCTGTTCGCCGGCGGTCTGGTCGCGGGAGTGCTGTGGGGCGTTGG
-CTGTATGCTGGTCACGCTGGTGGTCGCTAAGCGTCGAAATTATCGGGTTTTCTTCACCGTCCAAAAAGGC
-ATGGCGCTAAAAGTTGCCGTTGAGGCCATTCCCAGCCTGCTGCTGATCGTGATTATCGTCGGCGGCATTG
-TGCAGGGGATTTTCACCGCCATTGAAGCCTCCGCGATTGCCGTGGTGTATACATTATTGTTGACGATGGT
-GTTTTACCGCACGCTGAAAATTAAGGATTTGCCTTCGATTTTGCTCCAGACAGTGGTAATGACCGGGGTC
-ATCATGTTCCTGCTGGCAACCTCTTCGGCGATGTCCTTCTCGATGTCGATCACCAATATTCCTGCGGCGC
-TGAGCGATATGATCCTCGGTATTTCCGCCAATAAACTGGTTATCCTGTTAGTCATTACCGTCTTTTTGTT
-GATTATCGGCGCATTTATGGATATCGGTCCGGCCATTCTGATTTTTACCCCGATTCTGCTGCCGATCATG
-GCTAAACTGGGCGTCGATCCGGTGCATTTTGGCATTATCATGATCTATAACCTGGCGATTGGCACCATTA
-CGCCGCCAGTTGGCAGTGGTTTATATGTCGGGGCGAGCGTCGGTAAGGTCAAAGTTGAGGAAGTGATTAA
-ACCGTTGCTGCCTTTTTACGGCGCGATTATCGGCGTTCTGTTATTAATTACCTACATTCCGGAAATCACA
-CTGTTCTTACCCCGTCTACTGGGCATCATGTAA
diff --git a/Examples/2-res-Annotate-prodigal/tmp_files/genome4.fst_prodigal-split5N.fna-prodigalRes/GEN4.1111.00001.gff b/Examples/2-res-Annotate-prodigal/tmp_files/genome4.fst_prodigal-split5N.fna-prodigalRes/GEN4.1111.00001.gff
deleted file mode 100644
index 8d18ee18d50829eea540a74590cb3c173b6e5213..0000000000000000000000000000000000000000
--- a/Examples/2-res-Annotate-prodigal/tmp_files/genome4.fst_prodigal-split5N.fna-prodigalRes/GEN4.1111.00001.gff
+++ /dev/null
@@ -1,12 +0,0 @@
-##gff-version  3
-# Sequence Data: seqnum=1;seqlen=7134;seqhdr="g4_1"
-# Model Data: version=Prodigal.v2.6.3;run_type=Metagenomic;model="20|Escherichia_coli_UMN026|B|50.7|11|1";gc_cont=50.70;transl_table=11;uses_sd=1
-g4_1	Prodigal_v2.6.3	CDS	1	831	106.7	+	0	ID=1_1;partial=10;start_type=Edge;rbs_motif=None;rbs_spacer=None;gc_cont=0.579;conf=100.00;score=106.71;cscore=103.49;sscore=3.22;rscore=0.00;uscore=0.00;tscore=3.22;
-g4_1	Prodigal_v2.6.3	CDS	861	1241	42.3	+	0	ID=1_2;partial=00;start_type=ATG;rbs_motif=None;rbs_spacer=None;gc_cont=0.533;conf=100.00;score=43.30;cscore=49.63;sscore=-6.33;rscore=-8.50;uscore=-2.74;tscore=3.95;
-g4_1	Prodigal_v2.6.3	CDS	1271	2074	143.6	+	0	ID=1_3;partial=00;start_type=ATG;rbs_motif=AGGAG;rbs_spacer=5-10bp;gc_cont=0.591;conf=100.00;score=144.59;cscore=127.77;sscore=16.82;rscore=14.84;uscore=-2.92;tscore=3.95;
-g4_1	Prodigal_v2.6.3	CDS	2111	3514	138.1	+	0	ID=1_4;partial=00;start_type=ATG;rbs_motif=None;rbs_spacer=None;gc_cont=0.512;conf=100.00;score=138.96;cscore=143.16;sscore=-4.20;rscore=-8.50;uscore=-0.53;tscore=3.95;
-g4_1	Prodigal_v2.6.3	CDS	3535	4308	99.1	+	0	ID=1_5;partial=00;start_type=ATG;rbs_motif=3Base/5BMM;rbs_spacer=13-15bp;gc_cont=0.532;conf=100.00;score=100.11;cscore=105.95;sscore=-5.84;rscore=-6.58;uscore=-4.27;tscore=3.95;
-g4_1	Prodigal_v2.6.3	CDS	4327	5094	50.2	+	0	ID=1_6;partial=00;start_type=GTG;rbs_motif=None;rbs_spacer=None;gc_cont=0.544;conf=100.00;score=51.24;cscore=64.63;sscore=-13.39;rscore=-8.50;uscore=0.66;tscore=-6.63;
-g4_1	Prodigal_v2.6.3	CDS	5138	5398	23.6	+	0	ID=1_7;partial=00;start_type=ATG;rbs_motif=GGA/GAG/AGG;rbs_spacer=5-10bp;gc_cont=0.483;conf=99.64;score=24.44;cscore=15.14;sscore=9.29;rscore=2.79;uscore=1.75;tscore=3.95;
-g4_1	Prodigal_v2.6.3	CDS	5413	5994	54.9	+	0	ID=1_8;partial=00;start_type=ATG;rbs_motif=None;rbs_spacer=None;gc_cont=0.546;conf=100.00;score=56.05;cscore=59.63;sscore=-3.58;rscore=-8.50;uscore=-0.15;tscore=3.95;
-g4_1	Prodigal_v2.6.3	CDS	6052	7134	135.9	+	0	ID=1_9;partial=00;start_type=ATG;rbs_motif=None;rbs_spacer=None;gc_cont=0.525;conf=100.00;score=136.58;cscore=141.36;sscore=-4.77;rscore=-8.50;uscore=-0.88;tscore=3.95;
diff --git a/Examples/2-res-Annotate-prokka/Genes/EXAM.1216.00002.gen b/Examples/2-res-Annotate-prokka/Genes/EXAM.1216.00002.gen
deleted file mode 100644
index c5707189d49726c878363e570f73d854524df6ff..0000000000000000000000000000000000000000
--- a/Examples/2-res-Annotate-prokka/Genes/EXAM.1216.00002.gen
+++ /dev/null
@@ -1,158 +0,0 @@
->EXAM.1216.00002.0001b_00001 831 amiD_1 | N-acetylmuramoyl-L-alanine amidase AmiD | 3.5.1.28 | similar to AA sequence:UniProtKB:P75820 | COG:COG3023
-ATGAGAGCGCTACTGTGGCTGGTGGGTCTTGCGTTGCTGTTAACAGGCTGCGCGAGCGAA
-AAAGGAATTATCGATGAAGAGGGATATCAGCTTGATACCCGACATCGGGCGCAGGCGGCC
-TATCCGCGCATTAAAGTCCTGGTGATTCACTATACGGCGGAAAACTTTGACGTTTCGCTG
-GCGACGTTAACGGGCCGCAACGTCAGTTCGCATTACCTGATTCCCGCAACCCCGCCATTA
-TATGGCGGTAAACCGCGCATCTGGCAACTGGTGCCGGAACAGGATCAGGCCTGGCATGCG
-GGCGTCAGTTTCTGGCGAGGCGCCACGCGTCTCAATGATACGTCTATTGGCATTGAGCTG
-GAAAATCGCGGCTGGCGAATGTCCGGCGGGGTGAAATCTTTCGCGCCGTTTGAATCCGCG
-CAAATTCAGGCATTGATTCCGTTAGCGAAGGACATTATCGCGCGCTATGACATCAAACCG
-CAGAATGTGGTGGCCCATGCGGATATCGCGCCGCAGCGTAAAGACGATCCCGGCCCGCGC
-TTCCCGTGGCGCGAGCTGGCGGCACAGGGGATTGGCGCCTGGCCTGACGCCCAGCGTGTG
-GCGTTTTATCTGGCTGGACGCGCGCCGTATACGCCAGTCGATACCGCAACGGTGCTTGCG
-TTACTCTCGCGCTATGGCTATGAAGTCAAAGCCGATATGACGGCGCGCGAGCAACAGCGG
-GTGATTATGGCGTTCCAGATGCACTTCCGTCCGGCGCAATGGAACGGTATCGCAGATGCC
-GAAACGCAGGCGATTGCCGAAGCATTACTGGAGAAGTACGGCCAGGATTAA
->EXAM.1216.00002.0001i_00002 831 amiD_2 | N-acetylmuramoyl-L-alanine amidase AmiD | 3.5.1.28 | similar to AA sequence:UniProtKB:P75820 | COG:COG3023
-ATGAGAGCGCTACTGTGGCTGGTGGGTCTTGCGTTGCTGTTAACAGGCTGCGCGAGCGAA
-AAAGGAATTATCGATGAAGAGGGATATCAGCTTGATACCCGACATCGGGCGCAGGCGGCC
-TATCCGCGCATTAAAGTCCTGGTGATTCACTATACGGCGGAAAACTTTGACGTTTCGCTG
-GCGACGTTAACGGGCCGCAACGTCAGTTCGCATTACCTGATTCCCGCAACCCCGCCATTA
-TATGGCGGTAAACCGCGCATCTGGCAACTGGTGCCGGAACAGGATCAGGCCTGGCATGCG
-GGCGTCAGTTTCTGGCGAGGCGCCACGCGTCTCAATGATACGTCTATTGGCATTGAGCTG
-GAAAATCGCGGCTGGCGAATGTCCGGCGGGGTGAAATCTTTCGCGCCGTTTGAATCCGCG
-CAAATTCAGGCATTGATTCCGTTAGCGAAGGACATTATCGCGCGCTATGACATCAAACCG
-CAGAATGTGGTGGCCCATGCGGATATCGCGCCGCAGCGTAAAGACGATCCCGGCCCGCGC
-TTCCCGTGGCGCGAGCTGGCGGCACAGGGGATTGGCGCCTGGCCTGACGCCCAGCGTGTG
-GCGTTTTATCTGGCTGGACGCGCGCCGTATACGCCAGTCGATACCGCAACGGTGCTTGCG
-TTACTCTCGCGCTATGGCTATGAAGTCAAAGCCGATATGACGGCGCGCGAGCAACAGCGG
-GTGATTATGGCGTTCCAGATGCACTTCCGTCCGGCGCAATGGAACGGTATCGCAGATGCC
-GAAACGCAGGCGATTGCCGAAGCATTACTGGAGAAGTACGGCCAGGATTAA
->EXAM.1216.00002.0001i_00003 474 hpcD | 5-carboxymethyl-2-hydroxymuconate Delta-isomerase | 5.3.3.10 | similar to AA sequence:UniProtKB:Q05354 | NA
-ATGCCGAAACGCAGGCGATTGCCGAAGCATTACTGGAGAAGTACGGCCAGGATTAACAGG
-GCGCGGTATCGCGAGGACTCTCTCTTCGAGGACATGCCGCACTTTATTGCTGAATGTACT
-GAAAATATTCGCGAGCAGGCTGATTTACCCGGCCTGTTCAGCAAGGTAAACGAGGCGCTG
-GCCGCCAGCGGGATTTTCCCCATCGGCGGTATCCGCAGTCGCGCCCACTGGCTGGATACC
-TGGCAGATGGCTGACGGTAAGCATGATTACGCGTTTGTGCATATGACGCTGAAAATCGGC
-GCCGGGCGCAGCCTGGAGAGCCGTCAGGAAGTCGGCGAAATGCTGTTCGGGCTGATTAAA
-GCCCACTTCGCCGACCTGATGGAGAACCGCTATCTGGCGCTGTCGTTTGAGATTGCCGAG
-TTACATCCAACGCTCAATTACAAACAAAACAACGTACACGCGTTATTTAAATAG
->EXAM.1216.00002.0001i_00004 225 pspB | Phage shock protein B | NA | similar to AA sequence:UniProtKB:P0AFM9 | NA
-ATGAGCGCGCTATTTCTGGCCATCCCGTTAACCATTTTTGTGTTGTTTGTGTTACCGATT
-TGGCTGTGGCTGCATTACAGCAACCGCGCCGGTCGGGGAGAACTGTCGCAAAGCGAGCAG
-CAACGCTTACTGCAACTCACAGACGACGCGCAACGTATGCGCGAGCGCATTCAGGCGCTG
-GAAGACATTCTTGATGCAGAGCATCCGAACTGGAGAGAGCGCTAA
->EXAM.1216.00002.0001i_00005 1404 NA | hypothetical protein | NA | NA | NA
-ATGCCCGCGACTAAATTCTCCCGACGTACCCTCCTGACGGCAGGTTCTGCGCTTGCTGTT
-CTTCCTTTCCTGCGCGCCTTGCCGGTACAGGCGCGTGAACCTCGCGAGACCGTCGATATT
-AAGGATTATCCGGCGGATGACGGTATCGCCTCGTTCAAACAGGCCTTCGCCGACGGACAG
-ACCGTGGTCGTACCGCCAGGATGGGTGTGTGAAAATATCAATGCGGCGATAACGATTCCG
-GCGGGAAAAACGCTGCGGGTACAGGGCGCGGTGCGTGGGAATGGCCGGGGACGGTTTATT
-TTGCAGGACGGGTGTCAGGTGGTGGGGGAGCAGGGCGGCAGTCTGCACAATGTGACGCTG
-GATGTTCGCGGGTCGGACTGTGTGATTAAAGGCGTGGCGATGAGCGGCTTTGGCCCCGTC
-GCGCAAATTTTCATCGGTGGTAAGGAACCGCAGGTGATGCGTAATCTCATTATCGATGAC
-ATCACCGTTACCCACGCCAACTACGCCATTCTCCGCCAGGGATTTCATAACCAAATGGAC
-GGCGCGAGGATTACGCATAGCCGCTTTAGCGATTTACAGGGGGACGCCATTGAGTGGAAT
-GTCGCGATTCACGACCGCGATATCCTGATTTCCGATCATGTCATCGAACGCATTGATTGT
-ACCAATGGCAAAATCAACTGGGGGATCGGCATCGGGCTGGCGGGTAGCACCTATGACAAC
-AGTTATCCTGAAGACCAGGCAGTAAAAAACTTTGTGGTGGCCAATATTACCGGATCTGAT
-TGCCGACAGCTTGTGCACGTAGAAAATGGCAAACATTTCGTCATTCGCAATGTCAAAGCC
-AAAAACATCACGCCCGATTTCAGTAAAAATGCGGGTATTGATAACGCAACGATCGCAATT
-TATGGCTGTGATAATTTCGTCATTGATAATATTGATATGACGAATAGTGCCGGGATGCTC
-ATCGGCTATGGCGTCGTTAAAGGAAAATACCTGTCAATTCCGCAAAACTTTAAATTAAAC
-GCTATTCGGTTGGATAATCGCCAGGTTGCTTATAAATTACGCGGCATTCAAATTTCCTCC
-GGCAACACCCCCTCTTTTGTCGCCATCACCAATGTACGGATGACGCGTGCTACGCTGGAA
-CTGCATAATCAACCGCAGCACCTCTTCCTGCGTAATATCAACGTGATGCAAACTTCAGCG
-ATTGGCCCGGCGTTAAAAATGCATTTCGATTTGCGTAAAGATGTCCGTGGTCAATTTATG
-GCCCGCCAGGACACGCTGCTTTCCCTCGCTAATGTTCATGCCATCAATGAAAACGGGCAG
-AGTTCCGTGGATATCGACAGGATTAATCACCAAACCGTGAATGTCGAAGCAGTGAATTTT
-TCGCTGCCGAAGCGGGGAGGGTAA
->EXAM.1216.00002.0001i_00006 774 hisP | Histidine transport ATP-binding protein HisP | NA | similar to AA sequence:UniProtKB:P02915 | COG:COG4598
-ATGTCAGAAAATAAATTACACGTTATCGATTTGCACAAACGCTACGGCGGTCATGAAGTG
-CTGAAAGGGGTATCGCTGCAGGCCCGCGCCGGAGATGTGATTAGCATCATCGGCTCGTCC
-GGCTCCGGTAAAAGCACTTTTTTGCGCTGTATTAACTTCCTCGAAAAACCGAGCGAAGAC
-GCGATTATCGTGAACGGTCAGAACATTAATCTGGTGCGCGACAAAGACGGGCAGCTCAAA
-GTGGCGGATAAAAATCAGCTACGCTTGTTGCGTACCCGCCTGACGATGGTGTTTCAGCAC
-TTTAACCTCTGGAGCCACATGACGGTGCTGGAAAATGTGATGGAAGCGCCGATTCAGGTA
-CTGGGATTAAGCAAGCACGACGCGCGCGAGCGGGCGTTGAAATATCTGGCGAAGGTGGGG
-ATTGATGAGCGCGCTCAGGGCAAATATCCCGTTCATCTCTCCGGTGGCCAACAGCAGCGC
-GTTTCTATTGCGCGCGCGCTGGCGATGGAACCTGACGTTTTACTGTTCGATGAACCCACT
-TCGGCGCTCGATCCTGAACTGGTCGGCGAAGTGTTGCGCATCATGCAACAACTGGCGGAA
-GAAGGCAAAACGATGGTGGTGGTCACGCATGAAATGGGCTTCGTTCGCCATGTCTCTTCG
-CACGTTATTTTTCTGCATCAGGGGAAAATTGAAGAAGAGGGCGATCCGGAGCAGGTGTTC
-GGCAATCCGCAAAGCCCGCGTTTACAGCAATTCCTGAAAGGCTCGCTGAAATAA
->EXAM.1216.00002.0001i_00007 792 trmD | tRNA (guanine-N(1)-)-methyltransferase | 2.1.1.228 | similar to AA sequence:UniProtKB:P0A873 | COG:COG0336
-ATGCGCGCGATATATCGGCGATGCGTGTTTATTGGCATCGTTAGCCTGTTTCCTGAAATG
-TTCCGCGCAATTACCGATTACGGGGTAACTGGCCGGGCAGTAAAAAATGGCCTGCTGAAC
-ATCCAAAGCTGGAGTCCTCGCGACTTCACGCATGACCGGCACCGTACCGTGGACGATCGT
-CCTTACGGCGGCGGACCAGGGATGTTAATGATGGTGCAACCCTTGCGGGACGCCATTCAC
-GCAGCAAAAGCCGCGGCAGGTGAAGGCGCTAAAGTGATTTATCTGTCGCCTCAGGGACGC
-AAGCTTGATCAAGCGGGCGTTAGCGAGCTGGCCACGAATCAGAAGCTTATTCTGGTGTGT
-GGTCGCTACGAAGGCGTAGATGAGCGCGTAATTCAGACCGAAATTGACGAAGAATGGTCA
-ATTGGCGATTACGTTCTCAGCGGTGGCGAACTACCGGCAATGACGCTGATTGACTCCGTC
-GCCCGGTTTATACCGGGAGTTCTGGGGCATGAAGCATCAGCAATCGAAGATTCGTTTGCT
-GATGGGTTGCTGGATTGTCCGCACTATACGCGCCCTGAAGTGTTAGAGGGGATGGAAGTA
-CCGCCAGTATTGCTGTCGGGAAACCATGCTGAGATACGTCGCTGGCGTTTGAAACAGTCG
-CTGGGCCGAACCTGGCTTAGAAGACCTGAACTTCTGGAAAACCTGGCTCTGACTGAAGAG
-CAAGCAAGGTTGCTGGCGGAGTTCAAAACAGAACACGCACAACAGCAGCATAAACATGAT
-GGGATGGCATAG
->EXAM.1216.00002.0001b_00008 288 NA | hypothetical protein | NA | NA | NA
-ATGAATAATCATTTTGGGAAAGGGTTAATGGCCGGGTTGCACGCGCCATATGCATATAGC
-GCGCATCATGCGGTGAATTTCTGTTCTGAGTATAAACGTGGCTTTGTATTGGGTTTTACA
-CACCGTATGTTCGAAAAGACCGGCGATCGTCAACTTAGCGCGTGGGAGGCTGGAATTCTG
-ACGCGTCGCTATGGTCTGGATAAAGAAATGGTGATGGATTTCTTTAAAGAGAATCATTCC
-GGGATGGCGGTTCGCTTCTTTATGGCCGGTTATCGACTCGAAGGTTGA
->EXAM.1216.00002.0002b_00009 582 NA | hypothetical protein | NA | NA | NA
-ATGTCTACGCTTCTCTATTTGCACGGATTCAACAGTTCCCCTCGCTCGGCAAAAGCGTGC
-CAGCTAAAAAACTGGCTGGCGGAGCGTCATCCGCATGTTGAGATGATCGTCCCTCAACTA
-CCGCCGTATCCTGCCGATGCGGCGGAGTTGCTGGAGTCTCTCGTGCTTGAGCATGGCGGT
-GCGCCATTAGGGCTGGTAGGATCGTCGCTGGGTGGTTATTACGCCACCTGGCTGTCGCAA
-TGTTTTATGCTGCCGGCTGTGGTGGTGAATCCCGCCGTGCGGCCCTTTGAATTACTGACC
-GACTATCTCGGTCAGAACGAGAACCCCTACACCGGGCAGCAATATGTGCTAGAGTCTCGC
-CATATTTATGATCTTAAAGTCATGCAGATTGACCCGCTGGAAGCGCCGGACCTGATCTGG
-CTACTGCAACAGACGGGCGATGAAGTGCTGGATTACCGCCAGGCGGTGGCATATTACGCC
-TCCTGCCGTCAGACAGTGACCGAGGGTGGTAATCACGCATTCACGGGCTTCGAAGATTAT
-TTCAACCAGATTGTCGATTTTCTTGGACTGCACAGTTGCTGA
->EXAM.1216.00002.0002b_00010 1308 dctM | C4-dicarboxylate TRAP transporter large permease protein DctM | NA | similar to AA sequence:UniProtKB:O07838 | COG:COG1593
-ATGATTGACCCTATTTTTGCGTCCTGTACGCTAATTGCCGTCTTTGTTGTTTTACTGGCC
-ATGGGCGCGCCTATCGGGATCTGCATCGTTATCGCCTCTTTCAGCACCATGATGCTGGTA
-CTGCCTTTCGATATTTCGATGTTCGCCACCGCGCAAAAAATGTTCTCCAGCCTGGACAGT
-TTTGCCTTGCTGGCCGTGCCGTTCTTCGTTTTGTCCGGGGTGATCATGAATAGCGGGGGA
-ATTGCCGCCCGGCTGATCAATTTTGCCAAACTGTTTACTGGCAAACTGCCCGGTTCGCTC
-TCTTATACCAACATCGTCGGCAATATGATGTTCGGTGCAATTTCCGGATCGGCAATTGCC
-GCCTCAACCTCCATCGGCGGCGTGATGGTGCCGATGAGCGCGCGCGAAGGTTACGATCGC
-GGCTTTGCGGCCGCGGTGAATATCGCCTCCGCGCCGACGGGAATGTTAATTCCGCCCACC
-ACGGCTTTTATCCTTTATGCGCTGGCAAGCGGGGGAACATCGATTGCCGCTCTGTTCGCC
-GGCGGTCTGGTCGCGGGAGTGCTGTGGGGCGTTGGCTGTATGCTGGTCACGCTGGTAGTC
-GCTAAGCGTCGAAATTATCGGGTTTTCTTCACCGTCCAAAAAGGCATGGCGCTAAAAGTT
-GCCGTTGAGGCCATTCCCAGCCTGTTACTGATCGTGATTATCGTCGGCGGCATTGTGCAG
-GGGATTTTCACCGCCATTGAAGCCTCCGCGATTGCCGTGGTGTATACGTTATTGCTGACG
-ATGGTGTTTTACCGCACGCTGAAAATTAAGGATTTGCCTTCGATTTTGCTCCAGACAGTG
-GTAATGACCGGGGTCATCATGTTCCTGCTGGCAACCTCTTCGGCGATGTCCTTCTCAATG
-TCGATCACCAATATTCCTGCGGCGCTGAGCGATATGATCCTCGGTATTTCCGCCAATAAA
-CTGGTTATCCTGTTAGTCATTACCGTCTTTTTGTTGATTATCGGCGCATTTATGGATATC
-GGTCCGGCCATTCTGATTTTTACCCCGATTCTGCTGCCGATCATGGCTAAACTGGGCGTC
-GATCCGGTGCATTTGGGCATTATCATGATCTATAACCTGGCGATTGGCACCATTACGCCG
-CCAGTTGGCAGTGGTTTATATGTCGGGGCGAGCGTCGGTAAGGTCAAAGTTGAGGAAGTG
-ATTAAACCGTTGCTGCCTTTTTACGGCGCGATTATCGGCGTTCTGTTATTAATTACCTAC
-ATTCCGGAAATCATACTGTTCTTACCCCGTCTACTGGGCATCATGTAA
->EXAM.1216.00002.0003b_00011 255 NA | hypothetical protein | NA | NA | NA
-ATGATAATTAATGGGAAATTAATTAAAGCAAAAGACTTAGCTAAGGCTGCAGGTGTATCT
-CGTTCAACAGTGATTAAATATTACGGCATTAGCCGTGAGAATTACGAAAGGGTAGCAACT
-GAAAGAAGGAAGCTTGCTTTTGAACTAAGAGCATCAGGTTTAAAATGGAAAGAAGTTGCT
-GAAAAAATGAACACGACAAAATATAGCGCAATTGCATATTATAGACGATATTTAGCATTA
-GAGAAAAACAAATAA
->EXAM.1216.00002.0003b_00012 780 NA | IS21 family transposase ISSen3 | NA | similar to AA sequence:ISfinder:ISSen3 | NA
-ATGGTCGAACTGCAACATCAACGGCTGATGGTGCTTGCCGAACAGCTCCAGCTGGACAGT
-CTTATCGGCGCAGCGCCGGCGCTGTCGCAACAGGCGGTGGATCAGGAATGGAGCTACATG
-GACTTCCTGGAGCACCTGTTACATGAGGAGAAACTGGCCCGGCATCAGCGTAAACAGGCG
-ATGTACACGCGGATGGCAGCCTTCCCGGCGGTAAAGACGTTCGAGGAGTACGACTTCACC
-TTCGCCACCGGCGCTCCTCAGAAGCAAATCCAGTCGCTGCGATCCCTGAGCTTCATAGAG
-CGTAACGAAAACATCGTGTTGCTGGGGCCATCGGGCGTGGGAAAAACGCATCTGGCGATA
-GCCATGGGCTACGAAGCAGTACGGGCGGGCATCAAGGTTCGCTTCACAACAGCAGCGGAC
-CTGCTGCTACAGCTGTCCACTTCACAGCGTCAGGGCCGTTACAAAACGACTCTCAATCGT
-GGTGTCATGGCCCCGAAGCTGCTTATCATCGATGAAATAGGTTATCTGCCGTTCAGTCAG
-GAGGAAGCCAAGCTGTTCTTCCAGGTCATCGCCAAACGTTACGAGAAGAGCGCGATGATC
-CTGACCTCCAACCTGCCGTTCGGGCAGTGGGATCAGACGTTCGCCGGTGATGCAGCGCTG
-ACATCGGCGATGCTGGACCGGATCTTACATCACTCACACGTCGTGCAAATAAAAGGGGAA
-AGCTATCGACTGAAGCAGAAACGAAAGGCCGGGGTTATAGCTGAAGCTAATCCTGAGTAA
diff --git a/Examples/2-res-Annotate-prokka/Genes/EXAM.1219.00001.gen b/Examples/2-res-Annotate-prokka/Genes/EXAM.1219.00001.gen
deleted file mode 100644
index f37fdbc34f13641a86980ab1d9e84dae65db691d..0000000000000000000000000000000000000000
--- a/Examples/2-res-Annotate-prokka/Genes/EXAM.1219.00001.gen
+++ /dev/null
@@ -1,169 +0,0 @@
->EXAM.1219.00001.0001b_00001 1668 glnS | Glutamine--tRNA ligase | 6.1.1.18 | similar to AA sequence:UniProtKB:P00962 | COG:COG0008
-ATGAGTGAGGCTGAAGCCCGCCCGACTAACTTTATTCGTCAGATTATTGATGAAGATCTG
-GCGAGTGGTAAACATACCACTGTCCATACCCGTTTTCCGCCGGAGCCGAATGGCTATCTG
-CATATCGGCCACGCGAAATCTATCTGCCTGAACTTTGGCATCGCGCAAGATTATCAGGGC
-CAGTGCAACCTGCGTTTCGATGACACCAACCCGGTAAAAGAAGATATCGAGTACGTTGAT
-TCGATCAAAAACGACGTCGAGTGGTTAGGCTTTCACTGGTCTGGCGATATTCGCTACTCC
-TCCGATTACTTTGACCAACTGCACGCCTATGCGGTCGAGCTAATCAATAAAGGCCTGGCC
-TATGTTGATGAGCTGACGCCGGAGCAGATCCGTGAATACCGCGGTACGCTGACCGCGCCG
-GGTAAAAACAGCCCGTTCCGCGATCGCAGCGTCGAAGAGAACCTCGCGCTATTTGAAAAA
-ATGCGTACCGGCGGTTTTGAAGAGGGTAAAGCCTGTCTGCGCGCTAAAATCGACATGGCG
-TCGCCGTTTATCGTGATGCGCGATCCGGTGCTGTATCGCATTAAATTCGCCGAGCATCAT
-CAGACTGGCAACAAGTGGTGCATCTATCCGATGTACGACTTTACTCACTGCATCAGCGAT
-GCGCTGGAAGGCATTACTCATTCTCTGTGTACGCTGGAGTTCCAGGATAACCGTCGTCTG
-TACGACTGGGTGCTGGACAACATCACCATTCCGGTTCACCCGCGCCAGTACGAATTCTCG
-CGCCTGAATCTGGAATACACCGTGATGTCCAAGCGTAAGCTGAACCTGCTGGTGACCGAC
-AAACACGTCGAAGGTTGGGACGATCCGCGTATGCCGACTATTTCCGGTCTGCGCCGTCGC
-GGCTATACCGCGGCTTCTATTCGTGAGTTCTGCAAACGCATCGGCGTCACCAAGCAGGAC
-AACACTATTGAGATGGCGTCGCTGGAATCCTGCATTCGCGAAGATCTGAACGAAAACGCG
-CCGCGCGCGATGGCGGTAATCGATCCGGTAAAACTGGTTATCGAAAATTACCCGCAGGGT
-GAGAGCGAAATGGTTACCATGCCTAACCATCCGAATAAACCGGAGATGGGCAGCCGTGAA
-GTGCCGTTTAGCGGTGAGATCTGGATCGATCGCGCAGATTTCCGCGAAGAAGCGAACAAA
-CAGTACAAACGTCTGGTGATGGGCAAAGAAGTGCGTCTGCGTAATGCCTACGTCATTAAA
-GCGGAGCGCGTAGAGAAGGATGCCGAAGGGAATATCACCACCATCTTCTGTACCTATGAT
-GCTGATACGCTGAGTAAAGATCCGGCTGACGGGCGTAAAGTGAAAGGCGTAATCCACTGG
-GTTAGCGCAGCACATGCGCTGCCGATTGAAATTCGTCTCTACGACCGTCTGTTCAGCGTG
-CCGAATCCGGGCGCCGCGGAGGACTTCCTGTCTGTTATCAACCCCGAATCATTAGTGATT
-AAGCAGGGGTATGGCGAGCCGTCGCTGAAAGCGGCGGTAGCAGGAAAAGCTTTCCAGTTT
-GAACGTGAAGGCTACTTCTGCCTCGACAGCCGCTATGCAACGGCCGATAAGCTGGTCTTT
-AACCGCACCGTGGGCCTGCGTGATACCTGGGCGAAAGCGGGCGAGTAA
->EXAM.1219.00001.0001b_00002 831 amiD | N-acetylmuramoyl-L-alanine amidase AmiD | 3.5.1.28 | similar to AA sequence:UniProtKB:P75820 | COG:COG3023
-ATGAAAGCGCTACTGTGGCTGGTGGGTCTCGCGTTGCTGTTAACAGGCTGCGCGAGCGAA
-AAAGGAATTATCGATAAAGAGGGATATCAGCTTGATACCCGACATCGGGCGCAGGCGGCC
-TATCCGCGCATTAAAGTCCTGGTGATTCACTATACGGCGGAAAACTTTGACGTTTCGCTG
-GCGACGTTAACGGGTCGCAACGTCAGTTCGCATTACCTGATTCCCGCAACCCCGCCATTA
-TATGGCGGTAAACCGCGCATCTGGCAACTGGTGCCGGAACAGGATCAGGCCTGGCATGCG
-GGCGTCAGTTTCTGGCGAGGCGCCACGCGTCTCAATGATACGTCTATTGGCATTGAGCTG
-GAAAATCGTGGTTGGCGAATGTCCGGCGGGGTGAAATCTTTCGCGCCGTTTGAATCCGCG
-CAAATTCAGGCATTGATTCCGTTAGCGAAGGATATTATCGCGCGCTATAACATCAAACCG
-CAGAATGTGGTGGCCCATGCGGATATCGCGCCGCAGCGTAAAGACGATCCCGGCCCGCGC
-TTCCCGTGGCGCGAGCTGGCGGCGCAGGGGATTAGCGCCTGGCCTGACGCCCAGCGTGTG
-GCGTTTTATCTGGCTGGACGCGCGCCGTATACGCCAGTCGATACCGCAACGGTGCTTGCG
-TTACTCTCGCGCTATGGCTATGAAGTCAAAGCCGATATGACGGCACGCGAGCAGCAGCGG
-GTGATTATGGCGTTCCAGATGCACTTCCGTCCGGCGCAATGGAACGGTATCGCAGATGCC
-GAAACGCAGGCGATTGCCGAAGCATTACTGGAGAAGTACGGCCAGGATTAA
->EXAM.1219.00001.0002b_00003 381 hpcD | 5-carboxymethyl-2-hydroxymuconate Delta-isomerase | 5.3.3.10 | similar to AA sequence:UniProtKB:Q05354 | NA
-ATGCCGCACTTTATTGCTGAATGTACTGAAAATATTCGCGAGCAGGCTGATTTACCCGGC
-CTGTTCAGCAAGGTAAACGAGGCGCTGGCCGCCAGCGGGATTTTCCCCATCGGCGGTATC
-CGCAGTCGCGCCCACTGGCTGGATACCTGGCAGATGGCTGACGGTAAGCATGATTACGCG
-TTTGTGCATATGACGCTGAAAATCGGCGCCGGGCGCAGCCTGGAGAGCCGTCAGGAAGTT
-GGCGAAATGCTGTTTGGGCTGATTAAAGCCCACTTCGCCGACCTGATGGAGAACCGCTAT
-CTGGCGCTGTCGTTTGAGATTGCCGAGCTACATCCGACGCTCAATTACAAACAAAACAAC
-GTACACGCGTTATTTAAATAG
->EXAM.1219.00001.0002i_00004 1410 NA | hypothetical protein | NA | NA | NA
-ATGAGCATGCCCGCGACTAAATTCTCCCGACGTACCCTCCTGACGGCAGGTTCTGCGCTT
-GCTGTTCTTCCTTTTCTGCGCGCCTTGCCGGTACAGGCGCGTGAACCTCGCGAGACCGTC
-GATATTAAGGATTATCCGGCGGATGACGGTATCGCCTCGTTCAAACAGGCCTTCGCCGAC
-GGACAGACCGTGGTCGTACCGCCAGGATGGGTGTGTGAAAATATCAATGCGGCGATAACG
-ATTCCGGCGGGAAAAACGCTGCGGGTACAGGGCGCGGTGCGTGGGAATGGCCGGGGACGG
-TTTATTTTGCAGGACGGGTGTCAGGTGGTGGGGGAGCAGGGCGGCAGTCTGCACAATGTG
-ACGCTGGATGTTCGCGGGTCGGACTGTGTGATTAAAGGCGTGGCGATGAGCGGCTTTGGC
-CCCGTCGCGCAAATTTTCATCGGTGGTAAGGAACCGCAGGTGATGCGTAATCTCATTATC
-GATGACATCACCGTTACCCACGCCAACTACGCCATTCTCCGCCAGGGATTTCATAACCAA
-ATGGATGGCGCGCGGATTACGCATAGCCGCTTTAGCGATTTACAGGGGGACGCCATTGAG
-TGGAATGTCGCGATTCACGACCGCGACATCCTGATTTCCGATCATGTCATCGAACGCATT
-AATTGTACCAATGGCAAAATCAACTGGGGGATCGGCATCGGGCTGGCGGGTAGCACCTAT
-GACAACAGTTATCCTGAAGACCAGGCAGTAAAAAACTTTGTGGTGGCCAATATTACCGGA
-TCTGATTGCCGACAGCTTGTGCACGTAGAAAATGGCAAACATTTCGTCATTCGCAATGTC
-AAAGCCAAAAACATCACGCCCGGTTTCAGTAAAAATGCGGGTATTGATAACGCAACGATC
-GCAATTTATGGCTGTGATAATTTCGTCATTGATAATATTGATATGACGAATAGTGCCGGG
-ATGCTCATCGGCTATGGCGTCGTTAAAGGAAAATACCTGTCAATTCCGCAAAACTTTAAA
-TTAAACGCTATTCGGTTGGATAATCGCCAGGTTGCTTATAAATTACGCGGCATTCAAATT
-TCCTCCGGCAACACCCCCTCTTTTGTCGCCATCACCAATGTACGGATGACGCGTGCTACG
-CTGGAACTGCATAATCAACCGCAGCACCTCTTTCTGCGCAATATCAACGTGATGCAAACT
-TCAGCGATTGGCCCGGCGTTAAAAATGCATTTCGATTTGCGTAAAGATGTACGTGGTCAA
-TTTATGGCCCGCCAGGACACGCTGCTTTCCCTCGCTAATGTTCATGCCATCAATGAAAAC
-GGGCAGAGTTCCGTGGATATCGACAGGATTAATCACCAAACCGTGAATGTCGAAGCAGTG
-AATTTTTCGCTGCCGAAGCGGGGAGGGTAA
->EXAM.1219.00001.0002i_00005 774 hisP | Histidine transport ATP-binding protein HisP | NA | similar to AA sequence:UniProtKB:P02915 | COG:COG4598
-ATGTCAGAAAATAAATTACACGTTATCGATTTGCACAAACGCTACGGCGGTCATGAAGTG
-CTGAAAGGGGTATCGCTGCAGGCCCGCGCCGGAGATGTGATTAGCATCATCGGCTCGTCC
-GGCTCCGGTAAAAGCACTTTTTTGCGCTGTATTAACTTCCTCGAAAAACCGAGCGAAGGC
-GCGATTATCGTGAACGGTCAGAACATTAATCTGGTGCGCGACAAAGATGGGCAGCTCAAA
-GTGGCGGATAAAAATCAGCTACGCTTGTTGCGTACCCGCCTGACGATGGTGTTTCAGCAC
-TTCAACCTCTGGAGCCACATGACGGTGCTGGAAAATGTGATGGAAGCGCCGATTCAGGTA
-CTGGGATTAAGCAAGCACGACGCGCGCGAGCGGGCGTTGAAATATCTGGCGAAGGTGGGG
-ATTGATGAGCGCGCTCAGGGCAAATATCCCGTCCATCTCTCCGGCGGCCAACAGCAGCGC
-GTTTCTATTGCGCGCGCGCTGGCGATGGAACCTGACGTTTTACTGTTCGATGAACCCACA
-TCGGCGCTCGATCCTGAACTGGTCGGCGAAGTGTTGCGCATCATGCAACAACTGGCGGAA
-GAAGGCAAAACGATGGTGGTGGTCACGCATGAAATGGGCTTCGCTCGCCATGTCTCTTCG
-CACGTTATTTTTCTGCATCAGGGGAAAATTGAAGAAGAGGGTGATCCGGAGCAGGTGTTC
-GGCAATCCGCAAAGCCCGCGTTTACAGCAATTCCTGAAAGGCTCGCTGAAATAA
->EXAM.1219.00001.0002i_00006 735 trmD_1 | tRNA (guanine-N(1)-)-methyltransferase | 2.1.1.228 | similar to AA sequence:UniProtKB:P0A873 | COG:COG0336
-ATGTTCCGCGCAATTACCGATTACGGGGTAACTGGCCGGGCAGTAAAAAAAGGCCTGCTG
-AACATCCAAAGCTGGAGTCCTCGCGACTTCGCGCATGACCGGCACCGTACCGTGGACGAC
-CGTCCTTACGGCGGCGGACCGGGGATGTTAATGATGGTGCAACCCTTGCGGGACGCCATT
-CACGCAGCAAAAGCCGCGGCAGGTGAAGGCGCTAAAGTGATTTATCTGTCGCCTCAGGGA
-CGCAAGCTTGATCAAGCGGGCGTTAGCGAGCTGGCCACGAATCAGAAGCTTATTCTGGTG
-TGTGGTCGCTACGAAGGCGTAGATGAGCGCGTAATTCAGACCGAAATTGACGAAGAATGG
-TCAATTGGCGATTACGTTCTCAGCGGTGGCGAACTACCGGCAATGACGCTGATTGACTCC
-GTCGCCCGGTTTATACCGGGGGTTCTGGGGCATGAGGCATCAGCAATCGAAGATTCGTTT
-GCTGATGGGTTGCTGGATTGTCCGCACTATACGCGCCCTGAAGTGTTAGAGGGGATGGAA
-GTACCGCCAGTATTGCTGTCGGGAAACCATGCTGAGATACGTCGCTGGCGTTTGAAACAG
-TCGCTGGGCCGAACCTGGCTTAGAAGACCTGAACTTCTGGAAAACCTGGCTCTGACTGAA
-GAGCAAGCAAGGTTGCTGGCGGAGTTCAAAACAGAACACGCACAACAGCAGCATAAACAT
-GATGGGATGGCATAG
->EXAM.1219.00001.0002i_00007 828 trmD_2 | tRNA (guanine-N(1)-)-methyltransferase | 2.1.1.228 | similar to AA sequence:UniProtKB:P0A873 | COG:COG0336
-ATGATGGGATGGCATAGCCGTCATATGGGCTCTCAGAGGAGACGCGCTAATGCGCAGTAC
-GTGTTTATTGGCATAGTTAGCCTGTTTCCTGAAATGTTCCGCGCAATTACCGATTACGGG
-GTAACTGGCCGGGCAGTAAAAAAAGGCCTGCTGAACATCCAAAGCTGGAGTCCTCGCGAC
-TTCGCGCATGACCGGCACCGTACCGTGGACGACCGTCCTTACGGCGGCGGACCGGGGATG
-TTAATGATGGTGCAACCCTTGCGGGACGCCATTCACGCAGCAAAAGCCGCGGCAGGTGAA
-GGCGCTAAAGTGATTTATCTGTCGCCTCAGGGACGCAAGCTTGATCAAGCGGGCGTTAGC
-GAGCTGGCCACGAATCAGAAGCTTATTCTGGTGTGTGGTCGCTACGAAGGCGTAGATGAG
-CGCGTAATTCAGACCGAAATTGACGAAGAATGGTCAATTGGCGATTACGTTCTCAGCGGT
-GGCGAACTACCGGCAATGACGCTGATTGACTCCGTCGCCCGGTTTATACCGGGGGTTCTG
-GGGCATGAGGCATCAGCAATCGAAGATTCGTTTGCTGATGGGTTGCTGGATTGTCCGCAC
-TATACGCGCCCTGAAGTGTTAGAGGGGATGGAAGTACCGCCAGTATTGCTGTCGGGAAAC
-CATGCTGAGATACGTCGCTGGCGTTTGAAACAGTCGCTGGGCCGAACCTGGCTTAGAAGA
-CCTGAACTTCTGGAAAACCTGGCTCTGACTGAAGAGCAAGCAAGGTTGCTGGCGGAGTTC
-AAAACAGAACACGCACAACAGCAGCATAAACATGATGGGATGGCATAG
->EXAM.1219.00001.0002i_00008 465 NA | hypothetical protein | NA | NA | NA
-ATGAAGTTTGTTGCGCCCGAACAGGCACCGGAACAGGCGGAGGTCATCAAAAATACGCCG
-TTCTGGCCTGATGTGGACCTGTCGGAATTTCGCAGTGTGATGCGCACTGACGGCACGGTG
-ACGCAGCCGCGTTTAAAGCAGGTCGTGCTGACGGCGATCTCTGAGGTTAACGCTGAGCTG
-TACGACTTCCGCAACCGTCAGCAGATGCTGGGCTGGCGGACACTTGCTGAGGTTCCCGCA
-GAAATGCTGGACGGTAAAAGCGAGCGTATCCGGCACTACCACAACGCTGTTTTTTGCTGG
-GCGCGCGCTGTGCTTAATGAGCGTTATCAGGACTATGACGCCACGGCGTCAGGCGTGAAG
-CGAGGGGAGGAGCTGGCGGAGGCCAGCGGCGATCTGTGGCGTGATGCCCGCTGGGCCATC
-AGCCGGGTGCAGGATGTACCGCACTGTACGGTGGAGCTTATCTGA
->EXAM.1219.00001.0002i_00009 261 NA | hypothetical protein | NA | NA | NA
-ATGGCCGGGTTGCACGCGCCATATGCATATAGCGCGCATCATGCGGTGAATTTCTGTTCT
-GAGTATAAACGTGGCTTTGTATTGGGTTTTACACACCGTATGTTCGAAAAGACCGGCGAT
-CGTCAACTTAGCGCGTGGGAGGCTGGAATTCTGACGCGTCGCTATGGTCTGGATAAAGAA
-ATGGTGATGGATTTCTTTAAAGAGAATCATTCCGGGATGGCGGTTCGCTTCTTTATGGCC
-GGTTATCGACTCGAAGGTTGA
->EXAM.1219.00001.0002i_00010 582 NA | hypothetical protein | NA | NA | NA
-ATGTCTACGCTTCTCTATTTGCACGGATTCAACAGTTCCCCTCGCTCGGCAAAAGCGTGC
-CAGCTAAAAAACTGGCTGGCGGAGCGTCATCCGCATGTTGAGATGATCGTCCCTCAGCTG
-CCGCCGTATCCTGCCGATGCGGCGGAGTTGCTGGAATCTCTCGTGCTTGAGCATGGCGGT
-GCGCCATTAGGGCTGGTAGGATCGTCGCTGGGTGGTTATTACGCCACCTGGCTGTCGCAA
-TGTTTTATGCTGCCGGCTGTGGTGGTGAATCCCGCCGTGCGGCCCTTTGAATTACTGACC
-GACTATCTCGGTCAGAACGAGAACCCCTACACCGGGCAGCAATATGTGCTAGAGTCTCGC
-CATATTTATGATCTTAAAGTCATGCAGATTGACCCGCTGGAAGCGCCGGACCTGATCTGG
-CTACTGCAACAGACGGGCGATGAAGTGCTGTATTACCGCCAGGCGGTGGCATATTACGCC
-TCCTGCCGTCAGACAGTGACCGAGGGTGGTAATCACGCATTCACGGGCTTCGAAGATTAT
-TTCAACCAGATTGTCGATTTTCTTGGACTGCACAGTTGCTGA
->EXAM.1219.00001.0002b_00011 1308 dctM | C4-dicarboxylate TRAP transporter large permease protein DctM | NA | similar to AA sequence:UniProtKB:O07838 | COG:COG1593
-ATGATTGACCCTATTTTTGCGTCCTGTACGCTAATTGCCGTCTTTGTTGTTTTACTGGCC
-ATGGGCGCGCCTATCGGGATCTGCATCGTTATCGCCTCTTTCAGCACCATGATGCTGGTA
-CTGCCTTTCGATATTTCGATGTTCGCCACCGCGCAAAAAATGTTCTCCAGCCTGGACAGT
-TTTGCCTTGCTGGCCGTGCCGTTCTTCGTTTTGTCCGGGGTGATCATGAATAGCGGGGGA
-ATTGCCGCCCGGCTGGTCAATTTTGCCAAACTGTTTACTGGCAAACTGCCCGGCTCGCTC
-TCTTATACCAACATCGTCGGCAATATGATGTTCGGTGCAATTTCCGGATCGGCGATTGCC
-GCCTCAACCTCCATCGGCGGCGTGATGGTGCCGATGAGCGCGCGCGAAGGTTACGATCGC
-GGCTTTGCGGCCGCGGTGAATATCGCCTCCGCGCCGACGGGAATGTTAATTCCGCCCACC
-ACGGCTTTTATCCTTTACGCGCTGGCAAGCGGGGGAACATCGATTGCCGCTCTGTTCGCC
-GGCGGTCTGGTCGCGGGAGTGCTGTGGGGCGTTGGCTGTATGCTGGTCACGCTGGTGGTC
-GCTAAGCGTCGAAATTATCGGGTTTTCTTCACCGTCCAAAAAGGTATGGCGCTAAAAGTT
-GCCGTTGAGGCCATTCCCAGCCTGCTGCTGATCGTGATTATTGTCGGCGGCATTGTGCAG
-GGGATTTTCACCGCCATTGAAGCCTCCGCGATTGCCGTGGTGTATACGTTATTGCTGACG
-ATGGTGTTTTACCGCACGCTGAAAATTAAGGATTTGCCTTCGATTTTGCTCCAGACAGTG
-GTAATGACCGGGGTCATCATGTTCCTGCTGGCAACCTCTTCGGCGATGTCCTTCTCGATG
-TCGATCACCAATATTCCTGCGGCGCTGAGCGATATGATCCTCGGTATTTCCGCCAATAAA
-CTGGTTATCCTGTTAGTCATTACCGTCTTTTTGTTGATTATCGGCGCATTTATGGATATT
-GGTCCGGCCATTCTGATTTTTACCCCGATTCTGCTGCCAATCATGGCTAAACTGGGCGTC
-GATCCGGTGCATTTCGGCATTATCATGATCTATAACCTGGCGATTGGCACCATTACGCCG
-CCAGTTGGCAGTGGTTTATATGTCGGGGCGAGCGTCGGTAAGGTCAAAGTTGAGGAAGTG
-ATTAAACCGTTGCTGCCTTTTTACGGCGCGATTATCGGCGTTCTGTTATTAATTACCTAC
-ATTCCGGAAATCACACTGTTCTTACCCCGTCTACTGGGCATCATGTAA
diff --git a/Examples/2-res-Annotate-prokka/Genes/GEN2.1219.00001.gen b/Examples/2-res-Annotate-prokka/Genes/GEN2.1219.00001.gen
deleted file mode 100644
index ee6a29abcdee2a5214c7c188082d284a502bcb4c..0000000000000000000000000000000000000000
--- a/Examples/2-res-Annotate-prokka/Genes/GEN2.1219.00001.gen
+++ /dev/null
@@ -1,185 +0,0 @@
->GEN2.1219.00001.0001b_00001 774 hisP | Histidine transport ATP-binding protein HisP | NA | similar to AA sequence:UniProtKB:P02915 | COG:COG4598
-ATGTCAGAAAATAAATTACACGTTATCGATTTGCACAAACGCTACGGCGGTCATGAAGTG
-CTGAAAGGGGTATCGCTGCAGGCCCGCGCCGGAGATGTGATTAGCATTATCGGCTCGTCC
-GGTTCCGGTAAAAGCACTTTTTTGCGCTGCATTAACTTCCTCGAAAAATCGAGCGAAGGC
-GCGATTATCGTGAACGGTCAGAACATTAATCTGGTGCGCGACAAAGACGGGCAGCTCAAA
-GTGGCGGATAAAAATCAGCTACGCTTGTTGCGTACCCGCCTGACGATGGTGTTTCAGCAC
-TTTAACCTCTGGAACCACATGACGGTGCTGGAAAATGTGATGGAAGCGCCGATTCAGGTA
-CTGGGATTAAGCAAGCACGACGCGCGCGAGCGGGCGTTGAAATATCTGGCGAAGGTGGGG
-ATTGATGAGCGCGCTCAGGGCAAATATCCCGTCCATCTCTCCGGCGGCCAACAGCAGCGC
-GTTTCTATTGCGCGCGCGCTGGCGATGGAACCTGACGTTTTACTGTTCGATGAACCCACA
-TCGGCGCTCGATCCTGAACTGGTCGGCGAAGTGTTGCGCATCATGCAACAACTGGCGGAA
-GAAGGCAAAACGATGGTGGTGGTCACGCATGAAATGGGCTTCGCCCGCCATGTCTCTTCG
-CACGTGATTTTTCTGCATCAGGGGAAAATTGAAGAAGAGGGCAATCCGGAGCAGGTGTTC
-GGCAATCCGCAAAGCCCGCGTTTACAGCAATTCCTGAAAGGCTCGCTGAAATAA
->GEN2.1219.00001.0001b_00002 1404 NA | hypothetical protein | NA | NA | NA
-ATGCCCGCGACTAAATTCTCCCGACGTACCCTCCTGACGGCAGGTTCCGCGCTTGCTGTT
-CTTCCTTTTCTGCGCGCCTTGCCGGTACAGGCGCGTGAACCTCGCCAGACCGTCGATATT
-AAGGATTATCCGGCGGATGACGGTATCGCCTCGTTCAAACAGGCCTTCGCCGACGGGCAG
-ACTGTGGTCGTGCCGTCAGGATGGGTGTGTGAAAATATCAATGCGGCGATAACGATTCCG
-GCGGGAAAAACGCTGCGGATACAGGGCGCGGTGCGTGGGAATGGCCGGGGACGGTTTATT
-TTGCTGGACGGGTGTCAGGTGGTGGGGGAGCAGGGCGGCAGTCTGCACAATGTGACGCTG
-GATGTTCGCGGGTCGGACTGTGTGATTAAAGGCGTGACGATGAGCGGCTTTGGCCCCGTC
-GCGCAAATTTTCATCGGCGGTAAGGAACCGCAGGTGATGCGTAATCTCATTATCGATGAC
-ATCACCGTTACCCACGCCAACTACGCCATTCTCCGCCAGGGATTTCATAACCAAATGGAC
-GGCGCGCGGATTACGCATAGTCGCTTTAGCGATTTGCAGGGGGACGCCATTGAGTGGAAT
-GTCGCGATTCATGACCGCGACATCCTGATTTCCGATCATGTCATCGAACGCATTGATTGT
-ACCAATGGCAAAATCAACTGGGGGATCGGCATCGGGCTGGCGGGTAGCGCCTATGACAAT
-AGTTATCCTGAAGACCAGGCAGTAAAAAACTTTGTGGTGGCCAATATTACCGGATCTGAT
-TGCCGACAACTGGTACACGTAGAAAATGGCAAACATTTCGTCATTCGCAATGTCAAAGCC
-AAAAACATCACGCCCGATTTCAGTAAAAATGCGGGTATTGATAACGCAACGATCGCCATT
-TATGGCTGTGATAATTTCGTCATTGATAATATTGATATGACGAATAGTGCCGGGATGCTC
-ATCGGCTATGGCGTCGTTAAAGGAAAATACCTGTCAATTCCGCAAAACTTTAAATTAAAC
-GCTATTCGGTTGGATAATCGCCAGGTTGCTTATAAATTACGCGGCATTCAAATTTCCTCC
-GGTAACGCCCCCTCATTTGTTGCCATCACCAATGTACGGATGACGCGTGCTACGCTGGAA
-CTGCATAATCAACCGCAGCACCTCTTTTTGCGTAATATCAACGTGATGCAAACTTCAGCG
-ATTGGCCCGGCGTTAAAAATGCATTTTGATTTGCGTAAAGATGTCCGTGGTCAATTTATG
-GCCCGCCAGGACACGCTGCTTTCCCTCGCTAATGTTCATGCCATCAATGAAAACGGGCAG
-AGTTCCGTGGATATCGACAGGATTAATCACCAAACCGTGAATGTCGAAGCAGTGAATTTT
-TCGCTGCCGAAGCGGGGAGGGTAA
->GEN2.1219.00001.0002b_00003 225 pspB | Phage shock protein B | NA | similar to AA sequence:UniProtKB:P0AFM9 | NA
-ATGAGCGCGCTATTTCTGGCCATCCCGTTAACCATTTTTGTGTTGTTTGTGTTACCGATT
-TGGCTGTGGCTGCATTACAGCAACCGCGCCGGTCGGGGAGAACTGTCGCAAAGCGAGCAG
-CAACGCTTACTGCAACTCACAGACGACGCGCAACGTATGCGCGAGCGCATTCAGGCGCTG
-GAAGATATTCTTGATGCAGAGCATCCGAACTGGAGAGAGCGCTAA
->GEN2.1219.00001.0002i_00004 381 hpcD | 5-carboxymethyl-2-hydroxymuconate Delta-isomerase | 5.3.3.10 | similar to AA sequence:UniProtKB:Q05354 | NA
-ATGCCGCACTTTATTGCTGAATGTACTGAAAATATTCGCGAGCAGGCTGATTTACCAAGC
-CTGTTCAGCAAGGTAAACGAGGCGCTGGCCGCCACCGGGATTTTCCCCATCGGCGGTATC
-CGCAGTCGCGCCCACTGGCTGGATACCTGGCAGATGGCTGACGGTAAGCATGATTACGCG
-TTTGTGCATATGACGCTGAAAATCGGCGCCGGGCGCAGCCTGGAGAGCCGTCAGGAAGTC
-GGCGAAATGCTGTTTGGGCTGATTAAAGCCCACTTCGCCGACCTGATGGAGAACCGCTAT
-CTGGCGCTGTCGTTTGAGATTGCCGAGTTACATCCAACGCTCAATTACAAACAAAACAAC
-GTACACGCGTTATTTAAATAG
->GEN2.1219.00001.0002i_00005 834 amiD | N-acetylmuramoyl-L-alanine amidase AmiD | 3.5.1.28 | similar to AA sequence:UniProtKB:P75820 | COG:COG3023
-ATGATGAAAGCGCTACTGTGGCTGGTTGGTCTCGCGTTGCTGTTAACAGGCTGCGCGAGC
-GAAAAAGGAATTATCGATAAAGAGGGATATCAGCTTGATACCCGACATCGGGCGCAGGCG
-GCCTATCCGCGCATTAAAGTCCTGGTGATTCACTATACGGCGGAAAACTTTGACGTTTCG
-CTGGCGACGTTAACGGGTCGCAACGTCAGTTCGCATTACCTGATTCCCGCAACCCCGCCA
-TTATATGGCGGTAAACCGCGCATCTGGCAACTGGTGCCGGAACAGGATCAGGCTTGGCAT
-GCGGGCGTCAGTTTCTGGCGAGGCGCCACGCGTCTCAATGATACGTCTATTGGCATTGAG
-CTGGAAAATCGCGGCTGGCGAATGTCCGGCGGGGTGAAATCTTTCGCGCCGTTTGAATCC
-GCGCAAATTCAGGCATTGATCCCGTTAGCGAAGGACATTATCGCGCGCTATGACATCAAA
-CCGCAGAATGTGGTGGCCCATGCGGATATCGCGCCGCAGCGTAAAGACGATCCCGGCCCG
-CGCTTCCCGTGGCGCGAGCTGGCGGCACAGGGGATTGGCGCCTGGCCTGACGCCCAGCGT
-GTGGCGTTTTATCTGGCTGGACGCGCGCCGTATACGCCAGTCGATACCGCAACGGTGCTT
-GCGTTACTCTCGCGCTATGGCTATGAAGTCAAAGCCGATATGACGGCGCGCGAGCAACAG
-CGGGTGATTATGGCGTTCCAGATGCACTTCCGTCCGGCGCAATGGAACGGTATCGCAGAT
-GCCGAAACGCAGGCGATTGCCGAAGCATTACTGGAGAAGTACGGCCAGGATTAA
->GEN2.1219.00001.0002b_00006 1668 glnS | Glutamine--tRNA ligase | 6.1.1.18 | similar to AA sequence:UniProtKB:P00962 | COG:COG0008
-ATGAGTGAGGCTGAAGCCCGCCCGACTAACTTTATTCGTCAGATTATTGATGAAGATCTG
-GCGAGTGGTAAACATACCACTGTCCATACCCGTTTTCCGCCGGAGCCGAATGGCTATCTG
-CACATCGGCCACGCGAAATCTATCTGCCTGAACTTTGGCATCGCGCAAGATTATCAGGGC
-CAGTGCAACCTGCGTTTCGATGACACCAACCCGGTAAAAGAAGATATCGAGTACGTTGAT
-TCGATCAAAAACGACGTCGAGTGGTTAGGCTTTCACTGGTCTGGCGATATTCGCTACTCC
-TCCGATTACTTTGACCAACTGCACGCCTATGCGGTCGAGCTCATCAATAAAGGCCTGGCC
-TACGTTGATGAGCTGACGCCGGAGCAGATCCGCGAATACCGTGGTACGCTGACCGCGCCG
-GGTAAAAACAGCCCGTTCCGCGATCGCAGCGTGGAAGAAAACCTCGCGCTATTTGAAAAA
-ATGCGTACCGGCGGTTTTGAAGAGGGTAAAGCCTGTCTGCGCGCTAAAATCGACATGGCG
-TCGCCGTTTATCGTGATGCGCGATCCGGTGCTGTATCGCATTAAATTCGCCGAGCATCAT
-CAGACCGGCACGAAGTGGTGCATCTATCCGATGTACGACTTTACTCACTGCATCAGCGAT
-GCGCTGGAAGGCATTACTCATTCTCTGTGTACGCTGGAGTTCCAGGACAACCGTCGTCTG
-TACGACTGGGTGCTGGACAACATCACCATTCCGGTTCACCCGCGCCAGTACGAATTCTCG
-CGCCTGAATCTGGAATACACCGTGATGTCCAAGCGTAAGCTGAACCTGCTGGTGACCGAC
-AAACACGTCGAAGGTTGGGATGATCCGCGTATGCCGACTATTTCCGGTCTGCGCCGTCGC
-GGCTATACCGCGGCTTCTATTCGTGAGTTCTGCAAACGCATCGGCGTCACCAAGCAGGAC
-AACACTATTGAGATGGCGTCGCTGGAATCCTGCATTCGCGAAGATCTGAACGAAAACGCG
-CCGCGCGCGATGGCGGTAATCGATCCGGTAAAACTGGTTATCGAAAACTACCCGCAGGGC
-GAGAGCGAAATGGTTACCATGCCTAACCATCCGAATAAACCGGAGATGGGCAGCCGTGAA
-GTGCCGTTTAGCGGTGAGATCTGGATCGATCGCGCGGATTTCCGCGAAGAAGCGAACAAA
-CAGTACAAACGTCTGGTGATGGGCAAAGAAGTGCGTCTGCGTAATGCCTACGTCATTAAA
-GCGGAGCGCGTAGAGAAGGATGCCGAAGGGAATATCACCACCATCTTCTGTACCTATGAT
-GCTGATACGCTGAGTAAAGATCCGGCTGACGGGCGTAAAGTGAAAGGCGTAATCCACTGG
-GTTAGCGTAGCACATGCGCTGCCGATTGAAATTCGTCTCTACGACCGTCTGTTCAGCGTG
-CCGAACCCGGGCGCCGCGGAGGACTTCCTGTCTGTTATCAACCCCGAATCATTAGTGATT
-AAGCAGGGGTATGGCGAGCCGTCGCTGAAAGCGGCGGTAGCAGGGAAAGCTTTCCAGTTT
-GAACGTGAAGGTTACTTCTGCCTTGACAGCCGCTATGCAACGGCCGATAAGCTGGTCTTT
-AACCGCACCGTGGGCCTGCGTGATACCTGGGCGAAAGCGGGCGAATAA
->GEN2.1219.00001.0003b_00007 768 trmD | tRNA (guanine-N(1)-)-methyltransferase | 2.1.1.228 | similar to AA sequence:UniProtKB:P0A873 | COG:COG0336
-GTGTTTATTGGCATCGTTAGCCTGTTTCCTGAAATGTTCCGCGCAATTACCGATTACGGG
-GTAACTGGCCGGGCAGTAAAAAAAGGCCTGCTGAACATCCAAAGCTGGAGTCCTCGCGAC
-TTCGCGCATGACCGGCACCGTACCGTGGACGACCGTCCTTACGGCGGCGGACCGGGGATG
-TTAATGATGGTGCAACCCTTGCGGGACGCCATTCATGCAGCAAAAGCCGCGGCAGGTGAA
-GGCGCTAAAGTGATTTATCTGTCGCCTCAGGGACGCAAGCTTGATCAAGCGGGCGTTAGC
-GAGCTGGCCACGAATCAGAAACTCATTCTGGTGTGTGGTCGCTACGAAGGCGTAGATGAG
-CGCGTAATTCAGGCCGAAATTGACGAAGAATGGTCAATTGGCGATTACGTTCTCAGCGGT
-GGCGAACTACCGGCAATGACGCTGATTGACTCCGTCGCCCGGTTTATACCGGGGGTTCTG
-GGGCATGAGGCATCAGCAATCGAAGATTCGTTTGCTGATGGGTTGCTGGATTGTCCGCAC
-TATACGCGCCCTGAAGTGTTAGAGGGGATGGAAGTACCGCCAGTATTGCTGTCGGGAAAC
-CATGCTGAGATACGTCGCTGGCGTTTGAAACAGTCACTGGGCCGAACCTGGCTTAGAAGA
-CCTGAACTTCTGGAAAACCTGGCTCTGACTGAAGAGCAAGCAAGGTTGCTGGCGGAGTTC
-AAAACAGAACACGCACAACAGCAGCATAAACATGATGGGATGGCATAG
->GEN2.1219.00001.0003i_00008 261 NA | hypothetical protein | NA | NA | NA
-ATGGCCGGGTTGCACGCGCCATATGCATATAGCGCGCATCATGCGGTGAATTTCTGTTCT
-GAGTATAAACGTGGCTTTGTATTGGGTTTTACACACCGTATGTTCGAAAAGACCGGCGAT
-CGTCAACTTAGCGCGTGGGAGGCCGGAATTCTGACGCGTCGCTATGGTCTGGATAAAGAA
-ATGGTGATGGATTTCTTTAAAGAGAATCATTCCGGGATGGCGGTTCGCTTCTTTATGGCT
-GGTTATCGACTCGAAGGTTGA
->GEN2.1219.00001.0003i_00009 582 NA | hypothetical protein | NA | NA | NA
-ATGTCTACGCTTCTCTATTTGCACGGATTCAACAGTTCCCCTCGCTCGGCAAAAGCGTGC
-CAGCTAAAAAACTGGCTGGCGGAGCGTCATCCGCATGTTGAGATGATCGTCCCTCAACTG
-CCGCCGTATCCTGCCGATGCGGCGGAGTTGCTGGAATCTCTCGTACTTGAGCATGGCGGT
-GCGCCATTAGGGCTGGTAGGATCGTCGCTGGGTGGTTATTACGCCACCTGGCTGTCGCAA
-TGTTTTATGCTGCCGGCTGTGGTGGTGAATCCCGCCGTGCGGCCCTTTGAATTACTGACC
-GACTATCTCGGTCAGAACGAGAACCCCTACACCGGGCAGCAATATGTGCTAGAGTCTCGC
-CATATTTATGATCTTAAAGTCATGCAGATTGACCCGCTGGAAGCGCCGGACCTGATCTGG
-CTACTGCAACAGACGGGCGATGAAGTGCTGGATTACCGCCAGGCGGTGGCATATTACGCC
-TCCTGCCGTCAGACAGTGACCGAGGGGGGTAATCACGCATTCACGGGCTTCGAAGATTAT
-TTCAACCAGATTGTCGATTTTCTTGGACTGCACAGTTGCTGA
->GEN2.1219.00001.0003b_00010 369 NA | hypothetical protein | NA | NA | NA
-ATGATGCGCACTGATGGCACGGTGACGCAGCCGCGTTTAAAGCAGGTTGCGCTGTCGGCA
-ATTTCGGAGGTCAACGCAGAGCTGTATGAGTTTCGCAGACGCCAGCAGATGCTGGGGTAT
-GCCTCGCTGGCAGAAGTCCCGGCGGAACAACTGGACGGCAAAAGCGAGCGCATTCAGCAC
-TATTTCAACGCGGTTTACTGCTGGGCACGCGCCATGCTCAACGAACGTTACCAGGACTAT
-GACGCCACGGCATCCGGTGTGAAGCGGGGCGAAGAACTGGCAGAAGCCAGCGGTGATTTG
-TGGCGTGACGCCCGCTGGGCCATCAGCCGGGTGCAGGATGCGCCGCACTGCACAGTGGAG
-CTTATCTGA
->GEN2.1219.00001.0004b_00011 1308 dctM | C4-dicarboxylate TRAP transporter large permease protein DctM | NA | similar to AA sequence:UniProtKB:O07838 | COG:COG1593
-ATGATTGACCCTATTTTTGCGTCCTGTACGCTAATTGCCGTCTTTGTTGTTTTACTGGCC
-ATGGGCGCGCCTATCGGGATCTGCATCGTTATCGCCTCTTTCAGCACCATGATGCTGGTA
-CTGCCTTTCGATATTTCGATGTTCGCCACCGCGCAAAAAATGTTCTCCAGCCTGGACAGT
-TTTGCCTTGCTGGCCGTGCCGTTCTTCGTTTTGTCCGGGGTGATCATGAATAGCGGGGGA
-ATTGCCGCCCGACTGGTCAATTTTGCCAAACTGTTTACTGGCAAACTGCCCGGCTCGCTC
-TCTTACACCAACATCGTCGGCAATATGATGTTCGGTGCAATTTCCGGATCGGCGATTGCC
-GCCTCAACCTCTATCGGCGGCGTGATGGTGCCGATGAGCGCGCGCGAAGGTTACGATCGC
-GGTTTTGCGGCCGCGGTGAATATCGCCTCCGCGCCGACGGGAATGTTAATTCCGCCCACC
-ACGGCTTTTATCCTTTATGCGCTGGCAAGCGGGGGAACATCGATTGCCGCTCTGTTCGCC
-GGCGGTCTGGTCGCGGGAGTGCTGTGGGGCGTTGGCTGTATGCTGGTCACGCTGGTGGTC
-GCTAAGCGTCGAAATTATCGGGTTTTCTTCACCGTCCAAAAAGGCATGGCGCTAAAAGTT
-GCCGTTGAGGCCATTCCCAGCCTGTTACTGATCGTGATTATTGTCGGCGGCATTGTGCAG
-GGGATTTTCACCGCCATTGAAGCCTCCGCGATTGCCGTGGTGTATACGTTATTGCTGACG
-ATAGTGTTTTACCGCACGCTGAAAATTAAGGATTTGCCTTCGATTTTGCTCCAGACAGTG
-GTAATGACCGGGGTCATCATGTTCCTGCTGGCAACCTCTTCGGCGATGTCCTTCTCGATG
-TCGATCACCAATATTCCTGCGGCGCTGAGCGATATGATCCTCGGTATTTCCGCCAATAAA
-CTGGTTATCCTGTTAGTCATTACCGTCTTTTTGTTGATTATCGGCGCATTTATGGATATC
-GGTCCGGCCATTCTGATTTTTACCCCGATTCTGCTGCCGATTATGACTAAACTGGGCGTC
-GATCCGGTGCATTTCGGCATTATCATGATCTATAACCTGGCGATAGGCACCATTACGCCG
-CCAGTTGGCAGTGGTTTATATGTCGGGGCGAGCGTCGGTAAGGTCAAAGTTGAGGACGTT
-ATCAAACCGTTGATGCCTTTTTACGGCGCGATTATCGGCGTTCTGTTATTAATTACCTAC
-ATTCCGGAAATCACACTGTTTTTACCCCGTCTACTGGGCATCATGTAA
->GEN2.1219.00001.0004i_00012 465 NA | hypothetical protein | NA | NA | NA
-ATGAAGTTTGTTGCGCCAGAACAGGCACCGGAACAGGCGGAGGTCATCAAAAATACGCCG
-TTCTGGCCTGATGTGAACCTGTCGGAATTTCGCAGTGTGATGCGCACTGACGGCACGGTG
-ACGCAGCCGCGTTTAAAGCAGGTCGTGCTGACGGCGATCTCTGAGGTTAACGCTGAGCTG
-TACGACTTCCGCAACCGTCAGCAGATGCTGGGCTGGCGGACACTTGCTGAGGTTCCCGCA
-GAAATGCTGGACGGTAAAAGCGAGCGTATCCGGCACTACCACAACGCTGTTTTTTGCTGG
-GCGCGCGCTGTGCTTAATGAGCGTTATCAGGACTATGACGCCACGGCGTCAGGCGTGAAG
-CGAGGGGAGGAGCTGGCGGAGGCCAGCGGCGATCTGTGGCGTGATGCCCGCTGGGCCATC
-AGCCGGGTGCAGGATGCACCGCACTGTACGGTGGAGCTTATCTGA
->GEN2.1219.00001.0004b_00013 1014 xerC | Tyrosine recombinase XerC | NA | protein motif:HAMAP:MF_01808 | NA
-ATGGAAACAAATATTACCTGGCAACAATTGATAGATGAATATTTCTTCGCAAAACCTCTG
-CGCTCAGCATCTGAATGGAGTTACACCAAAGTCTTCAAATCATTTGTACATTATATGGGG
-CCGTTAAGCTGCCCTAATGATGTGACATATCACAAAGTGCTTGCCTGGCGCCGTTTTCTT
-TTAAAAGAGAAAAAGCTGTCCGGACGTACCTGGAATAACAAGGTGGCGCATATGCGGGCC
-ATCTTTAACTACGGAATACAGCGAGGGTTACTGCACTATGACGAAAATCCGTTTAACAAT
-TCGGTAGTTAAACCGGACAAGAAGAGAAAGAAAACGCTCACTCAGGCACAGATTGAGTAT
-GCCTATCAGATCATGGAGCAGTATGAAAATCAGGAGAATACAGGGCTGGGACTGAAATAT
-TCCCGCTGCGCCTTATTTCCTGCATGGTTCTGGCTCACTGTCCTGGATACGCTCTATTAC
-ACAGGGATACGTCAGAACCAGTTATTACATATTCGGCTGAATGATGTTGATTTGAGAGAA
-GGGCAGATTCGGCTGATTACGGAGGGGTGTAAAAATCACAAAGAACACTATGTGCCGGTG
-ATCAGTTTTCTGCGTCCACGGCTGACCTGTTTAATGGAGAAAGCGCAGAGCGAAGGATTG
-AAAGGTAATGACCGCCTGTTCAATATTGCACTTTTTACCGGCAAAGATCCCGCCATTGGC
-GATGACATGGATTCTCCTCAGGTAAGAGCATTCTTCCGTCGTCTGTCCAAGGAGTGTCAG
-TTTGCGATCAGTCCTCATCGTTTCAGACACACGCTGGCCACGGAGATGATGAAAATGCCG
-GAACAGAATCTGCATATGGCGCAAAGTGTGCTGGGTCATTCAAACATGAAATCCACGCTG
-GAGTATGTGGAGAATGATATTGCAGTGATGGGGAGGGCTCTGGAAGCGCAGTTTATGCAG
-ATTAAGGCAGCACATGCCCGAAGCATTTACAGTGGGTTGACAAAGAATAGATAA
diff --git a/Examples/2-res-Annotate-prokka/Genes/GEN4.1111.00001.gen b/Examples/2-res-Annotate-prokka/Genes/GEN4.1111.00001.gen
deleted file mode 100644
index d5c426371e32800c11fc2fb1013a41642a4b0e09..0000000000000000000000000000000000000000
--- a/Examples/2-res-Annotate-prokka/Genes/GEN4.1111.00001.gen
+++ /dev/null
@@ -1,128 +0,0 @@
->GEN4.1111.00001.0001b_00001 831 amiD | N-acetylmuramoyl-L-alanine amidase AmiD | 3.5.1.28 | similar to AA sequence:UniProtKB:P75820 | COG:COG3023
-ATGAAAGCGCTACTGTGGCTGGTGGGTCTCGCGTTGCTGTTAACAGGCTGCGCGAGCGAA
-AAAGGAATTATCGATAAAGAGGGATATCAGCTTGATACCCGACATCGGGCGCAGGCGGCC
-TATCCGCGCATTAAAGTCCTGGTGATTCACTATACGGCGGAAAACTTTGACGTTTCGCTG
-GCGACGTTAACGGGCCGCAACGTCAGTTCGCATTACCTGATTCCCGCAACCCCGCCATTA
-TATGGCGGTAAACCGCGCATCTGGCAACTGGTGCCGGAACAGGATCAGGCCTGGCATGCG
-GGCGTCAGTTTCTGGCGAGGCGCCACGCGTCTCAATGATACGTCTATTGGCATTGAGCTG
-GAAAATCGCGGCTGGCGAATGTCCGGCGGGGTGAAATCTTTCGCGCCGTTTGAATCCGCG
-CAAATTCAGGCATTGATTCCGTTAGCGAAGGACATTATCGCGCGCTATGACATCAAACCG
-CAGAATGTGGTGGCCCATGCGGATATCGCGCCGCAGCGTAAAGACGATCCCGGCCCGCGC
-TTCCCGTGGCGCGAGCTGGCGGCGCAGGGGATTGGCGCCTGGCCTGACGCCCAGCGTGTG
-GCGTTTTATCTGGCTGGACGCGCGCCGTATACGCCAGTCGATACCGCAACGGTGCTTGCG
-TTACTCTCGCGCTATGGCTATGAAGTCAAAGCCGATATGACGGCGCGCGAGCAGCAGCGG
-GTGATTATGGCGTTCCAGATGCACTTCCGTCCGGCGCAATGGAACGGTATCGCAGATGCC
-GAAACGCAGGCGATTGCCGAAGCATTACTGGAGAAGTACGGCCAGGATTAA
->GEN4.1111.00001.0001i_00002 381 hpcD | 5-carboxymethyl-2-hydroxymuconate Delta-isomerase | 5.3.3.10 | similar to AA sequence:UniProtKB:Q05354 | NA
-ATGCCGCACTTTATTGCTGAATGTACTGAAAATATTCGCGAGCAGGCTGATTTACCCGGC
-CTGTTCAGCAAGGTAAACGAGGCGCTGGCCGCCAGCGGGATTTTCCCCATCGGCGGTATC
-CGCAGTCGCGCCCACTGGCTGGATACCTGGCAGATGGCTGACGGTAAGCATGATTATGCG
-TTTGTGCATATGACGCTGAAAATCGGTACCGGGCGCAGCCTGGAGAGCCGTCAGGAAGTC
-GGCGAAATGCTGTTTGGGCTGATTAAAGCCCACTTCGCCGACCTGATGGAGAACCGCTAT
-CTGGCGCTGTCGTTTGAGATTGCCGAGCTACATCCGACGCTCAATTACAAACAAAACAAC
-GTACACGCGTTATTTAAATAG
->GEN4.1111.00001.0001i_00003 804 hpcG | 2-oxo-hept-4-ene-1,7-dioate hydratase | 4.2.1.163 | similar to AA sequence:UniProtKB:P42270 | NA
-ATGCTCGATAAACAGACCCATACCCTGATCGCCCAGCGACTTAATCAGGCTGAAAAACAG
-CGTGAACAAATTCGCGCAGTGTCGCTGGATTATCCCAACATCACTATTGAAGATGCCTAT
-GCCGTACAGCGTGAATGGGTCAATATCAAGATCGCCGAAGGGCGCACGCTCAAAGGCCAC
-AAAATCGGCCTGACCTCAAAAGCGATGCAGGCCAGCTCGCAAATCAGCGAACCGGATTAC
-GGCGCGCTGCTTGACGATATGTTCTTCCATGACGGCGGCGATATCCCCACCGACCGTTTT
-ATCGTCCCGCGTATTGAAGTGGAGCTGGCGTTCGTGCTGGCGAAACCGCTGCGCGGCCCT
-CACTGCACGCTGTTCGACGTCTACAACGCCACGGATTATGTGATTCCGGCGCTGGAACTG
-ATTGACGCCCGCAGCCACAACATCGACCCGGAAACCCAGCGCCCGCGCAAAGTGTTCGAC
-ACCATTTCCGACAACGCCGCCAACGCCGGGGTGATCCTCGGTGGTCGCCCCATCAAACCA
-GACGAGCTGGATCTGCGCTGGATCTCCGCGCTGCTCTATCGCAACGGCGTGATCGAAGAA
-ACCGGCGTCGCCGCAGGCGTGCTGAATCATCCGGCCAACGGCGTGGCGTGGCTGGCGAAC
-AAGCTTGCCCCCTACGATGTCCAGCTTGAAGCCGGGCAGATCATCCTCGGCGGCTCGTTC
-ACCCGCCCGGTGCCGGCGAGCAAGGGCGACACCTTCCATGTCGATTACGGCAACATGGGC
-GCGATCAGTTGCCGGTTTGTGTAA
->GEN4.1111.00001.0001i_00004 1404 NA | hypothetical protein | NA | NA | NA
-ATGCCCGTGAATAAGTTCTCCCGACGTACCCTCCTGACGGCAGGTTCCGCGCTTGCTGTT
-CTTCCTTTTCTGCGCGCCTTGCCGGTACAGGCGCGTGAACCTCGCGAGACCGTCGATATT
-AAGGATTATCCGGCGGATGACGGTATCGCCTCGTTCAAACAGGCCTTCGCCGACGGACAG
-ACCGTGGTCTTACCGCCAGGATGGGTGTGTGAAAATATCAATGCGGCGATAACGATTCCG
-GCGGGAAAAACGCTGCGGGTACAGGGCGCGGTGCGTGGGAATGGCCGGGGACGGTTTATT
-TTGCAGGACGGGTGTCAGGTGGTGGGGGAGCAGGGCGGCAGTCTGCACAATGTGACGCTG
-GATGTTCGCGGGTCGGACTGTGTGATTAAAGGCGTGACGATGAGCGGCTTTGGCCCCGTC
-GCGCAAATTTTCATCGGCGGTAAGGAACCGCAGGTGATGCGTAATCTCATTATCGATGAC
-ATCACCGTTACCCACGCCAACTACGCCATTCTCCGCCAGGGATTTCATAACCAAATGGAC
-GGCGCGCGGATTACGCATAGCCGCTTTAGCGATTTGCAGGGGGACGCCATTGAGTGGAAT
-GTCGCGATTCACGACCGCGACATCCTGATTTCCGATCATGTCATCGAACGCATTGATTGT
-ACCAATGGCAAAATCAACTGGGGGATCGGCATCGGGCTGGCGGGTAGCACCTATGACAAC
-AGTTATCCTGAAGATCAGGCAGTAAAAAACTTTGTGGTGGCCAATATTACCGGATCTGAT
-TGCCGACAGCTGGTGCACGTAGAAAATGGCAAACATTTCGTCATTCGCAATGTCAAAGCC
-AAAAACATCACGCCCGATTTCAGTAAAAATGCGGGTATTGATAACGCAACGATCGCCATT
-TATGGCTGTGATAATTTCGTCATTGATAATATTGATATGACGAATAGTGCTGGGATGCTC
-ATCGGCTATGGCGTCGTTAAAGGAAAATACCTGTCAATTCCGCAAAACTTTAAATTAAAC
-GCTATTCGGTTGGATAATCGCCAGGTTGCTTATAAATTACGCGGCATTCAAATTTCCTCC
-GGCAACATCCCCTCTTTTGTCGCCATCACCAATGTACGGATGACGCGTGCTACGCTGGAA
-CTGCATAATCAACCGCAGCACCTCTTTCTGCGTAATATCAACGTGATGCAAACTTCAGCG
-ATTGGCCCGGCGTTAAAAATGCATTTCGATTTGCGTAAAGATGTCCGTGGTCAATTTATG
-GCCCGCCAGGACACGCTGCTTTCCCTCGCTAATGTTCATGCCATCAATGAAAACGGGCAG
-AGTTCCGTGGATATCGACAGGATTAATCACCAAACCGTGAATGTCGAAGCAGTGAATTTT
-TCGCTGCCGAAGCGGGGAGGGTAA
->GEN4.1111.00001.0001i_00005 774 hisP | Histidine transport ATP-binding protein HisP | NA | similar to AA sequence:UniProtKB:P02915 | COG:COG4598
-ATGTCAGAAAATAAATTACACGTTATCGATTTGCACAAACGCTACGGCGGTCATGAAGTG
-CTGAAAGGGGTATCGTTGCAGGCCCGCGCCGGAGATGTGATTAGCATCATCGGCTCGTCC
-GGCTCCGGTAAAAGCACTTTTTTGCGCTGTATTAACTTCCTCGAAAAACCGAGCGAAGGC
-GCGATTATCGTGAACGGTCAGAACATTAATCTGGTGCGCGACAAAGACGGGCAGCTCAAA
-GTGGCGGATAAAAATCAGCTACGCTTGTTGCGTACCCGCCTGACGATGGTGTTTCAGCAC
-TTTAACCTCTGGAGCCACATGACGGTGCTGGAAAATGTGATGGAAGCGCCGATTCAGGTA
-CTGGGATTAAGCAAGCACGACGCGCGCGAGCGGGCGTTGAAATATCTGGCGAAGGTGGGG
-ATTGATGAGCGCGCTCAGGGCAAATATCCCGTCCATCTCTCCGGCGGCCAACAGCAGCGC
-GTTTCTATTGCGCGCGCGCTGGCGATGGAACCTGACGTTTTACTGTTCGATGAACCCACA
-TCGGCGCTCGATCCTGAACTGGTCGGCGAAGTGTTGCGCATCATGCAACAACTGGCGGAA
-GAAGGCAAAACGATGGTGGTGGTCACGCATGAAATGGGCTTCGCCCGCCATGTCTCTTCG
-CACGTTATTTTTCTGCATCAGGGGAAAATTGAAGAAGAGGGCGATCCGGAGCAGGTGTTC
-GGCAATCCGCAAAGCCCGCGTTTACAGCAATTCCTGAAAGGCTCGCTGAAATAA
->GEN4.1111.00001.0001i_00006 768 trmD | tRNA (guanine-N(1)-)-methyltransferase | 2.1.1.228 | similar to AA sequence:UniProtKB:P0A873 | COG:COG0336
-GTGTTTATTGGCATCGTTAGCCTGTTTCCTGAAATGTTCCGCGCAATTACCGATTACGGG
-GTAACTGGCCGGGCAGTAAAAAAAGGCCTGCTGAACATCCAAAGCTGGAGTCCTCGCGAC
-TTCGCGCATGACCGGCACCGTACCGTGGACGACCGTCCTTACGGCGGCGGACCGGGGATG
-TTAATGATGGTGCAACCCTTGCGGGACGCCATTCACGCAGCAAAAGCCGCGGCAGGTGAA
-GGCGCTAAAGTGATTTATCTGTCGCCTCAGGGACGCAAGCTTGATCAAGCGGGCGTTAGC
-GAGCTGGCCACGAATCAGAAGCTTATTCTGGTGTGTGGTCGCTACGAAGGCGTAGATGAG
-CGCGTAATTCAGACCGAAATTGACGAAGAATGGTCAATTGGCGATTACGTTCTCAGCGGT
-GGCGAACTACCGGCAATGACGCTGATTGACTCCGTCGCCCGGTTTATACCGGGGGTTCTG
-GGGCATGAGGCATCAGCAATCGAAGATTCGTTTGCTGATGGGTTGCTGGATTGTCCGCAC
-TATACGCGCCCTGAAGTGTTAGAGGGGATGGAAGTACCGCCAGTATTGCTGTCGGGAAAC
-CATGCCGAGATACGTCGCTGGCGCTTGAAACAGTCGCTGGGCCGAACCTGGCTTAGAAGA
-CCTGAACTTCTGGAAAACCTGGCTCTGACTGAAGAGCAAGCAAGGTTGCTGGCGGAGTTC
-AAAACAGAACACGCACAACAGCAGCATAAACATGATGGGATGGCATAG
->GEN4.1111.00001.0001i_00007 261 NA | hypothetical protein | NA | NA | NA
-ATGGCTGGGTTGCACGCGCCATATGCATATAGCGCGCATCATGCGGTGAATTTCTGTTCT
-GAGTATAAACGTGGCTTTGTATTGGGTTTTACACACCGTATGTTCGAAAAGACCGGCGAT
-CGTCAACTTAGCGCGTGGGAGGCCGGAATTCTGACGCGTCGCTATGGTCTGGATAAAGAA
-ATGGTGATGGATTTCTTTAAAGAGAATCATTCCGGGATGGCGGTTCGCTTCTTTATGGTC
-GGTTATCGACTCGAAGGTTGA
->GEN4.1111.00001.0001i_00008 582 NA | hypothetical protein | NA | NA | NA
-ATGTCTACGCTTCTCTATTTGCACGGATTCAACAGTTCCCCTCGCTCGGCAAAAGCGTGC
-CAGCTAAAAAACTGGCTGGCGGAGCGTCATCCGCATGTCGAGATGATCGTCCCTCAACTA
-CCGCCGTATCCTGCCGATGCGGCGGAGTTGCTGGAATCTCTCGTGCTTGAGCATGGCGGT
-GCGCCATTAGGGCTGGTAGGATCGTCGCTGGGTGGTTATTACGCCACCTGGCTGTCGCAA
-TGTTTTATGCTGCCGGCTGTGGTGGTGAATCCCGCCGTGCGGCCCTTTGAATTACTGACC
-GACTATCTCGGTCAGAACGAGAACCCCTACACCGGGCAGCAATATGTGCTAGAGTCTCGC
-CATATTTATGATCTTAAAGTCATGCAGATTGACCCGCTGGAAGCGCCGGACCTGATCTGG
-CTACTGCAACAGACGGGCGATGAAGTGCTGGATTACCGCCAGGCGGTGGCATATTACGCC
-TCCTGCCGTCAGACAGTGACCGAGGGTGGTAATCACGCATTCACGGGCTTCGAAGATTAT
-TTCAACCAGATTGTCGATTTTCTTGGACTGCACAGTTGCTGA
->GEN4.1111.00001.0001b_00009 1083 dctM | C4-dicarboxylate TRAP transporter large permease protein DctM | NA | similar to AA sequence:UniProtKB:O07838 | COG:COG1593
-ATGAATAGCGGGGGAATTGCCGCCCGGCTGGTCAATTTTGCCAAACTGTTTACTGGCAAA
-CTGCCCGGCTCGCTCTCTTATACCAACATCGTCGGCAATATGATGTTCGGTGCAATTTCC
-GGATCGGCAATTGCCGCCTCAACCTCCATCGGCGGCGTGATGGTGCCGATGAGCGCGCGC
-GAAGGTTACGATCGCGGCTTTGCGGCCGCGGTGAATATCGCCTCCGCGCCGACGGGAATG
-TTAATTCCGCCCACCACGGCTTTTATCCTTTATGCGCTGGCAAGCGGGGGAACATCGATT
-GCCGCTCTGTTCGCCGGCGGTCTGGTCGCGGGAGTGCTGTGGGGCGTTGGCTGTATGCTG
-GTCACGCTGGTGGTCGCTAAGCGTCGAAATTATCGGGTTTTCTTCACCGTCCAAAAAGGC
-ATGGCGCTAAAAGTTGCCGTTGAGGCCATTCCCAGCCTGCTGCTGATCGTGATTATCGTC
-GGCGGCATTGTGCAGGGGATTTTCACCGCCATTGAAGCCTCCGCGATTGCCGTGGTGTAT
-ACATTATTGTTGACGATGGTGTTTTACCGCACGCTGAAAATTAAGGATTTGCCTTCGATT
-TTGCTCCAGACAGTGGTAATGACCGGGGTCATCATGTTCCTGCTGGCAACCTCTTCGGCG
-ATGTCCTTCTCGATGTCGATCACCAATATTCCTGCGGCGCTGAGCGATATGATCCTCGGT
-ATTTCCGCCAATAAACTGGTTATCCTGTTAGTCATTACCGTCTTTTTGTTGATTATCGGC
-GCATTTATGGATATCGGTCCGGCCATTCTGATTTTTACCCCGATTCTGCTGCCGATCATG
-GCTAAACTGGGCGTCGATCCGGTGCATTTTGGCATTATCATGATCTATAACCTGGCGATT
-GGCACCATTACGCCGCCAGTTGGCAGTGGTTTATATGTCGGGGCGAGCGTCGGTAAGGTC
-AAAGTTGAGGAAGTGATTAAACCGTTGCTGCCTTTTTACGGCGCGATTATCGGCGTTCTG
-TTATTAATTACCTACATTCCGGAAATCACACTGTTCTTACCCCGTCTACTGGGCATCATG
-TAA
diff --git a/Examples/2-res-Annotate-prokka/LSTINFO-list_genomes.lst b/Examples/2-res-Annotate-prokka/LSTINFO-list_genomes.lst
deleted file mode 100644
index 67619a47c008025fc5212b651528dff6739c7e1c..0000000000000000000000000000000000000000
--- a/Examples/2-res-Annotate-prokka/LSTINFO-list_genomes.lst
+++ /dev/null
@@ -1,5 +0,0 @@
-gembase_name	orig_name	to_annotate	gsize	nb_conts	L90
-EXAM.1219.00001	genome1.fst	Examples/2-res-Annotate-prokka/tmp_files/genome1.fst_prokka-split5N.fna	9808	2	2
-EXAM.1216.00002	genome3-chromo.fst-all.fna	Examples/2-res-Annotate-prokka/tmp_files/genome3-chromo.fst-all.fna_prokka-split5N.fna	8817	3	3
-GEN2.1219.00001	genome2.fst	Examples/2-res-Annotate-prokka/tmp_files/genome2.fst_prokka-split5N.fna	10717	5	4
-GEN4.1111.00001	genome4.fst	Examples/2-res-Annotate-prokka/tmp_files/genome4.fst_prokka-split5N.fna	7134	1	1
diff --git a/Examples/2-res-Annotate-prokka/LSTINFO/EXAM.1216.00002.lst b/Examples/2-res-Annotate-prokka/LSTINFO/EXAM.1216.00002.lst
deleted file mode 100644
index 99a7ae839a0c51d18a8b49b79d8498d69ee16f12..0000000000000000000000000000000000000000
--- a/Examples/2-res-Annotate-prokka/LSTINFO/EXAM.1216.00002.lst
+++ /dev/null
@@ -1,12 +0,0 @@
-1	831	D	CDS	EXAM.1216.00002.0001b_00001	amiD_1	| N-acetylmuramoyl-L-alanine amidase AmiD | 3.5.1.28 | similar to AA sequence:UniProtKB:P75820 | COG:COG3023
-880	1710	D	CDS	EXAM.1216.00002.0001i_00002	amiD_2	| N-acetylmuramoyl-L-alanine amidase AmiD | 3.5.1.28 | similar to AA sequence:UniProtKB:P75820 | COG:COG3023
-1655	2128	D	CDS	EXAM.1216.00002.0001i_00003	hpcD	| 5-carboxymethyl-2-hydroxymuconate Delta-isomerase | 5.3.3.10 | similar to AA sequence:UniProtKB:Q05354 | NA
-2172	2396	D	CDS	EXAM.1216.00002.0001i_00004	pspB	| Phage shock protein B | NA | similar to AA sequence:UniProtKB:P0AFM9 | NA
-2425	3828	D	CDS	EXAM.1216.00002.0001i_00005	NA	| hypothetical protein | NA | NA | NA
-3863	4636	D	CDS	EXAM.1216.00002.0001i_00006	hisP	| Histidine transport ATP-binding protein HisP | NA | similar to AA sequence:UniProtKB:P02915 | COG:COG4598
-4641	5432	D	CDS	EXAM.1216.00002.0001i_00007	trmD	| tRNA (guanine-N(1)-)-methyltransferase | 2.1.1.228 | similar to AA sequence:UniProtKB:P0A873 | COG:COG0336
-5460	5747	D	CDS	EXAM.1216.00002.0001b_00008	NA	| hypothetical protein | NA | NA | NA
-1	582	D	CDS	EXAM.1216.00002.0002b_00009	NA	| hypothetical protein | NA | NA | NA
-629	1936	D	CDS	EXAM.1216.00002.0002b_00010	dctM	| C4-dicarboxylate TRAP transporter large permease protein DctM | NA | similar to AA sequence:UniProtKB:O07838 | COG:COG1593
-26	280	D	CDS	EXAM.1216.00002.0003b_00011	NA	| hypothetical protein | NA | NA | NA
-323	1102	D	CDS	EXAM.1216.00002.0003b_00012	NA	| IS21 family transposase ISSen3 | NA | similar to AA sequence:ISfinder:ISSen3 | NA
diff --git a/Examples/2-res-Annotate-prokka/LSTINFO/EXAM.1219.00001.lst b/Examples/2-res-Annotate-prokka/LSTINFO/EXAM.1219.00001.lst
deleted file mode 100644
index 0542b84e9590fd94ba3c8fde90f4a0f8e32c67fc..0000000000000000000000000000000000000000
--- a/Examples/2-res-Annotate-prokka/LSTINFO/EXAM.1219.00001.lst
+++ /dev/null
@@ -1,11 +0,0 @@
-213	1880	D	CDS	EXAM.1219.00001.0001b_00001	glnS	| Glutamine--tRNA ligase | 6.1.1.18 | similar to AA sequence:UniProtKB:P00962 | COG:COG0008
-1916	2746	D	CDS	EXAM.1219.00001.0001b_00002	amiD	| N-acetylmuramoyl-L-alanine amidase AmiD | 3.5.1.28 | similar to AA sequence:UniProtKB:P75820 | COG:COG3023
-16	396	D	CDS	EXAM.1219.00001.0002b_00003	hpcD	| 5-carboxymethyl-2-hydroxymuconate Delta-isomerase | 5.3.3.10 | similar to AA sequence:UniProtKB:Q05354 | NA
-428	1837	D	CDS	EXAM.1219.00001.0002i_00004	NA	| hypothetical protein | NA | NA | NA
-1869	2642	D	CDS	EXAM.1219.00001.0002i_00005	hisP	| Histidine transport ATP-binding protein HisP | NA | similar to AA sequence:UniProtKB:P02915 | COG:COG4598
-2709	3443	D	CDS	EXAM.1219.00001.0002i_00006	trmD_1	| tRNA (guanine-N(1)-)-methyltransferase | 2.1.1.228 | similar to AA sequence:UniProtKB:P0A873 | COG:COG0336
-3427	4254	D	CDS	EXAM.1219.00001.0002i_00007	trmD_2	| tRNA (guanine-N(1)-)-methyltransferase | 2.1.1.228 | similar to AA sequence:UniProtKB:P0A873 | COG:COG0336
-4299	4763	D	CDS	EXAM.1219.00001.0002i_00008	NA	| hypothetical protein | NA | NA | NA
-4818	5078	D	CDS	EXAM.1219.00001.0002i_00009	NA	| hypothetical protein | NA | NA | NA
-5117	5698	D	CDS	EXAM.1219.00001.0002i_00010	NA	| hypothetical protein | NA | NA | NA
-5717	7024	D	CDS	EXAM.1219.00001.0002b_00011	dctM	| C4-dicarboxylate TRAP transporter large permease protein DctM | NA | similar to AA sequence:UniProtKB:O07838 | COG:COG1593
diff --git a/Examples/2-res-Annotate-prokka/LSTINFO/GEN2.1219.00001.lst b/Examples/2-res-Annotate-prokka/LSTINFO/GEN2.1219.00001.lst
deleted file mode 100644
index 27c116ecaf42e3e8926e9afebda9427682eb2309..0000000000000000000000000000000000000000
--- a/Examples/2-res-Annotate-prokka/LSTINFO/GEN2.1219.00001.lst
+++ /dev/null
@@ -1,13 +0,0 @@
-1	774	D	CDS	GEN2.1219.00001.0001b_00001	hisP	| Histidine transport ATP-binding protein HisP | NA | similar to AA sequence:UniProtKB:P02915 | COG:COG4598
-857	2260	D	CDS	GEN2.1219.00001.0001b_00002	NA	| hypothetical protein | NA | NA | NA
-28	252	D	CDS	GEN2.1219.00001.0002b_00003	pspB	| Phage shock protein B | NA | similar to AA sequence:UniProtKB:P0AFM9 | NA
-301	681	D	CDS	GEN2.1219.00001.0002i_00004	hpcD	| 5-carboxymethyl-2-hydroxymuconate Delta-isomerase | 5.3.3.10 | similar to AA sequence:UniProtKB:Q05354 | NA
-764	1597	D	CDS	GEN2.1219.00001.0002i_00005	amiD	| N-acetylmuramoyl-L-alanine amidase AmiD | 3.5.1.28 | similar to AA sequence:UniProtKB:P75820 | COG:COG3023
-1628	3295	D	CDS	GEN2.1219.00001.0002b_00006	glnS	| Glutamine--tRNA ligase | 6.1.1.18 | similar to AA sequence:UniProtKB:P00962 | COG:COG0008
-30	797	D	CDS	GEN2.1219.00001.0003b_00007	trmD	| tRNA (guanine-N(1)-)-methyltransferase | 2.1.1.228 | similar to AA sequence:UniProtKB:P0A873 | COG:COG0336
-862	1122	D	CDS	GEN2.1219.00001.0003i_00008	NA	| hypothetical protein | NA | NA | NA
-1170	1751	D	CDS	GEN2.1219.00001.0003i_00009	NA	| hypothetical protein | NA | NA | NA
-1895	2263	D	CDS	GEN2.1219.00001.0003b_00010	NA	| hypothetical protein | NA | NA | NA
-1	1308	D	CDS	GEN2.1219.00001.0004b_00011	dctM	| C4-dicarboxylate TRAP transporter large permease protein DctM | NA | similar to AA sequence:UniProtKB:O07838 | COG:COG1593
-1340	1804	D	CDS	GEN2.1219.00001.0004i_00012	NA	| hypothetical protein | NA | NA | NA
-1832	2845	D	CDS	GEN2.1219.00001.0004b_00013	xerC	| Tyrosine recombinase XerC | NA | protein motif:HAMAP:MF_01808 | NA
diff --git a/Examples/2-res-Annotate-prokka/LSTINFO/GEN4.1111.00001.lst b/Examples/2-res-Annotate-prokka/LSTINFO/GEN4.1111.00001.lst
deleted file mode 100644
index 068882455461dbe77996cfbb05cfeb1c2647cb96..0000000000000000000000000000000000000000
--- a/Examples/2-res-Annotate-prokka/LSTINFO/GEN4.1111.00001.lst
+++ /dev/null
@@ -1,9 +0,0 @@
-1	831	D	CDS	GEN4.1111.00001.0001b_00001	amiD	| N-acetylmuramoyl-L-alanine amidase AmiD | 3.5.1.28 | similar to AA sequence:UniProtKB:P75820 | COG:COG3023
-861	1241	D	CDS	GEN4.1111.00001.0001i_00002	hpcD	| 5-carboxymethyl-2-hydroxymuconate Delta-isomerase | 5.3.3.10 | similar to AA sequence:UniProtKB:Q05354 | NA
-1271	2074	D	CDS	GEN4.1111.00001.0001i_00003	hpcG	| 2-oxo-hept-4-ene-1,7-dioate hydratase | 4.2.1.163 | similar to AA sequence:UniProtKB:P42270 | NA
-2111	3514	D	CDS	GEN4.1111.00001.0001i_00004	NA	| hypothetical protein | NA | NA | NA
-3535	4308	D	CDS	GEN4.1111.00001.0001i_00005	hisP	| Histidine transport ATP-binding protein HisP | NA | similar to AA sequence:UniProtKB:P02915 | COG:COG4598
-4327	5094	D	CDS	GEN4.1111.00001.0001i_00006	trmD	| tRNA (guanine-N(1)-)-methyltransferase | 2.1.1.228 | similar to AA sequence:UniProtKB:P0A873 | COG:COG0336
-5138	5398	D	CDS	GEN4.1111.00001.0001i_00007	NA	| hypothetical protein | NA | NA | NA
-5413	5994	D	CDS	GEN4.1111.00001.0001i_00008	NA	| hypothetical protein | NA | NA | NA
-6052	7134	D	CDS	GEN4.1111.00001.0001b_00009	dctM	| C4-dicarboxylate TRAP transporter large permease protein DctM | NA | similar to AA sequence:UniProtKB:O07838 | COG:COG1593
diff --git a/Examples/2-res-Annotate-prokka/PanACoTA-annotate_list_genomes.log b/Examples/2-res-Annotate-prokka/PanACoTA-annotate_list_genomes.log
deleted file mode 100644
index 57106d77555795b93d6e4c21278c0d4aeb8d66bc..0000000000000000000000000000000000000000
--- a/Examples/2-res-Annotate-prokka/PanACoTA-annotate_list_genomes.log
+++ /dev/null
@@ -1,12 +0,0 @@
-[2019-12-09 13:15:20] :: INFO :: PanACoTA version 20190425
-[2019-12-09 13:15:20] :: INFO :: Command used
- 	 > PanACoTA annotate -r Examples/2-res-Annotate-prokka -n EXAM -d Examples/genomes_init -l Examples/input_files/list_genomes.lst
-[2019-12-09 13:15:20] :: INFO :: Let's start!
-[2019-12-09 13:15:20] :: INFO :: Cutting genomes at each time there are at least 5 'N' in a row, and then, calculating genome size, number of contigs and L90.
-[2019-12-09 13:15:20] :: INFO :: Generating distribution of L90 and #contigs graphs.
-[2019-12-09 13:15:21] :: INFO :: -> Original sequences folder ('orig_name' column): Examples/genomes_init 
-[2019-12-09 13:15:21] :: INFO :: 	-> If original sequence not found in Examples/genomes_init, look for it in Examples/2-res-Annotate-prokka/tmp_files, as it must be a concatenation of several input sequence files.
-[2019-12-09 13:15:21] :: INFO :: -> Folder with sequence files that will be used for annotation ('to_annotate' column): Examples/2-res-Annotate-prokka/tmp_files
-[2019-12-09 13:15:21] :: INFO :: Renaming kept genomes according to their quality.
-[2019-12-09 13:15:21] :: INFO :: Annotating all genomes with prokka
-[2019-12-09 13:15:38] :: INFO :: Annotation step done.
diff --git a/Examples/2-res-Annotate-prokka/PanACoTA-annotate_list_genomes.log.details b/Examples/2-res-Annotate-prokka/PanACoTA-annotate_list_genomes.log.details
deleted file mode 100644
index c95caa004b4547c45f372f9069d7eca738c8cde4..0000000000000000000000000000000000000000
--- a/Examples/2-res-Annotate-prokka/PanACoTA-annotate_list_genomes.log.details
+++ /dev/null
@@ -1,24 +0,0 @@
-[2019-12-09 13:15:20] :: INFO :: PanACoTA version 20190425
-[2019-12-09 13:15:20] :: INFO :: Command used
- 	 > PanACoTA annotate -r Examples/2-res-Annotate-prokka -n EXAM -d Examples/genomes_init -l Examples/input_files/list_genomes.lst
-[2019-12-09 13:15:20] :: INFO :: Let's start!
-[2019-12-09 13:15:20] :: INFO :: Cutting genomes at each time there are at least 5 'N' in a row, and then, calculating genome size, number of contigs and L90.
-[2019-12-09 13:15:20] :: INFO :: Generating distribution of L90 and #contigs graphs.
-[2019-12-09 13:15:21] :: INFO :: -> Original sequences folder ('orig_name' column): Examples/genomes_init 
-[2019-12-09 13:15:21] :: INFO :: 	-> If original sequence not found in Examples/genomes_init, look for it in Examples/2-res-Annotate-prokka/tmp_files, as it must be a concatenation of several input sequence files.
-[2019-12-09 13:15:21] :: INFO :: -> Folder with sequence files that will be used for annotation ('to_annotate' column): Examples/2-res-Annotate-prokka/tmp_files
-[2019-12-09 13:15:21] :: INFO :: Renaming kept genomes according to their quality.
-[2019-12-09 13:15:21] :: INFO :: Annotating all genomes with prokka
-[2019-12-09 13:15:21] :: DETAIL :: Start annotating EXAM.1219.00001 from Examples/2-res-Annotate-prokka/tmp_files/genome1.fst_prokka-split5N.fna with Prokka
-[2019-12-09 13:15:21] :: DETAIL :: Prokka command: prokka --outdir Examples/2-res-Annotate-prokka/tmp_files/genome1.fst_prokka-split5N.fna-prokkaRes --cpus 1 --prefix EXAM.1219.00001 Examples/2-res-Annotate-prokka/tmp_files/genome1.fst_prokka-split5N.fna
-[2019-12-09 13:15:25] :: DETAIL :: End annotating EXAM.1219.00001 from Examples/2-res-Annotate-prokka/tmp_files/genome1.fst_prokka-split5N.fna.
-[2019-12-09 13:15:25] :: DETAIL :: Start annotating GEN2.1219.00001 from Examples/2-res-Annotate-prokka/tmp_files/genome2.fst_prokka-split5N.fna with Prokka
-[2019-12-09 13:15:25] :: DETAIL :: Prokka command: prokka --outdir Examples/2-res-Annotate-prokka/tmp_files/genome2.fst_prokka-split5N.fna-prokkaRes --cpus 1 --prefix GEN2.1219.00001 Examples/2-res-Annotate-prokka/tmp_files/genome2.fst_prokka-split5N.fna
-[2019-12-09 13:15:30] :: DETAIL :: End annotating GEN2.1219.00001 from Examples/2-res-Annotate-prokka/tmp_files/genome2.fst_prokka-split5N.fna.
-[2019-12-09 13:15:30] :: DETAIL :: Start annotating EXAM.1216.00002 from Examples/2-res-Annotate-prokka/tmp_files/genome3-chromo.fst-all.fna_prokka-split5N.fna with Prokka
-[2019-12-09 13:15:30] :: DETAIL :: Prokka command: prokka --outdir Examples/2-res-Annotate-prokka/tmp_files/genome3-chromo.fst-all.fna_prokka-split5N.fna-prokkaRes --cpus 1 --prefix EXAM.1216.00002 Examples/2-res-Annotate-prokka/tmp_files/genome3-chromo.fst-all.fna_prokka-split5N.fna
-[2019-12-09 13:15:34] :: DETAIL :: End annotating EXAM.1216.00002 from Examples/2-res-Annotate-prokka/tmp_files/genome3-chromo.fst-all.fna_prokka-split5N.fna.
-[2019-12-09 13:15:34] :: DETAIL :: Start annotating GEN4.1111.00001 from Examples/2-res-Annotate-prokka/tmp_files/genome4.fst_prokka-split5N.fna with Prokka
-[2019-12-09 13:15:34] :: DETAIL :: Prokka command: prokka --outdir Examples/2-res-Annotate-prokka/tmp_files/genome4.fst_prokka-split5N.fna-prokkaRes --cpus 1 --prefix GEN4.1111.00001 Examples/2-res-Annotate-prokka/tmp_files/genome4.fst_prokka-split5N.fna
-[2019-12-09 13:15:38] :: DETAIL :: End annotating GEN4.1111.00001 from Examples/2-res-Annotate-prokka/tmp_files/genome4.fst_prokka-split5N.fna.
-[2019-12-09 13:15:38] :: INFO :: Annotation step done.
diff --git a/Examples/2-res-Annotate-prokka/PanACoTA-annotate_list_genomes.log.err b/Examples/2-res-Annotate-prokka/PanACoTA-annotate_list_genomes.log.err
deleted file mode 100644
index e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
diff --git a/Examples/2-res-Annotate-prokka/Proteins/EXAM.1216.00002.prt b/Examples/2-res-Annotate-prokka/Proteins/EXAM.1216.00002.prt
deleted file mode 100644
index 1107b946a2090f686e1d061674dc2e21af6e04f1..0000000000000000000000000000000000000000
--- a/Examples/2-res-Annotate-prokka/Proteins/EXAM.1216.00002.prt
+++ /dev/null
@@ -1,66 +0,0 @@
->EXAM.1216.00002.0001b_00001 831 amiD_1 | N-acetylmuramoyl-L-alanine amidase AmiD | 3.5.1.28 | similar to AA sequence:UniProtKB:P75820 | COG:COG3023
-MRALLWLVGLALLLTGCASEKGIIDEEGYQLDTRHRAQAAYPRIKVLVIHYTAENFDVSL
-ATLTGRNVSSHYLIPATPPLYGGKPRIWQLVPEQDQAWHAGVSFWRGATRLNDTSIGIEL
-ENRGWRMSGGVKSFAPFESAQIQALIPLAKDIIARYDIKPQNVVAHADIAPQRKDDPGPR
-FPWRELAAQGIGAWPDAQRVAFYLAGRAPYTPVDTATVLALLSRYGYEVKADMTAREQQR
-VIMAFQMHFRPAQWNGIADAETQAIAEALLEKYGQD
->EXAM.1216.00002.0001i_00002 831 amiD_2 | N-acetylmuramoyl-L-alanine amidase AmiD | 3.5.1.28 | similar to AA sequence:UniProtKB:P75820 | COG:COG3023
-MRALLWLVGLALLLTGCASEKGIIDEEGYQLDTRHRAQAAYPRIKVLVIHYTAENFDVSL
-ATLTGRNVSSHYLIPATPPLYGGKPRIWQLVPEQDQAWHAGVSFWRGATRLNDTSIGIEL
-ENRGWRMSGGVKSFAPFESAQIQALIPLAKDIIARYDIKPQNVVAHADIAPQRKDDPGPR
-FPWRELAAQGIGAWPDAQRVAFYLAGRAPYTPVDTATVLALLSRYGYEVKADMTAREQQR
-VIMAFQMHFRPAQWNGIADAETQAIAEALLEKYGQD
->EXAM.1216.00002.0001i_00003 474 hpcD | 5-carboxymethyl-2-hydroxymuconate Delta-isomerase | 5.3.3.10 | similar to AA sequence:UniProtKB:Q05354 | NA
-MPKRRRLPKHYWRSTARINRARYREDSLFEDMPHFIAECTENIREQADLPGLFSKVNEAL
-AASGIFPIGGIRSRAHWLDTWQMADGKHDYAFVHMTLKIGAGRSLESRQEVGEMLFGLIK
-AHFADLMENRYLALSFEIAELHPTLNYKQNNVHALFK
->EXAM.1216.00002.0001i_00004 225 pspB | Phage shock protein B | NA | similar to AA sequence:UniProtKB:P0AFM9 | NA
-MSALFLAIPLTIFVLFVLPIWLWLHYSNRAGRGELSQSEQQRLLQLTDDAQRMRERIQAL
-EDILDAEHPNWRER
->EXAM.1216.00002.0001i_00005 1404 NA | hypothetical protein | NA | NA | NA
-MPATKFSRRTLLTAGSALAVLPFLRALPVQAREPRETVDIKDYPADDGIASFKQAFADGQ
-TVVVPPGWVCENINAAITIPAGKTLRVQGAVRGNGRGRFILQDGCQVVGEQGGSLHNVTL
-DVRGSDCVIKGVAMSGFGPVAQIFIGGKEPQVMRNLIIDDITVTHANYAILRQGFHNQMD
-GARITHSRFSDLQGDAIEWNVAIHDRDILISDHVIERIDCTNGKINWGIGIGLAGSTYDN
-SYPEDQAVKNFVVANITGSDCRQLVHVENGKHFVIRNVKAKNITPDFSKNAGIDNATIAI
-YGCDNFVIDNIDMTNSAGMLIGYGVVKGKYLSIPQNFKLNAIRLDNRQVAYKLRGIQISS
-GNTPSFVAITNVRMTRATLELHNQPQHLFLRNINVMQTSAIGPALKMHFDLRKDVRGQFM
-ARQDTLLSLANVHAINENGQSSVDIDRINHQTVNVEAVNFSLPKRGG
->EXAM.1216.00002.0001i_00006 774 hisP | Histidine transport ATP-binding protein HisP | NA | similar to AA sequence:UniProtKB:P02915 | COG:COG4598
-MSENKLHVIDLHKRYGGHEVLKGVSLQARAGDVISIIGSSGSGKSTFLRCINFLEKPSED
-AIIVNGQNINLVRDKDGQLKVADKNQLRLLRTRLTMVFQHFNLWSHMTVLENVMEAPIQV
-LGLSKHDARERALKYLAKVGIDERAQGKYPVHLSGGQQQRVSIARALAMEPDVLLFDEPT
-SALDPELVGEVLRIMQQLAEEGKTMVVVTHEMGFVRHVSSHVIFLHQGKIEEEGDPEQVF
-GNPQSPRLQQFLKGSLK
->EXAM.1216.00002.0001i_00007 792 trmD | tRNA (guanine-N(1)-)-methyltransferase | 2.1.1.228 | similar to AA sequence:UniProtKB:P0A873 | COG:COG0336
-MRAIYRRCVFIGIVSLFPEMFRAITDYGVTGRAVKNGLLNIQSWSPRDFTHDRHRTVDDR
-PYGGGPGMLMMVQPLRDAIHAAKAAAGEGAKVIYLSPQGRKLDQAGVSELATNQKLILVC
-GRYEGVDERVIQTEIDEEWSIGDYVLSGGELPAMTLIDSVARFIPGVLGHEASAIEDSFA
-DGLLDCPHYTRPEVLEGMEVPPVLLSGNHAEIRRWRLKQSLGRTWLRRPELLENLALTEE
-QARLLAEFKTEHAQQQHKHDGMA
->EXAM.1216.00002.0001b_00008 288 NA | hypothetical protein | NA | NA | NA
-MNNHFGKGLMAGLHAPYAYSAHHAVNFCSEYKRGFVLGFTHRMFEKTGDRQLSAWEAGIL
-TRRYGLDKEMVMDFFKENHSGMAVRFFMAGYRLEG
->EXAM.1216.00002.0002b_00009 582 NA | hypothetical protein | NA | NA | NA
-MSTLLYLHGFNSSPRSAKACQLKNWLAERHPHVEMIVPQLPPYPADAAELLESLVLEHGG
-APLGLVGSSLGGYYATWLSQCFMLPAVVVNPAVRPFELLTDYLGQNENPYTGQQYVLESR
-HIYDLKVMQIDPLEAPDLIWLLQQTGDEVLDYRQAVAYYASCRQTVTEGGNHAFTGFEDY
-FNQIVDFLGLHSC
->EXAM.1216.00002.0002b_00010 1308 dctM | C4-dicarboxylate TRAP transporter large permease protein DctM | NA | similar to AA sequence:UniProtKB:O07838 | COG:COG1593
-MIDPIFASCTLIAVFVVLLAMGAPIGICIVIASFSTMMLVLPFDISMFATAQKMFSSLDS
-FALLAVPFFVLSGVIMNSGGIAARLINFAKLFTGKLPGSLSYTNIVGNMMFGAISGSAIA
-ASTSIGGVMVPMSAREGYDRGFAAAVNIASAPTGMLIPPTTAFILYALASGGTSIAALFA
-GGLVAGVLWGVGCMLVTLVVAKRRNYRVFFTVQKGMALKVAVEAIPSLLLIVIIVGGIVQ
-GIFTAIEASAIAVVYTLLLTMVFYRTLKIKDLPSILLQTVVMTGVIMFLLATSSAMSFSM
-SITNIPAALSDMILGISANKLVILLVITVFLLIIGAFMDIGPAILIFTPILLPIMAKLGV
-DPVHLGIIMIYNLAIGTITPPVGSGLYVGASVGKVKVEEVIKPLLPFYGAIIGVLLLITY
-IPEIILFLPRLLGIM
->EXAM.1216.00002.0003b_00011 255 NA | hypothetical protein | NA | NA | NA
-MIINGKLIKAKDLAKAAGVSRSTVIKYYGISRENYERVATERRKLAFELRASGLKWKEVA
-EKMNTTKYSAIAYYRRYLALEKNK
->EXAM.1216.00002.0003b_00012 780 NA | IS21 family transposase ISSen3 | NA | similar to AA sequence:ISfinder:ISSen3 | NA
-MVELQHQRLMVLAEQLQLDSLIGAAPALSQQAVDQEWSYMDFLEHLLHEEKLARHQRKQA
-MYTRMAAFPAVKTFEEYDFTFATGAPQKQIQSLRSLSFIERNENIVLLGPSGVGKTHLAI
-AMGYEAVRAGIKVRFTTAADLLLQLSTSQRQGRYKTTLNRGVMAPKLLIIDEIGYLPFSQ
-EEAKLFFQVIAKRYEKSAMILTSNLPFGQWDQTFAGDAALTSAMLDRILHHSHVVQIKGE
-SYRLKQKRKAGVIAEANPE
diff --git a/Examples/2-res-Annotate-prokka/Proteins/EXAM.1219.00001.prt b/Examples/2-res-Annotate-prokka/Proteins/EXAM.1219.00001.prt
deleted file mode 100644
index 1fc2a57a8df14c3f948bdc665a4f7fa1210ead68..0000000000000000000000000000000000000000
--- a/Examples/2-res-Annotate-prokka/Proteins/EXAM.1219.00001.prt
+++ /dev/null
@@ -1,69 +0,0 @@
->EXAM.1219.00001.0001b_00001 1668 glnS | Glutamine--tRNA ligase | 6.1.1.18 | similar to AA sequence:UniProtKB:P00962 | COG:COG0008
-MSEAEARPTNFIRQIIDEDLASGKHTTVHTRFPPEPNGYLHIGHAKSICLNFGIAQDYQG
-QCNLRFDDTNPVKEDIEYVDSIKNDVEWLGFHWSGDIRYSSDYFDQLHAYAVELINKGLA
-YVDELTPEQIREYRGTLTAPGKNSPFRDRSVEENLALFEKMRTGGFEEGKACLRAKIDMA
-SPFIVMRDPVLYRIKFAEHHQTGNKWCIYPMYDFTHCISDALEGITHSLCTLEFQDNRRL
-YDWVLDNITIPVHPRQYEFSRLNLEYTVMSKRKLNLLVTDKHVEGWDDPRMPTISGLRRR
-GYTAASIREFCKRIGVTKQDNTIEMASLESCIREDLNENAPRAMAVIDPVKLVIENYPQG
-ESEMVTMPNHPNKPEMGSREVPFSGEIWIDRADFREEANKQYKRLVMGKEVRLRNAYVIK
-AERVEKDAEGNITTIFCTYDADTLSKDPADGRKVKGVIHWVSAAHALPIEIRLYDRLFSV
-PNPGAAEDFLSVINPESLVIKQGYGEPSLKAAVAGKAFQFEREGYFCLDSRYATADKLVF
-NRTVGLRDTWAKAGE
->EXAM.1219.00001.0001b_00002 831 amiD | N-acetylmuramoyl-L-alanine amidase AmiD | 3.5.1.28 | similar to AA sequence:UniProtKB:P75820 | COG:COG3023
-MKALLWLVGLALLLTGCASEKGIIDKEGYQLDTRHRAQAAYPRIKVLVIHYTAENFDVSL
-ATLTGRNVSSHYLIPATPPLYGGKPRIWQLVPEQDQAWHAGVSFWRGATRLNDTSIGIEL
-ENRGWRMSGGVKSFAPFESAQIQALIPLAKDIIARYNIKPQNVVAHADIAPQRKDDPGPR
-FPWRELAAQGISAWPDAQRVAFYLAGRAPYTPVDTATVLALLSRYGYEVKADMTAREQQR
-VIMAFQMHFRPAQWNGIADAETQAIAEALLEKYGQD
->EXAM.1219.00001.0002b_00003 381 hpcD | 5-carboxymethyl-2-hydroxymuconate Delta-isomerase | 5.3.3.10 | similar to AA sequence:UniProtKB:Q05354 | NA
-MPHFIAECTENIREQADLPGLFSKVNEALAASGIFPIGGIRSRAHWLDTWQMADGKHDYA
-FVHMTLKIGAGRSLESRQEVGEMLFGLIKAHFADLMENRYLALSFEIAELHPTLNYKQNN
-VHALFK
->EXAM.1219.00001.0002i_00004 1410 NA | hypothetical protein | NA | NA | NA
-MSMPATKFSRRTLLTAGSALAVLPFLRALPVQAREPRETVDIKDYPADDGIASFKQAFAD
-GQTVVVPPGWVCENINAAITIPAGKTLRVQGAVRGNGRGRFILQDGCQVVGEQGGSLHNV
-TLDVRGSDCVIKGVAMSGFGPVAQIFIGGKEPQVMRNLIIDDITVTHANYAILRQGFHNQ
-MDGARITHSRFSDLQGDAIEWNVAIHDRDILISDHVIERINCTNGKINWGIGIGLAGSTY
-DNSYPEDQAVKNFVVANITGSDCRQLVHVENGKHFVIRNVKAKNITPGFSKNAGIDNATI
-AIYGCDNFVIDNIDMTNSAGMLIGYGVVKGKYLSIPQNFKLNAIRLDNRQVAYKLRGIQI
-SSGNTPSFVAITNVRMTRATLELHNQPQHLFLRNINVMQTSAIGPALKMHFDLRKDVRGQ
-FMARQDTLLSLANVHAINENGQSSVDIDRINHQTVNVEAVNFSLPKRGG
->EXAM.1219.00001.0002i_00005 774 hisP | Histidine transport ATP-binding protein HisP | NA | similar to AA sequence:UniProtKB:P02915 | COG:COG4598
-MSENKLHVIDLHKRYGGHEVLKGVSLQARAGDVISIIGSSGSGKSTFLRCINFLEKPSEG
-AIIVNGQNINLVRDKDGQLKVADKNQLRLLRTRLTMVFQHFNLWSHMTVLENVMEAPIQV
-LGLSKHDARERALKYLAKVGIDERAQGKYPVHLSGGQQQRVSIARALAMEPDVLLFDEPT
-SALDPELVGEVLRIMQQLAEEGKTMVVVTHEMGFARHVSSHVIFLHQGKIEEEGDPEQVF
-GNPQSPRLQQFLKGSLK
->EXAM.1219.00001.0002i_00006 735 trmD_1 | tRNA (guanine-N(1)-)-methyltransferase | 2.1.1.228 | similar to AA sequence:UniProtKB:P0A873 | COG:COG0336
-MFRAITDYGVTGRAVKKGLLNIQSWSPRDFAHDRHRTVDDRPYGGGPGMLMMVQPLRDAI
-HAAKAAAGEGAKVIYLSPQGRKLDQAGVSELATNQKLILVCGRYEGVDERVIQTEIDEEW
-SIGDYVLSGGELPAMTLIDSVARFIPGVLGHEASAIEDSFADGLLDCPHYTRPEVLEGME
-VPPVLLSGNHAEIRRWRLKQSLGRTWLRRPELLENLALTEEQARLLAEFKTEHAQQQHKH
-DGMA
->EXAM.1219.00001.0002i_00007 828 trmD_2 | tRNA (guanine-N(1)-)-methyltransferase | 2.1.1.228 | similar to AA sequence:UniProtKB:P0A873 | COG:COG0336
-MMGWHSRHMGSQRRRANAQYVFIGIVSLFPEMFRAITDYGVTGRAVKKGLLNIQSWSPRD
-FAHDRHRTVDDRPYGGGPGMLMMVQPLRDAIHAAKAAAGEGAKVIYLSPQGRKLDQAGVS
-ELATNQKLILVCGRYEGVDERVIQTEIDEEWSIGDYVLSGGELPAMTLIDSVARFIPGVL
-GHEASAIEDSFADGLLDCPHYTRPEVLEGMEVPPVLLSGNHAEIRRWRLKQSLGRTWLRR
-PELLENLALTEEQARLLAEFKTEHAQQQHKHDGMA
->EXAM.1219.00001.0002i_00008 465 NA | hypothetical protein | NA | NA | NA
-MKFVAPEQAPEQAEVIKNTPFWPDVDLSEFRSVMRTDGTVTQPRLKQVVLTAISEVNAEL
-YDFRNRQQMLGWRTLAEVPAEMLDGKSERIRHYHNAVFCWARAVLNERYQDYDATASGVK
-RGEELAEASGDLWRDARWAISRVQDVPHCTVELI
->EXAM.1219.00001.0002i_00009 261 NA | hypothetical protein | NA | NA | NA
-MAGLHAPYAYSAHHAVNFCSEYKRGFVLGFTHRMFEKTGDRQLSAWEAGILTRRYGLDKE
-MVMDFFKENHSGMAVRFFMAGYRLEG
->EXAM.1219.00001.0002i_00010 582 NA | hypothetical protein | NA | NA | NA
-MSTLLYLHGFNSSPRSAKACQLKNWLAERHPHVEMIVPQLPPYPADAAELLESLVLEHGG
-APLGLVGSSLGGYYATWLSQCFMLPAVVVNPAVRPFELLTDYLGQNENPYTGQQYVLESR
-HIYDLKVMQIDPLEAPDLIWLLQQTGDEVLYYRQAVAYYASCRQTVTEGGNHAFTGFEDY
-FNQIVDFLGLHSC
->EXAM.1219.00001.0002b_00011 1308 dctM | C4-dicarboxylate TRAP transporter large permease protein DctM | NA | similar to AA sequence:UniProtKB:O07838 | COG:COG1593
-MIDPIFASCTLIAVFVVLLAMGAPIGICIVIASFSTMMLVLPFDISMFATAQKMFSSLDS
-FALLAVPFFVLSGVIMNSGGIAARLVNFAKLFTGKLPGSLSYTNIVGNMMFGAISGSAIA
-ASTSIGGVMVPMSAREGYDRGFAAAVNIASAPTGMLIPPTTAFILYALASGGTSIAALFA
-GGLVAGVLWGVGCMLVTLVVAKRRNYRVFFTVQKGMALKVAVEAIPSLLLIVIIVGGIVQ
-GIFTAIEASAIAVVYTLLLTMVFYRTLKIKDLPSILLQTVVMTGVIMFLLATSSAMSFSM
-SITNIPAALSDMILGISANKLVILLVITVFLLIIGAFMDIGPAILIFTPILLPIMAKLGV
-DPVHFGIIMIYNLAIGTITPPVGSGLYVGASVGKVKVEEVIKPLLPFYGAIIGVLLLITY
-IPEITLFLPRLLGIM
diff --git a/Examples/2-res-Annotate-prokka/Proteins/GEN2.1219.00001.prt b/Examples/2-res-Annotate-prokka/Proteins/GEN2.1219.00001.prt
deleted file mode 100644
index a7ff6601e0ea205068e260ef22d39660c5805c1c..0000000000000000000000000000000000000000
--- a/Examples/2-res-Annotate-prokka/Proteins/GEN2.1219.00001.prt
+++ /dev/null
@@ -1,77 +0,0 @@
->GEN2.1219.00001.0001b_00001 774 hisP | Histidine transport ATP-binding protein HisP | NA | similar to AA sequence:UniProtKB:P02915 | COG:COG4598
-MSENKLHVIDLHKRYGGHEVLKGVSLQARAGDVISIIGSSGSGKSTFLRCINFLEKSSEG
-AIIVNGQNINLVRDKDGQLKVADKNQLRLLRTRLTMVFQHFNLWNHMTVLENVMEAPIQV
-LGLSKHDARERALKYLAKVGIDERAQGKYPVHLSGGQQQRVSIARALAMEPDVLLFDEPT
-SALDPELVGEVLRIMQQLAEEGKTMVVVTHEMGFARHVSSHVIFLHQGKIEEEGNPEQVF
-GNPQSPRLQQFLKGSLK
->GEN2.1219.00001.0001b_00002 1404 NA | hypothetical protein | NA | NA | NA
-MPATKFSRRTLLTAGSALAVLPFLRALPVQAREPRQTVDIKDYPADDGIASFKQAFADGQ
-TVVVPSGWVCENINAAITIPAGKTLRIQGAVRGNGRGRFILLDGCQVVGEQGGSLHNVTL
-DVRGSDCVIKGVTMSGFGPVAQIFIGGKEPQVMRNLIIDDITVTHANYAILRQGFHNQMD
-GARITHSRFSDLQGDAIEWNVAIHDRDILISDHVIERIDCTNGKINWGIGIGLAGSAYDN
-SYPEDQAVKNFVVANITGSDCRQLVHVENGKHFVIRNVKAKNITPDFSKNAGIDNATIAI
-YGCDNFVIDNIDMTNSAGMLIGYGVVKGKYLSIPQNFKLNAIRLDNRQVAYKLRGIQISS
-GNAPSFVAITNVRMTRATLELHNQPQHLFLRNINVMQTSAIGPALKMHFDLRKDVRGQFM
-ARQDTLLSLANVHAINENGQSSVDIDRINHQTVNVEAVNFSLPKRGG
->GEN2.1219.00001.0002b_00003 225 pspB | Phage shock protein B | NA | similar to AA sequence:UniProtKB:P0AFM9 | NA
-MSALFLAIPLTIFVLFVLPIWLWLHYSNRAGRGELSQSEQQRLLQLTDDAQRMRERIQAL
-EDILDAEHPNWRER
->GEN2.1219.00001.0002i_00004 381 hpcD | 5-carboxymethyl-2-hydroxymuconate Delta-isomerase | 5.3.3.10 | similar to AA sequence:UniProtKB:Q05354 | NA
-MPHFIAECTENIREQADLPSLFSKVNEALAATGIFPIGGIRSRAHWLDTWQMADGKHDYA
-FVHMTLKIGAGRSLESRQEVGEMLFGLIKAHFADLMENRYLALSFEIAELHPTLNYKQNN
-VHALFK
->GEN2.1219.00001.0002i_00005 834 amiD | N-acetylmuramoyl-L-alanine amidase AmiD | 3.5.1.28 | similar to AA sequence:UniProtKB:P75820 | COG:COG3023
-MMKALLWLVGLALLLTGCASEKGIIDKEGYQLDTRHRAQAAYPRIKVLVIHYTAENFDVS
-LATLTGRNVSSHYLIPATPPLYGGKPRIWQLVPEQDQAWHAGVSFWRGATRLNDTSIGIE
-LENRGWRMSGGVKSFAPFESAQIQALIPLAKDIIARYDIKPQNVVAHADIAPQRKDDPGP
-RFPWRELAAQGIGAWPDAQRVAFYLAGRAPYTPVDTATVLALLSRYGYEVKADMTAREQQ
-RVIMAFQMHFRPAQWNGIADAETQAIAEALLEKYGQD
->GEN2.1219.00001.0002b_00006 1668 glnS | Glutamine--tRNA ligase | 6.1.1.18 | similar to AA sequence:UniProtKB:P00962 | COG:COG0008
-MSEAEARPTNFIRQIIDEDLASGKHTTVHTRFPPEPNGYLHIGHAKSICLNFGIAQDYQG
-QCNLRFDDTNPVKEDIEYVDSIKNDVEWLGFHWSGDIRYSSDYFDQLHAYAVELINKGLA
-YVDELTPEQIREYRGTLTAPGKNSPFRDRSVEENLALFEKMRTGGFEEGKACLRAKIDMA
-SPFIVMRDPVLYRIKFAEHHQTGTKWCIYPMYDFTHCISDALEGITHSLCTLEFQDNRRL
-YDWVLDNITIPVHPRQYEFSRLNLEYTVMSKRKLNLLVTDKHVEGWDDPRMPTISGLRRR
-GYTAASIREFCKRIGVTKQDNTIEMASLESCIREDLNENAPRAMAVIDPVKLVIENYPQG
-ESEMVTMPNHPNKPEMGSREVPFSGEIWIDRADFREEANKQYKRLVMGKEVRLRNAYVIK
-AERVEKDAEGNITTIFCTYDADTLSKDPADGRKVKGVIHWVSVAHALPIEIRLYDRLFSV
-PNPGAAEDFLSVINPESLVIKQGYGEPSLKAAVAGKAFQFEREGYFCLDSRYATADKLVF
-NRTVGLRDTWAKAGE
->GEN2.1219.00001.0003b_00007 768 trmD | tRNA (guanine-N(1)-)-methyltransferase | 2.1.1.228 | similar to AA sequence:UniProtKB:P0A873 | COG:COG0336
-MFIGIVSLFPEMFRAITDYGVTGRAVKKGLLNIQSWSPRDFAHDRHRTVDDRPYGGGPGM
-LMMVQPLRDAIHAAKAAAGEGAKVIYLSPQGRKLDQAGVSELATNQKLILVCGRYEGVDE
-RVIQAEIDEEWSIGDYVLSGGELPAMTLIDSVARFIPGVLGHEASAIEDSFADGLLDCPH
-YTRPEVLEGMEVPPVLLSGNHAEIRRWRLKQSLGRTWLRRPELLENLALTEEQARLLAEF
-KTEHAQQQHKHDGMA
->GEN2.1219.00001.0003i_00008 261 NA | hypothetical protein | NA | NA | NA
-MAGLHAPYAYSAHHAVNFCSEYKRGFVLGFTHRMFEKTGDRQLSAWEAGILTRRYGLDKE
-MVMDFFKENHSGMAVRFFMAGYRLEG
->GEN2.1219.00001.0003i_00009 582 NA | hypothetical protein | NA | NA | NA
-MSTLLYLHGFNSSPRSAKACQLKNWLAERHPHVEMIVPQLPPYPADAAELLESLVLEHGG
-APLGLVGSSLGGYYATWLSQCFMLPAVVVNPAVRPFELLTDYLGQNENPYTGQQYVLESR
-HIYDLKVMQIDPLEAPDLIWLLQQTGDEVLDYRQAVAYYASCRQTVTEGGNHAFTGFEDY
-FNQIVDFLGLHSC
->GEN2.1219.00001.0003b_00010 369 NA | hypothetical protein | NA | NA | NA
-MMRTDGTVTQPRLKQVALSAISEVNAELYEFRRRQQMLGYASLAEVPAEQLDGKSERIQH
-YFNAVYCWARAMLNERYQDYDATASGVKRGEELAEASGDLWRDARWAISRVQDAPHCTVE
-LI
->GEN2.1219.00001.0004b_00011 1308 dctM | C4-dicarboxylate TRAP transporter large permease protein DctM | NA | similar to AA sequence:UniProtKB:O07838 | COG:COG1593
-MIDPIFASCTLIAVFVVLLAMGAPIGICIVIASFSTMMLVLPFDISMFATAQKMFSSLDS
-FALLAVPFFVLSGVIMNSGGIAARLVNFAKLFTGKLPGSLSYTNIVGNMMFGAISGSAIA
-ASTSIGGVMVPMSAREGYDRGFAAAVNIASAPTGMLIPPTTAFILYALASGGTSIAALFA
-GGLVAGVLWGVGCMLVTLVVAKRRNYRVFFTVQKGMALKVAVEAIPSLLLIVIIVGGIVQ
-GIFTAIEASAIAVVYTLLLTIVFYRTLKIKDLPSILLQTVVMTGVIMFLLATSSAMSFSM
-SITNIPAALSDMILGISANKLVILLVITVFLLIIGAFMDIGPAILIFTPILLPIMTKLGV
-DPVHFGIIMIYNLAIGTITPPVGSGLYVGASVGKVKVEDVIKPLMPFYGAIIGVLLLITY
-IPEITLFLPRLLGIM
->GEN2.1219.00001.0004i_00012 465 NA | hypothetical protein | NA | NA | NA
-MKFVAPEQAPEQAEVIKNTPFWPDVNLSEFRSVMRTDGTVTQPRLKQVVLTAISEVNAEL
-YDFRNRQQMLGWRTLAEVPAEMLDGKSERIRHYHNAVFCWARAVLNERYQDYDATASGVK
-RGEELAEASGDLWRDARWAISRVQDAPHCTVELI
->GEN2.1219.00001.0004b_00013 1014 xerC | Tyrosine recombinase XerC | NA | protein motif:HAMAP:MF_01808 | NA
-METNITWQQLIDEYFFAKPLRSASEWSYTKVFKSFVHYMGPLSCPNDVTYHKVLAWRRFL
-LKEKKLSGRTWNNKVAHMRAIFNYGIQRGLLHYDENPFNNSVVKPDKKRKKTLTQAQIEY
-AYQIMEQYENQENTGLGLKYSRCALFPAWFWLTVLDTLYYTGIRQNQLLHIRLNDVDLRE
-GQIRLITEGCKNHKEHYVPVISFLRPRLTCLMEKAQSEGLKGNDRLFNIALFTGKDPAIG
-DDMDSPQVRAFFRRLSKECQFAISPHRFRHTLATEMMKMPEQNLHMAQSVLGHSNMKSTL
-EYVENDIAVMGRALEAQFMQIKAAHARSIYSGLTKNR
diff --git a/Examples/2-res-Annotate-prokka/Proteins/GEN4.1111.00001.prt b/Examples/2-res-Annotate-prokka/Proteins/GEN4.1111.00001.prt
deleted file mode 100644
index 841d437809448de6299df1faef13f9da3d26df92..0000000000000000000000000000000000000000
--- a/Examples/2-res-Annotate-prokka/Proteins/GEN4.1111.00001.prt
+++ /dev/null
@@ -1,52 +0,0 @@
->GEN4.1111.00001.0001b_00001 831 amiD | N-acetylmuramoyl-L-alanine amidase AmiD | 3.5.1.28 | similar to AA sequence:UniProtKB:P75820 | COG:COG3023
-MKALLWLVGLALLLTGCASEKGIIDKEGYQLDTRHRAQAAYPRIKVLVIHYTAENFDVSL
-ATLTGRNVSSHYLIPATPPLYGGKPRIWQLVPEQDQAWHAGVSFWRGATRLNDTSIGIEL
-ENRGWRMSGGVKSFAPFESAQIQALIPLAKDIIARYDIKPQNVVAHADIAPQRKDDPGPR
-FPWRELAAQGIGAWPDAQRVAFYLAGRAPYTPVDTATVLALLSRYGYEVKADMTAREQQR
-VIMAFQMHFRPAQWNGIADAETQAIAEALLEKYGQD
->GEN4.1111.00001.0001i_00002 381 hpcD | 5-carboxymethyl-2-hydroxymuconate Delta-isomerase | 5.3.3.10 | similar to AA sequence:UniProtKB:Q05354 | NA
-MPHFIAECTENIREQADLPGLFSKVNEALAASGIFPIGGIRSRAHWLDTWQMADGKHDYA
-FVHMTLKIGTGRSLESRQEVGEMLFGLIKAHFADLMENRYLALSFEIAELHPTLNYKQNN
-VHALFK
->GEN4.1111.00001.0001i_00003 804 hpcG | 2-oxo-hept-4-ene-1,7-dioate hydratase | 4.2.1.163 | similar to AA sequence:UniProtKB:P42270 | NA
-MLDKQTHTLIAQRLNQAEKQREQIRAVSLDYPNITIEDAYAVQREWVNIKIAEGRTLKGH
-KIGLTSKAMQASSQISEPDYGALLDDMFFHDGGDIPTDRFIVPRIEVELAFVLAKPLRGP
-HCTLFDVYNATDYVIPALELIDARSHNIDPETQRPRKVFDTISDNAANAGVILGGRPIKP
-DELDLRWISALLYRNGVIEETGVAAGVLNHPANGVAWLANKLAPYDVQLEAGQIILGGSF
-TRPVPASKGDTFHVDYGNMGAISCRFV
->GEN4.1111.00001.0001i_00004 1404 NA | hypothetical protein | NA | NA | NA
-MPVNKFSRRTLLTAGSALAVLPFLRALPVQAREPRETVDIKDYPADDGIASFKQAFADGQ
-TVVLPPGWVCENINAAITIPAGKTLRVQGAVRGNGRGRFILQDGCQVVGEQGGSLHNVTL
-DVRGSDCVIKGVTMSGFGPVAQIFIGGKEPQVMRNLIIDDITVTHANYAILRQGFHNQMD
-GARITHSRFSDLQGDAIEWNVAIHDRDILISDHVIERIDCTNGKINWGIGIGLAGSTYDN
-SYPEDQAVKNFVVANITGSDCRQLVHVENGKHFVIRNVKAKNITPDFSKNAGIDNATIAI
-YGCDNFVIDNIDMTNSAGMLIGYGVVKGKYLSIPQNFKLNAIRLDNRQVAYKLRGIQISS
-GNIPSFVAITNVRMTRATLELHNQPQHLFLRNINVMQTSAIGPALKMHFDLRKDVRGQFM
-ARQDTLLSLANVHAINENGQSSVDIDRINHQTVNVEAVNFSLPKRGG
->GEN4.1111.00001.0001i_00005 774 hisP | Histidine transport ATP-binding protein HisP | NA | similar to AA sequence:UniProtKB:P02915 | COG:COG4598
-MSENKLHVIDLHKRYGGHEVLKGVSLQARAGDVISIIGSSGSGKSTFLRCINFLEKPSEG
-AIIVNGQNINLVRDKDGQLKVADKNQLRLLRTRLTMVFQHFNLWSHMTVLENVMEAPIQV
-LGLSKHDARERALKYLAKVGIDERAQGKYPVHLSGGQQQRVSIARALAMEPDVLLFDEPT
-SALDPELVGEVLRIMQQLAEEGKTMVVVTHEMGFARHVSSHVIFLHQGKIEEEGDPEQVF
-GNPQSPRLQQFLKGSLK
->GEN4.1111.00001.0001i_00006 768 trmD | tRNA (guanine-N(1)-)-methyltransferase | 2.1.1.228 | similar to AA sequence:UniProtKB:P0A873 | COG:COG0336
-MFIGIVSLFPEMFRAITDYGVTGRAVKKGLLNIQSWSPRDFAHDRHRTVDDRPYGGGPGM
-LMMVQPLRDAIHAAKAAAGEGAKVIYLSPQGRKLDQAGVSELATNQKLILVCGRYEGVDE
-RVIQTEIDEEWSIGDYVLSGGELPAMTLIDSVARFIPGVLGHEASAIEDSFADGLLDCPH
-YTRPEVLEGMEVPPVLLSGNHAEIRRWRLKQSLGRTWLRRPELLENLALTEEQARLLAEF
-KTEHAQQQHKHDGMA
->GEN4.1111.00001.0001i_00007 261 NA | hypothetical protein | NA | NA | NA
-MAGLHAPYAYSAHHAVNFCSEYKRGFVLGFTHRMFEKTGDRQLSAWEAGILTRRYGLDKE
-MVMDFFKENHSGMAVRFFMVGYRLEG
->GEN4.1111.00001.0001i_00008 582 NA | hypothetical protein | NA | NA | NA
-MSTLLYLHGFNSSPRSAKACQLKNWLAERHPHVEMIVPQLPPYPADAAELLESLVLEHGG
-APLGLVGSSLGGYYATWLSQCFMLPAVVVNPAVRPFELLTDYLGQNENPYTGQQYVLESR
-HIYDLKVMQIDPLEAPDLIWLLQQTGDEVLDYRQAVAYYASCRQTVTEGGNHAFTGFEDY
-FNQIVDFLGLHSC
->GEN4.1111.00001.0001b_00009 1083 dctM | C4-dicarboxylate TRAP transporter large permease protein DctM | NA | similar to AA sequence:UniProtKB:O07838 | COG:COG1593
-MNSGGIAARLVNFAKLFTGKLPGSLSYTNIVGNMMFGAISGSAIAASTSIGGVMVPMSAR
-EGYDRGFAAAVNIASAPTGMLIPPTTAFILYALASGGTSIAALFAGGLVAGVLWGVGCML
-VTLVVAKRRNYRVFFTVQKGMALKVAVEAIPSLLLIVIIVGGIVQGIFTAIEASAIAVVY
-TLLLTMVFYRTLKIKDLPSILLQTVVMTGVIMFLLATSSAMSFSMSITNIPAALSDMILG
-ISANKLVILLVITVFLLIIGAFMDIGPAILIFTPILLPIMAKLGVDPVHFGIIMIYNLAI
-GTITPPVGSGLYVGASVGKVKVEEVIKPLLPFYGAIIGVLLLITYIPEITLFLPRLLGIM
diff --git a/Examples/2-res-Annotate-prokka/QC_L90-list_genomes.png b/Examples/2-res-Annotate-prokka/QC_L90-list_genomes.png
deleted file mode 100644
index 98988190f52b4fc64da18473ed96bc3bf3751f04..0000000000000000000000000000000000000000
Binary files a/Examples/2-res-Annotate-prokka/QC_L90-list_genomes.png and /dev/null differ
diff --git a/Examples/2-res-Annotate-prokka/QC_nb-contigs-list_genomes.png b/Examples/2-res-Annotate-prokka/QC_nb-contigs-list_genomes.png
deleted file mode 100644
index 25433444de0c917cb715f8f4a67f9836a6e2afde..0000000000000000000000000000000000000000
Binary files a/Examples/2-res-Annotate-prokka/QC_nb-contigs-list_genomes.png and /dev/null differ
diff --git a/Examples/2-res-Annotate-prokka/Replicons/EXAM.1216.00002.fna b/Examples/2-res-Annotate-prokka/Replicons/EXAM.1216.00002.fna
deleted file mode 100644
index bd0e1394f21b9f26a5a6dbf61eb728bc620e97f1..0000000000000000000000000000000000000000
--- a/Examples/2-res-Annotate-prokka/Replicons/EXAM.1216.00002.fna
+++ /dev/null
@@ -1,6 +0,0 @@
->EXAM.1216.00002.0001	5747
-ATGAGAGCGCTACTGTGGCTGGTGGGTCTTGCGTTGCTGTTAACAGGCTGCGCGAGCGAAAAAGGAATTATCGATGAAGAGGGATATCAGCTTGATACCCGACATCGGGCGCAGGCGGCCTATCCGCGCATTAAAGTCCTGGTGATTCACTATACGGCGGAAAACTTTGACGTTTCGCTGGCGACGTTAACGGGCCGCAACGTCAGTTCGCATTACCTGATTCCCGCAACCCCGCCATTATATGGCGGTAAACCGCGCATCTGGCAACTGGTGCCGGAACAGGATCAGGCCTGGCATGCGGGCGTCAGTTTCTGGCGAGGCGCCACGCGTCTCAATGATACGTCTATTGGCATTGAGCTGGAAAATCGCGGCTGGCGAATGTCCGGCGGGGTGAAATCTTTCGCGCCGTTTGAATCCGCGCAAATTCAGGCATTGATTCCGTTAGCGAAGGACATTATCGCGCGCTATGACATCAAACCGCAGAATGTGGTGGCCCATGCGGATATCGCGCCGCAGCGTAAAGACGATCCCGGCCCGCGCTTCCCGTGGCGCGAGCTGGCGGCACAGGGGATTGGCGCCTGGCCTGACGCCCAGCGTGTGGCGTTTTATCTGGCTGGACGCGCGCCGTATACGCCAGTCGATACCGCAACGGTGCTTGCGTTACTCTCGCGCTATGGCTATGAAGTCAAAGCCGATATGACGGCGCGCGAGCAACAGCGGGTGATTATGGCGTTCCAGATGCACTTCCGTCCGGCGCAATGGAACGGTATCGCAGATGCCGAAACGCAGGCGATTGCCGAAGCATTACTGGAGAAGTACGGCCAGGATTAACGAGTCCGGGAGCGGCGAGATTCCGGGCAGAGGAGGCGGCTATAGCGGATGAGAGCGCTACTGTGGCTGGTGGGTCTTGCGTTGCTGTTAACAGGCTGCGCGAGCGAAAAAGGAATTATCGATGAAGAGGGATATCAGCTTGATACCCGACATCGGGCGCAGGCGGCCTATCCGCGCATTAAAGTCCTGGTGATTCACTATACGGCGGAAAACTTTGACGTTTCGCTGGCGACGTTAACGGGCCGCAACGTCAGTTCGCATTACCTGATTCCCGCAACCCCGCCATTATATGGCGGTAAACCGCGCATCTGGCAACTGGTGCCGGAACAGGATCAGGCCTGGCATGCGGGCGTCAGTTTCTGGCGAGGCGCCACGCGTCTCAATGATACGTCTATTGGCATTGAGCTGGAAAATCGCGGCTGGCGAATGTCCGGCGGGGTGAAATCTTTCGCGCCGTTTGAATCCGCGCAAATTCAGGCATTGATTCCGTTAGCGAAGGACATTATCGCGCGCTATGACATCAAACCGCAGAATGTGGTGGCCCATGCGGATATCGCGCCGCAGCGTAAAGACGATCCCGGCCCGCGCTTCCCGTGGCGCGAGCTGGCGGCACAGGGGATTGGCGCCTGGCCTGACGCCCAGCGTGTGGCGTTTTATCTGGCTGGACGCGCGCCGTATACGCCAGTCGATACCGCAACGGTGCTTGCGTTACTCTCGCGCTATGGCTATGAAGTCAAAGCCGATATGACGGCGCGCGAGCAACAGCGGGTGATTATGGCGTTCCAGATGCACTTCCGTCCGGCGCAATGGAACGGTATCGCAGATGCCGAAACGCAGGCGATTGCCGAAGCATTACTGGAGAAGTACGGCCAGGATTAACAGGGCGCGGTATCGCGAGGACTCTCTCTTCGAGGACATGCCGCACTTTATTGCTGAATGTACTGAAAATATTCGCGAGCAGGCTGATTTACCCGGCCTGTTCAGCAAGGTAAACGAGGCGCTGGCCGCCAGCGGGATTTTCCCCATCGGCGGTATCCGCAGTCGCGCCCACTGGCTGGATACCTGGCAGATGGCTGACGGTAAGCATGATTACGCGTTTGTGCATATGACGCTGAAAATCGGCGCCGGGCGCAGCCTGGAGAGCCGTCAGGAAGTCGGCGAAATGCTGTTCGGGCTGATTAAAGCCCACTTCGCCGACCTGATGGAGAACCGCTATCTGGCGCTGTCGTTTGAGATTGCCGAGTTACATCCAACGCTCAATTACAAACAAAACAACGTACACGCGTTATTTAAATAGCCCGAGTATTAGCGCGCGGCGGCGCTATAGGCGCGCTATAGGCATGAGCGCGCTATTTCTGGCCATCCCGTTAACCATTTTTGTGTTGTTTGTGTTACCGATTTGGCTGTGGCTGCATTACAGCAACCGCGCCGGTCGGGGAGAACTGTCGCAAAGCGAGCAGCAACGCTTACTGCAACTCACAGACGACGCGCAACGTATGCGCGAGCGCATTCAGGCGCTGGAAGACATTCTTGATGCAGAGCATCCGAACTGGAGAGAGCGCTAACGAGAGTCTCGGAGGAGCGGCGCTCTGGATGCCCGCGACTAAATTCTCCCGACGTACCCTCCTGACGGCAGGTTCTGCGCTTGCTGTTCTTCCTTTCCTGCGCGCCTTGCCGGTACAGGCGCGTGAACCTCGCGAGACCGTCGATATTAAGGATTATCCGGCGGATGACGGTATCGCCTCGTTCAAACAGGCCTTCGCCGACGGACAGACCGTGGTCGTACCGCCAGGATGGGTGTGTGAAAATATCAATGCGGCGATAACGATTCCGGCGGGAAAAACGCTGCGGGTACAGGGCGCGGTGCGTGGGAATGGCCGGGGACGGTTTATTTTGCAGGACGGGTGTCAGGTGGTGGGGGAGCAGGGCGGCAGTCTGCACAATGTGACGCTGGATGTTCGCGGGTCGGACTGTGTGATTAAAGGCGTGGCGATGAGCGGCTTTGGCCCCGTCGCGCAAATTTTCATCGGTGGTAAGGAACCGCAGGTGATGCGTAATCTCATTATCGATGACATCACCGTTACCCACGCCAACTACGCCATTCTCCGCCAGGGATTTCATAACCAAATGGACGGCGCGAGGATTACGCATAGCCGCTTTAGCGATTTACAGGGGGACGCCATTGAGTGGAATGTCGCGATTCACGACCGCGATATCCTGATTTCCGATCATGTCATCGAACGCATTGATTGTACCAATGGCAAAATCAACTGGGGGATCGGCATCGGGCTGGCGGGTAGCACCTATGACAACAGTTATCCTGAAGACCAGGCAGTAAAAAACTTTGTGGTGGCCAATATTACCGGATCTGATTGCCGACAGCTTGTGCACGTAGAAAATGGCAAACATTTCGTCATTCGCAATGTCAAAGCCAAAAACATCACGCCCGATTTCAGTAAAAATGCGGGTATTGATAACGCAACGATCGCAATTTATGGCTGTGATAATTTCGTCATTGATAATATTGATATGACGAATAGTGCCGGGATGCTCATCGGCTATGGCGTCGTTAAAGGAAAATACCTGTCAATTCCGCAAAACTTTAAATTAAACGCTATTCGGTTGGATAATCGCCAGGTTGCTTATAAATTACGCGGCATTCAAATTTCCTCCGGCAACACCCCCTCTTTTGTCGCCATCACCAATGTACGGATGACGCGTGCTACGCTGGAACTGCATAATCAACCGCAGCACCTCTTCCTGCGTAATATCAACGTGATGCAAACTTCAGCGATTGGCCCGGCGTTAAAAATGCATTTCGATTTGCGTAAAGATGTCCGTGGTCAATTTATGGCCCGCCAGGACACGCTGCTTTCCCTCGCTAATGTTCATGCCATCAATGAAAACGGGCAGAGTTCCGTGGATATCGACAGGATTAATCACCAAACCGTGAATGTCGAAGCAGTGAATTTTTCGCTGCCGAAGCGGGGAGGGTAACGCGTCTGCGCGCGCGGAGAGAGGCTCTCAGGACATGTCAGAAAATAAATTACACGTTATCGATTTGCACAAACGCTACGGCGGTCATGAAGTGCTGAAAGGGGTATCGCTGCAGGCCCGCGCCGGAGATGTGATTAGCATCATCGGCTCGTCCGGCTCCGGTAAAAGCACTTTTTTGCGCTGTATTAACTTCCTCGAAAAACCGAGCGAAGACGCGATTATCGTGAACGGTCAGAACATTAATCTGGTGCGCGACAAAGACGGGCAGCTCAAAGTGGCGGATAAAAATCAGCTACGCTTGTTGCGTACCCGCCTGACGATGGTGTTTCAGCACTTTAACCTCTGGAGCCACATGACGGTGCTGGAAAATGTGATGGAAGCGCCGATTCAGGTACTGGGATTAAGCAAGCACGACGCGCGCGAGCGGGCGTTGAAATATCTGGCGAAGGTGGGGATTGATGAGCGCGCTCAGGGCAAATATCCCGTTCATCTCTCCGGTGGCCAACAGCAGCGCGTTTCTATTGCGCGCGCGCTGGCGATGGAACCTGACGTTTTACTGTTCGATGAACCCACTTCGGCGCTCGATCCTGAACTGGTCGGCGAAGTGTTGCGCATCATGCAACAACTGGCGGAAGAAGGCAAAACGATGGTGGTGGTCACGCATGAAATGGGCTTCGTTCGCCATGTCTCTTCGCACGTTATTTTTCTGCATCAGGGGAAAATTGAAGAAGAGGGCGATCCGGAGCAGGTGTTCGGCAATCCGCAAAGCCCGCGTTTACAGCAATTCCTGAAAGGCTCGCTGAAATAACCGGATGCGCGCGATATATCGGCGATGCGTGTTTATTGGCATCGTTAGCCTGTTTCCTGAAATGTTCCGCGCAATTACCGATTACGGGGTAACTGGCCGGGCAGTAAAAAATGGCCTGCTGAACATCCAAAGCTGGAGTCCTCGCGACTTCACGCATGACCGGCACCGTACCGTGGACGATCGTCCTTACGGCGGCGGACCAGGGATGTTAATGATGGTGCAACCCTTGCGGGACGCCATTCACGCAGCAAAAGCCGCGGCAGGTGAAGGCGCTAAAGTGATTTATCTGTCGCCTCAGGGACGCAAGCTTGATCAAGCGGGCGTTAGCGAGCTGGCCACGAATCAGAAGCTTATTCTGGTGTGTGGTCGCTACGAAGGCGTAGATGAGCGCGTAATTCAGACCGAAATTGACGAAGAATGGTCAATTGGCGATTACGTTCTCAGCGGTGGCGAACTACCGGCAATGACGCTGATTGACTCCGTCGCCCGGTTTATACCGGGAGTTCTGGGGCATGAAGCATCAGCAATCGAAGATTCGTTTGCTGATGGGTTGCTGGATTGTCCGCACTATACGCGCCCTGAAGTGTTAGAGGGGATGGAAGTACCGCCAGTATTGCTGTCGGGAAACCATGCTGAGATACGTCGCTGGCGTTTGAAACAGTCGCTGGGCCGAACCTGGCTTAGAAGACCTGAACTTCTGGAAAACCTGGCTCTGACTGAAGAGCAAGCAAGGTTGCTGGCGGAGTTCAAAACAGAACACGCACAACAGCAGCATAAACATGATGGGATGGCATAGCCGGCTCTGCGAGAGAGGAGCGCTCGCATGAATAATCATTTTGGGAAAGGGTTAATGGCCGGGTTGCACGCGCCATATGCATATAGCGCGCATCATGCGGTGAATTTCTGTTCTGAGTATAAACGTGGCTTTGTATTGGGTTTTACACACCGTATGTTCGAAAAGACCGGCGATCGTCAACTTAGCGCGTGGGAGGCTGGAATTCTGACGCGTCGCTATGGTCTGGATAAAGAAATGGTGATGGATTTCTTTAAAGAGAATCATTCCGGGATGGCGGTTCGCTTCTTTATGGCCGGTTATCGACTCGAAGGTTGA
->EXAM.1216.00002.0002	1968
-ATGTCTACGCTTCTCTATTTGCACGGATTCAACAGTTCCCCTCGCTCGGCAAAAGCGTGCCAGCTAAAAAACTGGCTGGCGGAGCGTCATCCGCATGTTGAGATGATCGTCCCTCAACTACCGCCGTATCCTGCCGATGCGGCGGAGTTGCTGGAGTCTCTCGTGCTTGAGCATGGCGGTGCGCCATTAGGGCTGGTAGGATCGTCGCTGGGTGGTTATTACGCCACCTGGCTGTCGCAATGTTTTATGCTGCCGGCTGTGGTGGTGAATCCCGCCGTGCGGCCCTTTGAATTACTGACCGACTATCTCGGTCAGAACGAGAACCCCTACACCGGGCAGCAATATGTGCTAGAGTCTCGCCATATTTATGATCTTAAAGTCATGCAGATTGACCCGCTGGAAGCGCCGGACCTGATCTGGCTACTGCAACAGACGGGCGATGAAGTGCTGGATTACCGCCAGGCGGTGGCATATTACGCCTCCTGCCGTCAGACAGTGACCGAGGGTGGTAATCACGCATTCACGGGCTTCGAAGATTATTTCAACCAGATTGTCGATTTTCTTGGACTGCACAGTTGCTGACGCGTAGCGGCCGGAATCTTCTCGGAGAGGCGCTTCTCTCTCGGAGATGATTGACCCTATTTTTGCGTCCTGTACGCTAATTGCCGTCTTTGTTGTTTTACTGGCCATGGGCGCGCCTATCGGGATCTGCATCGTTATCGCCTCTTTCAGCACCATGATGCTGGTACTGCCTTTCGATATTTCGATGTTCGCCACCGCGCAAAAAATGTTCTCCAGCCTGGACAGTTTTGCCTTGCTGGCCGTGCCGTTCTTCGTTTTGTCCGGGGTGATCATGAATAGCGGGGGAATTGCCGCCCGGCTGATCAATTTTGCCAAACTGTTTACTGGCAAACTGCCCGGTTCGCTCTCTTATACCAACATCGTCGGCAATATGATGTTCGGTGCAATTTCCGGATCGGCAATTGCCGCCTCAACCTCCATCGGCGGCGTGATGGTGCCGATGAGCGCGCGCGAAGGTTACGATCGCGGCTTTGCGGCCGCGGTGAATATCGCCTCCGCGCCGACGGGAATGTTAATTCCGCCCACCACGGCTTTTATCCTTTATGCGCTGGCAAGCGGGGGAACATCGATTGCCGCTCTGTTCGCCGGCGGTCTGGTCGCGGGAGTGCTGTGGGGCGTTGGCTGTATGCTGGTCACGCTGGTAGTCGCTAAGCGTCGAAATTATCGGGTTTTCTTCACCGTCCAAAAAGGCATGGCGCTAAAAGTTGCCGTTGAGGCCATTCCCAGCCTGTTACTGATCGTGATTATCGTCGGCGGCATTGTGCAGGGGATTTTCACCGCCATTGAAGCCTCCGCGATTGCCGTGGTGTATACGTTATTGCTGACGATGGTGTTTTACCGCACGCTGAAAATTAAGGATTTGCCTTCGATTTTGCTCCAGACAGTGGTAATGACCGGGGTCATCATGTTCCTGCTGGCAACCTCTTCGGCGATGTCCTTCTCAATGTCGATCACCAATATTCCTGCGGCGCTGAGCGATATGATCCTCGGTATTTCCGCCAATAAACTGGTTATCCTGTTAGTCATTACCGTCTTTTTGTTGATTATCGGCGCATTTATGGATATCGGTCCGGCCATTCTGATTTTTACCCCGATTCTGCTGCCGATCATGGCTAAACTGGGCGTCGATCCGGTGCATTTGGGCATTATCATGATCTATAACCTGGCGATTGGCACCATTACGCCGCCAGTTGGCAGTGGTTTATATGTCGGGGCGAGCGTCGGTAAGGTCAAAGTTGAGGAAGTGATTAAACCGTTGCTGCCTTTTTACGGCGCGATTATCGGCGTTCTGTTATTAATTACCTACATTCCGGAAATCATACTGTTCTTACCCCGTCTACTGGGCATCATGTAAACCCGATGGCGCGCAGAGGCGCGAGTTCTGGA
->EXAM.1216.00002.0003	1102
-CACAGGGCTTAGAGGCGCTATGGCAATGATAATTAATGGGAAATTAATTAAAGCAAAAGACTTAGCTAAGGCTGCAGGTGTATCTCGTTCAACAGTGATTAAATATTACGGCATTAGCCGTGAGAATTACGAAAGGGTAGCAACTGAAAGAAGGAAGCTTGCTTTTGAACTAAGAGCATCAGGTTTAAAATGGAAAGAAGTTGCTGAAAAAATGAACACGACAAAATATAGCGCAATTGCATATTATAGACGATATTTAGCATTAGAGAAAAACAAATAACAGGCGCTAAGGCGGCGATCCTAGCGCGCGATCGCGCATGCGATGGTCGAACTGCAACATCAACGGCTGATGGTGCTTGCCGAACAGCTCCAGCTGGACAGTCTTATCGGCGCAGCGCCGGCGCTGTCGCAACAGGCGGTGGATCAGGAATGGAGCTACATGGACTTCCTGGAGCACCTGTTACATGAGGAGAAACTGGCCCGGCATCAGCGTAAACAGGCGATGTACACGCGGATGGCAGCCTTCCCGGCGGTAAAGACGTTCGAGGAGTACGACTTCACCTTCGCCACCGGCGCTCCTCAGAAGCAAATCCAGTCGCTGCGATCCCTGAGCTTCATAGAGCGTAACGAAAACATCGTGTTGCTGGGGCCATCGGGCGTGGGAAAAACGCATCTGGCGATAGCCATGGGCTACGAAGCAGTACGGGCGGGCATCAAGGTTCGCTTCACAACAGCAGCGGACCTGCTGCTACAGCTGTCCACTTCACAGCGTCAGGGCCGTTACAAAACGACTCTCAATCGTGGTGTCATGGCCCCGAAGCTGCTTATCATCGATGAAATAGGTTATCTGCCGTTCAGTCAGGAGGAAGCCAAGCTGTTCTTCCAGGTCATCGCCAAACGTTACGAGAAGAGCGCGATGATCCTGACCTCCAACCTGCCGTTCGGGCAGTGGGATCAGACGTTCGCCGGTGATGCAGCGCTGACATCGGCGATGCTGGACCGGATCTTACATCACTCACACGTCGTGCAAATAAAAGGGGAAAGCTATCGACTGAAGCAGAAACGAAAGGCCGGGGTTATAGCTGAAGCTAATCCTGAGTAA
diff --git a/Examples/2-res-Annotate-prokka/Replicons/EXAM.1219.00001.fna b/Examples/2-res-Annotate-prokka/Replicons/EXAM.1219.00001.fna
deleted file mode 100644
index 8245cff51e58bd17ae799d8507ae99b28b3e9fdd..0000000000000000000000000000000000000000
--- a/Examples/2-res-Annotate-prokka/Replicons/EXAM.1219.00001.fna
+++ /dev/null
@@ -1,4 +0,0 @@
->EXAM.1219.00001.0001	2784
-ATGTGTAAAAGCCGGAGGGGTTATCTTTTCCCGGCTTTTTATTATCAATTACTCATTAACTCCTGTTCCGTTCTTTTGCGTTTAATCACCGGAATATCTCCGGTATTGTTCAGCGCCCCGGAAATGTTTTTAACCACTGTTCTGCACTCCGTTTATTAAACGCGCTCAGCGCGCGCTCATATATCGCGCGCGCGCGCGCGCATATATATATAATGAGTGAGGCTGAAGCCCGCCCGACTAACTTTATTCGTCAGATTATTGATGAAGATCTGGCGAGTGGTAAACATACCACTGTCCATACCCGTTTTCCGCCGGAGCCGAATGGCTATCTGCATATCGGCCACGCGAAATCTATCTGCCTGAACTTTGGCATCGCGCAAGATTATCAGGGCCAGTGCAACCTGCGTTTCGATGACACCAACCCGGTAAAAGAAGATATCGAGTACGTTGATTCGATCAAAAACGACGTCGAGTGGTTAGGCTTTCACTGGTCTGGCGATATTCGCTACTCCTCCGATTACTTTGACCAACTGCACGCCTATGCGGTCGAGCTAATCAATAAAGGCCTGGCCTATGTTGATGAGCTGACGCCGGAGCAGATCCGTGAATACCGCGGTACGCTGACCGCGCCGGGTAAAAACAGCCCGTTCCGCGATCGCAGCGTCGAAGAGAACCTCGCGCTATTTGAAAAAATGCGTACCGGCGGTTTTGAAGAGGGTAAAGCCTGTCTGCGCGCTAAAATCGACATGGCGTCGCCGTTTATCGTGATGCGCGATCCGGTGCTGTATCGCATTAAATTCGCCGAGCATCATCAGACTGGCAACAAGTGGTGCATCTATCCGATGTACGACTTTACTCACTGCATCAGCGATGCGCTGGAAGGCATTACTCATTCTCTGTGTACGCTGGAGTTCCAGGATAACCGTCGTCTGTACGACTGGGTGCTGGACAACATCACCATTCCGGTTCACCCGCGCCAGTACGAATTCTCGCGCCTGAATCTGGAATACACCGTGATGTCCAAGCGTAAGCTGAACCTGCTGGTGACCGACAAACACGTCGAAGGTTGGGACGATCCGCGTATGCCGACTATTTCCGGTCTGCGCCGTCGCGGCTATACCGCGGCTTCTATTCGTGAGTTCTGCAAACGCATCGGCGTCACCAAGCAGGACAACACTATTGAGATGGCGTCGCTGGAATCCTGCATTCGCGAAGATCTGAACGAAAACGCGCCGCGCGCGATGGCGGTAATCGATCCGGTAAAACTGGTTATCGAAAATTACCCGCAGGGTGAGAGCGAAATGGTTACCATGCCTAACCATCCGAATAAACCGGAGATGGGCAGCCGTGAAGTGCCGTTTAGCGGTGAGATCTGGATCGATCGCGCAGATTTCCGCGAAGAAGCGAACAAACAGTACAAACGTCTGGTGATGGGCAAAGAAGTGCGTCTGCGTAATGCCTACGTCATTAAAGCGGAGCGCGTAGAGAAGGATGCCGAAGGGAATATCACCACCATCTTCTGTACCTATGATGCTGATACGCTGAGTAAAGATCCGGCTGACGGGCGTAAAGTGAAAGGCGTAATCCACTGGGTTAGCGCAGCACATGCGCTGCCGATTGAAATTCGTCTCTACGACCGTCTGTTCAGCGTGCCGAATCCGGGCGCCGCGGAGGACTTCCTGTCTGTTATCAACCCCGAATCATTAGTGATTAAGCAGGGGTATGGCGAGCCGTCGCTGAAAGCGGCGGTAGCAGGAAAAGCTTTCCAGTTTGAACGTGAAGGCTACTTCTGCCTCGACAGCCGCTATGCAACGGCCGATAAGCTGGTCTTTAACCGCACCGTGGGCCTGCGTGATACCTGGGCGAAAGCGGGCGAGTAACGCGCATAGGCGGCCTTCAAGGAGGCGCTAGGCGAATGAAAGCGCTACTGTGGCTGGTGGGTCTCGCGTTGCTGTTAACAGGCTGCGCGAGCGAAAAAGGAATTATCGATAAAGAGGGATATCAGCTTGATACCCGACATCGGGCGCAGGCGGCCTATCCGCGCATTAAAGTCCTGGTGATTCACTATACGGCGGAAAACTTTGACGTTTCGCTGGCGACGTTAACGGGTCGCAACGTCAGTTCGCATTACCTGATTCCCGCAACCCCGCCATTATATGGCGGTAAACCGCGCATCTGGCAACTGGTGCCGGAACAGGATCAGGCCTGGCATGCGGGCGTCAGTTTCTGGCGAGGCGCCACGCGTCTCAATGATACGTCTATTGGCATTGAGCTGGAAAATCGTGGTTGGCGAATGTCCGGCGGGGTGAAATCTTTCGCGCCGTTTGAATCCGCGCAAATTCAGGCATTGATTCCGTTAGCGAAGGATATTATCGCGCGCTATAACATCAAACCGCAGAATGTGGTGGCCCATGCGGATATCGCGCCGCAGCGTAAAGACGATCCCGGCCCGCGCTTCCCGTGGCGCGAGCTGGCGGCGCAGGGGATTAGCGCCTGGCCTGACGCCCAGCGTGTGGCGTTTTATCTGGCTGGACGCGCGCCGTATACGCCAGTCGATACCGCAACGGTGCTTGCGTTACTCTCGCGCTATGGCTATGAAGTCAAAGCCGATATGACGGCACGCGAGCAGCAGCGGGTGATTATGGCGTTCCAGATGCACTTCCGTCCGGCGCAATGGAACGGTATCGCAGATGCCGAAACGCAGGCGATTGCCGAAGCATTACTGGAGAAGTACGGCCAGGATTAACGCGATAGGCGCGCGAGATTACGCGCGCAGTATCGCGC
->EXAM.1219.00001.0002	7024
-CGCGCATAGCGCGCAATGCCGCACTTTATTGCTGAATGTACTGAAAATATTCGCGAGCAGGCTGATTTACCCGGCCTGTTCAGCAAGGTAAACGAGGCGCTGGCCGCCAGCGGGATTTTCCCCATCGGCGGTATCCGCAGTCGCGCCCACTGGCTGGATACCTGGCAGATGGCTGACGGTAAGCATGATTACGCGTTTGTGCATATGACGCTGAAAATCGGCGCCGGGCGCAGCCTGGAGAGCCGTCAGGAAGTTGGCGAAATGCTGTTTGGGCTGATTAAAGCCCACTTCGCCGACCTGATGGAGAACCGCTATCTGGCGCTGTCGTTTGAGATTGCCGAGCTACATCCGACGCTCAATTACAAACAAAACAACGTACACGCGTTATTTAAATAGCCGATATGAGGCGCGGCGCTATAAGGCGCTCATGAGCATGCCCGCGACTAAATTCTCCCGACGTACCCTCCTGACGGCAGGTTCTGCGCTTGCTGTTCTTCCTTTTCTGCGCGCCTTGCCGGTACAGGCGCGTGAACCTCGCGAGACCGTCGATATTAAGGATTATCCGGCGGATGACGGTATCGCCTCGTTCAAACAGGCCTTCGCCGACGGACAGACCGTGGTCGTACCGCCAGGATGGGTGTGTGAAAATATCAATGCGGCGATAACGATTCCGGCGGGAAAAACGCTGCGGGTACAGGGCGCGGTGCGTGGGAATGGCCGGGGACGGTTTATTTTGCAGGACGGGTGTCAGGTGGTGGGGGAGCAGGGCGGCAGTCTGCACAATGTGACGCTGGATGTTCGCGGGTCGGACTGTGTGATTAAAGGCGTGGCGATGAGCGGCTTTGGCCCCGTCGCGCAAATTTTCATCGGTGGTAAGGAACCGCAGGTGATGCGTAATCTCATTATCGATGACATCACCGTTACCCACGCCAACTACGCCATTCTCCGCCAGGGATTTCATAACCAAATGGATGGCGCGCGGATTACGCATAGCCGCTTTAGCGATTTACAGGGGGACGCCATTGAGTGGAATGTCGCGATTCACGACCGCGACATCCTGATTTCCGATCATGTCATCGAACGCATTAATTGTACCAATGGCAAAATCAACTGGGGGATCGGCATCGGGCTGGCGGGTAGCACCTATGACAACAGTTATCCTGAAGACCAGGCAGTAAAAAACTTTGTGGTGGCCAATATTACCGGATCTGATTGCCGACAGCTTGTGCACGTAGAAAATGGCAAACATTTCGTCATTCGCAATGTCAAAGCCAAAAACATCACGCCCGGTTTCAGTAAAAATGCGGGTATTGATAACGCAACGATCGCAATTTATGGCTGTGATAATTTCGTCATTGATAATATTGATATGACGAATAGTGCCGGGATGCTCATCGGCTATGGCGTCGTTAAAGGAAAATACCTGTCAATTCCGCAAAACTTTAAATTAAACGCTATTCGGTTGGATAATCGCCAGGTTGCTTATAAATTACGCGGCATTCAAATTTCCTCCGGCAACACCCCCTCTTTTGTCGCCATCACCAATGTACGGATGACGCGTGCTACGCTGGAACTGCATAATCAACCGCAGCACCTCTTTCTGCGCAATATCAACGTGATGCAAACTTCAGCGATTGGCCCGGCGTTAAAAATGCATTTCGATTTGCGTAAAGATGTACGTGGTCAATTTATGGCCCGCCAGGACACGCTGCTTTCCCTCGCTAATGTTCATGCCATCAATGAAAACGGGCAGAGTTCCGTGGATATCGACAGGATTAATCACCAAACCGTGAATGTCGAAGCAGTGAATTTTTCGCTGCCGAAGCGGGGAGGGTAACGAATTCCGCGGCATATAGCGGCGCGATAGCATGTCAGAAAATAAATTACACGTTATCGATTTGCACAAACGCTACGGCGGTCATGAAGTGCTGAAAGGGGTATCGCTGCAGGCCCGCGCCGGAGATGTGATTAGCATCATCGGCTCGTCCGGCTCCGGTAAAAGCACTTTTTTGCGCTGTATTAACTTCCTCGAAAAACCGAGCGAAGGCGCGATTATCGTGAACGGTCAGAACATTAATCTGGTGCGCGACAAAGATGGGCAGCTCAAAGTGGCGGATAAAAATCAGCTACGCTTGTTGCGTACCCGCCTGACGATGGTGTTTCAGCACTTCAACCTCTGGAGCCACATGACGGTGCTGGAAAATGTGATGGAAGCGCCGATTCAGGTACTGGGATTAAGCAAGCACGACGCGCGCGAGCGGGCGTTGAAATATCTGGCGAAGGTGGGGATTGATGAGCGCGCTCAGGGCAAATATCCCGTCCATCTCTCCGGCGGCCAACAGCAGCGCGTTTCTATTGCGCGCGCGCTGGCGATGGAACCTGACGTTTTACTGTTCGATGAACCCACATCGGCGCTCGATCCTGAACTGGTCGGCGAAGTGTTGCGCATCATGCAACAACTGGCGGAAGAAGGCAAAACGATGGTGGTGGTCACGCATGAAATGGGCTTCGCTCGCCATGTCTCTTCGCACGTTATTTTTCTGCATCAGGGGAAAATTGAAGAAGAGGGTGATCCGGAGCAGGTGTTCGGCAATCCGCAAAGCCCGCGTTTACAGCAATTCCTGAAAGGCTCGCTGAAATAACGCTCAGAGGCGCGCGCGCGCTATATACGCGCAGTGTTTATTGGCATAGTTAGCCTGTTTCCTGAAATGTTCCGCGCAATTACCGATTACGGGGTAACTGGCCGGGCAGTAAAAAAAGGCCTGCTGAACATCCAAAGCTGGAGTCCTCGCGACTTCGCGCATGACCGGCACCGTACCGTGGACGACCGTCCTTACGGCGGCGGACCGGGGATGTTAATGATGGTGCAACCCTTGCGGGACGCCATTCACGCAGCAAAAGCCGCGGCAGGTGAAGGCGCTAAAGTGATTTATCTGTCGCCTCAGGGACGCAAGCTTGATCAAGCGGGCGTTAGCGAGCTGGCCACGAATCAGAAGCTTATTCTGGTGTGTGGTCGCTACGAAGGCGTAGATGAGCGCGTAATTCAGACCGAAATTGACGAAGAATGGTCAATTGGCGATTACGTTCTCAGCGGTGGCGAACTACCGGCAATGACGCTGATTGACTCCGTCGCCCGGTTTATACCGGGGGTTCTGGGGCATGAGGCATCAGCAATCGAAGATTCGTTTGCTGATGGGTTGCTGGATTGTCCGCACTATACGCGCCCTGAAGTGTTAGAGGGGATGGAAGTACCGCCAGTATTGCTGTCGGGAAACCATGCTGAGATACGTCGCTGGCGTTTGAAACAGTCGCTGGGCCGAACCTGGCTTAGAAGACCTGAACTTCTGGAAAACCTGGCTCTGACTGAAGAGCAAGCAAGGTTGCTGGCGGAGTTCAAAACAGAACACGCACAACAGCAGCATAAACATGATGGGATGGCATAGCCGTCATATGGGCTCTCAGAGGAGACGCGCTAATGCGCAGTACGTGTTTATTGGCATAGTTAGCCTGTTTCCTGAAATGTTCCGCGCAATTACCGATTACGGGGTAACTGGCCGGGCAGTAAAAAAAGGCCTGCTGAACATCCAAAGCTGGAGTCCTCGCGACTTCGCGCATGACCGGCACCGTACCGTGGACGACCGTCCTTACGGCGGCGGACCGGGGATGTTAATGATGGTGCAACCCTTGCGGGACGCCATTCACGCAGCAAAAGCCGCGGCAGGTGAAGGCGCTAAAGTGATTTATCTGTCGCCTCAGGGACGCAAGCTTGATCAAGCGGGCGTTAGCGAGCTGGCCACGAATCAGAAGCTTATTCTGGTGTGTGGTCGCTACGAAGGCGTAGATGAGCGCGTAATTCAGACCGAAATTGACGAAGAATGGTCAATTGGCGATTACGTTCTCAGCGGTGGCGAACTACCGGCAATGACGCTGATTGACTCCGTCGCCCGGTTTATACCGGGGGTTCTGGGGCATGAGGCATCAGCAATCGAAGATTCGTTTGCTGATGGGTTGCTGGATTGTCCGCACTATACGCGCCCTGAAGTGTTAGAGGGGATGGAAGTACCGCCAGTATTGCTGTCGGGAAACCATGCTGAGATACGTCGCTGGCGTTTGAAACAGTCGCTGGGCCGAACCTGGCTTAGAAGACCTGAACTTCTGGAAAACCTGGCTCTGACTGAAGAGCAAGCAAGGTTGCTGGCGGAGTTCAAAACAGAACACGCACAACAGCAGCATAAACATGATGGGATGGCATAGCGCATACGCGCGCGATATATATTCGCGCAGAGGCGCGCATAGCGATGAAGTTTGTTGCGCCCGAACAGGCACCGGAACAGGCGGAGGTCATCAAAAATACGCCGTTCTGGCCTGATGTGGACCTGTCGGAATTTCGCAGTGTGATGCGCACTGACGGCACGGTGACGCAGCCGCGTTTAAAGCAGGTCGTGCTGACGGCGATCTCTGAGGTTAACGCTGAGCTGTACGACTTCCGCAACCGTCAGCAGATGCTGGGCTGGCGGACACTTGCTGAGGTTCCCGCAGAAATGCTGGACGGTAAAAGCGAGCGTATCCGGCACTACCACAACGCTGTTTTTTGCTGGGCGCGCGCTGTGCTTAATGAGCGTTATCAGGACTATGACGCCACGGCGTCAGGCGTGAAGCGAGGGGAGGAGCTGGCGGAGGCCAGCGGCGATCTGTGGCGTGATGCCCGCTGGGCCATCAGCCGGGTGCAGGATGTACCGCACTGTACGGTGGAGCTTATCTGAACGGCTAGCGCGTAGCGGCAGTCTCGGATGAATAATCATTTTGGGAAAGGGTTAATGGCCGGGTTGCACGCGCCATATGCATATAGCGCGCATCATGCGGTGAATTTCTGTTCTGAGTATAAACGTGGCTTTGTATTGGGTTTTACACACCGTATGTTCGAAAAGACCGGCGATCGTCAACTTAGCGCGTGGGAGGCTGGAATTCTGACGCGTCGCTATGGTCTGGATAAAGAAATGGTGATGGATTTCTTTAAAGAGAATCATTCCGGGATGGCGGTTCGCTTCTTTATGGCCGGTTATCGACTCGAAGGTTGACGATCGCGCGCAGGAGGAGAGCTCTCTTCTTCTAGAGCATGTCTACGCTTCTCTATTTGCACGGATTCAACAGTTCCCCTCGCTCGGCAAAAGCGTGCCAGCTAAAAAACTGGCTGGCGGAGCGTCATCCGCATGTTGAGATGATCGTCCCTCAGCTGCCGCCGTATCCTGCCGATGCGGCGGAGTTGCTGGAATCTCTCGTGCTTGAGCATGGCGGTGCGCCATTAGGGCTGGTAGGATCGTCGCTGGGTGGTTATTACGCCACCTGGCTGTCGCAATGTTTTATGCTGCCGGCTGTGGTGGTGAATCCCGCCGTGCGGCCCTTTGAATTACTGACCGACTATCTCGGTCAGAACGAGAACCCCTACACCGGGCAGCAATATGTGCTAGAGTCTCGCCATATTTATGATCTTAAAGTCATGCAGATTGACCCGCTGGAAGCGCCGGACCTGATCTGGCTACTGCAACAGACGGGCGATGAAGTGCTGTATTACCGCCAGGCGGTGGCATATTACGCCTCCTGCCGTCAGACAGTGACCGAGGGTGGTAATCACGCATTCACGGGCTTCGAAGATTATTTCAACCAGATTGTCGATTTTCTTGGACTGCACAGTTGCTGACGGCTATGCGCGCGCTCGATGATTGACCCTATTTTTGCGTCCTGTACGCTAATTGCCGTCTTTGTTGTTTTACTGGCCATGGGCGCGCCTATCGGGATCTGCATCGTTATCGCCTCTTTCAGCACCATGATGCTGGTACTGCCTTTCGATATTTCGATGTTCGCCACCGCGCAAAAAATGTTCTCCAGCCTGGACAGTTTTGCCTTGCTGGCCGTGCCGTTCTTCGTTTTGTCCGGGGTGATCATGAATAGCGGGGGAATTGCCGCCCGGCTGGTCAATTTTGCCAAACTGTTTACTGGCAAACTGCCCGGCTCGCTCTCTTATACCAACATCGTCGGCAATATGATGTTCGGTGCAATTTCCGGATCGGCGATTGCCGCCTCAACCTCCATCGGCGGCGTGATGGTGCCGATGAGCGCGCGCGAAGGTTACGATCGCGGCTTTGCGGCCGCGGTGAATATCGCCTCCGCGCCGACGGGAATGTTAATTCCGCCCACCACGGCTTTTATCCTTTACGCGCTGGCAAGCGGGGGAACATCGATTGCCGCTCTGTTCGCCGGCGGTCTGGTCGCGGGAGTGCTGTGGGGCGTTGGCTGTATGCTGGTCACGCTGGTGGTCGCTAAGCGTCGAAATTATCGGGTTTTCTTCACCGTCCAAAAAGGTATGGCGCTAAAAGTTGCCGTTGAGGCCATTCCCAGCCTGCTGCTGATCGTGATTATTGTCGGCGGCATTGTGCAGGGGATTTTCACCGCCATTGAAGCCTCCGCGATTGCCGTGGTGTATACGTTATTGCTGACGATGGTGTTTTACCGCACGCTGAAAATTAAGGATTTGCCTTCGATTTTGCTCCAGACAGTGGTAATGACCGGGGTCATCATGTTCCTGCTGGCAACCTCTTCGGCGATGTCCTTCTCGATGTCGATCACCAATATTCCTGCGGCGCTGAGCGATATGATCCTCGGTATTTCCGCCAATAAACTGGTTATCCTGTTAGTCATTACCGTCTTTTTGTTGATTATCGGCGCATTTATGGATATTGGTCCGGCCATTCTGATTTTTACCCCGATTCTGCTGCCAATCATGGCTAAACTGGGCGTCGATCCGGTGCATTTCGGCATTATCATGATCTATAACCTGGCGATTGGCACCATTACGCCGCCAGTTGGCAGTGGTTTATATGTCGGGGCGAGCGTCGGTAAGGTCAAAGTTGAGGAAGTGATTAAACCGTTGCTGCCTTTTTACGGCGCGATTATCGGCGTTCTGTTATTAATTACCTACATTCCGGAAATCACACTGTTCTTACCCCGTCTACTGGGCATCATGTAA
diff --git a/Examples/2-res-Annotate-prokka/Replicons/GEN2.1219.00001.fna b/Examples/2-res-Annotate-prokka/Replicons/GEN2.1219.00001.fna
deleted file mode 100644
index 8fe856eefd3b0b8ab18cac65ebb213940f127894..0000000000000000000000000000000000000000
--- a/Examples/2-res-Annotate-prokka/Replicons/GEN2.1219.00001.fna
+++ /dev/null
@@ -1,10 +0,0 @@
->GEN2.1219.00001.0001	2308
-ATGTCAGAAAATAAATTACACGTTATCGATTTGCACAAACGCTACGGCGGTCATGAAGTGCTGAAAGGGGTATCGCTGCAGGCCCGCGCCGGAGATGTGATTAGCATTATCGGCTCGTCCGGTTCCGGTAAAAGCACTTTTTTGCGCTGCATTAACTTCCTCGAAAAATCGAGCGAAGGCGCGATTATCGTGAACGGTCAGAACATTAATCTGGTGCGCGACAAAGACGGGCAGCTCAAAGTGGCGGATAAAAATCAGCTACGCTTGTTGCGTACCCGCCTGACGATGGTGTTTCAGCACTTTAACCTCTGGAACCACATGACGGTGCTGGAAAATGTGATGGAAGCGCCGATTCAGGTACTGGGATTAAGCAAGCACGACGCGCGCGAGCGGGCGTTGAAATATCTGGCGAAGGTGGGGATTGATGAGCGCGCTCAGGGCAAATATCCCGTCCATCTCTCCGGCGGCCAACAGCAGCGCGTTTCTATTGCGCGCGCGCTGGCGATGGAACCTGACGTTTTACTGTTCGATGAACCCACATCGGCGCTCGATCCTGAACTGGTCGGCGAAGTGTTGCGCATCATGCAACAACTGGCGGAAGAAGGCAAAACGATGGTGGTGGTCACGCATGAAATGGGCTTCGCCCGCCATGTCTCTTCGCACGTGATTTTTCTGCATCAGGGGAAAATTGAAGAAGAGGGCAATCCGGAGCAGGTGTTCGGCAATCCGCAAAGCCCGCGTTTACAGCAATTCCTGAAAGGCTCGCTGAAATAAACGCTAGAGGACGCGCCTCTCAGAGAGCGCGCTCTCTCAGAGAGGCGCGCGCCTCTTTCGCAGAGACCNNCGCTCATGAGCGATGCCCGCGACTAAATTCTCCCGACGTACCCTCCTGACGGCAGGTTCCGCGCTTGCTGTTCTTCCTTTTCTGCGCGCCTTGCCGGTACAGGCGCGTGAACCTCGCCAGACCGTCGATATTAAGGATTATCCGGCGGATGACGGTATCGCCTCGTTCAAACAGGCCTTCGCCGACGGGCAGACTGTGGTCGTGCCGTCAGGATGGGTGTGTGAAAATATCAATGCGGCGATAACGATTCCGGCGGGAAAAACGCTGCGGATACAGGGCGCGGTGCGTGGGAATGGCCGGGGACGGTTTATTTTGCTGGACGGGTGTCAGGTGGTGGGGGAGCAGGGCGGCAGTCTGCACAATGTGACGCTGGATGTTCGCGGGTCGGACTGTGTGATTAAAGGCGTGACGATGAGCGGCTTTGGCCCCGTCGCGCAAATTTTCATCGGCGGTAAGGAACCGCAGGTGATGCGTAATCTCATTATCGATGACATCACCGTTACCCACGCCAACTACGCCATTCTCCGCCAGGGATTTCATAACCAAATGGACGGCGCGCGGATTACGCATAGTCGCTTTAGCGATTTGCAGGGGGACGCCATTGAGTGGAATGTCGCGATTCATGACCGCGACATCCTGATTTCCGATCATGTCATCGAACGCATTGATTGTACCAATGGCAAAATCAACTGGGGGATCGGCATCGGGCTGGCGGGTAGCGCCTATGACAATAGTTATCCTGAAGACCAGGCAGTAAAAAACTTTGTGGTGGCCAATATTACCGGATCTGATTGCCGACAACTGGTACACGTAGAAAATGGCAAACATTTCGTCATTCGCAATGTCAAAGCCAAAAACATCACGCCCGATTTCAGTAAAAATGCGGGTATTGATAACGCAACGATCGCCATTTATGGCTGTGATAATTTCGTCATTGATAATATTGATATGACGAATAGTGCCGGGATGCTCATCGGCTATGGCGTCGTTAAAGGAAAATACCTGTCAATTCCGCAAAACTTTAAATTAAACGCTATTCGGTTGGATAATCGCCAGGTTGCTTATAAATTACGCGGCATTCAAATTTCCTCCGGTAACGCCCCCTCATTTGTTGCCATCACCAATGTACGGATGACGCGTGCTACGCTGGAACTGCATAATCAACCGCAGCACCTCTTTTTGCGTAATATCAACGTGATGCAAACTTCAGCGATTGGCCCGGCGTTAAAAATGCATTTTGATTTGCGTAAAGATGTCCGTGGTCAATTTATGGCCCGCCAGGACACGCTGCTTTCCCTCGCTAATGTTCATGCCATCAATGAAAACGGGCAGAGTTCCGTGGATATCGACAGGATTAATCACCAAACCGTGAATGTCGAAGCAGTGAATTTTTCGCTGCCGAAGCGGGGAGGGTAACACTCGCGCATAGAGAGCTCTCAGAGGAGCGCGCGCGCTATAGCGCGC
->GEN2.1219.00001.0002	3295
-CGCGATAATATAGCGCGCGCTCATAGCATGAGCGCGCTATTTCTGGCCATCCCGTTAACCATTTTTGTGTTGTTTGTGTTACCGATTTGGCTGTGGCTGCATTACAGCAACCGCGCCGGTCGGGGAGAACTGTCGCAAAGCGAGCAGCAACGCTTACTGCAACTCACAGACGACGCGCAACGTATGCGCGAGCGCATTCAGGCGCTGGAAGATATTCTTGATGCAGAGCATCCGAACTGGAGAGAGCGCTAACGCCATATTATAGCGCGCCTCATAAGAGCGGCCTATAGCGCGCTANNNATGCCGCACTTTATTGCTGAATGTACTGAAAATATTCGCGAGCAGGCTGATTTACCAAGCCTGTTCAGCAAGGTAAACGAGGCGCTGGCCGCCACCGGGATTTTCCCCATCGGCGGTATCCGCAGTCGCGCCCACTGGCTGGATACCTGGCAGATGGCTGACGGTAAGCATGATTACGCGTTTGTGCATATGACGCTGAAAATCGGCGCCGGGCGCAGCCTGGAGAGCCGTCAGGAAGTCGGCGAAATGCTGTTTGGGCTGATTAAAGCCCACTTCGCCGACCTGATGGAGAACCGCTATCTGGCGCTGTCGTTTGAGATTGCCGAGTTACATCCAACGCTCAATTACAAACAAAACAACGTACACGCGTTATTTAAATAGCCAGAGATTCGCGCGTTCAGAGAGGAGCTCTCTCATAGACGCGCGCATATGCGCTCTAGAGAGGCGCGCCTAATGGCGCGCTATGATGAAAGCGCTACTGTGGCTGGTTGGTCTCGCGTTGCTGTTAACAGGCTGCGCGAGCGAAAAAGGAATTATCGATAAAGAGGGATATCAGCTTGATACCCGACATCGGGCGCAGGCGGCCTATCCGCGCATTAAAGTCCTGGTGATTCACTATACGGCGGAAAACTTTGACGTTTCGCTGGCGACGTTAACGGGTCGCAACGTCAGTTCGCATTACCTGATTCCCGCAACCCCGCCATTATATGGCGGTAAACCGCGCATCTGGCAACTGGTGCCGGAACAGGATCAGGCTTGGCATGCGGGCGTCAGTTTCTGGCGAGGCGCCACGCGTCTCAATGATACGTCTATTGGCATTGAGCTGGAAAATCGCGGCTGGCGAATGTCCGGCGGGGTGAAATCTTTCGCGCCGTTTGAATCCGCGCAAATTCAGGCATTGATCCCGTTAGCGAAGGACATTATCGCGCGCTATGACATCAAACCGCAGAATGTGGTGGCCCATGCGGATATCGCGCCGCAGCGTAAAGACGATCCCGGCCCGCGCTTCCCGTGGCGCGAGCTGGCGGCACAGGGGATTGGCGCCTGGCCTGACGCCCAGCGTGTGGCGTTTTATCTGGCTGGACGCGCGCCGTATACGCCAGTCGATACCGCAACGGTGCTTGCGTTACTCTCGCGCTATGGCTATGAAGTCAAAGCCGATATGACGGCGCGCGAGCAACAGCGGGTGATTATGGCGTTCCAGATGCACTTCCGTCCGGCGCAATGGAACGGTATCGCAGATGCCGAAACGCAGGCGATTGCCGAAGCATTACTGGAGAAGTACGGCCAGGATTAACAAAGCGCTCTCAGAGAGAGCGCTCTGCAGATGAGTGAGGCTGAAGCCCGCCCGACTAACTTTATTCGTCAGATTATTGATGAAGATCTGGCGAGTGGTAAACATACCACTGTCCATACCCGTTTTCCGCCGGAGCCGAATGGCTATCTGCACATCGGCCACGCGAAATCTATCTGCCTGAACTTTGGCATCGCGCAAGATTATCAGGGCCAGTGCAACCTGCGTTTCGATGACACCAACCCGGTAAAAGAAGATATCGAGTACGTTGATTCGATCAAAAACGACGTCGAGTGGTTAGGCTTTCACTGGTCTGGCGATATTCGCTACTCCTCCGATTACTTTGACCAACTGCACGCCTATGCGGTCGAGCTCATCAATAAAGGCCTGGCCTACGTTGATGAGCTGACGCCGGAGCAGATCCGCGAATACCGTGGTACGCTGACCGCGCCGGGTAAAAACAGCCCGTTCCGCGATCGCAGCGTGGAAGAAAACCTCGCGCTATTTGAAAAAATGCGTACCGGCGGTTTTGAAGAGGGTAAAGCCTGTCTGCGCGCTAAAATCGACATGGCGTCGCCGTTTATCGTGATGCGCGATCCGGTGCTGTATCGCATTAAATTCGCCGAGCATCATCAGACCGGCACGAAGTGGTGCATCTATCCGATGTACGACTTTACTCACTGCATCAGCGATGCGCTGGAAGGCATTACTCATTCTCTGTGTACGCTGGAGTTCCAGGACAACCGTCGTCTGTACGACTGGGTGCTGGACAACATCACCATTCCGGTTCACCCGCGCCAGTACGAATTCTCGCGCCTGAATCTGGAATACACCGTGATGTCCAAGCGTAAGCTGAACCTGCTGGTGACCGACAAACACGTCGAAGGTTGGGATGATCCGCGTATGCCGACTATTTCCGGTCTGCGCCGTCGCGGCTATACCGCGGCTTCTATTCGTGAGTTCTGCAAACGCATCGGCGTCACCAAGCAGGACAACACTATTGAGATGGCGTCGCTGGAATCCTGCATTCGCGAAGATCTGAACGAAAACGCGCCGCGCGCGATGGCGGTAATCGATCCGGTAAAACTGGTTATCGAAAACTACCCGCAGGGCGAGAGCGAAATGGTTACCATGCCTAACCATCCGAATAAACCGGAGATGGGCAGCCGTGAAGTGCCGTTTAGCGGTGAGATCTGGATCGATCGCGCGGATTTCCGCGAAGAAGCGAACAAACAGTACAAACGTCTGGTGATGGGCAAAGAAGTGCGTCTGCGTAATGCCTACGTCATTAAAGCGGAGCGCGTAGAGAAGGATGCCGAAGGGAATATCACCACCATCTTCTGTACCTATGATGCTGATACGCTGAGTAAAGATCCGGCTGACGGGCGTAAAGTGAAAGGCGTAATCCACTGGGTTAGCGTAGCACATGCGCTGCCGATTGAAATTCGTCTCTACGACCGTCTGTTCAGCGTGCCGAACCCGGGCGCCGCGGAGGACTTCCTGTCTGTTATCAACCCCGAATCATTAGTGATTAAGCAGGGGTATGGCGAGCCGTCGCTGAAAGCGGCGGTAGCAGGGAAAGCTTTCCAGTTTGAACGTGAAGGTTACTTCTGCCTTGACAGCCGCTATGCAACGGCCGATAAGCTGGTCTTTAACCGCACCGTGGGCCTGCGTGATACCTGGGCGAAAGCGGGCGAATAA
->GEN2.1219.00001.0003	2263
-ACGCGCTATAGGGCTCTCAGAGAGTCTCAGTGTTTATTGGCATCGTTAGCCTGTTTCCTGAAATGTTCCGCGCAATTACCGATTACGGGGTAACTGGCCGGGCAGTAAAAAAAGGCCTGCTGAACATCCAAAGCTGGAGTCCTCGCGACTTCGCGCATGACCGGCACCGTACCGTGGACGACCGTCCTTACGGCGGCGGACCGGGGATGTTAATGATGGTGCAACCCTTGCGGGACGCCATTCATGCAGCAAAAGCCGCGGCAGGTGAAGGCGCTAAAGTGATTTATCTGTCGCCTCAGGGACGCAAGCTTGATCAAGCGGGCGTTAGCGAGCTGGCCACGAATCAGAAACTCATTCTGGTGTGTGGTCGCTACGAAGGCGTAGATGAGCGCGTAATTCAGGCCGAAATTGACGAAGAATGGTCAATTGGCGATTACGTTCTCAGCGGTGGCGAACTACCGGCAATGACGCTGATTGACTCCGTCGCCCGGTTTATACCGGGGGTTCTGGGGCATGAGGCATCAGCAATCGAAGATTCGTTTGCTGATGGGTTGCTGGATTGTCCGCACTATACGCGCCCTGAAGTGTTAGAGGGGATGGAAGTACCGCCAGTATTGCTGTCGGGAAACCATGCTGAGATACGTCGCTGGCGTTTGAAACAGTCACTGGGCCGAACCTGGCTTAGAAGACCTGAACTTCTGGAAAACCTGGCTCTGACTGAAGAGCAAGCAAGGTTGCTGGCGGAGTTCAAAACAGAACACGCACAACAGCAGCATAAACATGATGGGATGGCATAGCGAGATCGCGCATAGCGCGCGGCGAGATCCGCGAGACATGAATAATCATTTTGGGAAAGGGTTAATGGCCGGGTTGCACGCGCCATATGCATATAGCGCGCATCATGCGGTGAATTTCTGTTCTGAGTATAAACGTGGCTTTGTATTGGGTTTTACACACCGTATGTTCGAAAAGACCGGCGATCGTCAACTTAGCGCGTGGGAGGCCGGAATTCTGACGCGTCGCTATGGTCTGGATAAAGAAATGGTGATGGATTTCTTTAAAGAGAATCATTCCGGGATGGCGGTTCGCTTCTTTATGGCTGGTTATCGACTCGAAGGTTGAACGCCTCTAGAGCGCTAGAGGCGCGCGCGATATACGCGGCGCGAGACATGTCTACGCTTCTCTATTTGCACGGATTCAACAGTTCCCCTCGCTCGGCAAAAGCGTGCCAGCTAAAAAACTGGCTGGCGGAGCGTCATCCGCATGTTGAGATGATCGTCCCTCAACTGCCGCCGTATCCTGCCGATGCGGCGGAGTTGCTGGAATCTCTCGTACTTGAGCATGGCGGTGCGCCATTAGGGCTGGTAGGATCGTCGCTGGGTGGTTATTACGCCACCTGGCTGTCGCAATGTTTTATGCTGCCGGCTGTGGTGGTGAATCCCGCCGTGCGGCCCTTTGAATTACTGACCGACTATCTCGGTCAGAACGAGAACCCCTACACCGGGCAGCAATATGTGCTAGAGTCTCGCCATATTTATGATCTTAAAGTCATGCAGATTGACCCGCTGGAAGCGCCGGACCTGATCTGGCTACTGCAACAGACGGGCGATGAAGTGCTGGATTACCGCCAGGCGGTGGCATATTACGCCTCCTGCCGTCAGACAGTGACCGAGGGGGGTAATCACGCATTCACGGGCTTCGAAGATTATTTCAACCAGATTGTCGATTTTCTTGGACTGCACAGTTGCTGACCGGATATACGCGCGCGCGCTATATAGCGCGCGCGGCGATATAGCGCATGAAGTTTGTTGCGCCAGAACAGGCACCGGAACAGGCGGAAATCATCAGAAATACGCCGTTCTGGCCTGATGTGGACCTGTCGGAGTTTCGCAGCATGATGCGCACTGATGGCACGGTGACGCAGCCGCGTTTAAAGCAGGTTGCGCTGTCGGCAATTTCGGAGGTCAACGCAGAGCTGTATGAGTTTCGCAGACGCCAGCAGATGCTGGGGTATGCCTCGCTGGCAGAAGTCCCGGCGGAACAACTGGACGGCAAAAGCGAGCGCATTCAGCACTATTTCAACGCGGTTTACTGCTGGGCACGCGCCATGCTCAACGAACGTTACCAGGACTATGACGCCACGGCATCCGGTGTGAAGCGGGGCGAAGAACTGGCAGAAGCCAGCGGTGATTTGTGGCGTGACGCCCGCTGGGCCATCAGCCGGGTGCAGGATGCGCCGCACTGCACAGTGGAGCTTATCTGA
->GEN2.1219.00001.0004	2845
-ATGATTGACCCTATTTTTGCGTCCTGTACGCTAATTGCCGTCTTTGTTGTTTTACTGGCCATGGGCGCGCCTATCGGGATCTGCATCGTTATCGCCTCTTTCAGCACCATGATGCTGGTACTGCCTTTCGATATTTCGATGTTCGCCACCGCGCAAAAAATGTTCTCCAGCCTGGACAGTTTTGCCTTGCTGGCCGTGCCGTTCTTCGTTTTGTCCGGGGTGATCATGAATAGCGGGGGAATTGCCGCCCGACTGGTCAATTTTGCCAAACTGTTTACTGGCAAACTGCCCGGCTCGCTCTCTTACACCAACATCGTCGGCAATATGATGTTCGGTGCAATTTCCGGATCGGCGATTGCCGCCTCAACCTCTATCGGCGGCGTGATGGTGCCGATGAGCGCGCGCGAAGGTTACGATCGCGGTTTTGCGGCCGCGGTGAATATCGCCTCCGCGCCGACGGGAATGTTAATTCCGCCCACCACGGCTTTTATCCTTTATGCGCTGGCAAGCGGGGGAACATCGATTGCCGCTCTGTTCGCCGGCGGTCTGGTCGCGGGAGTGCTGTGGGGCGTTGGCTGTATGCTGGTCACGCTGGTGGTCGCTAAGCGTCGAAATTATCGGGTTTTCTTCACCGTCCAAAAAGGCATGGCGCTAAAAGTTGCCGTTGAGGCCATTCCCAGCCTGTTACTGATCGTGATTATTGTCGGCGGCATTGTGCAGGGGATTTTCACCGCCATTGAAGCCTCCGCGATTGCCGTGGTGTATACGTTATTGCTGACGATAGTGTTTTACCGCACGCTGAAAATTAAGGATTTGCCTTCGATTTTGCTCCAGACAGTGGTAATGACCGGGGTCATCATGTTCCTGCTGGCAACCTCTTCGGCGATGTCCTTCTCGATGTCGATCACCAATATTCCTGCGGCGCTGAGCGATATGATCCTCGGTATTTCCGCCAATAAACTGGTTATCCTGTTAGTCATTACCGTCTTTTTGTTGATTATCGGCGCATTTATGGATATCGGTCCGGCCATTCTGATTTTTACCCCGATTCTGCTGCCGATTATGACTAAACTGGGCGTCGATCCGGTGCATTTCGGCATTATCATGATCTATAACCTGGCGATAGGCACCATTACGCCGCCAGTTGGCAGTGGTTTATATGTCGGGGCGAGCGTCGGTAAGGTCAAAGTTGAGGACGTTATCAAACCGTTGATGCCTTTTTACGGCGCGATTATCGGCGTTCTGTTATTAATTACCTACATTCCGGAAATCACACTGTTTTTACCCCGTCTACTGGGCATCATGTAAACGCTCATAGGCGGCGCGCGCGCTCTCAGGAATGAAGTTTGTTGCGCCAGAACAGGCACCGGAACAGGCGGAGGTCATCAAAAATACGCCGTTCTGGCCTGATGTGAACCTGTCGGAATTTCGCAGTGTGATGCGCACTGACGGCACGGTGACGCAGCCGCGTTTAAAGCAGGTCGTGCTGACGGCGATCTCTGAGGTTAACGCTGAGCTGTACGACTTCCGCAACCGTCAGCAGATGCTGGGCTGGCGGACACTTGCTGAGGTTCCCGCAGAAATGCTGGACGGTAAAAGCGAGCGTATCCGGCACTACCACAACGCTGTTTTTTGCTGGGCGCGCGCTGTGCTTAATGAGCGTTATCAGGACTATGACGCCACGGCGTCAGGCGTGAAGCGAGGGGAGGAGCTGGCGGAGGCCAGCGGCGATCTGTGGCGTGATGCCCGCTGGGCCATCAGCCGGGTGCAGGATGCACCGCACTGTACGGTGGAGCTTATCTGACGCTCATAGGCGCGCGCTCATAGCGCGATGGAAACAAATATTACCTGGCAACAATTGATAGATGAATATTTCTTCGCAAAACCTCTGCGCTCAGCATCTGAATGGAGTTACACCAAAGTCTTCAAATCATTTGTACATTATATGGGGCCGTTAAGCTGCCCTAATGATGTGACATATCACAAAGTGCTTGCCTGGCGCCGTTTTCTTTTAAAAGAGAAAAAGCTGTCCGGACGTACCTGGAATAACAAGGTGGCGCATATGCGGGCCATCTTTAACTACGGAATACAGCGAGGGTTACTGCACTATGACGAAAATCCGTTTAACAATTCGGTAGTTAAACCGGACAAGAAGAGAAAGAAAACGCTCACTCAGGCACAGATTGAGTATGCCTATCAGATCATGGAGCAGTATGAAAATCAGGAGAATACAGGGCTGGGACTGAAATATTCCCGCTGCGCCTTATTTCCTGCATGGTTCTGGCTCACTGTCCTGGATACGCTCTATTACACAGGGATACGTCAGAACCAGTTATTACATATTCGGCTGAATGATGTTGATTTGAGAGAAGGGCAGATTCGGCTGATTACGGAGGGGTGTAAAAATCACAAAGAACACTATGTGCCGGTGATCAGTTTTCTGCGTCCACGGCTGACCTGTTTAATGGAGAAAGCGCAGAGCGAAGGATTGAAAGGTAATGACCGCCTGTTCAATATTGCACTTTTTACCGGCAAAGATCCCGCCATTGGCGATGACATGGATTCTCCTCAGGTAAGAGCATTCTTCCGTCGTCTGTCCAAGGAGTGTCAGTTTGCGATCAGTCCTCATCGTTTCAGACACACGCTGGCCACGGAGATGATGAAAATGCCGGAACAGAATCTGCATATGGCGCAAAGTGTGCTGGGTCATTCAAACATGAAATCCACGCTGGAGTATGTGGAGAATGATATTGCAGTGATGGGGAGGGCTCTGGAAGCGCAGTTTATGCAGATTAAGGCAGCACATGCCCGAAGCATTTACAGTGGGTTGACAAAGAATAGATAA
->GEN2.1219.00001.0005	6
-GATACA
diff --git a/Examples/2-res-Annotate-prokka/Replicons/GEN4.1111.00001.fna b/Examples/2-res-Annotate-prokka/Replicons/GEN4.1111.00001.fna
deleted file mode 100644
index 5bd3953cedaf5748f1d63155735c530cc8487f01..0000000000000000000000000000000000000000
--- a/Examples/2-res-Annotate-prokka/Replicons/GEN4.1111.00001.fna
+++ /dev/null
@@ -1,2 +0,0 @@
->GEN4.1111.00001.0001	7134
-ATGAAAGCGCTACTGTGGCTGGTGGGTCTCGCGTTGCTGTTAACAGGCTGCGCGAGCGAAAAAGGAATTATCGATAAAGAGGGATATCAGCTTGATACCCGACATCGGGCGCAGGCGGCCTATCCGCGCATTAAAGTCCTGGTGATTCACTATACGGCGGAAAACTTTGACGTTTCGCTGGCGACGTTAACGGGCCGCAACGTCAGTTCGCATTACCTGATTCCCGCAACCCCGCCATTATATGGCGGTAAACCGCGCATCTGGCAACTGGTGCCGGAACAGGATCAGGCCTGGCATGCGGGCGTCAGTTTCTGGCGAGGCGCCACGCGTCTCAATGATACGTCTATTGGCATTGAGCTGGAAAATCGCGGCTGGCGAATGTCCGGCGGGGTGAAATCTTTCGCGCCGTTTGAATCCGCGCAAATTCAGGCATTGATTCCGTTAGCGAAGGACATTATCGCGCGCTATGACATCAAACCGCAGAATGTGGTGGCCCATGCGGATATCGCGCCGCAGCGTAAAGACGATCCCGGCCCGCGCTTCCCGTGGCGCGAGCTGGCGGCGCAGGGGATTGGCGCCTGGCCTGACGCCCAGCGTGTGGCGTTTTATCTGGCTGGACGCGCGCCGTATACGCCAGTCGATACCGCAACGGTGCTTGCGTTACTCTCGCGCTATGGCTATGAAGTCAAAGCCGATATGACGGCGCGCGAGCAGCAGCGGGTGATTATGGCGTTCCAGATGCACTTCCGTCCGGCGCAATGGAACGGTATCGCAGATGCCGAAACGCAGGCGATTGCCGAAGCATTACTGGAGAAGTACGGCCAGGATTAACGCGATCGCGCGCATATCGCGCGCGATAGATGCCGCACTTTATTGCTGAATGTACTGAAAATATTCGCGAGCAGGCTGATTTACCCGGCCTGTTCAGCAAGGTAAACGAGGCGCTGGCCGCCAGCGGGATTTTCCCCATCGGCGGTATCCGCAGTCGCGCCCACTGGCTGGATACCTGGCAGATGGCTGACGGTAAGCATGATTATGCGTTTGTGCATATGACGCTGAAAATCGGTACCGGGCGCAGCCTGGAGAGCCGTCAGGAAGTCGGCGAAATGCTGTTTGGGCTGATTAAAGCCCACTTCGCCGACCTGATGGAGAACCGCTATCTGGCGCTGTCGTTTGAGATTGCCGAGCTACATCCGACGCTCAATTACAAACAAAACAACGTACACGCGTTATTTAAATAGCCGCATATGCGGCGCTCAGGAGCGCTAGCATGCTCGATAAACAGACCCATACCCTGATCGCCCAGCGACTTAATCAGGCTGAAAAACAGCGTGAACAAATTCGCGCAGTGTCGCTGGATTATCCCAACATCACTATTGAAGATGCCTATGCCGTACAGCGTGAATGGGTCAATATCAAGATCGCCGAAGGGCGCACGCTCAAAGGCCACAAAATCGGCCTGACCTCAAAAGCGATGCAGGCCAGCTCGCAAATCAGCGAACCGGATTACGGCGCGCTGCTTGACGATATGTTCTTCCATGACGGCGGCGATATCCCCACCGACCGTTTTATCGTCCCGCGTATTGAAGTGGAGCTGGCGTTCGTGCTGGCGAAACCGCTGCGCGGCCCTCACTGCACGCTGTTCGACGTCTACAACGCCACGGATTATGTGATTCCGGCGCTGGAACTGATTGACGCCCGCAGCCACAACATCGACCCGGAAACCCAGCGCCCGCGCAAAGTGTTCGACACCATTTCCGACAACGCCGCCAACGCCGGGGTGATCCTCGGTGGTCGCCCCATCAAACCAGACGAGCTGGATCTGCGCTGGATCTCCGCGCTGCTCTATCGCAACGGCGTGATCGAAGAAACCGGCGTCGCCGCAGGCGTGCTGAATCATCCGGCCAACGGCGTGGCGTGGCTGGCGAACAAGCTTGCCCCCTACGATGTCCAGCTTGAAGCCGGGCAGATCATCCTCGGCGGCTCGTTCACCCGCCCGGTGCCGGCGAGCAAGGGCGACACCTTCCATGTCGATTACGGCAACATGGGCGCGATCAGTTGCCGGTTTGTGTAACCAGATCCGCGCGCGCATATATATCGCGCGCATACGATGCCCGTGAATAAGTTCTCCCGACGTACCCTCCTGACGGCAGGTTCCGCGCTTGCTGTTCTTCCTTTTCTGCGCGCCTTGCCGGTACAGGCGCGTGAACCTCGCGAGACCGTCGATATTAAGGATTATCCGGCGGATGACGGTATCGCCTCGTTCAAACAGGCCTTCGCCGACGGACAGACCGTGGTCTTACCGCCAGGATGGGTGTGTGAAAATATCAATGCGGCGATAACGATTCCGGCGGGAAAAACGCTGCGGGTACAGGGCGCGGTGCGTGGGAATGGCCGGGGACGGTTTATTTTGCAGGACGGGTGTCAGGTGGTGGGGGAGCAGGGCGGCAGTCTGCACAATGTGACGCTGGATGTTCGCGGGTCGGACTGTGTGATTAAAGGCGTGACGATGAGCGGCTTTGGCCCCGTCGCGCAAATTTTCATCGGCGGTAAGGAACCGCAGGTGATGCGTAATCTCATTATCGATGACATCACCGTTACCCACGCCAACTACGCCATTCTCCGCCAGGGATTTCATAACCAAATGGACGGCGCGCGGATTACGCATAGCCGCTTTAGCGATTTGCAGGGGGACGCCATTGAGTGGAATGTCGCGATTCACGACCGCGACATCCTGATTTCCGATCATGTCATCGAACGCATTGATTGTACCAATGGCAAAATCAACTGGGGGATCGGCATCGGGCTGGCGGGTAGCACCTATGACAACAGTTATCCTGAAGATCAGGCAGTAAAAAACTTTGTGGTGGCCAATATTACCGGATCTGATTGCCGACAGCTGGTGCACGTAGAAAATGGCAAACATTTCGTCATTCGCAATGTCAAAGCCAAAAACATCACGCCCGATTTCAGTAAAAATGCGGGTATTGATAACGCAACGATCGCCATTTATGGCTGTGATAATTTCGTCATTGATAATATTGATATGACGAATAGTGCTGGGATGCTCATCGGCTATGGCGTCGTTAAAGGAAAATACCTGTCAATTCCGCAAAACTTTAAATTAAACGCTATTCGGTTGGATAATCGCCAGGTTGCTTATAAATTACGCGGCATTCAAATTTCCTCCGGCAACATCCCCTCTTTTGTCGCCATCACCAATGTACGGATGACGCGTGCTACGCTGGAACTGCATAATCAACCGCAGCACCTCTTTCTGCGTAATATCAACGTGATGCAAACTTCAGCGATTGGCCCGGCGTTAAAAATGCATTTCGATTTGCGTAAAGATGTCCGTGGTCAATTTATGGCCCGCCAGGACACGCTGCTTTCCCTCGCTAATGTTCATGCCATCAATGAAAACGGGCAGAGTTCCGTGGATATCGACAGGATTAATCACCAAACCGTGAATGTCGAAGCAGTGAATTTTTCGCTGCCGAAGCGGGGAGGGTAACAGAGCTCGCGCGATCGCGAATGTCAGAAAATAAATTACACGTTATCGATTTGCACAAACGCTACGGCGGTCATGAAGTGCTGAAAGGGGTATCGTTGCAGGCCCGCGCCGGAGATGTGATTAGCATCATCGGCTCGTCCGGCTCCGGTAAAAGCACTTTTTTGCGCTGTATTAACTTCCTCGAAAAACCGAGCGAAGGCGCGATTATCGTGAACGGTCAGAACATTAATCTGGTGCGCGACAAAGACGGGCAGCTCAAAGTGGCGGATAAAAATCAGCTACGCTTGTTGCGTACCCGCCTGACGATGGTGTTTCAGCACTTTAACCTCTGGAGCCACATGACGGTGCTGGAAAATGTGATGGAAGCGCCGATTCAGGTACTGGGATTAAGCAAGCACGACGCGCGCGAGCGGGCGTTGAAATATCTGGCGAAGGTGGGGATTGATGAGCGCGCTCAGGGCAAATATCCCGTCCATCTCTCCGGCGGCCAACAGCAGCGCGTTTCTATTGCGCGCGCGCTGGCGATGGAACCTGACGTTTTACTGTTCGATGAACCCACATCGGCGCTCGATCCTGAACTGGTCGGCGAAGTGTTGCGCATCATGCAACAACTGGCGGAAGAAGGCAAAACGATGGTGGTGGTCACGCATGAAATGGGCTTCGCCCGCCATGTCTCTTCGCACGTTATTTTTCTGCATCAGGGGAAAATTGAAGAAGAGGGCGATCCGGAGCAGGTGTTCGGCAATCCGCAAAGCCCGCGTTTACAGCAATTCCTGAAAGGCTCGCTGAAATAACAGATACGCGCATGGCGAGTGTTTATTGGCATCGTTAGCCTGTTTCCTGAAATGTTCCGCGCAATTACCGATTACGGGGTAACTGGCCGGGCAGTAAAAAAAGGCCTGCTGAACATCCAAAGCTGGAGTCCTCGCGACTTCGCGCATGACCGGCACCGTACCGTGGACGACCGTCCTTACGGCGGCGGACCGGGGATGTTAATGATGGTGCAACCCTTGCGGGACGCCATTCACGCAGCAAAAGCCGCGGCAGGTGAAGGCGCTAAAGTGATTTATCTGTCGCCTCAGGGACGCAAGCTTGATCAAGCGGGCGTTAGCGAGCTGGCCACGAATCAGAAGCTTATTCTGGTGTGTGGTCGCTACGAAGGCGTAGATGAGCGCGTAATTCAGACCGAAATTGACGAAGAATGGTCAATTGGCGATTACGTTCTCAGCGGTGGCGAACTACCGGCAATGACGCTGATTGACTCCGTCGCCCGGTTTATACCGGGGGTTCTGGGGCATGAGGCATCAGCAATCGAAGATTCGTTTGCTGATGGGTTGCTGGATTGTCCGCACTATACGCGCCCTGAAGTGTTAGAGGGGATGGAAGTACCGCCAGTATTGCTGTCGGGAAACCATGCCGAGATACGTCGCTGGCGCTTGAAACAGTCGCTGGGCCGAACCTGGCTTAGAAGACCTGAACTTCTGGAAAACCTGGCTCTGACTGAAGAGCAAGCAAGGTTGCTGGCGGAGTTCAAAACAGAACACGCACAACAGCAGCATAAACATGATGGGATGGCATAGCGATAGCGCTAGAGCGATGAATAATCATTTTGGGAAAGGGTTAATGGCTGGGTTGCACGCGCCATATGCATATAGCGCGCATCATGCGGTGAATTTCTGTTCTGAGTATAAACGTGGCTTTGTATTGGGTTTTACACACCGTATGTTCGAAAAGACCGGCGATCGTCAACTTAGCGCGTGGGAGGCCGGAATTCTGACGCGTCGCTATGGTCTGGATAAAGAAATGGTGATGGATTTCTTTAAAGAGAATCATTCCGGGATGGCGGTTCGCTTCTTTATGGTCGGTTATCGACTCGAAGGTTGACAGATGCGCGATCGATGTCTACGCTTCTCTATTTGCACGGATTCAACAGTTCCCCTCGCTCGGCAAAAGCGTGCCAGCTAAAAAACTGGCTGGCGGAGCGTCATCCGCATGTCGAGATGATCGTCCCTCAACTACCGCCGTATCCTGCCGATGCGGCGGAGTTGCTGGAATCTCTCGTGCTTGAGCATGGCGGTGCGCCATTAGGGCTGGTAGGATCGTCGCTGGGTGGTTATTACGCCACCTGGCTGTCGCAATGTTTTATGCTGCCGGCTGTGGTGGTGAATCCCGCCGTGCGGCCCTTTGAATTACTGACCGACTATCTCGGTCAGAACGAGAACCCCTACACCGGGCAGCAATATGTGCTAGAGTCTCGCCATATTTATGATCTTAAAGTCATGCAGATTGACCCGCTGGAAGCGCCGGACCTGATCTGGCTACTGCAACAGACGGGCGATGAAGTGCTGGATTACCGCCAGGCGGTGGCATATTACGCCTCCTGCCGTCAGACAGTGACCGAGGGTGGTAATCACGCATTCACGGGCTTCGAAGATTATTTCAACCAGATTGTCGATTTTCTTGGACTGCACAGTTGCTGACACGGATGCGCCATCGGCTTGCTGGCCGTGCCGTTCTTCGTTTTGTCCGGGGTGATCATGAATAGCGGGGGAATTGCCGCCCGGCTGGTCAATTTTGCCAAACTGTTTACTGGCAAACTGCCCGGCTCGCTCTCTTATACCAACATCGTCGGCAATATGATGTTCGGTGCAATTTCCGGATCGGCAATTGCCGCCTCAACCTCCATCGGCGGCGTGATGGTGCCGATGAGCGCGCGCGAAGGTTACGATCGCGGCTTTGCGGCCGCGGTGAATATCGCCTCCGCGCCGACGGGAATGTTAATTCCGCCCACCACGGCTTTTATCCTTTATGCGCTGGCAAGCGGGGGAACATCGATTGCCGCTCTGTTCGCCGGCGGTCTGGTCGCGGGAGTGCTGTGGGGCGTTGGCTGTATGCTGGTCACGCTGGTGGTCGCTAAGCGTCGAAATTATCGGGTTTTCTTCACCGTCCAAAAAGGCATGGCGCTAAAAGTTGCCGTTGAGGCCATTCCCAGCCTGCTGCTGATCGTGATTATCGTCGGCGGCATTGTGCAGGGGATTTTCACCGCCATTGAAGCCTCCGCGATTGCCGTGGTGTATACATTATTGTTGACGATGGTGTTTTACCGCACGCTGAAAATTAAGGATTTGCCTTCGATTTTGCTCCAGACAGTGGTAATGACCGGGGTCATCATGTTCCTGCTGGCAACCTCTTCGGCGATGTCCTTCTCGATGTCGATCACCAATATTCCTGCGGCGCTGAGCGATATGATCCTCGGTATTTCCGCCAATAAACTGGTTATCCTGTTAGTCATTACCGTCTTTTTGTTGATTATCGGCGCATTTATGGATATCGGTCCGGCCATTCTGATTTTTACCCCGATTCTGCTGCCGATCATGGCTAAACTGGGCGTCGATCCGGTGCATTTTGGCATTATCATGATCTATAACCTGGCGATTGGCACCATTACGCCGCCAGTTGGCAGTGGTTTATATGTCGGGGCGAGCGTCGGTAAGGTCAAAGTTGAGGAAGTGATTAAACCGTTGCTGCCTTTTTACGGCGCGATTATCGGCGTTCTGTTATTAATTACCTACATTCCGGAAATCACACTGTTCTTACCCCGTCTACTGGGCATCATGTAA
diff --git a/Examples/2-res-Annotate-prokka/discarded-list_genomes.lst b/Examples/2-res-Annotate-prokka/discarded-list_genomes.lst
deleted file mode 100644
index 16c2d0c0909dd12b783df1afa25997442caf0d99..0000000000000000000000000000000000000000
--- a/Examples/2-res-Annotate-prokka/discarded-list_genomes.lst
+++ /dev/null
@@ -1 +0,0 @@
-orig_name	to_annotate	gsize	nb_conts	L90
diff --git a/Examples/2-res-Annotate-prokka/gff3/EXAM.1216.00002.gff b/Examples/2-res-Annotate-prokka/gff3/EXAM.1216.00002.gff
deleted file mode 100644
index 5081652395712961d0253d562bb6ed1fb853b6bb..0000000000000000000000000000000000000000
--- a/Examples/2-res-Annotate-prokka/gff3/EXAM.1216.00002.gff
+++ /dev/null
@@ -1,16 +0,0 @@
-##gff-version  3
-##sequence-region	EXAM.1216.00002.0001	1	5747
-##sequence-region	EXAM.1216.00002.0002	1	1968
-##sequence-region	EXAM.1216.00002.0003	1	1102
-EXAM.1216.00002.0001	Prodigal:002006	CDS	1	831	.	+	0	ID=EXAM.1216.00002.0001b_00001;eC_number=3.5.1.28;Name=amiD_1;db_xref=COG:COG3023;gene=amiD_1;inference=ab initio prediction:Prodigal:002006,similar to AA sequence:UniProtKB:P75820;locus_tag=EXAM.1216.00002.0001b_00001;product=N-acetylmuramoyl-L-alanine amidase AmiD
-EXAM.1216.00002.0001	Prodigal:002006	CDS	880	1710	.	+	0	ID=EXAM.1216.00002.0001i_00002;eC_number=3.5.1.28;Name=amiD_2;db_xref=COG:COG3023;gene=amiD_2;inference=ab initio prediction:Prodigal:002006,similar to AA sequence:UniProtKB:P75820;locus_tag=EXAM.1216.00002.0001i_00002;product=N-acetylmuramoyl-L-alanine amidase AmiD
-EXAM.1216.00002.0001	Prodigal:002006	CDS	1655	2128	.	+	0	ID=EXAM.1216.00002.0001i_00003;eC_number=5.3.3.10;Name=hpcD;gene=hpcD;inference=ab initio prediction:Prodigal:002006,similar to AA sequence:UniProtKB:Q05354;locus_tag=EXAM.1216.00002.0001i_00003;product=5-carboxymethyl-2-hydroxymuconate Delta-isomerase
-EXAM.1216.00002.0001	Prodigal:002006	CDS	2172	2396	.	+	0	ID=EXAM.1216.00002.0001i_00004;Name=pspB;gene=pspB;inference=ab initio prediction:Prodigal:002006,similar to AA sequence:UniProtKB:P0AFM9;locus_tag=EXAM.1216.00002.0001i_00004;product=Phage shock protein B
-EXAM.1216.00002.0001	Prodigal:002006	CDS	2425	3828	.	+	0	ID=EXAM.1216.00002.0001i_00005;inference=ab initio prediction:Prodigal:002006;locus_tag=EXAM.1216.00002.0001i_00005;product=hypothetical protein
-EXAM.1216.00002.0001	Prodigal:002006	CDS	3863	4636	.	+	0	ID=EXAM.1216.00002.0001i_00006;Name=hisP;db_xref=COG:COG4598;gene=hisP;inference=ab initio prediction:Prodigal:002006,similar to AA sequence:UniProtKB:P02915;locus_tag=EXAM.1216.00002.0001i_00006;product=Histidine transport ATP-binding protein HisP
-EXAM.1216.00002.0001	Prodigal:002006	CDS	4641	5432	.	+	0	ID=EXAM.1216.00002.0001i_00007;eC_number=2.1.1.228;Name=trmD;db_xref=COG:COG0336;gene=trmD;inference=ab initio prediction:Prodigal:002006,similar to AA sequence:UniProtKB:P0A873;locus_tag=EXAM.1216.00002.0001i_00007;product=tRNA (guanine-N(1)-)-methyltransferase
-EXAM.1216.00002.0001	Prodigal:002006	CDS	5460	5747	.	+	0	ID=EXAM.1216.00002.0001b_00008;inference=ab initio prediction:Prodigal:002006;locus_tag=EXAM.1216.00002.0001b_00008;product=hypothetical protein
-EXAM.1216.00002.0002	Prodigal:002006	CDS	1	582	.	+	0	ID=EXAM.1216.00002.0002b_00009;inference=ab initio prediction:Prodigal:002006;locus_tag=EXAM.1216.00002.0002b_00009;product=hypothetical protein
-EXAM.1216.00002.0002	Prodigal:002006	CDS	629	1936	.	+	0	ID=EXAM.1216.00002.0002b_00010;Name=dctM;db_xref=COG:COG1593;gene=dctM;inference=ab initio prediction:Prodigal:002006,similar to AA sequence:UniProtKB:O07838;locus_tag=EXAM.1216.00002.0002b_00010;product=C4-dicarboxylate TRAP transporter large permease protein DctM
-EXAM.1216.00002.0003	Prodigal:002006	CDS	26	280	.	+	0	ID=EXAM.1216.00002.0003b_00011;inference=ab initio prediction:Prodigal:002006;locus_tag=EXAM.1216.00002.0003b_00011;product=hypothetical protein
-EXAM.1216.00002.0003	Prodigal:002006	CDS	323	1102	.	+	0	ID=EXAM.1216.00002.0003b_00012;inference=ab initio prediction:Prodigal:002006,similar to AA sequence:ISfinder:ISSen3;locus_tag=EXAM.1216.00002.0003b_00012;product=IS21 family transposase ISSen3
diff --git a/Examples/2-res-Annotate-prokka/gff3/EXAM.1219.00001.gff b/Examples/2-res-Annotate-prokka/gff3/EXAM.1219.00001.gff
deleted file mode 100644
index 732fff49bb2023f6a7ae292be4c6e1af27eb3cd5..0000000000000000000000000000000000000000
--- a/Examples/2-res-Annotate-prokka/gff3/EXAM.1219.00001.gff
+++ /dev/null
@@ -1,14 +0,0 @@
-##gff-version  3
-##sequence-region	EXAM.1219.00001.0001	1	2784
-##sequence-region	EXAM.1219.00001.0002	1	7024
-EXAM.1219.00001.0001	Prodigal:002006	CDS	213	1880	.	+	0	ID=EXAM.1219.00001.0001b_00001;eC_number=6.1.1.18;Name=glnS;db_xref=COG:COG0008;gene=glnS;inference=ab initio prediction:Prodigal:002006,similar to AA sequence:UniProtKB:P00962;locus_tag=EXAM.1219.00001.0001b_00001;product=Glutamine--tRNA ligase
-EXAM.1219.00001.0001	Prodigal:002006	CDS	1916	2746	.	+	0	ID=EXAM.1219.00001.0001b_00002;eC_number=3.5.1.28;Name=amiD;db_xref=COG:COG3023;gene=amiD;inference=ab initio prediction:Prodigal:002006,similar to AA sequence:UniProtKB:P75820;locus_tag=EXAM.1219.00001.0001b_00002;product=N-acetylmuramoyl-L-alanine amidase AmiD
-EXAM.1219.00001.0002	Prodigal:002006	CDS	16	396	.	+	0	ID=EXAM.1219.00001.0002b_00003;eC_number=5.3.3.10;Name=hpcD;gene=hpcD;inference=ab initio prediction:Prodigal:002006,similar to AA sequence:UniProtKB:Q05354;locus_tag=EXAM.1219.00001.0002b_00003;product=5-carboxymethyl-2-hydroxymuconate Delta-isomerase
-EXAM.1219.00001.0002	Prodigal:002006	CDS	428	1837	.	+	0	ID=EXAM.1219.00001.0002i_00004;inference=ab initio prediction:Prodigal:002006;locus_tag=EXAM.1219.00001.0002i_00004;product=hypothetical protein
-EXAM.1219.00001.0002	Prodigal:002006	CDS	1869	2642	.	+	0	ID=EXAM.1219.00001.0002i_00005;Name=hisP;db_xref=COG:COG4598;gene=hisP;inference=ab initio prediction:Prodigal:002006,similar to AA sequence:UniProtKB:P02915;locus_tag=EXAM.1219.00001.0002i_00005;product=Histidine transport ATP-binding protein HisP
-EXAM.1219.00001.0002	Prodigal:002006	CDS	2709	3443	.	+	0	ID=EXAM.1219.00001.0002i_00006;eC_number=2.1.1.228;Name=trmD_1;db_xref=COG:COG0336;gene=trmD_1;inference=ab initio prediction:Prodigal:002006,similar to AA sequence:UniProtKB:P0A873;locus_tag=EXAM.1219.00001.0002i_00006;product=tRNA (guanine-N(1)-)-methyltransferase
-EXAM.1219.00001.0002	Prodigal:002006	CDS	3427	4254	.	+	0	ID=EXAM.1219.00001.0002i_00007;eC_number=2.1.1.228;Name=trmD_2;db_xref=COG:COG0336;gene=trmD_2;inference=ab initio prediction:Prodigal:002006,similar to AA sequence:UniProtKB:P0A873;locus_tag=EXAM.1219.00001.0002i_00007;product=tRNA (guanine-N(1)-)-methyltransferase
-EXAM.1219.00001.0002	Prodigal:002006	CDS	4299	4763	.	+	0	ID=EXAM.1219.00001.0002i_00008;inference=ab initio prediction:Prodigal:002006;locus_tag=EXAM.1219.00001.0002i_00008;product=hypothetical protein
-EXAM.1219.00001.0002	Prodigal:002006	CDS	4818	5078	.	+	0	ID=EXAM.1219.00001.0002i_00009;inference=ab initio prediction:Prodigal:002006;locus_tag=EXAM.1219.00001.0002i_00009;product=hypothetical protein
-EXAM.1219.00001.0002	Prodigal:002006	CDS	5117	5698	.	+	0	ID=EXAM.1219.00001.0002i_00010;inference=ab initio prediction:Prodigal:002006;locus_tag=EXAM.1219.00001.0002i_00010;product=hypothetical protein
-EXAM.1219.00001.0002	Prodigal:002006	CDS	5717	7024	.	+	0	ID=EXAM.1219.00001.0002b_00011;Name=dctM;db_xref=COG:COG1593;gene=dctM;inference=ab initio prediction:Prodigal:002006,similar to AA sequence:UniProtKB:O07838;locus_tag=EXAM.1219.00001.0002b_00011;product=C4-dicarboxylate TRAP transporter large permease protein DctM
diff --git a/Examples/2-res-Annotate-prokka/gff3/GEN2.1219.00001.gff b/Examples/2-res-Annotate-prokka/gff3/GEN2.1219.00001.gff
deleted file mode 100644
index 5cfdc86106848a76edbcf6f182c2c6fd2e50cd37..0000000000000000000000000000000000000000
--- a/Examples/2-res-Annotate-prokka/gff3/GEN2.1219.00001.gff
+++ /dev/null
@@ -1,19 +0,0 @@
-##gff-version  3
-##sequence-region	GEN2.1219.00001.0001	1	2308
-##sequence-region	GEN2.1219.00001.0002	1	3295
-##sequence-region	GEN2.1219.00001.0003	1	2263
-##sequence-region	GEN2.1219.00001.0004	1	2845
-##sequence-region	GEN2.1219.00001.0005	1	6
-GEN2.1219.00001.0001	Prodigal:002006	CDS	1	774	.	+	0	ID=GEN2.1219.00001.0001b_00001;Name=hisP;db_xref=COG:COG4598;gene=hisP;inference=ab initio prediction:Prodigal:002006,similar to AA sequence:UniProtKB:P02915;locus_tag=GEN2.1219.00001.0001b_00001;product=Histidine transport ATP-binding protein HisP
-GEN2.1219.00001.0001	Prodigal:002006	CDS	857	2260	.	+	0	ID=GEN2.1219.00001.0001b_00002;inference=ab initio prediction:Prodigal:002006;locus_tag=GEN2.1219.00001.0001b_00002;product=hypothetical protein
-GEN2.1219.00001.0002	Prodigal:002006	CDS	28	252	.	+	0	ID=GEN2.1219.00001.0002b_00003;Name=pspB;gene=pspB;inference=ab initio prediction:Prodigal:002006,similar to AA sequence:UniProtKB:P0AFM9;locus_tag=GEN2.1219.00001.0002b_00003;product=Phage shock protein B
-GEN2.1219.00001.0002	Prodigal:002006	CDS	301	681	.	+	0	ID=GEN2.1219.00001.0002i_00004;eC_number=5.3.3.10;Name=hpcD;gene=hpcD;inference=ab initio prediction:Prodigal:002006,similar to AA sequence:UniProtKB:Q05354;locus_tag=GEN2.1219.00001.0002i_00004;product=5-carboxymethyl-2-hydroxymuconate Delta-isomerase
-GEN2.1219.00001.0002	Prodigal:002006	CDS	764	1597	.	+	0	ID=GEN2.1219.00001.0002i_00005;eC_number=3.5.1.28;Name=amiD;db_xref=COG:COG3023;gene=amiD;inference=ab initio prediction:Prodigal:002006,similar to AA sequence:UniProtKB:P75820;locus_tag=GEN2.1219.00001.0002i_00005;product=N-acetylmuramoyl-L-alanine amidase AmiD
-GEN2.1219.00001.0002	Prodigal:002006	CDS	1628	3295	.	+	0	ID=GEN2.1219.00001.0002b_00006;eC_number=6.1.1.18;Name=glnS;db_xref=COG:COG0008;gene=glnS;inference=ab initio prediction:Prodigal:002006,similar to AA sequence:UniProtKB:P00962;locus_tag=GEN2.1219.00001.0002b_00006;product=Glutamine--tRNA ligase
-GEN2.1219.00001.0003	Prodigal:002006	CDS	30	797	.	+	0	ID=GEN2.1219.00001.0003b_00007;eC_number=2.1.1.228;Name=trmD;db_xref=COG:COG0336;gene=trmD;inference=ab initio prediction:Prodigal:002006,similar to AA sequence:UniProtKB:P0A873;locus_tag=GEN2.1219.00001.0003b_00007;product=tRNA (guanine-N(1)-)-methyltransferase
-GEN2.1219.00001.0003	Prodigal:002006	CDS	862	1122	.	+	0	ID=GEN2.1219.00001.0003i_00008;inference=ab initio prediction:Prodigal:002006;locus_tag=GEN2.1219.00001.0003i_00008;product=hypothetical protein
-GEN2.1219.00001.0003	Prodigal:002006	CDS	1170	1751	.	+	0	ID=GEN2.1219.00001.0003i_00009;inference=ab initio prediction:Prodigal:002006;locus_tag=GEN2.1219.00001.0003i_00009;product=hypothetical protein
-GEN2.1219.00001.0003	Prodigal:002006	CDS	1895	2263	.	+	0	ID=GEN2.1219.00001.0003b_00010;inference=ab initio prediction:Prodigal:002006;locus_tag=GEN2.1219.00001.0003b_00010;product=hypothetical protein
-GEN2.1219.00001.0004	Prodigal:002006	CDS	1	1308	.	+	0	ID=GEN2.1219.00001.0004b_00011;Name=dctM;db_xref=COG:COG1593;gene=dctM;inference=ab initio prediction:Prodigal:002006,similar to AA sequence:UniProtKB:O07838;locus_tag=GEN2.1219.00001.0004b_00011;product=C4-dicarboxylate TRAP transporter large permease protein DctM
-GEN2.1219.00001.0004	Prodigal:002006	CDS	1340	1804	.	+	0	ID=GEN2.1219.00001.0004i_00012;inference=ab initio prediction:Prodigal:002006;locus_tag=GEN2.1219.00001.0004i_00012;product=hypothetical protein
-GEN2.1219.00001.0004	Prodigal:002006	CDS	1832	2845	.	+	0	ID=GEN2.1219.00001.0004b_00013;Name=xerC;gene=xerC;inference=ab initio prediction:Prodigal:002006,protein motif:HAMAP:MF_01808;locus_tag=GEN2.1219.00001.0004b_00013;product=Tyrosine recombinase XerC
diff --git a/Examples/2-res-Annotate-prokka/gff3/GEN4.1111.00001.gff b/Examples/2-res-Annotate-prokka/gff3/GEN4.1111.00001.gff
deleted file mode 100644
index dfc7d8ed03fbe31ca11b4106e1e5b80de23f3dbd..0000000000000000000000000000000000000000
--- a/Examples/2-res-Annotate-prokka/gff3/GEN4.1111.00001.gff
+++ /dev/null
@@ -1,11 +0,0 @@
-##gff-version  3
-##sequence-region	GEN4.1111.00001.0001	1	7134
-GEN4.1111.00001.0001	Prodigal:002006	CDS	1	831	.	+	0	ID=GEN4.1111.00001.0001b_00001;eC_number=3.5.1.28;Name=amiD;db_xref=COG:COG3023;gene=amiD;inference=ab initio prediction:Prodigal:002006,similar to AA sequence:UniProtKB:P75820;locus_tag=GEN4.1111.00001.0001b_00001;product=N-acetylmuramoyl-L-alanine amidase AmiD
-GEN4.1111.00001.0001	Prodigal:002006	CDS	861	1241	.	+	0	ID=GEN4.1111.00001.0001i_00002;eC_number=5.3.3.10;Name=hpcD;gene=hpcD;inference=ab initio prediction:Prodigal:002006,similar to AA sequence:UniProtKB:Q05354;locus_tag=GEN4.1111.00001.0001i_00002;product=5-carboxymethyl-2-hydroxymuconate Delta-isomerase
-GEN4.1111.00001.0001	Prodigal:002006	CDS	1271	2074	.	+	0	ID=GEN4.1111.00001.0001i_00003;eC_number=4.2.1.163;Name=hpcG;gene=hpcG;inference=ab initio prediction:Prodigal:002006,similar to AA sequence:UniProtKB:P42270;locus_tag=GEN4.1111.00001.0001i_00003;product=2-oxo-hept-4-ene-1%2C7-dioate hydratase
-GEN4.1111.00001.0001	Prodigal:002006	CDS	2111	3514	.	+	0	ID=GEN4.1111.00001.0001i_00004;inference=ab initio prediction:Prodigal:002006;locus_tag=GEN4.1111.00001.0001i_00004;product=hypothetical protein
-GEN4.1111.00001.0001	Prodigal:002006	CDS	3535	4308	.	+	0	ID=GEN4.1111.00001.0001i_00005;Name=hisP;db_xref=COG:COG4598;gene=hisP;inference=ab initio prediction:Prodigal:002006,similar to AA sequence:UniProtKB:P02915;locus_tag=GEN4.1111.00001.0001i_00005;product=Histidine transport ATP-binding protein HisP
-GEN4.1111.00001.0001	Prodigal:002006	CDS	4327	5094	.	+	0	ID=GEN4.1111.00001.0001i_00006;eC_number=2.1.1.228;Name=trmD;db_xref=COG:COG0336;gene=trmD;inference=ab initio prediction:Prodigal:002006,similar to AA sequence:UniProtKB:P0A873;locus_tag=GEN4.1111.00001.0001i_00006;product=tRNA (guanine-N(1)-)-methyltransferase
-GEN4.1111.00001.0001	Prodigal:002006	CDS	5138	5398	.	+	0	ID=GEN4.1111.00001.0001i_00007;inference=ab initio prediction:Prodigal:002006;locus_tag=GEN4.1111.00001.0001i_00007;product=hypothetical protein
-GEN4.1111.00001.0001	Prodigal:002006	CDS	5413	5994	.	+	0	ID=GEN4.1111.00001.0001i_00008;inference=ab initio prediction:Prodigal:002006;locus_tag=GEN4.1111.00001.0001i_00008;product=hypothetical protein
-GEN4.1111.00001.0001	Prodigal:002006	CDS	6052	7134	.	+	0	ID=GEN4.1111.00001.0001b_00009;Name=dctM;db_xref=COG:COG1593;gene=dctM;inference=ab initio prediction:Prodigal:002006,similar to AA sequence:UniProtKB:O07838;locus_tag=GEN4.1111.00001.0001b_00009;product=C4-dicarboxylate TRAP transporter large permease protein DctM
diff --git a/Examples/2-res-Annotate-prokka/tmp_files/genome1.fst_prokka-split5N.fna b/Examples/2-res-Annotate-prokka/tmp_files/genome1.fst_prokka-split5N.fna
deleted file mode 100644
index 11feaae3628ca13667c0d695bbcacd5a2139310d..0000000000000000000000000000000000000000
--- a/Examples/2-res-Annotate-prokka/tmp_files/genome1.fst_prokka-split5N.fna
+++ /dev/null
@@ -1,4 +0,0 @@
->genome1_1
-ATGTGTAAAAGCCGGAGGGGTTATCTTTTCCCGGCTTTTTATTATCAATTACTCATTAACTCCTGTTCCGTTCTTTTGCGTTTAATCACCGGAATATCTCCGGTATTGTTCAGCGCCCCGGAAATGTTTTTAACCACTGTTCTGCACTCCGTTTATTAAACGCGCTCAGCGCGCGCTCATATATCGCGCGCGCGCGCGCGCATATATATATAATGAGTGAGGCTGAAGCCCGCCCGACTAACTTTATTCGTCAGATTATTGATGAAGATCTGGCGAGTGGTAAACATACCACTGTCCATACCCGTTTTCCGCCGGAGCCGAATGGCTATCTGCATATCGGCCACGCGAAATCTATCTGCCTGAACTTTGGCATCGCGCAAGATTATCAGGGCCAGTGCAACCTGCGTTTCGATGACACCAACCCGGTAAAAGAAGATATCGAGTACGTTGATTCGATCAAAAACGACGTCGAGTGGTTAGGCTTTCACTGGTCTGGCGATATTCGCTACTCCTCCGATTACTTTGACCAACTGCACGCCTATGCGGTCGAGCTAATCAATAAAGGCCTGGCCTATGTTGATGAGCTGACGCCGGAGCAGATCCGTGAATACCGCGGTACGCTGACCGCGCCGGGTAAAAACAGCCCGTTCCGCGATCGCAGCGTCGAAGAGAACCTCGCGCTATTTGAAAAAATGCGTACCGGCGGTTTTGAAGAGGGTAAAGCCTGTCTGCGCGCTAAAATCGACATGGCGTCGCCGTTTATCGTGATGCGCGATCCGGTGCTGTATCGCATTAAATTCGCCGAGCATCATCAGACTGGCAACAAGTGGTGCATCTATCCGATGTACGACTTTACTCACTGCATCAGCGATGCGCTGGAAGGCATTACTCATTCTCTGTGTACGCTGGAGTTCCAGGATAACCGTCGTCTGTACGACTGGGTGCTGGACAACATCACCATTCCGGTTCACCCGCGCCAGTACGAATTCTCGCGCCTGAATCTGGAATACACCGTGATGTCCAAGCGTAAGCTGAACCTGCTGGTGACCGACAAACACGTCGAAGGTTGGGACGATCCGCGTATGCCGACTATTTCCGGTCTGCGCCGTCGCGGCTATACCGCGGCTTCTATTCGTGAGTTCTGCAAACGCATCGGCGTCACCAAGCAGGACAACACTATTGAGATGGCGTCGCTGGAATCCTGCATTCGCGAAGATCTGAACGAAAACGCGCCGCGCGCGATGGCGGTAATCGATCCGGTAAAACTGGTTATCGAAAATTACCCGCAGGGTGAGAGCGAAATGGTTACCATGCCTAACCATCCGAATAAACCGGAGATGGGCAGCCGTGAAGTGCCGTTTAGCGGTGAGATCTGGATCGATCGCGCAGATTTCCGCGAAGAAGCGAACAAACAGTACAAACGTCTGGTGATGGGCAAAGAAGTGCGTCTGCGTAATGCCTACGTCATTAAAGCGGAGCGCGTAGAGAAGGATGCCGAAGGGAATATCACCACCATCTTCTGTACCTATGATGCTGATACGCTGAGTAAAGATCCGGCTGACGGGCGTAAAGTGAAAGGCGTAATCCACTGGGTTAGCGCAGCACATGCGCTGCCGATTGAAATTCGTCTCTACGACCGTCTGTTCAGCGTGCCGAATCCGGGCGCCGCGGAGGACTTCCTGTCTGTTATCAACCCCGAATCATTAGTGATTAAGCAGGGGTATGGCGAGCCGTCGCTGAAAGCGGCGGTAGCAGGAAAAGCTTTCCAGTTTGAACGTGAAGGCTACTTCTGCCTCGACAGCCGCTATGCAACGGCCGATAAGCTGGTCTTTAACCGCACCGTGGGCCTGCGTGATACCTGGGCGAAAGCGGGCGAGTAACGCGCATAGGCGGCCTTCAAGGAGGCGCTAGGCGAATGAAAGCGCTACTGTGGCTGGTGGGTCTCGCGTTGCTGTTAACAGGCTGCGCGAGCGAAAAAGGAATTATCGATAAAGAGGGATATCAGCTTGATACCCGACATCGGGCGCAGGCGGCCTATCCGCGCATTAAAGTCCTGGTGATTCACTATACGGCGGAAAACTTTGACGTTTCGCTGGCGACGTTAACGGGTCGCAACGTCAGTTCGCATTACCTGATTCCCGCAACCCCGCCATTATATGGCGGTAAACCGCGCATCTGGCAACTGGTGCCGGAACAGGATCAGGCCTGGCATGCGGGCGTCAGTTTCTGGCGAGGCGCCACGCGTCTCAATGATACGTCTATTGGCATTGAGCTGGAAAATCGTGGTTGGCGAATGTCCGGCGGGGTGAAATCTTTCGCGCCGTTTGAATCCGCGCAAATTCAGGCATTGATTCCGTTAGCGAAGGATATTATCGCGCGCTATAACATCAAACCGCAGAATGTGGTGGCCCATGCGGATATCGCGCCGCAGCGTAAAGACGATCCCGGCCCGCGCTTCCCGTGGCGCGAGCTGGCGGCGCAGGGGATTAGCGCCTGGCCTGACGCCCAGCGTGTGGCGTTTTATCTGGCTGGACGCGCGCCGTATACGCCAGTCGATACCGCAACGGTGCTTGCGTTACTCTCGCGCTATGGCTATGAAGTCAAAGCCGATATGACGGCACGCGAGCAGCAGCGGGTGATTATGGCGTTCCAGATGCACTTCCGTCCGGCGCAATGGAACGGTATCGCAGATGCCGAAACGCAGGCGATTGCCGAAGCATTACTGGAGAAGTACGGCCAGGATTAACGCGATAGGCGCGCGAGATTACGCGCGCAGTATCGCGC
->genome1_2
-CGCGCATAGCGCGCAATGCCGCACTTTATTGCTGAATGTACTGAAAATATTCGCGAGCAGGCTGATTTACCCGGCCTGTTCAGCAAGGTAAACGAGGCGCTGGCCGCCAGCGGGATTTTCCCCATCGGCGGTATCCGCAGTCGCGCCCACTGGCTGGATACCTGGCAGATGGCTGACGGTAAGCATGATTACGCGTTTGTGCATATGACGCTGAAAATCGGCGCCGGGCGCAGCCTGGAGAGCCGTCAGGAAGTTGGCGAAATGCTGTTTGGGCTGATTAAAGCCCACTTCGCCGACCTGATGGAGAACCGCTATCTGGCGCTGTCGTTTGAGATTGCCGAGCTACATCCGACGCTCAATTACAAACAAAACAACGTACACGCGTTATTTAAATAGCCGATATGAGGCGCGGCGCTATAAGGCGCTCATGAGCATGCCCGCGACTAAATTCTCCCGACGTACCCTCCTGACGGCAGGTTCTGCGCTTGCTGTTCTTCCTTTTCTGCGCGCCTTGCCGGTACAGGCGCGTGAACCTCGCGAGACCGTCGATATTAAGGATTATCCGGCGGATGACGGTATCGCCTCGTTCAAACAGGCCTTCGCCGACGGACAGACCGTGGTCGTACCGCCAGGATGGGTGTGTGAAAATATCAATGCGGCGATAACGATTCCGGCGGGAAAAACGCTGCGGGTACAGGGCGCGGTGCGTGGGAATGGCCGGGGACGGTTTATTTTGCAGGACGGGTGTCAGGTGGTGGGGGAGCAGGGCGGCAGTCTGCACAATGTGACGCTGGATGTTCGCGGGTCGGACTGTGTGATTAAAGGCGTGGCGATGAGCGGCTTTGGCCCCGTCGCGCAAATTTTCATCGGTGGTAAGGAACCGCAGGTGATGCGTAATCTCATTATCGATGACATCACCGTTACCCACGCCAACTACGCCATTCTCCGCCAGGGATTTCATAACCAAATGGATGGCGCGCGGATTACGCATAGCCGCTTTAGCGATTTACAGGGGGACGCCATTGAGTGGAATGTCGCGATTCACGACCGCGACATCCTGATTTCCGATCATGTCATCGAACGCATTAATTGTACCAATGGCAAAATCAACTGGGGGATCGGCATCGGGCTGGCGGGTAGCACCTATGACAACAGTTATCCTGAAGACCAGGCAGTAAAAAACTTTGTGGTGGCCAATATTACCGGATCTGATTGCCGACAGCTTGTGCACGTAGAAAATGGCAAACATTTCGTCATTCGCAATGTCAAAGCCAAAAACATCACGCCCGGTTTCAGTAAAAATGCGGGTATTGATAACGCAACGATCGCAATTTATGGCTGTGATAATTTCGTCATTGATAATATTGATATGACGAATAGTGCCGGGATGCTCATCGGCTATGGCGTCGTTAAAGGAAAATACCTGTCAATTCCGCAAAACTTTAAATTAAACGCTATTCGGTTGGATAATCGCCAGGTTGCTTATAAATTACGCGGCATTCAAATTTCCTCCGGCAACACCCCCTCTTTTGTCGCCATCACCAATGTACGGATGACGCGTGCTACGCTGGAACTGCATAATCAACCGCAGCACCTCTTTCTGCGCAATATCAACGTGATGCAAACTTCAGCGATTGGCCCGGCGTTAAAAATGCATTTCGATTTGCGTAAAGATGTACGTGGTCAATTTATGGCCCGCCAGGACACGCTGCTTTCCCTCGCTAATGTTCATGCCATCAATGAAAACGGGCAGAGTTCCGTGGATATCGACAGGATTAATCACCAAACCGTGAATGTCGAAGCAGTGAATTTTTCGCTGCCGAAGCGGGGAGGGTAACGAATTCCGCGGCATATAGCGGCGCGATAGCATGTCAGAAAATAAATTACACGTTATCGATTTGCACAAACGCTACGGCGGTCATGAAGTGCTGAAAGGGGTATCGCTGCAGGCCCGCGCCGGAGATGTGATTAGCATCATCGGCTCGTCCGGCTCCGGTAAAAGCACTTTTTTGCGCTGTATTAACTTCCTCGAAAAACCGAGCGAAGGCGCGATTATCGTGAACGGTCAGAACATTAATCTGGTGCGCGACAAAGATGGGCAGCTCAAAGTGGCGGATAAAAATCAGCTACGCTTGTTGCGTACCCGCCTGACGATGGTGTTTCAGCACTTCAACCTCTGGAGCCACATGACGGTGCTGGAAAATGTGATGGAAGCGCCGATTCAGGTACTGGGATTAAGCAAGCACGACGCGCGCGAGCGGGCGTTGAAATATCTGGCGAAGGTGGGGATTGATGAGCGCGCTCAGGGCAAATATCCCGTCCATCTCTCCGGCGGCCAACAGCAGCGCGTTTCTATTGCGCGCGCGCTGGCGATGGAACCTGACGTTTTACTGTTCGATGAACCCACATCGGCGCTCGATCCTGAACTGGTCGGCGAAGTGTTGCGCATCATGCAACAACTGGCGGAAGAAGGCAAAACGATGGTGGTGGTCACGCATGAAATGGGCTTCGCTCGCCATGTCTCTTCGCACGTTATTTTTCTGCATCAGGGGAAAATTGAAGAAGAGGGTGATCCGGAGCAGGTGTTCGGCAATCCGCAAAGCCCGCGTTTACAGCAATTCCTGAAAGGCTCGCTGAAATAACGCTCAGAGGCGCGCGCGCGCTATATACGCGCAGTGTTTATTGGCATAGTTAGCCTGTTTCCTGAAATGTTCCGCGCAATTACCGATTACGGGGTAACTGGCCGGGCAGTAAAAAAAGGCCTGCTGAACATCCAAAGCTGGAGTCCTCGCGACTTCGCGCATGACCGGCACCGTACCGTGGACGACCGTCCTTACGGCGGCGGACCGGGGATGTTAATGATGGTGCAACCCTTGCGGGACGCCATTCACGCAGCAAAAGCCGCGGCAGGTGAAGGCGCTAAAGTGATTTATCTGTCGCCTCAGGGACGCAAGCTTGATCAAGCGGGCGTTAGCGAGCTGGCCACGAATCAGAAGCTTATTCTGGTGTGTGGTCGCTACGAAGGCGTAGATGAGCGCGTAATTCAGACCGAAATTGACGAAGAATGGTCAATTGGCGATTACGTTCTCAGCGGTGGCGAACTACCGGCAATGACGCTGATTGACTCCGTCGCCCGGTTTATACCGGGGGTTCTGGGGCATGAGGCATCAGCAATCGAAGATTCGTTTGCTGATGGGTTGCTGGATTGTCCGCACTATACGCGCCCTGAAGTGTTAGAGGGGATGGAAGTACCGCCAGTATTGCTGTCGGGAAACCATGCTGAGATACGTCGCTGGCGTTTGAAACAGTCGCTGGGCCGAACCTGGCTTAGAAGACCTGAACTTCTGGAAAACCTGGCTCTGACTGAAGAGCAAGCAAGGTTGCTGGCGGAGTTCAAAACAGAACACGCACAACAGCAGCATAAACATGATGGGATGGCATAGCCGTCATATGGGCTCTCAGAGGAGACGCGCTAATGCGCAGTACGTGTTTATTGGCATAGTTAGCCTGTTTCCTGAAATGTTCCGCGCAATTACCGATTACGGGGTAACTGGCCGGGCAGTAAAAAAAGGCCTGCTGAACATCCAAAGCTGGAGTCCTCGCGACTTCGCGCATGACCGGCACCGTACCGTGGACGACCGTCCTTACGGCGGCGGACCGGGGATGTTAATGATGGTGCAACCCTTGCGGGACGCCATTCACGCAGCAAAAGCCGCGGCAGGTGAAGGCGCTAAAGTGATTTATCTGTCGCCTCAGGGACGCAAGCTTGATCAAGCGGGCGTTAGCGAGCTGGCCACGAATCAGAAGCTTATTCTGGTGTGTGGTCGCTACGAAGGCGTAGATGAGCGCGTAATTCAGACCGAAATTGACGAAGAATGGTCAATTGGCGATTACGTTCTCAGCGGTGGCGAACTACCGGCAATGACGCTGATTGACTCCGTCGCCCGGTTTATACCGGGGGTTCTGGGGCATGAGGCATCAGCAATCGAAGATTCGTTTGCTGATGGGTTGCTGGATTGTCCGCACTATACGCGCCCTGAAGTGTTAGAGGGGATGGAAGTACCGCCAGTATTGCTGTCGGGAAACCATGCTGAGATACGTCGCTGGCGTTTGAAACAGTCGCTGGGCCGAACCTGGCTTAGAAGACCTGAACTTCTGGAAAACCTGGCTCTGACTGAAGAGCAAGCAAGGTTGCTGGCGGAGTTCAAAACAGAACACGCACAACAGCAGCATAAACATGATGGGATGGCATAGCGCATACGCGCGCGATATATATTCGCGCAGAGGCGCGCATAGCGATGAAGTTTGTTGCGCCCGAACAGGCACCGGAACAGGCGGAGGTCATCAAAAATACGCCGTTCTGGCCTGATGTGGACCTGTCGGAATTTCGCAGTGTGATGCGCACTGACGGCACGGTGACGCAGCCGCGTTTAAAGCAGGTCGTGCTGACGGCGATCTCTGAGGTTAACGCTGAGCTGTACGACTTCCGCAACCGTCAGCAGATGCTGGGCTGGCGGACACTTGCTGAGGTTCCCGCAGAAATGCTGGACGGTAAAAGCGAGCGTATCCGGCACTACCACAACGCTGTTTTTTGCTGGGCGCGCGCTGTGCTTAATGAGCGTTATCAGGACTATGACGCCACGGCGTCAGGCGTGAAGCGAGGGGAGGAGCTGGCGGAGGCCAGCGGCGATCTGTGGCGTGATGCCCGCTGGGCCATCAGCCGGGTGCAGGATGTACCGCACTGTACGGTGGAGCTTATCTGAACGGCTAGCGCGTAGCGGCAGTCTCGGATGAATAATCATTTTGGGAAAGGGTTAATGGCCGGGTTGCACGCGCCATATGCATATAGCGCGCATCATGCGGTGAATTTCTGTTCTGAGTATAAACGTGGCTTTGTATTGGGTTTTACACACCGTATGTTCGAAAAGACCGGCGATCGTCAACTTAGCGCGTGGGAGGCTGGAATTCTGACGCGTCGCTATGGTCTGGATAAAGAAATGGTGATGGATTTCTTTAAAGAGAATCATTCCGGGATGGCGGTTCGCTTCTTTATGGCCGGTTATCGACTCGAAGGTTGACGATCGCGCGCAGGAGGAGAGCTCTCTTCTTCTAGAGCATGTCTACGCTTCTCTATTTGCACGGATTCAACAGTTCCCCTCGCTCGGCAAAAGCGTGCCAGCTAAAAAACTGGCTGGCGGAGCGTCATCCGCATGTTGAGATGATCGTCCCTCAGCTGCCGCCGTATCCTGCCGATGCGGCGGAGTTGCTGGAATCTCTCGTGCTTGAGCATGGCGGTGCGCCATTAGGGCTGGTAGGATCGTCGCTGGGTGGTTATTACGCCACCTGGCTGTCGCAATGTTTTATGCTGCCGGCTGTGGTGGTGAATCCCGCCGTGCGGCCCTTTGAATTACTGACCGACTATCTCGGTCAGAACGAGAACCCCTACACCGGGCAGCAATATGTGCTAGAGTCTCGCCATATTTATGATCTTAAAGTCATGCAGATTGACCCGCTGGAAGCGCCGGACCTGATCTGGCTACTGCAACAGACGGGCGATGAAGTGCTGTATTACCGCCAGGCGGTGGCATATTACGCCTCCTGCCGTCAGACAGTGACCGAGGGTGGTAATCACGCATTCACGGGCTTCGAAGATTATTTCAACCAGATTGTCGATTTTCTTGGACTGCACAGTTGCTGACGGCTATGCGCGCGCTCGATGATTGACCCTATTTTTGCGTCCTGTACGCTAATTGCCGTCTTTGTTGTTTTACTGGCCATGGGCGCGCCTATCGGGATCTGCATCGTTATCGCCTCTTTCAGCACCATGATGCTGGTACTGCCTTTCGATATTTCGATGTTCGCCACCGCGCAAAAAATGTTCTCCAGCCTGGACAGTTTTGCCTTGCTGGCCGTGCCGTTCTTCGTTTTGTCCGGGGTGATCATGAATAGCGGGGGAATTGCCGCCCGGCTGGTCAATTTTGCCAAACTGTTTACTGGCAAACTGCCCGGCTCGCTCTCTTATACCAACATCGTCGGCAATATGATGTTCGGTGCAATTTCCGGATCGGCGATTGCCGCCTCAACCTCCATCGGCGGCGTGATGGTGCCGATGAGCGCGCGCGAAGGTTACGATCGCGGCTTTGCGGCCGCGGTGAATATCGCCTCCGCGCCGACGGGAATGTTAATTCCGCCCACCACGGCTTTTATCCTTTACGCGCTGGCAAGCGGGGGAACATCGATTGCCGCTCTGTTCGCCGGCGGTCTGGTCGCGGGAGTGCTGTGGGGCGTTGGCTGTATGCTGGTCACGCTGGTGGTCGCTAAGCGTCGAAATTATCGGGTTTTCTTCACCGTCCAAAAAGGTATGGCGCTAAAAGTTGCCGTTGAGGCCATTCCCAGCCTGCTGCTGATCGTGATTATTGTCGGCGGCATTGTGCAGGGGATTTTCACCGCCATTGAAGCCTCCGCGATTGCCGTGGTGTATACGTTATTGCTGACGATGGTGTTTTACCGCACGCTGAAAATTAAGGATTTGCCTTCGATTTTGCTCCAGACAGTGGTAATGACCGGGGTCATCATGTTCCTGCTGGCAACCTCTTCGGCGATGTCCTTCTCGATGTCGATCACCAATATTCCTGCGGCGCTGAGCGATATGATCCTCGGTATTTCCGCCAATAAACTGGTTATCCTGTTAGTCATTACCGTCTTTTTGTTGATTATCGGCGCATTTATGGATATTGGTCCGGCCATTCTGATTTTTACCCCGATTCTGCTGCCAATCATGGCTAAACTGGGCGTCGATCCGGTGCATTTCGGCATTATCATGATCTATAACCTGGCGATTGGCACCATTACGCCGCCAGTTGGCAGTGGTTTATATGTCGGGGCGAGCGTCGGTAAGGTCAAAGTTGAGGAAGTGATTAAACCGTTGCTGCCTTTTTACGGCGCGATTATCGGCGTTCTGTTATTAATTACCTACATTCCGGAAATCACACTGTTCTTACCCCGTCTACTGGGCATCATGTAA
diff --git a/Examples/2-res-Annotate-prokka/tmp_files/genome1.fst_prokka-split5N.fna-prokka.log b/Examples/2-res-Annotate-prokka/tmp_files/genome1.fst_prokka-split5N.fna-prokka.log
deleted file mode 100644
index 0aa974902a9cd21965ea0f7f27e1f6aa8a90e4bf..0000000000000000000000000000000000000000
--- a/Examples/2-res-Annotate-prokka/tmp_files/genome1.fst_prokka-split5N.fna-prokka.log
+++ /dev/null
@@ -1,130 +0,0 @@
-[13:15:21] This is prokka 1.14.5
-[13:15:21] Written by Torsten Seemann <torsten.seemann@gmail.com>
-[13:15:21] Homepage is https://github.com/tseemann/prokka
-[13:15:21] Local time is Mon Dec  9 13:15:21 2019
-[13:15:21] You are aperrin
-[13:15:21] Operating system is darwin
-[13:15:21] You have BioPerl 1.007002
-[13:15:21] System has 8 cores.
-[13:15:21] Will use maximum of 1 cores.
-[13:15:21] Annotating as >>> Bacteria <<<
-[13:15:21] Generating locus_tag from 'Examples/2-res-Annotate-prokka/tmp_files/genome1.fst_prokka-split5N.fna' contents.
-[13:15:21] Setting --locustag GKEGNCBE from MD5 04e07cbef9b8a6b8d550f0d6ed3a8746
-[13:15:21] Creating new output folder: Examples/2-res-Annotate-prokka/tmp_files/genome1.fst_prokka-split5N.fna-prokkaRes
-[13:15:21] Running: mkdir -p Examples\/2\-res\-Annotate\-prokka\/tmp_files\/genome1\.fst_prokka\-split5N\.fna\-prokkaRes
-[13:15:21] Using filename prefix: EXAM.1219.00001.XXX
-[13:15:21] Setting HMMER_NCPU=1
-[13:15:21] Writing log to: Examples/2-res-Annotate-prokka/tmp_files/genome1.fst_prokka-split5N.fna-prokkaRes/EXAM.1219.00001.log
-[13:15:21] Command: /usr/local/bin/prokka --outdir Examples/2-res-Annotate-prokka/tmp_files/genome1.fst_prokka-split5N.fna-prokkaRes --cpus 1 --prefix EXAM.1219.00001 Examples/2-res-Annotate-prokka/tmp_files/genome1.fst_prokka-split5N.fna
-[13:15:21] Appending to PATH: /Users/aperrin/Softwares/src/prokka-dec.19/bin/../binaries/darwin
-[13:15:21] Appending to PATH: /Users/aperrin/Softwares/src/prokka-dec.19/bin/../binaries/darwin/../common
-[13:15:21] Appending to PATH: /Users/aperrin/Softwares/src/prokka-dec.19/bin
-[13:15:21] Looking for 'aragorn' - found /usr/local/bin/aragorn
-[13:15:21] Determined aragorn version is 001002 from 'ARAGORN v1.2.38 Dean Laslett'
-[13:15:21] Looking for 'barrnap' - found /usr/local/bin/barrnap
-[13:15:21] Determined barrnap version is 000008 from 'barrnap 0.8'
-[13:15:21] Looking for 'blastp' - found /Users/aperrin/Softwares/bin/blastp
-[13:15:21] Determined blastp version is 002009 from 'blastp: 2.9.0+'
-[13:15:21] Looking for 'cmpress' - found /usr/local/bin/cmpress
-[13:15:21] Determined cmpress version is 001001 from '# INFERNAL 1.1.2 (July 2016)'
-[13:15:21] Looking for 'cmscan' - found /usr/local/bin/cmscan
-[13:15:21] Determined cmscan version is 001001 from '# INFERNAL 1.1.2 (July 2016)'
-[13:15:21] Looking for 'egrep' - found /usr/bin/egrep
-[13:15:21] Looking for 'find' - found /usr/bin/find
-[13:15:21] Looking for 'grep' - found /usr/bin/grep
-[13:15:21] Looking for 'hmmpress' - found /Users/aperrin/Softwares/src/prokka-dec.19/bin/../binaries/darwin/hmmpress
-[13:15:21] Determined hmmpress version is 003001 from '# HMMER 3.1b1 (May 2013); http://hmmer.org/'
-[13:15:21] Looking for 'hmmscan' - found /usr/local/bin/hmmscan
-[13:15:21] Determined hmmscan version is 003001 from '# HMMER 3.1b2 (February 2015); http://hmmer.org/'
-[13:15:21] Looking for 'java' - found /usr/bin/java
-[13:15:21] Looking for 'makeblastdb' - found /Users/aperrin/Softwares/bin/makeblastdb
-[13:15:21] Determined makeblastdb version is 002009 from 'makeblastdb: 2.9.0+'
-[13:15:21] Looking for 'minced' - found /Users/aperrin/Softwares/src/prokka-dec.19/bin/../binaries/darwin/../common/minced
-[13:15:22] Determined minced version is 002000 from 'minced 0.2.0'
-[13:15:22] Looking for 'parallel' - found /usr/local/bin/parallel
-[13:15:22] Determined parallel version is 20181022 from 'GNU parallel 20181022'
-[13:15:22] Looking for 'prodigal' - found /usr/local/bin/prodigal
-[13:15:22] Determined prodigal version is 002006 from 'Prodigal V2.6.3: February, 2016'
-[13:15:22] Looking for 'prokka-genbank_to_fasta_db' - found /Users/aperrin/Softwares/src/prokka-dec.19/bin/prokka-genbank_to_fasta_db
-[13:15:22] Looking for 'sed' - found /usr/bin/sed
-[13:15:22] Looking for 'tbl2asn' - found /Users/aperrin/Softwares/src/prokka-dec.19/bin/../binaries/darwin/tbl2asn
-[13:15:22] Determined tbl2asn version is 025007 from 'tbl2asn 25.7   arguments:'
-[13:15:22] Using genetic code table 11.
-[13:15:22] Loading and checking input file: Examples/2-res-Annotate-prokka/tmp_files/genome1.fst_prokka-split5N.fna
-[13:15:22] Wrote 2 contigs totalling 9808 bp.
-[13:15:22] Predicting tRNAs and tmRNAs
-[13:15:22] Running: aragorn -l -gc11  -w Examples\/2\-res\-Annotate\-prokka\/tmp_files\/genome1\.fst_prokka\-split5N\.fna\-prokkaRes\/EXAM\.1219\.00001\.fna
-[13:15:22] Found 0 tRNAs
-[13:15:22] Predicting Ribosomal RNAs
-[13:15:22] Running Barrnap with 1 threads
-[13:15:22] Found 0 rRNAs
-[13:15:22] Skipping ncRNA search, enable with --rfam if desired.
-[13:15:22] Total of 0 tRNA + rRNA features
-[13:15:22] Searching for CRISPR repeats
-[13:15:22] Found 0 CRISPRs
-[13:15:22] Predicting coding sequences
-[13:15:22] Contigs total 9808 bp, so using meta mode
-[13:15:22] Running: prodigal -i Examples\/2\-res\-Annotate\-prokka\/tmp_files\/genome1\.fst_prokka\-split5N\.fna\-prokkaRes\/EXAM\.1219\.00001\.fna -c -m -g 11 -p meta -f sco -q
-[13:15:22] Found 11 CDS
-[13:15:22] Connecting features back to sequences
-[13:15:22] Not using genus-specific database. Try --usegenus to enable it.
-[13:15:22] Annotating CDS, please be patient.
-[13:15:22] Will use 1 CPUs for similarity searching.
-[13:15:22] There are still 11 unannotated CDS left (started with 11)
-[13:15:22] Will use blast to search against /Users/aperrin/Softwares/src/prokka-dec.19/db/kingdom/Bacteria/IS with 1 CPUs
-[13:15:22] Running: cat Examples\/2\-res\-Annotate\-prokka\/tmp_files\/genome1\.fst_prokka\-split5N\.fna\-prokkaRes\/EXAM\.1219\.00001\.IS\.tmp\.94917\.faa | parallel --gnu --plain -j 1 --block 1558 --recstart '>' --pipe blastp -query - -db /Users/aperrin/Softwares/src/prokka-dec.19/db/kingdom/Bacteria/IS -evalue 1e-30 -qcov_hsp_perc 90 -num_threads 1 -num_descriptions 1 -num_alignments 1 -seg no > Examples\/2\-res\-Annotate\-prokka\/tmp_files\/genome1\.fst_prokka\-split5N\.fna\-prokkaRes\/EXAM\.1219\.00001\.IS\.tmp\.94917\.blast 2> /dev/null
-[13:15:23] Deleting unwanted file: Examples/2-res-Annotate-prokka/tmp_files/genome1.fst_prokka-split5N.fna-prokkaRes/EXAM.1219.00001.IS.tmp.94917.faa
-[13:15:23] Deleting unwanted file: Examples/2-res-Annotate-prokka/tmp_files/genome1.fst_prokka-split5N.fna-prokkaRes/EXAM.1219.00001.IS.tmp.94917.blast
-[13:15:23] There are still 11 unannotated CDS left (started with 11)
-[13:15:23] Will use blast to search against /Users/aperrin/Softwares/src/prokka-dec.19/db/kingdom/Bacteria/AMR with 1 CPUs
-[13:15:23] Running: cat Examples\/2\-res\-Annotate\-prokka\/tmp_files\/genome1\.fst_prokka\-split5N\.fna\-prokkaRes\/EXAM\.1219\.00001\.AMR\.tmp\.94917\.faa | parallel --gnu --plain -j 1 --block 1558 --recstart '>' --pipe blastp -query - -db /Users/aperrin/Softwares/src/prokka-dec.19/db/kingdom/Bacteria/AMR -evalue 1e-300 -qcov_hsp_perc 90 -num_threads 1 -num_descriptions 1 -num_alignments 1 -seg no > Examples\/2\-res\-Annotate\-prokka\/tmp_files\/genome1\.fst_prokka\-split5N\.fna\-prokkaRes\/EXAM\.1219\.00001\.AMR\.tmp\.94917\.blast 2> /dev/null
-[13:15:23] Deleting unwanted file: Examples/2-res-Annotate-prokka/tmp_files/genome1.fst_prokka-split5N.fna-prokkaRes/EXAM.1219.00001.AMR.tmp.94917.faa
-[13:15:23] Deleting unwanted file: Examples/2-res-Annotate-prokka/tmp_files/genome1.fst_prokka-split5N.fna-prokkaRes/EXAM.1219.00001.AMR.tmp.94917.blast
-[13:15:23] There are still 11 unannotated CDS left (started with 11)
-[13:15:23] Will use blast to search against /Users/aperrin/Softwares/src/prokka-dec.19/db/kingdom/Bacteria/sprot with 1 CPUs
-[13:15:23] Running: cat Examples\/2\-res\-Annotate\-prokka\/tmp_files\/genome1\.fst_prokka\-split5N\.fna\-prokkaRes\/EXAM\.1219\.00001\.sprot\.tmp\.94917\.faa | parallel --gnu --plain -j 1 --block 1558 --recstart '>' --pipe blastp -query - -db /Users/aperrin/Softwares/src/prokka-dec.19/db/kingdom/Bacteria/sprot -evalue 1e-09 -qcov_hsp_perc 80 -num_threads 1 -num_descriptions 1 -num_alignments 1 -seg no > Examples\/2\-res\-Annotate\-prokka\/tmp_files\/genome1\.fst_prokka\-split5N\.fna\-prokkaRes\/EXAM\.1219\.00001\.sprot\.tmp\.94917\.blast 2> /dev/null
-[13:15:25] Deleting unwanted file: Examples/2-res-Annotate-prokka/tmp_files/genome1.fst_prokka-split5N.fna-prokkaRes/EXAM.1219.00001.sprot.tmp.94917.faa
-[13:15:25] Deleting unwanted file: Examples/2-res-Annotate-prokka/tmp_files/genome1.fst_prokka-split5N.fna-prokkaRes/EXAM.1219.00001.sprot.tmp.94917.blast
-[13:15:25] There are still 4 unannotated CDS left (started with 11)
-[13:15:25] Will use hmmer3 to search against /Users/aperrin/Softwares/src/prokka-dec.19/db/hmm/HAMAP.hmm with 1 CPUs
-[13:15:25] Running: cat Examples\/2\-res\-Annotate\-prokka\/tmp_files\/genome1\.fst_prokka\-split5N\.fna\-prokkaRes\/EXAM\.1219\.00001\.HAMAP\.hmm\.tmp\.94917\.faa | parallel --gnu --plain -j 1 --block 459 --recstart '>' --pipe hmmscan --noali --notextw --acc -E 1e-09 --cpu 1 /Users/aperrin/Softwares/src/prokka-dec.19/db/hmm/HAMAP.hmm /dev/stdin > Examples\/2\-res\-Annotate\-prokka\/tmp_files\/genome1\.fst_prokka\-split5N\.fna\-prokkaRes\/EXAM\.1219\.00001\.HAMAP\.hmm\.tmp\.94917\.hmmer3 2> /dev/null
-[13:15:25] Deleting unwanted file: Examples/2-res-Annotate-prokka/tmp_files/genome1.fst_prokka-split5N.fna-prokkaRes/EXAM.1219.00001.HAMAP.hmm.tmp.94917.faa
-[13:15:25] Deleting unwanted file: Examples/2-res-Annotate-prokka/tmp_files/genome1.fst_prokka-split5N.fna-prokkaRes/EXAM.1219.00001.HAMAP.hmm.tmp.94917.hmmer3
-[13:15:25] Labelling remaining 4 proteins as 'hypothetical protein'
-[13:15:25] Possible /pseudo 'tRNA (guanine-N(1)-)-methyltransferase' at genome1_2 position 3427
-[13:15:25] Found 6 unique /gene codes.
-[13:15:25] Fixed 2 duplicate /gene - trmD_1 trmD_2
-[13:15:25] Fixed 1 colliding /gene names.
-[13:15:25] Adding /locus_tag identifiers
-[13:15:25] Assigned 11 locus_tags to CDS and RNA features.
-[13:15:25] Writing outputs to Examples/2-res-Annotate-prokka/tmp_files/genome1.fst_prokka-split5N.fna-prokkaRes/
-[13:15:25] Generating annotation statistics file
-[13:15:25] Generating Genbank and Sequin files
-[13:15:25] Running: tbl2asn -V b -a r10k -l paired-ends -M n -N 1 -y 'Annotated using prokka 1.14.5 from https://github.com/tseemann/prokka' -Z Examples\/2\-res\-Annotate\-prokka\/tmp_files\/genome1\.fst_prokka\-split5N\.fna\-prokkaRes\/EXAM\.1219\.00001\.err -i Examples\/2\-res\-Annotate\-prokka\/tmp_files\/genome1\.fst_prokka\-split5N\.fna\-prokkaRes\/EXAM\.1219\.00001\.fsa 2> /dev/null
-[13:15:25] Deleting unwanted file: Examples/2-res-Annotate-prokka/tmp_files/genome1.fst_prokka-split5N.fna-prokkaRes/errorsummary.val
-[13:15:25] Deleting unwanted file: Examples/2-res-Annotate-prokka/tmp_files/genome1.fst_prokka-split5N.fna-prokkaRes/EXAM.1219.00001.dr
-[13:15:25] Deleting unwanted file: Examples/2-res-Annotate-prokka/tmp_files/genome1.fst_prokka-split5N.fna-prokkaRes/EXAM.1219.00001.fixedproducts
-[13:15:25] Deleting unwanted file: Examples/2-res-Annotate-prokka/tmp_files/genome1.fst_prokka-split5N.fna-prokkaRes/EXAM.1219.00001.ecn
-[13:15:25] Deleting unwanted file: Examples/2-res-Annotate-prokka/tmp_files/genome1.fst_prokka-split5N.fna-prokkaRes/EXAM.1219.00001.val
-[13:15:25] Repairing broken .GBK output that tbl2asn produces...
-[13:15:25] Running: sed 's/COORDINATES: profile/COORDINATES:profile/' < Examples\/2\-res\-Annotate\-prokka\/tmp_files\/genome1\.fst_prokka\-split5N\.fna\-prokkaRes\/EXAM\.1219\.00001\.gbf > Examples\/2\-res\-Annotate\-prokka\/tmp_files\/genome1\.fst_prokka\-split5N\.fna\-prokkaRes\/EXAM\.1219\.00001\.gbk
-[13:15:25] Deleting unwanted file: Examples/2-res-Annotate-prokka/tmp_files/genome1.fst_prokka-split5N.fna-prokkaRes/EXAM.1219.00001.gbf
-[13:15:25] Output files:
-[13:15:25] Examples/2-res-Annotate-prokka/tmp_files/genome1.fst_prokka-split5N.fna-prokkaRes/EXAM.1219.00001.txt
-[13:15:25] Examples/2-res-Annotate-prokka/tmp_files/genome1.fst_prokka-split5N.fna-prokkaRes/EXAM.1219.00001.gff
-[13:15:25] Examples/2-res-Annotate-prokka/tmp_files/genome1.fst_prokka-split5N.fna-prokkaRes/EXAM.1219.00001.tbl
-[13:15:25] Examples/2-res-Annotate-prokka/tmp_files/genome1.fst_prokka-split5N.fna-prokkaRes/EXAM.1219.00001.sqn
-[13:15:25] Examples/2-res-Annotate-prokka/tmp_files/genome1.fst_prokka-split5N.fna-prokkaRes/EXAM.1219.00001.fna
-[13:15:25] Examples/2-res-Annotate-prokka/tmp_files/genome1.fst_prokka-split5N.fna-prokkaRes/EXAM.1219.00001.tsv
-[13:15:25] Examples/2-res-Annotate-prokka/tmp_files/genome1.fst_prokka-split5N.fna-prokkaRes/EXAM.1219.00001.err
-[13:15:25] Examples/2-res-Annotate-prokka/tmp_files/genome1.fst_prokka-split5N.fna-prokkaRes/EXAM.1219.00001.log
-[13:15:25] Examples/2-res-Annotate-prokka/tmp_files/genome1.fst_prokka-split5N.fna-prokkaRes/EXAM.1219.00001.ffn
-[13:15:25] Examples/2-res-Annotate-prokka/tmp_files/genome1.fst_prokka-split5N.fna-prokkaRes/EXAM.1219.00001.gbk
-[13:15:25] Examples/2-res-Annotate-prokka/tmp_files/genome1.fst_prokka-split5N.fna-prokkaRes/EXAM.1219.00001.fsa
-[13:15:25] Examples/2-res-Annotate-prokka/tmp_files/genome1.fst_prokka-split5N.fna-prokkaRes/EXAM.1219.00001.faa
-[13:15:25] Annotation finished successfully.
-[13:15:25] Walltime used: 0.07 minutes
-[13:15:25] If you use this result please cite the Prokka paper:
-[13:15:25] Seemann T (2014) Prokka: rapid prokaryotic genome annotation. Bioinformatics. 30(14):2068-9.
-[13:15:25] Type 'prokka --citation' for more details.
-[13:15:25] Thank you, come again.
diff --git a/Examples/2-res-Annotate-prokka/tmp_files/genome1.fst_prokka-split5N.fna-prokkaRes/EXAM.1219.00001.err b/Examples/2-res-Annotate-prokka/tmp_files/genome1.fst_prokka-split5N.fna-prokkaRes/EXAM.1219.00001.err
deleted file mode 100644
index 6f30173ddbc799ee7893d28fff8923f98a0a624f..0000000000000000000000000000000000000000
--- a/Examples/2-res-Annotate-prokka/tmp_files/genome1.fst_prokka-split5N.fna-prokkaRes/EXAM.1219.00001.err
+++ /dev/null
@@ -1,126 +0,0 @@
-Discrepancy Report Results
-
-Summary
-FATAL: MISSING_PROTEIN_ID:11 proteins have invalid IDs.
-DISC_SOURCE_QUALS_ASNDISC:strain (all present, all same)
-DISC_SOURCE_QUALS_ASNDISC:taxname (all present, all same)
-DISC_FEATURE_COUNT:CDS: 11 present
-DISC_COUNT_NUCLEOTIDES:2 nucleotide Bioseqs are present
-FEATURE_LOCATION_CONFLICT:11 features have inconsistent gene locations.
-OVERLAPPING_CDS:2 coding regions overlap another coding region with a similar or identical name.
-DISC_QUALITY_SCORES:Quality scores are missing on all sequences.
-ONCALLER_COMMENT_PRESENT:2 comment descriptors were found (all same)
-MISSING_GENOMEASSEMBLY_COMMENTS:2 bioseqs are missing GenomeAssembly structured comments
-MOLTYPE_NOT_MRNA:2 molecule types are not set as mRNA.
-TECHNIQUE_NOT_TSA:2 technique are not set as TSA
-MISSING_STRUCTURED_COMMENT:2 sequences do not include structured comments.
-MISSING_PROJECT:13 sequences do not include project.
-DISC_INCONSISTENT_MOLINFO_TECH:Molinfo Technique Report (some missing, all same)
-
-
-Detailed Report
-
-FATAL: DiscRep_ALL:MISSING_PROTEIN_ID::11 proteins halid nvalid IDs.
-Examples/2-res-Annotate-prokka/tmp_files/genome1.fst_prokka-split5N.fna-prokkaRes/EXAM.1219.00001:genome1_1_1 (length 555)
-Examples/2-res-Annotate-prokka/tmp_files/genome1.fst_prokka-split5N.fna-prokkaRes/EXAM.1219.00001:genome1_1_2 (length 276)
-Examples/2-res-Annotate-prokka/tmp_files/genome1.fst_prokka-split5N.fna-prokkaRes/EXAM.1219.00001:genome1_2_1 (length 126)
-Examples/2-res-Annotate-prokka/tmp_files/genome1.fst_prokka-split5N.fna-prokkaRes/EXAM.1219.00001:genome1_2_2 (length 469)
-Examples/2-res-Annotate-prokka/tmp_files/genome1.fst_prokka-split5N.fna-prokkaRes/EXAM.1219.00001:genome1_2_3 (length 257)
-Examples/2-res-Annotate-prokka/tmp_files/genome1.fst_prokka-split5N.fna-prokkaRes/EXAM.1219.00001:genome1_2_4 (length 244)
-Examples/2-res-Annotate-prokka/tmp_files/genome1.fst_prokka-split5N.fna-prokkaRes/EXAM.1219.00001:genome1_2_5 (length 275)
-Examples/2-res-Annotate-prokka/tmp_files/genome1.fst_prokka-split5N.fna-prokkaRes/EXAM.1219.00001:genome1_2_6 (length 154)
-Examples/2-res-Annotate-prokka/tmp_files/genome1.fst_prokka-split5N.fna-prokkaRes/EXAM.1219.00001:genome1_2_7 (length 86)
-Examples/2-res-Annotate-prokka/tmp_files/genome1.fst_prokka-split5N.fna-prokkaRes/EXAM.1219.00001:genome1_2_8 (length 193)
-Examples/2-res-Annotate-prokka/tmp_files/genome1.fst_prokka-split5N.fna-prokkaRes/EXAM.1219.00001:genome1_2_9 (length 435)
-
-DiscRep_ALL:DISC_SOURCE_QUALS_ASNDISC::strain (all present, all same)
-DiscRep_SUB:DISC_SOURCE_QUALS_ASNDISC::2 sources have 'strain' for strain
-DiscRep_ALL:DISC_SOURCE_QUALS_ASNDISC::taxname (all present, all same)
-DiscRep_SUB:DISC_SOURCE_QUALS_ASNDISC::2 sources have 'Genus species' for taxname
-DiscRep_ALL:DISC_FEATURE_COUNT::CDS: 11 present
-DiscRep_ALL:DISC_COUNT_NUCLEOTIDES::2 nucleotide Bioseqs are present
-Examples/2-res-Annotate-prokka/tmp_files/genome1.fst_prokka-split5N.fna-prokkaRes/EXAM.1219.00001:genome1_1 (length 2784)
-Examples/2-res-Annotate-prokka/tmp_files/genome1.fst_prokka-split5N.fna-prokkaRes/EXAM.1219.00001:genome1_2 (length 7024)
-
-DiscRep_ALL:FEATURE_LOCATION_CONFLICT::11 features have inconsistent gene locations.
-DiscRep_SUB:FEATURE_LOCATION_CONFLICT::Coding region xref gene does not exist
-Examples/2-res-Annotate-prokka/tmp_files/genome1.fst_prokka-split5N.fna-prokkaRes/EXAM.1219.00001:CDS	Glutamine--tRNA ligase	genome1_1:213-1880	GKEGNCBE_00001
-
-DiscRep_SUB:FEATURE_LOCATION_CONFLICT::Coding region xref gene does not exist
-Examples/2-res-Annotate-prokka/tmp_files/genome1.fst_prokka-split5N.fna-prokkaRes/EXAM.1219.00001:CDS	N-acetylmuramoyl-L-alanine amidase AmiD	genome1_1:1916-2746	GKEGNCBE_00002
-
-DiscRep_SUB:FEATURE_LOCATION_CONFLICT::Coding region xref gene does not exist
-Examples/2-res-Annotate-prokka/tmp_files/genome1.fst_prokka-split5N.fna-prokkaRes/EXAM.1219.00001:CDS	5-carboxymethyl-2-hydroxymuconate Delta-isomerase	genome1_2:16-396	GKEGNCBE_00003
-
-DiscRep_SUB:FEATURE_LOCATION_CONFLICT::Coding region xref gene does not exist
-Examples/2-res-Annotate-prokka/tmp_files/genome1.fst_prokka-split5N.fna-prokkaRes/EXAM.1219.00001:CDS	hypothetical protein	genome1_2:428-1837	GKEGNCBE_00004
-
-DiscRep_SUB:FEATURE_LOCATION_CONFLICT::Coding region xref gene does not exist
-Examples/2-res-Annotate-prokka/tmp_files/genome1.fst_prokka-split5N.fna-prokkaRes/EXAM.1219.00001:CDS	Histidine transport ATP-binding protein HisP	genome1_2:1869-2642	GKEGNCBE_00005
-
-DiscRep_SUB:FEATURE_LOCATION_CONFLICT::Coding region xref gene does not exist
-Examples/2-res-Annotate-prokka/tmp_files/genome1.fst_prokka-split5N.fna-prokkaRes/EXAM.1219.00001:CDS	tRNA (guanine-N(1)-)-methyltransferase	genome1_2:2709-3443	GKEGNCBE_00006
-
-DiscRep_SUB:FEATURE_LOCATION_CONFLICT::Coding region xref gene does not exist
-Examples/2-res-Annotate-prokka/tmp_files/genome1.fst_prokka-split5N.fna-prokkaRes/EXAM.1219.00001:CDS	tRNA (guanine-N(1)-)-methyltransferase	genome1_2:3427-4254	GKEGNCBE_00007
-
-DiscRep_SUB:FEATURE_LOCATION_CONFLICT::Coding region xref gene does not exist
-Examples/2-res-Annotate-prokka/tmp_files/genome1.fst_prokka-split5N.fna-prokkaRes/EXAM.1219.00001:CDS	hypothetical protein	genome1_2:4299-4763	GKEGNCBE_00008
-
-DiscRep_SUB:FEATURE_LOCATION_CONFLICT::Coding region xref gene does not exist
-Examples/2-res-Annotate-prokka/tmp_files/genome1.fst_prokka-split5N.fna-prokkaRes/EXAM.1219.00001:CDS	hypothetical protein	genome1_2:4818-5078	GKEGNCBE_00009
-
-DiscRep_SUB:FEATURE_LOCATION_CONFLICT::Coding region xref gene does not exist
-Examples/2-res-Annotate-prokka/tmp_files/genome1.fst_prokka-split5N.fna-prokkaRes/EXAM.1219.00001:CDS	hypothetical protein	genome1_2:5117-5698	GKEGNCBE_00010
-
-DiscRep_SUB:FEATURE_LOCATION_CONFLICT::Coding region xref gene does not exist
-Examples/2-res-Annotate-prokka/tmp_files/genome1.fst_prokka-split5N.fna-prokkaRes/EXAM.1219.00001:CDS	C4-dicarboxylate TRAP transporter large permease protein DctM	genome1_2:5717-7024	GKEGNCBE_00011
-
-DiscRep_ALL:OVERLAPPING_CDS::2 coding regions overlap another coding region with a similar or identical name.
-DiscRep_SUB:OVERLAPPING_CDS::2 coding regions overlap another coding region with a similar or identical name that do not have the appropriate note text
-Examples/2-res-Annotate-prokka/tmp_files/genome1.fst_prokka-split5N.fna-prokkaRes/EXAM.1219.00001:CDS	tRNA (guanine-N(1)-)-methyltransferase	genome1_2:2709-3443	GKEGNCBE_00006
-Examples/2-res-Annotate-prokka/tmp_files/genome1.fst_prokka-split5N.fna-prokkaRes/EXAM.1219.00001:CDS	tRNA (guanine-N(1)-)-methyltransferase	genome1_2:3427-4254	GKEGNCBE_00007
-
-DiscRep_ALL:DISC_QUALITY_SCORES::Quality scores are missing on all sequences.
-
-DiscRep_ALL:ONCALLER_COMMENT_PRESENT::2 comment descriptors were found (all same)
-Examples/2-res-Annotate-prokka/tmp_files/genome1.fst_prokka-split5N.fna-prokkaRes/EXAM.1219.00001:genome1_1:Annotated using prokka 1.14.5 from https://github.com/tseemann/prokka
-Examples/2-res-Annotate-prokka/tmp_files/genome1.fst_prokka-split5N.fna-prokkaRes/EXAM.1219.00001:genome1_2:Annotated using prokka 1.14.5 from https://github.com/tseemann/prokka
-
-DiscRep_ALL:MISSING_GENOMEASSEMBLY_COMMENTS::2 bioseqs are missing GenomeAssembly structured comments
-Examples/2-res-Annotate-prokka/tmp_files/genome1.fst_prokka-split5N.fna-prokkaRes/EXAM.1219.00001:genome1_1 (length 2784)
-Examples/2-res-Annotate-prokka/tmp_files/genome1.fst_prokka-split5N.fna-prokkaRes/EXAM.1219.00001:genome1_2 (length 7024)
-
-DiscRep_ALL:MOLTYPE_NOT_MRNA::2 molecule types are not set as mRNA.
-Examples/2-res-Annotate-prokka/tmp_files/genome1.fst_prokka-split5N.fna-prokkaRes/EXAM.1219.00001:genome1_1 (length 2784)
-Examples/2-res-Annotate-prokka/tmp_files/genome1.fst_prokka-split5N.fna-prokkaRes/EXAM.1219.00001:genome1_2 (length 7024)
-
-DiscRep_ALL:TECHNIQUE_NOT_TSA::2 technique are not set as TSA
-Examples/2-res-Annotate-prokka/tmp_files/genome1.fst_prokka-split5N.fna-prokkaRes/EXAM.1219.00001:genome1_1 (length 2784)
-Examples/2-res-Annotate-prokka/tmp_files/genome1.fst_prokka-split5N.fna-prokkaRes/EXAM.1219.00001:genome1_2 (length 7024)
-
-DiscRep_ALL:MISSING_STRUCTURED_COMMENT::2 sequences do not include structured comments.
-Examples/2-res-Annotate-prokka/tmp_files/genome1.fst_prokka-split5N.fna-prokkaRes/EXAM.1219.00001:genome1_1 (length 2784)
-Examples/2-res-Annotate-prokka/tmp_files/genome1.fst_prokka-split5N.fna-prokkaRes/EXAM.1219.00001:genome1_2 (length 7024)
-
-DiscRep_ALL:MISSING_PROJECT::13 sequences do not include project.
-Examples/2-res-Annotate-prokka/tmp_files/genome1.fst_prokka-split5N.fna-prokkaRes/EXAM.1219.00001:genome1_1 (length 2784)
-Examples/2-res-Annotate-prokka/tmp_files/genome1.fst_prokka-split5N.fna-prokkaRes/EXAM.1219.00001:genome1_1_1 (length 555)
-Examples/2-res-Annotate-prokka/tmp_files/genome1.fst_prokka-split5N.fna-prokkaRes/EXAM.1219.00001:genome1_1_2 (length 276)
-Examples/2-res-Annotate-prokka/tmp_files/genome1.fst_prokka-split5N.fna-prokkaRes/EXAM.1219.00001:genome1_2 (length 7024)
-Examples/2-res-Annotate-prokka/tmp_files/genome1.fst_prokka-split5N.fna-prokkaRes/EXAM.1219.00001:genome1_2_1 (length 126)
-Examples/2-res-Annotate-prokka/tmp_files/genome1.fst_prokka-split5N.fna-prokkaRes/EXAM.1219.00001:genome1_2_2 (length 469)
-Examples/2-res-Annotate-prokka/tmp_files/genome1.fst_prokka-split5N.fna-prokkaRes/EXAM.1219.00001:genome1_2_3 (length 257)
-Examples/2-res-Annotate-prokka/tmp_files/genome1.fst_prokka-split5N.fna-prokkaRes/EXAM.1219.00001:genome1_2_4 (length 244)
-Examples/2-res-Annotate-prokka/tmp_files/genome1.fst_prokka-split5N.fna-prokkaRes/EXAM.1219.00001:genome1_2_5 (length 275)
-Examples/2-res-Annotate-prokka/tmp_files/genome1.fst_prokka-split5N.fna-prokkaRes/EXAM.1219.00001:genome1_2_6 (length 154)
-Examples/2-res-Annotate-prokka/tmp_files/genome1.fst_prokka-split5N.fna-prokkaRes/EXAM.1219.00001:genome1_2_7 (length 86)
-Examples/2-res-Annotate-prokka/tmp_files/genome1.fst_prokka-split5N.fna-prokkaRes/EXAM.1219.00001:genome1_2_8 (length 193)
-Examples/2-res-Annotate-prokka/tmp_files/genome1.fst_prokka-split5N.fna-prokkaRes/EXAM.1219.00001:genome1_2_9 (length 435)
-
-DiscRep_ALL:DISC_INCONSISTENT_MOLINFO_TECH::Molinfo Technique Report (some missing, all same)
-DiscRep_SUB:DISC_INCONSISTENT_MOLINFO_TECH::technique (all missing)
-DiscRep_SUB:DISC_INCONSISTENT_MOLINFO_TECH::2 Molinfos are missing field technique
-Examples/2-res-Annotate-prokka/tmp_files/genome1.fst_prokka-split5N.fna-prokkaRes/EXAM.1219.00001:genome1_1 (length 2784)
-Examples/2-res-Annotate-prokka/tmp_files/genome1.fst_prokka-split5N.fna-prokkaRes/EXAM.1219.00001:genome1_2 (length 7024)
-
diff --git a/Examples/2-res-Annotate-prokka/tmp_files/genome1.fst_prokka-split5N.fna-prokkaRes/EXAM.1219.00001.faa b/Examples/2-res-Annotate-prokka/tmp_files/genome1.fst_prokka-split5N.fna-prokkaRes/EXAM.1219.00001.faa
deleted file mode 100644
index 2bb9f621de719842530393507763f132848a7e16..0000000000000000000000000000000000000000
--- a/Examples/2-res-Annotate-prokka/tmp_files/genome1.fst_prokka-split5N.fna-prokkaRes/EXAM.1219.00001.faa
+++ /dev/null
@@ -1,69 +0,0 @@
->GKEGNCBE_00001 Glutamine--tRNA ligase
-MSEAEARPTNFIRQIIDEDLASGKHTTVHTRFPPEPNGYLHIGHAKSICLNFGIAQDYQG
-QCNLRFDDTNPVKEDIEYVDSIKNDVEWLGFHWSGDIRYSSDYFDQLHAYAVELINKGLA
-YVDELTPEQIREYRGTLTAPGKNSPFRDRSVEENLALFEKMRTGGFEEGKACLRAKIDMA
-SPFIVMRDPVLYRIKFAEHHQTGNKWCIYPMYDFTHCISDALEGITHSLCTLEFQDNRRL
-YDWVLDNITIPVHPRQYEFSRLNLEYTVMSKRKLNLLVTDKHVEGWDDPRMPTISGLRRR
-GYTAASIREFCKRIGVTKQDNTIEMASLESCIREDLNENAPRAMAVIDPVKLVIENYPQG
-ESEMVTMPNHPNKPEMGSREVPFSGEIWIDRADFREEANKQYKRLVMGKEVRLRNAYVIK
-AERVEKDAEGNITTIFCTYDADTLSKDPADGRKVKGVIHWVSAAHALPIEIRLYDRLFSV
-PNPGAAEDFLSVINPESLVIKQGYGEPSLKAAVAGKAFQFEREGYFCLDSRYATADKLVF
-NRTVGLRDTWAKAGE
->GKEGNCBE_00002 N-acetylmuramoyl-L-alanine amidase AmiD
-MKALLWLVGLALLLTGCASEKGIIDKEGYQLDTRHRAQAAYPRIKVLVIHYTAENFDVSL
-ATLTGRNVSSHYLIPATPPLYGGKPRIWQLVPEQDQAWHAGVSFWRGATRLNDTSIGIEL
-ENRGWRMSGGVKSFAPFESAQIQALIPLAKDIIARYNIKPQNVVAHADIAPQRKDDPGPR
-FPWRELAAQGISAWPDAQRVAFYLAGRAPYTPVDTATVLALLSRYGYEVKADMTAREQQR
-VIMAFQMHFRPAQWNGIADAETQAIAEALLEKYGQD
->GKEGNCBE_00003 5-carboxymethyl-2-hydroxymuconate Delta-isomerase
-MPHFIAECTENIREQADLPGLFSKVNEALAASGIFPIGGIRSRAHWLDTWQMADGKHDYA
-FVHMTLKIGAGRSLESRQEVGEMLFGLIKAHFADLMENRYLALSFEIAELHPTLNYKQNN
-VHALFK
->GKEGNCBE_00004 hypothetical protein
-MSMPATKFSRRTLLTAGSALAVLPFLRALPVQAREPRETVDIKDYPADDGIASFKQAFAD
-GQTVVVPPGWVCENINAAITIPAGKTLRVQGAVRGNGRGRFILQDGCQVVGEQGGSLHNV
-TLDVRGSDCVIKGVAMSGFGPVAQIFIGGKEPQVMRNLIIDDITVTHANYAILRQGFHNQ
-MDGARITHSRFSDLQGDAIEWNVAIHDRDILISDHVIERINCTNGKINWGIGIGLAGSTY
-DNSYPEDQAVKNFVVANITGSDCRQLVHVENGKHFVIRNVKAKNITPGFSKNAGIDNATI
-AIYGCDNFVIDNIDMTNSAGMLIGYGVVKGKYLSIPQNFKLNAIRLDNRQVAYKLRGIQI
-SSGNTPSFVAITNVRMTRATLELHNQPQHLFLRNINVMQTSAIGPALKMHFDLRKDVRGQ
-FMARQDTLLSLANVHAINENGQSSVDIDRINHQTVNVEAVNFSLPKRGG
->GKEGNCBE_00005 Histidine transport ATP-binding protein HisP
-MSENKLHVIDLHKRYGGHEVLKGVSLQARAGDVISIIGSSGSGKSTFLRCINFLEKPSEG
-AIIVNGQNINLVRDKDGQLKVADKNQLRLLRTRLTMVFQHFNLWSHMTVLENVMEAPIQV
-LGLSKHDARERALKYLAKVGIDERAQGKYPVHLSGGQQQRVSIARALAMEPDVLLFDEPT
-SALDPELVGEVLRIMQQLAEEGKTMVVVTHEMGFARHVSSHVIFLHQGKIEEEGDPEQVF
-GNPQSPRLQQFLKGSLK
->GKEGNCBE_00006 tRNA (guanine-N(1)-)-methyltransferase
-MFRAITDYGVTGRAVKKGLLNIQSWSPRDFAHDRHRTVDDRPYGGGPGMLMMVQPLRDAI
-HAAKAAAGEGAKVIYLSPQGRKLDQAGVSELATNQKLILVCGRYEGVDERVIQTEIDEEW
-SIGDYVLSGGELPAMTLIDSVARFIPGVLGHEASAIEDSFADGLLDCPHYTRPEVLEGME
-VPPVLLSGNHAEIRRWRLKQSLGRTWLRRPELLENLALTEEQARLLAEFKTEHAQQQHKH
-DGMA
->GKEGNCBE_00007 tRNA (guanine-N(1)-)-methyltransferase
-MMGWHSRHMGSQRRRANAQYVFIGIVSLFPEMFRAITDYGVTGRAVKKGLLNIQSWSPRD
-FAHDRHRTVDDRPYGGGPGMLMMVQPLRDAIHAAKAAAGEGAKVIYLSPQGRKLDQAGVS
-ELATNQKLILVCGRYEGVDERVIQTEIDEEWSIGDYVLSGGELPAMTLIDSVARFIPGVL
-GHEASAIEDSFADGLLDCPHYTRPEVLEGMEVPPVLLSGNHAEIRRWRLKQSLGRTWLRR
-PELLENLALTEEQARLLAEFKTEHAQQQHKHDGMA
->GKEGNCBE_00008 hypothetical protein
-MKFVAPEQAPEQAEVIKNTPFWPDVDLSEFRSVMRTDGTVTQPRLKQVVLTAISEVNAEL
-YDFRNRQQMLGWRTLAEVPAEMLDGKSERIRHYHNAVFCWARAVLNERYQDYDATASGVK
-RGEELAEASGDLWRDARWAISRVQDVPHCTVELI
->GKEGNCBE_00009 hypothetical protein
-MAGLHAPYAYSAHHAVNFCSEYKRGFVLGFTHRMFEKTGDRQLSAWEAGILTRRYGLDKE
-MVMDFFKENHSGMAVRFFMAGYRLEG
->GKEGNCBE_00010 hypothetical protein
-MSTLLYLHGFNSSPRSAKACQLKNWLAERHPHVEMIVPQLPPYPADAAELLESLVLEHGG
-APLGLVGSSLGGYYATWLSQCFMLPAVVVNPAVRPFELLTDYLGQNENPYTGQQYVLESR
-HIYDLKVMQIDPLEAPDLIWLLQQTGDEVLYYRQAVAYYASCRQTVTEGGNHAFTGFEDY
-FNQIVDFLGLHSC
->GKEGNCBE_00011 C4-dicarboxylate TRAP transporter large permease protein DctM
-MIDPIFASCTLIAVFVVLLAMGAPIGICIVIASFSTMMLVLPFDISMFATAQKMFSSLDS
-FALLAVPFFVLSGVIMNSGGIAARLVNFAKLFTGKLPGSLSYTNIVGNMMFGAISGSAIA
-ASTSIGGVMVPMSAREGYDRGFAAAVNIASAPTGMLIPPTTAFILYALASGGTSIAALFA
-GGLVAGVLWGVGCMLVTLVVAKRRNYRVFFTVQKGMALKVAVEAIPSLLLIVIIVGGIVQ
-GIFTAIEASAIAVVYTLLLTMVFYRTLKIKDLPSILLQTVVMTGVIMFLLATSSAMSFSM
-SITNIPAALSDMILGISANKLVILLVITVFLLIIGAFMDIGPAILIFTPILLPIMAKLGV
-DPVHFGIIMIYNLAIGTITPPVGSGLYVGASVGKVKVEEVIKPLLPFYGAIIGVLLLITY
-IPEITLFLPRLLGIM
diff --git a/Examples/2-res-Annotate-prokka/tmp_files/genome1.fst_prokka-split5N.fna-prokkaRes/EXAM.1219.00001.ffn b/Examples/2-res-Annotate-prokka/tmp_files/genome1.fst_prokka-split5N.fna-prokkaRes/EXAM.1219.00001.ffn
deleted file mode 100644
index 8bf92ebb8dfd9e743a03a529ee7eda731975d893..0000000000000000000000000000000000000000
--- a/Examples/2-res-Annotate-prokka/tmp_files/genome1.fst_prokka-split5N.fna-prokkaRes/EXAM.1219.00001.ffn
+++ /dev/null
@@ -1,169 +0,0 @@
->GKEGNCBE_00001 Glutamine--tRNA ligase
-ATGAGTGAGGCTGAAGCCCGCCCGACTAACTTTATTCGTCAGATTATTGATGAAGATCTG
-GCGAGTGGTAAACATACCACTGTCCATACCCGTTTTCCGCCGGAGCCGAATGGCTATCTG
-CATATCGGCCACGCGAAATCTATCTGCCTGAACTTTGGCATCGCGCAAGATTATCAGGGC
-CAGTGCAACCTGCGTTTCGATGACACCAACCCGGTAAAAGAAGATATCGAGTACGTTGAT
-TCGATCAAAAACGACGTCGAGTGGTTAGGCTTTCACTGGTCTGGCGATATTCGCTACTCC
-TCCGATTACTTTGACCAACTGCACGCCTATGCGGTCGAGCTAATCAATAAAGGCCTGGCC
-TATGTTGATGAGCTGACGCCGGAGCAGATCCGTGAATACCGCGGTACGCTGACCGCGCCG
-GGTAAAAACAGCCCGTTCCGCGATCGCAGCGTCGAAGAGAACCTCGCGCTATTTGAAAAA
-ATGCGTACCGGCGGTTTTGAAGAGGGTAAAGCCTGTCTGCGCGCTAAAATCGACATGGCG
-TCGCCGTTTATCGTGATGCGCGATCCGGTGCTGTATCGCATTAAATTCGCCGAGCATCAT
-CAGACTGGCAACAAGTGGTGCATCTATCCGATGTACGACTTTACTCACTGCATCAGCGAT
-GCGCTGGAAGGCATTACTCATTCTCTGTGTACGCTGGAGTTCCAGGATAACCGTCGTCTG
-TACGACTGGGTGCTGGACAACATCACCATTCCGGTTCACCCGCGCCAGTACGAATTCTCG
-CGCCTGAATCTGGAATACACCGTGATGTCCAAGCGTAAGCTGAACCTGCTGGTGACCGAC
-AAACACGTCGAAGGTTGGGACGATCCGCGTATGCCGACTATTTCCGGTCTGCGCCGTCGC
-GGCTATACCGCGGCTTCTATTCGTGAGTTCTGCAAACGCATCGGCGTCACCAAGCAGGAC
-AACACTATTGAGATGGCGTCGCTGGAATCCTGCATTCGCGAAGATCTGAACGAAAACGCG
-CCGCGCGCGATGGCGGTAATCGATCCGGTAAAACTGGTTATCGAAAATTACCCGCAGGGT
-GAGAGCGAAATGGTTACCATGCCTAACCATCCGAATAAACCGGAGATGGGCAGCCGTGAA
-GTGCCGTTTAGCGGTGAGATCTGGATCGATCGCGCAGATTTCCGCGAAGAAGCGAACAAA
-CAGTACAAACGTCTGGTGATGGGCAAAGAAGTGCGTCTGCGTAATGCCTACGTCATTAAA
-GCGGAGCGCGTAGAGAAGGATGCCGAAGGGAATATCACCACCATCTTCTGTACCTATGAT
-GCTGATACGCTGAGTAAAGATCCGGCTGACGGGCGTAAAGTGAAAGGCGTAATCCACTGG
-GTTAGCGCAGCACATGCGCTGCCGATTGAAATTCGTCTCTACGACCGTCTGTTCAGCGTG
-CCGAATCCGGGCGCCGCGGAGGACTTCCTGTCTGTTATCAACCCCGAATCATTAGTGATT
-AAGCAGGGGTATGGCGAGCCGTCGCTGAAAGCGGCGGTAGCAGGAAAAGCTTTCCAGTTT
-GAACGTGAAGGCTACTTCTGCCTCGACAGCCGCTATGCAACGGCCGATAAGCTGGTCTTT
-AACCGCACCGTGGGCCTGCGTGATACCTGGGCGAAAGCGGGCGAGTAA
->GKEGNCBE_00002 N-acetylmuramoyl-L-alanine amidase AmiD
-ATGAAAGCGCTACTGTGGCTGGTGGGTCTCGCGTTGCTGTTAACAGGCTGCGCGAGCGAA
-AAAGGAATTATCGATAAAGAGGGATATCAGCTTGATACCCGACATCGGGCGCAGGCGGCC
-TATCCGCGCATTAAAGTCCTGGTGATTCACTATACGGCGGAAAACTTTGACGTTTCGCTG
-GCGACGTTAACGGGTCGCAACGTCAGTTCGCATTACCTGATTCCCGCAACCCCGCCATTA
-TATGGCGGTAAACCGCGCATCTGGCAACTGGTGCCGGAACAGGATCAGGCCTGGCATGCG
-GGCGTCAGTTTCTGGCGAGGCGCCACGCGTCTCAATGATACGTCTATTGGCATTGAGCTG
-GAAAATCGTGGTTGGCGAATGTCCGGCGGGGTGAAATCTTTCGCGCCGTTTGAATCCGCG
-CAAATTCAGGCATTGATTCCGTTAGCGAAGGATATTATCGCGCGCTATAACATCAAACCG
-CAGAATGTGGTGGCCCATGCGGATATCGCGCCGCAGCGTAAAGACGATCCCGGCCCGCGC
-TTCCCGTGGCGCGAGCTGGCGGCGCAGGGGATTAGCGCCTGGCCTGACGCCCAGCGTGTG
-GCGTTTTATCTGGCTGGACGCGCGCCGTATACGCCAGTCGATACCGCAACGGTGCTTGCG
-TTACTCTCGCGCTATGGCTATGAAGTCAAAGCCGATATGACGGCACGCGAGCAGCAGCGG
-GTGATTATGGCGTTCCAGATGCACTTCCGTCCGGCGCAATGGAACGGTATCGCAGATGCC
-GAAACGCAGGCGATTGCCGAAGCATTACTGGAGAAGTACGGCCAGGATTAA
->GKEGNCBE_00003 5-carboxymethyl-2-hydroxymuconate Delta-isomerase
-ATGCCGCACTTTATTGCTGAATGTACTGAAAATATTCGCGAGCAGGCTGATTTACCCGGC
-CTGTTCAGCAAGGTAAACGAGGCGCTGGCCGCCAGCGGGATTTTCCCCATCGGCGGTATC
-CGCAGTCGCGCCCACTGGCTGGATACCTGGCAGATGGCTGACGGTAAGCATGATTACGCG
-TTTGTGCATATGACGCTGAAAATCGGCGCCGGGCGCAGCCTGGAGAGCCGTCAGGAAGTT
-GGCGAAATGCTGTTTGGGCTGATTAAAGCCCACTTCGCCGACCTGATGGAGAACCGCTAT
-CTGGCGCTGTCGTTTGAGATTGCCGAGCTACATCCGACGCTCAATTACAAACAAAACAAC
-GTACACGCGTTATTTAAATAG
->GKEGNCBE_00004 hypothetical protein
-ATGAGCATGCCCGCGACTAAATTCTCCCGACGTACCCTCCTGACGGCAGGTTCTGCGCTT
-GCTGTTCTTCCTTTTCTGCGCGCCTTGCCGGTACAGGCGCGTGAACCTCGCGAGACCGTC
-GATATTAAGGATTATCCGGCGGATGACGGTATCGCCTCGTTCAAACAGGCCTTCGCCGAC
-GGACAGACCGTGGTCGTACCGCCAGGATGGGTGTGTGAAAATATCAATGCGGCGATAACG
-ATTCCGGCGGGAAAAACGCTGCGGGTACAGGGCGCGGTGCGTGGGAATGGCCGGGGACGG
-TTTATTTTGCAGGACGGGTGTCAGGTGGTGGGGGAGCAGGGCGGCAGTCTGCACAATGTG
-ACGCTGGATGTTCGCGGGTCGGACTGTGTGATTAAAGGCGTGGCGATGAGCGGCTTTGGC
-CCCGTCGCGCAAATTTTCATCGGTGGTAAGGAACCGCAGGTGATGCGTAATCTCATTATC
-GATGACATCACCGTTACCCACGCCAACTACGCCATTCTCCGCCAGGGATTTCATAACCAA
-ATGGATGGCGCGCGGATTACGCATAGCCGCTTTAGCGATTTACAGGGGGACGCCATTGAG
-TGGAATGTCGCGATTCACGACCGCGACATCCTGATTTCCGATCATGTCATCGAACGCATT
-AATTGTACCAATGGCAAAATCAACTGGGGGATCGGCATCGGGCTGGCGGGTAGCACCTAT
-GACAACAGTTATCCTGAAGACCAGGCAGTAAAAAACTTTGTGGTGGCCAATATTACCGGA
-TCTGATTGCCGACAGCTTGTGCACGTAGAAAATGGCAAACATTTCGTCATTCGCAATGTC
-AAAGCCAAAAACATCACGCCCGGTTTCAGTAAAAATGCGGGTATTGATAACGCAACGATC
-GCAATTTATGGCTGTGATAATTTCGTCATTGATAATATTGATATGACGAATAGTGCCGGG
-ATGCTCATCGGCTATGGCGTCGTTAAAGGAAAATACCTGTCAATTCCGCAAAACTTTAAA
-TTAAACGCTATTCGGTTGGATAATCGCCAGGTTGCTTATAAATTACGCGGCATTCAAATT
-TCCTCCGGCAACACCCCCTCTTTTGTCGCCATCACCAATGTACGGATGACGCGTGCTACG
-CTGGAACTGCATAATCAACCGCAGCACCTCTTTCTGCGCAATATCAACGTGATGCAAACT
-TCAGCGATTGGCCCGGCGTTAAAAATGCATTTCGATTTGCGTAAAGATGTACGTGGTCAA
-TTTATGGCCCGCCAGGACACGCTGCTTTCCCTCGCTAATGTTCATGCCATCAATGAAAAC
-GGGCAGAGTTCCGTGGATATCGACAGGATTAATCACCAAACCGTGAATGTCGAAGCAGTG
-AATTTTTCGCTGCCGAAGCGGGGAGGGTAA
->GKEGNCBE_00005 Histidine transport ATP-binding protein HisP
-ATGTCAGAAAATAAATTACACGTTATCGATTTGCACAAACGCTACGGCGGTCATGAAGTG
-CTGAAAGGGGTATCGCTGCAGGCCCGCGCCGGAGATGTGATTAGCATCATCGGCTCGTCC
-GGCTCCGGTAAAAGCACTTTTTTGCGCTGTATTAACTTCCTCGAAAAACCGAGCGAAGGC
-GCGATTATCGTGAACGGTCAGAACATTAATCTGGTGCGCGACAAAGATGGGCAGCTCAAA
-GTGGCGGATAAAAATCAGCTACGCTTGTTGCGTACCCGCCTGACGATGGTGTTTCAGCAC
-TTCAACCTCTGGAGCCACATGACGGTGCTGGAAAATGTGATGGAAGCGCCGATTCAGGTA
-CTGGGATTAAGCAAGCACGACGCGCGCGAGCGGGCGTTGAAATATCTGGCGAAGGTGGGG
-ATTGATGAGCGCGCTCAGGGCAAATATCCCGTCCATCTCTCCGGCGGCCAACAGCAGCGC
-GTTTCTATTGCGCGCGCGCTGGCGATGGAACCTGACGTTTTACTGTTCGATGAACCCACA
-TCGGCGCTCGATCCTGAACTGGTCGGCGAAGTGTTGCGCATCATGCAACAACTGGCGGAA
-GAAGGCAAAACGATGGTGGTGGTCACGCATGAAATGGGCTTCGCTCGCCATGTCTCTTCG
-CACGTTATTTTTCTGCATCAGGGGAAAATTGAAGAAGAGGGTGATCCGGAGCAGGTGTTC
-GGCAATCCGCAAAGCCCGCGTTTACAGCAATTCCTGAAAGGCTCGCTGAAATAA
->GKEGNCBE_00006 tRNA (guanine-N(1)-)-methyltransferase
-ATGTTCCGCGCAATTACCGATTACGGGGTAACTGGCCGGGCAGTAAAAAAAGGCCTGCTG
-AACATCCAAAGCTGGAGTCCTCGCGACTTCGCGCATGACCGGCACCGTACCGTGGACGAC
-CGTCCTTACGGCGGCGGACCGGGGATGTTAATGATGGTGCAACCCTTGCGGGACGCCATT
-CACGCAGCAAAAGCCGCGGCAGGTGAAGGCGCTAAAGTGATTTATCTGTCGCCTCAGGGA
-CGCAAGCTTGATCAAGCGGGCGTTAGCGAGCTGGCCACGAATCAGAAGCTTATTCTGGTG
-TGTGGTCGCTACGAAGGCGTAGATGAGCGCGTAATTCAGACCGAAATTGACGAAGAATGG
-TCAATTGGCGATTACGTTCTCAGCGGTGGCGAACTACCGGCAATGACGCTGATTGACTCC
-GTCGCCCGGTTTATACCGGGGGTTCTGGGGCATGAGGCATCAGCAATCGAAGATTCGTTT
-GCTGATGGGTTGCTGGATTGTCCGCACTATACGCGCCCTGAAGTGTTAGAGGGGATGGAA
-GTACCGCCAGTATTGCTGTCGGGAAACCATGCTGAGATACGTCGCTGGCGTTTGAAACAG
-TCGCTGGGCCGAACCTGGCTTAGAAGACCTGAACTTCTGGAAAACCTGGCTCTGACTGAA
-GAGCAAGCAAGGTTGCTGGCGGAGTTCAAAACAGAACACGCACAACAGCAGCATAAACAT
-GATGGGATGGCATAG
->GKEGNCBE_00007 tRNA (guanine-N(1)-)-methyltransferase
-ATGATGGGATGGCATAGCCGTCATATGGGCTCTCAGAGGAGACGCGCTAATGCGCAGTAC
-GTGTTTATTGGCATAGTTAGCCTGTTTCCTGAAATGTTCCGCGCAATTACCGATTACGGG
-GTAACTGGCCGGGCAGTAAAAAAAGGCCTGCTGAACATCCAAAGCTGGAGTCCTCGCGAC
-TTCGCGCATGACCGGCACCGTACCGTGGACGACCGTCCTTACGGCGGCGGACCGGGGATG
-TTAATGATGGTGCAACCCTTGCGGGACGCCATTCACGCAGCAAAAGCCGCGGCAGGTGAA
-GGCGCTAAAGTGATTTATCTGTCGCCTCAGGGACGCAAGCTTGATCAAGCGGGCGTTAGC
-GAGCTGGCCACGAATCAGAAGCTTATTCTGGTGTGTGGTCGCTACGAAGGCGTAGATGAG
-CGCGTAATTCAGACCGAAATTGACGAAGAATGGTCAATTGGCGATTACGTTCTCAGCGGT
-GGCGAACTACCGGCAATGACGCTGATTGACTCCGTCGCCCGGTTTATACCGGGGGTTCTG
-GGGCATGAGGCATCAGCAATCGAAGATTCGTTTGCTGATGGGTTGCTGGATTGTCCGCAC
-TATACGCGCCCTGAAGTGTTAGAGGGGATGGAAGTACCGCCAGTATTGCTGTCGGGAAAC
-CATGCTGAGATACGTCGCTGGCGTTTGAAACAGTCGCTGGGCCGAACCTGGCTTAGAAGA
-CCTGAACTTCTGGAAAACCTGGCTCTGACTGAAGAGCAAGCAAGGTTGCTGGCGGAGTTC
-AAAACAGAACACGCACAACAGCAGCATAAACATGATGGGATGGCATAG
->GKEGNCBE_00008 hypothetical protein
-ATGAAGTTTGTTGCGCCCGAACAGGCACCGGAACAGGCGGAGGTCATCAAAAATACGCCG
-TTCTGGCCTGATGTGGACCTGTCGGAATTTCGCAGTGTGATGCGCACTGACGGCACGGTG
-ACGCAGCCGCGTTTAAAGCAGGTCGTGCTGACGGCGATCTCTGAGGTTAACGCTGAGCTG
-TACGACTTCCGCAACCGTCAGCAGATGCTGGGCTGGCGGACACTTGCTGAGGTTCCCGCA
-GAAATGCTGGACGGTAAAAGCGAGCGTATCCGGCACTACCACAACGCTGTTTTTTGCTGG
-GCGCGCGCTGTGCTTAATGAGCGTTATCAGGACTATGACGCCACGGCGTCAGGCGTGAAG
-CGAGGGGAGGAGCTGGCGGAGGCCAGCGGCGATCTGTGGCGTGATGCCCGCTGGGCCATC
-AGCCGGGTGCAGGATGTACCGCACTGTACGGTGGAGCTTATCTGA
->GKEGNCBE_00009 hypothetical protein
-ATGGCCGGGTTGCACGCGCCATATGCATATAGCGCGCATCATGCGGTGAATTTCTGTTCT
-GAGTATAAACGTGGCTTTGTATTGGGTTTTACACACCGTATGTTCGAAAAGACCGGCGAT
-CGTCAACTTAGCGCGTGGGAGGCTGGAATTCTGACGCGTCGCTATGGTCTGGATAAAGAA
-ATGGTGATGGATTTCTTTAAAGAGAATCATTCCGGGATGGCGGTTCGCTTCTTTATGGCC
-GGTTATCGACTCGAAGGTTGA
->GKEGNCBE_00010 hypothetical protein
-ATGTCTACGCTTCTCTATTTGCACGGATTCAACAGTTCCCCTCGCTCGGCAAAAGCGTGC
-CAGCTAAAAAACTGGCTGGCGGAGCGTCATCCGCATGTTGAGATGATCGTCCCTCAGCTG
-CCGCCGTATCCTGCCGATGCGGCGGAGTTGCTGGAATCTCTCGTGCTTGAGCATGGCGGT
-GCGCCATTAGGGCTGGTAGGATCGTCGCTGGGTGGTTATTACGCCACCTGGCTGTCGCAA
-TGTTTTATGCTGCCGGCTGTGGTGGTGAATCCCGCCGTGCGGCCCTTTGAATTACTGACC
-GACTATCTCGGTCAGAACGAGAACCCCTACACCGGGCAGCAATATGTGCTAGAGTCTCGC
-CATATTTATGATCTTAAAGTCATGCAGATTGACCCGCTGGAAGCGCCGGACCTGATCTGG
-CTACTGCAACAGACGGGCGATGAAGTGCTGTATTACCGCCAGGCGGTGGCATATTACGCC
-TCCTGCCGTCAGACAGTGACCGAGGGTGGTAATCACGCATTCACGGGCTTCGAAGATTAT
-TTCAACCAGATTGTCGATTTTCTTGGACTGCACAGTTGCTGA
->GKEGNCBE_00011 C4-dicarboxylate TRAP transporter large permease protein DctM
-ATGATTGACCCTATTTTTGCGTCCTGTACGCTAATTGCCGTCTTTGTTGTTTTACTGGCC
-ATGGGCGCGCCTATCGGGATCTGCATCGTTATCGCCTCTTTCAGCACCATGATGCTGGTA
-CTGCCTTTCGATATTTCGATGTTCGCCACCGCGCAAAAAATGTTCTCCAGCCTGGACAGT
-TTTGCCTTGCTGGCCGTGCCGTTCTTCGTTTTGTCCGGGGTGATCATGAATAGCGGGGGA
-ATTGCCGCCCGGCTGGTCAATTTTGCCAAACTGTTTACTGGCAAACTGCCCGGCTCGCTC
-TCTTATACCAACATCGTCGGCAATATGATGTTCGGTGCAATTTCCGGATCGGCGATTGCC
-GCCTCAACCTCCATCGGCGGCGTGATGGTGCCGATGAGCGCGCGCGAAGGTTACGATCGC
-GGCTTTGCGGCCGCGGTGAATATCGCCTCCGCGCCGACGGGAATGTTAATTCCGCCCACC
-ACGGCTTTTATCCTTTACGCGCTGGCAAGCGGGGGAACATCGATTGCCGCTCTGTTCGCC
-GGCGGTCTGGTCGCGGGAGTGCTGTGGGGCGTTGGCTGTATGCTGGTCACGCTGGTGGTC
-GCTAAGCGTCGAAATTATCGGGTTTTCTTCACCGTCCAAAAAGGTATGGCGCTAAAAGTT
-GCCGTTGAGGCCATTCCCAGCCTGCTGCTGATCGTGATTATTGTCGGCGGCATTGTGCAG
-GGGATTTTCACCGCCATTGAAGCCTCCGCGATTGCCGTGGTGTATACGTTATTGCTGACG
-ATGGTGTTTTACCGCACGCTGAAAATTAAGGATTTGCCTTCGATTTTGCTCCAGACAGTG
-GTAATGACCGGGGTCATCATGTTCCTGCTGGCAACCTCTTCGGCGATGTCCTTCTCGATG
-TCGATCACCAATATTCCTGCGGCGCTGAGCGATATGATCCTCGGTATTTCCGCCAATAAA
-CTGGTTATCCTGTTAGTCATTACCGTCTTTTTGTTGATTATCGGCGCATTTATGGATATT
-GGTCCGGCCATTCTGATTTTTACCCCGATTCTGCTGCCAATCATGGCTAAACTGGGCGTC
-GATCCGGTGCATTTCGGCATTATCATGATCTATAACCTGGCGATTGGCACCATTACGCCG
-CCAGTTGGCAGTGGTTTATATGTCGGGGCGAGCGTCGGTAAGGTCAAAGTTGAGGAAGTG
-ATTAAACCGTTGCTGCCTTTTTACGGCGCGATTATCGGCGTTCTGTTATTAATTACCTAC
-ATTCCGGAAATCACACTGTTCTTACCCCGTCTACTGGGCATCATGTAA
diff --git a/Examples/2-res-Annotate-prokka/tmp_files/genome1.fst_prokka-split5N.fna-prokkaRes/EXAM.1219.00001.fna b/Examples/2-res-Annotate-prokka/tmp_files/genome1.fst_prokka-split5N.fna-prokkaRes/EXAM.1219.00001.fna
deleted file mode 100644
index 325b3340782ba0db58b1693fab267c634919957a..0000000000000000000000000000000000000000
--- a/Examples/2-res-Annotate-prokka/tmp_files/genome1.fst_prokka-split5N.fna-prokkaRes/EXAM.1219.00001.fna
+++ /dev/null
@@ -1,167 +0,0 @@
->genome1_1
-ATGTGTAAAAGCCGGAGGGGTTATCTTTTCCCGGCTTTTTATTATCAATTACTCATTAAC
-TCCTGTTCCGTTCTTTTGCGTTTAATCACCGGAATATCTCCGGTATTGTTCAGCGCCCCG
-GAAATGTTTTTAACCACTGTTCTGCACTCCGTTTATTAAACGCGCTCAGCGCGCGCTCAT
-ATATCGCGCGCGCGCGCGCGCATATATATATAATGAGTGAGGCTGAAGCCCGCCCGACTA
-ACTTTATTCGTCAGATTATTGATGAAGATCTGGCGAGTGGTAAACATACCACTGTCCATA
-CCCGTTTTCCGCCGGAGCCGAATGGCTATCTGCATATCGGCCACGCGAAATCTATCTGCC
-TGAACTTTGGCATCGCGCAAGATTATCAGGGCCAGTGCAACCTGCGTTTCGATGACACCA
-ACCCGGTAAAAGAAGATATCGAGTACGTTGATTCGATCAAAAACGACGTCGAGTGGTTAG
-GCTTTCACTGGTCTGGCGATATTCGCTACTCCTCCGATTACTTTGACCAACTGCACGCCT
-ATGCGGTCGAGCTAATCAATAAAGGCCTGGCCTATGTTGATGAGCTGACGCCGGAGCAGA
-TCCGTGAATACCGCGGTACGCTGACCGCGCCGGGTAAAAACAGCCCGTTCCGCGATCGCA
-GCGTCGAAGAGAACCTCGCGCTATTTGAAAAAATGCGTACCGGCGGTTTTGAAGAGGGTA
-AAGCCTGTCTGCGCGCTAAAATCGACATGGCGTCGCCGTTTATCGTGATGCGCGATCCGG
-TGCTGTATCGCATTAAATTCGCCGAGCATCATCAGACTGGCAACAAGTGGTGCATCTATC
-CGATGTACGACTTTACTCACTGCATCAGCGATGCGCTGGAAGGCATTACTCATTCTCTGT
-GTACGCTGGAGTTCCAGGATAACCGTCGTCTGTACGACTGGGTGCTGGACAACATCACCA
-TTCCGGTTCACCCGCGCCAGTACGAATTCTCGCGCCTGAATCTGGAATACACCGTGATGT
-CCAAGCGTAAGCTGAACCTGCTGGTGACCGACAAACACGTCGAAGGTTGGGACGATCCGC
-GTATGCCGACTATTTCCGGTCTGCGCCGTCGCGGCTATACCGCGGCTTCTATTCGTGAGT
-TCTGCAAACGCATCGGCGTCACCAAGCAGGACAACACTATTGAGATGGCGTCGCTGGAAT
-CCTGCATTCGCGAAGATCTGAACGAAAACGCGCCGCGCGCGATGGCGGTAATCGATCCGG
-TAAAACTGGTTATCGAAAATTACCCGCAGGGTGAGAGCGAAATGGTTACCATGCCTAACC
-ATCCGAATAAACCGGAGATGGGCAGCCGTGAAGTGCCGTTTAGCGGTGAGATCTGGATCG
-ATCGCGCAGATTTCCGCGAAGAAGCGAACAAACAGTACAAACGTCTGGTGATGGGCAAAG
-AAGTGCGTCTGCGTAATGCCTACGTCATTAAAGCGGAGCGCGTAGAGAAGGATGCCGAAG
-GGAATATCACCACCATCTTCTGTACCTATGATGCTGATACGCTGAGTAAAGATCCGGCTG
-ACGGGCGTAAAGTGAAAGGCGTAATCCACTGGGTTAGCGCAGCACATGCGCTGCCGATTG
-AAATTCGTCTCTACGACCGTCTGTTCAGCGTGCCGAATCCGGGCGCCGCGGAGGACTTCC
-TGTCTGTTATCAACCCCGAATCATTAGTGATTAAGCAGGGGTATGGCGAGCCGTCGCTGA
-AAGCGGCGGTAGCAGGAAAAGCTTTCCAGTTTGAACGTGAAGGCTACTTCTGCCTCGACA
-GCCGCTATGCAACGGCCGATAAGCTGGTCTTTAACCGCACCGTGGGCCTGCGTGATACCT
-GGGCGAAAGCGGGCGAGTAACGCGCATAGGCGGCCTTCAAGGAGGCGCTAGGCGAATGAA
-AGCGCTACTGTGGCTGGTGGGTCTCGCGTTGCTGTTAACAGGCTGCGCGAGCGAAAAAGG
-AATTATCGATAAAGAGGGATATCAGCTTGATACCCGACATCGGGCGCAGGCGGCCTATCC
-GCGCATTAAAGTCCTGGTGATTCACTATACGGCGGAAAACTTTGACGTTTCGCTGGCGAC
-GTTAACGGGTCGCAACGTCAGTTCGCATTACCTGATTCCCGCAACCCCGCCATTATATGG
-CGGTAAACCGCGCATCTGGCAACTGGTGCCGGAACAGGATCAGGCCTGGCATGCGGGCGT
-CAGTTTCTGGCGAGGCGCCACGCGTCTCAATGATACGTCTATTGGCATTGAGCTGGAAAA
-TCGTGGTTGGCGAATGTCCGGCGGGGTGAAATCTTTCGCGCCGTTTGAATCCGCGCAAAT
-TCAGGCATTGATTCCGTTAGCGAAGGATATTATCGCGCGCTATAACATCAAACCGCAGAA
-TGTGGTGGCCCATGCGGATATCGCGCCGCAGCGTAAAGACGATCCCGGCCCGCGCTTCCC
-GTGGCGCGAGCTGGCGGCGCAGGGGATTAGCGCCTGGCCTGACGCCCAGCGTGTGGCGTT
-TTATCTGGCTGGACGCGCGCCGTATACGCCAGTCGATACCGCAACGGTGCTTGCGTTACT
-CTCGCGCTATGGCTATGAAGTCAAAGCCGATATGACGGCACGCGAGCAGCAGCGGGTGAT
-TATGGCGTTCCAGATGCACTTCCGTCCGGCGCAATGGAACGGTATCGCAGATGCCGAAAC
-GCAGGCGATTGCCGAAGCATTACTGGAGAAGTACGGCCAGGATTAACGCGATAGGCGCGC
-GAGATTACGCGCGCAGTATCGCGC
->genome1_2
-CGCGCATAGCGCGCAATGCCGCACTTTATTGCTGAATGTACTGAAAATATTCGCGAGCAG
-GCTGATTTACCCGGCCTGTTCAGCAAGGTAAACGAGGCGCTGGCCGCCAGCGGGATTTTC
-CCCATCGGCGGTATCCGCAGTCGCGCCCACTGGCTGGATACCTGGCAGATGGCTGACGGT
-AAGCATGATTACGCGTTTGTGCATATGACGCTGAAAATCGGCGCCGGGCGCAGCCTGGAG
-AGCCGTCAGGAAGTTGGCGAAATGCTGTTTGGGCTGATTAAAGCCCACTTCGCCGACCTG
-ATGGAGAACCGCTATCTGGCGCTGTCGTTTGAGATTGCCGAGCTACATCCGACGCTCAAT
-TACAAACAAAACAACGTACACGCGTTATTTAAATAGCCGATATGAGGCGCGGCGCTATAA
-GGCGCTCATGAGCATGCCCGCGACTAAATTCTCCCGACGTACCCTCCTGACGGCAGGTTC
-TGCGCTTGCTGTTCTTCCTTTTCTGCGCGCCTTGCCGGTACAGGCGCGTGAACCTCGCGA
-GACCGTCGATATTAAGGATTATCCGGCGGATGACGGTATCGCCTCGTTCAAACAGGCCTT
-CGCCGACGGACAGACCGTGGTCGTACCGCCAGGATGGGTGTGTGAAAATATCAATGCGGC
-GATAACGATTCCGGCGGGAAAAACGCTGCGGGTACAGGGCGCGGTGCGTGGGAATGGCCG
-GGGACGGTTTATTTTGCAGGACGGGTGTCAGGTGGTGGGGGAGCAGGGCGGCAGTCTGCA
-CAATGTGACGCTGGATGTTCGCGGGTCGGACTGTGTGATTAAAGGCGTGGCGATGAGCGG
-CTTTGGCCCCGTCGCGCAAATTTTCATCGGTGGTAAGGAACCGCAGGTGATGCGTAATCT
-CATTATCGATGACATCACCGTTACCCACGCCAACTACGCCATTCTCCGCCAGGGATTTCA
-TAACCAAATGGATGGCGCGCGGATTACGCATAGCCGCTTTAGCGATTTACAGGGGGACGC
-CATTGAGTGGAATGTCGCGATTCACGACCGCGACATCCTGATTTCCGATCATGTCATCGA
-ACGCATTAATTGTACCAATGGCAAAATCAACTGGGGGATCGGCATCGGGCTGGCGGGTAG
-CACCTATGACAACAGTTATCCTGAAGACCAGGCAGTAAAAAACTTTGTGGTGGCCAATAT
-TACCGGATCTGATTGCCGACAGCTTGTGCACGTAGAAAATGGCAAACATTTCGTCATTCG
-CAATGTCAAAGCCAAAAACATCACGCCCGGTTTCAGTAAAAATGCGGGTATTGATAACGC
-AACGATCGCAATTTATGGCTGTGATAATTTCGTCATTGATAATATTGATATGACGAATAG
-TGCCGGGATGCTCATCGGCTATGGCGTCGTTAAAGGAAAATACCTGTCAATTCCGCAAAA
-CTTTAAATTAAACGCTATTCGGTTGGATAATCGCCAGGTTGCTTATAAATTACGCGGCAT
-TCAAATTTCCTCCGGCAACACCCCCTCTTTTGTCGCCATCACCAATGTACGGATGACGCG
-TGCTACGCTGGAACTGCATAATCAACCGCAGCACCTCTTTCTGCGCAATATCAACGTGAT
-GCAAACTTCAGCGATTGGCCCGGCGTTAAAAATGCATTTCGATTTGCGTAAAGATGTACG
-TGGTCAATTTATGGCCCGCCAGGACACGCTGCTTTCCCTCGCTAATGTTCATGCCATCAA
-TGAAAACGGGCAGAGTTCCGTGGATATCGACAGGATTAATCACCAAACCGTGAATGTCGA
-AGCAGTGAATTTTTCGCTGCCGAAGCGGGGAGGGTAACGAATTCCGCGGCATATAGCGGC
-GCGATAGCATGTCAGAAAATAAATTACACGTTATCGATTTGCACAAACGCTACGGCGGTC
-ATGAAGTGCTGAAAGGGGTATCGCTGCAGGCCCGCGCCGGAGATGTGATTAGCATCATCG
-GCTCGTCCGGCTCCGGTAAAAGCACTTTTTTGCGCTGTATTAACTTCCTCGAAAAACCGA
-GCGAAGGCGCGATTATCGTGAACGGTCAGAACATTAATCTGGTGCGCGACAAAGATGGGC
-AGCTCAAAGTGGCGGATAAAAATCAGCTACGCTTGTTGCGTACCCGCCTGACGATGGTGT
-TTCAGCACTTCAACCTCTGGAGCCACATGACGGTGCTGGAAAATGTGATGGAAGCGCCGA
-TTCAGGTACTGGGATTAAGCAAGCACGACGCGCGCGAGCGGGCGTTGAAATATCTGGCGA
-AGGTGGGGATTGATGAGCGCGCTCAGGGCAAATATCCCGTCCATCTCTCCGGCGGCCAAC
-AGCAGCGCGTTTCTATTGCGCGCGCGCTGGCGATGGAACCTGACGTTTTACTGTTCGATG
-AACCCACATCGGCGCTCGATCCTGAACTGGTCGGCGAAGTGTTGCGCATCATGCAACAAC
-TGGCGGAAGAAGGCAAAACGATGGTGGTGGTCACGCATGAAATGGGCTTCGCTCGCCATG
-TCTCTTCGCACGTTATTTTTCTGCATCAGGGGAAAATTGAAGAAGAGGGTGATCCGGAGC
-AGGTGTTCGGCAATCCGCAAAGCCCGCGTTTACAGCAATTCCTGAAAGGCTCGCTGAAAT
-AACGCTCAGAGGCGCGCGCGCGCTATATACGCGCAGTGTTTATTGGCATAGTTAGCCTGT
-TTCCTGAAATGTTCCGCGCAATTACCGATTACGGGGTAACTGGCCGGGCAGTAAAAAAAG
-GCCTGCTGAACATCCAAAGCTGGAGTCCTCGCGACTTCGCGCATGACCGGCACCGTACCG
-TGGACGACCGTCCTTACGGCGGCGGACCGGGGATGTTAATGATGGTGCAACCCTTGCGGG
-ACGCCATTCACGCAGCAAAAGCCGCGGCAGGTGAAGGCGCTAAAGTGATTTATCTGTCGC
-CTCAGGGACGCAAGCTTGATCAAGCGGGCGTTAGCGAGCTGGCCACGAATCAGAAGCTTA
-TTCTGGTGTGTGGTCGCTACGAAGGCGTAGATGAGCGCGTAATTCAGACCGAAATTGACG
-AAGAATGGTCAATTGGCGATTACGTTCTCAGCGGTGGCGAACTACCGGCAATGACGCTGA
-TTGACTCCGTCGCCCGGTTTATACCGGGGGTTCTGGGGCATGAGGCATCAGCAATCGAAG
-ATTCGTTTGCTGATGGGTTGCTGGATTGTCCGCACTATACGCGCCCTGAAGTGTTAGAGG
-GGATGGAAGTACCGCCAGTATTGCTGTCGGGAAACCATGCTGAGATACGTCGCTGGCGTT
-TGAAACAGTCGCTGGGCCGAACCTGGCTTAGAAGACCTGAACTTCTGGAAAACCTGGCTC
-TGACTGAAGAGCAAGCAAGGTTGCTGGCGGAGTTCAAAACAGAACACGCACAACAGCAGC
-ATAAACATGATGGGATGGCATAGCCGTCATATGGGCTCTCAGAGGAGACGCGCTAATGCG
-CAGTACGTGTTTATTGGCATAGTTAGCCTGTTTCCTGAAATGTTCCGCGCAATTACCGAT
-TACGGGGTAACTGGCCGGGCAGTAAAAAAAGGCCTGCTGAACATCCAAAGCTGGAGTCCT
-CGCGACTTCGCGCATGACCGGCACCGTACCGTGGACGACCGTCCTTACGGCGGCGGACCG
-GGGATGTTAATGATGGTGCAACCCTTGCGGGACGCCATTCACGCAGCAAAAGCCGCGGCA
-GGTGAAGGCGCTAAAGTGATTTATCTGTCGCCTCAGGGACGCAAGCTTGATCAAGCGGGC
-GTTAGCGAGCTGGCCACGAATCAGAAGCTTATTCTGGTGTGTGGTCGCTACGAAGGCGTA
-GATGAGCGCGTAATTCAGACCGAAATTGACGAAGAATGGTCAATTGGCGATTACGTTCTC
-AGCGGTGGCGAACTACCGGCAATGACGCTGATTGACTCCGTCGCCCGGTTTATACCGGGG
-GTTCTGGGGCATGAGGCATCAGCAATCGAAGATTCGTTTGCTGATGGGTTGCTGGATTGT
-CCGCACTATACGCGCCCTGAAGTGTTAGAGGGGATGGAAGTACCGCCAGTATTGCTGTCG
-GGAAACCATGCTGAGATACGTCGCTGGCGTTTGAAACAGTCGCTGGGCCGAACCTGGCTT
-AGAAGACCTGAACTTCTGGAAAACCTGGCTCTGACTGAAGAGCAAGCAAGGTTGCTGGCG
-GAGTTCAAAACAGAACACGCACAACAGCAGCATAAACATGATGGGATGGCATAGCGCATA
-CGCGCGCGATATATATTCGCGCAGAGGCGCGCATAGCGATGAAGTTTGTTGCGCCCGAAC
-AGGCACCGGAACAGGCGGAGGTCATCAAAAATACGCCGTTCTGGCCTGATGTGGACCTGT
-CGGAATTTCGCAGTGTGATGCGCACTGACGGCACGGTGACGCAGCCGCGTTTAAAGCAGG
-TCGTGCTGACGGCGATCTCTGAGGTTAACGCTGAGCTGTACGACTTCCGCAACCGTCAGC
-AGATGCTGGGCTGGCGGACACTTGCTGAGGTTCCCGCAGAAATGCTGGACGGTAAAAGCG
-AGCGTATCCGGCACTACCACAACGCTGTTTTTTGCTGGGCGCGCGCTGTGCTTAATGAGC
-GTTATCAGGACTATGACGCCACGGCGTCAGGCGTGAAGCGAGGGGAGGAGCTGGCGGAGG
-CCAGCGGCGATCTGTGGCGTGATGCCCGCTGGGCCATCAGCCGGGTGCAGGATGTACCGC
-ACTGTACGGTGGAGCTTATCTGAACGGCTAGCGCGTAGCGGCAGTCTCGGATGAATAATC
-ATTTTGGGAAAGGGTTAATGGCCGGGTTGCACGCGCCATATGCATATAGCGCGCATCATG
-CGGTGAATTTCTGTTCTGAGTATAAACGTGGCTTTGTATTGGGTTTTACACACCGTATGT
-TCGAAAAGACCGGCGATCGTCAACTTAGCGCGTGGGAGGCTGGAATTCTGACGCGTCGCT
-ATGGTCTGGATAAAGAAATGGTGATGGATTTCTTTAAAGAGAATCATTCCGGGATGGCGG
-TTCGCTTCTTTATGGCCGGTTATCGACTCGAAGGTTGACGATCGCGCGCAGGAGGAGAGC
-TCTCTTCTTCTAGAGCATGTCTACGCTTCTCTATTTGCACGGATTCAACAGTTCCCCTCG
-CTCGGCAAAAGCGTGCCAGCTAAAAAACTGGCTGGCGGAGCGTCATCCGCATGTTGAGAT
-GATCGTCCCTCAGCTGCCGCCGTATCCTGCCGATGCGGCGGAGTTGCTGGAATCTCTCGT
-GCTTGAGCATGGCGGTGCGCCATTAGGGCTGGTAGGATCGTCGCTGGGTGGTTATTACGC
-CACCTGGCTGTCGCAATGTTTTATGCTGCCGGCTGTGGTGGTGAATCCCGCCGTGCGGCC
-CTTTGAATTACTGACCGACTATCTCGGTCAGAACGAGAACCCCTACACCGGGCAGCAATA
-TGTGCTAGAGTCTCGCCATATTTATGATCTTAAAGTCATGCAGATTGACCCGCTGGAAGC
-GCCGGACCTGATCTGGCTACTGCAACAGACGGGCGATGAAGTGCTGTATTACCGCCAGGC
-GGTGGCATATTACGCCTCCTGCCGTCAGACAGTGACCGAGGGTGGTAATCACGCATTCAC
-GGGCTTCGAAGATTATTTCAACCAGATTGTCGATTTTCTTGGACTGCACAGTTGCTGACG
-GCTATGCGCGCGCTCGATGATTGACCCTATTTTTGCGTCCTGTACGCTAATTGCCGTCTT
-TGTTGTTTTACTGGCCATGGGCGCGCCTATCGGGATCTGCATCGTTATCGCCTCTTTCAG
-CACCATGATGCTGGTACTGCCTTTCGATATTTCGATGTTCGCCACCGCGCAAAAAATGTT
-CTCCAGCCTGGACAGTTTTGCCTTGCTGGCCGTGCCGTTCTTCGTTTTGTCCGGGGTGAT
-CATGAATAGCGGGGGAATTGCCGCCCGGCTGGTCAATTTTGCCAAACTGTTTACTGGCAA
-ACTGCCCGGCTCGCTCTCTTATACCAACATCGTCGGCAATATGATGTTCGGTGCAATTTC
-CGGATCGGCGATTGCCGCCTCAACCTCCATCGGCGGCGTGATGGTGCCGATGAGCGCGCG
-CGAAGGTTACGATCGCGGCTTTGCGGCCGCGGTGAATATCGCCTCCGCGCCGACGGGAAT
-GTTAATTCCGCCCACCACGGCTTTTATCCTTTACGCGCTGGCAAGCGGGGGAACATCGAT
-TGCCGCTCTGTTCGCCGGCGGTCTGGTCGCGGGAGTGCTGTGGGGCGTTGGCTGTATGCT
-GGTCACGCTGGTGGTCGCTAAGCGTCGAAATTATCGGGTTTTCTTCACCGTCCAAAAAGG
-TATGGCGCTAAAAGTTGCCGTTGAGGCCATTCCCAGCCTGCTGCTGATCGTGATTATTGT
-CGGCGGCATTGTGCAGGGGATTTTCACCGCCATTGAAGCCTCCGCGATTGCCGTGGTGTA
-TACGTTATTGCTGACGATGGTGTTTTACCGCACGCTGAAAATTAAGGATTTGCCTTCGAT
-TTTGCTCCAGACAGTGGTAATGACCGGGGTCATCATGTTCCTGCTGGCAACCTCTTCGGC
-GATGTCCTTCTCGATGTCGATCACCAATATTCCTGCGGCGCTGAGCGATATGATCCTCGG
-TATTTCCGCCAATAAACTGGTTATCCTGTTAGTCATTACCGTCTTTTTGTTGATTATCGG
-CGCATTTATGGATATTGGTCCGGCCATTCTGATTTTTACCCCGATTCTGCTGCCAATCAT
-GGCTAAACTGGGCGTCGATCCGGTGCATTTCGGCATTATCATGATCTATAACCTGGCGAT
-TGGCACCATTACGCCGCCAGTTGGCAGTGGTTTATATGTCGGGGCGAGCGTCGGTAAGGT
-CAAAGTTGAGGAAGTGATTAAACCGTTGCTGCCTTTTTACGGCGCGATTATCGGCGTTCT
-GTTATTAATTACCTACATTCCGGAAATCACACTGTTCTTACCCCGTCTACTGGGCATCAT
-GTAA
diff --git a/Examples/2-res-Annotate-prokka/tmp_files/genome1.fst_prokka-split5N.fna-prokkaRes/EXAM.1219.00001.fsa b/Examples/2-res-Annotate-prokka/tmp_files/genome1.fst_prokka-split5N.fna-prokkaRes/EXAM.1219.00001.fsa
deleted file mode 100644
index ca5e180abfba3f98289887814c4d89b20e9e1bb6..0000000000000000000000000000000000000000
--- a/Examples/2-res-Annotate-prokka/tmp_files/genome1.fst_prokka-split5N.fna-prokkaRes/EXAM.1219.00001.fsa
+++ /dev/null
@@ -1,167 +0,0 @@
->genome1_1 [gcode=11] [organism=Genus species] [strain=strain]
-ATGTGTAAAAGCCGGAGGGGTTATCTTTTCCCGGCTTTTTATTATCAATTACTCATTAAC
-TCCTGTTCCGTTCTTTTGCGTTTAATCACCGGAATATCTCCGGTATTGTTCAGCGCCCCG
-GAAATGTTTTTAACCACTGTTCTGCACTCCGTTTATTAAACGCGCTCAGCGCGCGCTCAT
-ATATCGCGCGCGCGCGCGCGCATATATATATAATGAGTGAGGCTGAAGCCCGCCCGACTA
-ACTTTATTCGTCAGATTATTGATGAAGATCTGGCGAGTGGTAAACATACCACTGTCCATA
-CCCGTTTTCCGCCGGAGCCGAATGGCTATCTGCATATCGGCCACGCGAAATCTATCTGCC
-TGAACTTTGGCATCGCGCAAGATTATCAGGGCCAGTGCAACCTGCGTTTCGATGACACCA
-ACCCGGTAAAAGAAGATATCGAGTACGTTGATTCGATCAAAAACGACGTCGAGTGGTTAG
-GCTTTCACTGGTCTGGCGATATTCGCTACTCCTCCGATTACTTTGACCAACTGCACGCCT
-ATGCGGTCGAGCTAATCAATAAAGGCCTGGCCTATGTTGATGAGCTGACGCCGGAGCAGA
-TCCGTGAATACCGCGGTACGCTGACCGCGCCGGGTAAAAACAGCCCGTTCCGCGATCGCA
-GCGTCGAAGAGAACCTCGCGCTATTTGAAAAAATGCGTACCGGCGGTTTTGAAGAGGGTA
-AAGCCTGTCTGCGCGCTAAAATCGACATGGCGTCGCCGTTTATCGTGATGCGCGATCCGG
-TGCTGTATCGCATTAAATTCGCCGAGCATCATCAGACTGGCAACAAGTGGTGCATCTATC
-CGATGTACGACTTTACTCACTGCATCAGCGATGCGCTGGAAGGCATTACTCATTCTCTGT
-GTACGCTGGAGTTCCAGGATAACCGTCGTCTGTACGACTGGGTGCTGGACAACATCACCA
-TTCCGGTTCACCCGCGCCAGTACGAATTCTCGCGCCTGAATCTGGAATACACCGTGATGT
-CCAAGCGTAAGCTGAACCTGCTGGTGACCGACAAACACGTCGAAGGTTGGGACGATCCGC
-GTATGCCGACTATTTCCGGTCTGCGCCGTCGCGGCTATACCGCGGCTTCTATTCGTGAGT
-TCTGCAAACGCATCGGCGTCACCAAGCAGGACAACACTATTGAGATGGCGTCGCTGGAAT
-CCTGCATTCGCGAAGATCTGAACGAAAACGCGCCGCGCGCGATGGCGGTAATCGATCCGG
-TAAAACTGGTTATCGAAAATTACCCGCAGGGTGAGAGCGAAATGGTTACCATGCCTAACC
-ATCCGAATAAACCGGAGATGGGCAGCCGTGAAGTGCCGTTTAGCGGTGAGATCTGGATCG
-ATCGCGCAGATTTCCGCGAAGAAGCGAACAAACAGTACAAACGTCTGGTGATGGGCAAAG
-AAGTGCGTCTGCGTAATGCCTACGTCATTAAAGCGGAGCGCGTAGAGAAGGATGCCGAAG
-GGAATATCACCACCATCTTCTGTACCTATGATGCTGATACGCTGAGTAAAGATCCGGCTG
-ACGGGCGTAAAGTGAAAGGCGTAATCCACTGGGTTAGCGCAGCACATGCGCTGCCGATTG
-AAATTCGTCTCTACGACCGTCTGTTCAGCGTGCCGAATCCGGGCGCCGCGGAGGACTTCC
-TGTCTGTTATCAACCCCGAATCATTAGTGATTAAGCAGGGGTATGGCGAGCCGTCGCTGA
-AAGCGGCGGTAGCAGGAAAAGCTTTCCAGTTTGAACGTGAAGGCTACTTCTGCCTCGACA
-GCCGCTATGCAACGGCCGATAAGCTGGTCTTTAACCGCACCGTGGGCCTGCGTGATACCT
-GGGCGAAAGCGGGCGAGTAACGCGCATAGGCGGCCTTCAAGGAGGCGCTAGGCGAATGAA
-AGCGCTACTGTGGCTGGTGGGTCTCGCGTTGCTGTTAACAGGCTGCGCGAGCGAAAAAGG
-AATTATCGATAAAGAGGGATATCAGCTTGATACCCGACATCGGGCGCAGGCGGCCTATCC
-GCGCATTAAAGTCCTGGTGATTCACTATACGGCGGAAAACTTTGACGTTTCGCTGGCGAC
-GTTAACGGGTCGCAACGTCAGTTCGCATTACCTGATTCCCGCAACCCCGCCATTATATGG
-CGGTAAACCGCGCATCTGGCAACTGGTGCCGGAACAGGATCAGGCCTGGCATGCGGGCGT
-CAGTTTCTGGCGAGGCGCCACGCGTCTCAATGATACGTCTATTGGCATTGAGCTGGAAAA
-TCGTGGTTGGCGAATGTCCGGCGGGGTGAAATCTTTCGCGCCGTTTGAATCCGCGCAAAT
-TCAGGCATTGATTCCGTTAGCGAAGGATATTATCGCGCGCTATAACATCAAACCGCAGAA
-TGTGGTGGCCCATGCGGATATCGCGCCGCAGCGTAAAGACGATCCCGGCCCGCGCTTCCC
-GTGGCGCGAGCTGGCGGCGCAGGGGATTAGCGCCTGGCCTGACGCCCAGCGTGTGGCGTT
-TTATCTGGCTGGACGCGCGCCGTATACGCCAGTCGATACCGCAACGGTGCTTGCGTTACT
-CTCGCGCTATGGCTATGAAGTCAAAGCCGATATGACGGCACGCGAGCAGCAGCGGGTGAT
-TATGGCGTTCCAGATGCACTTCCGTCCGGCGCAATGGAACGGTATCGCAGATGCCGAAAC
-GCAGGCGATTGCCGAAGCATTACTGGAGAAGTACGGCCAGGATTAACGCGATAGGCGCGC
-GAGATTACGCGCGCAGTATCGCGC
->genome1_2 [gcode=11] [organism=Genus species] [strain=strain]
-CGCGCATAGCGCGCAATGCCGCACTTTATTGCTGAATGTACTGAAAATATTCGCGAGCAG
-GCTGATTTACCCGGCCTGTTCAGCAAGGTAAACGAGGCGCTGGCCGCCAGCGGGATTTTC
-CCCATCGGCGGTATCCGCAGTCGCGCCCACTGGCTGGATACCTGGCAGATGGCTGACGGT
-AAGCATGATTACGCGTTTGTGCATATGACGCTGAAAATCGGCGCCGGGCGCAGCCTGGAG
-AGCCGTCAGGAAGTTGGCGAAATGCTGTTTGGGCTGATTAAAGCCCACTTCGCCGACCTG
-ATGGAGAACCGCTATCTGGCGCTGTCGTTTGAGATTGCCGAGCTACATCCGACGCTCAAT
-TACAAACAAAACAACGTACACGCGTTATTTAAATAGCCGATATGAGGCGCGGCGCTATAA
-GGCGCTCATGAGCATGCCCGCGACTAAATTCTCCCGACGTACCCTCCTGACGGCAGGTTC
-TGCGCTTGCTGTTCTTCCTTTTCTGCGCGCCTTGCCGGTACAGGCGCGTGAACCTCGCGA
-GACCGTCGATATTAAGGATTATCCGGCGGATGACGGTATCGCCTCGTTCAAACAGGCCTT
-CGCCGACGGACAGACCGTGGTCGTACCGCCAGGATGGGTGTGTGAAAATATCAATGCGGC
-GATAACGATTCCGGCGGGAAAAACGCTGCGGGTACAGGGCGCGGTGCGTGGGAATGGCCG
-GGGACGGTTTATTTTGCAGGACGGGTGTCAGGTGGTGGGGGAGCAGGGCGGCAGTCTGCA
-CAATGTGACGCTGGATGTTCGCGGGTCGGACTGTGTGATTAAAGGCGTGGCGATGAGCGG
-CTTTGGCCCCGTCGCGCAAATTTTCATCGGTGGTAAGGAACCGCAGGTGATGCGTAATCT
-CATTATCGATGACATCACCGTTACCCACGCCAACTACGCCATTCTCCGCCAGGGATTTCA
-TAACCAAATGGATGGCGCGCGGATTACGCATAGCCGCTTTAGCGATTTACAGGGGGACGC
-CATTGAGTGGAATGTCGCGATTCACGACCGCGACATCCTGATTTCCGATCATGTCATCGA
-ACGCATTAATTGTACCAATGGCAAAATCAACTGGGGGATCGGCATCGGGCTGGCGGGTAG
-CACCTATGACAACAGTTATCCTGAAGACCAGGCAGTAAAAAACTTTGTGGTGGCCAATAT
-TACCGGATCTGATTGCCGACAGCTTGTGCACGTAGAAAATGGCAAACATTTCGTCATTCG
-CAATGTCAAAGCCAAAAACATCACGCCCGGTTTCAGTAAAAATGCGGGTATTGATAACGC
-AACGATCGCAATTTATGGCTGTGATAATTTCGTCATTGATAATATTGATATGACGAATAG
-TGCCGGGATGCTCATCGGCTATGGCGTCGTTAAAGGAAAATACCTGTCAATTCCGCAAAA
-CTTTAAATTAAACGCTATTCGGTTGGATAATCGCCAGGTTGCTTATAAATTACGCGGCAT
-TCAAATTTCCTCCGGCAACACCCCCTCTTTTGTCGCCATCACCAATGTACGGATGACGCG
-TGCTACGCTGGAACTGCATAATCAACCGCAGCACCTCTTTCTGCGCAATATCAACGTGAT
-GCAAACTTCAGCGATTGGCCCGGCGTTAAAAATGCATTTCGATTTGCGTAAAGATGTACG
-TGGTCAATTTATGGCCCGCCAGGACACGCTGCTTTCCCTCGCTAATGTTCATGCCATCAA
-TGAAAACGGGCAGAGTTCCGTGGATATCGACAGGATTAATCACCAAACCGTGAATGTCGA
-AGCAGTGAATTTTTCGCTGCCGAAGCGGGGAGGGTAACGAATTCCGCGGCATATAGCGGC
-GCGATAGCATGTCAGAAAATAAATTACACGTTATCGATTTGCACAAACGCTACGGCGGTC
-ATGAAGTGCTGAAAGGGGTATCGCTGCAGGCCCGCGCCGGAGATGTGATTAGCATCATCG
-GCTCGTCCGGCTCCGGTAAAAGCACTTTTTTGCGCTGTATTAACTTCCTCGAAAAACCGA
-GCGAAGGCGCGATTATCGTGAACGGTCAGAACATTAATCTGGTGCGCGACAAAGATGGGC
-AGCTCAAAGTGGCGGATAAAAATCAGCTACGCTTGTTGCGTACCCGCCTGACGATGGTGT
-TTCAGCACTTCAACCTCTGGAGCCACATGACGGTGCTGGAAAATGTGATGGAAGCGCCGA
-TTCAGGTACTGGGATTAAGCAAGCACGACGCGCGCGAGCGGGCGTTGAAATATCTGGCGA
-AGGTGGGGATTGATGAGCGCGCTCAGGGCAAATATCCCGTCCATCTCTCCGGCGGCCAAC
-AGCAGCGCGTTTCTATTGCGCGCGCGCTGGCGATGGAACCTGACGTTTTACTGTTCGATG
-AACCCACATCGGCGCTCGATCCTGAACTGGTCGGCGAAGTGTTGCGCATCATGCAACAAC
-TGGCGGAAGAAGGCAAAACGATGGTGGTGGTCACGCATGAAATGGGCTTCGCTCGCCATG
-TCTCTTCGCACGTTATTTTTCTGCATCAGGGGAAAATTGAAGAAGAGGGTGATCCGGAGC
-AGGTGTTCGGCAATCCGCAAAGCCCGCGTTTACAGCAATTCCTGAAAGGCTCGCTGAAAT
-AACGCTCAGAGGCGCGCGCGCGCTATATACGCGCAGTGTTTATTGGCATAGTTAGCCTGT
-TTCCTGAAATGTTCCGCGCAATTACCGATTACGGGGTAACTGGCCGGGCAGTAAAAAAAG
-GCCTGCTGAACATCCAAAGCTGGAGTCCTCGCGACTTCGCGCATGACCGGCACCGTACCG
-TGGACGACCGTCCTTACGGCGGCGGACCGGGGATGTTAATGATGGTGCAACCCTTGCGGG
-ACGCCATTCACGCAGCAAAAGCCGCGGCAGGTGAAGGCGCTAAAGTGATTTATCTGTCGC
-CTCAGGGACGCAAGCTTGATCAAGCGGGCGTTAGCGAGCTGGCCACGAATCAGAAGCTTA
-TTCTGGTGTGTGGTCGCTACGAAGGCGTAGATGAGCGCGTAATTCAGACCGAAATTGACG
-AAGAATGGTCAATTGGCGATTACGTTCTCAGCGGTGGCGAACTACCGGCAATGACGCTGA
-TTGACTCCGTCGCCCGGTTTATACCGGGGGTTCTGGGGCATGAGGCATCAGCAATCGAAG
-ATTCGTTTGCTGATGGGTTGCTGGATTGTCCGCACTATACGCGCCCTGAAGTGTTAGAGG
-GGATGGAAGTACCGCCAGTATTGCTGTCGGGAAACCATGCTGAGATACGTCGCTGGCGTT
-TGAAACAGTCGCTGGGCCGAACCTGGCTTAGAAGACCTGAACTTCTGGAAAACCTGGCTC
-TGACTGAAGAGCAAGCAAGGTTGCTGGCGGAGTTCAAAACAGAACACGCACAACAGCAGC
-ATAAACATGATGGGATGGCATAGCCGTCATATGGGCTCTCAGAGGAGACGCGCTAATGCG
-CAGTACGTGTTTATTGGCATAGTTAGCCTGTTTCCTGAAATGTTCCGCGCAATTACCGAT
-TACGGGGTAACTGGCCGGGCAGTAAAAAAAGGCCTGCTGAACATCCAAAGCTGGAGTCCT
-CGCGACTTCGCGCATGACCGGCACCGTACCGTGGACGACCGTCCTTACGGCGGCGGACCG
-GGGATGTTAATGATGGTGCAACCCTTGCGGGACGCCATTCACGCAGCAAAAGCCGCGGCA
-GGTGAAGGCGCTAAAGTGATTTATCTGTCGCCTCAGGGACGCAAGCTTGATCAAGCGGGC
-GTTAGCGAGCTGGCCACGAATCAGAAGCTTATTCTGGTGTGTGGTCGCTACGAAGGCGTA
-GATGAGCGCGTAATTCAGACCGAAATTGACGAAGAATGGTCAATTGGCGATTACGTTCTC
-AGCGGTGGCGAACTACCGGCAATGACGCTGATTGACTCCGTCGCCCGGTTTATACCGGGG
-GTTCTGGGGCATGAGGCATCAGCAATCGAAGATTCGTTTGCTGATGGGTTGCTGGATTGT
-CCGCACTATACGCGCCCTGAAGTGTTAGAGGGGATGGAAGTACCGCCAGTATTGCTGTCG
-GGAAACCATGCTGAGATACGTCGCTGGCGTTTGAAACAGTCGCTGGGCCGAACCTGGCTT
-AGAAGACCTGAACTTCTGGAAAACCTGGCTCTGACTGAAGAGCAAGCAAGGTTGCTGGCG
-GAGTTCAAAACAGAACACGCACAACAGCAGCATAAACATGATGGGATGGCATAGCGCATA
-CGCGCGCGATATATATTCGCGCAGAGGCGCGCATAGCGATGAAGTTTGTTGCGCCCGAAC
-AGGCACCGGAACAGGCGGAGGTCATCAAAAATACGCCGTTCTGGCCTGATGTGGACCTGT
-CGGAATTTCGCAGTGTGATGCGCACTGACGGCACGGTGACGCAGCCGCGTTTAAAGCAGG
-TCGTGCTGACGGCGATCTCTGAGGTTAACGCTGAGCTGTACGACTTCCGCAACCGTCAGC
-AGATGCTGGGCTGGCGGACACTTGCTGAGGTTCCCGCAGAAATGCTGGACGGTAAAAGCG
-AGCGTATCCGGCACTACCACAACGCTGTTTTTTGCTGGGCGCGCGCTGTGCTTAATGAGC
-GTTATCAGGACTATGACGCCACGGCGTCAGGCGTGAAGCGAGGGGAGGAGCTGGCGGAGG
-CCAGCGGCGATCTGTGGCGTGATGCCCGCTGGGCCATCAGCCGGGTGCAGGATGTACCGC
-ACTGTACGGTGGAGCTTATCTGAACGGCTAGCGCGTAGCGGCAGTCTCGGATGAATAATC
-ATTTTGGGAAAGGGTTAATGGCCGGGTTGCACGCGCCATATGCATATAGCGCGCATCATG
-CGGTGAATTTCTGTTCTGAGTATAAACGTGGCTTTGTATTGGGTTTTACACACCGTATGT
-TCGAAAAGACCGGCGATCGTCAACTTAGCGCGTGGGAGGCTGGAATTCTGACGCGTCGCT
-ATGGTCTGGATAAAGAAATGGTGATGGATTTCTTTAAAGAGAATCATTCCGGGATGGCGG
-TTCGCTTCTTTATGGCCGGTTATCGACTCGAAGGTTGACGATCGCGCGCAGGAGGAGAGC
-TCTCTTCTTCTAGAGCATGTCTACGCTTCTCTATTTGCACGGATTCAACAGTTCCCCTCG
-CTCGGCAAAAGCGTGCCAGCTAAAAAACTGGCTGGCGGAGCGTCATCCGCATGTTGAGAT
-GATCGTCCCTCAGCTGCCGCCGTATCCTGCCGATGCGGCGGAGTTGCTGGAATCTCTCGT
-GCTTGAGCATGGCGGTGCGCCATTAGGGCTGGTAGGATCGTCGCTGGGTGGTTATTACGC
-CACCTGGCTGTCGCAATGTTTTATGCTGCCGGCTGTGGTGGTGAATCCCGCCGTGCGGCC
-CTTTGAATTACTGACCGACTATCTCGGTCAGAACGAGAACCCCTACACCGGGCAGCAATA
-TGTGCTAGAGTCTCGCCATATTTATGATCTTAAAGTCATGCAGATTGACCCGCTGGAAGC
-GCCGGACCTGATCTGGCTACTGCAACAGACGGGCGATGAAGTGCTGTATTACCGCCAGGC
-GGTGGCATATTACGCCTCCTGCCGTCAGACAGTGACCGAGGGTGGTAATCACGCATTCAC
-GGGCTTCGAAGATTATTTCAACCAGATTGTCGATTTTCTTGGACTGCACAGTTGCTGACG
-GCTATGCGCGCGCTCGATGATTGACCCTATTTTTGCGTCCTGTACGCTAATTGCCGTCTT
-TGTTGTTTTACTGGCCATGGGCGCGCCTATCGGGATCTGCATCGTTATCGCCTCTTTCAG
-CACCATGATGCTGGTACTGCCTTTCGATATTTCGATGTTCGCCACCGCGCAAAAAATGTT
-CTCCAGCCTGGACAGTTTTGCCTTGCTGGCCGTGCCGTTCTTCGTTTTGTCCGGGGTGAT
-CATGAATAGCGGGGGAATTGCCGCCCGGCTGGTCAATTTTGCCAAACTGTTTACTGGCAA
-ACTGCCCGGCTCGCTCTCTTATACCAACATCGTCGGCAATATGATGTTCGGTGCAATTTC
-CGGATCGGCGATTGCCGCCTCAACCTCCATCGGCGGCGTGATGGTGCCGATGAGCGCGCG
-CGAAGGTTACGATCGCGGCTTTGCGGCCGCGGTGAATATCGCCTCCGCGCCGACGGGAAT
-GTTAATTCCGCCCACCACGGCTTTTATCCTTTACGCGCTGGCAAGCGGGGGAACATCGAT
-TGCCGCTCTGTTCGCCGGCGGTCTGGTCGCGGGAGTGCTGTGGGGCGTTGGCTGTATGCT
-GGTCACGCTGGTGGTCGCTAAGCGTCGAAATTATCGGGTTTTCTTCACCGTCCAAAAAGG
-TATGGCGCTAAAAGTTGCCGTTGAGGCCATTCCCAGCCTGCTGCTGATCGTGATTATTGT
-CGGCGGCATTGTGCAGGGGATTTTCACCGCCATTGAAGCCTCCGCGATTGCCGTGGTGTA
-TACGTTATTGCTGACGATGGTGTTTTACCGCACGCTGAAAATTAAGGATTTGCCTTCGAT
-TTTGCTCCAGACAGTGGTAATGACCGGGGTCATCATGTTCCTGCTGGCAACCTCTTCGGC
-GATGTCCTTCTCGATGTCGATCACCAATATTCCTGCGGCGCTGAGCGATATGATCCTCGG
-TATTTCCGCCAATAAACTGGTTATCCTGTTAGTCATTACCGTCTTTTTGTTGATTATCGG
-CGCATTTATGGATATTGGTCCGGCCATTCTGATTTTTACCCCGATTCTGCTGCCAATCAT
-GGCTAAACTGGGCGTCGATCCGGTGCATTTCGGCATTATCATGATCTATAACCTGGCGAT
-TGGCACCATTACGCCGCCAGTTGGCAGTGGTTTATATGTCGGGGCGAGCGTCGGTAAGGT
-CAAAGTTGAGGAAGTGATTAAACCGTTGCTGCCTTTTTACGGCGCGATTATCGGCGTTCT
-GTTATTAATTACCTACATTCCGGAAATCACACTGTTCTTACCCCGTCTACTGGGCATCAT
-GTAA
diff --git a/Examples/2-res-Annotate-prokka/tmp_files/genome1.fst_prokka-split5N.fna-prokkaRes/EXAM.1219.00001.gbk b/Examples/2-res-Annotate-prokka/tmp_files/genome1.fst_prokka-split5N.fna-prokkaRes/EXAM.1219.00001.gbk
deleted file mode 100644
index d1e2048a35df5f0b5cb752ba35e3e95bfdfdb725..0000000000000000000000000000000000000000
--- a/Examples/2-res-Annotate-prokka/tmp_files/genome1.fst_prokka-split5N.fna-prokkaRes/EXAM.1219.00001.gbk
+++ /dev/null
@@ -1,352 +0,0 @@
-LOCUS       genome1_1               2784 bp    DNA     linear       09-DEC-2019
-DEFINITION  Genus species strain strain.
-ACCESSION   
-VERSION
-KEYWORDS    .
-SOURCE      Genus species
-  ORGANISM  Genus species
-            Unclassified.
-COMMENT     Annotated using prokka 1.14.5 from
-            https://github.com/tseemann/prokka.
-FEATURES             Location/Qualifiers
-     source          1..2784
-                     /organism="Genus species"
-                     /mol_type="genomic DNA"
-                     /strain="strain"
-     CDS             213..1880
-                     /gene="glnS"
-                     /locus_tag="GKEGNCBE_00001"
-                     /EC_number="6.1.1.18"
-                     /inference="ab initio prediction:Prodigal:002006"
-                     /inference="similar to AA sequence:UniProtKB:P00962"
-                     /codon_start=1
-                     /transl_table=11
-                     /product="Glutamine--tRNA ligase"
-                     /db_xref="COG:COG0008"
-                     /translation="MSEAEARPTNFIRQIIDEDLASGKHTTVHTRFPPEPNGYLHIGH
-                     AKSICLNFGIAQDYQGQCNLRFDDTNPVKEDIEYVDSIKNDVEWLGFHWSGDIRYSSD
-                     YFDQLHAYAVELINKGLAYVDELTPEQIREYRGTLTAPGKNSPFRDRSVEENLALFEK
-                     MRTGGFEEGKACLRAKIDMASPFIVMRDPVLYRIKFAEHHQTGNKWCIYPMYDFTHCI
-                     SDALEGITHSLCTLEFQDNRRLYDWVLDNITIPVHPRQYEFSRLNLEYTVMSKRKLNL
-                     LVTDKHVEGWDDPRMPTISGLRRRGYTAASIREFCKRIGVTKQDNTIEMASLESCIRE
-                     DLNENAPRAMAVIDPVKLVIENYPQGESEMVTMPNHPNKPEMGSREVPFSGEIWIDRA
-                     DFREEANKQYKRLVMGKEVRLRNAYVIKAERVEKDAEGNITTIFCTYDADTLSKDPAD
-                     GRKVKGVIHWVSAAHALPIEIRLYDRLFSVPNPGAAEDFLSVINPESLVIKQGYGEPS
-                     LKAAVAGKAFQFEREGYFCLDSRYATADKLVFNRTVGLRDTWAKAGE"
-     CDS             1916..2746
-                     /gene="amiD"
-                     /locus_tag="GKEGNCBE_00002"
-                     /EC_number="3.5.1.28"
-                     /inference="ab initio prediction:Prodigal:002006"
-                     /inference="similar to AA sequence:UniProtKB:P75820"
-                     /codon_start=1
-                     /transl_table=11
-                     /product="N-acetylmuramoyl-L-alanine amidase AmiD"
-                     /db_xref="COG:COG3023"
-                     /translation="MKALLWLVGLALLLTGCASEKGIIDKEGYQLDTRHRAQAAYPRI
-                     KVLVIHYTAENFDVSLATLTGRNVSSHYLIPATPPLYGGKPRIWQLVPEQDQAWHAGV
-                     SFWRGATRLNDTSIGIELENRGWRMSGGVKSFAPFESAQIQALIPLAKDIIARYNIKP
-                     QNVVAHADIAPQRKDDPGPRFPWRELAAQGISAWPDAQRVAFYLAGRAPYTPVDTATV
-                     LALLSRYGYEVKADMTAREQQRVIMAFQMHFRPAQWNGIADAETQAIAEALLEKYGQD
-                     "
-ORIGIN      
-        1 atgtgtaaaa gccggagggg ttatcttttc ccggcttttt attatcaatt actcattaac
-       61 tcctgttccg ttcttttgcg tttaatcacc ggaatatctc cggtattgtt cagcgccccg
-      121 gaaatgtttt taaccactgt tctgcactcc gtttattaaa cgcgctcagc gcgcgctcat
-      181 atatcgcgcg cgcgcgcgcg catatatata taatgagtga ggctgaagcc cgcccgacta
-      241 actttattcg tcagattatt gatgaagatc tggcgagtgg taaacatacc actgtccata
-      301 cccgttttcc gccggagccg aatggctatc tgcatatcgg ccacgcgaaa tctatctgcc
-      361 tgaactttgg catcgcgcaa gattatcagg gccagtgcaa cctgcgtttc gatgacacca
-      421 acccggtaaa agaagatatc gagtacgttg attcgatcaa aaacgacgtc gagtggttag
-      481 gctttcactg gtctggcgat attcgctact cctccgatta ctttgaccaa ctgcacgcct
-      541 atgcggtcga gctaatcaat aaaggcctgg cctatgttga tgagctgacg ccggagcaga
-      601 tccgtgaata ccgcggtacg ctgaccgcgc cgggtaaaaa cagcccgttc cgcgatcgca
-      661 gcgtcgaaga gaacctcgcg ctatttgaaa aaatgcgtac cggcggtttt gaagagggta
-      721 aagcctgtct gcgcgctaaa atcgacatgg cgtcgccgtt tatcgtgatg cgcgatccgg
-      781 tgctgtatcg cattaaattc gccgagcatc atcagactgg caacaagtgg tgcatctatc
-      841 cgatgtacga ctttactcac tgcatcagcg atgcgctgga aggcattact cattctctgt
-      901 gtacgctgga gttccaggat aaccgtcgtc tgtacgactg ggtgctggac aacatcacca
-      961 ttccggttca cccgcgccag tacgaattct cgcgcctgaa tctggaatac accgtgatgt
-     1021 ccaagcgtaa gctgaacctg ctggtgaccg acaaacacgt cgaaggttgg gacgatccgc
-     1081 gtatgccgac tatttccggt ctgcgccgtc gcggctatac cgcggcttct attcgtgagt
-     1141 tctgcaaacg catcggcgtc accaagcagg acaacactat tgagatggcg tcgctggaat
-     1201 cctgcattcg cgaagatctg aacgaaaacg cgccgcgcgc gatggcggta atcgatccgg
-     1261 taaaactggt tatcgaaaat tacccgcagg gtgagagcga aatggttacc atgcctaacc
-     1321 atccgaataa accggagatg ggcagccgtg aagtgccgtt tagcggtgag atctggatcg
-     1381 atcgcgcaga tttccgcgaa gaagcgaaca aacagtacaa acgtctggtg atgggcaaag
-     1441 aagtgcgtct gcgtaatgcc tacgtcatta aagcggagcg cgtagagaag gatgccgaag
-     1501 ggaatatcac caccatcttc tgtacctatg atgctgatac gctgagtaaa gatccggctg
-     1561 acgggcgtaa agtgaaaggc gtaatccact gggttagcgc agcacatgcg ctgccgattg
-     1621 aaattcgtct ctacgaccgt ctgttcagcg tgccgaatcc gggcgccgcg gaggacttcc
-     1681 tgtctgttat caaccccgaa tcattagtga ttaagcaggg gtatggcgag ccgtcgctga
-     1741 aagcggcggt agcaggaaaa gctttccagt ttgaacgtga aggctacttc tgcctcgaca
-     1801 gccgctatgc aacggccgat aagctggtct ttaaccgcac cgtgggcctg cgtgatacct
-     1861 gggcgaaagc gggcgagtaa cgcgcatagg cggccttcaa ggaggcgcta ggcgaatgaa
-     1921 agcgctactg tggctggtgg gtctcgcgtt gctgttaaca ggctgcgcga gcgaaaaagg
-     1981 aattatcgat aaagagggat atcagcttga tacccgacat cgggcgcagg cggcctatcc
-     2041 gcgcattaaa gtcctggtga ttcactatac ggcggaaaac tttgacgttt cgctggcgac
-     2101 gttaacgggt cgcaacgtca gttcgcatta cctgattccc gcaaccccgc cattatatgg
-     2161 cggtaaaccg cgcatctggc aactggtgcc ggaacaggat caggcctggc atgcgggcgt
-     2221 cagtttctgg cgaggcgcca cgcgtctcaa tgatacgtct attggcattg agctggaaaa
-     2281 tcgtggttgg cgaatgtccg gcggggtgaa atctttcgcg ccgtttgaat ccgcgcaaat
-     2341 tcaggcattg attccgttag cgaaggatat tatcgcgcgc tataacatca aaccgcagaa
-     2401 tgtggtggcc catgcggata tcgcgccgca gcgtaaagac gatcccggcc cgcgcttccc
-     2461 gtggcgcgag ctggcggcgc aggggattag cgcctggcct gacgcccagc gtgtggcgtt
-     2521 ttatctggct ggacgcgcgc cgtatacgcc agtcgatacc gcaacggtgc ttgcgttact
-     2581 ctcgcgctat ggctatgaag tcaaagccga tatgacggca cgcgagcagc agcgggtgat
-     2641 tatggcgttc cagatgcact tccgtccggc gcaatggaac ggtatcgcag atgccgaaac
-     2701 gcaggcgatt gccgaagcat tactggagaa gtacggccag gattaacgcg ataggcgcgc
-     2761 gagattacgc gcgcagtatc gcgc
-//
-LOCUS       genome1_2               7024 bp    DNA     linear       09-DEC-2019
-DEFINITION  Genus species strain strain.
-ACCESSION   
-VERSION
-KEYWORDS    .
-SOURCE      Genus species
-  ORGANISM  Genus species
-            Unclassified.
-COMMENT     Annotated using prokka 1.14.5 from
-            https://github.com/tseemann/prokka.
-FEATURES             Location/Qualifiers
-     source          1..7024
-                     /organism="Genus species"
-                     /mol_type="genomic DNA"
-                     /strain="strain"
-     CDS             16..396
-                     /gene="hpcD"
-                     /locus_tag="GKEGNCBE_00003"
-                     /EC_number="5.3.3.10"
-                     /inference="ab initio prediction:Prodigal:002006"
-                     /inference="similar to AA sequence:UniProtKB:Q05354"
-                     /codon_start=1
-                     /transl_table=11
-                     /product="5-carboxymethyl-2-hydroxymuconate
-                     Delta-isomerase"
-                     /translation="MPHFIAECTENIREQADLPGLFSKVNEALAASGIFPIGGIRSRA
-                     HWLDTWQMADGKHDYAFVHMTLKIGAGRSLESRQEVGEMLFGLIKAHFADLMENRYLA
-                     LSFEIAELHPTLNYKQNNVHALFK"
-     CDS             428..1837
-                     /locus_tag="GKEGNCBE_00004"
-                     /inference="ab initio prediction:Prodigal:002006"
-                     /codon_start=1
-                     /transl_table=11
-                     /product="hypothetical protein"
-                     /translation="MSMPATKFSRRTLLTAGSALAVLPFLRALPVQAREPRETVDIKD
-                     YPADDGIASFKQAFADGQTVVVPPGWVCENINAAITIPAGKTLRVQGAVRGNGRGRFI
-                     LQDGCQVVGEQGGSLHNVTLDVRGSDCVIKGVAMSGFGPVAQIFIGGKEPQVMRNLII
-                     DDITVTHANYAILRQGFHNQMDGARITHSRFSDLQGDAIEWNVAIHDRDILISDHVIE
-                     RINCTNGKINWGIGIGLAGSTYDNSYPEDQAVKNFVVANITGSDCRQLVHVENGKHFV
-                     IRNVKAKNITPGFSKNAGIDNATIAIYGCDNFVIDNIDMTNSAGMLIGYGVVKGKYLS
-                     IPQNFKLNAIRLDNRQVAYKLRGIQISSGNTPSFVAITNVRMTRATLELHNQPQHLFL
-                     RNINVMQTSAIGPALKMHFDLRKDVRGQFMARQDTLLSLANVHAINENGQSSVDIDRI
-                     NHQTVNVEAVNFSLPKRGG"
-     CDS             1869..2642
-                     /gene="hisP"
-                     /locus_tag="GKEGNCBE_00005"
-                     /inference="ab initio prediction:Prodigal:002006"
-                     /inference="similar to AA sequence:UniProtKB:P02915"
-                     /codon_start=1
-                     /transl_table=11
-                     /product="Histidine transport ATP-binding protein HisP"
-                     /db_xref="COG:COG4598"
-                     /translation="MSENKLHVIDLHKRYGGHEVLKGVSLQARAGDVISIIGSSGSGK
-                     STFLRCINFLEKPSEGAIIVNGQNINLVRDKDGQLKVADKNQLRLLRTRLTMVFQHFN
-                     LWSHMTVLENVMEAPIQVLGLSKHDARERALKYLAKVGIDERAQGKYPVHLSGGQQQR
-                     VSIARALAMEPDVLLFDEPTSALDPELVGEVLRIMQQLAEEGKTMVVVTHEMGFARHV
-                     SSHVIFLHQGKIEEEGDPEQVFGNPQSPRLQQFLKGSLK"
-     CDS             2709..3443
-                     /gene="trmD_1"
-                     /locus_tag="GKEGNCBE_00006"
-                     /EC_number="2.1.1.228"
-                     /inference="ab initio prediction:Prodigal:002006"
-                     /inference="similar to AA sequence:UniProtKB:P0A873"
-                     /codon_start=1
-                     /transl_table=11
-                     /product="tRNA (guanine-N(1)-)-methyltransferase"
-                     /db_xref="COG:COG0336"
-                     /translation="MFRAITDYGVTGRAVKKGLLNIQSWSPRDFAHDRHRTVDDRPYG
-                     GGPGMLMMVQPLRDAIHAAKAAAGEGAKVIYLSPQGRKLDQAGVSELATNQKLILVCG
-                     RYEGVDERVIQTEIDEEWSIGDYVLSGGELPAMTLIDSVARFIPGVLGHEASAIEDSF
-                     ADGLLDCPHYTRPEVLEGMEVPPVLLSGNHAEIRRWRLKQSLGRTWLRRPELLENLAL
-                     TEEQARLLAEFKTEHAQQQHKHDGMA"
-     CDS             3427..4254
-                     /gene="trmD_2"
-                     /locus_tag="GKEGNCBE_00007"
-                     /EC_number="2.1.1.228"
-                     /inference="ab initio prediction:Prodigal:002006"
-                     /inference="similar to AA sequence:UniProtKB:P0A873"
-                     /codon_start=1
-                     /transl_table=11
-                     /product="tRNA (guanine-N(1)-)-methyltransferase"
-                     /db_xref="COG:COG0336"
-                     /translation="MMGWHSRHMGSQRRRANAQYVFIGIVSLFPEMFRAITDYGVTGR
-                     AVKKGLLNIQSWSPRDFAHDRHRTVDDRPYGGGPGMLMMVQPLRDAIHAAKAAAGEGA
-                     KVIYLSPQGRKLDQAGVSELATNQKLILVCGRYEGVDERVIQTEIDEEWSIGDYVLSG
-                     GELPAMTLIDSVARFIPGVLGHEASAIEDSFADGLLDCPHYTRPEVLEGMEVPPVLLS
-                     GNHAEIRRWRLKQSLGRTWLRRPELLENLALTEEQARLLAEFKTEHAQQQHKHDGMA"
-     CDS             4299..4763
-                     /locus_tag="GKEGNCBE_00008"
-                     /inference="ab initio prediction:Prodigal:002006"
-                     /codon_start=1
-                     /transl_table=11
-                     /product="hypothetical protein"
-                     /translation="MKFVAPEQAPEQAEVIKNTPFWPDVDLSEFRSVMRTDGTVTQPR
-                     LKQVVLTAISEVNAELYDFRNRQQMLGWRTLAEVPAEMLDGKSERIRHYHNAVFCWAR
-                     AVLNERYQDYDATASGVKRGEELAEASGDLWRDARWAISRVQDVPHCTVELI"
-     CDS             4818..5078
-                     /locus_tag="GKEGNCBE_00009"
-                     /inference="ab initio prediction:Prodigal:002006"
-                     /codon_start=1
-                     /transl_table=11
-                     /product="hypothetical protein"
-                     /translation="MAGLHAPYAYSAHHAVNFCSEYKRGFVLGFTHRMFEKTGDRQLS
-                     AWEAGILTRRYGLDKEMVMDFFKENHSGMAVRFFMAGYRLEG"
-     CDS             5117..5698
-                     /locus_tag="GKEGNCBE_00010"
-                     /inference="ab initio prediction:Prodigal:002006"
-                     /codon_start=1
-                     /transl_table=11
-                     /product="hypothetical protein"
-                     /translation="MSTLLYLHGFNSSPRSAKACQLKNWLAERHPHVEMIVPQLPPYP
-                     ADAAELLESLVLEHGGAPLGLVGSSLGGYYATWLSQCFMLPAVVVNPAVRPFELLTDY
-                     LGQNENPYTGQQYVLESRHIYDLKVMQIDPLEAPDLIWLLQQTGDEVLYYRQAVAYYA
-                     SCRQTVTEGGNHAFTGFEDYFNQIVDFLGLHSC"
-     CDS             5717..7024
-                     /gene="dctM"
-                     /locus_tag="GKEGNCBE_00011"
-                     /inference="ab initio prediction:Prodigal:002006"
-                     /inference="similar to AA sequence:UniProtKB:O07838"
-                     /codon_start=1
-                     /transl_table=11
-                     /product="C4-dicarboxylate TRAP transporter large permease
-                     protein DctM"
-                     /db_xref="COG:COG1593"
-                     /translation="MIDPIFASCTLIAVFVVLLAMGAPIGICIVIASFSTMMLVLPFD
-                     ISMFATAQKMFSSLDSFALLAVPFFVLSGVIMNSGGIAARLVNFAKLFTGKLPGSLSY
-                     TNIVGNMMFGAISGSAIAASTSIGGVMVPMSAREGYDRGFAAAVNIASAPTGMLIPPT
-                     TAFILYALASGGTSIAALFAGGLVAGVLWGVGCMLVTLVVAKRRNYRVFFTVQKGMAL
-                     KVAVEAIPSLLLIVIIVGGIVQGIFTAIEASAIAVVYTLLLTMVFYRTLKIKDLPSIL
-                     LQTVVMTGVIMFLLATSSAMSFSMSITNIPAALSDMILGISANKLVILLVITVFLLII
-                     GAFMDIGPAILIFTPILLPIMAKLGVDPVHFGIIMIYNLAIGTITPPVGSGLYVGASV
-                     GKVKVEEVIKPLLPFYGAIIGVLLLITYIPEITLFLPRLLGIM"
-ORIGIN      
-        1 cgcgcatagc gcgcaatgcc gcactttatt gctgaatgta ctgaaaatat tcgcgagcag
-       61 gctgatttac ccggcctgtt cagcaaggta aacgaggcgc tggccgccag cgggattttc
-      121 cccatcggcg gtatccgcag tcgcgcccac tggctggata cctggcagat ggctgacggt
-      181 aagcatgatt acgcgtttgt gcatatgacg ctgaaaatcg gcgccgggcg cagcctggag
-      241 agccgtcagg aagttggcga aatgctgttt gggctgatta aagcccactt cgccgacctg
-      301 atggagaacc gctatctggc gctgtcgttt gagattgccg agctacatcc gacgctcaat
-      361 tacaaacaaa acaacgtaca cgcgttattt aaatagccga tatgaggcgc ggcgctataa
-      421 ggcgctcatg agcatgcccg cgactaaatt ctcccgacgt accctcctga cggcaggttc
-      481 tgcgcttgct gttcttcctt ttctgcgcgc cttgccggta caggcgcgtg aacctcgcga
-      541 gaccgtcgat attaaggatt atccggcgga tgacggtatc gcctcgttca aacaggcctt
-      601 cgccgacgga cagaccgtgg tcgtaccgcc aggatgggtg tgtgaaaata tcaatgcggc
-      661 gataacgatt ccggcgggaa aaacgctgcg ggtacagggc gcggtgcgtg ggaatggccg
-      721 gggacggttt attttgcagg acgggtgtca ggtggtgggg gagcagggcg gcagtctgca
-      781 caatgtgacg ctggatgttc gcgggtcgga ctgtgtgatt aaaggcgtgg cgatgagcgg
-      841 ctttggcccc gtcgcgcaaa ttttcatcgg tggtaaggaa ccgcaggtga tgcgtaatct
-      901 cattatcgat gacatcaccg ttacccacgc caactacgcc attctccgcc agggatttca
-      961 taaccaaatg gatggcgcgc ggattacgca tagccgcttt agcgatttac agggggacgc
-     1021 cattgagtgg aatgtcgcga ttcacgaccg cgacatcctg atttccgatc atgtcatcga
-     1081 acgcattaat tgtaccaatg gcaaaatcaa ctgggggatc ggcatcgggc tggcgggtag
-     1141 cacctatgac aacagttatc ctgaagacca ggcagtaaaa aactttgtgg tggccaatat
-     1201 taccggatct gattgccgac agcttgtgca cgtagaaaat ggcaaacatt tcgtcattcg
-     1261 caatgtcaaa gccaaaaaca tcacgcccgg tttcagtaaa aatgcgggta ttgataacgc
-     1321 aacgatcgca atttatggct gtgataattt cgtcattgat aatattgata tgacgaatag
-     1381 tgccgggatg ctcatcggct atggcgtcgt taaaggaaaa tacctgtcaa ttccgcaaaa
-     1441 ctttaaatta aacgctattc ggttggataa tcgccaggtt gcttataaat tacgcggcat
-     1501 tcaaatttcc tccggcaaca ccccctcttt tgtcgccatc accaatgtac ggatgacgcg
-     1561 tgctacgctg gaactgcata atcaaccgca gcacctcttt ctgcgcaata tcaacgtgat
-     1621 gcaaacttca gcgattggcc cggcgttaaa aatgcatttc gatttgcgta aagatgtacg
-     1681 tggtcaattt atggcccgcc aggacacgct gctttccctc gctaatgttc atgccatcaa
-     1741 tgaaaacggg cagagttccg tggatatcga caggattaat caccaaaccg tgaatgtcga
-     1801 agcagtgaat ttttcgctgc cgaagcgggg agggtaacga attccgcggc atatagcggc
-     1861 gcgatagcat gtcagaaaat aaattacacg ttatcgattt gcacaaacgc tacggcggtc
-     1921 atgaagtgct gaaaggggta tcgctgcagg cccgcgccgg agatgtgatt agcatcatcg
-     1981 gctcgtccgg ctccggtaaa agcacttttt tgcgctgtat taacttcctc gaaaaaccga
-     2041 gcgaaggcgc gattatcgtg aacggtcaga acattaatct ggtgcgcgac aaagatgggc
-     2101 agctcaaagt ggcggataaa aatcagctac gcttgttgcg tacccgcctg acgatggtgt
-     2161 ttcagcactt caacctctgg agccacatga cggtgctgga aaatgtgatg gaagcgccga
-     2221 ttcaggtact gggattaagc aagcacgacg cgcgcgagcg ggcgttgaaa tatctggcga
-     2281 aggtggggat tgatgagcgc gctcagggca aatatcccgt ccatctctcc ggcggccaac
-     2341 agcagcgcgt ttctattgcg cgcgcgctgg cgatggaacc tgacgtttta ctgttcgatg
-     2401 aacccacatc ggcgctcgat cctgaactgg tcggcgaagt gttgcgcatc atgcaacaac
-     2461 tggcggaaga aggcaaaacg atggtggtgg tcacgcatga aatgggcttc gctcgccatg
-     2521 tctcttcgca cgttattttt ctgcatcagg ggaaaattga agaagagggt gatccggagc
-     2581 aggtgttcgg caatccgcaa agcccgcgtt tacagcaatt cctgaaaggc tcgctgaaat
-     2641 aacgctcaga ggcgcgcgcg cgctatatac gcgcagtgtt tattggcata gttagcctgt
-     2701 ttcctgaaat gttccgcgca attaccgatt acggggtaac tggccgggca gtaaaaaaag
-     2761 gcctgctgaa catccaaagc tggagtcctc gcgacttcgc gcatgaccgg caccgtaccg
-     2821 tggacgaccg tccttacggc ggcggaccgg ggatgttaat gatggtgcaa cccttgcggg
-     2881 acgccattca cgcagcaaaa gccgcggcag gtgaaggcgc taaagtgatt tatctgtcgc
-     2941 ctcagggacg caagcttgat caagcgggcg ttagcgagct ggccacgaat cagaagctta
-     3001 ttctggtgtg tggtcgctac gaaggcgtag atgagcgcgt aattcagacc gaaattgacg
-     3061 aagaatggtc aattggcgat tacgttctca gcggtggcga actaccggca atgacgctga
-     3121 ttgactccgt cgcccggttt ataccggggg ttctggggca tgaggcatca gcaatcgaag
-     3181 attcgtttgc tgatgggttg ctggattgtc cgcactatac gcgccctgaa gtgttagagg
-     3241 ggatggaagt accgccagta ttgctgtcgg gaaaccatgc tgagatacgt cgctggcgtt
-     3301 tgaaacagtc gctgggccga acctggctta gaagacctga acttctggaa aacctggctc
-     3361 tgactgaaga gcaagcaagg ttgctggcgg agttcaaaac agaacacgca caacagcagc
-     3421 ataaacatga tgggatggca tagccgtcat atgggctctc agaggagacg cgctaatgcg
-     3481 cagtacgtgt ttattggcat agttagcctg tttcctgaaa tgttccgcgc aattaccgat
-     3541 tacggggtaa ctggccgggc agtaaaaaaa ggcctgctga acatccaaag ctggagtcct
-     3601 cgcgacttcg cgcatgaccg gcaccgtacc gtggacgacc gtccttacgg cggcggaccg
-     3661 gggatgttaa tgatggtgca acccttgcgg gacgccattc acgcagcaaa agccgcggca
-     3721 ggtgaaggcg ctaaagtgat ttatctgtcg cctcagggac gcaagcttga tcaagcgggc
-     3781 gttagcgagc tggccacgaa tcagaagctt attctggtgt gtggtcgcta cgaaggcgta
-     3841 gatgagcgcg taattcagac cgaaattgac gaagaatggt caattggcga ttacgttctc
-     3901 agcggtggcg aactaccggc aatgacgctg attgactccg tcgcccggtt tataccgggg
-     3961 gttctggggc atgaggcatc agcaatcgaa gattcgtttg ctgatgggtt gctggattgt
-     4021 ccgcactata cgcgccctga agtgttagag gggatggaag taccgccagt attgctgtcg
-     4081 ggaaaccatg ctgagatacg tcgctggcgt ttgaaacagt cgctgggccg aacctggctt
-     4141 agaagacctg aacttctgga aaacctggct ctgactgaag agcaagcaag gttgctggcg
-     4201 gagttcaaaa cagaacacgc acaacagcag cataaacatg atgggatggc atagcgcata
-     4261 cgcgcgcgat atatattcgc gcagaggcgc gcatagcgat gaagtttgtt gcgcccgaac
-     4321 aggcaccgga acaggcggag gtcatcaaaa atacgccgtt ctggcctgat gtggacctgt
-     4381 cggaatttcg cagtgtgatg cgcactgacg gcacggtgac gcagccgcgt ttaaagcagg
-     4441 tcgtgctgac ggcgatctct gaggttaacg ctgagctgta cgacttccgc aaccgtcagc
-     4501 agatgctggg ctggcggaca cttgctgagg ttcccgcaga aatgctggac ggtaaaagcg
-     4561 agcgtatccg gcactaccac aacgctgttt tttgctgggc gcgcgctgtg cttaatgagc
-     4621 gttatcagga ctatgacgcc acggcgtcag gcgtgaagcg aggggaggag ctggcggagg
-     4681 ccagcggcga tctgtggcgt gatgcccgct gggccatcag ccgggtgcag gatgtaccgc
-     4741 actgtacggt ggagcttatc tgaacggcta gcgcgtagcg gcagtctcgg atgaataatc
-     4801 attttgggaa agggttaatg gccgggttgc acgcgccata tgcatatagc gcgcatcatg
-     4861 cggtgaattt ctgttctgag tataaacgtg gctttgtatt gggttttaca caccgtatgt
-     4921 tcgaaaagac cggcgatcgt caacttagcg cgtgggaggc tggaattctg acgcgtcgct
-     4981 atggtctgga taaagaaatg gtgatggatt tctttaaaga gaatcattcc gggatggcgg
-     5041 ttcgcttctt tatggccggt tatcgactcg aaggttgacg atcgcgcgca ggaggagagc
-     5101 tctcttcttc tagagcatgt ctacgcttct ctatttgcac ggattcaaca gttcccctcg
-     5161 ctcggcaaaa gcgtgccagc taaaaaactg gctggcggag cgtcatccgc atgttgagat
-     5221 gatcgtccct cagctgccgc cgtatcctgc cgatgcggcg gagttgctgg aatctctcgt
-     5281 gcttgagcat ggcggtgcgc cattagggct ggtaggatcg tcgctgggtg gttattacgc
-     5341 cacctggctg tcgcaatgtt ttatgctgcc ggctgtggtg gtgaatcccg ccgtgcggcc
-     5401 ctttgaatta ctgaccgact atctcggtca gaacgagaac ccctacaccg ggcagcaata
-     5461 tgtgctagag tctcgccata tttatgatct taaagtcatg cagattgacc cgctggaagc
-     5521 gccggacctg atctggctac tgcaacagac gggcgatgaa gtgctgtatt accgccaggc
-     5581 ggtggcatat tacgcctcct gccgtcagac agtgaccgag ggtggtaatc acgcattcac
-     5641 gggcttcgaa gattatttca accagattgt cgattttctt ggactgcaca gttgctgacg
-     5701 gctatgcgcg cgctcgatga ttgaccctat ttttgcgtcc tgtacgctaa ttgccgtctt
-     5761 tgttgtttta ctggccatgg gcgcgcctat cgggatctgc atcgttatcg cctctttcag
-     5821 caccatgatg ctggtactgc ctttcgatat ttcgatgttc gccaccgcgc aaaaaatgtt
-     5881 ctccagcctg gacagttttg ccttgctggc cgtgccgttc ttcgttttgt ccggggtgat
-     5941 catgaatagc gggggaattg ccgcccggct ggtcaatttt gccaaactgt ttactggcaa
-     6001 actgcccggc tcgctctctt ataccaacat cgtcggcaat atgatgttcg gtgcaatttc
-     6061 cggatcggcg attgccgcct caacctccat cggcggcgtg atggtgccga tgagcgcgcg
-     6121 cgaaggttac gatcgcggct ttgcggccgc ggtgaatatc gcctccgcgc cgacgggaat
-     6181 gttaattccg cccaccacgg cttttatcct ttacgcgctg gcaagcgggg gaacatcgat
-     6241 tgccgctctg ttcgccggcg gtctggtcgc gggagtgctg tggggcgttg gctgtatgct
-     6301 ggtcacgctg gtggtcgcta agcgtcgaaa ttatcgggtt ttcttcaccg tccaaaaagg
-     6361 tatggcgcta aaagttgccg ttgaggccat tcccagcctg ctgctgatcg tgattattgt
-     6421 cggcggcatt gtgcagggga ttttcaccgc cattgaagcc tccgcgattg ccgtggtgta
-     6481 tacgttattg ctgacgatgg tgttttaccg cacgctgaaa attaaggatt tgccttcgat
-     6541 tttgctccag acagtggtaa tgaccggggt catcatgttc ctgctggcaa cctcttcggc
-     6601 gatgtccttc tcgatgtcga tcaccaatat tcctgcggcg ctgagcgata tgatcctcgg
-     6661 tatttccgcc aataaactgg ttatcctgtt agtcattacc gtctttttgt tgattatcgg
-     6721 cgcatttatg gatattggtc cggccattct gatttttacc ccgattctgc tgccaatcat
-     6781 ggctaaactg ggcgtcgatc cggtgcattt cggcattatc atgatctata acctggcgat
-     6841 tggcaccatt acgccgccag ttggcagtgg tttatatgtc ggggcgagcg tcggtaaggt
-     6901 caaagttgag gaagtgatta aaccgttgct gcctttttac ggcgcgatta tcggcgttct
-     6961 gttattaatt acctacattc cggaaatcac actgttctta ccccgtctac tgggcatcat
-     7021 gtaa
-//
diff --git a/Examples/2-res-Annotate-prokka/tmp_files/genome1.fst_prokka-split5N.fna-prokkaRes/EXAM.1219.00001.gff b/Examples/2-res-Annotate-prokka/tmp_files/genome1.fst_prokka-split5N.fna-prokkaRes/EXAM.1219.00001.gff
deleted file mode 100644
index a99171c4434be5516afb462181a1680d423e5c61..0000000000000000000000000000000000000000
--- a/Examples/2-res-Annotate-prokka/tmp_files/genome1.fst_prokka-split5N.fna-prokkaRes/EXAM.1219.00001.gff
+++ /dev/null
@@ -1,182 +0,0 @@
-##gff-version 3
-##sequence-region genome1_1 1 2784
-##sequence-region genome1_2 1 7024
-genome1_1	Prodigal:002006	CDS	213	1880	.	+	0	ID=GKEGNCBE_00001;eC_number=6.1.1.18;Name=glnS;db_xref=COG:COG0008;gene=glnS;inference=ab initio prediction:Prodigal:002006,similar to AA sequence:UniProtKB:P00962;locus_tag=GKEGNCBE_00001;product=Glutamine--tRNA ligase
-genome1_1	Prodigal:002006	CDS	1916	2746	.	+	0	ID=GKEGNCBE_00002;eC_number=3.5.1.28;Name=amiD;db_xref=COG:COG3023;gene=amiD;inference=ab initio prediction:Prodigal:002006,similar to AA sequence:UniProtKB:P75820;locus_tag=GKEGNCBE_00002;product=N-acetylmuramoyl-L-alanine amidase AmiD
-genome1_2	Prodigal:002006	CDS	16	396	.	+	0	ID=GKEGNCBE_00003;eC_number=5.3.3.10;Name=hpcD;gene=hpcD;inference=ab initio prediction:Prodigal:002006,similar to AA sequence:UniProtKB:Q05354;locus_tag=GKEGNCBE_00003;product=5-carboxymethyl-2-hydroxymuconate Delta-isomerase
-genome1_2	Prodigal:002006	CDS	428	1837	.	+	0	ID=GKEGNCBE_00004;inference=ab initio prediction:Prodigal:002006;locus_tag=GKEGNCBE_00004;product=hypothetical protein
-genome1_2	Prodigal:002006	CDS	1869	2642	.	+	0	ID=GKEGNCBE_00005;Name=hisP;db_xref=COG:COG4598;gene=hisP;inference=ab initio prediction:Prodigal:002006,similar to AA sequence:UniProtKB:P02915;locus_tag=GKEGNCBE_00005;product=Histidine transport ATP-binding protein HisP
-genome1_2	Prodigal:002006	CDS	2709	3443	.	+	0	ID=GKEGNCBE_00006;eC_number=2.1.1.228;Name=trmD_1;db_xref=COG:COG0336;gene=trmD_1;inference=ab initio prediction:Prodigal:002006,similar to AA sequence:UniProtKB:P0A873;locus_tag=GKEGNCBE_00006;product=tRNA (guanine-N(1)-)-methyltransferase
-genome1_2	Prodigal:002006	CDS	3427	4254	.	+	0	ID=GKEGNCBE_00007;eC_number=2.1.1.228;Name=trmD_2;db_xref=COG:COG0336;gene=trmD_2;inference=ab initio prediction:Prodigal:002006,similar to AA sequence:UniProtKB:P0A873;locus_tag=GKEGNCBE_00007;product=tRNA (guanine-N(1)-)-methyltransferase
-genome1_2	Prodigal:002006	CDS	4299	4763	.	+	0	ID=GKEGNCBE_00008;inference=ab initio prediction:Prodigal:002006;locus_tag=GKEGNCBE_00008;product=hypothetical protein
-genome1_2	Prodigal:002006	CDS	4818	5078	.	+	0	ID=GKEGNCBE_00009;inference=ab initio prediction:Prodigal:002006;locus_tag=GKEGNCBE_00009;product=hypothetical protein
-genome1_2	Prodigal:002006	CDS	5117	5698	.	+	0	ID=GKEGNCBE_00010;inference=ab initio prediction:Prodigal:002006;locus_tag=GKEGNCBE_00010;product=hypothetical protein
-genome1_2	Prodigal:002006	CDS	5717	7024	.	+	0	ID=GKEGNCBE_00011;Name=dctM;db_xref=COG:COG1593;gene=dctM;inference=ab initio prediction:Prodigal:002006,similar to AA sequence:UniProtKB:O07838;locus_tag=GKEGNCBE_00011;product=C4-dicarboxylate TRAP transporter large permease protein DctM
-##FASTA
->genome1_1
-ATGTGTAAAAGCCGGAGGGGTTATCTTTTCCCGGCTTTTTATTATCAATTACTCATTAAC
-TCCTGTTCCGTTCTTTTGCGTTTAATCACCGGAATATCTCCGGTATTGTTCAGCGCCCCG
-GAAATGTTTTTAACCACTGTTCTGCACTCCGTTTATTAAACGCGCTCAGCGCGCGCTCAT
-ATATCGCGCGCGCGCGCGCGCATATATATATAATGAGTGAGGCTGAAGCCCGCCCGACTA
-ACTTTATTCGTCAGATTATTGATGAAGATCTGGCGAGTGGTAAACATACCACTGTCCATA
-CCCGTTTTCCGCCGGAGCCGAATGGCTATCTGCATATCGGCCACGCGAAATCTATCTGCC
-TGAACTTTGGCATCGCGCAAGATTATCAGGGCCAGTGCAACCTGCGTTTCGATGACACCA
-ACCCGGTAAAAGAAGATATCGAGTACGTTGATTCGATCAAAAACGACGTCGAGTGGTTAG
-GCTTTCACTGGTCTGGCGATATTCGCTACTCCTCCGATTACTTTGACCAACTGCACGCCT
-ATGCGGTCGAGCTAATCAATAAAGGCCTGGCCTATGTTGATGAGCTGACGCCGGAGCAGA
-TCCGTGAATACCGCGGTACGCTGACCGCGCCGGGTAAAAACAGCCCGTTCCGCGATCGCA
-GCGTCGAAGAGAACCTCGCGCTATTTGAAAAAATGCGTACCGGCGGTTTTGAAGAGGGTA
-AAGCCTGTCTGCGCGCTAAAATCGACATGGCGTCGCCGTTTATCGTGATGCGCGATCCGG
-TGCTGTATCGCATTAAATTCGCCGAGCATCATCAGACTGGCAACAAGTGGTGCATCTATC
-CGATGTACGACTTTACTCACTGCATCAGCGATGCGCTGGAAGGCATTACTCATTCTCTGT
-GTACGCTGGAGTTCCAGGATAACCGTCGTCTGTACGACTGGGTGCTGGACAACATCACCA
-TTCCGGTTCACCCGCGCCAGTACGAATTCTCGCGCCTGAATCTGGAATACACCGTGATGT
-CCAAGCGTAAGCTGAACCTGCTGGTGACCGACAAACACGTCGAAGGTTGGGACGATCCGC
-GTATGCCGACTATTTCCGGTCTGCGCCGTCGCGGCTATACCGCGGCTTCTATTCGTGAGT
-TCTGCAAACGCATCGGCGTCACCAAGCAGGACAACACTATTGAGATGGCGTCGCTGGAAT
-CCTGCATTCGCGAAGATCTGAACGAAAACGCGCCGCGCGCGATGGCGGTAATCGATCCGG
-TAAAACTGGTTATCGAAAATTACCCGCAGGGTGAGAGCGAAATGGTTACCATGCCTAACC
-ATCCGAATAAACCGGAGATGGGCAGCCGTGAAGTGCCGTTTAGCGGTGAGATCTGGATCG
-ATCGCGCAGATTTCCGCGAAGAAGCGAACAAACAGTACAAACGTCTGGTGATGGGCAAAG
-AAGTGCGTCTGCGTAATGCCTACGTCATTAAAGCGGAGCGCGTAGAGAAGGATGCCGAAG
-GGAATATCACCACCATCTTCTGTACCTATGATGCTGATACGCTGAGTAAAGATCCGGCTG
-ACGGGCGTAAAGTGAAAGGCGTAATCCACTGGGTTAGCGCAGCACATGCGCTGCCGATTG
-AAATTCGTCTCTACGACCGTCTGTTCAGCGTGCCGAATCCGGGCGCCGCGGAGGACTTCC
-TGTCTGTTATCAACCCCGAATCATTAGTGATTAAGCAGGGGTATGGCGAGCCGTCGCTGA
-AAGCGGCGGTAGCAGGAAAAGCTTTCCAGTTTGAACGTGAAGGCTACTTCTGCCTCGACA
-GCCGCTATGCAACGGCCGATAAGCTGGTCTTTAACCGCACCGTGGGCCTGCGTGATACCT
-GGGCGAAAGCGGGCGAGTAACGCGCATAGGCGGCCTTCAAGGAGGCGCTAGGCGAATGAA
-AGCGCTACTGTGGCTGGTGGGTCTCGCGTTGCTGTTAACAGGCTGCGCGAGCGAAAAAGG
-AATTATCGATAAAGAGGGATATCAGCTTGATACCCGACATCGGGCGCAGGCGGCCTATCC
-GCGCATTAAAGTCCTGGTGATTCACTATACGGCGGAAAACTTTGACGTTTCGCTGGCGAC
-GTTAACGGGTCGCAACGTCAGTTCGCATTACCTGATTCCCGCAACCCCGCCATTATATGG
-CGGTAAACCGCGCATCTGGCAACTGGTGCCGGAACAGGATCAGGCCTGGCATGCGGGCGT
-CAGTTTCTGGCGAGGCGCCACGCGTCTCAATGATACGTCTATTGGCATTGAGCTGGAAAA
-TCGTGGTTGGCGAATGTCCGGCGGGGTGAAATCTTTCGCGCCGTTTGAATCCGCGCAAAT
-TCAGGCATTGATTCCGTTAGCGAAGGATATTATCGCGCGCTATAACATCAAACCGCAGAA
-TGTGGTGGCCCATGCGGATATCGCGCCGCAGCGTAAAGACGATCCCGGCCCGCGCTTCCC
-GTGGCGCGAGCTGGCGGCGCAGGGGATTAGCGCCTGGCCTGACGCCCAGCGTGTGGCGTT
-TTATCTGGCTGGACGCGCGCCGTATACGCCAGTCGATACCGCAACGGTGCTTGCGTTACT
-CTCGCGCTATGGCTATGAAGTCAAAGCCGATATGACGGCACGCGAGCAGCAGCGGGTGAT
-TATGGCGTTCCAGATGCACTTCCGTCCGGCGCAATGGAACGGTATCGCAGATGCCGAAAC
-GCAGGCGATTGCCGAAGCATTACTGGAGAAGTACGGCCAGGATTAACGCGATAGGCGCGC
-GAGATTACGCGCGCAGTATCGCGC
->genome1_2
-CGCGCATAGCGCGCAATGCCGCACTTTATTGCTGAATGTACTGAAAATATTCGCGAGCAG
-GCTGATTTACCCGGCCTGTTCAGCAAGGTAAACGAGGCGCTGGCCGCCAGCGGGATTTTC
-CCCATCGGCGGTATCCGCAGTCGCGCCCACTGGCTGGATACCTGGCAGATGGCTGACGGT
-AAGCATGATTACGCGTTTGTGCATATGACGCTGAAAATCGGCGCCGGGCGCAGCCTGGAG
-AGCCGTCAGGAAGTTGGCGAAATGCTGTTTGGGCTGATTAAAGCCCACTTCGCCGACCTG
-ATGGAGAACCGCTATCTGGCGCTGTCGTTTGAGATTGCCGAGCTACATCCGACGCTCAAT
-TACAAACAAAACAACGTACACGCGTTATTTAAATAGCCGATATGAGGCGCGGCGCTATAA
-GGCGCTCATGAGCATGCCCGCGACTAAATTCTCCCGACGTACCCTCCTGACGGCAGGTTC
-TGCGCTTGCTGTTCTTCCTTTTCTGCGCGCCTTGCCGGTACAGGCGCGTGAACCTCGCGA
-GACCGTCGATATTAAGGATTATCCGGCGGATGACGGTATCGCCTCGTTCAAACAGGCCTT
-CGCCGACGGACAGACCGTGGTCGTACCGCCAGGATGGGTGTGTGAAAATATCAATGCGGC
-GATAACGATTCCGGCGGGAAAAACGCTGCGGGTACAGGGCGCGGTGCGTGGGAATGGCCG
-GGGACGGTTTATTTTGCAGGACGGGTGTCAGGTGGTGGGGGAGCAGGGCGGCAGTCTGCA
-CAATGTGACGCTGGATGTTCGCGGGTCGGACTGTGTGATTAAAGGCGTGGCGATGAGCGG
-CTTTGGCCCCGTCGCGCAAATTTTCATCGGTGGTAAGGAACCGCAGGTGATGCGTAATCT
-CATTATCGATGACATCACCGTTACCCACGCCAACTACGCCATTCTCCGCCAGGGATTTCA
-TAACCAAATGGATGGCGCGCGGATTACGCATAGCCGCTTTAGCGATTTACAGGGGGACGC
-CATTGAGTGGAATGTCGCGATTCACGACCGCGACATCCTGATTTCCGATCATGTCATCGA
-ACGCATTAATTGTACCAATGGCAAAATCAACTGGGGGATCGGCATCGGGCTGGCGGGTAG
-CACCTATGACAACAGTTATCCTGAAGACCAGGCAGTAAAAAACTTTGTGGTGGCCAATAT
-TACCGGATCTGATTGCCGACAGCTTGTGCACGTAGAAAATGGCAAACATTTCGTCATTCG
-CAATGTCAAAGCCAAAAACATCACGCCCGGTTTCAGTAAAAATGCGGGTATTGATAACGC
-AACGATCGCAATTTATGGCTGTGATAATTTCGTCATTGATAATATTGATATGACGAATAG
-TGCCGGGATGCTCATCGGCTATGGCGTCGTTAAAGGAAAATACCTGTCAATTCCGCAAAA
-CTTTAAATTAAACGCTATTCGGTTGGATAATCGCCAGGTTGCTTATAAATTACGCGGCAT
-TCAAATTTCCTCCGGCAACACCCCCTCTTTTGTCGCCATCACCAATGTACGGATGACGCG
-TGCTACGCTGGAACTGCATAATCAACCGCAGCACCTCTTTCTGCGCAATATCAACGTGAT
-GCAAACTTCAGCGATTGGCCCGGCGTTAAAAATGCATTTCGATTTGCGTAAAGATGTACG
-TGGTCAATTTATGGCCCGCCAGGACACGCTGCTTTCCCTCGCTAATGTTCATGCCATCAA
-TGAAAACGGGCAGAGTTCCGTGGATATCGACAGGATTAATCACCAAACCGTGAATGTCGA
-AGCAGTGAATTTTTCGCTGCCGAAGCGGGGAGGGTAACGAATTCCGCGGCATATAGCGGC
-GCGATAGCATGTCAGAAAATAAATTACACGTTATCGATTTGCACAAACGCTACGGCGGTC
-ATGAAGTGCTGAAAGGGGTATCGCTGCAGGCCCGCGCCGGAGATGTGATTAGCATCATCG
-GCTCGTCCGGCTCCGGTAAAAGCACTTTTTTGCGCTGTATTAACTTCCTCGAAAAACCGA
-GCGAAGGCGCGATTATCGTGAACGGTCAGAACATTAATCTGGTGCGCGACAAAGATGGGC
-AGCTCAAAGTGGCGGATAAAAATCAGCTACGCTTGTTGCGTACCCGCCTGACGATGGTGT
-TTCAGCACTTCAACCTCTGGAGCCACATGACGGTGCTGGAAAATGTGATGGAAGCGCCGA
-TTCAGGTACTGGGATTAAGCAAGCACGACGCGCGCGAGCGGGCGTTGAAATATCTGGCGA
-AGGTGGGGATTGATGAGCGCGCTCAGGGCAAATATCCCGTCCATCTCTCCGGCGGCCAAC
-AGCAGCGCGTTTCTATTGCGCGCGCGCTGGCGATGGAACCTGACGTTTTACTGTTCGATG
-AACCCACATCGGCGCTCGATCCTGAACTGGTCGGCGAAGTGTTGCGCATCATGCAACAAC
-TGGCGGAAGAAGGCAAAACGATGGTGGTGGTCACGCATGAAATGGGCTTCGCTCGCCATG
-TCTCTTCGCACGTTATTTTTCTGCATCAGGGGAAAATTGAAGAAGAGGGTGATCCGGAGC
-AGGTGTTCGGCAATCCGCAAAGCCCGCGTTTACAGCAATTCCTGAAAGGCTCGCTGAAAT
-AACGCTCAGAGGCGCGCGCGCGCTATATACGCGCAGTGTTTATTGGCATAGTTAGCCTGT
-TTCCTGAAATGTTCCGCGCAATTACCGATTACGGGGTAACTGGCCGGGCAGTAAAAAAAG
-GCCTGCTGAACATCCAAAGCTGGAGTCCTCGCGACTTCGCGCATGACCGGCACCGTACCG
-TGGACGACCGTCCTTACGGCGGCGGACCGGGGATGTTAATGATGGTGCAACCCTTGCGGG
-ACGCCATTCACGCAGCAAAAGCCGCGGCAGGTGAAGGCGCTAAAGTGATTTATCTGTCGC
-CTCAGGGACGCAAGCTTGATCAAGCGGGCGTTAGCGAGCTGGCCACGAATCAGAAGCTTA
-TTCTGGTGTGTGGTCGCTACGAAGGCGTAGATGAGCGCGTAATTCAGACCGAAATTGACG
-AAGAATGGTCAATTGGCGATTACGTTCTCAGCGGTGGCGAACTACCGGCAATGACGCTGA
-TTGACTCCGTCGCCCGGTTTATACCGGGGGTTCTGGGGCATGAGGCATCAGCAATCGAAG
-ATTCGTTTGCTGATGGGTTGCTGGATTGTCCGCACTATACGCGCCCTGAAGTGTTAGAGG
-GGATGGAAGTACCGCCAGTATTGCTGTCGGGAAACCATGCTGAGATACGTCGCTGGCGTT
-TGAAACAGTCGCTGGGCCGAACCTGGCTTAGAAGACCTGAACTTCTGGAAAACCTGGCTC
-TGACTGAAGAGCAAGCAAGGTTGCTGGCGGAGTTCAAAACAGAACACGCACAACAGCAGC
-ATAAACATGATGGGATGGCATAGCCGTCATATGGGCTCTCAGAGGAGACGCGCTAATGCG
-CAGTACGTGTTTATTGGCATAGTTAGCCTGTTTCCTGAAATGTTCCGCGCAATTACCGAT
-TACGGGGTAACTGGCCGGGCAGTAAAAAAAGGCCTGCTGAACATCCAAAGCTGGAGTCCT
-CGCGACTTCGCGCATGACCGGCACCGTACCGTGGACGACCGTCCTTACGGCGGCGGACCG
-GGGATGTTAATGATGGTGCAACCCTTGCGGGACGCCATTCACGCAGCAAAAGCCGCGGCA
-GGTGAAGGCGCTAAAGTGATTTATCTGTCGCCTCAGGGACGCAAGCTTGATCAAGCGGGC
-GTTAGCGAGCTGGCCACGAATCAGAAGCTTATTCTGGTGTGTGGTCGCTACGAAGGCGTA
-GATGAGCGCGTAATTCAGACCGAAATTGACGAAGAATGGTCAATTGGCGATTACGTTCTC
-AGCGGTGGCGAACTACCGGCAATGACGCTGATTGACTCCGTCGCCCGGTTTATACCGGGG
-GTTCTGGGGCATGAGGCATCAGCAATCGAAGATTCGTTTGCTGATGGGTTGCTGGATTGT
-CCGCACTATACGCGCCCTGAAGTGTTAGAGGGGATGGAAGTACCGCCAGTATTGCTGTCG
-GGAAACCATGCTGAGATACGTCGCTGGCGTTTGAAACAGTCGCTGGGCCGAACCTGGCTT
-AGAAGACCTGAACTTCTGGAAAACCTGGCTCTGACTGAAGAGCAAGCAAGGTTGCTGGCG
-GAGTTCAAAACAGAACACGCACAACAGCAGCATAAACATGATGGGATGGCATAGCGCATA
-CGCGCGCGATATATATTCGCGCAGAGGCGCGCATAGCGATGAAGTTTGTTGCGCCCGAAC
-AGGCACCGGAACAGGCGGAGGTCATCAAAAATACGCCGTTCTGGCCTGATGTGGACCTGT
-CGGAATTTCGCAGTGTGATGCGCACTGACGGCACGGTGACGCAGCCGCGTTTAAAGCAGG
-TCGTGCTGACGGCGATCTCTGAGGTTAACGCTGAGCTGTACGACTTCCGCAACCGTCAGC
-AGATGCTGGGCTGGCGGACACTTGCTGAGGTTCCCGCAGAAATGCTGGACGGTAAAAGCG
-AGCGTATCCGGCACTACCACAACGCTGTTTTTTGCTGGGCGCGCGCTGTGCTTAATGAGC
-GTTATCAGGACTATGACGCCACGGCGTCAGGCGTGAAGCGAGGGGAGGAGCTGGCGGAGG
-CCAGCGGCGATCTGTGGCGTGATGCCCGCTGGGCCATCAGCCGGGTGCAGGATGTACCGC
-ACTGTACGGTGGAGCTTATCTGAACGGCTAGCGCGTAGCGGCAGTCTCGGATGAATAATC
-ATTTTGGGAAAGGGTTAATGGCCGGGTTGCACGCGCCATATGCATATAGCGCGCATCATG
-CGGTGAATTTCTGTTCTGAGTATAAACGTGGCTTTGTATTGGGTTTTACACACCGTATGT
-TCGAAAAGACCGGCGATCGTCAACTTAGCGCGTGGGAGGCTGGAATTCTGACGCGTCGCT
-ATGGTCTGGATAAAGAAATGGTGATGGATTTCTTTAAAGAGAATCATTCCGGGATGGCGG
-TTCGCTTCTTTATGGCCGGTTATCGACTCGAAGGTTGACGATCGCGCGCAGGAGGAGAGC
-TCTCTTCTTCTAGAGCATGTCTACGCTTCTCTATTTGCACGGATTCAACAGTTCCCCTCG
-CTCGGCAAAAGCGTGCCAGCTAAAAAACTGGCTGGCGGAGCGTCATCCGCATGTTGAGAT
-GATCGTCCCTCAGCTGCCGCCGTATCCTGCCGATGCGGCGGAGTTGCTGGAATCTCTCGT
-GCTTGAGCATGGCGGTGCGCCATTAGGGCTGGTAGGATCGTCGCTGGGTGGTTATTACGC
-CACCTGGCTGTCGCAATGTTTTATGCTGCCGGCTGTGGTGGTGAATCCCGCCGTGCGGCC
-CTTTGAATTACTGACCGACTATCTCGGTCAGAACGAGAACCCCTACACCGGGCAGCAATA
-TGTGCTAGAGTCTCGCCATATTTATGATCTTAAAGTCATGCAGATTGACCCGCTGGAAGC
-GCCGGACCTGATCTGGCTACTGCAACAGACGGGCGATGAAGTGCTGTATTACCGCCAGGC
-GGTGGCATATTACGCCTCCTGCCGTCAGACAGTGACCGAGGGTGGTAATCACGCATTCAC
-GGGCTTCGAAGATTATTTCAACCAGATTGTCGATTTTCTTGGACTGCACAGTTGCTGACG
-GCTATGCGCGCGCTCGATGATTGACCCTATTTTTGCGTCCTGTACGCTAATTGCCGTCTT
-TGTTGTTTTACTGGCCATGGGCGCGCCTATCGGGATCTGCATCGTTATCGCCTCTTTCAG
-CACCATGATGCTGGTACTGCCTTTCGATATTTCGATGTTCGCCACCGCGCAAAAAATGTT
-CTCCAGCCTGGACAGTTTTGCCTTGCTGGCCGTGCCGTTCTTCGTTTTGTCCGGGGTGAT
-CATGAATAGCGGGGGAATTGCCGCCCGGCTGGTCAATTTTGCCAAACTGTTTACTGGCAA
-ACTGCCCGGCTCGCTCTCTTATACCAACATCGTCGGCAATATGATGTTCGGTGCAATTTC
-CGGATCGGCGATTGCCGCCTCAACCTCCATCGGCGGCGTGATGGTGCCGATGAGCGCGCG
-CGAAGGTTACGATCGCGGCTTTGCGGCCGCGGTGAATATCGCCTCCGCGCCGACGGGAAT
-GTTAATTCCGCCCACCACGGCTTTTATCCTTTACGCGCTGGCAAGCGGGGGAACATCGAT
-TGCCGCTCTGTTCGCCGGCGGTCTGGTCGCGGGAGTGCTGTGGGGCGTTGGCTGTATGCT
-GGTCACGCTGGTGGTCGCTAAGCGTCGAAATTATCGGGTTTTCTTCACCGTCCAAAAAGG
-TATGGCGCTAAAAGTTGCCGTTGAGGCCATTCCCAGCCTGCTGCTGATCGTGATTATTGT
-CGGCGGCATTGTGCAGGGGATTTTCACCGCCATTGAAGCCTCCGCGATTGCCGTGGTGTA
-TACGTTATTGCTGACGATGGTGTTTTACCGCACGCTGAAAATTAAGGATTTGCCTTCGAT
-TTTGCTCCAGACAGTGGTAATGACCGGGGTCATCATGTTCCTGCTGGCAACCTCTTCGGC
-GATGTCCTTCTCGATGTCGATCACCAATATTCCTGCGGCGCTGAGCGATATGATCCTCGG
-TATTTCCGCCAATAAACTGGTTATCCTGTTAGTCATTACCGTCTTTTTGTTGATTATCGG
-CGCATTTATGGATATTGGTCCGGCCATTCTGATTTTTACCCCGATTCTGCTGCCAATCAT
-GGCTAAACTGGGCGTCGATCCGGTGCATTTCGGCATTATCATGATCTATAACCTGGCGAT
-TGGCACCATTACGCCGCCAGTTGGCAGTGGTTTATATGTCGGGGCGAGCGTCGGTAAGGT
-CAAAGTTGAGGAAGTGATTAAACCGTTGCTGCCTTTTTACGGCGCGATTATCGGCGTTCT
-GTTATTAATTACCTACATTCCGGAAATCACACTGTTCTTACCCCGTCTACTGGGCATCAT
-GTAA
diff --git a/Examples/2-res-Annotate-prokka/tmp_files/genome1.fst_prokka-split5N.fna-prokkaRes/EXAM.1219.00001.log b/Examples/2-res-Annotate-prokka/tmp_files/genome1.fst_prokka-split5N.fna-prokkaRes/EXAM.1219.00001.log
deleted file mode 100644
index 0aa974902a9cd21965ea0f7f27e1f6aa8a90e4bf..0000000000000000000000000000000000000000
--- a/Examples/2-res-Annotate-prokka/tmp_files/genome1.fst_prokka-split5N.fna-prokkaRes/EXAM.1219.00001.log
+++ /dev/null
@@ -1,130 +0,0 @@
-[13:15:21] This is prokka 1.14.5
-[13:15:21] Written by Torsten Seemann <torsten.seemann@gmail.com>
-[13:15:21] Homepage is https://github.com/tseemann/prokka
-[13:15:21] Local time is Mon Dec  9 13:15:21 2019
-[13:15:21] You are aperrin
-[13:15:21] Operating system is darwin
-[13:15:21] You have BioPerl 1.007002
-[13:15:21] System has 8 cores.
-[13:15:21] Will use maximum of 1 cores.
-[13:15:21] Annotating as >>> Bacteria <<<
-[13:15:21] Generating locus_tag from 'Examples/2-res-Annotate-prokka/tmp_files/genome1.fst_prokka-split5N.fna' contents.
-[13:15:21] Setting --locustag GKEGNCBE from MD5 04e07cbef9b8a6b8d550f0d6ed3a8746
-[13:15:21] Creating new output folder: Examples/2-res-Annotate-prokka/tmp_files/genome1.fst_prokka-split5N.fna-prokkaRes
-[13:15:21] Running: mkdir -p Examples\/2\-res\-Annotate\-prokka\/tmp_files\/genome1\.fst_prokka\-split5N\.fna\-prokkaRes
-[13:15:21] Using filename prefix: EXAM.1219.00001.XXX
-[13:15:21] Setting HMMER_NCPU=1
-[13:15:21] Writing log to: Examples/2-res-Annotate-prokka/tmp_files/genome1.fst_prokka-split5N.fna-prokkaRes/EXAM.1219.00001.log
-[13:15:21] Command: /usr/local/bin/prokka --outdir Examples/2-res-Annotate-prokka/tmp_files/genome1.fst_prokka-split5N.fna-prokkaRes --cpus 1 --prefix EXAM.1219.00001 Examples/2-res-Annotate-prokka/tmp_files/genome1.fst_prokka-split5N.fna
-[13:15:21] Appending to PATH: /Users/aperrin/Softwares/src/prokka-dec.19/bin/../binaries/darwin
-[13:15:21] Appending to PATH: /Users/aperrin/Softwares/src/prokka-dec.19/bin/../binaries/darwin/../common
-[13:15:21] Appending to PATH: /Users/aperrin/Softwares/src/prokka-dec.19/bin
-[13:15:21] Looking for 'aragorn' - found /usr/local/bin/aragorn
-[13:15:21] Determined aragorn version is 001002 from 'ARAGORN v1.2.38 Dean Laslett'
-[13:15:21] Looking for 'barrnap' - found /usr/local/bin/barrnap
-[13:15:21] Determined barrnap version is 000008 from 'barrnap 0.8'
-[13:15:21] Looking for 'blastp' - found /Users/aperrin/Softwares/bin/blastp
-[13:15:21] Determined blastp version is 002009 from 'blastp: 2.9.0+'
-[13:15:21] Looking for 'cmpress' - found /usr/local/bin/cmpress
-[13:15:21] Determined cmpress version is 001001 from '# INFERNAL 1.1.2 (July 2016)'
-[13:15:21] Looking for 'cmscan' - found /usr/local/bin/cmscan
-[13:15:21] Determined cmscan version is 001001 from '# INFERNAL 1.1.2 (July 2016)'
-[13:15:21] Looking for 'egrep' - found /usr/bin/egrep
-[13:15:21] Looking for 'find' - found /usr/bin/find
-[13:15:21] Looking for 'grep' - found /usr/bin/grep
-[13:15:21] Looking for 'hmmpress' - found /Users/aperrin/Softwares/src/prokka-dec.19/bin/../binaries/darwin/hmmpress
-[13:15:21] Determined hmmpress version is 003001 from '# HMMER 3.1b1 (May 2013); http://hmmer.org/'
-[13:15:21] Looking for 'hmmscan' - found /usr/local/bin/hmmscan
-[13:15:21] Determined hmmscan version is 003001 from '# HMMER 3.1b2 (February 2015); http://hmmer.org/'
-[13:15:21] Looking for 'java' - found /usr/bin/java
-[13:15:21] Looking for 'makeblastdb' - found /Users/aperrin/Softwares/bin/makeblastdb
-[13:15:21] Determined makeblastdb version is 002009 from 'makeblastdb: 2.9.0+'
-[13:15:21] Looking for 'minced' - found /Users/aperrin/Softwares/src/prokka-dec.19/bin/../binaries/darwin/../common/minced
-[13:15:22] Determined minced version is 002000 from 'minced 0.2.0'
-[13:15:22] Looking for 'parallel' - found /usr/local/bin/parallel
-[13:15:22] Determined parallel version is 20181022 from 'GNU parallel 20181022'
-[13:15:22] Looking for 'prodigal' - found /usr/local/bin/prodigal
-[13:15:22] Determined prodigal version is 002006 from 'Prodigal V2.6.3: February, 2016'
-[13:15:22] Looking for 'prokka-genbank_to_fasta_db' - found /Users/aperrin/Softwares/src/prokka-dec.19/bin/prokka-genbank_to_fasta_db
-[13:15:22] Looking for 'sed' - found /usr/bin/sed
-[13:15:22] Looking for 'tbl2asn' - found /Users/aperrin/Softwares/src/prokka-dec.19/bin/../binaries/darwin/tbl2asn
-[13:15:22] Determined tbl2asn version is 025007 from 'tbl2asn 25.7   arguments:'
-[13:15:22] Using genetic code table 11.
-[13:15:22] Loading and checking input file: Examples/2-res-Annotate-prokka/tmp_files/genome1.fst_prokka-split5N.fna
-[13:15:22] Wrote 2 contigs totalling 9808 bp.
-[13:15:22] Predicting tRNAs and tmRNAs
-[13:15:22] Running: aragorn -l -gc11  -w Examples\/2\-res\-Annotate\-prokka\/tmp_files\/genome1\.fst_prokka\-split5N\.fna\-prokkaRes\/EXAM\.1219\.00001\.fna
-[13:15:22] Found 0 tRNAs
-[13:15:22] Predicting Ribosomal RNAs
-[13:15:22] Running Barrnap with 1 threads
-[13:15:22] Found 0 rRNAs
-[13:15:22] Skipping ncRNA search, enable with --rfam if desired.
-[13:15:22] Total of 0 tRNA + rRNA features
-[13:15:22] Searching for CRISPR repeats
-[13:15:22] Found 0 CRISPRs
-[13:15:22] Predicting coding sequences
-[13:15:22] Contigs total 9808 bp, so using meta mode
-[13:15:22] Running: prodigal -i Examples\/2\-res\-Annotate\-prokka\/tmp_files\/genome1\.fst_prokka\-split5N\.fna\-prokkaRes\/EXAM\.1219\.00001\.fna -c -m -g 11 -p meta -f sco -q
-[13:15:22] Found 11 CDS
-[13:15:22] Connecting features back to sequences
-[13:15:22] Not using genus-specific database. Try --usegenus to enable it.
-[13:15:22] Annotating CDS, please be patient.
-[13:15:22] Will use 1 CPUs for similarity searching.
-[13:15:22] There are still 11 unannotated CDS left (started with 11)
-[13:15:22] Will use blast to search against /Users/aperrin/Softwares/src/prokka-dec.19/db/kingdom/Bacteria/IS with 1 CPUs
-[13:15:22] Running: cat Examples\/2\-res\-Annotate\-prokka\/tmp_files\/genome1\.fst_prokka\-split5N\.fna\-prokkaRes\/EXAM\.1219\.00001\.IS\.tmp\.94917\.faa | parallel --gnu --plain -j 1 --block 1558 --recstart '>' --pipe blastp -query - -db /Users/aperrin/Softwares/src/prokka-dec.19/db/kingdom/Bacteria/IS -evalue 1e-30 -qcov_hsp_perc 90 -num_threads 1 -num_descriptions 1 -num_alignments 1 -seg no > Examples\/2\-res\-Annotate\-prokka\/tmp_files\/genome1\.fst_prokka\-split5N\.fna\-prokkaRes\/EXAM\.1219\.00001\.IS\.tmp\.94917\.blast 2> /dev/null
-[13:15:23] Deleting unwanted file: Examples/2-res-Annotate-prokka/tmp_files/genome1.fst_prokka-split5N.fna-prokkaRes/EXAM.1219.00001.IS.tmp.94917.faa
-[13:15:23] Deleting unwanted file: Examples/2-res-Annotate-prokka/tmp_files/genome1.fst_prokka-split5N.fna-prokkaRes/EXAM.1219.00001.IS.tmp.94917.blast
-[13:15:23] There are still 11 unannotated CDS left (started with 11)
-[13:15:23] Will use blast to search against /Users/aperrin/Softwares/src/prokka-dec.19/db/kingdom/Bacteria/AMR with 1 CPUs
-[13:15:23] Running: cat Examples\/2\-res\-Annotate\-prokka\/tmp_files\/genome1\.fst_prokka\-split5N\.fna\-prokkaRes\/EXAM\.1219\.00001\.AMR\.tmp\.94917\.faa | parallel --gnu --plain -j 1 --block 1558 --recstart '>' --pipe blastp -query - -db /Users/aperrin/Softwares/src/prokka-dec.19/db/kingdom/Bacteria/AMR -evalue 1e-300 -qcov_hsp_perc 90 -num_threads 1 -num_descriptions 1 -num_alignments 1 -seg no > Examples\/2\-res\-Annotate\-prokka\/tmp_files\/genome1\.fst_prokka\-split5N\.fna\-prokkaRes\/EXAM\.1219\.00001\.AMR\.tmp\.94917\.blast 2> /dev/null
-[13:15:23] Deleting unwanted file: Examples/2-res-Annotate-prokka/tmp_files/genome1.fst_prokka-split5N.fna-prokkaRes/EXAM.1219.00001.AMR.tmp.94917.faa
-[13:15:23] Deleting unwanted file: Examples/2-res-Annotate-prokka/tmp_files/genome1.fst_prokka-split5N.fna-prokkaRes/EXAM.1219.00001.AMR.tmp.94917.blast
-[13:15:23] There are still 11 unannotated CDS left (started with 11)
-[13:15:23] Will use blast to search against /Users/aperrin/Softwares/src/prokka-dec.19/db/kingdom/Bacteria/sprot with 1 CPUs
-[13:15:23] Running: cat Examples\/2\-res\-Annotate\-prokka\/tmp_files\/genome1\.fst_prokka\-split5N\.fna\-prokkaRes\/EXAM\.1219\.00001\.sprot\.tmp\.94917\.faa | parallel --gnu --plain -j 1 --block 1558 --recstart '>' --pipe blastp -query - -db /Users/aperrin/Softwares/src/prokka-dec.19/db/kingdom/Bacteria/sprot -evalue 1e-09 -qcov_hsp_perc 80 -num_threads 1 -num_descriptions 1 -num_alignments 1 -seg no > Examples\/2\-res\-Annotate\-prokka\/tmp_files\/genome1\.fst_prokka\-split5N\.fna\-prokkaRes\/EXAM\.1219\.00001\.sprot\.tmp\.94917\.blast 2> /dev/null
-[13:15:25] Deleting unwanted file: Examples/2-res-Annotate-prokka/tmp_files/genome1.fst_prokka-split5N.fna-prokkaRes/EXAM.1219.00001.sprot.tmp.94917.faa
-[13:15:25] Deleting unwanted file: Examples/2-res-Annotate-prokka/tmp_files/genome1.fst_prokka-split5N.fna-prokkaRes/EXAM.1219.00001.sprot.tmp.94917.blast
-[13:15:25] There are still 4 unannotated CDS left (started with 11)
-[13:15:25] Will use hmmer3 to search against /Users/aperrin/Softwares/src/prokka-dec.19/db/hmm/HAMAP.hmm with 1 CPUs
-[13:15:25] Running: cat Examples\/2\-res\-Annotate\-prokka\/tmp_files\/genome1\.fst_prokka\-split5N\.fna\-prokkaRes\/EXAM\.1219\.00001\.HAMAP\.hmm\.tmp\.94917\.faa | parallel --gnu --plain -j 1 --block 459 --recstart '>' --pipe hmmscan --noali --notextw --acc -E 1e-09 --cpu 1 /Users/aperrin/Softwares/src/prokka-dec.19/db/hmm/HAMAP.hmm /dev/stdin > Examples\/2\-res\-Annotate\-prokka\/tmp_files\/genome1\.fst_prokka\-split5N\.fna\-prokkaRes\/EXAM\.1219\.00001\.HAMAP\.hmm\.tmp\.94917\.hmmer3 2> /dev/null
-[13:15:25] Deleting unwanted file: Examples/2-res-Annotate-prokka/tmp_files/genome1.fst_prokka-split5N.fna-prokkaRes/EXAM.1219.00001.HAMAP.hmm.tmp.94917.faa
-[13:15:25] Deleting unwanted file: Examples/2-res-Annotate-prokka/tmp_files/genome1.fst_prokka-split5N.fna-prokkaRes/EXAM.1219.00001.HAMAP.hmm.tmp.94917.hmmer3
-[13:15:25] Labelling remaining 4 proteins as 'hypothetical protein'
-[13:15:25] Possible /pseudo 'tRNA (guanine-N(1)-)-methyltransferase' at genome1_2 position 3427
-[13:15:25] Found 6 unique /gene codes.
-[13:15:25] Fixed 2 duplicate /gene - trmD_1 trmD_2
-[13:15:25] Fixed 1 colliding /gene names.
-[13:15:25] Adding /locus_tag identifiers
-[13:15:25] Assigned 11 locus_tags to CDS and RNA features.
-[13:15:25] Writing outputs to Examples/2-res-Annotate-prokka/tmp_files/genome1.fst_prokka-split5N.fna-prokkaRes/
-[13:15:25] Generating annotation statistics file
-[13:15:25] Generating Genbank and Sequin files
-[13:15:25] Running: tbl2asn -V b -a r10k -l paired-ends -M n -N 1 -y 'Annotated using prokka 1.14.5 from https://github.com/tseemann/prokka' -Z Examples\/2\-res\-Annotate\-prokka\/tmp_files\/genome1\.fst_prokka\-split5N\.fna\-prokkaRes\/EXAM\.1219\.00001\.err -i Examples\/2\-res\-Annotate\-prokka\/tmp_files\/genome1\.fst_prokka\-split5N\.fna\-prokkaRes\/EXAM\.1219\.00001\.fsa 2> /dev/null
-[13:15:25] Deleting unwanted file: Examples/2-res-Annotate-prokka/tmp_files/genome1.fst_prokka-split5N.fna-prokkaRes/errorsummary.val
-[13:15:25] Deleting unwanted file: Examples/2-res-Annotate-prokka/tmp_files/genome1.fst_prokka-split5N.fna-prokkaRes/EXAM.1219.00001.dr
-[13:15:25] Deleting unwanted file: Examples/2-res-Annotate-prokka/tmp_files/genome1.fst_prokka-split5N.fna-prokkaRes/EXAM.1219.00001.fixedproducts
-[13:15:25] Deleting unwanted file: Examples/2-res-Annotate-prokka/tmp_files/genome1.fst_prokka-split5N.fna-prokkaRes/EXAM.1219.00001.ecn
-[13:15:25] Deleting unwanted file: Examples/2-res-Annotate-prokka/tmp_files/genome1.fst_prokka-split5N.fna-prokkaRes/EXAM.1219.00001.val
-[13:15:25] Repairing broken .GBK output that tbl2asn produces...
-[13:15:25] Running: sed 's/COORDINATES: profile/COORDINATES:profile/' < Examples\/2\-res\-Annotate\-prokka\/tmp_files\/genome1\.fst_prokka\-split5N\.fna\-prokkaRes\/EXAM\.1219\.00001\.gbf > Examples\/2\-res\-Annotate\-prokka\/tmp_files\/genome1\.fst_prokka\-split5N\.fna\-prokkaRes\/EXAM\.1219\.00001\.gbk
-[13:15:25] Deleting unwanted file: Examples/2-res-Annotate-prokka/tmp_files/genome1.fst_prokka-split5N.fna-prokkaRes/EXAM.1219.00001.gbf
-[13:15:25] Output files:
-[13:15:25] Examples/2-res-Annotate-prokka/tmp_files/genome1.fst_prokka-split5N.fna-prokkaRes/EXAM.1219.00001.txt
-[13:15:25] Examples/2-res-Annotate-prokka/tmp_files/genome1.fst_prokka-split5N.fna-prokkaRes/EXAM.1219.00001.gff
-[13:15:25] Examples/2-res-Annotate-prokka/tmp_files/genome1.fst_prokka-split5N.fna-prokkaRes/EXAM.1219.00001.tbl
-[13:15:25] Examples/2-res-Annotate-prokka/tmp_files/genome1.fst_prokka-split5N.fna-prokkaRes/EXAM.1219.00001.sqn
-[13:15:25] Examples/2-res-Annotate-prokka/tmp_files/genome1.fst_prokka-split5N.fna-prokkaRes/EXAM.1219.00001.fna
-[13:15:25] Examples/2-res-Annotate-prokka/tmp_files/genome1.fst_prokka-split5N.fna-prokkaRes/EXAM.1219.00001.tsv
-[13:15:25] Examples/2-res-Annotate-prokka/tmp_files/genome1.fst_prokka-split5N.fna-prokkaRes/EXAM.1219.00001.err
-[13:15:25] Examples/2-res-Annotate-prokka/tmp_files/genome1.fst_prokka-split5N.fna-prokkaRes/EXAM.1219.00001.log
-[13:15:25] Examples/2-res-Annotate-prokka/tmp_files/genome1.fst_prokka-split5N.fna-prokkaRes/EXAM.1219.00001.ffn
-[13:15:25] Examples/2-res-Annotate-prokka/tmp_files/genome1.fst_prokka-split5N.fna-prokkaRes/EXAM.1219.00001.gbk
-[13:15:25] Examples/2-res-Annotate-prokka/tmp_files/genome1.fst_prokka-split5N.fna-prokkaRes/EXAM.1219.00001.fsa
-[13:15:25] Examples/2-res-Annotate-prokka/tmp_files/genome1.fst_prokka-split5N.fna-prokkaRes/EXAM.1219.00001.faa
-[13:15:25] Annotation finished successfully.
-[13:15:25] Walltime used: 0.07 minutes
-[13:15:25] If you use this result please cite the Prokka paper:
-[13:15:25] Seemann T (2014) Prokka: rapid prokaryotic genome annotation. Bioinformatics. 30(14):2068-9.
-[13:15:25] Type 'prokka --citation' for more details.
-[13:15:25] Thank you, come again.
diff --git a/Examples/2-res-Annotate-prokka/tmp_files/genome1.fst_prokka-split5N.fna-prokkaRes/EXAM.1219.00001.sqn b/Examples/2-res-Annotate-prokka/tmp_files/genome1.fst_prokka-split5N.fna-prokkaRes/EXAM.1219.00001.sqn
deleted file mode 100644
index f494125efd584126706b97ee44e17f04e84bdf70..0000000000000000000000000000000000000000
--- a/Examples/2-res-Annotate-prokka/tmp_files/genome1.fst_prokka-split5N.fna-prokkaRes/EXAM.1219.00001.sqn
+++ /dev/null
@@ -1,1072 +0,0 @@
-Seq-entry ::= set {
-  class genbank ,
-  seq-set {
-    set {
-      class nuc-prot ,
-      descr {
-        source {
-          org {
-            taxname "Genus species" ,
-            orgname {
-              mod {
-                {
-                  subtype strain ,
-                  subname "strain" } } ,
-              gcode 11 } } } ,
-        comment "Annotated using prokka 1.14.5 from
- https://github.com/tseemann/prokka" ,
-        user {
-          type
-            str "NcbiCleanup" ,
-          data {
-            {
-              label
-                str "method" ,
-              data
-                str "SeriousSeqEntryCleanup" } ,
-            {
-              label
-                str "version" ,
-              data
-                int 8 } ,
-            {
-              label
-                str "month" ,
-              data
-                int 12 } ,
-            {
-              label
-                str "day" ,
-              data
-                int 9 } ,
-            {
-              label
-                str "year" ,
-              data
-                int 2019 } } } ,
-        create-date
-          std {
-            year 2019 ,
-            month 12 ,
-            day 9 } } ,
-      seq-set {
-        seq {
-          id {
-            local
-              str "genome1_1" } ,
-          descr {
-            molinfo {
-              biomol genomic } } ,
-          inst {
-            repr raw ,
-            mol dna ,
-            length 2784 ,
-            seq-data
-              iupacna "ATGTGTAAAAGCCGGAGGGGTTATCTTTTCCCGGCTTTTTATTATCAATTACTCA
-TTAACTCCTGTTCCGTTCTTTTGCGTTTAATCACCGGAATATCTCCGGTATTGTTCAGCGCCCCGGAAATGTTTTTAA
-CCACTGTTCTGCACTCCGTTTATTAAACGCGCTCAGCGCGCGCTCATATATCGCGCGCGCGCGCGCGCATATATATAT
-AATGAGTGAGGCTGAAGCCCGCCCGACTAACTTTATTCGTCAGATTATTGATGAAGATCTGGCGAGTGGTAAACATAC
-CACTGTCCATACCCGTTTTCCGCCGGAGCCGAATGGCTATCTGCATATCGGCCACGCGAAATCTATCTGCCTGAACTT
-TGGCATCGCGCAAGATTATCAGGGCCAGTGCAACCTGCGTTTCGATGACACCAACCCGGTAAAAGAAGATATCGAGTA
-CGTTGATTCGATCAAAAACGACGTCGAGTGGTTAGGCTTTCACTGGTCTGGCGATATTCGCTACTCCTCCGATTACTT
-TGACCAACTGCACGCCTATGCGGTCGAGCTAATCAATAAAGGCCTGGCCTATGTTGATGAGCTGACGCCGGAGCAGAT
-CCGTGAATACCGCGGTACGCTGACCGCGCCGGGTAAAAACAGCCCGTTCCGCGATCGCAGCGTCGAAGAGAACCTCGC
-GCTATTTGAAAAAATGCGTACCGGCGGTTTTGAAGAGGGTAAAGCCTGTCTGCGCGCTAAAATCGACATGGCGTCGCC
-GTTTATCGTGATGCGCGATCCGGTGCTGTATCGCATTAAATTCGCCGAGCATCATCAGACTGGCAACAAGTGGTGCAT
-CTATCCGATGTACGACTTTACTCACTGCATCAGCGATGCGCTGGAAGGCATTACTCATTCTCTGTGTACGCTGGAGTT
-CCAGGATAACCGTCGTCTGTACGACTGGGTGCTGGACAACATCACCATTCCGGTTCACCCGCGCCAGTACGAATTCTC
-GCGCCTGAATCTGGAATACACCGTGATGTCCAAGCGTAAGCTGAACCTGCTGGTGACCGACAAACACGTCGAAGGTTG
-GGACGATCCGCGTATGCCGACTATTTCCGGTCTGCGCCGTCGCGGCTATACCGCGGCTTCTATTCGTGAGTTCTGCAA
-ACGCATCGGCGTCACCAAGCAGGACAACACTATTGAGATGGCGTCGCTGGAATCCTGCATTCGCGAAGATCTGAACGA
-AAACGCGCCGCGCGCGATGGCGGTAATCGATCCGGTAAAACTGGTTATCGAAAATTACCCGCAGGGTGAGAGCGAAAT
-GGTTACCATGCCTAACCATCCGAATAAACCGGAGATGGGCAGCCGTGAAGTGCCGTTTAGCGGTGAGATCTGGATCGA
-TCGCGCAGATTTCCGCGAAGAAGCGAACAAACAGTACAAACGTCTGGTGATGGGCAAAGAAGTGCGTCTGCGTAATGC
-CTACGTCATTAAAGCGGAGCGCGTAGAGAAGGATGCCGAAGGGAATATCACCACCATCTTCTGTACCTATGATGCTGA
-TACGCTGAGTAAAGATCCGGCTGACGGGCGTAAAGTGAAAGGCGTAATCCACTGGGTTAGCGCAGCACATGCGCTGCC
-GATTGAAATTCGTCTCTACGACCGTCTGTTCAGCGTGCCGAATCCGGGCGCCGCGGAGGACTTCCTGTCTGTTATCAA
-CCCCGAATCATTAGTGATTAAGCAGGGGTATGGCGAGCCGTCGCTGAAAGCGGCGGTAGCAGGAAAAGCTTTCCAGTT
-TGAACGTGAAGGCTACTTCTGCCTCGACAGCCGCTATGCAACGGCCGATAAGCTGGTCTTTAACCGCACCGTGGGCCT
-GCGTGATACCTGGGCGAAAGCGGGCGAGTAACGCGCATAGGCGGCCTTCAAGGAGGCGCTAGGCGAATGAAAGCGCTA
-CTGTGGCTGGTGGGTCTCGCGTTGCTGTTAACAGGCTGCGCGAGCGAAAAAGGAATTATCGATAAAGAGGGATATCAG
-CTTGATACCCGACATCGGGCGCAGGCGGCCTATCCGCGCATTAAAGTCCTGGTGATTCACTATACGGCGGAAAACTTT
-GACGTTTCGCTGGCGACGTTAACGGGTCGCAACGTCAGTTCGCATTACCTGATTCCCGCAACCCCGCCATTATATGGC
-GGTAAACCGCGCATCTGGCAACTGGTGCCGGAACAGGATCAGGCCTGGCATGCGGGCGTCAGTTTCTGGCGAGGCGCC
-ACGCGTCTCAATGATACGTCTATTGGCATTGAGCTGGAAAATCGTGGTTGGCGAATGTCCGGCGGGGTGAAATCTTTC
-GCGCCGTTTGAATCCGCGCAAATTCAGGCATTGATTCCGTTAGCGAAGGATATTATCGCGCGCTATAACATCAAACCG
-CAGAATGTGGTGGCCCATGCGGATATCGCGCCGCAGCGTAAAGACGATCCCGGCCCGCGCTTCCCGTGGCGCGAGCTG
-GCGGCGCAGGGGATTAGCGCCTGGCCTGACGCCCAGCGTGTGGCGTTTTATCTGGCTGGACGCGCGCCGTATACGCCA
-GTCGATACCGCAACGGTGCTTGCGTTACTCTCGCGCTATGGCTATGAAGTCAAAGCCGATATGACGGCACGCGAGCAG
-CAGCGGGTGATTATGGCGTTCCAGATGCACTTCCGTCCGGCGCAATGGAACGGTATCGCAGATGCCGAAACGCAGGCG
-ATTGCCGAAGCATTACTGGAGAAGTACGGCCAGGATTAACGCGATAGGCGCGCGAGATTACGCGCGCAGTATCGCGC" } } ,
-        seq {
-          id {
-            local
-              str "genome1_1_1" } ,
-          descr {
-            title "Glutamine--tRNA ligase [Genus species]" ,
-            molinfo {
-              biomol peptide ,
-              tech concept-trans } } ,
-          inst {
-            repr raw ,
-            mol aa ,
-            length 555 ,
-            seq-data
-              ncbieaa "MSEAEARPTNFIRQIIDEDLASGKHTTVHTRFPPEPNGYLHIGHAKSICLNFGIA
-QDYQGQCNLRFDDTNPVKEDIEYVDSIKNDVEWLGFHWSGDIRYSSDYFDQLHAYAVELINKGLAYVDELTPEQIREY
-RGTLTAPGKNSPFRDRSVEENLALFEKMRTGGFEEGKACLRAKIDMASPFIVMRDPVLYRIKFAEHHQTGNKWCIYPM
-YDFTHCISDALEGITHSLCTLEFQDNRRLYDWVLDNITIPVHPRQYEFSRLNLEYTVMSKRKLNLLVTDKHVEGWDDP
-RMPTISGLRRRGYTAASIREFCKRIGVTKQDNTIEMASLESCIREDLNENAPRAMAVIDPVKLVIENYPQGESEMVTM
-PNHPNKPEMGSREVPFSGEIWIDRADFREEANKQYKRLVMGKEVRLRNAYVIKAERVEKDAEGNITTIFCTYDADTLS
-KDPADGRKVKGVIHWVSAAHALPIEIRLYDRLFSVPNPGAAEDFLSVINPESLVIKQGYGEPSLKAAVAGKAFQFERE
-GYFCLDSRYATADKLVFNRTVGLRDTWAKAGE" } ,
-          annot {
-            {
-              data
-                ftable {
-                  {
-                    id
-                      local
-                        id 3 ,
-                    data
-                      prot {
-                        name {
-                          "Glutamine--tRNA ligase" } ,
-                        ec {
-                          "6.1.1.18" } } ,
-                    location
-                      int {
-                        from 0 ,
-                        to 554 ,
-                        id
-                          local
-                            str "genome1_1_1" } } } } } } ,
-        seq {
-          id {
-            local
-              str "genome1_1_2" } ,
-          descr {
-            title "N-acetylmuramoyl-L-alanine amidase AmiD [Genus species]" ,
-            molinfo {
-              biomol peptide ,
-              tech concept-trans } } ,
-          inst {
-            repr raw ,
-            mol aa ,
-            length 276 ,
-            seq-data
-              ncbieaa "MKALLWLVGLALLLTGCASEKGIIDKEGYQLDTRHRAQAAYPRIKVLVIHYTAEN
-FDVSLATLTGRNVSSHYLIPATPPLYGGKPRIWQLVPEQDQAWHAGVSFWRGATRLNDTSIGIELENRGWRMSGGVKS
-FAPFESAQIQALIPLAKDIIARYNIKPQNVVAHADIAPQRKDDPGPRFPWRELAAQGISAWPDAQRVAFYLAGRAPYT
-PVDTATVLALLSRYGYEVKADMTAREQQRVIMAFQMHFRPAQWNGIADAETQAIAEALLEKYGQD" } ,
-          annot {
-            {
-              data
-                ftable {
-                  {
-                    id
-                      local
-                        id 4 ,
-                    data
-                      prot {
-                        name {
-                          "N-acetylmuramoyl-L-alanine amidase AmiD" } ,
-                        ec {
-                          "3.5.1.28" } } ,
-                    location
-                      int {
-                        from 0 ,
-                        to 275 ,
-                        id
-                          local
-                            str "genome1_1_2" } } } } } } } ,
-      annot {
-        {
-          data
-            ftable {
-              {
-                id
-                  local
-                    id 1 ,
-                data
-                  cdregion {
-                    frame one ,
-                    code {
-                      id 11 } } ,
-                product
-                  whole
-                    local
-                      str "genome1_1_1" ,
-                location
-                  int {
-                    from 212 ,
-                    to 1879 ,
-                    strand plus ,
-                    id
-                      local
-                        str "genome1_1" } ,
-                qual {
-                  {
-                    qual "inference" ,
-                    val "ab initio prediction:Prodigal:002006" } ,
-                  {
-                    qual "inference" ,
-                    val "similar to AA sequence:UniProtKB:P00962" } } ,
-                xref {
-                  {
-                    data
-                      gene {
-                        locus "glnS" ,
-                        locus-tag "GKEGNCBE_00001" } } } ,
-                dbxref {
-                  {
-                    db "COG" ,
-                    tag
-                      str "COG0008" } } } ,
-              {
-                id
-                  local
-                    id 2 ,
-                data
-                  cdregion {
-                    frame one ,
-                    code {
-                      id 11 } } ,
-                product
-                  whole
-                    local
-                      str "genome1_1_2" ,
-                location
-                  int {
-                    from 1915 ,
-                    to 2745 ,
-                    strand plus ,
-                    id
-                      local
-                        str "genome1_1" } ,
-                qual {
-                  {
-                    qual "inference" ,
-                    val "ab initio prediction:Prodigal:002006" } ,
-                  {
-                    qual "inference" ,
-                    val "similar to AA sequence:UniProtKB:P75820" } } ,
-                xref {
-                  {
-                    data
-                      gene {
-                        locus "amiD" ,
-                        locus-tag "GKEGNCBE_00002" } } } ,
-                dbxref {
-                  {
-                    db "COG" ,
-                    tag
-                      str "COG3023" } } } } } } } ,
-    set {
-      class nuc-prot ,
-      descr {
-        source {
-          org {
-            taxname "Genus species" ,
-            orgname {
-              mod {
-                {
-                  subtype strain ,
-                  subname "strain" } } ,
-              gcode 11 } } } ,
-        comment "Annotated using prokka 1.14.5 from
- https://github.com/tseemann/prokka" ,
-        user {
-          type
-            str "NcbiCleanup" ,
-          data {
-            {
-              label
-                str "method" ,
-              data
-                str "SeriousSeqEntryCleanup" } ,
-            {
-              label
-                str "version" ,
-              data
-                int 8 } ,
-            {
-              label
-                str "month" ,
-              data
-                int 12 } ,
-            {
-              label
-                str "day" ,
-              data
-                int 9 } ,
-            {
-              label
-                str "year" ,
-              data
-                int 2019 } } } ,
-        create-date
-          std {
-            year 2019 ,
-            month 12 ,
-            day 9 } } ,
-      seq-set {
-        seq {
-          id {
-            local
-              str "genome1_2" } ,
-          descr {
-            molinfo {
-              biomol genomic } } ,
-          inst {
-            repr raw ,
-            mol dna ,
-            length 7024 ,
-            seq-data
-              iupacna "CGCGCATAGCGCGCAATGCCGCACTTTATTGCTGAATGTACTGAAAATATTCGCG
-AGCAGGCTGATTTACCCGGCCTGTTCAGCAAGGTAAACGAGGCGCTGGCCGCCAGCGGGATTTTCCCCATCGGCGGTA
-TCCGCAGTCGCGCCCACTGGCTGGATACCTGGCAGATGGCTGACGGTAAGCATGATTACGCGTTTGTGCATATGACGC
-TGAAAATCGGCGCCGGGCGCAGCCTGGAGAGCCGTCAGGAAGTTGGCGAAATGCTGTTTGGGCTGATTAAAGCCCACT
-TCGCCGACCTGATGGAGAACCGCTATCTGGCGCTGTCGTTTGAGATTGCCGAGCTACATCCGACGCTCAATTACAAAC
-AAAACAACGTACACGCGTTATTTAAATAGCCGATATGAGGCGCGGCGCTATAAGGCGCTCATGAGCATGCCCGCGACT
-AAATTCTCCCGACGTACCCTCCTGACGGCAGGTTCTGCGCTTGCTGTTCTTCCTTTTCTGCGCGCCTTGCCGGTACAG
-GCGCGTGAACCTCGCGAGACCGTCGATATTAAGGATTATCCGGCGGATGACGGTATCGCCTCGTTCAAACAGGCCTTC
-GCCGACGGACAGACCGTGGTCGTACCGCCAGGATGGGTGTGTGAAAATATCAATGCGGCGATAACGATTCCGGCGGGA
-AAAACGCTGCGGGTACAGGGCGCGGTGCGTGGGAATGGCCGGGGACGGTTTATTTTGCAGGACGGGTGTCAGGTGGTG
-GGGGAGCAGGGCGGCAGTCTGCACAATGTGACGCTGGATGTTCGCGGGTCGGACTGTGTGATTAAAGGCGTGGCGATG
-AGCGGCTTTGGCCCCGTCGCGCAAATTTTCATCGGTGGTAAGGAACCGCAGGTGATGCGTAATCTCATTATCGATGAC
-ATCACCGTTACCCACGCCAACTACGCCATTCTCCGCCAGGGATTTCATAACCAAATGGATGGCGCGCGGATTACGCAT
-AGCCGCTTTAGCGATTTACAGGGGGACGCCATTGAGTGGAATGTCGCGATTCACGACCGCGACATCCTGATTTCCGAT
-CATGTCATCGAACGCATTAATTGTACCAATGGCAAAATCAACTGGGGGATCGGCATCGGGCTGGCGGGTAGCACCTAT
-GACAACAGTTATCCTGAAGACCAGGCAGTAAAAAACTTTGTGGTGGCCAATATTACCGGATCTGATTGCCGACAGCTT
-GTGCACGTAGAAAATGGCAAACATTTCGTCATTCGCAATGTCAAAGCCAAAAACATCACGCCCGGTTTCAGTAAAAAT
-GCGGGTATTGATAACGCAACGATCGCAATTTATGGCTGTGATAATTTCGTCATTGATAATATTGATATGACGAATAGT
-GCCGGGATGCTCATCGGCTATGGCGTCGTTAAAGGAAAATACCTGTCAATTCCGCAAAACTTTAAATTAAACGCTATT
-CGGTTGGATAATCGCCAGGTTGCTTATAAATTACGCGGCATTCAAATTTCCTCCGGCAACACCCCCTCTTTTGTCGCC
-ATCACCAATGTACGGATGACGCGTGCTACGCTGGAACTGCATAATCAACCGCAGCACCTCTTTCTGCGCAATATCAAC
-GTGATGCAAACTTCAGCGATTGGCCCGGCGTTAAAAATGCATTTCGATTTGCGTAAAGATGTACGTGGTCAATTTATG
-GCCCGCCAGGACACGCTGCTTTCCCTCGCTAATGTTCATGCCATCAATGAAAACGGGCAGAGTTCCGTGGATATCGAC
-AGGATTAATCACCAAACCGTGAATGTCGAAGCAGTGAATTTTTCGCTGCCGAAGCGGGGAGGGTAACGAATTCCGCGG
-CATATAGCGGCGCGATAGCATGTCAGAAAATAAATTACACGTTATCGATTTGCACAAACGCTACGGCGGTCATGAAGT
-GCTGAAAGGGGTATCGCTGCAGGCCCGCGCCGGAGATGTGATTAGCATCATCGGCTCGTCCGGCTCCGGTAAAAGCAC
-TTTTTTGCGCTGTATTAACTTCCTCGAAAAACCGAGCGAAGGCGCGATTATCGTGAACGGTCAGAACATTAATCTGGT
-GCGCGACAAAGATGGGCAGCTCAAAGTGGCGGATAAAAATCAGCTACGCTTGTTGCGTACCCGCCTGACGATGGTGTT
-TCAGCACTTCAACCTCTGGAGCCACATGACGGTGCTGGAAAATGTGATGGAAGCGCCGATTCAGGTACTGGGATTAAG
-CAAGCACGACGCGCGCGAGCGGGCGTTGAAATATCTGGCGAAGGTGGGGATTGATGAGCGCGCTCAGGGCAAATATCC
-CGTCCATCTCTCCGGCGGCCAACAGCAGCGCGTTTCTATTGCGCGCGCGCTGGCGATGGAACCTGACGTTTTACTGTT
-CGATGAACCCACATCGGCGCTCGATCCTGAACTGGTCGGCGAAGTGTTGCGCATCATGCAACAACTGGCGGAAGAAGG
-CAAAACGATGGTGGTGGTCACGCATGAAATGGGCTTCGCTCGCCATGTCTCTTCGCACGTTATTTTTCTGCATCAGGG
-GAAAATTGAAGAAGAGGGTGATCCGGAGCAGGTGTTCGGCAATCCGCAAAGCCCGCGTTTACAGCAATTCCTGAAAGG
-CTCGCTGAAATAACGCTCAGAGGCGCGCGCGCGCTATATACGCGCAGTGTTTATTGGCATAGTTAGCCTGTTTCCTGA
-AATGTTCCGCGCAATTACCGATTACGGGGTAACTGGCCGGGCAGTAAAAAAAGGCCTGCTGAACATCCAAAGCTGGAG
-TCCTCGCGACTTCGCGCATGACCGGCACCGTACCGTGGACGACCGTCCTTACGGCGGCGGACCGGGGATGTTAATGAT
-GGTGCAACCCTTGCGGGACGCCATTCACGCAGCAAAAGCCGCGGCAGGTGAAGGCGCTAAAGTGATTTATCTGTCGCC
-TCAGGGACGCAAGCTTGATCAAGCGGGCGTTAGCGAGCTGGCCACGAATCAGAAGCTTATTCTGGTGTGTGGTCGCTA
-CGAAGGCGTAGATGAGCGCGTAATTCAGACCGAAATTGACGAAGAATGGTCAATTGGCGATTACGTTCTCAGCGGTGG
-CGAACTACCGGCAATGACGCTGATTGACTCCGTCGCCCGGTTTATACCGGGGGTTCTGGGGCATGAGGCATCAGCAAT
-CGAAGATTCGTTTGCTGATGGGTTGCTGGATTGTCCGCACTATACGCGCCCTGAAGTGTTAGAGGGGATGGAAGTACC
-GCCAGTATTGCTGTCGGGAAACCATGCTGAGATACGTCGCTGGCGTTTGAAACAGTCGCTGGGCCGAACCTGGCTTAG
-AAGACCTGAACTTCTGGAAAACCTGGCTCTGACTGAAGAGCAAGCAAGGTTGCTGGCGGAGTTCAAAACAGAACACGC
-ACAACAGCAGCATAAACATGATGGGATGGCATAGCCGTCATATGGGCTCTCAGAGGAGACGCGCTAATGCGCAGTACG
-TGTTTATTGGCATAGTTAGCCTGTTTCCTGAAATGTTCCGCGCAATTACCGATTACGGGGTAACTGGCCGGGCAGTAA
-AAAAAGGCCTGCTGAACATCCAAAGCTGGAGTCCTCGCGACTTCGCGCATGACCGGCACCGTACCGTGGACGACCGTC
-CTTACGGCGGCGGACCGGGGATGTTAATGATGGTGCAACCCTTGCGGGACGCCATTCACGCAGCAAAAGCCGCGGCAG
-GTGAAGGCGCTAAAGTGATTTATCTGTCGCCTCAGGGACGCAAGCTTGATCAAGCGGGCGTTAGCGAGCTGGCCACGA
-ATCAGAAGCTTATTCTGGTGTGTGGTCGCTACGAAGGCGTAGATGAGCGCGTAATTCAGACCGAAATTGACGAAGAAT
-GGTCAATTGGCGATTACGTTCTCAGCGGTGGCGAACTACCGGCAATGACGCTGATTGACTCCGTCGCCCGGTTTATAC
-CGGGGGTTCTGGGGCATGAGGCATCAGCAATCGAAGATTCGTTTGCTGATGGGTTGCTGGATTGTCCGCACTATACGC
-GCCCTGAAGTGTTAGAGGGGATGGAAGTACCGCCAGTATTGCTGTCGGGAAACCATGCTGAGATACGTCGCTGGCGTT
-TGAAACAGTCGCTGGGCCGAACCTGGCTTAGAAGACCTGAACTTCTGGAAAACCTGGCTCTGACTGAAGAGCAAGCAA
-GGTTGCTGGCGGAGTTCAAAACAGAACACGCACAACAGCAGCATAAACATGATGGGATGGCATAGCGCATACGCGCGC
-GATATATATTCGCGCAGAGGCGCGCATAGCGATGAAGTTTGTTGCGCCCGAACAGGCACCGGAACAGGCGGAGGTCAT
-CAAAAATACGCCGTTCTGGCCTGATGTGGACCTGTCGGAATTTCGCAGTGTGATGCGCACTGACGGCACGGTGACGCA
-GCCGCGTTTAAAGCAGGTCGTGCTGACGGCGATCTCTGAGGTTAACGCTGAGCTGTACGACTTCCGCAACCGTCAGCA
-GATGCTGGGCTGGCGGACACTTGCTGAGGTTCCCGCAGAAATGCTGGACGGTAAAAGCGAGCGTATCCGGCACTACCA
-CAACGCTGTTTTTTGCTGGGCGCGCGCTGTGCTTAATGAGCGTTATCAGGACTATGACGCCACGGCGTCAGGCGTGAA
-GCGAGGGGAGGAGCTGGCGGAGGCCAGCGGCGATCTGTGGCGTGATGCCCGCTGGGCCATCAGCCGGGTGCAGGATGT
-ACCGCACTGTACGGTGGAGCTTATCTGAACGGCTAGCGCGTAGCGGCAGTCTCGGATGAATAATCATTTTGGGAAAGG
-GTTAATGGCCGGGTTGCACGCGCCATATGCATATAGCGCGCATCATGCGGTGAATTTCTGTTCTGAGTATAAACGTGG
-CTTTGTATTGGGTTTTACACACCGTATGTTCGAAAAGACCGGCGATCGTCAACTTAGCGCGTGGGAGGCTGGAATTCT
-GACGCGTCGCTATGGTCTGGATAAAGAAATGGTGATGGATTTCTTTAAAGAGAATCATTCCGGGATGGCGGTTCGCTT
-CTTTATGGCCGGTTATCGACTCGAAGGTTGACGATCGCGCGCAGGAGGAGAGCTCTCTTCTTCTAGAGCATGTCTACG
-CTTCTCTATTTGCACGGATTCAACAGTTCCCCTCGCTCGGCAAAAGCGTGCCAGCTAAAAAACTGGCTGGCGGAGCGT
-CATCCGCATGTTGAGATGATCGTCCCTCAGCTGCCGCCGTATCCTGCCGATGCGGCGGAGTTGCTGGAATCTCTCGTG
-CTTGAGCATGGCGGTGCGCCATTAGGGCTGGTAGGATCGTCGCTGGGTGGTTATTACGCCACCTGGCTGTCGCAATGT
-TTTATGCTGCCGGCTGTGGTGGTGAATCCCGCCGTGCGGCCCTTTGAATTACTGACCGACTATCTCGGTCAGAACGAG
-AACCCCTACACCGGGCAGCAATATGTGCTAGAGTCTCGCCATATTTATGATCTTAAAGTCATGCAGATTGACCCGCTG
-GAAGCGCCGGACCTGATCTGGCTACTGCAACAGACGGGCGATGAAGTGCTGTATTACCGCCAGGCGGTGGCATATTAC
-GCCTCCTGCCGTCAGACAGTGACCGAGGGTGGTAATCACGCATTCACGGGCTTCGAAGATTATTTCAACCAGATTGTC
-GATTTTCTTGGACTGCACAGTTGCTGACGGCTATGCGCGCGCTCGATGATTGACCCTATTTTTGCGTCCTGTACGCTA
-ATTGCCGTCTTTGTTGTTTTACTGGCCATGGGCGCGCCTATCGGGATCTGCATCGTTATCGCCTCTTTCAGCACCATG
-ATGCTGGTACTGCCTTTCGATATTTCGATGTTCGCCACCGCGCAAAAAATGTTCTCCAGCCTGGACAGTTTTGCCTTG
-CTGGCCGTGCCGTTCTTCGTTTTGTCCGGGGTGATCATGAATAGCGGGGGAATTGCCGCCCGGCTGGTCAATTTTGCC
-AAACTGTTTACTGGCAAACTGCCCGGCTCGCTCTCTTATACCAACATCGTCGGCAATATGATGTTCGGTGCAATTTCC
-GGATCGGCGATTGCCGCCTCAACCTCCATCGGCGGCGTGATGGTGCCGATGAGCGCGCGCGAAGGTTACGATCGCGGC
-TTTGCGGCCGCGGTGAATATCGCCTCCGCGCCGACGGGAATGTTAATTCCGCCCACCACGGCTTTTATCCTTTACGCG
-CTGGCAAGCGGGGGAACATCGATTGCCGCTCTGTTCGCCGGCGGTCTGGTCGCGGGAGTGCTGTGGGGCGTTGGCTGT
-ATGCTGGTCACGCTGGTGGTCGCTAAGCGTCGAAATTATCGGGTTTTCTTCACCGTCCAAAAAGGTATGGCGCTAAAA
-GTTGCCGTTGAGGCCATTCCCAGCCTGCTGCTGATCGTGATTATTGTCGGCGGCATTGTGCAGGGGATTTTCACCGCC
-ATTGAAGCCTCCGCGATTGCCGTGGTGTATACGTTATTGCTGACGATGGTGTTTTACCGCACGCTGAAAATTAAGGAT
-TTGCCTTCGATTTTGCTCCAGACAGTGGTAATGACCGGGGTCATCATGTTCCTGCTGGCAACCTCTTCGGCGATGTCC
-TTCTCGATGTCGATCACCAATATTCCTGCGGCGCTGAGCGATATGATCCTCGGTATTTCCGCCAATAAACTGGTTATC
-CTGTTAGTCATTACCGTCTTTTTGTTGATTATCGGCGCATTTATGGATATTGGTCCGGCCATTCTGATTTTTACCCCG
-ATTCTGCTGCCAATCATGGCTAAACTGGGCGTCGATCCGGTGCATTTCGGCATTATCATGATCTATAACCTGGCGATT
-GGCACCATTACGCCGCCAGTTGGCAGTGGTTTATATGTCGGGGCGAGCGTCGGTAAGGTCAAAGTTGAGGAAGTGATT
-AAACCGTTGCTGCCTTTTTACGGCGCGATTATCGGCGTTCTGTTATTAATTACCTACATTCCGGAAATCACACTGTTC
-TTACCCCGTCTACTGGGCATCATGTAA" } } ,
-        seq {
-          id {
-            local
-              str "genome1_2_1" } ,
-          descr {
-            title "5-carboxymethyl-2-hydroxymuconate Delta-isomerase [Genus
- species]" ,
-            molinfo {
-              biomol peptide ,
-              tech concept-trans } } ,
-          inst {
-            repr raw ,
-            mol aa ,
-            length 126 ,
-            seq-data
-              ncbieaa "MPHFIAECTENIREQADLPGLFSKVNEALAASGIFPIGGIRSRAHWLDTWQMADG
-KHDYAFVHMTLKIGAGRSLESRQEVGEMLFGLIKAHFADLMENRYLALSFEIAELHPTLNYKQNNVHALFK" } ,
-          annot {
-            {
-              data
-                ftable {
-                  {
-                    id
-                      local
-                        id 14 ,
-                    data
-                      prot {
-                        name {
-                          "5-carboxymethyl-2-hydroxymuconate Delta-isomerase" } ,
-                        ec {
-                          "5.3.3.10" } } ,
-                    location
-                      int {
-                        from 0 ,
-                        to 125 ,
-                        id
-                          local
-                            str "genome1_2_1" } } } } } } ,
-        seq {
-          id {
-            local
-              str "genome1_2_2" } ,
-          descr {
-            title "hypothetical protein GKEGNCBE_00004 [Genus species]" ,
-            molinfo {
-              biomol peptide ,
-              tech concept-trans } } ,
-          inst {
-            repr raw ,
-            mol aa ,
-            length 469 ,
-            seq-data
-              ncbieaa "MSMPATKFSRRTLLTAGSALAVLPFLRALPVQAREPRETVDIKDYPADDGIASFK
-QAFADGQTVVVPPGWVCENINAAITIPAGKTLRVQGAVRGNGRGRFILQDGCQVVGEQGGSLHNVTLDVRGSDCVIKG
-VAMSGFGPVAQIFIGGKEPQVMRNLIIDDITVTHANYAILRQGFHNQMDGARITHSRFSDLQGDAIEWNVAIHDRDIL
-ISDHVIERINCTNGKINWGIGIGLAGSTYDNSYPEDQAVKNFVVANITGSDCRQLVHVENGKHFVIRNVKAKNITPGF
-SKNAGIDNATIAIYGCDNFVIDNIDMTNSAGMLIGYGVVKGKYLSIPQNFKLNAIRLDNRQVAYKLRGIQISSGNTPS
-FVAITNVRMTRATLELHNQPQHLFLRNINVMQTSAIGPALKMHFDLRKDVRGQFMARQDTLLSLANVHAINENGQSSV
-DIDRINHQTVNVEAVNFSLPKRGG" } ,
-          annot {
-            {
-              data
-                ftable {
-                  {
-                    id
-                      local
-                        id 15 ,
-                    data
-                      prot {
-                        name {
-                          "hypothetical protein" } } ,
-                    location
-                      int {
-                        from 0 ,
-                        to 468 ,
-                        id
-                          local
-                            str "genome1_2_2" } } } } } } ,
-        seq {
-          id {
-            local
-              str "genome1_2_3" } ,
-          descr {
-            title "Histidine transport ATP-binding protein HisP [Genus
- species]" ,
-            molinfo {
-              biomol peptide ,
-              tech concept-trans } } ,
-          inst {
-            repr raw ,
-            mol aa ,
-            length 257 ,
-            seq-data
-              ncbieaa "MSENKLHVIDLHKRYGGHEVLKGVSLQARAGDVISIIGSSGSGKSTFLRCINFLE
-KPSEGAIIVNGQNINLVRDKDGQLKVADKNQLRLLRTRLTMVFQHFNLWSHMTVLENVMEAPIQVLGLSKHDARERAL
-KYLAKVGIDERAQGKYPVHLSGGQQQRVSIARALAMEPDVLLFDEPTSALDPELVGEVLRIMQQLAEEGKTMVVVTHE
-MGFARHVSSHVIFLHQGKIEEEGDPEQVFGNPQSPRLQQFLKGSLK" } ,
-          annot {
-            {
-              data
-                ftable {
-                  {
-                    id
-                      local
-                        id 16 ,
-                    data
-                      prot {
-                        name {
-                          "Histidine transport ATP-binding protein HisP" } } ,
-                    location
-                      int {
-                        from 0 ,
-                        to 256 ,
-                        id
-                          local
-                            str "genome1_2_3" } } } } } } ,
-        seq {
-          id {
-            local
-              str "genome1_2_4" } ,
-          descr {
-            title "tRNA (guanine-N(1)-)-methyltransferase [Genus species]" ,
-            molinfo {
-              biomol peptide ,
-              tech concept-trans } } ,
-          inst {
-            repr raw ,
-            mol aa ,
-            length 244 ,
-            seq-data
-              ncbieaa "MFRAITDYGVTGRAVKKGLLNIQSWSPRDFAHDRHRTVDDRPYGGGPGMLMMVQP
-LRDAIHAAKAAAGEGAKVIYLSPQGRKLDQAGVSELATNQKLILVCGRYEGVDERVIQTEIDEEWSIGDYVLSGGELP
-AMTLIDSVARFIPGVLGHEASAIEDSFADGLLDCPHYTRPEVLEGMEVPPVLLSGNHAEIRRWRLKQSLGRTWLRRPE
-LLENLALTEEQARLLAEFKTEHAQQQHKHDGMA" } ,
-          annot {
-            {
-              data
-                ftable {
-                  {
-                    id
-                      local
-                        id 17 ,
-                    data
-                      prot {
-                        name {
-                          "tRNA (guanine-N(1)-)-methyltransferase" } ,
-                        ec {
-                          "2.1.1.228" } } ,
-                    location
-                      int {
-                        from 0 ,
-                        to 243 ,
-                        id
-                          local
-                            str "genome1_2_4" } } } } } } ,
-        seq {
-          id {
-            local
-              str "genome1_2_5" } ,
-          descr {
-            title "tRNA (guanine-N(1)-)-methyltransferase [Genus species]" ,
-            molinfo {
-              biomol peptide ,
-              tech concept-trans } } ,
-          inst {
-            repr raw ,
-            mol aa ,
-            length 275 ,
-            seq-data
-              ncbieaa "MMGWHSRHMGSQRRRANAQYVFIGIVSLFPEMFRAITDYGVTGRAVKKGLLNIQS
-WSPRDFAHDRHRTVDDRPYGGGPGMLMMVQPLRDAIHAAKAAAGEGAKVIYLSPQGRKLDQAGVSELATNQKLILVCG
-RYEGVDERVIQTEIDEEWSIGDYVLSGGELPAMTLIDSVARFIPGVLGHEASAIEDSFADGLLDCPHYTRPEVLEGME
-VPPVLLSGNHAEIRRWRLKQSLGRTWLRRPELLENLALTEEQARLLAEFKTEHAQQQHKHDGMA" } ,
-          annot {
-            {
-              data
-                ftable {
-                  {
-                    id
-                      local
-                        id 18 ,
-                    data
-                      prot {
-                        name {
-                          "tRNA (guanine-N(1)-)-methyltransferase" } ,
-                        ec {
-                          "2.1.1.228" } } ,
-                    location
-                      int {
-                        from 0 ,
-                        to 274 ,
-                        id
-                          local
-                            str "genome1_2_5" } } } } } } ,
-        seq {
-          id {
-            local
-              str "genome1_2_6" } ,
-          descr {
-            title "hypothetical protein GKEGNCBE_00008 [Genus species]" ,
-            molinfo {
-              biomol peptide ,
-              tech concept-trans } } ,
-          inst {
-            repr raw ,
-            mol aa ,
-            length 154 ,
-            seq-data
-              ncbieaa "MKFVAPEQAPEQAEVIKNTPFWPDVDLSEFRSVMRTDGTVTQPRLKQVVLTAISE
-VNAELYDFRNRQQMLGWRTLAEVPAEMLDGKSERIRHYHNAVFCWARAVLNERYQDYDATASGVKRGEELAEASGDLW
-RDARWAISRVQDVPHCTVELI" } ,
-          annot {
-            {
-              data
-                ftable {
-                  {
-                    id
-                      local
-                        id 19 ,
-                    data
-                      prot {
-                        name {
-                          "hypothetical protein" } } ,
-                    location
-                      int {
-                        from 0 ,
-                        to 153 ,
-                        id
-                          local
-                            str "genome1_2_6" } } } } } } ,
-        seq {
-          id {
-            local
-              str "genome1_2_7" } ,
-          descr {
-            title "hypothetical protein GKEGNCBE_00009 [Genus species]" ,
-            molinfo {
-              biomol peptide ,
-              tech concept-trans } } ,
-          inst {
-            repr raw ,
-            mol aa ,
-            length 86 ,
-            seq-data
-              ncbieaa "MAGLHAPYAYSAHHAVNFCSEYKRGFVLGFTHRMFEKTGDRQLSAWEAGILTRRY
-GLDKEMVMDFFKENHSGMAVRFFMAGYRLEG" } ,
-          annot {
-            {
-              data
-                ftable {
-                  {
-                    id
-                      local
-                        id 20 ,
-                    data
-                      prot {
-                        name {
-                          "hypothetical protein" } } ,
-                    location
-                      int {
-                        from 0 ,
-                        to 85 ,
-                        id
-                          local
-                            str "genome1_2_7" } } } } } } ,
-        seq {
-          id {
-            local
-              str "genome1_2_8" } ,
-          descr {
-            title "hypothetical protein GKEGNCBE_00010 [Genus species]" ,
-            molinfo {
-              biomol peptide ,
-              tech concept-trans } } ,
-          inst {
-            repr raw ,
-            mol aa ,
-            length 193 ,
-            seq-data
-              ncbieaa "MSTLLYLHGFNSSPRSAKACQLKNWLAERHPHVEMIVPQLPPYPADAAELLESLV
-LEHGGAPLGLVGSSLGGYYATWLSQCFMLPAVVVNPAVRPFELLTDYLGQNENPYTGQQYVLESRHIYDLKVMQIDPL
-EAPDLIWLLQQTGDEVLYYRQAVAYYASCRQTVTEGGNHAFTGFEDYFNQIVDFLGLHSC" } ,
-          annot {
-            {
-              data
-                ftable {
-                  {
-                    id
-                      local
-                        id 21 ,
-                    data
-                      prot {
-                        name {
-                          "hypothetical protein" } } ,
-                    location
-                      int {
-                        from 0 ,
-                        to 192 ,
-                        id
-                          local
-                            str "genome1_2_8" } } } } } } ,
-        seq {
-          id {
-            local
-              str "genome1_2_9" } ,
-          descr {
-            title "C4-dicarboxylate TRAP transporter large permease protein
- DctM [Genus species]" ,
-            molinfo {
-              biomol peptide ,
-              tech concept-trans } } ,
-          inst {
-            repr raw ,
-            mol aa ,
-            length 435 ,
-            seq-data
-              ncbieaa "MIDPIFASCTLIAVFVVLLAMGAPIGICIVIASFSTMMLVLPFDISMFATAQKMF
-SSLDSFALLAVPFFVLSGVIMNSGGIAARLVNFAKLFTGKLPGSLSYTNIVGNMMFGAISGSAIAASTSIGGVMVPMS
-AREGYDRGFAAAVNIASAPTGMLIPPTTAFILYALASGGTSIAALFAGGLVAGVLWGVGCMLVTLVVAKRRNYRVFFT
-VQKGMALKVAVEAIPSLLLIVIIVGGIVQGIFTAIEASAIAVVYTLLLTMVFYRTLKIKDLPSILLQTVVMTGVIMFL
-LATSSAMSFSMSITNIPAALSDMILGISANKLVILLVITVFLLIIGAFMDIGPAILIFTPILLPIMAKLGVDPVHFGI
-IMIYNLAIGTITPPVGSGLYVGASVGKVKVEEVIKPLLPFYGAIIGVLLLITYIPEITLFLPRLLGIM" } ,
-          annot {
-            {
-              data
-                ftable {
-                  {
-                    id
-                      local
-                        id 22 ,
-                    data
-                      prot {
-                        name {
-                          "C4-dicarboxylate TRAP transporter large permease
- protein DctM" } } ,
-                    location
-                      int {
-                        from 0 ,
-                        to 434 ,
-                        id
-                          local
-                            str "genome1_2_9" } } } } } } } ,
-      annot {
-        {
-          data
-            ftable {
-              {
-                id
-                  local
-                    id 5 ,
-                data
-                  cdregion {
-                    frame one ,
-                    code {
-                      id 11 } } ,
-                product
-                  whole
-                    local
-                      str "genome1_2_1" ,
-                location
-                  int {
-                    from 15 ,
-                    to 395 ,
-                    strand plus ,
-                    id
-                      local
-                        str "genome1_2" } ,
-                qual {
-                  {
-                    qual "inference" ,
-                    val "ab initio prediction:Prodigal:002006" } ,
-                  {
-                    qual "inference" ,
-                    val "similar to AA sequence:UniProtKB:Q05354" } } ,
-                xref {
-                  {
-                    data
-                      gene {
-                        locus "hpcD" ,
-                        locus-tag "GKEGNCBE_00003" } } } } ,
-              {
-                id
-                  local
-                    id 6 ,
-                data
-                  cdregion {
-                    frame one ,
-                    code {
-                      id 11 } } ,
-                product
-                  whole
-                    local
-                      str "genome1_2_2" ,
-                location
-                  int {
-                    from 427 ,
-                    to 1836 ,
-                    strand plus ,
-                    id
-                      local
-                        str "genome1_2" } ,
-                qual {
-                  {
-                    qual "inference" ,
-                    val "ab initio prediction:Prodigal:002006" } } ,
-                xref {
-                  {
-                    data
-                      gene {
-                        locus-tag "GKEGNCBE_00004" } } } } ,
-              {
-                id
-                  local
-                    id 7 ,
-                data
-                  cdregion {
-                    frame one ,
-                    code {
-                      id 11 } } ,
-                product
-                  whole
-                    local
-                      str "genome1_2_3" ,
-                location
-                  int {
-                    from 1868 ,
-                    to 2641 ,
-                    strand plus ,
-                    id
-                      local
-                        str "genome1_2" } ,
-                qual {
-                  {
-                    qual "inference" ,
-                    val "ab initio prediction:Prodigal:002006" } ,
-                  {
-                    qual "inference" ,
-                    val "similar to AA sequence:UniProtKB:P02915" } } ,
-                xref {
-                  {
-                    data
-                      gene {
-                        locus "hisP" ,
-                        locus-tag "GKEGNCBE_00005" } } } ,
-                dbxref {
-                  {
-                    db "COG" ,
-                    tag
-                      str "COG4598" } } } ,
-              {
-                id
-                  local
-                    id 8 ,
-                data
-                  cdregion {
-                    frame one ,
-                    code {
-                      id 11 } } ,
-                product
-                  whole
-                    local
-                      str "genome1_2_4" ,
-                location
-                  int {
-                    from 2708 ,
-                    to 3442 ,
-                    strand plus ,
-                    id
-                      local
-                        str "genome1_2" } ,
-                qual {
-                  {
-                    qual "inference" ,
-                    val "ab initio prediction:Prodigal:002006" } ,
-                  {
-                    qual "inference" ,
-                    val "similar to AA sequence:UniProtKB:P0A873" } } ,
-                xref {
-                  {
-                    data
-                      gene {
-                        locus "trmD_1" ,
-                        locus-tag "GKEGNCBE_00006" } } } ,
-                dbxref {
-                  {
-                    db "COG" ,
-                    tag
-                      str "COG0336" } } } ,
-              {
-                id
-                  local
-                    id 9 ,
-                data
-                  cdregion {
-                    frame one ,
-                    code {
-                      id 11 } } ,
-                product
-                  whole
-                    local
-                      str "genome1_2_5" ,
-                location
-                  int {
-                    from 3426 ,
-                    to 4253 ,
-                    strand plus ,
-                    id
-                      local
-                        str "genome1_2" } ,
-                qual {
-                  {
-                    qual "inference" ,
-                    val "ab initio prediction:Prodigal:002006" } ,
-                  {
-                    qual "inference" ,
-                    val "similar to AA sequence:UniProtKB:P0A873" } } ,
-                xref {
-                  {
-                    data
-                      gene {
-                        locus "trmD_2" ,
-                        locus-tag "GKEGNCBE_00007" } } } ,
-                dbxref {
-                  {
-                    db "COG" ,
-                    tag
-                      str "COG0336" } } } ,
-              {
-                id
-                  local
-                    id 10 ,
-                data
-                  cdregion {
-                    frame one ,
-                    code {
-                      id 11 } } ,
-                product
-                  whole
-                    local
-                      str "genome1_2_6" ,
-                location
-                  int {
-                    from 4298 ,
-                    to 4762 ,
-                    strand plus ,
-                    id
-                      local
-                        str "genome1_2" } ,
-                qual {
-                  {
-                    qual "inference" ,
-                    val "ab initio prediction:Prodigal:002006" } } ,
-                xref {
-                  {
-                    data
-                      gene {
-                        locus-tag "GKEGNCBE_00008" } } } } ,
-              {
-                id
-                  local
-                    id 11 ,
-                data
-                  cdregion {
-                    frame one ,
-                    code {
-                      id 11 } } ,
-                product
-                  whole
-                    local
-                      str "genome1_2_7" ,
-                location
-                  int {
-                    from 4817 ,
-                    to 5077 ,
-                    strand plus ,
-                    id
-                      local
-                        str "genome1_2" } ,
-                qual {
-                  {
-                    qual "inference" ,
-                    val "ab initio prediction:Prodigal:002006" } } ,
-                xref {
-                  {
-                    data
-                      gene {
-                        locus-tag "GKEGNCBE_00009" } } } } ,
-              {
-                id
-                  local
-                    id 12 ,
-                data
-                  cdregion {
-                    frame one ,
-                    code {
-                      id 11 } } ,
-                product
-                  whole
-                    local
-                      str "genome1_2_8" ,
-                location
-                  int {
-                    from 5116 ,
-                    to 5697 ,
-                    strand plus ,
-                    id
-                      local
-                        str "genome1_2" } ,
-                qual {
-                  {
-                    qual "inference" ,
-                    val "ab initio prediction:Prodigal:002006" } } ,
-                xref {
-                  {
-                    data
-                      gene {
-                        locus-tag "GKEGNCBE_00010" } } } } ,
-              {
-                id
-                  local
-                    id 13 ,
-                data
-                  cdregion {
-                    frame one ,
-                    code {
-                      id 11 } } ,
-                product
-                  whole
-                    local
-                      str "genome1_2_9" ,
-                location
-                  int {
-                    from 5716 ,
-                    to 7023 ,
-                    strand plus ,
-                    id
-                      local
-                        str "genome1_2" } ,
-                qual {
-                  {
-                    qual "inference" ,
-                    val "ab initio prediction:Prodigal:002006" } ,
-                  {
-                    qual "inference" ,
-                    val "similar to AA sequence:UniProtKB:O07838" } } ,
-                xref {
-                  {
-                    data
-                      gene {
-                        locus "dctM" ,
-                        locus-tag "GKEGNCBE_00011" } } } ,
-                dbxref {
-                  {
-                    db "COG" ,
-                    tag
-                      str "COG1593" } } } } } } } } }
diff --git a/Examples/2-res-Annotate-prokka/tmp_files/genome1.fst_prokka-split5N.fna-prokkaRes/EXAM.1219.00001.tbl b/Examples/2-res-Annotate-prokka/tmp_files/genome1.fst_prokka-split5N.fna-prokkaRes/EXAM.1219.00001.tbl
deleted file mode 100644
index da5d7ed36978f3b923bc5408e492c121d7c7c130..0000000000000000000000000000000000000000
--- a/Examples/2-res-Annotate-prokka/tmp_files/genome1.fst_prokka-split5N.fna-prokkaRes/EXAM.1219.00001.tbl
+++ /dev/null
@@ -1,71 +0,0 @@
->Feature genome1_1
-213	1880	CDS
-			EC_number	6.1.1.18
-			db_xref	COG:COG0008
-			gene	glnS
-			inference	ab initio prediction:Prodigal:002006
-			inference	similar to AA sequence:UniProtKB:P00962
-			locus_tag	GKEGNCBE_00001
-			product	Glutamine--tRNA ligase
-1916	2746	CDS
-			EC_number	3.5.1.28
-			db_xref	COG:COG3023
-			gene	amiD
-			inference	ab initio prediction:Prodigal:002006
-			inference	similar to AA sequence:UniProtKB:P75820
-			locus_tag	GKEGNCBE_00002
-			product	N-acetylmuramoyl-L-alanine amidase AmiD
->Feature genome1_2
-16	396	CDS
-			EC_number	5.3.3.10
-			gene	hpcD
-			inference	ab initio prediction:Prodigal:002006
-			inference	similar to AA sequence:UniProtKB:Q05354
-			locus_tag	GKEGNCBE_00003
-			product	5-carboxymethyl-2-hydroxymuconate Delta-isomerase
-428	1837	CDS
-			inference	ab initio prediction:Prodigal:002006
-			locus_tag	GKEGNCBE_00004
-			product	hypothetical protein
-1869	2642	CDS
-			db_xref	COG:COG4598
-			gene	hisP
-			inference	ab initio prediction:Prodigal:002006
-			inference	similar to AA sequence:UniProtKB:P02915
-			locus_tag	GKEGNCBE_00005
-			product	Histidine transport ATP-binding protein HisP
-2709	3443	CDS
-			EC_number	2.1.1.228
-			db_xref	COG:COG0336
-			gene	trmD_1
-			inference	ab initio prediction:Prodigal:002006
-			inference	similar to AA sequence:UniProtKB:P0A873
-			locus_tag	GKEGNCBE_00006
-			product	tRNA (guanine-N(1)-)-methyltransferase
-3427	4254	CDS
-			EC_number	2.1.1.228
-			db_xref	COG:COG0336
-			gene	trmD_2
-			inference	ab initio prediction:Prodigal:002006
-			inference	similar to AA sequence:UniProtKB:P0A873
-			locus_tag	GKEGNCBE_00007
-			product	tRNA (guanine-N(1)-)-methyltransferase
-4299	4763	CDS
-			inference	ab initio prediction:Prodigal:002006
-			locus_tag	GKEGNCBE_00008
-			product	hypothetical protein
-4818	5078	CDS
-			inference	ab initio prediction:Prodigal:002006
-			locus_tag	GKEGNCBE_00009
-			product	hypothetical protein
-5117	5698	CDS
-			inference	ab initio prediction:Prodigal:002006
-			locus_tag	GKEGNCBE_00010
-			product	hypothetical protein
-5717	7024	CDS
-			db_xref	COG:COG1593
-			gene	dctM
-			inference	ab initio prediction:Prodigal:002006
-			inference	similar to AA sequence:UniProtKB:O07838
-			locus_tag	GKEGNCBE_00011
-			product	C4-dicarboxylate TRAP transporter large permease protein DctM
diff --git a/Examples/2-res-Annotate-prokka/tmp_files/genome1.fst_prokka-split5N.fna-prokkaRes/EXAM.1219.00001.tsv b/Examples/2-res-Annotate-prokka/tmp_files/genome1.fst_prokka-split5N.fna-prokkaRes/EXAM.1219.00001.tsv
deleted file mode 100644
index f71d90c382bab07dddd2ad815ac182c57bae9b46..0000000000000000000000000000000000000000
--- a/Examples/2-res-Annotate-prokka/tmp_files/genome1.fst_prokka-split5N.fna-prokkaRes/EXAM.1219.00001.tsv
+++ /dev/null
@@ -1,12 +0,0 @@
-locus_tag	ftype	length_bp	gene	EC_number	COG	product
-GKEGNCBE_00001	CDS	1668	glnS	6.1.1.18	COG0008	Glutamine--tRNA ligase
-GKEGNCBE_00002	CDS	831	amiD	3.5.1.28	COG3023	N-acetylmuramoyl-L-alanine amidase AmiD
-GKEGNCBE_00003	CDS	381	hpcD	5.3.3.10		5-carboxymethyl-2-hydroxymuconate Delta-isomerase
-GKEGNCBE_00004	CDS	1410				hypothetical protein
-GKEGNCBE_00005	CDS	774	hisP		COG4598	Histidine transport ATP-binding protein HisP
-GKEGNCBE_00006	CDS	735	trmD_1	2.1.1.228	COG0336	tRNA (guanine-N(1)-)-methyltransferase
-GKEGNCBE_00007	CDS	828	trmD_2	2.1.1.228	COG0336	tRNA (guanine-N(1)-)-methyltransferase
-GKEGNCBE_00008	CDS	465				hypothetical protein
-GKEGNCBE_00009	CDS	261				hypothetical protein
-GKEGNCBE_00010	CDS	582				hypothetical protein
-GKEGNCBE_00011	CDS	1308	dctM		COG1593	C4-dicarboxylate TRAP transporter large permease protein DctM
diff --git a/Examples/2-res-Annotate-prokka/tmp_files/genome1.fst_prokka-split5N.fna-prokkaRes/EXAM.1219.00001.txt b/Examples/2-res-Annotate-prokka/tmp_files/genome1.fst_prokka-split5N.fna-prokkaRes/EXAM.1219.00001.txt
deleted file mode 100644
index 9cd2780b0722866f0837937f638f91238d44ab84..0000000000000000000000000000000000000000
--- a/Examples/2-res-Annotate-prokka/tmp_files/genome1.fst_prokka-split5N.fna-prokkaRes/EXAM.1219.00001.txt
+++ /dev/null
@@ -1,4 +0,0 @@
-organism: Genus species strain 
-contigs: 2
-bases: 9808
-CDS: 11
diff --git a/Examples/2-res-Annotate-prokka/tmp_files/genome2.fst_prokka-split5N.fna b/Examples/2-res-Annotate-prokka/tmp_files/genome2.fst_prokka-split5N.fna
deleted file mode 100644
index eac6e2ca510efa36060430b2d3181f31039f4814..0000000000000000000000000000000000000000
--- a/Examples/2-res-Annotate-prokka/tmp_files/genome2.fst_prokka-split5N.fna
+++ /dev/null
@@ -1,10 +0,0 @@
->this_is_genome_1
-ATGTCAGAAAATAAATTACACGTTATCGATTTGCACAAACGCTACGGCGGTCATGAAGTGCTGAAAGGGGTATCGCTGCAGGCCCGCGCCGGAGATGTGATTAGCATTATCGGCTCGTCCGGTTCCGGTAAAAGCACTTTTTTGCGCTGCATTAACTTCCTCGAAAAATCGAGCGAAGGCGCGATTATCGTGAACGGTCAGAACATTAATCTGGTGCGCGACAAAGACGGGCAGCTCAAAGTGGCGGATAAAAATCAGCTACGCTTGTTGCGTACCCGCCTGACGATGGTGTTTCAGCACTTTAACCTCTGGAACCACATGACGGTGCTGGAAAATGTGATGGAAGCGCCGATTCAGGTACTGGGATTAAGCAAGCACGACGCGCGCGAGCGGGCGTTGAAATATCTGGCGAAGGTGGGGATTGATGAGCGCGCTCAGGGCAAATATCCCGTCCATCTCTCCGGCGGCCAACAGCAGCGCGTTTCTATTGCGCGCGCGCTGGCGATGGAACCTGACGTTTTACTGTTCGATGAACCCACATCGGCGCTCGATCCTGAACTGGTCGGCGAAGTGTTGCGCATCATGCAACAACTGGCGGAAGAAGGCAAAACGATGGTGGTGGTCACGCATGAAATGGGCTTCGCCCGCCATGTCTCTTCGCACGTGATTTTTCTGCATCAGGGGAAAATTGAAGAAGAGGGCAATCCGGAGCAGGTGTTCGGCAATCCGCAAAGCCCGCGTTTACAGCAATTCCTGAAAGGCTCGCTGAAATAAACGCTAGAGGACGCGCCTCTCAGAGAGCGCGCTCTCTCAGAGAGGCGCGCGCCTCTTTCGCAGAGACCNNCGCTCATGAGCGATGCCCGCGACTAAATTCTCCCGACGTACCCTCCTGACGGCAGGTTCCGCGCTTGCTGTTCTTCCTTTTCTGCGCGCCTTGCCGGTACAGGCGCGTGAACCTCGCCAGACCGTCGATATTAAGGATTATCCGGCGGATGACGGTATCGCCTCGTTCAAACAGGCCTTCGCCGACGGGCAGACTGTGGTCGTGCCGTCAGGATGGGTGTGTGAAAATATCAATGCGGCGATAACGATTCCGGCGGGAAAAACGCTGCGGATACAGGGCGCGGTGCGTGGGAATGGCCGGGGACGGTTTATTTTGCTGGACGGGTGTCAGGTGGTGGGGGAGCAGGGCGGCAGTCTGCACAATGTGACGCTGGATGTTCGCGGGTCGGACTGTGTGATTAAAGGCGTGACGATGAGCGGCTTTGGCCCCGTCGCGCAAATTTTCATCGGCGGTAAGGAACCGCAGGTGATGCGTAATCTCATTATCGATGACATCACCGTTACCCACGCCAACTACGCCATTCTCCGCCAGGGATTTCATAACCAAATGGACGGCGCGCGGATTACGCATAGTCGCTTTAGCGATTTGCAGGGGGACGCCATTGAGTGGAATGTCGCGATTCATGACCGCGACATCCTGATTTCCGATCATGTCATCGAACGCATTGATTGTACCAATGGCAAAATCAACTGGGGGATCGGCATCGGGCTGGCGGGTAGCGCCTATGACAATAGTTATCCTGAAGACCAGGCAGTAAAAAACTTTGTGGTGGCCAATATTACCGGATCTGATTGCCGACAACTGGTACACGTAGAAAATGGCAAACATTTCGTCATTCGCAATGTCAAAGCCAAAAACATCACGCCCGATTTCAGTAAAAATGCGGGTATTGATAACGCAACGATCGCCATTTATGGCTGTGATAATTTCGTCATTGATAATATTGATATGACGAATAGTGCCGGGATGCTCATCGGCTATGGCGTCGTTAAAGGAAAATACCTGTCAATTCCGCAAAACTTTAAATTAAACGCTATTCGGTTGGATAATCGCCAGGTTGCTTATAAATTACGCGGCATTCAAATTTCCTCCGGTAACGCCCCCTCATTTGTTGCCATCACCAATGTACGGATGACGCGTGCTACGCTGGAACTGCATAATCAACCGCAGCACCTCTTTTTGCGTAATATCAACGTGATGCAAACTTCAGCGATTGGCCCGGCGTTAAAAATGCATTTTGATTTGCGTAAAGATGTCCGTGGTCAATTTATGGCCCGCCAGGACACGCTGCTTTCCCTCGCTAATGTTCATGCCATCAATGAAAACGGGCAGAGTTCCGTGGATATCGACAGGATTAATCACCAAACCGTGAATGTCGAAGCAGTGAATTTTTCGCTGCCGAAGCGGGGAGGGTAACACTCGCGCATAGAGAGCTCTCAGAGGAGCGCGCGCGCTATAGCGCGC
->this_is_genome_2
-CGCGATAATATAGCGCGCGCTCATAGCATGAGCGCGCTATTTCTGGCCATCCCGTTAACCATTTTTGTGTTGTTTGTGTTACCGATTTGGCTGTGGCTGCATTACAGCAACCGCGCCGGTCGGGGAGAACTGTCGCAAAGCGAGCAGCAACGCTTACTGCAACTCACAGACGACGCGCAACGTATGCGCGAGCGCATTCAGGCGCTGGAAGATATTCTTGATGCAGAGCATCCGAACTGGAGAGAGCGCTAACGCCATATTATAGCGCGCCTCATAAGAGCGGCCTATAGCGCGCTANNNATGCCGCACTTTATTGCTGAATGTACTGAAAATATTCGCGAGCAGGCTGATTTACCAAGCCTGTTCAGCAAGGTAAACGAGGCGCTGGCCGCCACCGGGATTTTCCCCATCGGCGGTATCCGCAGTCGCGCCCACTGGCTGGATACCTGGCAGATGGCTGACGGTAAGCATGATTACGCGTTTGTGCATATGACGCTGAAAATCGGCGCCGGGCGCAGCCTGGAGAGCCGTCAGGAAGTCGGCGAAATGCTGTTTGGGCTGATTAAAGCCCACTTCGCCGACCTGATGGAGAACCGCTATCTGGCGCTGTCGTTTGAGATTGCCGAGTTACATCCAACGCTCAATTACAAACAAAACAACGTACACGCGTTATTTAAATAGCCAGAGATTCGCGCGTTCAGAGAGGAGCTCTCTCATAGACGCGCGCATATGCGCTCTAGAGAGGCGCGCCTAATGGCGCGCTATGATGAAAGCGCTACTGTGGCTGGTTGGTCTCGCGTTGCTGTTAACAGGCTGCGCGAGCGAAAAAGGAATTATCGATAAAGAGGGATATCAGCTTGATACCCGACATCGGGCGCAGGCGGCCTATCCGCGCATTAAAGTCCTGGTGATTCACTATACGGCGGAAAACTTTGACGTTTCGCTGGCGACGTTAACGGGTCGCAACGTCAGTTCGCATTACCTGATTCCCGCAACCCCGCCATTATATGGCGGTAAACCGCGCATCTGGCAACTGGTGCCGGAACAGGATCAGGCTTGGCATGCGGGCGTCAGTTTCTGGCGAGGCGCCACGCGTCTCAATGATACGTCTATTGGCATTGAGCTGGAAAATCGCGGCTGGCGAATGTCCGGCGGGGTGAAATCTTTCGCGCCGTTTGAATCCGCGCAAATTCAGGCATTGATCCCGTTAGCGAAGGACATTATCGCGCGCTATGACATCAAACCGCAGAATGTGGTGGCCCATGCGGATATCGCGCCGCAGCGTAAAGACGATCCCGGCCCGCGCTTCCCGTGGCGCGAGCTGGCGGCACAGGGGATTGGCGCCTGGCCTGACGCCCAGCGTGTGGCGTTTTATCTGGCTGGACGCGCGCCGTATACGCCAGTCGATACCGCAACGGTGCTTGCGTTACTCTCGCGCTATGGCTATGAAGTCAAAGCCGATATGACGGCGCGCGAGCAACAGCGGGTGATTATGGCGTTCCAGATGCACTTCCGTCCGGCGCAATGGAACGGTATCGCAGATGCCGAAACGCAGGCGATTGCCGAAGCATTACTGGAGAAGTACGGCCAGGATTAACAAAGCGCTCTCAGAGAGAGCGCTCTGCAGATGAGTGAGGCTGAAGCCCGCCCGACTAACTTTATTCGTCAGATTATTGATGAAGATCTGGCGAGTGGTAAACATACCACTGTCCATACCCGTTTTCCGCCGGAGCCGAATGGCTATCTGCACATCGGCCACGCGAAATCTATCTGCCTGAACTTTGGCATCGCGCAAGATTATCAGGGCCAGTGCAACCTGCGTTTCGATGACACCAACCCGGTAAAAGAAGATATCGAGTACGTTGATTCGATCAAAAACGACGTCGAGTGGTTAGGCTTTCACTGGTCTGGCGATATTCGCTACTCCTCCGATTACTTTGACCAACTGCACGCCTATGCGGTCGAGCTCATCAATAAAGGCCTGGCCTACGTTGATGAGCTGACGCCGGAGCAGATCCGCGAATACCGTGGTACGCTGACCGCGCCGGGTAAAAACAGCCCGTTCCGCGATCGCAGCGTGGAAGAAAACCTCGCGCTATTTGAAAAAATGCGTACCGGCGGTTTTGAAGAGGGTAAAGCCTGTCTGCGCGCTAAAATCGACATGGCGTCGCCGTTTATCGTGATGCGCGATCCGGTGCTGTATCGCATTAAATTCGCCGAGCATCATCAGACCGGCACGAAGTGGTGCATCTATCCGATGTACGACTTTACTCACTGCATCAGCGATGCGCTGGAAGGCATTACTCATTCTCTGTGTACGCTGGAGTTCCAGGACAACCGTCGTCTGTACGACTGGGTGCTGGACAACATCACCATTCCGGTTCACCCGCGCCAGTACGAATTCTCGCGCCTGAATCTGGAATACACCGTGATGTCCAAGCGTAAGCTGAACCTGCTGGTGACCGACAAACACGTCGAAGGTTGGGATGATCCGCGTATGCCGACTATTTCCGGTCTGCGCCGTCGCGGCTATACCGCGGCTTCTATTCGTGAGTTCTGCAAACGCATCGGCGTCACCAAGCAGGACAACACTATTGAGATGGCGTCGCTGGAATCCTGCATTCGCGAAGATCTGAACGAAAACGCGCCGCGCGCGATGGCGGTAATCGATCCGGTAAAACTGGTTATCGAAAACTACCCGCAGGGCGAGAGCGAAATGGTTACCATGCCTAACCATCCGAATAAACCGGAGATGGGCAGCCGTGAAGTGCCGTTTAGCGGTGAGATCTGGATCGATCGCGCGGATTTCCGCGAAGAAGCGAACAAACAGTACAAACGTCTGGTGATGGGCAAAGAAGTGCGTCTGCGTAATGCCTACGTCATTAAAGCGGAGCGCGTAGAGAAGGATGCCGAAGGGAATATCACCACCATCTTCTGTACCTATGATGCTGATACGCTGAGTAAAGATCCGGCTGACGGGCGTAAAGTGAAAGGCGTAATCCACTGGGTTAGCGTAGCACATGCGCTGCCGATTGAAATTCGTCTCTACGACCGTCTGTTCAGCGTGCCGAACCCGGGCGCCGCGGAGGACTTCCTGTCTGTTATCAACCCCGAATCATTAGTGATTAAGCAGGGGTATGGCGAGCCGTCGCTGAAAGCGGCGGTAGCAGGGAAAGCTTTCCAGTTTGAACGTGAAGGTTACTTCTGCCTTGACAGCCGCTATGCAACGGCCGATAAGCTGGTCTTTAACCGCACCGTGGGCCTGCGTGATACCTGGGCGAAAGCGGGCGAATAA
->this_is_genome_3
-ACGCGCTATAGGGCTCTCAGAGAGTCTCAGTGTTTATTGGCATCGTTAGCCTGTTTCCTGAAATGTTCCGCGCAATTACCGATTACGGGGTAACTGGCCGGGCAGTAAAAAAAGGCCTGCTGAACATCCAAAGCTGGAGTCCTCGCGACTTCGCGCATGACCGGCACCGTACCGTGGACGACCGTCCTTACGGCGGCGGACCGGGGATGTTAATGATGGTGCAACCCTTGCGGGACGCCATTCATGCAGCAAAAGCCGCGGCAGGTGAAGGCGCTAAAGTGATTTATCTGTCGCCTCAGGGACGCAAGCTTGATCAAGCGGGCGTTAGCGAGCTGGCCACGAATCAGAAACTCATTCTGGTGTGTGGTCGCTACGAAGGCGTAGATGAGCGCGTAATTCAGGCCGAAATTGACGAAGAATGGTCAATTGGCGATTACGTTCTCAGCGGTGGCGAACTACCGGCAATGACGCTGATTGACTCCGTCGCCCGGTTTATACCGGGGGTTCTGGGGCATGAGGCATCAGCAATCGAAGATTCGTTTGCTGATGGGTTGCTGGATTGTCCGCACTATACGCGCCCTGAAGTGTTAGAGGGGATGGAAGTACCGCCAGTATTGCTGTCGGGAAACCATGCTGAGATACGTCGCTGGCGTTTGAAACAGTCACTGGGCCGAACCTGGCTTAGAAGACCTGAACTTCTGGAAAACCTGGCTCTGACTGAAGAGCAAGCAAGGTTGCTGGCGGAGTTCAAAACAGAACACGCACAACAGCAGCATAAACATGATGGGATGGCATAGCGAGATCGCGCATAGCGCGCGGCGAGATCCGCGAGACATGAATAATCATTTTGGGAAAGGGTTAATGGCCGGGTTGCACGCGCCATATGCATATAGCGCGCATCATGCGGTGAATTTCTGTTCTGAGTATAAACGTGGCTTTGTATTGGGTTTTACACACCGTATGTTCGAAAAGACCGGCGATCGTCAACTTAGCGCGTGGGAGGCCGGAATTCTGACGCGTCGCTATGGTCTGGATAAAGAAATGGTGATGGATTTCTTTAAAGAGAATCATTCCGGGATGGCGGTTCGCTTCTTTATGGCTGGTTATCGACTCGAAGGTTGAACGCCTCTAGAGCGCTAGAGGCGCGCGCGATATACGCGGCGCGAGACATGTCTACGCTTCTCTATTTGCACGGATTCAACAGTTCCCCTCGCTCGGCAAAAGCGTGCCAGCTAAAAAACTGGCTGGCGGAGCGTCATCCGCATGTTGAGATGATCGTCCCTCAACTGCCGCCGTATCCTGCCGATGCGGCGGAGTTGCTGGAATCTCTCGTACTTGAGCATGGCGGTGCGCCATTAGGGCTGGTAGGATCGTCGCTGGGTGGTTATTACGCCACCTGGCTGTCGCAATGTTTTATGCTGCCGGCTGTGGTGGTGAATCCCGCCGTGCGGCCCTTTGAATTACTGACCGACTATCTCGGTCAGAACGAGAACCCCTACACCGGGCAGCAATATGTGCTAGAGTCTCGCCATATTTATGATCTTAAAGTCATGCAGATTGACCCGCTGGAAGCGCCGGACCTGATCTGGCTACTGCAACAGACGGGCGATGAAGTGCTGGATTACCGCCAGGCGGTGGCATATTACGCCTCCTGCCGTCAGACAGTGACCGAGGGGGGTAATCACGCATTCACGGGCTTCGAAGATTATTTCAACCAGATTGTCGATTTTCTTGGACTGCACAGTTGCTGACCGGATATACGCGCGCGCGCTATATAGCGCGCGCGGCGATATAGCGCATGAAGTTTGTTGCGCCAGAACAGGCACCGGAACAGGCGGAAATCATCAGAAATACGCCGTTCTGGCCTGATGTGGACCTGTCGGAGTTTCGCAGCATGATGCGCACTGATGGCACGGTGACGCAGCCGCGTTTAAAGCAGGTTGCGCTGTCGGCAATTTCGGAGGTCAACGCAGAGCTGTATGAGTTTCGCAGACGCCAGCAGATGCTGGGGTATGCCTCGCTGGCAGAAGTCCCGGCGGAACAACTGGACGGCAAAAGCGAGCGCATTCAGCACTATTTCAACGCGGTTTACTGCTGGGCACGCGCCATGCTCAACGAACGTTACCAGGACTATGACGCCACGGCATCCGGTGTGAAGCGGGGCGAAGAACTGGCAGAAGCCAGCGGTGATTTGTGGCGTGACGCCCGCTGGGCCATCAGCCGGGTGCAGGATGCGCCGCACTGCACAGTGGAGCTTATCTGA
->this_is_genome_4
-ATGATTGACCCTATTTTTGCGTCCTGTACGCTAATTGCCGTCTTTGTTGTTTTACTGGCCATGGGCGCGCCTATCGGGATCTGCATCGTTATCGCCTCTTTCAGCACCATGATGCTGGTACTGCCTTTCGATATTTCGATGTTCGCCACCGCGCAAAAAATGTTCTCCAGCCTGGACAGTTTTGCCTTGCTGGCCGTGCCGTTCTTCGTTTTGTCCGGGGTGATCATGAATAGCGGGGGAATTGCCGCCCGACTGGTCAATTTTGCCAAACTGTTTACTGGCAAACTGCCCGGCTCGCTCTCTTACACCAACATCGTCGGCAATATGATGTTCGGTGCAATTTCCGGATCGGCGATTGCCGCCTCAACCTCTATCGGCGGCGTGATGGTGCCGATGAGCGCGCGCGAAGGTTACGATCGCGGTTTTGCGGCCGCGGTGAATATCGCCTCCGCGCCGACGGGAATGTTAATTCCGCCCACCACGGCTTTTATCCTTTATGCGCTGGCAAGCGGGGGAACATCGATTGCCGCTCTGTTCGCCGGCGGTCTGGTCGCGGGAGTGCTGTGGGGCGTTGGCTGTATGCTGGTCACGCTGGTGGTCGCTAAGCGTCGAAATTATCGGGTTTTCTTCACCGTCCAAAAAGGCATGGCGCTAAAAGTTGCCGTTGAGGCCATTCCCAGCCTGTTACTGATCGTGATTATTGTCGGCGGCATTGTGCAGGGGATTTTCACCGCCATTGAAGCCTCCGCGATTGCCGTGGTGTATACGTTATTGCTGACGATAGTGTTTTACCGCACGCTGAAAATTAAGGATTTGCCTTCGATTTTGCTCCAGACAGTGGTAATGACCGGGGTCATCATGTTCCTGCTGGCAACCTCTTCGGCGATGTCCTTCTCGATGTCGATCACCAATATTCCTGCGGCGCTGAGCGATATGATCCTCGGTATTTCCGCCAATAAACTGGTTATCCTGTTAGTCATTACCGTCTTTTTGTTGATTATCGGCGCATTTATGGATATCGGTCCGGCCATTCTGATTTTTACCCCGATTCTGCTGCCGATTATGACTAAACTGGGCGTCGATCCGGTGCATTTCGGCATTATCATGATCTATAACCTGGCGATAGGCACCATTACGCCGCCAGTTGGCAGTGGTTTATATGTCGGGGCGAGCGTCGGTAAGGTCAAAGTTGAGGACGTTATCAAACCGTTGATGCCTTTTTACGGCGCGATTATCGGCGTTCTGTTATTAATTACCTACATTCCGGAAATCACACTGTTTTTACCCCGTCTACTGGGCATCATGTAAACGCTCATAGGCGGCGCGCGCGCTCTCAGGAATGAAGTTTGTTGCGCCAGAACAGGCACCGGAACAGGCGGAGGTCATCAAAAATACGCCGTTCTGGCCTGATGTGAACCTGTCGGAATTTCGCAGTGTGATGCGCACTGACGGCACGGTGACGCAGCCGCGTTTAAAGCAGGTCGTGCTGACGGCGATCTCTGAGGTTAACGCTGAGCTGTACGACTTCCGCAACCGTCAGCAGATGCTGGGCTGGCGGACACTTGCTGAGGTTCCCGCAGAAATGCTGGACGGTAAAAGCGAGCGTATCCGGCACTACCACAACGCTGTTTTTTGCTGGGCGCGCGCTGTGCTTAATGAGCGTTATCAGGACTATGACGCCACGGCGTCAGGCGTGAAGCGAGGGGAGGAGCTGGCGGAGGCCAGCGGCGATCTGTGGCGTGATGCCCGCTGGGCCATCAGCCGGGTGCAGGATGCACCGCACTGTACGGTGGAGCTTATCTGACGCTCATAGGCGCGCGCTCATAGCGCGATGGAAACAAATATTACCTGGCAACAATTGATAGATGAATATTTCTTCGCAAAACCTCTGCGCTCAGCATCTGAATGGAGTTACACCAAAGTCTTCAAATCATTTGTACATTATATGGGGCCGTTAAGCTGCCCTAATGATGTGACATATCACAAAGTGCTTGCCTGGCGCCGTTTTCTTTTAAAAGAGAAAAAGCTGTCCGGACGTACCTGGAATAACAAGGTGGCGCATATGCGGGCCATCTTTAACTACGGAATACAGCGAGGGTTACTGCACTATGACGAAAATCCGTTTAACAATTCGGTAGTTAAACCGGACAAGAAGAGAAAGAAAACGCTCACTCAGGCACAGATTGAGTATGCCTATCAGATCATGGAGCAGTATGAAAATCAGGAGAATACAGGGCTGGGACTGAAATATTCCCGCTGCGCCTTATTTCCTGCATGGTTCTGGCTCACTGTCCTGGATACGCTCTATTACACAGGGATACGTCAGAACCAGTTATTACATATTCGGCTGAATGATGTTGATTTGAGAGAAGGGCAGATTCGGCTGATTACGGAGGGGTGTAAAAATCACAAAGAACACTATGTGCCGGTGATCAGTTTTCTGCGTCCACGGCTGACCTGTTTAATGGAGAAAGCGCAGAGCGAAGGATTGAAAGGTAATGACCGCCTGTTCAATATTGCACTTTTTACCGGCAAAGATCCCGCCATTGGCGATGACATGGATTCTCCTCAGGTAAGAGCATTCTTCCGTCGTCTGTCCAAGGAGTGTCAGTTTGCGATCAGTCCTCATCGTTTCAGACACACGCTGGCCACGGAGATGATGAAAATGCCGGAACAGAATCTGCATATGGCGCAAAGTGTGCTGGGTCATTCAAACATGAAATCCACGCTGGAGTATGTGGAGAATGATATTGCAGTGATGGGGAGGGCTCTGGAAGCGCAGTTTATGCAGATTAAGGCAGCACATGCCCGAAGCATTTACAGTGGGTTGACAAAGAATAGATAA
->genome2_small_5
-GATACA
diff --git a/Examples/2-res-Annotate-prokka/tmp_files/genome2.fst_prokka-split5N.fna-prokka.log b/Examples/2-res-Annotate-prokka/tmp_files/genome2.fst_prokka-split5N.fna-prokka.log
deleted file mode 100644
index 251627a3eb8cf38b0943f63ac55c0d7eb5f2d73b..0000000000000000000000000000000000000000
--- a/Examples/2-res-Annotate-prokka/tmp_files/genome2.fst_prokka-split5N.fna-prokka.log
+++ /dev/null
@@ -1,128 +0,0 @@
-[13:15:26] This is prokka 1.14.5
-[13:15:26] Written by Torsten Seemann <torsten.seemann@gmail.com>
-[13:15:26] Homepage is https://github.com/tseemann/prokka
-[13:15:26] Local time is Mon Dec  9 13:15:26 2019
-[13:15:26] You are aperrin
-[13:15:26] Operating system is darwin
-[13:15:26] You have BioPerl 1.007002
-[13:15:26] System has 8 cores.
-[13:15:26] Will use maximum of 1 cores.
-[13:15:26] Annotating as >>> Bacteria <<<
-[13:15:26] Generating locus_tag from 'Examples/2-res-Annotate-prokka/tmp_files/genome2.fst_prokka-split5N.fna' contents.
-[13:15:26] Setting --locustag AMHDIIJN from MD5 a61d2237f76cf8056ab8e698ba010fa3
-[13:15:26] Creating new output folder: Examples/2-res-Annotate-prokka/tmp_files/genome2.fst_prokka-split5N.fna-prokkaRes
-[13:15:26] Running: mkdir -p Examples\/2\-res\-Annotate\-prokka\/tmp_files\/genome2\.fst_prokka\-split5N\.fna\-prokkaRes
-[13:15:26] Using filename prefix: GEN2.1219.00001.XXX
-[13:15:26] Setting HMMER_NCPU=1
-[13:15:26] Writing log to: Examples/2-res-Annotate-prokka/tmp_files/genome2.fst_prokka-split5N.fna-prokkaRes/GEN2.1219.00001.log
-[13:15:26] Command: /usr/local/bin/prokka --outdir Examples/2-res-Annotate-prokka/tmp_files/genome2.fst_prokka-split5N.fna-prokkaRes --cpus 1 --prefix GEN2.1219.00001 Examples/2-res-Annotate-prokka/tmp_files/genome2.fst_prokka-split5N.fna
-[13:15:26] Appending to PATH: /Users/aperrin/Softwares/src/prokka-dec.19/bin/../binaries/darwin
-[13:15:26] Appending to PATH: /Users/aperrin/Softwares/src/prokka-dec.19/bin/../binaries/darwin/../common
-[13:15:26] Appending to PATH: /Users/aperrin/Softwares/src/prokka-dec.19/bin
-[13:15:26] Looking for 'aragorn' - found /usr/local/bin/aragorn
-[13:15:26] Determined aragorn version is 001002 from 'ARAGORN v1.2.38 Dean Laslett'
-[13:15:26] Looking for 'barrnap' - found /usr/local/bin/barrnap
-[13:15:26] Determined barrnap version is 000008 from 'barrnap 0.8'
-[13:15:26] Looking for 'blastp' - found /Users/aperrin/Softwares/bin/blastp
-[13:15:26] Determined blastp version is 002009 from 'blastp: 2.9.0+'
-[13:15:26] Looking for 'cmpress' - found /usr/local/bin/cmpress
-[13:15:26] Determined cmpress version is 001001 from '# INFERNAL 1.1.2 (July 2016)'
-[13:15:26] Looking for 'cmscan' - found /usr/local/bin/cmscan
-[13:15:26] Determined cmscan version is 001001 from '# INFERNAL 1.1.2 (July 2016)'
-[13:15:26] Looking for 'egrep' - found /usr/bin/egrep
-[13:15:26] Looking for 'find' - found /usr/bin/find
-[13:15:26] Looking for 'grep' - found /usr/bin/grep
-[13:15:26] Looking for 'hmmpress' - found /Users/aperrin/Softwares/src/prokka-dec.19/bin/../binaries/darwin/hmmpress
-[13:15:26] Determined hmmpress version is 003001 from '# HMMER 3.1b1 (May 2013); http://hmmer.org/'
-[13:15:26] Looking for 'hmmscan' - found /usr/local/bin/hmmscan
-[13:15:26] Determined hmmscan version is 003001 from '# HMMER 3.1b2 (February 2015); http://hmmer.org/'
-[13:15:26] Looking for 'java' - found /usr/bin/java
-[13:15:26] Looking for 'makeblastdb' - found /Users/aperrin/Softwares/bin/makeblastdb
-[13:15:26] Determined makeblastdb version is 002009 from 'makeblastdb: 2.9.0+'
-[13:15:26] Looking for 'minced' - found /Users/aperrin/Softwares/src/prokka-dec.19/bin/../binaries/darwin/../common/minced
-[13:15:26] Determined minced version is 002000 from 'minced 0.2.0'
-[13:15:26] Looking for 'parallel' - found /usr/local/bin/parallel
-[13:15:26] Determined parallel version is 20181022 from 'GNU parallel 20181022'
-[13:15:26] Looking for 'prodigal' - found /usr/local/bin/prodigal
-[13:15:26] Determined prodigal version is 002006 from 'Prodigal V2.6.3: February, 2016'
-[13:15:26] Looking for 'prokka-genbank_to_fasta_db' - found /Users/aperrin/Softwares/src/prokka-dec.19/bin/prokka-genbank_to_fasta_db
-[13:15:26] Looking for 'sed' - found /usr/bin/sed
-[13:15:26] Looking for 'tbl2asn' - found /Users/aperrin/Softwares/src/prokka-dec.19/bin/../binaries/darwin/tbl2asn
-[13:15:26] Determined tbl2asn version is 025007 from 'tbl2asn 25.7   arguments:'
-[13:15:26] Using genetic code table 11.
-[13:15:26] Loading and checking input file: Examples/2-res-Annotate-prokka/tmp_files/genome2.fst_prokka-split5N.fna
-[13:15:26] Wrote 5 contigs totalling 10717 bp.
-[13:15:26] Predicting tRNAs and tmRNAs
-[13:15:26] Running: aragorn -l -gc11  -w Examples\/2\-res\-Annotate\-prokka\/tmp_files\/genome2\.fst_prokka\-split5N\.fna\-prokkaRes\/GEN2\.1219\.00001\.fna
-[13:15:26] Found 0 tRNAs
-[13:15:26] Predicting Ribosomal RNAs
-[13:15:26] Running Barrnap with 1 threads
-[13:15:26] Found 0 rRNAs
-[13:15:26] Skipping ncRNA search, enable with --rfam if desired.
-[13:15:26] Total of 0 tRNA + rRNA features
-[13:15:26] Searching for CRISPR repeats
-[13:15:27] Found 0 CRISPRs
-[13:15:27] Predicting coding sequences
-[13:15:27] Contigs total 10717 bp, so using meta mode
-[13:15:27] Running: prodigal -i Examples\/2\-res\-Annotate\-prokka\/tmp_files\/genome2\.fst_prokka\-split5N\.fna\-prokkaRes\/GEN2\.1219\.00001\.fna -c -m -g 11 -p meta -f sco -q
-[13:15:27] Found 13 CDS
-[13:15:27] Connecting features back to sequences
-[13:15:27] Not using genus-specific database. Try --usegenus to enable it.
-[13:15:27] Annotating CDS, please be patient.
-[13:15:27] Will use 1 CPUs for similarity searching.
-[13:15:27] There are still 13 unannotated CDS left (started with 13)
-[13:15:27] Will use blast to search against /Users/aperrin/Softwares/src/prokka-dec.19/db/kingdom/Bacteria/IS with 1 CPUs
-[13:15:27] Running: cat Examples\/2\-res\-Annotate\-prokka\/tmp_files\/genome2\.fst_prokka\-split5N\.fna\-prokkaRes\/GEN2\.1219\.00001\.IS\.tmp\.95071\.faa | parallel --gnu --plain -j 1 --block 1697 --recstart '>' --pipe blastp -query - -db /Users/aperrin/Softwares/src/prokka-dec.19/db/kingdom/Bacteria/IS -evalue 1e-30 -qcov_hsp_perc 90 -num_threads 1 -num_descriptions 1 -num_alignments 1 -seg no > Examples\/2\-res\-Annotate\-prokka\/tmp_files\/genome2\.fst_prokka\-split5N\.fna\-prokkaRes\/GEN2\.1219\.00001\.IS\.tmp\.95071\.blast 2> /dev/null
-[13:15:27] Deleting unwanted file: Examples/2-res-Annotate-prokka/tmp_files/genome2.fst_prokka-split5N.fna-prokkaRes/GEN2.1219.00001.IS.tmp.95071.faa
-[13:15:27] Deleting unwanted file: Examples/2-res-Annotate-prokka/tmp_files/genome2.fst_prokka-split5N.fna-prokkaRes/GEN2.1219.00001.IS.tmp.95071.blast
-[13:15:27] There are still 13 unannotated CDS left (started with 13)
-[13:15:27] Will use blast to search against /Users/aperrin/Softwares/src/prokka-dec.19/db/kingdom/Bacteria/AMR with 1 CPUs
-[13:15:27] Running: cat Examples\/2\-res\-Annotate\-prokka\/tmp_files\/genome2\.fst_prokka\-split5N\.fna\-prokkaRes\/GEN2\.1219\.00001\.AMR\.tmp\.95071\.faa | parallel --gnu --plain -j 1 --block 1697 --recstart '>' --pipe blastp -query - -db /Users/aperrin/Softwares/src/prokka-dec.19/db/kingdom/Bacteria/AMR -evalue 1e-300 -qcov_hsp_perc 90 -num_threads 1 -num_descriptions 1 -num_alignments 1 -seg no > Examples\/2\-res\-Annotate\-prokka\/tmp_files\/genome2\.fst_prokka\-split5N\.fna\-prokkaRes\/GEN2\.1219\.00001\.AMR\.tmp\.95071\.blast 2> /dev/null
-[13:15:28] Deleting unwanted file: Examples/2-res-Annotate-prokka/tmp_files/genome2.fst_prokka-split5N.fna-prokkaRes/GEN2.1219.00001.AMR.tmp.95071.faa
-[13:15:28] Deleting unwanted file: Examples/2-res-Annotate-prokka/tmp_files/genome2.fst_prokka-split5N.fna-prokkaRes/GEN2.1219.00001.AMR.tmp.95071.blast
-[13:15:28] There are still 13 unannotated CDS left (started with 13)
-[13:15:28] Will use blast to search against /Users/aperrin/Softwares/src/prokka-dec.19/db/kingdom/Bacteria/sprot with 1 CPUs
-[13:15:28] Running: cat Examples\/2\-res\-Annotate\-prokka\/tmp_files\/genome2\.fst_prokka\-split5N\.fna\-prokkaRes\/GEN2\.1219\.00001\.sprot\.tmp\.95071\.faa | parallel --gnu --plain -j 1 --block 1697 --recstart '>' --pipe blastp -query - -db /Users/aperrin/Softwares/src/prokka-dec.19/db/kingdom/Bacteria/sprot -evalue 1e-09 -qcov_hsp_perc 80 -num_threads 1 -num_descriptions 1 -num_alignments 1 -seg no > Examples\/2\-res\-Annotate\-prokka\/tmp_files\/genome2\.fst_prokka\-split5N\.fna\-prokkaRes\/GEN2\.1219\.00001\.sprot\.tmp\.95071\.blast 2> /dev/null
-[13:15:29] Deleting unwanted file: Examples/2-res-Annotate-prokka/tmp_files/genome2.fst_prokka-split5N.fna-prokkaRes/GEN2.1219.00001.sprot.tmp.95071.faa
-[13:15:29] Deleting unwanted file: Examples/2-res-Annotate-prokka/tmp_files/genome2.fst_prokka-split5N.fna-prokkaRes/GEN2.1219.00001.sprot.tmp.95071.blast
-[13:15:29] There are still 6 unannotated CDS left (started with 13)
-[13:15:29] Will use hmmer3 to search against /Users/aperrin/Softwares/src/prokka-dec.19/db/hmm/HAMAP.hmm with 1 CPUs
-[13:15:29] Running: cat Examples\/2\-res\-Annotate\-prokka\/tmp_files\/genome2\.fst_prokka\-split5N\.fna\-prokkaRes\/GEN2\.1219\.00001\.HAMAP\.hmm\.tmp\.95071\.faa | parallel --gnu --plain -j 1 --block 691 --recstart '>' --pipe hmmscan --noali --notextw --acc -E 1e-09 --cpu 1 /Users/aperrin/Softwares/src/prokka-dec.19/db/hmm/HAMAP.hmm /dev/stdin > Examples\/2\-res\-Annotate\-prokka\/tmp_files\/genome2\.fst_prokka\-split5N\.fna\-prokkaRes\/GEN2\.1219\.00001\.HAMAP\.hmm\.tmp\.95071\.hmmer3 2> /dev/null
-[13:15:30] Deleting unwanted file: Examples/2-res-Annotate-prokka/tmp_files/genome2.fst_prokka-split5N.fna-prokkaRes/GEN2.1219.00001.HAMAP.hmm.tmp.95071.faa
-[13:15:30] Deleting unwanted file: Examples/2-res-Annotate-prokka/tmp_files/genome2.fst_prokka-split5N.fna-prokkaRes/GEN2.1219.00001.HAMAP.hmm.tmp.95071.hmmer3
-[13:15:30] Labelling remaining 5 proteins as 'hypothetical protein'
-[13:15:30] Found 8 unique /gene codes.
-[13:15:30] Fixed 0 colliding /gene names.
-[13:15:30] Adding /locus_tag identifiers
-[13:15:30] Assigned 13 locus_tags to CDS and RNA features.
-[13:15:30] Writing outputs to Examples/2-res-Annotate-prokka/tmp_files/genome2.fst_prokka-split5N.fna-prokkaRes/
-[13:15:30] Generating annotation statistics file
-[13:15:30] Generating Genbank and Sequin files
-[13:15:30] Running: tbl2asn -V b -a r10k -l paired-ends -M n -N 1 -y 'Annotated using prokka 1.14.5 from https://github.com/tseemann/prokka' -Z Examples\/2\-res\-Annotate\-prokka\/tmp_files\/genome2\.fst_prokka\-split5N\.fna\-prokkaRes\/GEN2\.1219\.00001\.err -i Examples\/2\-res\-Annotate\-prokka\/tmp_files\/genome2\.fst_prokka\-split5N\.fna\-prokkaRes\/GEN2\.1219\.00001\.fsa 2> /dev/null
-[13:15:30] Deleting unwanted file: Examples/2-res-Annotate-prokka/tmp_files/genome2.fst_prokka-split5N.fna-prokkaRes/errorsummary.val
-[13:15:30] Deleting unwanted file: Examples/2-res-Annotate-prokka/tmp_files/genome2.fst_prokka-split5N.fna-prokkaRes/GEN2.1219.00001.dr
-[13:15:30] Deleting unwanted file: Examples/2-res-Annotate-prokka/tmp_files/genome2.fst_prokka-split5N.fna-prokkaRes/GEN2.1219.00001.fixedproducts
-[13:15:30] Deleting unwanted file: Examples/2-res-Annotate-prokka/tmp_files/genome2.fst_prokka-split5N.fna-prokkaRes/GEN2.1219.00001.ecn
-[13:15:30] Deleting unwanted file: Examples/2-res-Annotate-prokka/tmp_files/genome2.fst_prokka-split5N.fna-prokkaRes/GEN2.1219.00001.val
-[13:15:30] Repairing broken .GBK output that tbl2asn produces...
-[13:15:30] Running: sed 's/COORDINATES: profile/COORDINATES:profile/' < Examples\/2\-res\-Annotate\-prokka\/tmp_files\/genome2\.fst_prokka\-split5N\.fna\-prokkaRes\/GEN2\.1219\.00001\.gbf > Examples\/2\-res\-Annotate\-prokka\/tmp_files\/genome2\.fst_prokka\-split5N\.fna\-prokkaRes\/GEN2\.1219\.00001\.gbk
-[13:15:30] Deleting unwanted file: Examples/2-res-Annotate-prokka/tmp_files/genome2.fst_prokka-split5N.fna-prokkaRes/GEN2.1219.00001.gbf
-[13:15:30] Output files:
-[13:15:30] Examples/2-res-Annotate-prokka/tmp_files/genome2.fst_prokka-split5N.fna-prokkaRes/GEN2.1219.00001.tsv
-[13:15:30] Examples/2-res-Annotate-prokka/tmp_files/genome2.fst_prokka-split5N.fna-prokkaRes/GEN2.1219.00001.fna
-[13:15:30] Examples/2-res-Annotate-prokka/tmp_files/genome2.fst_prokka-split5N.fna-prokkaRes/GEN2.1219.00001.err
-[13:15:30] Examples/2-res-Annotate-prokka/tmp_files/genome2.fst_prokka-split5N.fna-prokkaRes/GEN2.1219.00001.gff
-[13:15:30] Examples/2-res-Annotate-prokka/tmp_files/genome2.fst_prokka-split5N.fna-prokkaRes/GEN2.1219.00001.sqn
-[13:15:30] Examples/2-res-Annotate-prokka/tmp_files/genome2.fst_prokka-split5N.fna-prokkaRes/GEN2.1219.00001.tbl
-[13:15:30] Examples/2-res-Annotate-prokka/tmp_files/genome2.fst_prokka-split5N.fna-prokkaRes/GEN2.1219.00001.txt
-[13:15:30] Examples/2-res-Annotate-prokka/tmp_files/genome2.fst_prokka-split5N.fna-prokkaRes/GEN2.1219.00001.faa
-[13:15:30] Examples/2-res-Annotate-prokka/tmp_files/genome2.fst_prokka-split5N.fna-prokkaRes/GEN2.1219.00001.fsa
-[13:15:30] Examples/2-res-Annotate-prokka/tmp_files/genome2.fst_prokka-split5N.fna-prokkaRes/GEN2.1219.00001.gbk
-[13:15:30] Examples/2-res-Annotate-prokka/tmp_files/genome2.fst_prokka-split5N.fna-prokkaRes/GEN2.1219.00001.log
-[13:15:30] Examples/2-res-Annotate-prokka/tmp_files/genome2.fst_prokka-split5N.fna-prokkaRes/GEN2.1219.00001.ffn
-[13:15:30] Annotation finished successfully.
-[13:15:30] Walltime used: 0.07 minutes
-[13:15:30] If you use this result please cite the Prokka paper:
-[13:15:30] Seemann T (2014) Prokka: rapid prokaryotic genome annotation. Bioinformatics. 30(14):2068-9.
-[13:15:30] Type 'prokka --citation' for more details.
-[13:15:30] Thank you, come again.
diff --git a/Examples/2-res-Annotate-prokka/tmp_files/genome2.fst_prokka-split5N.fna-prokkaRes/GEN2.1219.00001.err b/Examples/2-res-Annotate-prokka/tmp_files/genome2.fst_prokka-split5N.fna-prokkaRes/GEN2.1219.00001.err
deleted file mode 100644
index 7a0763633247dc67fba0e59e65d36a35ef9a10ca..0000000000000000000000000000000000000000
--- a/Examples/2-res-Annotate-prokka/tmp_files/genome2.fst_prokka-split5N.fna-prokkaRes/GEN2.1219.00001.err
+++ /dev/null
@@ -1,170 +0,0 @@
-Discrepancy Report Results
-
-Summary
-FATAL: MISSING_PROTEIN_ID:13 proteins have invalid IDs.
-DISC_SOURCE_QUALS_ASNDISC:strain (all present, all same)
-DISC_SOURCE_QUALS_ASNDISC:taxname (all present, all same)
-DISC_FEATURE_COUNT:CDS: 13 present
-DISC_COUNT_NUCLEOTIDES:5 nucleotide Bioseqs are present
-FEATURE_LOCATION_CONFLICT:13 features have inconsistent gene locations.
-SHORT_CONTIG:1 contigs are shorter than 200 nt.
-SHORT_SEQUENCES:1 sequences are shorter than 50 nt.
-NO_ANNOTATION:1 bioseqs have no features
-DISC_QUALITY_SCORES:Quality scores are missing on all sequences.
-ONCALLER_COMMENT_PRESENT:5 comment descriptors were found (all same)
-MISSING_GENOMEASSEMBLY_COMMENTS:5 bioseqs are missing GenomeAssembly structured comments
-SHORT_SEQUENCES_200:1 sequences are shorter than 200 bp.
-MOLTYPE_NOT_MRNA:5 molecule types are not set as mRNA.
-TECHNIQUE_NOT_TSA:5 technique are not set as TSA
-MISSING_STRUCTURED_COMMENT:5 sequences do not include structured comments.
-MISSING_PROJECT:18 sequences do not include project.
-DISC_INCONSISTENT_MOLINFO_TECH:Molinfo Technique Report (some missing, all same)
-
-
-Detailed Report
-
-FATAL: DiscRep_ALL:MISSING_PROTEIN_ID::13 proteins halid nvalid IDs.
-Examples/2-res-Annotate-prokka/tmp_files/genome2.fst_prokka-split5N.fna-prokkaRes/GEN2.1219.00001:this_is_genome_1_1 (length 257)
-Examples/2-res-Annotate-prokka/tmp_files/genome2.fst_prokka-split5N.fna-prokkaRes/GEN2.1219.00001:this_is_genome_1_2 (length 467)
-Examples/2-res-Annotate-prokka/tmp_files/genome2.fst_prokka-split5N.fna-prokkaRes/GEN2.1219.00001:this_is_genome_2_1 (length 74)
-Examples/2-res-Annotate-prokka/tmp_files/genome2.fst_prokka-split5N.fna-prokkaRes/GEN2.1219.00001:this_is_genome_2_2 (length 126)
-Examples/2-res-Annotate-prokka/tmp_files/genome2.fst_prokka-split5N.fna-prokkaRes/GEN2.1219.00001:this_is_genome_2_3 (length 277)
-Examples/2-res-Annotate-prokka/tmp_files/genome2.fst_prokka-split5N.fna-prokkaRes/GEN2.1219.00001:this_is_genome_2_4 (length 555)
-Examples/2-res-Annotate-prokka/tmp_files/genome2.fst_prokka-split5N.fna-prokkaRes/GEN2.1219.00001:this_is_genome_3_1 (length 255)
-Examples/2-res-Annotate-prokka/tmp_files/genome2.fst_prokka-split5N.fna-prokkaRes/GEN2.1219.00001:this_is_genome_3_2 (length 86)
-Examples/2-res-Annotate-prokka/tmp_files/genome2.fst_prokka-split5N.fna-prokkaRes/GEN2.1219.00001:this_is_genome_3_3 (length 193)
-Examples/2-res-Annotate-prokka/tmp_files/genome2.fst_prokka-split5N.fna-prokkaRes/GEN2.1219.00001:this_is_genome_3_4 (length 122)
-Examples/2-res-Annotate-prokka/tmp_files/genome2.fst_prokka-split5N.fna-prokkaRes/GEN2.1219.00001:this_is_genome_4_1 (length 435)
-Examples/2-res-Annotate-prokka/tmp_files/genome2.fst_prokka-split5N.fna-prokkaRes/GEN2.1219.00001:this_is_genome_4_2 (length 154)
-Examples/2-res-Annotate-prokka/tmp_files/genome2.fst_prokka-split5N.fna-prokkaRes/GEN2.1219.00001:this_is_genome_4_3 (length 337)
-
-DiscRep_ALL:DISC_SOURCE_QUALS_ASNDISC::strain (all present, all same)
-DiscRep_SUB:DISC_SOURCE_QUALS_ASNDISC::5 sources have 'strain' for strain
-DiscRep_ALL:DISC_SOURCE_QUALS_ASNDISC::taxname (all present, all same)
-DiscRep_SUB:DISC_SOURCE_QUALS_ASNDISC::5 sources have 'Genus species' for taxname
-DiscRep_ALL:DISC_FEATURE_COUNT::CDS: 13 present
-DiscRep_ALL:DISC_COUNT_NUCLEOTIDES::5 nucleotide Bioseqs are present
-Examples/2-res-Annotate-prokka/tmp_files/genome2.fst_prokka-split5N.fna-prokkaRes/GEN2.1219.00001:this_is_genome_1 (length 2308, 2 other)
-Examples/2-res-Annotate-prokka/tmp_files/genome2.fst_prokka-split5N.fna-prokkaRes/GEN2.1219.00001:this_is_genome_2 (length 3295, 3 other)
-Examples/2-res-Annotate-prokka/tmp_files/genome2.fst_prokka-split5N.fna-prokkaRes/GEN2.1219.00001:this_is_genome_3 (length 2263)
-Examples/2-res-Annotate-prokka/tmp_files/genome2.fst_prokka-split5N.fna-prokkaRes/GEN2.1219.00001:this_is_genome_4 (length 2845)
-Examples/2-res-Annotate-prokka/tmp_files/genome2.fst_prokka-split5N.fna-prokkaRes/GEN2.1219.00001:genome2_small_5 (length 6)
-
-DiscRep_ALL:FEATURE_LOCATION_CONFLICT::13 features have inconsistent gene locations.
-DiscRep_SUB:FEATURE_LOCATION_CONFLICT::Coding region xref gene does not exist
-Examples/2-res-Annotate-prokka/tmp_files/genome2.fst_prokka-split5N.fna-prokkaRes/GEN2.1219.00001:CDS	Histidine transport ATP-binding protein HisP	this_is_genome_1:1-774	AMHDIIJN_00001
-
-DiscRep_SUB:FEATURE_LOCATION_CONFLICT::Coding region xref gene does not exist
-Examples/2-res-Annotate-prokka/tmp_files/genome2.fst_prokka-split5N.fna-prokkaRes/GEN2.1219.00001:CDS	hypothetical protein	this_is_genome_1:857-2260	AMHDIIJN_00002
-
-DiscRep_SUB:FEATURE_LOCATION_CONFLICT::Coding region xref gene does not exist
-Examples/2-res-Annotate-prokka/tmp_files/genome2.fst_prokka-split5N.fna-prokkaRes/GEN2.1219.00001:CDS	Phage shock protein B	this_is_genome_2:28-252	AMHDIIJN_00003
-
-DiscRep_SUB:FEATURE_LOCATION_CONFLICT::Coding region xref gene does not exist
-Examples/2-res-Annotate-prokka/tmp_files/genome2.fst_prokka-split5N.fna-prokkaRes/GEN2.1219.00001:CDS	5-carboxymethyl-2-hydroxymuconate Delta-isomerase	this_is_genome_2:301-681	AMHDIIJN_00004
-
-DiscRep_SUB:FEATURE_LOCATION_CONFLICT::Coding region xref gene does not exist
-Examples/2-res-Annotate-prokka/tmp_files/genome2.fst_prokka-split5N.fna-prokkaRes/GEN2.1219.00001:CDS	N-acetylmuramoyl-L-alanine amidase AmiD	this_is_genome_2:764-1597	AMHDIIJN_00005
-
-DiscRep_SUB:FEATURE_LOCATION_CONFLICT::Coding region xref gene does not exist
-Examples/2-res-Annotate-prokka/tmp_files/genome2.fst_prokka-split5N.fna-prokkaRes/GEN2.1219.00001:CDS	Glutamine--tRNA ligase	this_is_genome_2:1628-3295	AMHDIIJN_00006
-
-DiscRep_SUB:FEATURE_LOCATION_CONFLICT::Coding region xref gene does not exist
-Examples/2-res-Annotate-prokka/tmp_files/genome2.fst_prokka-split5N.fna-prokkaRes/GEN2.1219.00001:CDS	tRNA (guanine-N(1)-)-methyltransferase	this_is_genome_3:30-797	AMHDIIJN_00007
-
-DiscRep_SUB:FEATURE_LOCATION_CONFLICT::Coding region xref gene does not exist
-Examples/2-res-Annotate-prokka/tmp_files/genome2.fst_prokka-split5N.fna-prokkaRes/GEN2.1219.00001:CDS	hypothetical protein	this_is_genome_3:862-1122	AMHDIIJN_00008
-
-DiscRep_SUB:FEATURE_LOCATION_CONFLICT::Coding region xref gene does not exist
-Examples/2-res-Annotate-prokka/tmp_files/genome2.fst_prokka-split5N.fna-prokkaRes/GEN2.1219.00001:CDS	hypothetical protein	this_is_genome_3:1170-1751	AMHDIIJN_00009
-
-DiscRep_SUB:FEATURE_LOCATION_CONFLICT::Coding region xref gene does not exist
-Examples/2-res-Annotate-prokka/tmp_files/genome2.fst_prokka-split5N.fna-prokkaRes/GEN2.1219.00001:CDS	hypothetical protein	this_is_genome_3:1895-2263	AMHDIIJN_00010
-
-DiscRep_SUB:FEATURE_LOCATION_CONFLICT::Coding region xref gene does not exist
-Examples/2-res-Annotate-prokka/tmp_files/genome2.fst_prokka-split5N.fna-prokkaRes/GEN2.1219.00001:CDS	C4-dicarboxylate TRAP transporter large permease protein DctM	this_is_genome_4:1-1308	AMHDIIJN_00011
-
-DiscRep_SUB:FEATURE_LOCATION_CONFLICT::Coding region xref gene does not exist
-Examples/2-res-Annotate-prokka/tmp_files/genome2.fst_prokka-split5N.fna-prokkaRes/GEN2.1219.00001:CDS	hypothetical protein	this_is_genome_4:1340-1804	AMHDIIJN_00012
-
-DiscRep_SUB:FEATURE_LOCATION_CONFLICT::Coding region xref gene does not exist
-Examples/2-res-Annotate-prokka/tmp_files/genome2.fst_prokka-split5N.fna-prokkaRes/GEN2.1219.00001:CDS	Tyrosine recombinase XerC	this_is_genome_4:1832-2845	AMHDIIJN_00013
-
-DiscRep_ALL:SHORT_CONTIG::1 contigs are shorter than 200 nt.
-Examples/2-res-Annotate-prokka/tmp_files/genome2.fst_prokka-split5N.fna-prokkaRes/GEN2.1219.00001:genome2_small_5 (length 6)
-
-DiscRep_ALL:SHORT_SEQUENCES::1 sequences are shorter than 50 nt.
-Examples/2-res-Annotate-prokka/tmp_files/genome2.fst_prokka-split5N.fna-prokkaRes/GEN2.1219.00001:genome2_small_5 (length 6)
-
-DiscRep_ALL:NO_ANNOTATION::1 bioseqs have no features
-Examples/2-res-Annotate-prokka/tmp_files/genome2.fst_prokka-split5N.fna-prokkaRes/GEN2.1219.00001:genome2_small_5 (length 6)
-
-DiscRep_ALL:DISC_QUALITY_SCORES::Quality scores are missing on all sequences.
-
-DiscRep_ALL:ONCALLER_COMMENT_PRESENT::5 comment descriptors were found (all same)
-Examples/2-res-Annotate-prokka/tmp_files/genome2.fst_prokka-split5N.fna-prokkaRes/GEN2.1219.00001:this_is_genome_1:Annotated using prokka 1.14.5 from https://github.com/tseemann/prokka
-Examples/2-res-Annotate-prokka/tmp_files/genome2.fst_prokka-split5N.fna-prokkaRes/GEN2.1219.00001:this_is_genome_2:Annotated using prokka 1.14.5 from https://github.com/tseemann/prokka
-Examples/2-res-Annotate-prokka/tmp_files/genome2.fst_prokka-split5N.fna-prokkaRes/GEN2.1219.00001:this_is_genome_3:Annotated using prokka 1.14.5 from https://github.com/tseemann/prokka
-Examples/2-res-Annotate-prokka/tmp_files/genome2.fst_prokka-split5N.fna-prokkaRes/GEN2.1219.00001:this_is_genome_4:Annotated using prokka 1.14.5 from https://github.com/tseemann/prokka
-Examples/2-res-Annotate-prokka/tmp_files/genome2.fst_prokka-split5N.fna-prokkaRes/GEN2.1219.00001:genome2_small_5:Annotated using prokka 1.14.5 from https://github.com/tseemann/prokka
-
-DiscRep_ALL:MISSING_GENOMEASSEMBLY_COMMENTS::5 bioseqs are missing GenomeAssembly structured comments
-Examples/2-res-Annotate-prokka/tmp_files/genome2.fst_prokka-split5N.fna-prokkaRes/GEN2.1219.00001:this_is_genome_1 (length 2308, 2 other)
-Examples/2-res-Annotate-prokka/tmp_files/genome2.fst_prokka-split5N.fna-prokkaRes/GEN2.1219.00001:this_is_genome_2 (length 3295, 3 other)
-Examples/2-res-Annotate-prokka/tmp_files/genome2.fst_prokka-split5N.fna-prokkaRes/GEN2.1219.00001:this_is_genome_3 (length 2263)
-Examples/2-res-Annotate-prokka/tmp_files/genome2.fst_prokka-split5N.fna-prokkaRes/GEN2.1219.00001:this_is_genome_4 (length 2845)
-Examples/2-res-Annotate-prokka/tmp_files/genome2.fst_prokka-split5N.fna-prokkaRes/GEN2.1219.00001:genome2_small_5 (length 6)
-
-DiscRep_ALL:SHORT_SEQUENCES_200::1 sequences are shorter than 200 bp.
-Examples/2-res-Annotate-prokka/tmp_files/genome2.fst_prokka-split5N.fna-prokkaRes/GEN2.1219.00001:genome2_small_5 (length 6)
-
-DiscRep_ALL:MOLTYPE_NOT_MRNA::5 molecule types are not set as mRNA.
-Examples/2-res-Annotate-prokka/tmp_files/genome2.fst_prokka-split5N.fna-prokkaRes/GEN2.1219.00001:this_is_genome_1 (length 2308, 2 other)
-Examples/2-res-Annotate-prokka/tmp_files/genome2.fst_prokka-split5N.fna-prokkaRes/GEN2.1219.00001:this_is_genome_2 (length 3295, 3 other)
-Examples/2-res-Annotate-prokka/tmp_files/genome2.fst_prokka-split5N.fna-prokkaRes/GEN2.1219.00001:this_is_genome_3 (length 2263)
-Examples/2-res-Annotate-prokka/tmp_files/genome2.fst_prokka-split5N.fna-prokkaRes/GEN2.1219.00001:this_is_genome_4 (length 2845)
-Examples/2-res-Annotate-prokka/tmp_files/genome2.fst_prokka-split5N.fna-prokkaRes/GEN2.1219.00001:genome2_small_5 (length 6)
-
-DiscRep_ALL:TECHNIQUE_NOT_TSA::5 technique are not set as TSA
-Examples/2-res-Annotate-prokka/tmp_files/genome2.fst_prokka-split5N.fna-prokkaRes/GEN2.1219.00001:this_is_genome_1 (length 2308, 2 other)
-Examples/2-res-Annotate-prokka/tmp_files/genome2.fst_prokka-split5N.fna-prokkaRes/GEN2.1219.00001:this_is_genome_2 (length 3295, 3 other)
-Examples/2-res-Annotate-prokka/tmp_files/genome2.fst_prokka-split5N.fna-prokkaRes/GEN2.1219.00001:this_is_genome_3 (length 2263)
-Examples/2-res-Annotate-prokka/tmp_files/genome2.fst_prokka-split5N.fna-prokkaRes/GEN2.1219.00001:this_is_genome_4 (length 2845)
-Examples/2-res-Annotate-prokka/tmp_files/genome2.fst_prokka-split5N.fna-prokkaRes/GEN2.1219.00001:genome2_small_5 (length 6)
-
-DiscRep_ALL:MISSING_STRUCTURED_COMMENT::5 sequences do not include structured comments.
-Examples/2-res-Annotate-prokka/tmp_files/genome2.fst_prokka-split5N.fna-prokkaRes/GEN2.1219.00001:this_is_genome_1 (length 2308, 2 other)
-Examples/2-res-Annotate-prokka/tmp_files/genome2.fst_prokka-split5N.fna-prokkaRes/GEN2.1219.00001:this_is_genome_2 (length 3295, 3 other)
-Examples/2-res-Annotate-prokka/tmp_files/genome2.fst_prokka-split5N.fna-prokkaRes/GEN2.1219.00001:this_is_genome_3 (length 2263)
-Examples/2-res-Annotate-prokka/tmp_files/genome2.fst_prokka-split5N.fna-prokkaRes/GEN2.1219.00001:this_is_genome_4 (length 2845)
-Examples/2-res-Annotate-prokka/tmp_files/genome2.fst_prokka-split5N.fna-prokkaRes/GEN2.1219.00001:genome2_small_5 (length 6)
-
-DiscRep_ALL:MISSING_PROJECT::18 sequences do not include project.
-Examples/2-res-Annotate-prokka/tmp_files/genome2.fst_prokka-split5N.fna-prokkaRes/GEN2.1219.00001:this_is_genome_1 (length 2308, 2 other)
-Examples/2-res-Annotate-prokka/tmp_files/genome2.fst_prokka-split5N.fna-prokkaRes/GEN2.1219.00001:this_is_genome_1_1 (length 257)
-Examples/2-res-Annotate-prokka/tmp_files/genome2.fst_prokka-split5N.fna-prokkaRes/GEN2.1219.00001:this_is_genome_1_2 (length 467)
-Examples/2-res-Annotate-prokka/tmp_files/genome2.fst_prokka-split5N.fna-prokkaRes/GEN2.1219.00001:this_is_genome_2 (length 3295, 3 other)
-Examples/2-res-Annotate-prokka/tmp_files/genome2.fst_prokka-split5N.fna-prokkaRes/GEN2.1219.00001:this_is_genome_2_1 (length 74)
-Examples/2-res-Annotate-prokka/tmp_files/genome2.fst_prokka-split5N.fna-prokkaRes/GEN2.1219.00001:this_is_genome_2_2 (length 126)
-Examples/2-res-Annotate-prokka/tmp_files/genome2.fst_prokka-split5N.fna-prokkaRes/GEN2.1219.00001:this_is_genome_2_3 (length 277)
-Examples/2-res-Annotate-prokka/tmp_files/genome2.fst_prokka-split5N.fna-prokkaRes/GEN2.1219.00001:this_is_genome_2_4 (length 555)
-Examples/2-res-Annotate-prokka/tmp_files/genome2.fst_prokka-split5N.fna-prokkaRes/GEN2.1219.00001:this_is_genome_3 (length 2263)
-Examples/2-res-Annotate-prokka/tmp_files/genome2.fst_prokka-split5N.fna-prokkaRes/GEN2.1219.00001:this_is_genome_3_1 (length 255)
-Examples/2-res-Annotate-prokka/tmp_files/genome2.fst_prokka-split5N.fna-prokkaRes/GEN2.1219.00001:this_is_genome_3_2 (length 86)
-Examples/2-res-Annotate-prokka/tmp_files/genome2.fst_prokka-split5N.fna-prokkaRes/GEN2.1219.00001:this_is_genome_3_3 (length 193)
-Examples/2-res-Annotate-prokka/tmp_files/genome2.fst_prokka-split5N.fna-prokkaRes/GEN2.1219.00001:this_is_genome_3_4 (length 122)
-Examples/2-res-Annotate-prokka/tmp_files/genome2.fst_prokka-split5N.fna-prokkaRes/GEN2.1219.00001:this_is_genome_4 (length 2845)
-Examples/2-res-Annotate-prokka/tmp_files/genome2.fst_prokka-split5N.fna-prokkaRes/GEN2.1219.00001:this_is_genome_4_1 (length 435)
-Examples/2-res-Annotate-prokka/tmp_files/genome2.fst_prokka-split5N.fna-prokkaRes/GEN2.1219.00001:this_is_genome_4_2 (length 154)
-Examples/2-res-Annotate-prokka/tmp_files/genome2.fst_prokka-split5N.fna-prokkaRes/GEN2.1219.00001:this_is_genome_4_3 (length 337)
-Examples/2-res-Annotate-prokka/tmp_files/genome2.fst_prokka-split5N.fna-prokkaRes/GEN2.1219.00001:genome2_small_5 (length 6)
-
-DiscRep_ALL:DISC_INCONSISTENT_MOLINFO_TECH::Molinfo Technique Report (some missing, all same)
-DiscRep_SUB:DISC_INCONSISTENT_MOLINFO_TECH::technique (all missing)
-DiscRep_SUB:DISC_INCONSISTENT_MOLINFO_TECH::5 Molinfos are missing field technique
-Examples/2-res-Annotate-prokka/tmp_files/genome2.fst_prokka-split5N.fna-prokkaRes/GEN2.1219.00001:genome2_small_5 (length 6)
-Examples/2-res-Annotate-prokka/tmp_files/genome2.fst_prokka-split5N.fna-prokkaRes/GEN2.1219.00001:this_is_genome_1 (length 2308, 2 other)
-Examples/2-res-Annotate-prokka/tmp_files/genome2.fst_prokka-split5N.fna-prokkaRes/GEN2.1219.00001:this_is_genome_2 (length 3295, 3 other)
-Examples/2-res-Annotate-prokka/tmp_files/genome2.fst_prokka-split5N.fna-prokkaRes/GEN2.1219.00001:this_is_genome_3 (length 2263)
-Examples/2-res-Annotate-prokka/tmp_files/genome2.fst_prokka-split5N.fna-prokkaRes/GEN2.1219.00001:this_is_genome_4 (length 2845)
-
diff --git a/Examples/2-res-Annotate-prokka/tmp_files/genome2.fst_prokka-split5N.fna-prokkaRes/GEN2.1219.00001.faa b/Examples/2-res-Annotate-prokka/tmp_files/genome2.fst_prokka-split5N.fna-prokkaRes/GEN2.1219.00001.faa
deleted file mode 100644
index c0920321a10a6a1b43adabda156ab19ba6f3c39a..0000000000000000000000000000000000000000
--- a/Examples/2-res-Annotate-prokka/tmp_files/genome2.fst_prokka-split5N.fna-prokkaRes/GEN2.1219.00001.faa
+++ /dev/null
@@ -1,77 +0,0 @@
->AMHDIIJN_00001 Histidine transport ATP-binding protein HisP
-MSENKLHVIDLHKRYGGHEVLKGVSLQARAGDVISIIGSSGSGKSTFLRCINFLEKSSEG
-AIIVNGQNINLVRDKDGQLKVADKNQLRLLRTRLTMVFQHFNLWNHMTVLENVMEAPIQV
-LGLSKHDARERALKYLAKVGIDERAQGKYPVHLSGGQQQRVSIARALAMEPDVLLFDEPT
-SALDPELVGEVLRIMQQLAEEGKTMVVVTHEMGFARHVSSHVIFLHQGKIEEEGNPEQVF
-GNPQSPRLQQFLKGSLK
->AMHDIIJN_00002 hypothetical protein
-MPATKFSRRTLLTAGSALAVLPFLRALPVQAREPRQTVDIKDYPADDGIASFKQAFADGQ
-TVVVPSGWVCENINAAITIPAGKTLRIQGAVRGNGRGRFILLDGCQVVGEQGGSLHNVTL
-DVRGSDCVIKGVTMSGFGPVAQIFIGGKEPQVMRNLIIDDITVTHANYAILRQGFHNQMD
-GARITHSRFSDLQGDAIEWNVAIHDRDILISDHVIERIDCTNGKINWGIGIGLAGSAYDN
-SYPEDQAVKNFVVANITGSDCRQLVHVENGKHFVIRNVKAKNITPDFSKNAGIDNATIAI
-YGCDNFVIDNIDMTNSAGMLIGYGVVKGKYLSIPQNFKLNAIRLDNRQVAYKLRGIQISS
-GNAPSFVAITNVRMTRATLELHNQPQHLFLRNINVMQTSAIGPALKMHFDLRKDVRGQFM
-ARQDTLLSLANVHAINENGQSSVDIDRINHQTVNVEAVNFSLPKRGG
->AMHDIIJN_00003 Phage shock protein B
-MSALFLAIPLTIFVLFVLPIWLWLHYSNRAGRGELSQSEQQRLLQLTDDAQRMRERIQAL
-EDILDAEHPNWRER
->AMHDIIJN_00004 5-carboxymethyl-2-hydroxymuconate Delta-isomerase
-MPHFIAECTENIREQADLPSLFSKVNEALAATGIFPIGGIRSRAHWLDTWQMADGKHDYA
-FVHMTLKIGAGRSLESRQEVGEMLFGLIKAHFADLMENRYLALSFEIAELHPTLNYKQNN
-VHALFK
->AMHDIIJN_00005 N-acetylmuramoyl-L-alanine amidase AmiD
-MMKALLWLVGLALLLTGCASEKGIIDKEGYQLDTRHRAQAAYPRIKVLVIHYTAENFDVS
-LATLTGRNVSSHYLIPATPPLYGGKPRIWQLVPEQDQAWHAGVSFWRGATRLNDTSIGIE
-LENRGWRMSGGVKSFAPFESAQIQALIPLAKDIIARYDIKPQNVVAHADIAPQRKDDPGP
-RFPWRELAAQGIGAWPDAQRVAFYLAGRAPYTPVDTATVLALLSRYGYEVKADMTAREQQ
-RVIMAFQMHFRPAQWNGIADAETQAIAEALLEKYGQD
->AMHDIIJN_00006 Glutamine--tRNA ligase
-MSEAEARPTNFIRQIIDEDLASGKHTTVHTRFPPEPNGYLHIGHAKSICLNFGIAQDYQG
-QCNLRFDDTNPVKEDIEYVDSIKNDVEWLGFHWSGDIRYSSDYFDQLHAYAVELINKGLA
-YVDELTPEQIREYRGTLTAPGKNSPFRDRSVEENLALFEKMRTGGFEEGKACLRAKIDMA
-SPFIVMRDPVLYRIKFAEHHQTGTKWCIYPMYDFTHCISDALEGITHSLCTLEFQDNRRL
-YDWVLDNITIPVHPRQYEFSRLNLEYTVMSKRKLNLLVTDKHVEGWDDPRMPTISGLRRR
-GYTAASIREFCKRIGVTKQDNTIEMASLESCIREDLNENAPRAMAVIDPVKLVIENYPQG
-ESEMVTMPNHPNKPEMGSREVPFSGEIWIDRADFREEANKQYKRLVMGKEVRLRNAYVIK
-AERVEKDAEGNITTIFCTYDADTLSKDPADGRKVKGVIHWVSVAHALPIEIRLYDRLFSV
-PNPGAAEDFLSVINPESLVIKQGYGEPSLKAAVAGKAFQFEREGYFCLDSRYATADKLVF
-NRTVGLRDTWAKAGE
->AMHDIIJN_00007 tRNA (guanine-N(1)-)-methyltransferase
-MFIGIVSLFPEMFRAITDYGVTGRAVKKGLLNIQSWSPRDFAHDRHRTVDDRPYGGGPGM
-LMMVQPLRDAIHAAKAAAGEGAKVIYLSPQGRKLDQAGVSELATNQKLILVCGRYEGVDE
-RVIQAEIDEEWSIGDYVLSGGELPAMTLIDSVARFIPGVLGHEASAIEDSFADGLLDCPH
-YTRPEVLEGMEVPPVLLSGNHAEIRRWRLKQSLGRTWLRRPELLENLALTEEQARLLAEF
-KTEHAQQQHKHDGMA
->AMHDIIJN_00008 hypothetical protein
-MAGLHAPYAYSAHHAVNFCSEYKRGFVLGFTHRMFEKTGDRQLSAWEAGILTRRYGLDKE
-MVMDFFKENHSGMAVRFFMAGYRLEG
->AMHDIIJN_00009 hypothetical protein
-MSTLLYLHGFNSSPRSAKACQLKNWLAERHPHVEMIVPQLPPYPADAAELLESLVLEHGG
-APLGLVGSSLGGYYATWLSQCFMLPAVVVNPAVRPFELLTDYLGQNENPYTGQQYVLESR
-HIYDLKVMQIDPLEAPDLIWLLQQTGDEVLDYRQAVAYYASCRQTVTEGGNHAFTGFEDY
-FNQIVDFLGLHSC
->AMHDIIJN_00010 hypothetical protein
-MMRTDGTVTQPRLKQVALSAISEVNAELYEFRRRQQMLGYASLAEVPAEQLDGKSERIQH
-YFNAVYCWARAMLNERYQDYDATASGVKRGEELAEASGDLWRDARWAISRVQDAPHCTVE
-LI
->AMHDIIJN_00011 C4-dicarboxylate TRAP transporter large permease protein DctM
-MIDPIFASCTLIAVFVVLLAMGAPIGICIVIASFSTMMLVLPFDISMFATAQKMFSSLDS
-FALLAVPFFVLSGVIMNSGGIAARLVNFAKLFTGKLPGSLSYTNIVGNMMFGAISGSAIA
-ASTSIGGVMVPMSAREGYDRGFAAAVNIASAPTGMLIPPTTAFILYALASGGTSIAALFA
-GGLVAGVLWGVGCMLVTLVVAKRRNYRVFFTVQKGMALKVAVEAIPSLLLIVIIVGGIVQ
-GIFTAIEASAIAVVYTLLLTIVFYRTLKIKDLPSILLQTVVMTGVIMFLLATSSAMSFSM
-SITNIPAALSDMILGISANKLVILLVITVFLLIIGAFMDIGPAILIFTPILLPIMTKLGV
-DPVHFGIIMIYNLAIGTITPPVGSGLYVGASVGKVKVEDVIKPLMPFYGAIIGVLLLITY
-IPEITLFLPRLLGIM
->AMHDIIJN_00012 hypothetical protein
-MKFVAPEQAPEQAEVIKNTPFWPDVNLSEFRSVMRTDGTVTQPRLKQVVLTAISEVNAEL
-YDFRNRQQMLGWRTLAEVPAEMLDGKSERIRHYHNAVFCWARAVLNERYQDYDATASGVK
-RGEELAEASGDLWRDARWAISRVQDAPHCTVELI
->AMHDIIJN_00013 Tyrosine recombinase XerC
-METNITWQQLIDEYFFAKPLRSASEWSYTKVFKSFVHYMGPLSCPNDVTYHKVLAWRRFL
-LKEKKLSGRTWNNKVAHMRAIFNYGIQRGLLHYDENPFNNSVVKPDKKRKKTLTQAQIEY
-AYQIMEQYENQENTGLGLKYSRCALFPAWFWLTVLDTLYYTGIRQNQLLHIRLNDVDLRE
-GQIRLITEGCKNHKEHYVPVISFLRPRLTCLMEKAQSEGLKGNDRLFNIALFTGKDPAIG
-DDMDSPQVRAFFRRLSKECQFAISPHRFRHTLATEMMKMPEQNLHMAQSVLGHSNMKSTL
-EYVENDIAVMGRALEAQFMQIKAAHARSIYSGLTKNR
diff --git a/Examples/2-res-Annotate-prokka/tmp_files/genome2.fst_prokka-split5N.fna-prokkaRes/GEN2.1219.00001.ffn b/Examples/2-res-Annotate-prokka/tmp_files/genome2.fst_prokka-split5N.fna-prokkaRes/GEN2.1219.00001.ffn
deleted file mode 100644
index 4892107f9017bbcf5bd646c557664037c1597eee..0000000000000000000000000000000000000000
--- a/Examples/2-res-Annotate-prokka/tmp_files/genome2.fst_prokka-split5N.fna-prokkaRes/GEN2.1219.00001.ffn
+++ /dev/null
@@ -1,185 +0,0 @@
->AMHDIIJN_00001 Histidine transport ATP-binding protein HisP
-ATGTCAGAAAATAAATTACACGTTATCGATTTGCACAAACGCTACGGCGGTCATGAAGTG
-CTGAAAGGGGTATCGCTGCAGGCCCGCGCCGGAGATGTGATTAGCATTATCGGCTCGTCC
-GGTTCCGGTAAAAGCACTTTTTTGCGCTGCATTAACTTCCTCGAAAAATCGAGCGAAGGC
-GCGATTATCGTGAACGGTCAGAACATTAATCTGGTGCGCGACAAAGACGGGCAGCTCAAA
-GTGGCGGATAAAAATCAGCTACGCTTGTTGCGTACCCGCCTGACGATGGTGTTTCAGCAC
-TTTAACCTCTGGAACCACATGACGGTGCTGGAAAATGTGATGGAAGCGCCGATTCAGGTA
-CTGGGATTAAGCAAGCACGACGCGCGCGAGCGGGCGTTGAAATATCTGGCGAAGGTGGGG
-ATTGATGAGCGCGCTCAGGGCAAATATCCCGTCCATCTCTCCGGCGGCCAACAGCAGCGC
-GTTTCTATTGCGCGCGCGCTGGCGATGGAACCTGACGTTTTACTGTTCGATGAACCCACA
-TCGGCGCTCGATCCTGAACTGGTCGGCGAAGTGTTGCGCATCATGCAACAACTGGCGGAA
-GAAGGCAAAACGATGGTGGTGGTCACGCATGAAATGGGCTTCGCCCGCCATGTCTCTTCG
-CACGTGATTTTTCTGCATCAGGGGAAAATTGAAGAAGAGGGCAATCCGGAGCAGGTGTTC
-GGCAATCCGCAAAGCCCGCGTTTACAGCAATTCCTGAAAGGCTCGCTGAAATAA
->AMHDIIJN_00002 hypothetical protein
-ATGCCCGCGACTAAATTCTCCCGACGTACCCTCCTGACGGCAGGTTCCGCGCTTGCTGTT
-CTTCCTTTTCTGCGCGCCTTGCCGGTACAGGCGCGTGAACCTCGCCAGACCGTCGATATT
-AAGGATTATCCGGCGGATGACGGTATCGCCTCGTTCAAACAGGCCTTCGCCGACGGGCAG
-ACTGTGGTCGTGCCGTCAGGATGGGTGTGTGAAAATATCAATGCGGCGATAACGATTCCG
-GCGGGAAAAACGCTGCGGATACAGGGCGCGGTGCGTGGGAATGGCCGGGGACGGTTTATT
-TTGCTGGACGGGTGTCAGGTGGTGGGGGAGCAGGGCGGCAGTCTGCACAATGTGACGCTG
-GATGTTCGCGGGTCGGACTGTGTGATTAAAGGCGTGACGATGAGCGGCTTTGGCCCCGTC
-GCGCAAATTTTCATCGGCGGTAAGGAACCGCAGGTGATGCGTAATCTCATTATCGATGAC
-ATCACCGTTACCCACGCCAACTACGCCATTCTCCGCCAGGGATTTCATAACCAAATGGAC
-GGCGCGCGGATTACGCATAGTCGCTTTAGCGATTTGCAGGGGGACGCCATTGAGTGGAAT
-GTCGCGATTCATGACCGCGACATCCTGATTTCCGATCATGTCATCGAACGCATTGATTGT
-ACCAATGGCAAAATCAACTGGGGGATCGGCATCGGGCTGGCGGGTAGCGCCTATGACAAT
-AGTTATCCTGAAGACCAGGCAGTAAAAAACTTTGTGGTGGCCAATATTACCGGATCTGAT
-TGCCGACAACTGGTACACGTAGAAAATGGCAAACATTTCGTCATTCGCAATGTCAAAGCC
-AAAAACATCACGCCCGATTTCAGTAAAAATGCGGGTATTGATAACGCAACGATCGCCATT
-TATGGCTGTGATAATTTCGTCATTGATAATATTGATATGACGAATAGTGCCGGGATGCTC
-ATCGGCTATGGCGTCGTTAAAGGAAAATACCTGTCAATTCCGCAAAACTTTAAATTAAAC
-GCTATTCGGTTGGATAATCGCCAGGTTGCTTATAAATTACGCGGCATTCAAATTTCCTCC
-GGTAACGCCCCCTCATTTGTTGCCATCACCAATGTACGGATGACGCGTGCTACGCTGGAA
-CTGCATAATCAACCGCAGCACCTCTTTTTGCGTAATATCAACGTGATGCAAACTTCAGCG
-ATTGGCCCGGCGTTAAAAATGCATTTTGATTTGCGTAAAGATGTCCGTGGTCAATTTATG
-GCCCGCCAGGACACGCTGCTTTCCCTCGCTAATGTTCATGCCATCAATGAAAACGGGCAG
-AGTTCCGTGGATATCGACAGGATTAATCACCAAACCGTGAATGTCGAAGCAGTGAATTTT
-TCGCTGCCGAAGCGGGGAGGGTAA
->AMHDIIJN_00003 Phage shock protein B
-ATGAGCGCGCTATTTCTGGCCATCCCGTTAACCATTTTTGTGTTGTTTGTGTTACCGATT
-TGGCTGTGGCTGCATTACAGCAACCGCGCCGGTCGGGGAGAACTGTCGCAAAGCGAGCAG
-CAACGCTTACTGCAACTCACAGACGACGCGCAACGTATGCGCGAGCGCATTCAGGCGCTG
-GAAGATATTCTTGATGCAGAGCATCCGAACTGGAGAGAGCGCTAA
->AMHDIIJN_00004 5-carboxymethyl-2-hydroxymuconate Delta-isomerase
-ATGCCGCACTTTATTGCTGAATGTACTGAAAATATTCGCGAGCAGGCTGATTTACCAAGC
-CTGTTCAGCAAGGTAAACGAGGCGCTGGCCGCCACCGGGATTTTCCCCATCGGCGGTATC
-CGCAGTCGCGCCCACTGGCTGGATACCTGGCAGATGGCTGACGGTAAGCATGATTACGCG
-TTTGTGCATATGACGCTGAAAATCGGCGCCGGGCGCAGCCTGGAGAGCCGTCAGGAAGTC
-GGCGAAATGCTGTTTGGGCTGATTAAAGCCCACTTCGCCGACCTGATGGAGAACCGCTAT
-CTGGCGCTGTCGTTTGAGATTGCCGAGTTACATCCAACGCTCAATTACAAACAAAACAAC
-GTACACGCGTTATTTAAATAG
->AMHDIIJN_00005 N-acetylmuramoyl-L-alanine amidase AmiD
-ATGATGAAAGCGCTACTGTGGCTGGTTGGTCTCGCGTTGCTGTTAACAGGCTGCGCGAGC
-GAAAAAGGAATTATCGATAAAGAGGGATATCAGCTTGATACCCGACATCGGGCGCAGGCG
-GCCTATCCGCGCATTAAAGTCCTGGTGATTCACTATACGGCGGAAAACTTTGACGTTTCG
-CTGGCGACGTTAACGGGTCGCAACGTCAGTTCGCATTACCTGATTCCCGCAACCCCGCCA
-TTATATGGCGGTAAACCGCGCATCTGGCAACTGGTGCCGGAACAGGATCAGGCTTGGCAT
-GCGGGCGTCAGTTTCTGGCGAGGCGCCACGCGTCTCAATGATACGTCTATTGGCATTGAG
-CTGGAAAATCGCGGCTGGCGAATGTCCGGCGGGGTGAAATCTTTCGCGCCGTTTGAATCC
-GCGCAAATTCAGGCATTGATCCCGTTAGCGAAGGACATTATCGCGCGCTATGACATCAAA
-CCGCAGAATGTGGTGGCCCATGCGGATATCGCGCCGCAGCGTAAAGACGATCCCGGCCCG
-CGCTTCCCGTGGCGCGAGCTGGCGGCACAGGGGATTGGCGCCTGGCCTGACGCCCAGCGT
-GTGGCGTTTTATCTGGCTGGACGCGCGCCGTATACGCCAGTCGATACCGCAACGGTGCTT
-GCGTTACTCTCGCGCTATGGCTATGAAGTCAAAGCCGATATGACGGCGCGCGAGCAACAG
-CGGGTGATTATGGCGTTCCAGATGCACTTCCGTCCGGCGCAATGGAACGGTATCGCAGAT
-GCCGAAACGCAGGCGATTGCCGAAGCATTACTGGAGAAGTACGGCCAGGATTAA
->AMHDIIJN_00006 Glutamine--tRNA ligase
-ATGAGTGAGGCTGAAGCCCGCCCGACTAACTTTATTCGTCAGATTATTGATGAAGATCTG
-GCGAGTGGTAAACATACCACTGTCCATACCCGTTTTCCGCCGGAGCCGAATGGCTATCTG
-CACATCGGCCACGCGAAATCTATCTGCCTGAACTTTGGCATCGCGCAAGATTATCAGGGC
-CAGTGCAACCTGCGTTTCGATGACACCAACCCGGTAAAAGAAGATATCGAGTACGTTGAT
-TCGATCAAAAACGACGTCGAGTGGTTAGGCTTTCACTGGTCTGGCGATATTCGCTACTCC
-TCCGATTACTTTGACCAACTGCACGCCTATGCGGTCGAGCTCATCAATAAAGGCCTGGCC
-TACGTTGATGAGCTGACGCCGGAGCAGATCCGCGAATACCGTGGTACGCTGACCGCGCCG
-GGTAAAAACAGCCCGTTCCGCGATCGCAGCGTGGAAGAAAACCTCGCGCTATTTGAAAAA
-ATGCGTACCGGCGGTTTTGAAGAGGGTAAAGCCTGTCTGCGCGCTAAAATCGACATGGCG
-TCGCCGTTTATCGTGATGCGCGATCCGGTGCTGTATCGCATTAAATTCGCCGAGCATCAT
-CAGACCGGCACGAAGTGGTGCATCTATCCGATGTACGACTTTACTCACTGCATCAGCGAT
-GCGCTGGAAGGCATTACTCATTCTCTGTGTACGCTGGAGTTCCAGGACAACCGTCGTCTG
-TACGACTGGGTGCTGGACAACATCACCATTCCGGTTCACCCGCGCCAGTACGAATTCTCG
-CGCCTGAATCTGGAATACACCGTGATGTCCAAGCGTAAGCTGAACCTGCTGGTGACCGAC
-AAACACGTCGAAGGTTGGGATGATCCGCGTATGCCGACTATTTCCGGTCTGCGCCGTCGC
-GGCTATACCGCGGCTTCTATTCGTGAGTTCTGCAAACGCATCGGCGTCACCAAGCAGGAC
-AACACTATTGAGATGGCGTCGCTGGAATCCTGCATTCGCGAAGATCTGAACGAAAACGCG
-CCGCGCGCGATGGCGGTAATCGATCCGGTAAAACTGGTTATCGAAAACTACCCGCAGGGC
-GAGAGCGAAATGGTTACCATGCCTAACCATCCGAATAAACCGGAGATGGGCAGCCGTGAA
-GTGCCGTTTAGCGGTGAGATCTGGATCGATCGCGCGGATTTCCGCGAAGAAGCGAACAAA
-CAGTACAAACGTCTGGTGATGGGCAAAGAAGTGCGTCTGCGTAATGCCTACGTCATTAAA
-GCGGAGCGCGTAGAGAAGGATGCCGAAGGGAATATCACCACCATCTTCTGTACCTATGAT
-GCTGATACGCTGAGTAAAGATCCGGCTGACGGGCGTAAAGTGAAAGGCGTAATCCACTGG
-GTTAGCGTAGCACATGCGCTGCCGATTGAAATTCGTCTCTACGACCGTCTGTTCAGCGTG
-CCGAACCCGGGCGCCGCGGAGGACTTCCTGTCTGTTATCAACCCCGAATCATTAGTGATT
-AAGCAGGGGTATGGCGAGCCGTCGCTGAAAGCGGCGGTAGCAGGGAAAGCTTTCCAGTTT
-GAACGTGAAGGTTACTTCTGCCTTGACAGCCGCTATGCAACGGCCGATAAGCTGGTCTTT
-AACCGCACCGTGGGCCTGCGTGATACCTGGGCGAAAGCGGGCGAATAA
->AMHDIIJN_00007 tRNA (guanine-N(1)-)-methyltransferase
-GTGTTTATTGGCATCGTTAGCCTGTTTCCTGAAATGTTCCGCGCAATTACCGATTACGGG
-GTAACTGGCCGGGCAGTAAAAAAAGGCCTGCTGAACATCCAAAGCTGGAGTCCTCGCGAC
-TTCGCGCATGACCGGCACCGTACCGTGGACGACCGTCCTTACGGCGGCGGACCGGGGATG
-TTAATGATGGTGCAACCCTTGCGGGACGCCATTCATGCAGCAAAAGCCGCGGCAGGTGAA
-GGCGCTAAAGTGATTTATCTGTCGCCTCAGGGACGCAAGCTTGATCAAGCGGGCGTTAGC
-GAGCTGGCCACGAATCAGAAACTCATTCTGGTGTGTGGTCGCTACGAAGGCGTAGATGAG
-CGCGTAATTCAGGCCGAAATTGACGAAGAATGGTCAATTGGCGATTACGTTCTCAGCGGT
-GGCGAACTACCGGCAATGACGCTGATTGACTCCGTCGCCCGGTTTATACCGGGGGTTCTG
-GGGCATGAGGCATCAGCAATCGAAGATTCGTTTGCTGATGGGTTGCTGGATTGTCCGCAC
-TATACGCGCCCTGAAGTGTTAGAGGGGATGGAAGTACCGCCAGTATTGCTGTCGGGAAAC
-CATGCTGAGATACGTCGCTGGCGTTTGAAACAGTCACTGGGCCGAACCTGGCTTAGAAGA
-CCTGAACTTCTGGAAAACCTGGCTCTGACTGAAGAGCAAGCAAGGTTGCTGGCGGAGTTC
-AAAACAGAACACGCACAACAGCAGCATAAACATGATGGGATGGCATAG
->AMHDIIJN_00008 hypothetical protein
-ATGGCCGGGTTGCACGCGCCATATGCATATAGCGCGCATCATGCGGTGAATTTCTGTTCT
-GAGTATAAACGTGGCTTTGTATTGGGTTTTACACACCGTATGTTCGAAAAGACCGGCGAT
-CGTCAACTTAGCGCGTGGGAGGCCGGAATTCTGACGCGTCGCTATGGTCTGGATAAAGAA
-ATGGTGATGGATTTCTTTAAAGAGAATCATTCCGGGATGGCGGTTCGCTTCTTTATGGCT
-GGTTATCGACTCGAAGGTTGA
->AMHDIIJN_00009 hypothetical protein
-ATGTCTACGCTTCTCTATTTGCACGGATTCAACAGTTCCCCTCGCTCGGCAAAAGCGTGC
-CAGCTAAAAAACTGGCTGGCGGAGCGTCATCCGCATGTTGAGATGATCGTCCCTCAACTG
-CCGCCGTATCCTGCCGATGCGGCGGAGTTGCTGGAATCTCTCGTACTTGAGCATGGCGGT
-GCGCCATTAGGGCTGGTAGGATCGTCGCTGGGTGGTTATTACGCCACCTGGCTGTCGCAA
-TGTTTTATGCTGCCGGCTGTGGTGGTGAATCCCGCCGTGCGGCCCTTTGAATTACTGACC
-GACTATCTCGGTCAGAACGAGAACCCCTACACCGGGCAGCAATATGTGCTAGAGTCTCGC
-CATATTTATGATCTTAAAGTCATGCAGATTGACCCGCTGGAAGCGCCGGACCTGATCTGG
-CTACTGCAACAGACGGGCGATGAAGTGCTGGATTACCGCCAGGCGGTGGCATATTACGCC
-TCCTGCCGTCAGACAGTGACCGAGGGGGGTAATCACGCATTCACGGGCTTCGAAGATTAT
-TTCAACCAGATTGTCGATTTTCTTGGACTGCACAGTTGCTGA
->AMHDIIJN_00010 hypothetical protein
-ATGATGCGCACTGATGGCACGGTGACGCAGCCGCGTTTAAAGCAGGTTGCGCTGTCGGCA
-ATTTCGGAGGTCAACGCAGAGCTGTATGAGTTTCGCAGACGCCAGCAGATGCTGGGGTAT
-GCCTCGCTGGCAGAAGTCCCGGCGGAACAACTGGACGGCAAAAGCGAGCGCATTCAGCAC
-TATTTCAACGCGGTTTACTGCTGGGCACGCGCCATGCTCAACGAACGTTACCAGGACTAT
-GACGCCACGGCATCCGGTGTGAAGCGGGGCGAAGAACTGGCAGAAGCCAGCGGTGATTTG
-TGGCGTGACGCCCGCTGGGCCATCAGCCGGGTGCAGGATGCGCCGCACTGCACAGTGGAG
-CTTATCTGA
->AMHDIIJN_00011 C4-dicarboxylate TRAP transporter large permease protein DctM
-ATGATTGACCCTATTTTTGCGTCCTGTACGCTAATTGCCGTCTTTGTTGTTTTACTGGCC
-ATGGGCGCGCCTATCGGGATCTGCATCGTTATCGCCTCTTTCAGCACCATGATGCTGGTA
-CTGCCTTTCGATATTTCGATGTTCGCCACCGCGCAAAAAATGTTCTCCAGCCTGGACAGT
-TTTGCCTTGCTGGCCGTGCCGTTCTTCGTTTTGTCCGGGGTGATCATGAATAGCGGGGGA
-ATTGCCGCCCGACTGGTCAATTTTGCCAAACTGTTTACTGGCAAACTGCCCGGCTCGCTC
-TCTTACACCAACATCGTCGGCAATATGATGTTCGGTGCAATTTCCGGATCGGCGATTGCC
-GCCTCAACCTCTATCGGCGGCGTGATGGTGCCGATGAGCGCGCGCGAAGGTTACGATCGC
-GGTTTTGCGGCCGCGGTGAATATCGCCTCCGCGCCGACGGGAATGTTAATTCCGCCCACC
-ACGGCTTTTATCCTTTATGCGCTGGCAAGCGGGGGAACATCGATTGCCGCTCTGTTCGCC
-GGCGGTCTGGTCGCGGGAGTGCTGTGGGGCGTTGGCTGTATGCTGGTCACGCTGGTGGTC
-GCTAAGCGTCGAAATTATCGGGTTTTCTTCACCGTCCAAAAAGGCATGGCGCTAAAAGTT
-GCCGTTGAGGCCATTCCCAGCCTGTTACTGATCGTGATTATTGTCGGCGGCATTGTGCAG
-GGGATTTTCACCGCCATTGAAGCCTCCGCGATTGCCGTGGTGTATACGTTATTGCTGACG
-ATAGTGTTTTACCGCACGCTGAAAATTAAGGATTTGCCTTCGATTTTGCTCCAGACAGTG
-GTAATGACCGGGGTCATCATGTTCCTGCTGGCAACCTCTTCGGCGATGTCCTTCTCGATG
-TCGATCACCAATATTCCTGCGGCGCTGAGCGATATGATCCTCGGTATTTCCGCCAATAAA
-CTGGTTATCCTGTTAGTCATTACCGTCTTTTTGTTGATTATCGGCGCATTTATGGATATC
-GGTCCGGCCATTCTGATTTTTACCCCGATTCTGCTGCCGATTATGACTAAACTGGGCGTC
-GATCCGGTGCATTTCGGCATTATCATGATCTATAACCTGGCGATAGGCACCATTACGCCG
-CCAGTTGGCAGTGGTTTATATGTCGGGGCGAGCGTCGGTAAGGTCAAAGTTGAGGACGTT
-ATCAAACCGTTGATGCCTTTTTACGGCGCGATTATCGGCGTTCTGTTATTAATTACCTAC
-ATTCCGGAAATCACACTGTTTTTACCCCGTCTACTGGGCATCATGTAA
->AMHDIIJN_00012 hypothetical protein
-ATGAAGTTTGTTGCGCCAGAACAGGCACCGGAACAGGCGGAGGTCATCAAAAATACGCCG
-TTCTGGCCTGATGTGAACCTGTCGGAATTTCGCAGTGTGATGCGCACTGACGGCACGGTG
-ACGCAGCCGCGTTTAAAGCAGGTCGTGCTGACGGCGATCTCTGAGGTTAACGCTGAGCTG
-TACGACTTCCGCAACCGTCAGCAGATGCTGGGCTGGCGGACACTTGCTGAGGTTCCCGCA
-GAAATGCTGGACGGTAAAAGCGAGCGTATCCGGCACTACCACAACGCTGTTTTTTGCTGG
-GCGCGCGCTGTGCTTAATGAGCGTTATCAGGACTATGACGCCACGGCGTCAGGCGTGAAG
-CGAGGGGAGGAGCTGGCGGAGGCCAGCGGCGATCTGTGGCGTGATGCCCGCTGGGCCATC
-AGCCGGGTGCAGGATGCACCGCACTGTACGGTGGAGCTTATCTGA
->AMHDIIJN_00013 Tyrosine recombinase XerC
-ATGGAAACAAATATTACCTGGCAACAATTGATAGATGAATATTTCTTCGCAAAACCTCTG
-CGCTCAGCATCTGAATGGAGTTACACCAAAGTCTTCAAATCATTTGTACATTATATGGGG
-CCGTTAAGCTGCCCTAATGATGTGACATATCACAAAGTGCTTGCCTGGCGCCGTTTTCTT
-TTAAAAGAGAAAAAGCTGTCCGGACGTACCTGGAATAACAAGGTGGCGCATATGCGGGCC
-ATCTTTAACTACGGAATACAGCGAGGGTTACTGCACTATGACGAAAATCCGTTTAACAAT
-TCGGTAGTTAAACCGGACAAGAAGAGAAAGAAAACGCTCACTCAGGCACAGATTGAGTAT
-GCCTATCAGATCATGGAGCAGTATGAAAATCAGGAGAATACAGGGCTGGGACTGAAATAT
-TCCCGCTGCGCCTTATTTCCTGCATGGTTCTGGCTCACTGTCCTGGATACGCTCTATTAC
-ACAGGGATACGTCAGAACCAGTTATTACATATTCGGCTGAATGATGTTGATTTGAGAGAA
-GGGCAGATTCGGCTGATTACGGAGGGGTGTAAAAATCACAAAGAACACTATGTGCCGGTG
-ATCAGTTTTCTGCGTCCACGGCTGACCTGTTTAATGGAGAAAGCGCAGAGCGAAGGATTG
-AAAGGTAATGACCGCCTGTTCAATATTGCACTTTTTACCGGCAAAGATCCCGCCATTGGC
-GATGACATGGATTCTCCTCAGGTAAGAGCATTCTTCCGTCGTCTGTCCAAGGAGTGTCAG
-TTTGCGATCAGTCCTCATCGTTTCAGACACACGCTGGCCACGGAGATGATGAAAATGCCG
-GAACAGAATCTGCATATGGCGCAAAGTGTGCTGGGTCATTCAAACATGAAATCCACGCTG
-GAGTATGTGGAGAATGATATTGCAGTGATGGGGAGGGCTCTGGAAGCGCAGTTTATGCAG
-ATTAAGGCAGCACATGCCCGAAGCATTTACAGTGGGTTGACAAAGAATAGATAA
diff --git a/Examples/2-res-Annotate-prokka/tmp_files/genome2.fst_prokka-split5N.fna-prokkaRes/GEN2.1219.00001.fna b/Examples/2-res-Annotate-prokka/tmp_files/genome2.fst_prokka-split5N.fna-prokkaRes/GEN2.1219.00001.fna
deleted file mode 100644
index 064642eada56fa671b1a4258e63797795318bb9a..0000000000000000000000000000000000000000
--- a/Examples/2-res-Annotate-prokka/tmp_files/genome2.fst_prokka-split5N.fna-prokkaRes/GEN2.1219.00001.fna
+++ /dev/null
@@ -1,186 +0,0 @@
->this_is_genome_1
-ATGTCAGAAAATAAATTACACGTTATCGATTTGCACAAACGCTACGGCGGTCATGAAGTG
-CTGAAAGGGGTATCGCTGCAGGCCCGCGCCGGAGATGTGATTAGCATTATCGGCTCGTCC
-GGTTCCGGTAAAAGCACTTTTTTGCGCTGCATTAACTTCCTCGAAAAATCGAGCGAAGGC
-GCGATTATCGTGAACGGTCAGAACATTAATCTGGTGCGCGACAAAGACGGGCAGCTCAAA
-GTGGCGGATAAAAATCAGCTACGCTTGTTGCGTACCCGCCTGACGATGGTGTTTCAGCAC
-TTTAACCTCTGGAACCACATGACGGTGCTGGAAAATGTGATGGAAGCGCCGATTCAGGTA
-CTGGGATTAAGCAAGCACGACGCGCGCGAGCGGGCGTTGAAATATCTGGCGAAGGTGGGG
-ATTGATGAGCGCGCTCAGGGCAAATATCCCGTCCATCTCTCCGGCGGCCAACAGCAGCGC
-GTTTCTATTGCGCGCGCGCTGGCGATGGAACCTGACGTTTTACTGTTCGATGAACCCACA
-TCGGCGCTCGATCCTGAACTGGTCGGCGAAGTGTTGCGCATCATGCAACAACTGGCGGAA
-GAAGGCAAAACGATGGTGGTGGTCACGCATGAAATGGGCTTCGCCCGCCATGTCTCTTCG
-CACGTGATTTTTCTGCATCAGGGGAAAATTGAAGAAGAGGGCAATCCGGAGCAGGTGTTC
-GGCAATCCGCAAAGCCCGCGTTTACAGCAATTCCTGAAAGGCTCGCTGAAATAAACGCTA
-GAGGACGCGCCTCTCAGAGAGCGCGCTCTCTCAGAGAGGCGCGCGCCTCTTTCGCAGAGA
-CCNNCGCTCATGAGCGATGCCCGCGACTAAATTCTCCCGACGTACCCTCCTGACGGCAGG
-TTCCGCGCTTGCTGTTCTTCCTTTTCTGCGCGCCTTGCCGGTACAGGCGCGTGAACCTCG
-CCAGACCGTCGATATTAAGGATTATCCGGCGGATGACGGTATCGCCTCGTTCAAACAGGC
-CTTCGCCGACGGGCAGACTGTGGTCGTGCCGTCAGGATGGGTGTGTGAAAATATCAATGC
-GGCGATAACGATTCCGGCGGGAAAAACGCTGCGGATACAGGGCGCGGTGCGTGGGAATGG
-CCGGGGACGGTTTATTTTGCTGGACGGGTGTCAGGTGGTGGGGGAGCAGGGCGGCAGTCT
-GCACAATGTGACGCTGGATGTTCGCGGGTCGGACTGTGTGATTAAAGGCGTGACGATGAG
-CGGCTTTGGCCCCGTCGCGCAAATTTTCATCGGCGGTAAGGAACCGCAGGTGATGCGTAA
-TCTCATTATCGATGACATCACCGTTACCCACGCCAACTACGCCATTCTCCGCCAGGGATT
-TCATAACCAAATGGACGGCGCGCGGATTACGCATAGTCGCTTTAGCGATTTGCAGGGGGA
-CGCCATTGAGTGGAATGTCGCGATTCATGACCGCGACATCCTGATTTCCGATCATGTCAT
-CGAACGCATTGATTGTACCAATGGCAAAATCAACTGGGGGATCGGCATCGGGCTGGCGGG
-TAGCGCCTATGACAATAGTTATCCTGAAGACCAGGCAGTAAAAAACTTTGTGGTGGCCAA
-TATTACCGGATCTGATTGCCGACAACTGGTACACGTAGAAAATGGCAAACATTTCGTCAT
-TCGCAATGTCAAAGCCAAAAACATCACGCCCGATTTCAGTAAAAATGCGGGTATTGATAA
-CGCAACGATCGCCATTTATGGCTGTGATAATTTCGTCATTGATAATATTGATATGACGAA
-TAGTGCCGGGATGCTCATCGGCTATGGCGTCGTTAAAGGAAAATACCTGTCAATTCCGCA
-AAACTTTAAATTAAACGCTATTCGGTTGGATAATCGCCAGGTTGCTTATAAATTACGCGG
-CATTCAAATTTCCTCCGGTAACGCCCCCTCATTTGTTGCCATCACCAATGTACGGATGAC
-GCGTGCTACGCTGGAACTGCATAATCAACCGCAGCACCTCTTTTTGCGTAATATCAACGT
-GATGCAAACTTCAGCGATTGGCCCGGCGTTAAAAATGCATTTTGATTTGCGTAAAGATGT
-CCGTGGTCAATTTATGGCCCGCCAGGACACGCTGCTTTCCCTCGCTAATGTTCATGCCAT
-CAATGAAAACGGGCAGAGTTCCGTGGATATCGACAGGATTAATCACCAAACCGTGAATGT
-CGAAGCAGTGAATTTTTCGCTGCCGAAGCGGGGAGGGTAACACTCGCGCATAGAGAGCTC
-TCAGAGGAGCGCGCGCGCTATAGCGCGC
->this_is_genome_2
-CGCGATAATATAGCGCGCGCTCATAGCATGAGCGCGCTATTTCTGGCCATCCCGTTAACC
-ATTTTTGTGTTGTTTGTGTTACCGATTTGGCTGTGGCTGCATTACAGCAACCGCGCCGGT
-CGGGGAGAACTGTCGCAAAGCGAGCAGCAACGCTTACTGCAACTCACAGACGACGCGCAA
-CGTATGCGCGAGCGCATTCAGGCGCTGGAAGATATTCTTGATGCAGAGCATCCGAACTGG
-AGAGAGCGCTAACGCCATATTATAGCGCGCCTCATAAGAGCGGCCTATAGCGCGCTANNN
-ATGCCGCACTTTATTGCTGAATGTACTGAAAATATTCGCGAGCAGGCTGATTTACCAAGC
-CTGTTCAGCAAGGTAAACGAGGCGCTGGCCGCCACCGGGATTTTCCCCATCGGCGGTATC
-CGCAGTCGCGCCCACTGGCTGGATACCTGGCAGATGGCTGACGGTAAGCATGATTACGCG
-TTTGTGCATATGACGCTGAAAATCGGCGCCGGGCGCAGCCTGGAGAGCCGTCAGGAAGTC
-GGCGAAATGCTGTTTGGGCTGATTAAAGCCCACTTCGCCGACCTGATGGAGAACCGCTAT
-CTGGCGCTGTCGTTTGAGATTGCCGAGTTACATCCAACGCTCAATTACAAACAAAACAAC
-GTACACGCGTTATTTAAATAGCCAGAGATTCGCGCGTTCAGAGAGGAGCTCTCTCATAGA
-CGCGCGCATATGCGCTCTAGAGAGGCGCGCCTAATGGCGCGCTATGATGAAAGCGCTACT
-GTGGCTGGTTGGTCTCGCGTTGCTGTTAACAGGCTGCGCGAGCGAAAAAGGAATTATCGA
-TAAAGAGGGATATCAGCTTGATACCCGACATCGGGCGCAGGCGGCCTATCCGCGCATTAA
-AGTCCTGGTGATTCACTATACGGCGGAAAACTTTGACGTTTCGCTGGCGACGTTAACGGG
-TCGCAACGTCAGTTCGCATTACCTGATTCCCGCAACCCCGCCATTATATGGCGGTAAACC
-GCGCATCTGGCAACTGGTGCCGGAACAGGATCAGGCTTGGCATGCGGGCGTCAGTTTCTG
-GCGAGGCGCCACGCGTCTCAATGATACGTCTATTGGCATTGAGCTGGAAAATCGCGGCTG
-GCGAATGTCCGGCGGGGTGAAATCTTTCGCGCCGTTTGAATCCGCGCAAATTCAGGCATT
-GATCCCGTTAGCGAAGGACATTATCGCGCGCTATGACATCAAACCGCAGAATGTGGTGGC
-CCATGCGGATATCGCGCCGCAGCGTAAAGACGATCCCGGCCCGCGCTTCCCGTGGCGCGA
-GCTGGCGGCACAGGGGATTGGCGCCTGGCCTGACGCCCAGCGTGTGGCGTTTTATCTGGC
-TGGACGCGCGCCGTATACGCCAGTCGATACCGCAACGGTGCTTGCGTTACTCTCGCGCTA
-TGGCTATGAAGTCAAAGCCGATATGACGGCGCGCGAGCAACAGCGGGTGATTATGGCGTT
-CCAGATGCACTTCCGTCCGGCGCAATGGAACGGTATCGCAGATGCCGAAACGCAGGCGAT
-TGCCGAAGCATTACTGGAGAAGTACGGCCAGGATTAACAAAGCGCTCTCAGAGAGAGCGC
-TCTGCAGATGAGTGAGGCTGAAGCCCGCCCGACTAACTTTATTCGTCAGATTATTGATGA
-AGATCTGGCGAGTGGTAAACATACCACTGTCCATACCCGTTTTCCGCCGGAGCCGAATGG
-CTATCTGCACATCGGCCACGCGAAATCTATCTGCCTGAACTTTGGCATCGCGCAAGATTA
-TCAGGGCCAGTGCAACCTGCGTTTCGATGACACCAACCCGGTAAAAGAAGATATCGAGTA
-CGTTGATTCGATCAAAAACGACGTCGAGTGGTTAGGCTTTCACTGGTCTGGCGATATTCG
-CTACTCCTCCGATTACTTTGACCAACTGCACGCCTATGCGGTCGAGCTCATCAATAAAGG
-CCTGGCCTACGTTGATGAGCTGACGCCGGAGCAGATCCGCGAATACCGTGGTACGCTGAC
-CGCGCCGGGTAAAAACAGCCCGTTCCGCGATCGCAGCGTGGAAGAAAACCTCGCGCTATT
-TGAAAAAATGCGTACCGGCGGTTTTGAAGAGGGTAAAGCCTGTCTGCGCGCTAAAATCGA
-CATGGCGTCGCCGTTTATCGTGATGCGCGATCCGGTGCTGTATCGCATTAAATTCGCCGA
-GCATCATCAGACCGGCACGAAGTGGTGCATCTATCCGATGTACGACTTTACTCACTGCAT
-CAGCGATGCGCTGGAAGGCATTACTCATTCTCTGTGTACGCTGGAGTTCCAGGACAACCG
-TCGTCTGTACGACTGGGTGCTGGACAACATCACCATTCCGGTTCACCCGCGCCAGTACGA
-ATTCTCGCGCCTGAATCTGGAATACACCGTGATGTCCAAGCGTAAGCTGAACCTGCTGGT
-GACCGACAAACACGTCGAAGGTTGGGATGATCCGCGTATGCCGACTATTTCCGGTCTGCG
-CCGTCGCGGCTATACCGCGGCTTCTATTCGTGAGTTCTGCAAACGCATCGGCGTCACCAA
-GCAGGACAACACTATTGAGATGGCGTCGCTGGAATCCTGCATTCGCGAAGATCTGAACGA
-AAACGCGCCGCGCGCGATGGCGGTAATCGATCCGGTAAAACTGGTTATCGAAAACTACCC
-GCAGGGCGAGAGCGAAATGGTTACCATGCCTAACCATCCGAATAAACCGGAGATGGGCAG
-CCGTGAAGTGCCGTTTAGCGGTGAGATCTGGATCGATCGCGCGGATTTCCGCGAAGAAGC
-GAACAAACAGTACAAACGTCTGGTGATGGGCAAAGAAGTGCGTCTGCGTAATGCCTACGT
-CATTAAAGCGGAGCGCGTAGAGAAGGATGCCGAAGGGAATATCACCACCATCTTCTGTAC
-CTATGATGCTGATACGCTGAGTAAAGATCCGGCTGACGGGCGTAAAGTGAAAGGCGTAAT
-CCACTGGGTTAGCGTAGCACATGCGCTGCCGATTGAAATTCGTCTCTACGACCGTCTGTT
-CAGCGTGCCGAACCCGGGCGCCGCGGAGGACTTCCTGTCTGTTATCAACCCCGAATCATT
-AGTGATTAAGCAGGGGTATGGCGAGCCGTCGCTGAAAGCGGCGGTAGCAGGGAAAGCTTT
-CCAGTTTGAACGTGAAGGTTACTTCTGCCTTGACAGCCGCTATGCAACGGCCGATAAGCT
-GGTCTTTAACCGCACCGTGGGCCTGCGTGATACCTGGGCGAAAGCGGGCGAATAA
->this_is_genome_3
-ACGCGCTATAGGGCTCTCAGAGAGTCTCAGTGTTTATTGGCATCGTTAGCCTGTTTCCTG
-AAATGTTCCGCGCAATTACCGATTACGGGGTAACTGGCCGGGCAGTAAAAAAAGGCCTGC
-TGAACATCCAAAGCTGGAGTCCTCGCGACTTCGCGCATGACCGGCACCGTACCGTGGACG
-ACCGTCCTTACGGCGGCGGACCGGGGATGTTAATGATGGTGCAACCCTTGCGGGACGCCA
-TTCATGCAGCAAAAGCCGCGGCAGGTGAAGGCGCTAAAGTGATTTATCTGTCGCCTCAGG
-GACGCAAGCTTGATCAAGCGGGCGTTAGCGAGCTGGCCACGAATCAGAAACTCATTCTGG
-TGTGTGGTCGCTACGAAGGCGTAGATGAGCGCGTAATTCAGGCCGAAATTGACGAAGAAT
-GGTCAATTGGCGATTACGTTCTCAGCGGTGGCGAACTACCGGCAATGACGCTGATTGACT
-CCGTCGCCCGGTTTATACCGGGGGTTCTGGGGCATGAGGCATCAGCAATCGAAGATTCGT
-TTGCTGATGGGTTGCTGGATTGTCCGCACTATACGCGCCCTGAAGTGTTAGAGGGGATGG
-AAGTACCGCCAGTATTGCTGTCGGGAAACCATGCTGAGATACGTCGCTGGCGTTTGAAAC
-AGTCACTGGGCCGAACCTGGCTTAGAAGACCTGAACTTCTGGAAAACCTGGCTCTGACTG
-AAGAGCAAGCAAGGTTGCTGGCGGAGTTCAAAACAGAACACGCACAACAGCAGCATAAAC
-ATGATGGGATGGCATAGCGAGATCGCGCATAGCGCGCGGCGAGATCCGCGAGACATGAAT
-AATCATTTTGGGAAAGGGTTAATGGCCGGGTTGCACGCGCCATATGCATATAGCGCGCAT
-CATGCGGTGAATTTCTGTTCTGAGTATAAACGTGGCTTTGTATTGGGTTTTACACACCGT
-ATGTTCGAAAAGACCGGCGATCGTCAACTTAGCGCGTGGGAGGCCGGAATTCTGACGCGT
-CGCTATGGTCTGGATAAAGAAATGGTGATGGATTTCTTTAAAGAGAATCATTCCGGGATG
-GCGGTTCGCTTCTTTATGGCTGGTTATCGACTCGAAGGTTGAACGCCTCTAGAGCGCTAG
-AGGCGCGCGCGATATACGCGGCGCGAGACATGTCTACGCTTCTCTATTTGCACGGATTCA
-ACAGTTCCCCTCGCTCGGCAAAAGCGTGCCAGCTAAAAAACTGGCTGGCGGAGCGTCATC
-CGCATGTTGAGATGATCGTCCCTCAACTGCCGCCGTATCCTGCCGATGCGGCGGAGTTGC
-TGGAATCTCTCGTACTTGAGCATGGCGGTGCGCCATTAGGGCTGGTAGGATCGTCGCTGG
-GTGGTTATTACGCCACCTGGCTGTCGCAATGTTTTATGCTGCCGGCTGTGGTGGTGAATC
-CCGCCGTGCGGCCCTTTGAATTACTGACCGACTATCTCGGTCAGAACGAGAACCCCTACA
-CCGGGCAGCAATATGTGCTAGAGTCTCGCCATATTTATGATCTTAAAGTCATGCAGATTG
-ACCCGCTGGAAGCGCCGGACCTGATCTGGCTACTGCAACAGACGGGCGATGAAGTGCTGG
-ATTACCGCCAGGCGGTGGCATATTACGCCTCCTGCCGTCAGACAGTGACCGAGGGGGGTA
-ATCACGCATTCACGGGCTTCGAAGATTATTTCAACCAGATTGTCGATTTTCTTGGACTGC
-ACAGTTGCTGACCGGATATACGCGCGCGCGCTATATAGCGCGCGCGGCGATATAGCGCAT
-GAAGTTTGTTGCGCCAGAACAGGCACCGGAACAGGCGGAAATCATCAGAAATACGCCGTT
-CTGGCCTGATGTGGACCTGTCGGAGTTTCGCAGCATGATGCGCACTGATGGCACGGTGAC
-GCAGCCGCGTTTAAAGCAGGTTGCGCTGTCGGCAATTTCGGAGGTCAACGCAGAGCTGTA
-TGAGTTTCGCAGACGCCAGCAGATGCTGGGGTATGCCTCGCTGGCAGAAGTCCCGGCGGA
-ACAACTGGACGGCAAAAGCGAGCGCATTCAGCACTATTTCAACGCGGTTTACTGCTGGGC
-ACGCGCCATGCTCAACGAACGTTACCAGGACTATGACGCCACGGCATCCGGTGTGAAGCG
-GGGCGAAGAACTGGCAGAAGCCAGCGGTGATTTGTGGCGTGACGCCCGCTGGGCCATCAG
-CCGGGTGCAGGATGCGCCGCACTGCACAGTGGAGCTTATCTGA
->this_is_genome_4
-ATGATTGACCCTATTTTTGCGTCCTGTACGCTAATTGCCGTCTTTGTTGTTTTACTGGCC
-ATGGGCGCGCCTATCGGGATCTGCATCGTTATCGCCTCTTTCAGCACCATGATGCTGGTA
-CTGCCTTTCGATATTTCGATGTTCGCCACCGCGCAAAAAATGTTCTCCAGCCTGGACAGT
-TTTGCCTTGCTGGCCGTGCCGTTCTTCGTTTTGTCCGGGGTGATCATGAATAGCGGGGGA
-ATTGCCGCCCGACTGGTCAATTTTGCCAAACTGTTTACTGGCAAACTGCCCGGCTCGCTC
-TCTTACACCAACATCGTCGGCAATATGATGTTCGGTGCAATTTCCGGATCGGCGATTGCC
-GCCTCAACCTCTATCGGCGGCGTGATGGTGCCGATGAGCGCGCGCGAAGGTTACGATCGC
-GGTTTTGCGGCCGCGGTGAATATCGCCTCCGCGCCGACGGGAATGTTAATTCCGCCCACC
-ACGGCTTTTATCCTTTATGCGCTGGCAAGCGGGGGAACATCGATTGCCGCTCTGTTCGCC
-GGCGGTCTGGTCGCGGGAGTGCTGTGGGGCGTTGGCTGTATGCTGGTCACGCTGGTGGTC
-GCTAAGCGTCGAAATTATCGGGTTTTCTTCACCGTCCAAAAAGGCATGGCGCTAAAAGTT
-GCCGTTGAGGCCATTCCCAGCCTGTTACTGATCGTGATTATTGTCGGCGGCATTGTGCAG
-GGGATTTTCACCGCCATTGAAGCCTCCGCGATTGCCGTGGTGTATACGTTATTGCTGACG
-ATAGTGTTTTACCGCACGCTGAAAATTAAGGATTTGCCTTCGATTTTGCTCCAGACAGTG
-GTAATGACCGGGGTCATCATGTTCCTGCTGGCAACCTCTTCGGCGATGTCCTTCTCGATG
-TCGATCACCAATATTCCTGCGGCGCTGAGCGATATGATCCTCGGTATTTCCGCCAATAAA
-CTGGTTATCCTGTTAGTCATTACCGTCTTTTTGTTGATTATCGGCGCATTTATGGATATC
-GGTCCGGCCATTCTGATTTTTACCCCGATTCTGCTGCCGATTATGACTAAACTGGGCGTC
-GATCCGGTGCATTTCGGCATTATCATGATCTATAACCTGGCGATAGGCACCATTACGCCG
-CCAGTTGGCAGTGGTTTATATGTCGGGGCGAGCGTCGGTAAGGTCAAAGTTGAGGACGTT
-ATCAAACCGTTGATGCCTTTTTACGGCGCGATTATCGGCGTTCTGTTATTAATTACCTAC
-ATTCCGGAAATCACACTGTTTTTACCCCGTCTACTGGGCATCATGTAAACGCTCATAGGC
-GGCGCGCGCGCTCTCAGGAATGAAGTTTGTTGCGCCAGAACAGGCACCGGAACAGGCGGA
-GGTCATCAAAAATACGCCGTTCTGGCCTGATGTGAACCTGTCGGAATTTCGCAGTGTGAT
-GCGCACTGACGGCACGGTGACGCAGCCGCGTTTAAAGCAGGTCGTGCTGACGGCGATCTC
-TGAGGTTAACGCTGAGCTGTACGACTTCCGCAACCGTCAGCAGATGCTGGGCTGGCGGAC
-ACTTGCTGAGGTTCCCGCAGAAATGCTGGACGGTAAAAGCGAGCGTATCCGGCACTACCA
-CAACGCTGTTTTTTGCTGGGCGCGCGCTGTGCTTAATGAGCGTTATCAGGACTATGACGC
-CACGGCGTCAGGCGTGAAGCGAGGGGAGGAGCTGGCGGAGGCCAGCGGCGATCTGTGGCG
-TGATGCCCGCTGGGCCATCAGCCGGGTGCAGGATGCACCGCACTGTACGGTGGAGCTTAT
-CTGACGCTCATAGGCGCGCGCTCATAGCGCGATGGAAACAAATATTACCTGGCAACAATT
-GATAGATGAATATTTCTTCGCAAAACCTCTGCGCTCAGCATCTGAATGGAGTTACACCAA
-AGTCTTCAAATCATTTGTACATTATATGGGGCCGTTAAGCTGCCCTAATGATGTGACATA
-TCACAAAGTGCTTGCCTGGCGCCGTTTTCTTTTAAAAGAGAAAAAGCTGTCCGGACGTAC
-CTGGAATAACAAGGTGGCGCATATGCGGGCCATCTTTAACTACGGAATACAGCGAGGGTT
-ACTGCACTATGACGAAAATCCGTTTAACAATTCGGTAGTTAAACCGGACAAGAAGAGAAA
-GAAAACGCTCACTCAGGCACAGATTGAGTATGCCTATCAGATCATGGAGCAGTATGAAAA
-TCAGGAGAATACAGGGCTGGGACTGAAATATTCCCGCTGCGCCTTATTTCCTGCATGGTT
-CTGGCTCACTGTCCTGGATACGCTCTATTACACAGGGATACGTCAGAACCAGTTATTACA
-TATTCGGCTGAATGATGTTGATTTGAGAGAAGGGCAGATTCGGCTGATTACGGAGGGGTG
-TAAAAATCACAAAGAACACTATGTGCCGGTGATCAGTTTTCTGCGTCCACGGCTGACCTG
-TTTAATGGAGAAAGCGCAGAGCGAAGGATTGAAAGGTAATGACCGCCTGTTCAATATTGC
-ACTTTTTACCGGCAAAGATCCCGCCATTGGCGATGACATGGATTCTCCTCAGGTAAGAGC
-ATTCTTCCGTCGTCTGTCCAAGGAGTGTCAGTTTGCGATCAGTCCTCATCGTTTCAGACA
-CACGCTGGCCACGGAGATGATGAAAATGCCGGAACAGAATCTGCATATGGCGCAAAGTGT
-GCTGGGTCATTCAAACATGAAATCCACGCTGGAGTATGTGGAGAATGATATTGCAGTGAT
-GGGGAGGGCTCTGGAAGCGCAGTTTATGCAGATTAAGGCAGCACATGCCCGAAGCATTTA
-CAGTGGGTTGACAAAGAATAGATAA
->genome2_small_5
-GATACA
diff --git a/Examples/2-res-Annotate-prokka/tmp_files/genome2.fst_prokka-split5N.fna-prokkaRes/GEN2.1219.00001.fsa b/Examples/2-res-Annotate-prokka/tmp_files/genome2.fst_prokka-split5N.fna-prokkaRes/GEN2.1219.00001.fsa
deleted file mode 100644
index 9472a1ff05fa5e203242d624c1fca11189d02fa6..0000000000000000000000000000000000000000
--- a/Examples/2-res-Annotate-prokka/tmp_files/genome2.fst_prokka-split5N.fna-prokkaRes/GEN2.1219.00001.fsa
+++ /dev/null
@@ -1,186 +0,0 @@
->this_is_genome_1 [gcode=11] [organism=Genus species] [strain=strain]
-ATGTCAGAAAATAAATTACACGTTATCGATTTGCACAAACGCTACGGCGGTCATGAAGTG
-CTGAAAGGGGTATCGCTGCAGGCCCGCGCCGGAGATGTGATTAGCATTATCGGCTCGTCC
-GGTTCCGGTAAAAGCACTTTTTTGCGCTGCATTAACTTCCTCGAAAAATCGAGCGAAGGC
-GCGATTATCGTGAACGGTCAGAACATTAATCTGGTGCGCGACAAAGACGGGCAGCTCAAA
-GTGGCGGATAAAAATCAGCTACGCTTGTTGCGTACCCGCCTGACGATGGTGTTTCAGCAC
-TTTAACCTCTGGAACCACATGACGGTGCTGGAAAATGTGATGGAAGCGCCGATTCAGGTA
-CTGGGATTAAGCAAGCACGACGCGCGCGAGCGGGCGTTGAAATATCTGGCGAAGGTGGGG
-ATTGATGAGCGCGCTCAGGGCAAATATCCCGTCCATCTCTCCGGCGGCCAACAGCAGCGC
-GTTTCTATTGCGCGCGCGCTGGCGATGGAACCTGACGTTTTACTGTTCGATGAACCCACA
-TCGGCGCTCGATCCTGAACTGGTCGGCGAAGTGTTGCGCATCATGCAACAACTGGCGGAA
-GAAGGCAAAACGATGGTGGTGGTCACGCATGAAATGGGCTTCGCCCGCCATGTCTCTTCG
-CACGTGATTTTTCTGCATCAGGGGAAAATTGAAGAAGAGGGCAATCCGGAGCAGGTGTTC
-GGCAATCCGCAAAGCCCGCGTTTACAGCAATTCCTGAAAGGCTCGCTGAAATAAACGCTA
-GAGGACGCGCCTCTCAGAGAGCGCGCTCTCTCAGAGAGGCGCGCGCCTCTTTCGCAGAGA
-CCNNCGCTCATGAGCGATGCCCGCGACTAAATTCTCCCGACGTACCCTCCTGACGGCAGG
-TTCCGCGCTTGCTGTTCTTCCTTTTCTGCGCGCCTTGCCGGTACAGGCGCGTGAACCTCG
-CCAGACCGTCGATATTAAGGATTATCCGGCGGATGACGGTATCGCCTCGTTCAAACAGGC
-CTTCGCCGACGGGCAGACTGTGGTCGTGCCGTCAGGATGGGTGTGTGAAAATATCAATGC
-GGCGATAACGATTCCGGCGGGAAAAACGCTGCGGATACAGGGCGCGGTGCGTGGGAATGG
-CCGGGGACGGTTTATTTTGCTGGACGGGTGTCAGGTGGTGGGGGAGCAGGGCGGCAGTCT
-GCACAATGTGACGCTGGATGTTCGCGGGTCGGACTGTGTGATTAAAGGCGTGACGATGAG
-CGGCTTTGGCCCCGTCGCGCAAATTTTCATCGGCGGTAAGGAACCGCAGGTGATGCGTAA
-TCTCATTATCGATGACATCACCGTTACCCACGCCAACTACGCCATTCTCCGCCAGGGATT
-TCATAACCAAATGGACGGCGCGCGGATTACGCATAGTCGCTTTAGCGATTTGCAGGGGGA
-CGCCATTGAGTGGAATGTCGCGATTCATGACCGCGACATCCTGATTTCCGATCATGTCAT
-CGAACGCATTGATTGTACCAATGGCAAAATCAACTGGGGGATCGGCATCGGGCTGGCGGG
-TAGCGCCTATGACAATAGTTATCCTGAAGACCAGGCAGTAAAAAACTTTGTGGTGGCCAA
-TATTACCGGATCTGATTGCCGACAACTGGTACACGTAGAAAATGGCAAACATTTCGTCAT
-TCGCAATGTCAAAGCCAAAAACATCACGCCCGATTTCAGTAAAAATGCGGGTATTGATAA
-CGCAACGATCGCCATTTATGGCTGTGATAATTTCGTCATTGATAATATTGATATGACGAA
-TAGTGCCGGGATGCTCATCGGCTATGGCGTCGTTAAAGGAAAATACCTGTCAATTCCGCA
-AAACTTTAAATTAAACGCTATTCGGTTGGATAATCGCCAGGTTGCTTATAAATTACGCGG
-CATTCAAATTTCCTCCGGTAACGCCCCCTCATTTGTTGCCATCACCAATGTACGGATGAC
-GCGTGCTACGCTGGAACTGCATAATCAACCGCAGCACCTCTTTTTGCGTAATATCAACGT
-GATGCAAACTTCAGCGATTGGCCCGGCGTTAAAAATGCATTTTGATTTGCGTAAAGATGT
-CCGTGGTCAATTTATGGCCCGCCAGGACACGCTGCTTTCCCTCGCTAATGTTCATGCCAT
-CAATGAAAACGGGCAGAGTTCCGTGGATATCGACAGGATTAATCACCAAACCGTGAATGT
-CGAAGCAGTGAATTTTTCGCTGCCGAAGCGGGGAGGGTAACACTCGCGCATAGAGAGCTC
-TCAGAGGAGCGCGCGCGCTATAGCGCGC
->this_is_genome_2 [gcode=11] [organism=Genus species] [strain=strain]
-CGCGATAATATAGCGCGCGCTCATAGCATGAGCGCGCTATTTCTGGCCATCCCGTTAACC
-ATTTTTGTGTTGTTTGTGTTACCGATTTGGCTGTGGCTGCATTACAGCAACCGCGCCGGT
-CGGGGAGAACTGTCGCAAAGCGAGCAGCAACGCTTACTGCAACTCACAGACGACGCGCAA
-CGTATGCGCGAGCGCATTCAGGCGCTGGAAGATATTCTTGATGCAGAGCATCCGAACTGG
-AGAGAGCGCTAACGCCATATTATAGCGCGCCTCATAAGAGCGGCCTATAGCGCGCTANNN
-ATGCCGCACTTTATTGCTGAATGTACTGAAAATATTCGCGAGCAGGCTGATTTACCAAGC
-CTGTTCAGCAAGGTAAACGAGGCGCTGGCCGCCACCGGGATTTTCCCCATCGGCGGTATC
-CGCAGTCGCGCCCACTGGCTGGATACCTGGCAGATGGCTGACGGTAAGCATGATTACGCG
-TTTGTGCATATGACGCTGAAAATCGGCGCCGGGCGCAGCCTGGAGAGCCGTCAGGAAGTC
-GGCGAAATGCTGTTTGGGCTGATTAAAGCCCACTTCGCCGACCTGATGGAGAACCGCTAT
-CTGGCGCTGTCGTTTGAGATTGCCGAGTTACATCCAACGCTCAATTACAAACAAAACAAC
-GTACACGCGTTATTTAAATAGCCAGAGATTCGCGCGTTCAGAGAGGAGCTCTCTCATAGA
-CGCGCGCATATGCGCTCTAGAGAGGCGCGCCTAATGGCGCGCTATGATGAAAGCGCTACT
-GTGGCTGGTTGGTCTCGCGTTGCTGTTAACAGGCTGCGCGAGCGAAAAAGGAATTATCGA
-TAAAGAGGGATATCAGCTTGATACCCGACATCGGGCGCAGGCGGCCTATCCGCGCATTAA
-AGTCCTGGTGATTCACTATACGGCGGAAAACTTTGACGTTTCGCTGGCGACGTTAACGGG
-TCGCAACGTCAGTTCGCATTACCTGATTCCCGCAACCCCGCCATTATATGGCGGTAAACC
-GCGCATCTGGCAACTGGTGCCGGAACAGGATCAGGCTTGGCATGCGGGCGTCAGTTTCTG
-GCGAGGCGCCACGCGTCTCAATGATACGTCTATTGGCATTGAGCTGGAAAATCGCGGCTG
-GCGAATGTCCGGCGGGGTGAAATCTTTCGCGCCGTTTGAATCCGCGCAAATTCAGGCATT
-GATCCCGTTAGCGAAGGACATTATCGCGCGCTATGACATCAAACCGCAGAATGTGGTGGC
-CCATGCGGATATCGCGCCGCAGCGTAAAGACGATCCCGGCCCGCGCTTCCCGTGGCGCGA
-GCTGGCGGCACAGGGGATTGGCGCCTGGCCTGACGCCCAGCGTGTGGCGTTTTATCTGGC
-TGGACGCGCGCCGTATACGCCAGTCGATACCGCAACGGTGCTTGCGTTACTCTCGCGCTA
-TGGCTATGAAGTCAAAGCCGATATGACGGCGCGCGAGCAACAGCGGGTGATTATGGCGTT
-CCAGATGCACTTCCGTCCGGCGCAATGGAACGGTATCGCAGATGCCGAAACGCAGGCGAT
-TGCCGAAGCATTACTGGAGAAGTACGGCCAGGATTAACAAAGCGCTCTCAGAGAGAGCGC
-TCTGCAGATGAGTGAGGCTGAAGCCCGCCCGACTAACTTTATTCGTCAGATTATTGATGA
-AGATCTGGCGAGTGGTAAACATACCACTGTCCATACCCGTTTTCCGCCGGAGCCGAATGG
-CTATCTGCACATCGGCCACGCGAAATCTATCTGCCTGAACTTTGGCATCGCGCAAGATTA
-TCAGGGCCAGTGCAACCTGCGTTTCGATGACACCAACCCGGTAAAAGAAGATATCGAGTA
-CGTTGATTCGATCAAAAACGACGTCGAGTGGTTAGGCTTTCACTGGTCTGGCGATATTCG
-CTACTCCTCCGATTACTTTGACCAACTGCACGCCTATGCGGTCGAGCTCATCAATAAAGG
-CCTGGCCTACGTTGATGAGCTGACGCCGGAGCAGATCCGCGAATACCGTGGTACGCTGAC
-CGCGCCGGGTAAAAACAGCCCGTTCCGCGATCGCAGCGTGGAAGAAAACCTCGCGCTATT
-TGAAAAAATGCGTACCGGCGGTTTTGAAGAGGGTAAAGCCTGTCTGCGCGCTAAAATCGA
-CATGGCGTCGCCGTTTATCGTGATGCGCGATCCGGTGCTGTATCGCATTAAATTCGCCGA
-GCATCATCAGACCGGCACGAAGTGGTGCATCTATCCGATGTACGACTTTACTCACTGCAT
-CAGCGATGCGCTGGAAGGCATTACTCATTCTCTGTGTACGCTGGAGTTCCAGGACAACCG
-TCGTCTGTACGACTGGGTGCTGGACAACATCACCATTCCGGTTCACCCGCGCCAGTACGA
-ATTCTCGCGCCTGAATCTGGAATACACCGTGATGTCCAAGCGTAAGCTGAACCTGCTGGT
-GACCGACAAACACGTCGAAGGTTGGGATGATCCGCGTATGCCGACTATTTCCGGTCTGCG
-CCGTCGCGGCTATACCGCGGCTTCTATTCGTGAGTTCTGCAAACGCATCGGCGTCACCAA
-GCAGGACAACACTATTGAGATGGCGTCGCTGGAATCCTGCATTCGCGAAGATCTGAACGA
-AAACGCGCCGCGCGCGATGGCGGTAATCGATCCGGTAAAACTGGTTATCGAAAACTACCC
-GCAGGGCGAGAGCGAAATGGTTACCATGCCTAACCATCCGAATAAACCGGAGATGGGCAG
-CCGTGAAGTGCCGTTTAGCGGTGAGATCTGGATCGATCGCGCGGATTTCCGCGAAGAAGC
-GAACAAACAGTACAAACGTCTGGTGATGGGCAAAGAAGTGCGTCTGCGTAATGCCTACGT
-CATTAAAGCGGAGCGCGTAGAGAAGGATGCCGAAGGGAATATCACCACCATCTTCTGTAC
-CTATGATGCTGATACGCTGAGTAAAGATCCGGCTGACGGGCGTAAAGTGAAAGGCGTAAT
-CCACTGGGTTAGCGTAGCACATGCGCTGCCGATTGAAATTCGTCTCTACGACCGTCTGTT
-CAGCGTGCCGAACCCGGGCGCCGCGGAGGACTTCCTGTCTGTTATCAACCCCGAATCATT
-AGTGATTAAGCAGGGGTATGGCGAGCCGTCGCTGAAAGCGGCGGTAGCAGGGAAAGCTTT
-CCAGTTTGAACGTGAAGGTTACTTCTGCCTTGACAGCCGCTATGCAACGGCCGATAAGCT
-GGTCTTTAACCGCACCGTGGGCCTGCGTGATACCTGGGCGAAAGCGGGCGAATAA
->this_is_genome_3 [gcode=11] [organism=Genus species] [strain=strain]
-ACGCGCTATAGGGCTCTCAGAGAGTCTCAGTGTTTATTGGCATCGTTAGCCTGTTTCCTG
-AAATGTTCCGCGCAATTACCGATTACGGGGTAACTGGCCGGGCAGTAAAAAAAGGCCTGC
-TGAACATCCAAAGCTGGAGTCCTCGCGACTTCGCGCATGACCGGCACCGTACCGTGGACG
-ACCGTCCTTACGGCGGCGGACCGGGGATGTTAATGATGGTGCAACCCTTGCGGGACGCCA
-TTCATGCAGCAAAAGCCGCGGCAGGTGAAGGCGCTAAAGTGATTTATCTGTCGCCTCAGG
-GACGCAAGCTTGATCAAGCGGGCGTTAGCGAGCTGGCCACGAATCAGAAACTCATTCTGG
-TGTGTGGTCGCTACGAAGGCGTAGATGAGCGCGTAATTCAGGCCGAAATTGACGAAGAAT
-GGTCAATTGGCGATTACGTTCTCAGCGGTGGCGAACTACCGGCAATGACGCTGATTGACT
-CCGTCGCCCGGTTTATACCGGGGGTTCTGGGGCATGAGGCATCAGCAATCGAAGATTCGT
-TTGCTGATGGGTTGCTGGATTGTCCGCACTATACGCGCCCTGAAGTGTTAGAGGGGATGG
-AAGTACCGCCAGTATTGCTGTCGGGAAACCATGCTGAGATACGTCGCTGGCGTTTGAAAC
-AGTCACTGGGCCGAACCTGGCTTAGAAGACCTGAACTTCTGGAAAACCTGGCTCTGACTG
-AAGAGCAAGCAAGGTTGCTGGCGGAGTTCAAAACAGAACACGCACAACAGCAGCATAAAC
-ATGATGGGATGGCATAGCGAGATCGCGCATAGCGCGCGGCGAGATCCGCGAGACATGAAT
-AATCATTTTGGGAAAGGGTTAATGGCCGGGTTGCACGCGCCATATGCATATAGCGCGCAT
-CATGCGGTGAATTTCTGTTCTGAGTATAAACGTGGCTTTGTATTGGGTTTTACACACCGT
-ATGTTCGAAAAGACCGGCGATCGTCAACTTAGCGCGTGGGAGGCCGGAATTCTGACGCGT
-CGCTATGGTCTGGATAAAGAAATGGTGATGGATTTCTTTAAAGAGAATCATTCCGGGATG
-GCGGTTCGCTTCTTTATGGCTGGTTATCGACTCGAAGGTTGAACGCCTCTAGAGCGCTAG
-AGGCGCGCGCGATATACGCGGCGCGAGACATGTCTACGCTTCTCTATTTGCACGGATTCA
-ACAGTTCCCCTCGCTCGGCAAAAGCGTGCCAGCTAAAAAACTGGCTGGCGGAGCGTCATC
-CGCATGTTGAGATGATCGTCCCTCAACTGCCGCCGTATCCTGCCGATGCGGCGGAGTTGC
-TGGAATCTCTCGTACTTGAGCATGGCGGTGCGCCATTAGGGCTGGTAGGATCGTCGCTGG
-GTGGTTATTACGCCACCTGGCTGTCGCAATGTTTTATGCTGCCGGCTGTGGTGGTGAATC
-CCGCCGTGCGGCCCTTTGAATTACTGACCGACTATCTCGGTCAGAACGAGAACCCCTACA
-CCGGGCAGCAATATGTGCTAGAGTCTCGCCATATTTATGATCTTAAAGTCATGCAGATTG
-ACCCGCTGGAAGCGCCGGACCTGATCTGGCTACTGCAACAGACGGGCGATGAAGTGCTGG
-ATTACCGCCAGGCGGTGGCATATTACGCCTCCTGCCGTCAGACAGTGACCGAGGGGGGTA
-ATCACGCATTCACGGGCTTCGAAGATTATTTCAACCAGATTGTCGATTTTCTTGGACTGC
-ACAGTTGCTGACCGGATATACGCGCGCGCGCTATATAGCGCGCGCGGCGATATAGCGCAT
-GAAGTTTGTTGCGCCAGAACAGGCACCGGAACAGGCGGAAATCATCAGAAATACGCCGTT
-CTGGCCTGATGTGGACCTGTCGGAGTTTCGCAGCATGATGCGCACTGATGGCACGGTGAC
-GCAGCCGCGTTTAAAGCAGGTTGCGCTGTCGGCAATTTCGGAGGTCAACGCAGAGCTGTA
-TGAGTTTCGCAGACGCCAGCAGATGCTGGGGTATGCCTCGCTGGCAGAAGTCCCGGCGGA
-ACAACTGGACGGCAAAAGCGAGCGCATTCAGCACTATTTCAACGCGGTTTACTGCTGGGC
-ACGCGCCATGCTCAACGAACGTTACCAGGACTATGACGCCACGGCATCCGGTGTGAAGCG
-GGGCGAAGAACTGGCAGAAGCCAGCGGTGATTTGTGGCGTGACGCCCGCTGGGCCATCAG
-CCGGGTGCAGGATGCGCCGCACTGCACAGTGGAGCTTATCTGA
->this_is_genome_4 [gcode=11] [organism=Genus species] [strain=strain]
-ATGATTGACCCTATTTTTGCGTCCTGTACGCTAATTGCCGTCTTTGTTGTTTTACTGGCC
-ATGGGCGCGCCTATCGGGATCTGCATCGTTATCGCCTCTTTCAGCACCATGATGCTGGTA
-CTGCCTTTCGATATTTCGATGTTCGCCACCGCGCAAAAAATGTTCTCCAGCCTGGACAGT
-TTTGCCTTGCTGGCCGTGCCGTTCTTCGTTTTGTCCGGGGTGATCATGAATAGCGGGGGA
-ATTGCCGCCCGACTGGTCAATTTTGCCAAACTGTTTACTGGCAAACTGCCCGGCTCGCTC
-TCTTACACCAACATCGTCGGCAATATGATGTTCGGTGCAATTTCCGGATCGGCGATTGCC
-GCCTCAACCTCTATCGGCGGCGTGATGGTGCCGATGAGCGCGCGCGAAGGTTACGATCGC
-GGTTTTGCGGCCGCGGTGAATATCGCCTCCGCGCCGACGGGAATGTTAATTCCGCCCACC
-ACGGCTTTTATCCTTTATGCGCTGGCAAGCGGGGGAACATCGATTGCCGCTCTGTTCGCC
-GGCGGTCTGGTCGCGGGAGTGCTGTGGGGCGTTGGCTGTATGCTGGTCACGCTGGTGGTC
-GCTAAGCGTCGAAATTATCGGGTTTTCTTCACCGTCCAAAAAGGCATGGCGCTAAAAGTT
-GCCGTTGAGGCCATTCCCAGCCTGTTACTGATCGTGATTATTGTCGGCGGCATTGTGCAG
-GGGATTTTCACCGCCATTGAAGCCTCCGCGATTGCCGTGGTGTATACGTTATTGCTGACG
-ATAGTGTTTTACCGCACGCTGAAAATTAAGGATTTGCCTTCGATTTTGCTCCAGACAGTG
-GTAATGACCGGGGTCATCATGTTCCTGCTGGCAACCTCTTCGGCGATGTCCTTCTCGATG
-TCGATCACCAATATTCCTGCGGCGCTGAGCGATATGATCCTCGGTATTTCCGCCAATAAA
-CTGGTTATCCTGTTAGTCATTACCGTCTTTTTGTTGATTATCGGCGCATTTATGGATATC
-GGTCCGGCCATTCTGATTTTTACCCCGATTCTGCTGCCGATTATGACTAAACTGGGCGTC
-GATCCGGTGCATTTCGGCATTATCATGATCTATAACCTGGCGATAGGCACCATTACGCCG
-CCAGTTGGCAGTGGTTTATATGTCGGGGCGAGCGTCGGTAAGGTCAAAGTTGAGGACGTT
-ATCAAACCGTTGATGCCTTTTTACGGCGCGATTATCGGCGTTCTGTTATTAATTACCTAC
-ATTCCGGAAATCACACTGTTTTTACCCCGTCTACTGGGCATCATGTAAACGCTCATAGGC
-GGCGCGCGCGCTCTCAGGAATGAAGTTTGTTGCGCCAGAACAGGCACCGGAACAGGCGGA
-GGTCATCAAAAATACGCCGTTCTGGCCTGATGTGAACCTGTCGGAATTTCGCAGTGTGAT
-GCGCACTGACGGCACGGTGACGCAGCCGCGTTTAAAGCAGGTCGTGCTGACGGCGATCTC
-TGAGGTTAACGCTGAGCTGTACGACTTCCGCAACCGTCAGCAGATGCTGGGCTGGCGGAC
-ACTTGCTGAGGTTCCCGCAGAAATGCTGGACGGTAAAAGCGAGCGTATCCGGCACTACCA
-CAACGCTGTTTTTTGCTGGGCGCGCGCTGTGCTTAATGAGCGTTATCAGGACTATGACGC
-CACGGCGTCAGGCGTGAAGCGAGGGGAGGAGCTGGCGGAGGCCAGCGGCGATCTGTGGCG
-TGATGCCCGCTGGGCCATCAGCCGGGTGCAGGATGCACCGCACTGTACGGTGGAGCTTAT
-CTGACGCTCATAGGCGCGCGCTCATAGCGCGATGGAAACAAATATTACCTGGCAACAATT
-GATAGATGAATATTTCTTCGCAAAACCTCTGCGCTCAGCATCTGAATGGAGTTACACCAA
-AGTCTTCAAATCATTTGTACATTATATGGGGCCGTTAAGCTGCCCTAATGATGTGACATA
-TCACAAAGTGCTTGCCTGGCGCCGTTTTCTTTTAAAAGAGAAAAAGCTGTCCGGACGTAC
-CTGGAATAACAAGGTGGCGCATATGCGGGCCATCTTTAACTACGGAATACAGCGAGGGTT
-ACTGCACTATGACGAAAATCCGTTTAACAATTCGGTAGTTAAACCGGACAAGAAGAGAAA
-GAAAACGCTCACTCAGGCACAGATTGAGTATGCCTATCAGATCATGGAGCAGTATGAAAA
-TCAGGAGAATACAGGGCTGGGACTGAAATATTCCCGCTGCGCCTTATTTCCTGCATGGTT
-CTGGCTCACTGTCCTGGATACGCTCTATTACACAGGGATACGTCAGAACCAGTTATTACA
-TATTCGGCTGAATGATGTTGATTTGAGAGAAGGGCAGATTCGGCTGATTACGGAGGGGTG
-TAAAAATCACAAAGAACACTATGTGCCGGTGATCAGTTTTCTGCGTCCACGGCTGACCTG
-TTTAATGGAGAAAGCGCAGAGCGAAGGATTGAAAGGTAATGACCGCCTGTTCAATATTGC
-ACTTTTTACCGGCAAAGATCCCGCCATTGGCGATGACATGGATTCTCCTCAGGTAAGAGC
-ATTCTTCCGTCGTCTGTCCAAGGAGTGTCAGTTTGCGATCAGTCCTCATCGTTTCAGACA
-CACGCTGGCCACGGAGATGATGAAAATGCCGGAACAGAATCTGCATATGGCGCAAAGTGT
-GCTGGGTCATTCAAACATGAAATCCACGCTGGAGTATGTGGAGAATGATATTGCAGTGAT
-GGGGAGGGCTCTGGAAGCGCAGTTTATGCAGATTAAGGCAGCACATGCCCGAAGCATTTA
-CAGTGGGTTGACAAAGAATAGATAA
->genome2_small_5 [gcode=11] [organism=Genus species] [strain=strain]
-GATACA
diff --git a/Examples/2-res-Annotate-prokka/tmp_files/genome2.fst_prokka-split5N.fna-prokkaRes/GEN2.1219.00001.gbk b/Examples/2-res-Annotate-prokka/tmp_files/genome2.fst_prokka-split5N.fna-prokkaRes/GEN2.1219.00001.gbk
deleted file mode 100644
index dff9ee40ef8bab67c8f358ce83b20ebdb452f6df..0000000000000000000000000000000000000000
--- a/Examples/2-res-Annotate-prokka/tmp_files/genome2.fst_prokka-split5N.fna-prokkaRes/GEN2.1219.00001.gbk
+++ /dev/null
@@ -1,438 +0,0 @@
-LOCUS       this_is_genome_1        2308 bp    DNA     linear       09-DEC-2019
-DEFINITION  Genus species strain strain.
-ACCESSION   
-VERSION
-KEYWORDS    .
-SOURCE      Genus species
-  ORGANISM  Genus species
-            Unclassified.
-COMMENT     Annotated using prokka 1.14.5 from
-            https://github.com/tseemann/prokka.
-FEATURES             Location/Qualifiers
-     source          1..2308
-                     /organism="Genus species"
-                     /mol_type="genomic DNA"
-                     /strain="strain"
-     CDS             1..774
-                     /gene="hisP"
-                     /locus_tag="AMHDIIJN_00001"
-                     /inference="ab initio prediction:Prodigal:002006"
-                     /inference="similar to AA sequence:UniProtKB:P02915"
-                     /codon_start=1
-                     /transl_table=11
-                     /product="Histidine transport ATP-binding protein HisP"
-                     /db_xref="COG:COG4598"
-                     /translation="MSENKLHVIDLHKRYGGHEVLKGVSLQARAGDVISIIGSSGSGK
-                     STFLRCINFLEKSSEGAIIVNGQNINLVRDKDGQLKVADKNQLRLLRTRLTMVFQHFN
-                     LWNHMTVLENVMEAPIQVLGLSKHDARERALKYLAKVGIDERAQGKYPVHLSGGQQQR
-                     VSIARALAMEPDVLLFDEPTSALDPELVGEVLRIMQQLAEEGKTMVVVTHEMGFARHV
-                     SSHVIFLHQGKIEEEGNPEQVFGNPQSPRLQQFLKGSLK"
-     CDS             857..2260
-                     /locus_tag="AMHDIIJN_00002"
-                     /inference="ab initio prediction:Prodigal:002006"
-                     /codon_start=1
-                     /transl_table=11
-                     /product="hypothetical protein"
-                     /translation="MPATKFSRRTLLTAGSALAVLPFLRALPVQAREPRQTVDIKDYP
-                     ADDGIASFKQAFADGQTVVVPSGWVCENINAAITIPAGKTLRIQGAVRGNGRGRFILL
-                     DGCQVVGEQGGSLHNVTLDVRGSDCVIKGVTMSGFGPVAQIFIGGKEPQVMRNLIIDD
-                     ITVTHANYAILRQGFHNQMDGARITHSRFSDLQGDAIEWNVAIHDRDILISDHVIERI
-                     DCTNGKINWGIGIGLAGSAYDNSYPEDQAVKNFVVANITGSDCRQLVHVENGKHFVIR
-                     NVKAKNITPDFSKNAGIDNATIAIYGCDNFVIDNIDMTNSAGMLIGYGVVKGKYLSIP
-                     QNFKLNAIRLDNRQVAYKLRGIQISSGNAPSFVAITNVRMTRATLELHNQPQHLFLRN
-                     INVMQTSAIGPALKMHFDLRKDVRGQFMARQDTLLSLANVHAINENGQSSVDIDRINH
-                     QTVNVEAVNFSLPKRGG"
-ORIGIN      
-        1 atgtcagaaa ataaattaca cgttatcgat ttgcacaaac gctacggcgg tcatgaagtg
-       61 ctgaaagggg tatcgctgca ggcccgcgcc ggagatgtga ttagcattat cggctcgtcc
-      121 ggttccggta aaagcacttt tttgcgctgc attaacttcc tcgaaaaatc gagcgaaggc
-      181 gcgattatcg tgaacggtca gaacattaat ctggtgcgcg acaaagacgg gcagctcaaa
-      241 gtggcggata aaaatcagct acgcttgttg cgtacccgcc tgacgatggt gtttcagcac
-      301 tttaacctct ggaaccacat gacggtgctg gaaaatgtga tggaagcgcc gattcaggta
-      361 ctgggattaa gcaagcacga cgcgcgcgag cgggcgttga aatatctggc gaaggtgggg
-      421 attgatgagc gcgctcaggg caaatatccc gtccatctct ccggcggcca acagcagcgc
-      481 gtttctattg cgcgcgcgct ggcgatggaa cctgacgttt tactgttcga tgaacccaca
-      541 tcggcgctcg atcctgaact ggtcggcgaa gtgttgcgca tcatgcaaca actggcggaa
-      601 gaaggcaaaa cgatggtggt ggtcacgcat gaaatgggct tcgcccgcca tgtctcttcg
-      661 cacgtgattt ttctgcatca ggggaaaatt gaagaagagg gcaatccgga gcaggtgttc
-      721 ggcaatccgc aaagcccgcg tttacagcaa ttcctgaaag gctcgctgaa ataaacgcta
-      781 gaggacgcgc ctctcagaga gcgcgctctc tcagagaggc gcgcgcctct ttcgcagaga
-      841 ccnncgctca tgagcgatgc ccgcgactaa attctcccga cgtaccctcc tgacggcagg
-      901 ttccgcgctt gctgttcttc cttttctgcg cgccttgccg gtacaggcgc gtgaacctcg
-      961 ccagaccgtc gatattaagg attatccggc ggatgacggt atcgcctcgt tcaaacaggc
-     1021 cttcgccgac gggcagactg tggtcgtgcc gtcaggatgg gtgtgtgaaa atatcaatgc
-     1081 ggcgataacg attccggcgg gaaaaacgct gcggatacag ggcgcggtgc gtgggaatgg
-     1141 ccggggacgg tttattttgc tggacgggtg tcaggtggtg ggggagcagg gcggcagtct
-     1201 gcacaatgtg acgctggatg ttcgcgggtc ggactgtgtg attaaaggcg tgacgatgag
-     1261 cggctttggc cccgtcgcgc aaattttcat cggcggtaag gaaccgcagg tgatgcgtaa
-     1321 tctcattatc gatgacatca ccgttaccca cgccaactac gccattctcc gccagggatt
-     1381 tcataaccaa atggacggcg cgcggattac gcatagtcgc tttagcgatt tgcaggggga
-     1441 cgccattgag tggaatgtcg cgattcatga ccgcgacatc ctgatttccg atcatgtcat
-     1501 cgaacgcatt gattgtacca atggcaaaat caactggggg atcggcatcg ggctggcggg
-     1561 tagcgcctat gacaatagtt atcctgaaga ccaggcagta aaaaactttg tggtggccaa
-     1621 tattaccgga tctgattgcc gacaactggt acacgtagaa aatggcaaac atttcgtcat
-     1681 tcgcaatgtc aaagccaaaa acatcacgcc cgatttcagt aaaaatgcgg gtattgataa
-     1741 cgcaacgatc gccatttatg gctgtgataa tttcgtcatt gataatattg atatgacgaa
-     1801 tagtgccggg atgctcatcg gctatggcgt cgttaaagga aaatacctgt caattccgca
-     1861 aaactttaaa ttaaacgcta ttcggttgga taatcgccag gttgcttata aattacgcgg
-     1921 cattcaaatt tcctccggta acgccccctc atttgttgcc atcaccaatg tacggatgac
-     1981 gcgtgctacg ctggaactgc ataatcaacc gcagcacctc tttttgcgta atatcaacgt
-     2041 gatgcaaact tcagcgattg gcccggcgtt aaaaatgcat tttgatttgc gtaaagatgt
-     2101 ccgtggtcaa tttatggccc gccaggacac gctgctttcc ctcgctaatg ttcatgccat
-     2161 caatgaaaac gggcagagtt ccgtggatat cgacaggatt aatcaccaaa ccgtgaatgt
-     2221 cgaagcagtg aatttttcgc tgccgaagcg gggagggtaa cactcgcgca tagagagctc
-     2281 tcagaggagc gcgcgcgcta tagcgcgc
-//
-LOCUS       this_is_genome_2        3295 bp    DNA     linear       09-DEC-2019
-DEFINITION  Genus species strain strain.
-ACCESSION   
-VERSION
-KEYWORDS    .
-SOURCE      Genus species
-  ORGANISM  Genus species
-            Unclassified.
-COMMENT     Annotated using prokka 1.14.5 from
-            https://github.com/tseemann/prokka.
-FEATURES             Location/Qualifiers
-     source          1..3295
-                     /organism="Genus species"
-                     /mol_type="genomic DNA"
-                     /strain="strain"
-     CDS             28..252
-                     /gene="pspB"
-                     /locus_tag="AMHDIIJN_00003"
-                     /inference="ab initio prediction:Prodigal:002006"
-                     /inference="similar to AA sequence:UniProtKB:P0AFM9"
-                     /codon_start=1
-                     /transl_table=11
-                     /product="Phage shock protein B"
-                     /translation="MSALFLAIPLTIFVLFVLPIWLWLHYSNRAGRGELSQSEQQRLL
-                     QLTDDAQRMRERIQALEDILDAEHPNWRER"
-     CDS             301..681
-                     /gene="hpcD"
-                     /locus_tag="AMHDIIJN_00004"
-                     /EC_number="5.3.3.10"
-                     /inference="ab initio prediction:Prodigal:002006"
-                     /inference="similar to AA sequence:UniProtKB:Q05354"
-                     /codon_start=1
-                     /transl_table=11
-                     /product="5-carboxymethyl-2-hydroxymuconate
-                     Delta-isomerase"
-                     /translation="MPHFIAECTENIREQADLPSLFSKVNEALAATGIFPIGGIRSRA
-                     HWLDTWQMADGKHDYAFVHMTLKIGAGRSLESRQEVGEMLFGLIKAHFADLMENRYLA
-                     LSFEIAELHPTLNYKQNNVHALFK"
-     CDS             764..1597
-                     /gene="amiD"
-                     /locus_tag="AMHDIIJN_00005"
-                     /EC_number="3.5.1.28"
-                     /inference="ab initio prediction:Prodigal:002006"
-                     /inference="similar to AA sequence:UniProtKB:P75820"
-                     /codon_start=1
-                     /transl_table=11
-                     /product="N-acetylmuramoyl-L-alanine amidase AmiD"
-                     /db_xref="COG:COG3023"
-                     /translation="MMKALLWLVGLALLLTGCASEKGIIDKEGYQLDTRHRAQAAYPR
-                     IKVLVIHYTAENFDVSLATLTGRNVSSHYLIPATPPLYGGKPRIWQLVPEQDQAWHAG
-                     VSFWRGATRLNDTSIGIELENRGWRMSGGVKSFAPFESAQIQALIPLAKDIIARYDIK
-                     PQNVVAHADIAPQRKDDPGPRFPWRELAAQGIGAWPDAQRVAFYLAGRAPYTPVDTAT
-                     VLALLSRYGYEVKADMTAREQQRVIMAFQMHFRPAQWNGIADAETQAIAEALLEKYGQ
-                     D"
-     CDS             1628..3295
-                     /gene="glnS"
-                     /locus_tag="AMHDIIJN_00006"
-                     /EC_number="6.1.1.18"
-                     /inference="ab initio prediction:Prodigal:002006"
-                     /inference="similar to AA sequence:UniProtKB:P00962"
-                     /codon_start=1
-                     /transl_table=11
-                     /product="Glutamine--tRNA ligase"
-                     /db_xref="COG:COG0008"
-                     /translation="MSEAEARPTNFIRQIIDEDLASGKHTTVHTRFPPEPNGYLHIGH
-                     AKSICLNFGIAQDYQGQCNLRFDDTNPVKEDIEYVDSIKNDVEWLGFHWSGDIRYSSD
-                     YFDQLHAYAVELINKGLAYVDELTPEQIREYRGTLTAPGKNSPFRDRSVEENLALFEK
-                     MRTGGFEEGKACLRAKIDMASPFIVMRDPVLYRIKFAEHHQTGTKWCIYPMYDFTHCI
-                     SDALEGITHSLCTLEFQDNRRLYDWVLDNITIPVHPRQYEFSRLNLEYTVMSKRKLNL
-                     LVTDKHVEGWDDPRMPTISGLRRRGYTAASIREFCKRIGVTKQDNTIEMASLESCIRE
-                     DLNENAPRAMAVIDPVKLVIENYPQGESEMVTMPNHPNKPEMGSREVPFSGEIWIDRA
-                     DFREEANKQYKRLVMGKEVRLRNAYVIKAERVEKDAEGNITTIFCTYDADTLSKDPAD
-                     GRKVKGVIHWVSVAHALPIEIRLYDRLFSVPNPGAAEDFLSVINPESLVIKQGYGEPS
-                     LKAAVAGKAFQFEREGYFCLDSRYATADKLVFNRTVGLRDTWAKAGE"
-ORIGIN      
-        1 cgcgataata tagcgcgcgc tcatagcatg agcgcgctat ttctggccat cccgttaacc
-       61 atttttgtgt tgtttgtgtt accgatttgg ctgtggctgc attacagcaa ccgcgccggt
-      121 cggggagaac tgtcgcaaag cgagcagcaa cgcttactgc aactcacaga cgacgcgcaa
-      181 cgtatgcgcg agcgcattca ggcgctggaa gatattcttg atgcagagca tccgaactgg
-      241 agagagcgct aacgccatat tatagcgcgc ctcataagag cggcctatag cgcgctannn
-      301 atgccgcact ttattgctga atgtactgaa aatattcgcg agcaggctga tttaccaagc
-      361 ctgttcagca aggtaaacga ggcgctggcc gccaccggga ttttccccat cggcggtatc
-      421 cgcagtcgcg cccactggct ggatacctgg cagatggctg acggtaagca tgattacgcg
-      481 tttgtgcata tgacgctgaa aatcggcgcc gggcgcagcc tggagagccg tcaggaagtc
-      541 ggcgaaatgc tgtttgggct gattaaagcc cacttcgccg acctgatgga gaaccgctat
-      601 ctggcgctgt cgtttgagat tgccgagtta catccaacgc tcaattacaa acaaaacaac
-      661 gtacacgcgt tatttaaata gccagagatt cgcgcgttca gagaggagct ctctcataga
-      721 cgcgcgcata tgcgctctag agaggcgcgc ctaatggcgc gctatgatga aagcgctact
-      781 gtggctggtt ggtctcgcgt tgctgttaac aggctgcgcg agcgaaaaag gaattatcga
-      841 taaagaggga tatcagcttg atacccgaca tcgggcgcag gcggcctatc cgcgcattaa
-      901 agtcctggtg attcactata cggcggaaaa ctttgacgtt tcgctggcga cgttaacggg
-      961 tcgcaacgtc agttcgcatt acctgattcc cgcaaccccg ccattatatg gcggtaaacc
-     1021 gcgcatctgg caactggtgc cggaacagga tcaggcttgg catgcgggcg tcagtttctg
-     1081 gcgaggcgcc acgcgtctca atgatacgtc tattggcatt gagctggaaa atcgcggctg
-     1141 gcgaatgtcc ggcggggtga aatctttcgc gccgtttgaa tccgcgcaaa ttcaggcatt
-     1201 gatcccgtta gcgaaggaca ttatcgcgcg ctatgacatc aaaccgcaga atgtggtggc
-     1261 ccatgcggat atcgcgccgc agcgtaaaga cgatcccggc ccgcgcttcc cgtggcgcga
-     1321 gctggcggca caggggattg gcgcctggcc tgacgcccag cgtgtggcgt tttatctggc
-     1381 tggacgcgcg ccgtatacgc cagtcgatac cgcaacggtg cttgcgttac tctcgcgcta
-     1441 tggctatgaa gtcaaagccg atatgacggc gcgcgagcaa cagcgggtga ttatggcgtt
-     1501 ccagatgcac ttccgtccgg cgcaatggaa cggtatcgca gatgccgaaa cgcaggcgat
-     1561 tgccgaagca ttactggaga agtacggcca ggattaacaa agcgctctca gagagagcgc
-     1621 tctgcagatg agtgaggctg aagcccgccc gactaacttt attcgtcaga ttattgatga
-     1681 agatctggcg agtggtaaac ataccactgt ccatacccgt tttccgccgg agccgaatgg
-     1741 ctatctgcac atcggccacg cgaaatctat ctgcctgaac tttggcatcg cgcaagatta
-     1801 tcagggccag tgcaacctgc gtttcgatga caccaacccg gtaaaagaag atatcgagta
-     1861 cgttgattcg atcaaaaacg acgtcgagtg gttaggcttt cactggtctg gcgatattcg
-     1921 ctactcctcc gattactttg accaactgca cgcctatgcg gtcgagctca tcaataaagg
-     1981 cctggcctac gttgatgagc tgacgccgga gcagatccgc gaataccgtg gtacgctgac
-     2041 cgcgccgggt aaaaacagcc cgttccgcga tcgcagcgtg gaagaaaacc tcgcgctatt
-     2101 tgaaaaaatg cgtaccggcg gttttgaaga gggtaaagcc tgtctgcgcg ctaaaatcga
-     2161 catggcgtcg ccgtttatcg tgatgcgcga tccggtgctg tatcgcatta aattcgccga
-     2221 gcatcatcag accggcacga agtggtgcat ctatccgatg tacgacttta ctcactgcat
-     2281 cagcgatgcg ctggaaggca ttactcattc tctgtgtacg ctggagttcc aggacaaccg
-     2341 tcgtctgtac gactgggtgc tggacaacat caccattccg gttcacccgc gccagtacga
-     2401 attctcgcgc ctgaatctgg aatacaccgt gatgtccaag cgtaagctga acctgctggt
-     2461 gaccgacaaa cacgtcgaag gttgggatga tccgcgtatg ccgactattt ccggtctgcg
-     2521 ccgtcgcggc tataccgcgg cttctattcg tgagttctgc aaacgcatcg gcgtcaccaa
-     2581 gcaggacaac actattgaga tggcgtcgct ggaatcctgc attcgcgaag atctgaacga
-     2641 aaacgcgccg cgcgcgatgg cggtaatcga tccggtaaaa ctggttatcg aaaactaccc
-     2701 gcagggcgag agcgaaatgg ttaccatgcc taaccatccg aataaaccgg agatgggcag
-     2761 ccgtgaagtg ccgtttagcg gtgagatctg gatcgatcgc gcggatttcc gcgaagaagc
-     2821 gaacaaacag tacaaacgtc tggtgatggg caaagaagtg cgtctgcgta atgcctacgt
-     2881 cattaaagcg gagcgcgtag agaaggatgc cgaagggaat atcaccacca tcttctgtac
-     2941 ctatgatgct gatacgctga gtaaagatcc ggctgacggg cgtaaagtga aaggcgtaat
-     3001 ccactgggtt agcgtagcac atgcgctgcc gattgaaatt cgtctctacg accgtctgtt
-     3061 cagcgtgccg aacccgggcg ccgcggagga cttcctgtct gttatcaacc ccgaatcatt
-     3121 agtgattaag caggggtatg gcgagccgtc gctgaaagcg gcggtagcag ggaaagcttt
-     3181 ccagtttgaa cgtgaaggtt acttctgcct tgacagccgc tatgcaacgg ccgataagct
-     3241 ggtctttaac cgcaccgtgg gcctgcgtga tacctgggcg aaagcgggcg aataa
-//
-LOCUS       this_is_genome_3        2263 bp    DNA     linear       09-DEC-2019
-DEFINITION  Genus species strain strain.
-ACCESSION   
-VERSION
-KEYWORDS    .
-SOURCE      Genus species
-  ORGANISM  Genus species
-            Unclassified.
-COMMENT     Annotated using prokka 1.14.5 from
-            https://github.com/tseemann/prokka.
-FEATURES             Location/Qualifiers
-     source          1..2263
-                     /organism="Genus species"
-                     /mol_type="genomic DNA"
-                     /strain="strain"
-     CDS             30..797
-                     /gene="trmD"
-                     /locus_tag="AMHDIIJN_00007"
-                     /EC_number="2.1.1.228"
-                     /inference="ab initio prediction:Prodigal:002006"
-                     /inference="similar to AA sequence:UniProtKB:P0A873"
-                     /codon_start=1
-                     /transl_table=11
-                     /product="tRNA (guanine-N(1)-)-methyltransferase"
-                     /db_xref="COG:COG0336"
-                     /translation="MFIGIVSLFPEMFRAITDYGVTGRAVKKGLLNIQSWSPRDFAHD
-                     RHRTVDDRPYGGGPGMLMMVQPLRDAIHAAKAAAGEGAKVIYLSPQGRKLDQAGVSEL
-                     ATNQKLILVCGRYEGVDERVIQAEIDEEWSIGDYVLSGGELPAMTLIDSVARFIPGVL
-                     GHEASAIEDSFADGLLDCPHYTRPEVLEGMEVPPVLLSGNHAEIRRWRLKQSLGRTWL
-                     RRPELLENLALTEEQARLLAEFKTEHAQQQHKHDGMA"
-     CDS             862..1122
-                     /locus_tag="AMHDIIJN_00008"
-                     /inference="ab initio prediction:Prodigal:002006"
-                     /codon_start=1
-                     /transl_table=11
-                     /product="hypothetical protein"
-                     /translation="MAGLHAPYAYSAHHAVNFCSEYKRGFVLGFTHRMFEKTGDRQLS
-                     AWEAGILTRRYGLDKEMVMDFFKENHSGMAVRFFMAGYRLEG"
-     CDS             1170..1751
-                     /locus_tag="AMHDIIJN_00009"
-                     /inference="ab initio prediction:Prodigal:002006"
-                     /codon_start=1
-                     /transl_table=11
-                     /product="hypothetical protein"
-                     /translation="MSTLLYLHGFNSSPRSAKACQLKNWLAERHPHVEMIVPQLPPYP
-                     ADAAELLESLVLEHGGAPLGLVGSSLGGYYATWLSQCFMLPAVVVNPAVRPFELLTDY
-                     LGQNENPYTGQQYVLESRHIYDLKVMQIDPLEAPDLIWLLQQTGDEVLDYRQAVAYYA
-                     SCRQTVTEGGNHAFTGFEDYFNQIVDFLGLHSC"
-     CDS             1895..2263
-                     /locus_tag="AMHDIIJN_00010"
-                     /inference="ab initio prediction:Prodigal:002006"
-                     /codon_start=1
-                     /transl_table=11
-                     /product="hypothetical protein"
-                     /translation="MMRTDGTVTQPRLKQVALSAISEVNAELYEFRRRQQMLGYASLA
-                     EVPAEQLDGKSERIQHYFNAVYCWARAMLNERYQDYDATASGVKRGEELAEASGDLWR
-                     DARWAISRVQDAPHCTVELI"
-ORIGIN      
-        1 acgcgctata gggctctcag agagtctcag tgtttattgg catcgttagc ctgtttcctg
-       61 aaatgttccg cgcaattacc gattacgggg taactggccg ggcagtaaaa aaaggcctgc
-      121 tgaacatcca aagctggagt cctcgcgact tcgcgcatga ccggcaccgt accgtggacg
-      181 accgtcctta cggcggcgga ccggggatgt taatgatggt gcaacccttg cgggacgcca
-      241 ttcatgcagc aaaagccgcg gcaggtgaag gcgctaaagt gatttatctg tcgcctcagg
-      301 gacgcaagct tgatcaagcg ggcgttagcg agctggccac gaatcagaaa ctcattctgg
-      361 tgtgtggtcg ctacgaaggc gtagatgagc gcgtaattca ggccgaaatt gacgaagaat
-      421 ggtcaattgg cgattacgtt ctcagcggtg gcgaactacc ggcaatgacg ctgattgact
-      481 ccgtcgcccg gtttataccg ggggttctgg ggcatgaggc atcagcaatc gaagattcgt
-      541 ttgctgatgg gttgctggat tgtccgcact atacgcgccc tgaagtgtta gaggggatgg
-      601 aagtaccgcc agtattgctg tcgggaaacc atgctgagat acgtcgctgg cgtttgaaac
-      661 agtcactggg ccgaacctgg cttagaagac ctgaacttct ggaaaacctg gctctgactg
-      721 aagagcaagc aaggttgctg gcggagttca aaacagaaca cgcacaacag cagcataaac
-      781 atgatgggat ggcatagcga gatcgcgcat agcgcgcggc gagatccgcg agacatgaat
-      841 aatcattttg ggaaagggtt aatggccggg ttgcacgcgc catatgcata tagcgcgcat
-      901 catgcggtga atttctgttc tgagtataaa cgtggctttg tattgggttt tacacaccgt
-      961 atgttcgaaa agaccggcga tcgtcaactt agcgcgtggg aggccggaat tctgacgcgt
-     1021 cgctatggtc tggataaaga aatggtgatg gatttcttta aagagaatca ttccgggatg
-     1081 gcggttcgct tctttatggc tggttatcga ctcgaaggtt gaacgcctct agagcgctag
-     1141 aggcgcgcgc gatatacgcg gcgcgagaca tgtctacgct tctctatttg cacggattca
-     1201 acagttcccc tcgctcggca aaagcgtgcc agctaaaaaa ctggctggcg gagcgtcatc
-     1261 cgcatgttga gatgatcgtc cctcaactgc cgccgtatcc tgccgatgcg gcggagttgc
-     1321 tggaatctct cgtacttgag catggcggtg cgccattagg gctggtagga tcgtcgctgg
-     1381 gtggttatta cgccacctgg ctgtcgcaat gttttatgct gccggctgtg gtggtgaatc
-     1441 ccgccgtgcg gccctttgaa ttactgaccg actatctcgg tcagaacgag aacccctaca
-     1501 ccgggcagca atatgtgcta gagtctcgcc atatttatga tcttaaagtc atgcagattg
-     1561 acccgctgga agcgccggac ctgatctggc tactgcaaca gacgggcgat gaagtgctgg
-     1621 attaccgcca ggcggtggca tattacgcct cctgccgtca gacagtgacc gaggggggta
-     1681 atcacgcatt cacgggcttc gaagattatt tcaaccagat tgtcgatttt cttggactgc
-     1741 acagttgctg accggatata cgcgcgcgcg ctatatagcg cgcgcggcga tatagcgcat
-     1801 gaagtttgtt gcgccagaac aggcaccgga acaggcggaa atcatcagaa atacgccgtt
-     1861 ctggcctgat gtggacctgt cggagtttcg cagcatgatg cgcactgatg gcacggtgac
-     1921 gcagccgcgt ttaaagcagg ttgcgctgtc ggcaatttcg gaggtcaacg cagagctgta
-     1981 tgagtttcgc agacgccagc agatgctggg gtatgcctcg ctggcagaag tcccggcgga
-     2041 acaactggac ggcaaaagcg agcgcattca gcactatttc aacgcggttt actgctgggc
-     2101 acgcgccatg ctcaacgaac gttaccagga ctatgacgcc acggcatccg gtgtgaagcg
-     2161 gggcgaagaa ctggcagaag ccagcggtga tttgtggcgt gacgcccgct gggccatcag
-     2221 ccgggtgcag gatgcgccgc actgcacagt ggagcttatc tga
-//
-LOCUS       this_is_genome_4        2845 bp    DNA     linear       09-DEC-2019
-DEFINITION  Genus species strain strain.
-ACCESSION   
-VERSION
-KEYWORDS    .
-SOURCE      Genus species
-  ORGANISM  Genus species
-            Unclassified.
-COMMENT     Annotated using prokka 1.14.5 from
-            https://github.com/tseemann/prokka.
-FEATURES             Location/Qualifiers
-     source          1..2845
-                     /organism="Genus species"
-                     /mol_type="genomic DNA"
-                     /strain="strain"
-     CDS             1..1308
-                     /gene="dctM"
-                     /locus_tag="AMHDIIJN_00011"
-                     /inference="ab initio prediction:Prodigal:002006"
-                     /inference="similar to AA sequence:UniProtKB:O07838"
-                     /codon_start=1
-                     /transl_table=11
-                     /product="C4-dicarboxylate TRAP transporter large permease
-                     protein DctM"
-                     /db_xref="COG:COG1593"
-                     /translation="MIDPIFASCTLIAVFVVLLAMGAPIGICIVIASFSTMMLVLPFD
-                     ISMFATAQKMFSSLDSFALLAVPFFVLSGVIMNSGGIAARLVNFAKLFTGKLPGSLSY
-                     TNIVGNMMFGAISGSAIAASTSIGGVMVPMSAREGYDRGFAAAVNIASAPTGMLIPPT
-                     TAFILYALASGGTSIAALFAGGLVAGVLWGVGCMLVTLVVAKRRNYRVFFTVQKGMAL
-                     KVAVEAIPSLLLIVIIVGGIVQGIFTAIEASAIAVVYTLLLTIVFYRTLKIKDLPSIL
-                     LQTVVMTGVIMFLLATSSAMSFSMSITNIPAALSDMILGISANKLVILLVITVFLLII
-                     GAFMDIGPAILIFTPILLPIMTKLGVDPVHFGIIMIYNLAIGTITPPVGSGLYVGASV
-                     GKVKVEDVIKPLMPFYGAIIGVLLLITYIPEITLFLPRLLGIM"
-     CDS             1340..1804
-                     /locus_tag="AMHDIIJN_00012"
-                     /inference="ab initio prediction:Prodigal:002006"
-                     /codon_start=1
-                     /transl_table=11
-                     /product="hypothetical protein"
-                     /translation="MKFVAPEQAPEQAEVIKNTPFWPDVNLSEFRSVMRTDGTVTQPR
-                     LKQVVLTAISEVNAELYDFRNRQQMLGWRTLAEVPAEMLDGKSERIRHYHNAVFCWAR
-                     AVLNERYQDYDATASGVKRGEELAEASGDLWRDARWAISRVQDAPHCTVELI"
-     CDS             1832..2845
-                     /gene="xerC"
-                     /locus_tag="AMHDIIJN_00013"
-                     /inference="ab initio prediction:Prodigal:002006"
-                     /inference="protein motif:HAMAP:MF_01808"
-                     /codon_start=1
-                     /transl_table=11
-                     /product="Tyrosine recombinase XerC"
-                     /translation="METNITWQQLIDEYFFAKPLRSASEWSYTKVFKSFVHYMGPLSC
-                     PNDVTYHKVLAWRRFLLKEKKLSGRTWNNKVAHMRAIFNYGIQRGLLHYDENPFNNSV
-                     VKPDKKRKKTLTQAQIEYAYQIMEQYENQENTGLGLKYSRCALFPAWFWLTVLDTLYY
-                     TGIRQNQLLHIRLNDVDLREGQIRLITEGCKNHKEHYVPVISFLRPRLTCLMEKAQSE
-                     GLKGNDRLFNIALFTGKDPAIGDDMDSPQVRAFFRRLSKECQFAISPHRFRHTLATEM
-                     MKMPEQNLHMAQSVLGHSNMKSTLEYVENDIAVMGRALEAQFMQIKAAHARSIYSGLT
-                     KNR"
-ORIGIN      
-        1 atgattgacc ctatttttgc gtcctgtacg ctaattgccg tctttgttgt tttactggcc
-       61 atgggcgcgc ctatcgggat ctgcatcgtt atcgcctctt tcagcaccat gatgctggta
-      121 ctgcctttcg atatttcgat gttcgccacc gcgcaaaaaa tgttctccag cctggacagt
-      181 tttgccttgc tggccgtgcc gttcttcgtt ttgtccgggg tgatcatgaa tagcggggga
-      241 attgccgccc gactggtcaa ttttgccaaa ctgtttactg gcaaactgcc cggctcgctc
-      301 tcttacacca acatcgtcgg caatatgatg ttcggtgcaa tttccggatc ggcgattgcc
-      361 gcctcaacct ctatcggcgg cgtgatggtg ccgatgagcg cgcgcgaagg ttacgatcgc
-      421 ggttttgcgg ccgcggtgaa tatcgcctcc gcgccgacgg gaatgttaat tccgcccacc
-      481 acggctttta tcctttatgc gctggcaagc gggggaacat cgattgccgc tctgttcgcc
-      541 ggcggtctgg tcgcgggagt gctgtggggc gttggctgta tgctggtcac gctggtggtc
-      601 gctaagcgtc gaaattatcg ggttttcttc accgtccaaa aaggcatggc gctaaaagtt
-      661 gccgttgagg ccattcccag cctgttactg atcgtgatta ttgtcggcgg cattgtgcag
-      721 gggattttca ccgccattga agcctccgcg attgccgtgg tgtatacgtt attgctgacg
-      781 atagtgtttt accgcacgct gaaaattaag gatttgcctt cgattttgct ccagacagtg
-      841 gtaatgaccg gggtcatcat gttcctgctg gcaacctctt cggcgatgtc cttctcgatg
-      901 tcgatcacca atattcctgc ggcgctgagc gatatgatcc tcggtatttc cgccaataaa
-      961 ctggttatcc tgttagtcat taccgtcttt ttgttgatta tcggcgcatt tatggatatc
-     1021 ggtccggcca ttctgatttt taccccgatt ctgctgccga ttatgactaa actgggcgtc
-     1081 gatccggtgc atttcggcat tatcatgatc tataacctgg cgataggcac cattacgccg
-     1141 ccagttggca gtggtttata tgtcggggcg agcgtcggta aggtcaaagt tgaggacgtt
-     1201 atcaaaccgt tgatgccttt ttacggcgcg attatcggcg ttctgttatt aattacctac
-     1261 attccggaaa tcacactgtt tttaccccgt ctactgggca tcatgtaaac gctcataggc
-     1321 ggcgcgcgcg ctctcaggaa tgaagtttgt tgcgccagaa caggcaccgg aacaggcgga
-     1381 ggtcatcaaa aatacgccgt tctggcctga tgtgaacctg tcggaatttc gcagtgtgat
-     1441 gcgcactgac ggcacggtga cgcagccgcg tttaaagcag gtcgtgctga cggcgatctc
-     1501 tgaggttaac gctgagctgt acgacttccg caaccgtcag cagatgctgg gctggcggac
-     1561 acttgctgag gttcccgcag aaatgctgga cggtaaaagc gagcgtatcc ggcactacca
-     1621 caacgctgtt ttttgctggg cgcgcgctgt gcttaatgag cgttatcagg actatgacgc
-     1681 cacggcgtca ggcgtgaagc gaggggagga gctggcggag gccagcggcg atctgtggcg
-     1741 tgatgcccgc tgggccatca gccgggtgca ggatgcaccg cactgtacgg tggagcttat
-     1801 ctgacgctca taggcgcgcg ctcatagcgc gatggaaaca aatattacct ggcaacaatt
-     1861 gatagatgaa tatttcttcg caaaacctct gcgctcagca tctgaatgga gttacaccaa
-     1921 agtcttcaaa tcatttgtac attatatggg gccgttaagc tgccctaatg atgtgacata
-     1981 tcacaaagtg cttgcctggc gccgttttct tttaaaagag aaaaagctgt ccggacgtac
-     2041 ctggaataac aaggtggcgc atatgcgggc catctttaac tacggaatac agcgagggtt
-     2101 actgcactat gacgaaaatc cgtttaacaa ttcggtagtt aaaccggaca agaagagaaa
-     2161 gaaaacgctc actcaggcac agattgagta tgcctatcag atcatggagc agtatgaaaa
-     2221 tcaggagaat acagggctgg gactgaaata ttcccgctgc gccttatttc ctgcatggtt
-     2281 ctggctcact gtcctggata cgctctatta cacagggata cgtcagaacc agttattaca
-     2341 tattcggctg aatgatgttg atttgagaga agggcagatt cggctgatta cggaggggtg
-     2401 taaaaatcac aaagaacact atgtgccggt gatcagtttt ctgcgtccac ggctgacctg
-     2461 tttaatggag aaagcgcaga gcgaaggatt gaaaggtaat gaccgcctgt tcaatattgc
-     2521 actttttacc ggcaaagatc ccgccattgg cgatgacatg gattctcctc aggtaagagc
-     2581 attcttccgt cgtctgtcca aggagtgtca gtttgcgatc agtcctcatc gtttcagaca
-     2641 cacgctggcc acggagatga tgaaaatgcc ggaacagaat ctgcatatgg cgcaaagtgt
-     2701 gctgggtcat tcaaacatga aatccacgct ggagtatgtg gagaatgata ttgcagtgat
-     2761 ggggagggct ctggaagcgc agtttatgca gattaaggca gcacatgccc gaagcattta
-     2821 cagtgggttg acaaagaata gataa
-//
-LOCUS       genome2_small_5            6 bp    DNA     linear       09-DEC-2019
-DEFINITION  Genus species strain strain.
-ACCESSION   
-VERSION
-KEYWORDS    .
-SOURCE      Genus species
-  ORGANISM  Genus species
-            Unclassified.
-COMMENT     Annotated using prokka 1.14.5 from
-            https://github.com/tseemann/prokka.
-FEATURES             Location/Qualifiers
-     source          1..6
-                     /organism="Genus species"
-                     /mol_type="genomic DNA"
-                     /strain="strain"
-ORIGIN      
-        1 gataca
-//
diff --git a/Examples/2-res-Annotate-prokka/tmp_files/genome2.fst_prokka-split5N.fna-prokkaRes/GEN2.1219.00001.gff b/Examples/2-res-Annotate-prokka/tmp_files/genome2.fst_prokka-split5N.fna-prokkaRes/GEN2.1219.00001.gff
deleted file mode 100644
index 8e3120cbe1b13faf8b667f2f28fda7922258fce7..0000000000000000000000000000000000000000
--- a/Examples/2-res-Annotate-prokka/tmp_files/genome2.fst_prokka-split5N.fna-prokkaRes/GEN2.1219.00001.gff
+++ /dev/null
@@ -1,206 +0,0 @@
-##gff-version 3
-##sequence-region this_is_genome_1 1 2308
-##sequence-region this_is_genome_2 1 3295
-##sequence-region this_is_genome_3 1 2263
-##sequence-region this_is_genome_4 1 2845
-##sequence-region genome2_small_5 1 6
-this_is_genome_1	Prodigal:002006	CDS	1	774	.	+	0	ID=AMHDIIJN_00001;Name=hisP;db_xref=COG:COG4598;gene=hisP;inference=ab initio prediction:Prodigal:002006,similar to AA sequence:UniProtKB:P02915;locus_tag=AMHDIIJN_00001;product=Histidine transport ATP-binding protein HisP
-this_is_genome_1	Prodigal:002006	CDS	857	2260	.	+	0	ID=AMHDIIJN_00002;inference=ab initio prediction:Prodigal:002006;locus_tag=AMHDIIJN_00002;product=hypothetical protein
-this_is_genome_2	Prodigal:002006	CDS	28	252	.	+	0	ID=AMHDIIJN_00003;Name=pspB;gene=pspB;inference=ab initio prediction:Prodigal:002006,similar to AA sequence:UniProtKB:P0AFM9;locus_tag=AMHDIIJN_00003;product=Phage shock protein B
-this_is_genome_2	Prodigal:002006	CDS	301	681	.	+	0	ID=AMHDIIJN_00004;eC_number=5.3.3.10;Name=hpcD;gene=hpcD;inference=ab initio prediction:Prodigal:002006,similar to AA sequence:UniProtKB:Q05354;locus_tag=AMHDIIJN_00004;product=5-carboxymethyl-2-hydroxymuconate Delta-isomerase
-this_is_genome_2	Prodigal:002006	CDS	764	1597	.	+	0	ID=AMHDIIJN_00005;eC_number=3.5.1.28;Name=amiD;db_xref=COG:COG3023;gene=amiD;inference=ab initio prediction:Prodigal:002006,similar to AA sequence:UniProtKB:P75820;locus_tag=AMHDIIJN_00005;product=N-acetylmuramoyl-L-alanine amidase AmiD
-this_is_genome_2	Prodigal:002006	CDS	1628	3295	.	+	0	ID=AMHDIIJN_00006;eC_number=6.1.1.18;Name=glnS;db_xref=COG:COG0008;gene=glnS;inference=ab initio prediction:Prodigal:002006,similar to AA sequence:UniProtKB:P00962;locus_tag=AMHDIIJN_00006;product=Glutamine--tRNA ligase
-this_is_genome_3	Prodigal:002006	CDS	30	797	.	+	0	ID=AMHDIIJN_00007;eC_number=2.1.1.228;Name=trmD;db_xref=COG:COG0336;gene=trmD;inference=ab initio prediction:Prodigal:002006,similar to AA sequence:UniProtKB:P0A873;locus_tag=AMHDIIJN_00007;product=tRNA (guanine-N(1)-)-methyltransferase
-this_is_genome_3	Prodigal:002006	CDS	862	1122	.	+	0	ID=AMHDIIJN_00008;inference=ab initio prediction:Prodigal:002006;locus_tag=AMHDIIJN_00008;product=hypothetical protein
-this_is_genome_3	Prodigal:002006	CDS	1170	1751	.	+	0	ID=AMHDIIJN_00009;inference=ab initio prediction:Prodigal:002006;locus_tag=AMHDIIJN_00009;product=hypothetical protein
-this_is_genome_3	Prodigal:002006	CDS	1895	2263	.	+	0	ID=AMHDIIJN_00010;inference=ab initio prediction:Prodigal:002006;locus_tag=AMHDIIJN_00010;product=hypothetical protein
-this_is_genome_4	Prodigal:002006	CDS	1	1308	.	+	0	ID=AMHDIIJN_00011;Name=dctM;db_xref=COG:COG1593;gene=dctM;inference=ab initio prediction:Prodigal:002006,similar to AA sequence:UniProtKB:O07838;locus_tag=AMHDIIJN_00011;product=C4-dicarboxylate TRAP transporter large permease protein DctM
-this_is_genome_4	Prodigal:002006	CDS	1340	1804	.	+	0	ID=AMHDIIJN_00012;inference=ab initio prediction:Prodigal:002006;locus_tag=AMHDIIJN_00012;product=hypothetical protein
-this_is_genome_4	Prodigal:002006	CDS	1832	2845	.	+	0	ID=AMHDIIJN_00013;Name=xerC;gene=xerC;inference=ab initio prediction:Prodigal:002006,protein motif:HAMAP:MF_01808;locus_tag=AMHDIIJN_00013;product=Tyrosine recombinase XerC
-##FASTA
->this_is_genome_1
-ATGTCAGAAAATAAATTACACGTTATCGATTTGCACAAACGCTACGGCGGTCATGAAGTG
-CTGAAAGGGGTATCGCTGCAGGCCCGCGCCGGAGATGTGATTAGCATTATCGGCTCGTCC
-GGTTCCGGTAAAAGCACTTTTTTGCGCTGCATTAACTTCCTCGAAAAATCGAGCGAAGGC
-GCGATTATCGTGAACGGTCAGAACATTAATCTGGTGCGCGACAAAGACGGGCAGCTCAAA
-GTGGCGGATAAAAATCAGCTACGCTTGTTGCGTACCCGCCTGACGATGGTGTTTCAGCAC
-TTTAACCTCTGGAACCACATGACGGTGCTGGAAAATGTGATGGAAGCGCCGATTCAGGTA
-CTGGGATTAAGCAAGCACGACGCGCGCGAGCGGGCGTTGAAATATCTGGCGAAGGTGGGG
-ATTGATGAGCGCGCTCAGGGCAAATATCCCGTCCATCTCTCCGGCGGCCAACAGCAGCGC
-GTTTCTATTGCGCGCGCGCTGGCGATGGAACCTGACGTTTTACTGTTCGATGAACCCACA
-TCGGCGCTCGATCCTGAACTGGTCGGCGAAGTGTTGCGCATCATGCAACAACTGGCGGAA
-GAAGGCAAAACGATGGTGGTGGTCACGCATGAAATGGGCTTCGCCCGCCATGTCTCTTCG
-CACGTGATTTTTCTGCATCAGGGGAAAATTGAAGAAGAGGGCAATCCGGAGCAGGTGTTC
-GGCAATCCGCAAAGCCCGCGTTTACAGCAATTCCTGAAAGGCTCGCTGAAATAAACGCTA
-GAGGACGCGCCTCTCAGAGAGCGCGCTCTCTCAGAGAGGCGCGCGCCTCTTTCGCAGAGA
-CCNNCGCTCATGAGCGATGCCCGCGACTAAATTCTCCCGACGTACCCTCCTGACGGCAGG
-TTCCGCGCTTGCTGTTCTTCCTTTTCTGCGCGCCTTGCCGGTACAGGCGCGTGAACCTCG
-CCAGACCGTCGATATTAAGGATTATCCGGCGGATGACGGTATCGCCTCGTTCAAACAGGC
-CTTCGCCGACGGGCAGACTGTGGTCGTGCCGTCAGGATGGGTGTGTGAAAATATCAATGC
-GGCGATAACGATTCCGGCGGGAAAAACGCTGCGGATACAGGGCGCGGTGCGTGGGAATGG
-CCGGGGACGGTTTATTTTGCTGGACGGGTGTCAGGTGGTGGGGGAGCAGGGCGGCAGTCT
-GCACAATGTGACGCTGGATGTTCGCGGGTCGGACTGTGTGATTAAAGGCGTGACGATGAG
-CGGCTTTGGCCCCGTCGCGCAAATTTTCATCGGCGGTAAGGAACCGCAGGTGATGCGTAA
-TCTCATTATCGATGACATCACCGTTACCCACGCCAACTACGCCATTCTCCGCCAGGGATT
-TCATAACCAAATGGACGGCGCGCGGATTACGCATAGTCGCTTTAGCGATTTGCAGGGGGA
-CGCCATTGAGTGGAATGTCGCGATTCATGACCGCGACATCCTGATTTCCGATCATGTCAT
-CGAACGCATTGATTGTACCAATGGCAAAATCAACTGGGGGATCGGCATCGGGCTGGCGGG
-TAGCGCCTATGACAATAGTTATCCTGAAGACCAGGCAGTAAAAAACTTTGTGGTGGCCAA
-TATTACCGGATCTGATTGCCGACAACTGGTACACGTAGAAAATGGCAAACATTTCGTCAT
-TCGCAATGTCAAAGCCAAAAACATCACGCCCGATTTCAGTAAAAATGCGGGTATTGATAA
-CGCAACGATCGCCATTTATGGCTGTGATAATTTCGTCATTGATAATATTGATATGACGAA
-TAGTGCCGGGATGCTCATCGGCTATGGCGTCGTTAAAGGAAAATACCTGTCAATTCCGCA
-AAACTTTAAATTAAACGCTATTCGGTTGGATAATCGCCAGGTTGCTTATAAATTACGCGG
-CATTCAAATTTCCTCCGGTAACGCCCCCTCATTTGTTGCCATCACCAATGTACGGATGAC
-GCGTGCTACGCTGGAACTGCATAATCAACCGCAGCACCTCTTTTTGCGTAATATCAACGT
-GATGCAAACTTCAGCGATTGGCCCGGCGTTAAAAATGCATTTTGATTTGCGTAAAGATGT
-CCGTGGTCAATTTATGGCCCGCCAGGACACGCTGCTTTCCCTCGCTAATGTTCATGCCAT
-CAATGAAAACGGGCAGAGTTCCGTGGATATCGACAGGATTAATCACCAAACCGTGAATGT
-CGAAGCAGTGAATTTTTCGCTGCCGAAGCGGGGAGGGTAACACTCGCGCATAGAGAGCTC
-TCAGAGGAGCGCGCGCGCTATAGCGCGC
->this_is_genome_2
-CGCGATAATATAGCGCGCGCTCATAGCATGAGCGCGCTATTTCTGGCCATCCCGTTAACC
-ATTTTTGTGTTGTTTGTGTTACCGATTTGGCTGTGGCTGCATTACAGCAACCGCGCCGGT
-CGGGGAGAACTGTCGCAAAGCGAGCAGCAACGCTTACTGCAACTCACAGACGACGCGCAA
-CGTATGCGCGAGCGCATTCAGGCGCTGGAAGATATTCTTGATGCAGAGCATCCGAACTGG
-AGAGAGCGCTAACGCCATATTATAGCGCGCCTCATAAGAGCGGCCTATAGCGCGCTANNN
-ATGCCGCACTTTATTGCTGAATGTACTGAAAATATTCGCGAGCAGGCTGATTTACCAAGC
-CTGTTCAGCAAGGTAAACGAGGCGCTGGCCGCCACCGGGATTTTCCCCATCGGCGGTATC
-CGCAGTCGCGCCCACTGGCTGGATACCTGGCAGATGGCTGACGGTAAGCATGATTACGCG
-TTTGTGCATATGACGCTGAAAATCGGCGCCGGGCGCAGCCTGGAGAGCCGTCAGGAAGTC
-GGCGAAATGCTGTTTGGGCTGATTAAAGCCCACTTCGCCGACCTGATGGAGAACCGCTAT
-CTGGCGCTGTCGTTTGAGATTGCCGAGTTACATCCAACGCTCAATTACAAACAAAACAAC
-GTACACGCGTTATTTAAATAGCCAGAGATTCGCGCGTTCAGAGAGGAGCTCTCTCATAGA
-CGCGCGCATATGCGCTCTAGAGAGGCGCGCCTAATGGCGCGCTATGATGAAAGCGCTACT
-GTGGCTGGTTGGTCTCGCGTTGCTGTTAACAGGCTGCGCGAGCGAAAAAGGAATTATCGA
-TAAAGAGGGATATCAGCTTGATACCCGACATCGGGCGCAGGCGGCCTATCCGCGCATTAA
-AGTCCTGGTGATTCACTATACGGCGGAAAACTTTGACGTTTCGCTGGCGACGTTAACGGG
-TCGCAACGTCAGTTCGCATTACCTGATTCCCGCAACCCCGCCATTATATGGCGGTAAACC
-GCGCATCTGGCAACTGGTGCCGGAACAGGATCAGGCTTGGCATGCGGGCGTCAGTTTCTG
-GCGAGGCGCCACGCGTCTCAATGATACGTCTATTGGCATTGAGCTGGAAAATCGCGGCTG
-GCGAATGTCCGGCGGGGTGAAATCTTTCGCGCCGTTTGAATCCGCGCAAATTCAGGCATT
-GATCCCGTTAGCGAAGGACATTATCGCGCGCTATGACATCAAACCGCAGAATGTGGTGGC
-CCATGCGGATATCGCGCCGCAGCGTAAAGACGATCCCGGCCCGCGCTTCCCGTGGCGCGA
-GCTGGCGGCACAGGGGATTGGCGCCTGGCCTGACGCCCAGCGTGTGGCGTTTTATCTGGC
-TGGACGCGCGCCGTATACGCCAGTCGATACCGCAACGGTGCTTGCGTTACTCTCGCGCTA
-TGGCTATGAAGTCAAAGCCGATATGACGGCGCGCGAGCAACAGCGGGTGATTATGGCGTT
-CCAGATGCACTTCCGTCCGGCGCAATGGAACGGTATCGCAGATGCCGAAACGCAGGCGAT
-TGCCGAAGCATTACTGGAGAAGTACGGCCAGGATTAACAAAGCGCTCTCAGAGAGAGCGC
-TCTGCAGATGAGTGAGGCTGAAGCCCGCCCGACTAACTTTATTCGTCAGATTATTGATGA
-AGATCTGGCGAGTGGTAAACATACCACTGTCCATACCCGTTTTCCGCCGGAGCCGAATGG
-CTATCTGCACATCGGCCACGCGAAATCTATCTGCCTGAACTTTGGCATCGCGCAAGATTA
-TCAGGGCCAGTGCAACCTGCGTTTCGATGACACCAACCCGGTAAAAGAAGATATCGAGTA
-CGTTGATTCGATCAAAAACGACGTCGAGTGGTTAGGCTTTCACTGGTCTGGCGATATTCG
-CTACTCCTCCGATTACTTTGACCAACTGCACGCCTATGCGGTCGAGCTCATCAATAAAGG
-CCTGGCCTACGTTGATGAGCTGACGCCGGAGCAGATCCGCGAATACCGTGGTACGCTGAC
-CGCGCCGGGTAAAAACAGCCCGTTCCGCGATCGCAGCGTGGAAGAAAACCTCGCGCTATT
-TGAAAAAATGCGTACCGGCGGTTTTGAAGAGGGTAAAGCCTGTCTGCGCGCTAAAATCGA
-CATGGCGTCGCCGTTTATCGTGATGCGCGATCCGGTGCTGTATCGCATTAAATTCGCCGA
-GCATCATCAGACCGGCACGAAGTGGTGCATCTATCCGATGTACGACTTTACTCACTGCAT
-CAGCGATGCGCTGGAAGGCATTACTCATTCTCTGTGTACGCTGGAGTTCCAGGACAACCG
-TCGTCTGTACGACTGGGTGCTGGACAACATCACCATTCCGGTTCACCCGCGCCAGTACGA
-ATTCTCGCGCCTGAATCTGGAATACACCGTGATGTCCAAGCGTAAGCTGAACCTGCTGGT
-GACCGACAAACACGTCGAAGGTTGGGATGATCCGCGTATGCCGACTATTTCCGGTCTGCG
-CCGTCGCGGCTATACCGCGGCTTCTATTCGTGAGTTCTGCAAACGCATCGGCGTCACCAA
-GCAGGACAACACTATTGAGATGGCGTCGCTGGAATCCTGCATTCGCGAAGATCTGAACGA
-AAACGCGCCGCGCGCGATGGCGGTAATCGATCCGGTAAAACTGGTTATCGAAAACTACCC
-GCAGGGCGAGAGCGAAATGGTTACCATGCCTAACCATCCGAATAAACCGGAGATGGGCAG
-CCGTGAAGTGCCGTTTAGCGGTGAGATCTGGATCGATCGCGCGGATTTCCGCGAAGAAGC
-GAACAAACAGTACAAACGTCTGGTGATGGGCAAAGAAGTGCGTCTGCGTAATGCCTACGT
-CATTAAAGCGGAGCGCGTAGAGAAGGATGCCGAAGGGAATATCACCACCATCTTCTGTAC
-CTATGATGCTGATACGCTGAGTAAAGATCCGGCTGACGGGCGTAAAGTGAAAGGCGTAAT
-CCACTGGGTTAGCGTAGCACATGCGCTGCCGATTGAAATTCGTCTCTACGACCGTCTGTT
-CAGCGTGCCGAACCCGGGCGCCGCGGAGGACTTCCTGTCTGTTATCAACCCCGAATCATT
-AGTGATTAAGCAGGGGTATGGCGAGCCGTCGCTGAAAGCGGCGGTAGCAGGGAAAGCTTT
-CCAGTTTGAACGTGAAGGTTACTTCTGCCTTGACAGCCGCTATGCAACGGCCGATAAGCT
-GGTCTTTAACCGCACCGTGGGCCTGCGTGATACCTGGGCGAAAGCGGGCGAATAA
->this_is_genome_3
-ACGCGCTATAGGGCTCTCAGAGAGTCTCAGTGTTTATTGGCATCGTTAGCCTGTTTCCTG
-AAATGTTCCGCGCAATTACCGATTACGGGGTAACTGGCCGGGCAGTAAAAAAAGGCCTGC
-TGAACATCCAAAGCTGGAGTCCTCGCGACTTCGCGCATGACCGGCACCGTACCGTGGACG
-ACCGTCCTTACGGCGGCGGACCGGGGATGTTAATGATGGTGCAACCCTTGCGGGACGCCA
-TTCATGCAGCAAAAGCCGCGGCAGGTGAAGGCGCTAAAGTGATTTATCTGTCGCCTCAGG
-GACGCAAGCTTGATCAAGCGGGCGTTAGCGAGCTGGCCACGAATCAGAAACTCATTCTGG
-TGTGTGGTCGCTACGAAGGCGTAGATGAGCGCGTAATTCAGGCCGAAATTGACGAAGAAT
-GGTCAATTGGCGATTACGTTCTCAGCGGTGGCGAACTACCGGCAATGACGCTGATTGACT
-CCGTCGCCCGGTTTATACCGGGGGTTCTGGGGCATGAGGCATCAGCAATCGAAGATTCGT
-TTGCTGATGGGTTGCTGGATTGTCCGCACTATACGCGCCCTGAAGTGTTAGAGGGGATGG
-AAGTACCGCCAGTATTGCTGTCGGGAAACCATGCTGAGATACGTCGCTGGCGTTTGAAAC
-AGTCACTGGGCCGAACCTGGCTTAGAAGACCTGAACTTCTGGAAAACCTGGCTCTGACTG
-AAGAGCAAGCAAGGTTGCTGGCGGAGTTCAAAACAGAACACGCACAACAGCAGCATAAAC
-ATGATGGGATGGCATAGCGAGATCGCGCATAGCGCGCGGCGAGATCCGCGAGACATGAAT
-AATCATTTTGGGAAAGGGTTAATGGCCGGGTTGCACGCGCCATATGCATATAGCGCGCAT
-CATGCGGTGAATTTCTGTTCTGAGTATAAACGTGGCTTTGTATTGGGTTTTACACACCGT
-ATGTTCGAAAAGACCGGCGATCGTCAACTTAGCGCGTGGGAGGCCGGAATTCTGACGCGT
-CGCTATGGTCTGGATAAAGAAATGGTGATGGATTTCTTTAAAGAGAATCATTCCGGGATG
-GCGGTTCGCTTCTTTATGGCTGGTTATCGACTCGAAGGTTGAACGCCTCTAGAGCGCTAG
-AGGCGCGCGCGATATACGCGGCGCGAGACATGTCTACGCTTCTCTATTTGCACGGATTCA
-ACAGTTCCCCTCGCTCGGCAAAAGCGTGCCAGCTAAAAAACTGGCTGGCGGAGCGTCATC
-CGCATGTTGAGATGATCGTCCCTCAACTGCCGCCGTATCCTGCCGATGCGGCGGAGTTGC
-TGGAATCTCTCGTACTTGAGCATGGCGGTGCGCCATTAGGGCTGGTAGGATCGTCGCTGG
-GTGGTTATTACGCCACCTGGCTGTCGCAATGTTTTATGCTGCCGGCTGTGGTGGTGAATC
-CCGCCGTGCGGCCCTTTGAATTACTGACCGACTATCTCGGTCAGAACGAGAACCCCTACA
-CCGGGCAGCAATATGTGCTAGAGTCTCGCCATATTTATGATCTTAAAGTCATGCAGATTG
-ACCCGCTGGAAGCGCCGGACCTGATCTGGCTACTGCAACAGACGGGCGATGAAGTGCTGG
-ATTACCGCCAGGCGGTGGCATATTACGCCTCCTGCCGTCAGACAGTGACCGAGGGGGGTA
-ATCACGCATTCACGGGCTTCGAAGATTATTTCAACCAGATTGTCGATTTTCTTGGACTGC
-ACAGTTGCTGACCGGATATACGCGCGCGCGCTATATAGCGCGCGCGGCGATATAGCGCAT
-GAAGTTTGTTGCGCCAGAACAGGCACCGGAACAGGCGGAAATCATCAGAAATACGCCGTT
-CTGGCCTGATGTGGACCTGTCGGAGTTTCGCAGCATGATGCGCACTGATGGCACGGTGAC
-GCAGCCGCGTTTAAAGCAGGTTGCGCTGTCGGCAATTTCGGAGGTCAACGCAGAGCTGTA
-TGAGTTTCGCAGACGCCAGCAGATGCTGGGGTATGCCTCGCTGGCAGAAGTCCCGGCGGA
-ACAACTGGACGGCAAAAGCGAGCGCATTCAGCACTATTTCAACGCGGTTTACTGCTGGGC
-ACGCGCCATGCTCAACGAACGTTACCAGGACTATGACGCCACGGCATCCGGTGTGAAGCG
-GGGCGAAGAACTGGCAGAAGCCAGCGGTGATTTGTGGCGTGACGCCCGCTGGGCCATCAG
-CCGGGTGCAGGATGCGCCGCACTGCACAGTGGAGCTTATCTGA
->this_is_genome_4
-ATGATTGACCCTATTTTTGCGTCCTGTACGCTAATTGCCGTCTTTGTTGTTTTACTGGCC
-ATGGGCGCGCCTATCGGGATCTGCATCGTTATCGCCTCTTTCAGCACCATGATGCTGGTA
-CTGCCTTTCGATATTTCGATGTTCGCCACCGCGCAAAAAATGTTCTCCAGCCTGGACAGT
-TTTGCCTTGCTGGCCGTGCCGTTCTTCGTTTTGTCCGGGGTGATCATGAATAGCGGGGGA
-ATTGCCGCCCGACTGGTCAATTTTGCCAAACTGTTTACTGGCAAACTGCCCGGCTCGCTC
-TCTTACACCAACATCGTCGGCAATATGATGTTCGGTGCAATTTCCGGATCGGCGATTGCC
-GCCTCAACCTCTATCGGCGGCGTGATGGTGCCGATGAGCGCGCGCGAAGGTTACGATCGC
-GGTTTTGCGGCCGCGGTGAATATCGCCTCCGCGCCGACGGGAATGTTAATTCCGCCCACC
-ACGGCTTTTATCCTTTATGCGCTGGCAAGCGGGGGAACATCGATTGCCGCTCTGTTCGCC
-GGCGGTCTGGTCGCGGGAGTGCTGTGGGGCGTTGGCTGTATGCTGGTCACGCTGGTGGTC
-GCTAAGCGTCGAAATTATCGGGTTTTCTTCACCGTCCAAAAAGGCATGGCGCTAAAAGTT
-GCCGTTGAGGCCATTCCCAGCCTGTTACTGATCGTGATTATTGTCGGCGGCATTGTGCAG
-GGGATTTTCACCGCCATTGAAGCCTCCGCGATTGCCGTGGTGTATACGTTATTGCTGACG
-ATAGTGTTTTACCGCACGCTGAAAATTAAGGATTTGCCTTCGATTTTGCTCCAGACAGTG
-GTAATGACCGGGGTCATCATGTTCCTGCTGGCAACCTCTTCGGCGATGTCCTTCTCGATG
-TCGATCACCAATATTCCTGCGGCGCTGAGCGATATGATCCTCGGTATTTCCGCCAATAAA
-CTGGTTATCCTGTTAGTCATTACCGTCTTTTTGTTGATTATCGGCGCATTTATGGATATC
-GGTCCGGCCATTCTGATTTTTACCCCGATTCTGCTGCCGATTATGACTAAACTGGGCGTC
-GATCCGGTGCATTTCGGCATTATCATGATCTATAACCTGGCGATAGGCACCATTACGCCG
-CCAGTTGGCAGTGGTTTATATGTCGGGGCGAGCGTCGGTAAGGTCAAAGTTGAGGACGTT
-ATCAAACCGTTGATGCCTTTTTACGGCGCGATTATCGGCGTTCTGTTATTAATTACCTAC
-ATTCCGGAAATCACACTGTTTTTACCCCGTCTACTGGGCATCATGTAAACGCTCATAGGC
-GGCGCGCGCGCTCTCAGGAATGAAGTTTGTTGCGCCAGAACAGGCACCGGAACAGGCGGA
-GGTCATCAAAAATACGCCGTTCTGGCCTGATGTGAACCTGTCGGAATTTCGCAGTGTGAT
-GCGCACTGACGGCACGGTGACGCAGCCGCGTTTAAAGCAGGTCGTGCTGACGGCGATCTC
-TGAGGTTAACGCTGAGCTGTACGACTTCCGCAACCGTCAGCAGATGCTGGGCTGGCGGAC
-ACTTGCTGAGGTTCCCGCAGAAATGCTGGACGGTAAAAGCGAGCGTATCCGGCACTACCA
-CAACGCTGTTTTTTGCTGGGCGCGCGCTGTGCTTAATGAGCGTTATCAGGACTATGACGC
-CACGGCGTCAGGCGTGAAGCGAGGGGAGGAGCTGGCGGAGGCCAGCGGCGATCTGTGGCG
-TGATGCCCGCTGGGCCATCAGCCGGGTGCAGGATGCACCGCACTGTACGGTGGAGCTTAT
-CTGACGCTCATAGGCGCGCGCTCATAGCGCGATGGAAACAAATATTACCTGGCAACAATT
-GATAGATGAATATTTCTTCGCAAAACCTCTGCGCTCAGCATCTGAATGGAGTTACACCAA
-AGTCTTCAAATCATTTGTACATTATATGGGGCCGTTAAGCTGCCCTAATGATGTGACATA
-TCACAAAGTGCTTGCCTGGCGCCGTTTTCTTTTAAAAGAGAAAAAGCTGTCCGGACGTAC
-CTGGAATAACAAGGTGGCGCATATGCGGGCCATCTTTAACTACGGAATACAGCGAGGGTT
-ACTGCACTATGACGAAAATCCGTTTAACAATTCGGTAGTTAAACCGGACAAGAAGAGAAA
-GAAAACGCTCACTCAGGCACAGATTGAGTATGCCTATCAGATCATGGAGCAGTATGAAAA
-TCAGGAGAATACAGGGCTGGGACTGAAATATTCCCGCTGCGCCTTATTTCCTGCATGGTT
-CTGGCTCACTGTCCTGGATACGCTCTATTACACAGGGATACGTCAGAACCAGTTATTACA
-TATTCGGCTGAATGATGTTGATTTGAGAGAAGGGCAGATTCGGCTGATTACGGAGGGGTG
-TAAAAATCACAAAGAACACTATGTGCCGGTGATCAGTTTTCTGCGTCCACGGCTGACCTG
-TTTAATGGAGAAAGCGCAGAGCGAAGGATTGAAAGGTAATGACCGCCTGTTCAATATTGC
-ACTTTTTACCGGCAAAGATCCCGCCATTGGCGATGACATGGATTCTCCTCAGGTAAGAGC
-ATTCTTCCGTCGTCTGTCCAAGGAGTGTCAGTTTGCGATCAGTCCTCATCGTTTCAGACA
-CACGCTGGCCACGGAGATGATGAAAATGCCGGAACAGAATCTGCATATGGCGCAAAGTGT
-GCTGGGTCATTCAAACATGAAATCCACGCTGGAGTATGTGGAGAATGATATTGCAGTGAT
-GGGGAGGGCTCTGGAAGCGCAGTTTATGCAGATTAAGGCAGCACATGCCCGAAGCATTTA
-CAGTGGGTTGACAAAGAATAGATAA
->genome2_small_5
-GATACA
diff --git a/Examples/2-res-Annotate-prokka/tmp_files/genome2.fst_prokka-split5N.fna-prokkaRes/GEN2.1219.00001.log b/Examples/2-res-Annotate-prokka/tmp_files/genome2.fst_prokka-split5N.fna-prokkaRes/GEN2.1219.00001.log
deleted file mode 100644
index 251627a3eb8cf38b0943f63ac55c0d7eb5f2d73b..0000000000000000000000000000000000000000
--- a/Examples/2-res-Annotate-prokka/tmp_files/genome2.fst_prokka-split5N.fna-prokkaRes/GEN2.1219.00001.log
+++ /dev/null
@@ -1,128 +0,0 @@
-[13:15:26] This is prokka 1.14.5
-[13:15:26] Written by Torsten Seemann <torsten.seemann@gmail.com>
-[13:15:26] Homepage is https://github.com/tseemann/prokka
-[13:15:26] Local time is Mon Dec  9 13:15:26 2019
-[13:15:26] You are aperrin
-[13:15:26] Operating system is darwin
-[13:15:26] You have BioPerl 1.007002
-[13:15:26] System has 8 cores.
-[13:15:26] Will use maximum of 1 cores.
-[13:15:26] Annotating as >>> Bacteria <<<
-[13:15:26] Generating locus_tag from 'Examples/2-res-Annotate-prokka/tmp_files/genome2.fst_prokka-split5N.fna' contents.
-[13:15:26] Setting --locustag AMHDIIJN from MD5 a61d2237f76cf8056ab8e698ba010fa3
-[13:15:26] Creating new output folder: Examples/2-res-Annotate-prokka/tmp_files/genome2.fst_prokka-split5N.fna-prokkaRes
-[13:15:26] Running: mkdir -p Examples\/2\-res\-Annotate\-prokka\/tmp_files\/genome2\.fst_prokka\-split5N\.fna\-prokkaRes
-[13:15:26] Using filename prefix: GEN2.1219.00001.XXX
-[13:15:26] Setting HMMER_NCPU=1
-[13:15:26] Writing log to: Examples/2-res-Annotate-prokka/tmp_files/genome2.fst_prokka-split5N.fna-prokkaRes/GEN2.1219.00001.log
-[13:15:26] Command: /usr/local/bin/prokka --outdir Examples/2-res-Annotate-prokka/tmp_files/genome2.fst_prokka-split5N.fna-prokkaRes --cpus 1 --prefix GEN2.1219.00001 Examples/2-res-Annotate-prokka/tmp_files/genome2.fst_prokka-split5N.fna
-[13:15:26] Appending to PATH: /Users/aperrin/Softwares/src/prokka-dec.19/bin/../binaries/darwin
-[13:15:26] Appending to PATH: /Users/aperrin/Softwares/src/prokka-dec.19/bin/../binaries/darwin/../common
-[13:15:26] Appending to PATH: /Users/aperrin/Softwares/src/prokka-dec.19/bin
-[13:15:26] Looking for 'aragorn' - found /usr/local/bin/aragorn
-[13:15:26] Determined aragorn version is 001002 from 'ARAGORN v1.2.38 Dean Laslett'
-[13:15:26] Looking for 'barrnap' - found /usr/local/bin/barrnap
-[13:15:26] Determined barrnap version is 000008 from 'barrnap 0.8'
-[13:15:26] Looking for 'blastp' - found /Users/aperrin/Softwares/bin/blastp
-[13:15:26] Determined blastp version is 002009 from 'blastp: 2.9.0+'
-[13:15:26] Looking for 'cmpress' - found /usr/local/bin/cmpress
-[13:15:26] Determined cmpress version is 001001 from '# INFERNAL 1.1.2 (July 2016)'
-[13:15:26] Looking for 'cmscan' - found /usr/local/bin/cmscan
-[13:15:26] Determined cmscan version is 001001 from '# INFERNAL 1.1.2 (July 2016)'
-[13:15:26] Looking for 'egrep' - found /usr/bin/egrep
-[13:15:26] Looking for 'find' - found /usr/bin/find
-[13:15:26] Looking for 'grep' - found /usr/bin/grep
-[13:15:26] Looking for 'hmmpress' - found /Users/aperrin/Softwares/src/prokka-dec.19/bin/../binaries/darwin/hmmpress
-[13:15:26] Determined hmmpress version is 003001 from '# HMMER 3.1b1 (May 2013); http://hmmer.org/'
-[13:15:26] Looking for 'hmmscan' - found /usr/local/bin/hmmscan
-[13:15:26] Determined hmmscan version is 003001 from '# HMMER 3.1b2 (February 2015); http://hmmer.org/'
-[13:15:26] Looking for 'java' - found /usr/bin/java
-[13:15:26] Looking for 'makeblastdb' - found /Users/aperrin/Softwares/bin/makeblastdb
-[13:15:26] Determined makeblastdb version is 002009 from 'makeblastdb: 2.9.0+'
-[13:15:26] Looking for 'minced' - found /Users/aperrin/Softwares/src/prokka-dec.19/bin/../binaries/darwin/../common/minced
-[13:15:26] Determined minced version is 002000 from 'minced 0.2.0'
-[13:15:26] Looking for 'parallel' - found /usr/local/bin/parallel
-[13:15:26] Determined parallel version is 20181022 from 'GNU parallel 20181022'
-[13:15:26] Looking for 'prodigal' - found /usr/local/bin/prodigal
-[13:15:26] Determined prodigal version is 002006 from 'Prodigal V2.6.3: February, 2016'
-[13:15:26] Looking for 'prokka-genbank_to_fasta_db' - found /Users/aperrin/Softwares/src/prokka-dec.19/bin/prokka-genbank_to_fasta_db
-[13:15:26] Looking for 'sed' - found /usr/bin/sed
-[13:15:26] Looking for 'tbl2asn' - found /Users/aperrin/Softwares/src/prokka-dec.19/bin/../binaries/darwin/tbl2asn
-[13:15:26] Determined tbl2asn version is 025007 from 'tbl2asn 25.7   arguments:'
-[13:15:26] Using genetic code table 11.
-[13:15:26] Loading and checking input file: Examples/2-res-Annotate-prokka/tmp_files/genome2.fst_prokka-split5N.fna
-[13:15:26] Wrote 5 contigs totalling 10717 bp.
-[13:15:26] Predicting tRNAs and tmRNAs
-[13:15:26] Running: aragorn -l -gc11  -w Examples\/2\-res\-Annotate\-prokka\/tmp_files\/genome2\.fst_prokka\-split5N\.fna\-prokkaRes\/GEN2\.1219\.00001\.fna
-[13:15:26] Found 0 tRNAs
-[13:15:26] Predicting Ribosomal RNAs
-[13:15:26] Running Barrnap with 1 threads
-[13:15:26] Found 0 rRNAs
-[13:15:26] Skipping ncRNA search, enable with --rfam if desired.
-[13:15:26] Total of 0 tRNA + rRNA features
-[13:15:26] Searching for CRISPR repeats
-[13:15:27] Found 0 CRISPRs
-[13:15:27] Predicting coding sequences
-[13:15:27] Contigs total 10717 bp, so using meta mode
-[13:15:27] Running: prodigal -i Examples\/2\-res\-Annotate\-prokka\/tmp_files\/genome2\.fst_prokka\-split5N\.fna\-prokkaRes\/GEN2\.1219\.00001\.fna -c -m -g 11 -p meta -f sco -q
-[13:15:27] Found 13 CDS
-[13:15:27] Connecting features back to sequences
-[13:15:27] Not using genus-specific database. Try --usegenus to enable it.
-[13:15:27] Annotating CDS, please be patient.
-[13:15:27] Will use 1 CPUs for similarity searching.
-[13:15:27] There are still 13 unannotated CDS left (started with 13)
-[13:15:27] Will use blast to search against /Users/aperrin/Softwares/src/prokka-dec.19/db/kingdom/Bacteria/IS with 1 CPUs
-[13:15:27] Running: cat Examples\/2\-res\-Annotate\-prokka\/tmp_files\/genome2\.fst_prokka\-split5N\.fna\-prokkaRes\/GEN2\.1219\.00001\.IS\.tmp\.95071\.faa | parallel --gnu --plain -j 1 --block 1697 --recstart '>' --pipe blastp -query - -db /Users/aperrin/Softwares/src/prokka-dec.19/db/kingdom/Bacteria/IS -evalue 1e-30 -qcov_hsp_perc 90 -num_threads 1 -num_descriptions 1 -num_alignments 1 -seg no > Examples\/2\-res\-Annotate\-prokka\/tmp_files\/genome2\.fst_prokka\-split5N\.fna\-prokkaRes\/GEN2\.1219\.00001\.IS\.tmp\.95071\.blast 2> /dev/null
-[13:15:27] Deleting unwanted file: Examples/2-res-Annotate-prokka/tmp_files/genome2.fst_prokka-split5N.fna-prokkaRes/GEN2.1219.00001.IS.tmp.95071.faa
-[13:15:27] Deleting unwanted file: Examples/2-res-Annotate-prokka/tmp_files/genome2.fst_prokka-split5N.fna-prokkaRes/GEN2.1219.00001.IS.tmp.95071.blast
-[13:15:27] There are still 13 unannotated CDS left (started with 13)
-[13:15:27] Will use blast to search against /Users/aperrin/Softwares/src/prokka-dec.19/db/kingdom/Bacteria/AMR with 1 CPUs
-[13:15:27] Running: cat Examples\/2\-res\-Annotate\-prokka\/tmp_files\/genome2\.fst_prokka\-split5N\.fna\-prokkaRes\/GEN2\.1219\.00001\.AMR\.tmp\.95071\.faa | parallel --gnu --plain -j 1 --block 1697 --recstart '>' --pipe blastp -query - -db /Users/aperrin/Softwares/src/prokka-dec.19/db/kingdom/Bacteria/AMR -evalue 1e-300 -qcov_hsp_perc 90 -num_threads 1 -num_descriptions 1 -num_alignments 1 -seg no > Examples\/2\-res\-Annotate\-prokka\/tmp_files\/genome2\.fst_prokka\-split5N\.fna\-prokkaRes\/GEN2\.1219\.00001\.AMR\.tmp\.95071\.blast 2> /dev/null
-[13:15:28] Deleting unwanted file: Examples/2-res-Annotate-prokka/tmp_files/genome2.fst_prokka-split5N.fna-prokkaRes/GEN2.1219.00001.AMR.tmp.95071.faa
-[13:15:28] Deleting unwanted file: Examples/2-res-Annotate-prokka/tmp_files/genome2.fst_prokka-split5N.fna-prokkaRes/GEN2.1219.00001.AMR.tmp.95071.blast
-[13:15:28] There are still 13 unannotated CDS left (started with 13)
-[13:15:28] Will use blast to search against /Users/aperrin/Softwares/src/prokka-dec.19/db/kingdom/Bacteria/sprot with 1 CPUs
-[13:15:28] Running: cat Examples\/2\-res\-Annotate\-prokka\/tmp_files\/genome2\.fst_prokka\-split5N\.fna\-prokkaRes\/GEN2\.1219\.00001\.sprot\.tmp\.95071\.faa | parallel --gnu --plain -j 1 --block 1697 --recstart '>' --pipe blastp -query - -db /Users/aperrin/Softwares/src/prokka-dec.19/db/kingdom/Bacteria/sprot -evalue 1e-09 -qcov_hsp_perc 80 -num_threads 1 -num_descriptions 1 -num_alignments 1 -seg no > Examples\/2\-res\-Annotate\-prokka\/tmp_files\/genome2\.fst_prokka\-split5N\.fna\-prokkaRes\/GEN2\.1219\.00001\.sprot\.tmp\.95071\.blast 2> /dev/null
-[13:15:29] Deleting unwanted file: Examples/2-res-Annotate-prokka/tmp_files/genome2.fst_prokka-split5N.fna-prokkaRes/GEN2.1219.00001.sprot.tmp.95071.faa
-[13:15:29] Deleting unwanted file: Examples/2-res-Annotate-prokka/tmp_files/genome2.fst_prokka-split5N.fna-prokkaRes/GEN2.1219.00001.sprot.tmp.95071.blast
-[13:15:29] There are still 6 unannotated CDS left (started with 13)
-[13:15:29] Will use hmmer3 to search against /Users/aperrin/Softwares/src/prokka-dec.19/db/hmm/HAMAP.hmm with 1 CPUs
-[13:15:29] Running: cat Examples\/2\-res\-Annotate\-prokka\/tmp_files\/genome2\.fst_prokka\-split5N\.fna\-prokkaRes\/GEN2\.1219\.00001\.HAMAP\.hmm\.tmp\.95071\.faa | parallel --gnu --plain -j 1 --block 691 --recstart '>' --pipe hmmscan --noali --notextw --acc -E 1e-09 --cpu 1 /Users/aperrin/Softwares/src/prokka-dec.19/db/hmm/HAMAP.hmm /dev/stdin > Examples\/2\-res\-Annotate\-prokka\/tmp_files\/genome2\.fst_prokka\-split5N\.fna\-prokkaRes\/GEN2\.1219\.00001\.HAMAP\.hmm\.tmp\.95071\.hmmer3 2> /dev/null
-[13:15:30] Deleting unwanted file: Examples/2-res-Annotate-prokka/tmp_files/genome2.fst_prokka-split5N.fna-prokkaRes/GEN2.1219.00001.HAMAP.hmm.tmp.95071.faa
-[13:15:30] Deleting unwanted file: Examples/2-res-Annotate-prokka/tmp_files/genome2.fst_prokka-split5N.fna-prokkaRes/GEN2.1219.00001.HAMAP.hmm.tmp.95071.hmmer3
-[13:15:30] Labelling remaining 5 proteins as 'hypothetical protein'
-[13:15:30] Found 8 unique /gene codes.
-[13:15:30] Fixed 0 colliding /gene names.
-[13:15:30] Adding /locus_tag identifiers
-[13:15:30] Assigned 13 locus_tags to CDS and RNA features.
-[13:15:30] Writing outputs to Examples/2-res-Annotate-prokka/tmp_files/genome2.fst_prokka-split5N.fna-prokkaRes/
-[13:15:30] Generating annotation statistics file
-[13:15:30] Generating Genbank and Sequin files
-[13:15:30] Running: tbl2asn -V b -a r10k -l paired-ends -M n -N 1 -y 'Annotated using prokka 1.14.5 from https://github.com/tseemann/prokka' -Z Examples\/2\-res\-Annotate\-prokka\/tmp_files\/genome2\.fst_prokka\-split5N\.fna\-prokkaRes\/GEN2\.1219\.00001\.err -i Examples\/2\-res\-Annotate\-prokka\/tmp_files\/genome2\.fst_prokka\-split5N\.fna\-prokkaRes\/GEN2\.1219\.00001\.fsa 2> /dev/null
-[13:15:30] Deleting unwanted file: Examples/2-res-Annotate-prokka/tmp_files/genome2.fst_prokka-split5N.fna-prokkaRes/errorsummary.val
-[13:15:30] Deleting unwanted file: Examples/2-res-Annotate-prokka/tmp_files/genome2.fst_prokka-split5N.fna-prokkaRes/GEN2.1219.00001.dr
-[13:15:30] Deleting unwanted file: Examples/2-res-Annotate-prokka/tmp_files/genome2.fst_prokka-split5N.fna-prokkaRes/GEN2.1219.00001.fixedproducts
-[13:15:30] Deleting unwanted file: Examples/2-res-Annotate-prokka/tmp_files/genome2.fst_prokka-split5N.fna-prokkaRes/GEN2.1219.00001.ecn
-[13:15:30] Deleting unwanted file: Examples/2-res-Annotate-prokka/tmp_files/genome2.fst_prokka-split5N.fna-prokkaRes/GEN2.1219.00001.val
-[13:15:30] Repairing broken .GBK output that tbl2asn produces...
-[13:15:30] Running: sed 's/COORDINATES: profile/COORDINATES:profile/' < Examples\/2\-res\-Annotate\-prokka\/tmp_files\/genome2\.fst_prokka\-split5N\.fna\-prokkaRes\/GEN2\.1219\.00001\.gbf > Examples\/2\-res\-Annotate\-prokka\/tmp_files\/genome2\.fst_prokka\-split5N\.fna\-prokkaRes\/GEN2\.1219\.00001\.gbk
-[13:15:30] Deleting unwanted file: Examples/2-res-Annotate-prokka/tmp_files/genome2.fst_prokka-split5N.fna-prokkaRes/GEN2.1219.00001.gbf
-[13:15:30] Output files:
-[13:15:30] Examples/2-res-Annotate-prokka/tmp_files/genome2.fst_prokka-split5N.fna-prokkaRes/GEN2.1219.00001.tsv
-[13:15:30] Examples/2-res-Annotate-prokka/tmp_files/genome2.fst_prokka-split5N.fna-prokkaRes/GEN2.1219.00001.fna
-[13:15:30] Examples/2-res-Annotate-prokka/tmp_files/genome2.fst_prokka-split5N.fna-prokkaRes/GEN2.1219.00001.err
-[13:15:30] Examples/2-res-Annotate-prokka/tmp_files/genome2.fst_prokka-split5N.fna-prokkaRes/GEN2.1219.00001.gff
-[13:15:30] Examples/2-res-Annotate-prokka/tmp_files/genome2.fst_prokka-split5N.fna-prokkaRes/GEN2.1219.00001.sqn
-[13:15:30] Examples/2-res-Annotate-prokka/tmp_files/genome2.fst_prokka-split5N.fna-prokkaRes/GEN2.1219.00001.tbl
-[13:15:30] Examples/2-res-Annotate-prokka/tmp_files/genome2.fst_prokka-split5N.fna-prokkaRes/GEN2.1219.00001.txt
-[13:15:30] Examples/2-res-Annotate-prokka/tmp_files/genome2.fst_prokka-split5N.fna-prokkaRes/GEN2.1219.00001.faa
-[13:15:30] Examples/2-res-Annotate-prokka/tmp_files/genome2.fst_prokka-split5N.fna-prokkaRes/GEN2.1219.00001.fsa
-[13:15:30] Examples/2-res-Annotate-prokka/tmp_files/genome2.fst_prokka-split5N.fna-prokkaRes/GEN2.1219.00001.gbk
-[13:15:30] Examples/2-res-Annotate-prokka/tmp_files/genome2.fst_prokka-split5N.fna-prokkaRes/GEN2.1219.00001.log
-[13:15:30] Examples/2-res-Annotate-prokka/tmp_files/genome2.fst_prokka-split5N.fna-prokkaRes/GEN2.1219.00001.ffn
-[13:15:30] Annotation finished successfully.
-[13:15:30] Walltime used: 0.07 minutes
-[13:15:30] If you use this result please cite the Prokka paper:
-[13:15:30] Seemann T (2014) Prokka: rapid prokaryotic genome annotation. Bioinformatics. 30(14):2068-9.
-[13:15:30] Type 'prokka --citation' for more details.
-[13:15:30] Thank you, come again.
diff --git a/Examples/2-res-Annotate-prokka/tmp_files/genome2.fst_prokka-split5N.fna-prokkaRes/GEN2.1219.00001.sqn b/Examples/2-res-Annotate-prokka/tmp_files/genome2.fst_prokka-split5N.fna-prokkaRes/GEN2.1219.00001.sqn
deleted file mode 100644
index b84374d8320d2a1199a66dbd722201c5b3593591..0000000000000000000000000000000000000000
--- a/Examples/2-res-Annotate-prokka/tmp_files/genome2.fst_prokka-split5N.fna-prokkaRes/GEN2.1219.00001.sqn
+++ /dev/null
@@ -1,1401 +0,0 @@
-Seq-entry ::= set {
-  class genbank ,
-  seq-set {
-    set {
-      class nuc-prot ,
-      descr {
-        source {
-          org {
-            taxname "Genus species" ,
-            orgname {
-              mod {
-                {
-                  subtype strain ,
-                  subname "strain" } } ,
-              gcode 11 } } } ,
-        comment "Annotated using prokka 1.14.5 from
- https://github.com/tseemann/prokka" ,
-        user {
-          type
-            str "NcbiCleanup" ,
-          data {
-            {
-              label
-                str "method" ,
-              data
-                str "SeriousSeqEntryCleanup" } ,
-            {
-              label
-                str "version" ,
-              data
-                int 8 } ,
-            {
-              label
-                str "month" ,
-              data
-                int 12 } ,
-            {
-              label
-                str "day" ,
-              data
-                int 9 } ,
-            {
-              label
-                str "year" ,
-              data
-                int 2019 } } } ,
-        create-date
-          std {
-            year 2019 ,
-            month 12 ,
-            day 9 } } ,
-      seq-set {
-        seq {
-          id {
-            local
-              str "this_is_genome_1" } ,
-          descr {
-            molinfo {
-              biomol genomic } } ,
-          inst {
-            repr raw ,
-            mol dna ,
-            length 2308 ,
-            seq-data
-              iupacna "ATGTCAGAAAATAAATTACACGTTATCGATTTGCACAAACGCTACGGCGGTCATG
-AAGTGCTGAAAGGGGTATCGCTGCAGGCCCGCGCCGGAGATGTGATTAGCATTATCGGCTCGTCCGGTTCCGGTAAAA
-GCACTTTTTTGCGCTGCATTAACTTCCTCGAAAAATCGAGCGAAGGCGCGATTATCGTGAACGGTCAGAACATTAATC
-TGGTGCGCGACAAAGACGGGCAGCTCAAAGTGGCGGATAAAAATCAGCTACGCTTGTTGCGTACCCGCCTGACGATGG
-TGTTTCAGCACTTTAACCTCTGGAACCACATGACGGTGCTGGAAAATGTGATGGAAGCGCCGATTCAGGTACTGGGAT
-TAAGCAAGCACGACGCGCGCGAGCGGGCGTTGAAATATCTGGCGAAGGTGGGGATTGATGAGCGCGCTCAGGGCAAAT
-ATCCCGTCCATCTCTCCGGCGGCCAACAGCAGCGCGTTTCTATTGCGCGCGCGCTGGCGATGGAACCTGACGTTTTAC
-TGTTCGATGAACCCACATCGGCGCTCGATCCTGAACTGGTCGGCGAAGTGTTGCGCATCATGCAACAACTGGCGGAAG
-AAGGCAAAACGATGGTGGTGGTCACGCATGAAATGGGCTTCGCCCGCCATGTCTCTTCGCACGTGATTTTTCTGCATC
-AGGGGAAAATTGAAGAAGAGGGCAATCCGGAGCAGGTGTTCGGCAATCCGCAAAGCCCGCGTTTACAGCAATTCCTGA
-AAGGCTCGCTGAAATAAACGCTAGAGGACGCGCCTCTCAGAGAGCGCGCTCTCTCAGAGAGGCGCGCGCCTCTTTCGC
-AGAGACCNNCGCTCATGAGCGATGCCCGCGACTAAATTCTCCCGACGTACCCTCCTGACGGCAGGTTCCGCGCTTGCT
-GTTCTTCCTTTTCTGCGCGCCTTGCCGGTACAGGCGCGTGAACCTCGCCAGACCGTCGATATTAAGGATTATCCGGCG
-GATGACGGTATCGCCTCGTTCAAACAGGCCTTCGCCGACGGGCAGACTGTGGTCGTGCCGTCAGGATGGGTGTGTGAA
-AATATCAATGCGGCGATAACGATTCCGGCGGGAAAAACGCTGCGGATACAGGGCGCGGTGCGTGGGAATGGCCGGGGA
-CGGTTTATTTTGCTGGACGGGTGTCAGGTGGTGGGGGAGCAGGGCGGCAGTCTGCACAATGTGACGCTGGATGTTCGC
-GGGTCGGACTGTGTGATTAAAGGCGTGACGATGAGCGGCTTTGGCCCCGTCGCGCAAATTTTCATCGGCGGTAAGGAA
-CCGCAGGTGATGCGTAATCTCATTATCGATGACATCACCGTTACCCACGCCAACTACGCCATTCTCCGCCAGGGATTT
-CATAACCAAATGGACGGCGCGCGGATTACGCATAGTCGCTTTAGCGATTTGCAGGGGGACGCCATTGAGTGGAATGTC
-GCGATTCATGACCGCGACATCCTGATTTCCGATCATGTCATCGAACGCATTGATTGTACCAATGGCAAAATCAACTGG
-GGGATCGGCATCGGGCTGGCGGGTAGCGCCTATGACAATAGTTATCCTGAAGACCAGGCAGTAAAAAACTTTGTGGTG
-GCCAATATTACCGGATCTGATTGCCGACAACTGGTACACGTAGAAAATGGCAAACATTTCGTCATTCGCAATGTCAAA
-GCCAAAAACATCACGCCCGATTTCAGTAAAAATGCGGGTATTGATAACGCAACGATCGCCATTTATGGCTGTGATAAT
-TTCGTCATTGATAATATTGATATGACGAATAGTGCCGGGATGCTCATCGGCTATGGCGTCGTTAAAGGAAAATACCTG
-TCAATTCCGCAAAACTTTAAATTAAACGCTATTCGGTTGGATAATCGCCAGGTTGCTTATAAATTACGCGGCATTCAA
-ATTTCCTCCGGTAACGCCCCCTCATTTGTTGCCATCACCAATGTACGGATGACGCGTGCTACGCTGGAACTGCATAAT
-CAACCGCAGCACCTCTTTTTGCGTAATATCAACGTGATGCAAACTTCAGCGATTGGCCCGGCGTTAAAAATGCATTTT
-GATTTGCGTAAAGATGTCCGTGGTCAATTTATGGCCCGCCAGGACACGCTGCTTTCCCTCGCTAATGTTCATGCCATC
-AATGAAAACGGGCAGAGTTCCGTGGATATCGACAGGATTAATCACCAAACCGTGAATGTCGAAGCAGTGAATTTTTCG
-CTGCCGAAGCGGGGAGGGTAACACTCGCGCATAGAGAGCTCTCAGAGGAGCGCGCGCGCTATAGCGCGC" } } ,
-        seq {
-          id {
-            local
-              str "this_is_genome_1_1" } ,
-          descr {
-            title "Histidine transport ATP-binding protein HisP [Genus
- species]" ,
-            molinfo {
-              biomol peptide ,
-              tech concept-trans } } ,
-          inst {
-            repr raw ,
-            mol aa ,
-            length 257 ,
-            seq-data
-              ncbieaa "MSENKLHVIDLHKRYGGHEVLKGVSLQARAGDVISIIGSSGSGKSTFLRCINFLE
-KSSEGAIIVNGQNINLVRDKDGQLKVADKNQLRLLRTRLTMVFQHFNLWNHMTVLENVMEAPIQVLGLSKHDARERAL
-KYLAKVGIDERAQGKYPVHLSGGQQQRVSIARALAMEPDVLLFDEPTSALDPELVGEVLRIMQQLAEEGKTMVVVTHE
-MGFARHVSSHVIFLHQGKIEEEGNPEQVFGNPQSPRLQQFLKGSLK" } ,
-          annot {
-            {
-              data
-                ftable {
-                  {
-                    id
-                      local
-                        id 3 ,
-                    data
-                      prot {
-                        name {
-                          "Histidine transport ATP-binding protein HisP" } } ,
-                    location
-                      int {
-                        from 0 ,
-                        to 256 ,
-                        id
-                          local
-                            str "this_is_genome_1_1" } } } } } } ,
-        seq {
-          id {
-            local
-              str "this_is_genome_1_2" } ,
-          descr {
-            title "hypothetical protein AMHDIIJN_00002 [Genus species]" ,
-            molinfo {
-              biomol peptide ,
-              tech concept-trans } } ,
-          inst {
-            repr raw ,
-            mol aa ,
-            length 467 ,
-            seq-data
-              ncbieaa "MPATKFSRRTLLTAGSALAVLPFLRALPVQAREPRQTVDIKDYPADDGIASFKQA
-FADGQTVVVPSGWVCENINAAITIPAGKTLRIQGAVRGNGRGRFILLDGCQVVGEQGGSLHNVTLDVRGSDCVIKGVT
-MSGFGPVAQIFIGGKEPQVMRNLIIDDITVTHANYAILRQGFHNQMDGARITHSRFSDLQGDAIEWNVAIHDRDILIS
-DHVIERIDCTNGKINWGIGIGLAGSAYDNSYPEDQAVKNFVVANITGSDCRQLVHVENGKHFVIRNVKAKNITPDFSK
-NAGIDNATIAIYGCDNFVIDNIDMTNSAGMLIGYGVVKGKYLSIPQNFKLNAIRLDNRQVAYKLRGIQISSGNAPSFV
-AITNVRMTRATLELHNQPQHLFLRNINVMQTSAIGPALKMHFDLRKDVRGQFMARQDTLLSLANVHAINENGQSSVDI
-DRINHQTVNVEAVNFSLPKRGG" } ,
-          annot {
-            {
-              data
-                ftable {
-                  {
-                    id
-                      local
-                        id 4 ,
-                    data
-                      prot {
-                        name {
-                          "hypothetical protein" } } ,
-                    location
-                      int {
-                        from 0 ,
-                        to 466 ,
-                        id
-                          local
-                            str "this_is_genome_1_2" } } } } } } } ,
-      annot {
-        {
-          data
-            ftable {
-              {
-                id
-                  local
-                    id 1 ,
-                data
-                  cdregion {
-                    frame one ,
-                    code {
-                      id 11 } } ,
-                product
-                  whole
-                    local
-                      str "this_is_genome_1_1" ,
-                location
-                  int {
-                    from 0 ,
-                    to 773 ,
-                    strand plus ,
-                    id
-                      local
-                        str "this_is_genome_1" } ,
-                qual {
-                  {
-                    qual "inference" ,
-                    val "ab initio prediction:Prodigal:002006" } ,
-                  {
-                    qual "inference" ,
-                    val "similar to AA sequence:UniProtKB:P02915" } } ,
-                xref {
-                  {
-                    data
-                      gene {
-                        locus "hisP" ,
-                        locus-tag "AMHDIIJN_00001" } } } ,
-                dbxref {
-                  {
-                    db "COG" ,
-                    tag
-                      str "COG4598" } } } ,
-              {
-                id
-                  local
-                    id 2 ,
-                data
-                  cdregion {
-                    frame one ,
-                    code {
-                      id 11 } } ,
-                product
-                  whole
-                    local
-                      str "this_is_genome_1_2" ,
-                location
-                  int {
-                    from 856 ,
-                    to 2259 ,
-                    strand plus ,
-                    id
-                      local
-                        str "this_is_genome_1" } ,
-                qual {
-                  {
-                    qual "inference" ,
-                    val "ab initio prediction:Prodigal:002006" } } ,
-                xref {
-                  {
-                    data
-                      gene {
-                        locus-tag "AMHDIIJN_00002" } } } } } } } } ,
-    set {
-      class nuc-prot ,
-      descr {
-        source {
-          org {
-            taxname "Genus species" ,
-            orgname {
-              mod {
-                {
-                  subtype strain ,
-                  subname "strain" } } ,
-              gcode 11 } } } ,
-        comment "Annotated using prokka 1.14.5 from
- https://github.com/tseemann/prokka" ,
-        user {
-          type
-            str "NcbiCleanup" ,
-          data {
-            {
-              label
-                str "method" ,
-              data
-                str "SeriousSeqEntryCleanup" } ,
-            {
-              label
-                str "version" ,
-              data
-                int 8 } ,
-            {
-              label
-                str "month" ,
-              data
-                int 12 } ,
-            {
-              label
-                str "day" ,
-              data
-                int 9 } ,
-            {
-              label
-                str "year" ,
-              data
-                int 2019 } } } ,
-        create-date
-          std {
-            year 2019 ,
-            month 12 ,
-            day 9 } } ,
-      seq-set {
-        seq {
-          id {
-            local
-              str "this_is_genome_2" } ,
-          descr {
-            molinfo {
-              biomol genomic } } ,
-          inst {
-            repr raw ,
-            mol dna ,
-            length 3295 ,
-            seq-data
-              iupacna "CGCGATAATATAGCGCGCGCTCATAGCATGAGCGCGCTATTTCTGGCCATCCCGT
-TAACCATTTTTGTGTTGTTTGTGTTACCGATTTGGCTGTGGCTGCATTACAGCAACCGCGCCGGTCGGGGAGAACTGT
-CGCAAAGCGAGCAGCAACGCTTACTGCAACTCACAGACGACGCGCAACGTATGCGCGAGCGCATTCAGGCGCTGGAAG
-ATATTCTTGATGCAGAGCATCCGAACTGGAGAGAGCGCTAACGCCATATTATAGCGCGCCTCATAAGAGCGGCCTATA
-GCGCGCTANNNATGCCGCACTTTATTGCTGAATGTACTGAAAATATTCGCGAGCAGGCTGATTTACCAAGCCTGTTCA
-GCAAGGTAAACGAGGCGCTGGCCGCCACCGGGATTTTCCCCATCGGCGGTATCCGCAGTCGCGCCCACTGGCTGGATA
-CCTGGCAGATGGCTGACGGTAAGCATGATTACGCGTTTGTGCATATGACGCTGAAAATCGGCGCCGGGCGCAGCCTGG
-AGAGCCGTCAGGAAGTCGGCGAAATGCTGTTTGGGCTGATTAAAGCCCACTTCGCCGACCTGATGGAGAACCGCTATC
-TGGCGCTGTCGTTTGAGATTGCCGAGTTACATCCAACGCTCAATTACAAACAAAACAACGTACACGCGTTATTTAAAT
-AGCCAGAGATTCGCGCGTTCAGAGAGGAGCTCTCTCATAGACGCGCGCATATGCGCTCTAGAGAGGCGCGCCTAATGG
-CGCGCTATGATGAAAGCGCTACTGTGGCTGGTTGGTCTCGCGTTGCTGTTAACAGGCTGCGCGAGCGAAAAAGGAATT
-ATCGATAAAGAGGGATATCAGCTTGATACCCGACATCGGGCGCAGGCGGCCTATCCGCGCATTAAAGTCCTGGTGATT
-CACTATACGGCGGAAAACTTTGACGTTTCGCTGGCGACGTTAACGGGTCGCAACGTCAGTTCGCATTACCTGATTCCC
-GCAACCCCGCCATTATATGGCGGTAAACCGCGCATCTGGCAACTGGTGCCGGAACAGGATCAGGCTTGGCATGCGGGC
-GTCAGTTTCTGGCGAGGCGCCACGCGTCTCAATGATACGTCTATTGGCATTGAGCTGGAAAATCGCGGCTGGCGAATG
-TCCGGCGGGGTGAAATCTTTCGCGCCGTTTGAATCCGCGCAAATTCAGGCATTGATCCCGTTAGCGAAGGACATTATC
-GCGCGCTATGACATCAAACCGCAGAATGTGGTGGCCCATGCGGATATCGCGCCGCAGCGTAAAGACGATCCCGGCCCG
-CGCTTCCCGTGGCGCGAGCTGGCGGCACAGGGGATTGGCGCCTGGCCTGACGCCCAGCGTGTGGCGTTTTATCTGGCT
-GGACGCGCGCCGTATACGCCAGTCGATACCGCAACGGTGCTTGCGTTACTCTCGCGCTATGGCTATGAAGTCAAAGCC
-GATATGACGGCGCGCGAGCAACAGCGGGTGATTATGGCGTTCCAGATGCACTTCCGTCCGGCGCAATGGAACGGTATC
-GCAGATGCCGAAACGCAGGCGATTGCCGAAGCATTACTGGAGAAGTACGGCCAGGATTAACAAAGCGCTCTCAGAGAG
-AGCGCTCTGCAGATGAGTGAGGCTGAAGCCCGCCCGACTAACTTTATTCGTCAGATTATTGATGAAGATCTGGCGAGT
-GGTAAACATACCACTGTCCATACCCGTTTTCCGCCGGAGCCGAATGGCTATCTGCACATCGGCCACGCGAAATCTATC
-TGCCTGAACTTTGGCATCGCGCAAGATTATCAGGGCCAGTGCAACCTGCGTTTCGATGACACCAACCCGGTAAAAGAA
-GATATCGAGTACGTTGATTCGATCAAAAACGACGTCGAGTGGTTAGGCTTTCACTGGTCTGGCGATATTCGCTACTCC
-TCCGATTACTTTGACCAACTGCACGCCTATGCGGTCGAGCTCATCAATAAAGGCCTGGCCTACGTTGATGAGCTGACG
-CCGGAGCAGATCCGCGAATACCGTGGTACGCTGACCGCGCCGGGTAAAAACAGCCCGTTCCGCGATCGCAGCGTGGAA
-GAAAACCTCGCGCTATTTGAAAAAATGCGTACCGGCGGTTTTGAAGAGGGTAAAGCCTGTCTGCGCGCTAAAATCGAC
-ATGGCGTCGCCGTTTATCGTGATGCGCGATCCGGTGCTGTATCGCATTAAATTCGCCGAGCATCATCAGACCGGCACG
-AAGTGGTGCATCTATCCGATGTACGACTTTACTCACTGCATCAGCGATGCGCTGGAAGGCATTACTCATTCTCTGTGT
-ACGCTGGAGTTCCAGGACAACCGTCGTCTGTACGACTGGGTGCTGGACAACATCACCATTCCGGTTCACCCGCGCCAG
-TACGAATTCTCGCGCCTGAATCTGGAATACACCGTGATGTCCAAGCGTAAGCTGAACCTGCTGGTGACCGACAAACAC
-GTCGAAGGTTGGGATGATCCGCGTATGCCGACTATTTCCGGTCTGCGCCGTCGCGGCTATACCGCGGCTTCTATTCGT
-GAGTTCTGCAAACGCATCGGCGTCACCAAGCAGGACAACACTATTGAGATGGCGTCGCTGGAATCCTGCATTCGCGAA
-GATCTGAACGAAAACGCGCCGCGCGCGATGGCGGTAATCGATCCGGTAAAACTGGTTATCGAAAACTACCCGCAGGGC
-GAGAGCGAAATGGTTACCATGCCTAACCATCCGAATAAACCGGAGATGGGCAGCCGTGAAGTGCCGTTTAGCGGTGAG
-ATCTGGATCGATCGCGCGGATTTCCGCGAAGAAGCGAACAAACAGTACAAACGTCTGGTGATGGGCAAAGAAGTGCGT
-CTGCGTAATGCCTACGTCATTAAAGCGGAGCGCGTAGAGAAGGATGCCGAAGGGAATATCACCACCATCTTCTGTACC
-TATGATGCTGATACGCTGAGTAAAGATCCGGCTGACGGGCGTAAAGTGAAAGGCGTAATCCACTGGGTTAGCGTAGCA
-CATGCGCTGCCGATTGAAATTCGTCTCTACGACCGTCTGTTCAGCGTGCCGAACCCGGGCGCCGCGGAGGACTTCCTG
-TCTGTTATCAACCCCGAATCATTAGTGATTAAGCAGGGGTATGGCGAGCCGTCGCTGAAAGCGGCGGTAGCAGGGAAA
-GCTTTCCAGTTTGAACGTGAAGGTTACTTCTGCCTTGACAGCCGCTATGCAACGGCCGATAAGCTGGTCTTTAACCGC
-ACCGTGGGCCTGCGTGATACCTGGGCGAAAGCGGGCGAATAA" } } ,
-        seq {
-          id {
-            local
-              str "this_is_genome_2_1" } ,
-          descr {
-            title "Phage shock protein B [Genus species]" ,
-            molinfo {
-              biomol peptide ,
-              tech concept-trans } } ,
-          inst {
-            repr raw ,
-            mol aa ,
-            length 74 ,
-            seq-data
-              ncbieaa "MSALFLAIPLTIFVLFVLPIWLWLHYSNRAGRGELSQSEQQRLLQLTDDAQRMRE
-RIQALEDILDAEHPNWRER" } ,
-          annot {
-            {
-              data
-                ftable {
-                  {
-                    id
-                      local
-                        id 9 ,
-                    data
-                      prot {
-                        name {
-                          "Phage shock protein B" } } ,
-                    location
-                      int {
-                        from 0 ,
-                        to 73 ,
-                        id
-                          local
-                            str "this_is_genome_2_1" } } } } } } ,
-        seq {
-          id {
-            local
-              str "this_is_genome_2_2" } ,
-          descr {
-            title "5-carboxymethyl-2-hydroxymuconate Delta-isomerase [Genus
- species]" ,
-            molinfo {
-              biomol peptide ,
-              tech concept-trans } } ,
-          inst {
-            repr raw ,
-            mol aa ,
-            length 126 ,
-            seq-data
-              ncbieaa "MPHFIAECTENIREQADLPSLFSKVNEALAATGIFPIGGIRSRAHWLDTWQMADG
-KHDYAFVHMTLKIGAGRSLESRQEVGEMLFGLIKAHFADLMENRYLALSFEIAELHPTLNYKQNNVHALFK" } ,
-          annot {
-            {
-              data
-                ftable {
-                  {
-                    id
-                      local
-                        id 10 ,
-                    data
-                      prot {
-                        name {
-                          "5-carboxymethyl-2-hydroxymuconate Delta-isomerase" } ,
-                        ec {
-                          "5.3.3.10" } } ,
-                    location
-                      int {
-                        from 0 ,
-                        to 125 ,
-                        id
-                          local
-                            str "this_is_genome_2_2" } } } } } } ,
-        seq {
-          id {
-            local
-              str "this_is_genome_2_3" } ,
-          descr {
-            title "N-acetylmuramoyl-L-alanine amidase AmiD [Genus species]" ,
-            molinfo {
-              biomol peptide ,
-              tech concept-trans } } ,
-          inst {
-            repr raw ,
-            mol aa ,
-            length 277 ,
-            seq-data
-              ncbieaa "MMKALLWLVGLALLLTGCASEKGIIDKEGYQLDTRHRAQAAYPRIKVLVIHYTAE
-NFDVSLATLTGRNVSSHYLIPATPPLYGGKPRIWQLVPEQDQAWHAGVSFWRGATRLNDTSIGIELENRGWRMSGGVK
-SFAPFESAQIQALIPLAKDIIARYDIKPQNVVAHADIAPQRKDDPGPRFPWRELAAQGIGAWPDAQRVAFYLAGRAPY
-TPVDTATVLALLSRYGYEVKADMTAREQQRVIMAFQMHFRPAQWNGIADAETQAIAEALLEKYGQD" } ,
-          annot {
-            {
-              data
-                ftable {
-                  {
-                    id
-                      local
-                        id 11 ,
-                    data
-                      prot {
-                        name {
-                          "N-acetylmuramoyl-L-alanine amidase AmiD" } ,
-                        ec {
-                          "3.5.1.28" } } ,
-                    location
-                      int {
-                        from 0 ,
-                        to 276 ,
-                        id
-                          local
-                            str "this_is_genome_2_3" } } } } } } ,
-        seq {
-          id {
-            local
-              str "this_is_genome_2_4" } ,
-          descr {
-            title "Glutamine--tRNA ligase [Genus species]" ,
-            molinfo {
-              biomol peptide ,
-              tech concept-trans } } ,
-          inst {
-            repr raw ,
-            mol aa ,
-            length 555 ,
-            seq-data
-              ncbieaa "MSEAEARPTNFIRQIIDEDLASGKHTTVHTRFPPEPNGYLHIGHAKSICLNFGIA
-QDYQGQCNLRFDDTNPVKEDIEYVDSIKNDVEWLGFHWSGDIRYSSDYFDQLHAYAVELINKGLAYVDELTPEQIREY
-RGTLTAPGKNSPFRDRSVEENLALFEKMRTGGFEEGKACLRAKIDMASPFIVMRDPVLYRIKFAEHHQTGTKWCIYPM
-YDFTHCISDALEGITHSLCTLEFQDNRRLYDWVLDNITIPVHPRQYEFSRLNLEYTVMSKRKLNLLVTDKHVEGWDDP
-RMPTISGLRRRGYTAASIREFCKRIGVTKQDNTIEMASLESCIREDLNENAPRAMAVIDPVKLVIENYPQGESEMVTM
-PNHPNKPEMGSREVPFSGEIWIDRADFREEANKQYKRLVMGKEVRLRNAYVIKAERVEKDAEGNITTIFCTYDADTLS
-KDPADGRKVKGVIHWVSVAHALPIEIRLYDRLFSVPNPGAAEDFLSVINPESLVIKQGYGEPSLKAAVAGKAFQFERE
-GYFCLDSRYATADKLVFNRTVGLRDTWAKAGE" } ,
-          annot {
-            {
-              data
-                ftable {
-                  {
-                    id
-                      local
-                        id 12 ,
-                    data
-                      prot {
-                        name {
-                          "Glutamine--tRNA ligase" } ,
-                        ec {
-                          "6.1.1.18" } } ,
-                    location
-                      int {
-                        from 0 ,
-                        to 554 ,
-                        id
-                          local
-                            str "this_is_genome_2_4" } } } } } } } ,
-      annot {
-        {
-          data
-            ftable {
-              {
-                id
-                  local
-                    id 5 ,
-                data
-                  cdregion {
-                    frame one ,
-                    code {
-                      id 11 } } ,
-                product
-                  whole
-                    local
-                      str "this_is_genome_2_1" ,
-                location
-                  int {
-                    from 27 ,
-                    to 251 ,
-                    strand plus ,
-                    id
-                      local
-                        str "this_is_genome_2" } ,
-                qual {
-                  {
-                    qual "inference" ,
-                    val "ab initio prediction:Prodigal:002006" } ,
-                  {
-                    qual "inference" ,
-                    val "similar to AA sequence:UniProtKB:P0AFM9" } } ,
-                xref {
-                  {
-                    data
-                      gene {
-                        locus "pspB" ,
-                        locus-tag "AMHDIIJN_00003" } } } } ,
-              {
-                id
-                  local
-                    id 6 ,
-                data
-                  cdregion {
-                    frame one ,
-                    code {
-                      id 11 } } ,
-                product
-                  whole
-                    local
-                      str "this_is_genome_2_2" ,
-                location
-                  int {
-                    from 300 ,
-                    to 680 ,
-                    strand plus ,
-                    id
-                      local
-                        str "this_is_genome_2" } ,
-                qual {
-                  {
-                    qual "inference" ,
-                    val "ab initio prediction:Prodigal:002006" } ,
-                  {
-                    qual "inference" ,
-                    val "similar to AA sequence:UniProtKB:Q05354" } } ,
-                xref {
-                  {
-                    data
-                      gene {
-                        locus "hpcD" ,
-                        locus-tag "AMHDIIJN_00004" } } } } ,
-              {
-                id
-                  local
-                    id 7 ,
-                data
-                  cdregion {
-                    frame one ,
-                    code {
-                      id 11 } } ,
-                product
-                  whole
-                    local
-                      str "this_is_genome_2_3" ,
-                location
-                  int {
-                    from 763 ,
-                    to 1596 ,
-                    strand plus ,
-                    id
-                      local
-                        str "this_is_genome_2" } ,
-                qual {
-                  {
-                    qual "inference" ,
-                    val "ab initio prediction:Prodigal:002006" } ,
-                  {
-                    qual "inference" ,
-                    val "similar to AA sequence:UniProtKB:P75820" } } ,
-                xref {
-                  {
-                    data
-                      gene {
-                        locus "amiD" ,
-                        locus-tag "AMHDIIJN_00005" } } } ,
-                dbxref {
-                  {
-                    db "COG" ,
-                    tag
-                      str "COG3023" } } } ,
-              {
-                id
-                  local
-                    id 8 ,
-                data
-                  cdregion {
-                    frame one ,
-                    code {
-                      id 11 } } ,
-                product
-                  whole
-                    local
-                      str "this_is_genome_2_4" ,
-                location
-                  int {
-                    from 1627 ,
-                    to 3294 ,
-                    strand plus ,
-                    id
-                      local
-                        str "this_is_genome_2" } ,
-                qual {
-                  {
-                    qual "inference" ,
-                    val "ab initio prediction:Prodigal:002006" } ,
-                  {
-                    qual "inference" ,
-                    val "similar to AA sequence:UniProtKB:P00962" } } ,
-                xref {
-                  {
-                    data
-                      gene {
-                        locus "glnS" ,
-                        locus-tag "AMHDIIJN_00006" } } } ,
-                dbxref {
-                  {
-                    db "COG" ,
-                    tag
-                      str "COG0008" } } } } } } } ,
-    set {
-      class nuc-prot ,
-      descr {
-        source {
-          org {
-            taxname "Genus species" ,
-            orgname {
-              mod {
-                {
-                  subtype strain ,
-                  subname "strain" } } ,
-              gcode 11 } } } ,
-        comment "Annotated using prokka 1.14.5 from
- https://github.com/tseemann/prokka" ,
-        user {
-          type
-            str "NcbiCleanup" ,
-          data {
-            {
-              label
-                str "method" ,
-              data
-                str "SeriousSeqEntryCleanup" } ,
-            {
-              label
-                str "version" ,
-              data
-                int 8 } ,
-            {
-              label
-                str "month" ,
-              data
-                int 12 } ,
-            {
-              label
-                str "day" ,
-              data
-                int 9 } ,
-            {
-              label
-                str "year" ,
-              data
-                int 2019 } } } ,
-        create-date
-          std {
-            year 2019 ,
-            month 12 ,
-            day 9 } } ,
-      seq-set {
-        seq {
-          id {
-            local
-              str "this_is_genome_3" } ,
-          descr {
-            molinfo {
-              biomol genomic } } ,
-          inst {
-            repr raw ,
-            mol dna ,
-            length 2263 ,
-            seq-data
-              iupacna "ACGCGCTATAGGGCTCTCAGAGAGTCTCAGTGTTTATTGGCATCGTTAGCCTGTT
-TCCTGAAATGTTCCGCGCAATTACCGATTACGGGGTAACTGGCCGGGCAGTAAAAAAAGGCCTGCTGAACATCCAAAG
-CTGGAGTCCTCGCGACTTCGCGCATGACCGGCACCGTACCGTGGACGACCGTCCTTACGGCGGCGGACCGGGGATGTT
-AATGATGGTGCAACCCTTGCGGGACGCCATTCATGCAGCAAAAGCCGCGGCAGGTGAAGGCGCTAAAGTGATTTATCT
-GTCGCCTCAGGGACGCAAGCTTGATCAAGCGGGCGTTAGCGAGCTGGCCACGAATCAGAAACTCATTCTGGTGTGTGG
-TCGCTACGAAGGCGTAGATGAGCGCGTAATTCAGGCCGAAATTGACGAAGAATGGTCAATTGGCGATTACGTTCTCAG
-CGGTGGCGAACTACCGGCAATGACGCTGATTGACTCCGTCGCCCGGTTTATACCGGGGGTTCTGGGGCATGAGGCATC
-AGCAATCGAAGATTCGTTTGCTGATGGGTTGCTGGATTGTCCGCACTATACGCGCCCTGAAGTGTTAGAGGGGATGGA
-AGTACCGCCAGTATTGCTGTCGGGAAACCATGCTGAGATACGTCGCTGGCGTTTGAAACAGTCACTGGGCCGAACCTG
-GCTTAGAAGACCTGAACTTCTGGAAAACCTGGCTCTGACTGAAGAGCAAGCAAGGTTGCTGGCGGAGTTCAAAACAGA
-ACACGCACAACAGCAGCATAAACATGATGGGATGGCATAGCGAGATCGCGCATAGCGCGCGGCGAGATCCGCGAGACA
-TGAATAATCATTTTGGGAAAGGGTTAATGGCCGGGTTGCACGCGCCATATGCATATAGCGCGCATCATGCGGTGAATT
-TCTGTTCTGAGTATAAACGTGGCTTTGTATTGGGTTTTACACACCGTATGTTCGAAAAGACCGGCGATCGTCAACTTA
-GCGCGTGGGAGGCCGGAATTCTGACGCGTCGCTATGGTCTGGATAAAGAAATGGTGATGGATTTCTTTAAAGAGAATC
-ATTCCGGGATGGCGGTTCGCTTCTTTATGGCTGGTTATCGACTCGAAGGTTGAACGCCTCTAGAGCGCTAGAGGCGCG
-CGCGATATACGCGGCGCGAGACATGTCTACGCTTCTCTATTTGCACGGATTCAACAGTTCCCCTCGCTCGGCAAAAGC
-GTGCCAGCTAAAAAACTGGCTGGCGGAGCGTCATCCGCATGTTGAGATGATCGTCCCTCAACTGCCGCCGTATCCTGC
-CGATGCGGCGGAGTTGCTGGAATCTCTCGTACTTGAGCATGGCGGTGCGCCATTAGGGCTGGTAGGATCGTCGCTGGG
-TGGTTATTACGCCACCTGGCTGTCGCAATGTTTTATGCTGCCGGCTGTGGTGGTGAATCCCGCCGTGCGGCCCTTTGA
-ATTACTGACCGACTATCTCGGTCAGAACGAGAACCCCTACACCGGGCAGCAATATGTGCTAGAGTCTCGCCATATTTA
-TGATCTTAAAGTCATGCAGATTGACCCGCTGGAAGCGCCGGACCTGATCTGGCTACTGCAACAGACGGGCGATGAAGT
-GCTGGATTACCGCCAGGCGGTGGCATATTACGCCTCCTGCCGTCAGACAGTGACCGAGGGGGGTAATCACGCATTCAC
-GGGCTTCGAAGATTATTTCAACCAGATTGTCGATTTTCTTGGACTGCACAGTTGCTGACCGGATATACGCGCGCGCGC
-TATATAGCGCGCGCGGCGATATAGCGCATGAAGTTTGTTGCGCCAGAACAGGCACCGGAACAGGCGGAAATCATCAGA
-AATACGCCGTTCTGGCCTGATGTGGACCTGTCGGAGTTTCGCAGCATGATGCGCACTGATGGCACGGTGACGCAGCCG
-CGTTTAAAGCAGGTTGCGCTGTCGGCAATTTCGGAGGTCAACGCAGAGCTGTATGAGTTTCGCAGACGCCAGCAGATG
-CTGGGGTATGCCTCGCTGGCAGAAGTCCCGGCGGAACAACTGGACGGCAAAAGCGAGCGCATTCAGCACTATTTCAAC
-GCGGTTTACTGCTGGGCACGCGCCATGCTCAACGAACGTTACCAGGACTATGACGCCACGGCATCCGGTGTGAAGCGG
-GGCGAAGAACTGGCAGAAGCCAGCGGTGATTTGTGGCGTGACGCCCGCTGGGCCATCAGCCGGGTGCAGGATGCGCCG
-CACTGCACAGTGGAGCTTATCTGA" } } ,
-        seq {
-          id {
-            local
-              str "this_is_genome_3_1" } ,
-          descr {
-            title "tRNA (guanine-N(1)-)-methyltransferase [Genus species]" ,
-            molinfo {
-              biomol peptide ,
-              tech concept-trans } } ,
-          inst {
-            repr raw ,
-            mol aa ,
-            length 255 ,
-            seq-data
-              ncbieaa "MFIGIVSLFPEMFRAITDYGVTGRAVKKGLLNIQSWSPRDFAHDRHRTVDDRPYG
-GGPGMLMMVQPLRDAIHAAKAAAGEGAKVIYLSPQGRKLDQAGVSELATNQKLILVCGRYEGVDERVIQAEIDEEWSI
-GDYVLSGGELPAMTLIDSVARFIPGVLGHEASAIEDSFADGLLDCPHYTRPEVLEGMEVPPVLLSGNHAEIRRWRLKQ
-SLGRTWLRRPELLENLALTEEQARLLAEFKTEHAQQQHKHDGMA" } ,
-          annot {
-            {
-              data
-                ftable {
-                  {
-                    id
-                      local
-                        id 17 ,
-                    data
-                      prot {
-                        name {
-                          "tRNA (guanine-N(1)-)-methyltransferase" } ,
-                        ec {
-                          "2.1.1.228" } } ,
-                    location
-                      int {
-                        from 0 ,
-                        to 254 ,
-                        id
-                          local
-                            str "this_is_genome_3_1" } } } } } } ,
-        seq {
-          id {
-            local
-              str "this_is_genome_3_2" } ,
-          descr {
-            title "hypothetical protein AMHDIIJN_00008 [Genus species]" ,
-            molinfo {
-              biomol peptide ,
-              tech concept-trans } } ,
-          inst {
-            repr raw ,
-            mol aa ,
-            length 86 ,
-            seq-data
-              ncbieaa "MAGLHAPYAYSAHHAVNFCSEYKRGFVLGFTHRMFEKTGDRQLSAWEAGILTRRY
-GLDKEMVMDFFKENHSGMAVRFFMAGYRLEG" } ,
-          annot {
-            {
-              data
-                ftable {
-                  {
-                    id
-                      local
-                        id 18 ,
-                    data
-                      prot {
-                        name {
-                          "hypothetical protein" } } ,
-                    location
-                      int {
-                        from 0 ,
-                        to 85 ,
-                        id
-                          local
-                            str "this_is_genome_3_2" } } } } } } ,
-        seq {
-          id {
-            local
-              str "this_is_genome_3_3" } ,
-          descr {
-            title "hypothetical protein AMHDIIJN_00009 [Genus species]" ,
-            molinfo {
-              biomol peptide ,
-              tech concept-trans } } ,
-          inst {
-            repr raw ,
-            mol aa ,
-            length 193 ,
-            seq-data
-              ncbieaa "MSTLLYLHGFNSSPRSAKACQLKNWLAERHPHVEMIVPQLPPYPADAAELLESLV
-LEHGGAPLGLVGSSLGGYYATWLSQCFMLPAVVVNPAVRPFELLTDYLGQNENPYTGQQYVLESRHIYDLKVMQIDPL
-EAPDLIWLLQQTGDEVLDYRQAVAYYASCRQTVTEGGNHAFTGFEDYFNQIVDFLGLHSC" } ,
-          annot {
-            {
-              data
-                ftable {
-                  {
-                    id
-                      local
-                        id 19 ,
-                    data
-                      prot {
-                        name {
-                          "hypothetical protein" } } ,
-                    location
-                      int {
-                        from 0 ,
-                        to 192 ,
-                        id
-                          local
-                            str "this_is_genome_3_3" } } } } } } ,
-        seq {
-          id {
-            local
-              str "this_is_genome_3_4" } ,
-          descr {
-            title "hypothetical protein AMHDIIJN_00010 [Genus species]" ,
-            molinfo {
-              biomol peptide ,
-              tech concept-trans } } ,
-          inst {
-            repr raw ,
-            mol aa ,
-            length 122 ,
-            seq-data
-              ncbieaa "MMRTDGTVTQPRLKQVALSAISEVNAELYEFRRRQQMLGYASLAEVPAEQLDGKS
-ERIQHYFNAVYCWARAMLNERYQDYDATASGVKRGEELAEASGDLWRDARWAISRVQDAPHCTVELI" } ,
-          annot {
-            {
-              data
-                ftable {
-                  {
-                    id
-                      local
-                        id 20 ,
-                    data
-                      prot {
-                        name {
-                          "hypothetical protein" } } ,
-                    location
-                      int {
-                        from 0 ,
-                        to 121 ,
-                        id
-                          local
-                            str "this_is_genome_3_4" } } } } } } } ,
-      annot {
-        {
-          data
-            ftable {
-              {
-                id
-                  local
-                    id 13 ,
-                data
-                  cdregion {
-                    frame one ,
-                    code {
-                      id 11 } } ,
-                product
-                  whole
-                    local
-                      str "this_is_genome_3_1" ,
-                location
-                  int {
-                    from 29 ,
-                    to 796 ,
-                    strand plus ,
-                    id
-                      local
-                        str "this_is_genome_3" } ,
-                qual {
-                  {
-                    qual "inference" ,
-                    val "ab initio prediction:Prodigal:002006" } ,
-                  {
-                    qual "inference" ,
-                    val "similar to AA sequence:UniProtKB:P0A873" } } ,
-                xref {
-                  {
-                    data
-                      gene {
-                        locus "trmD" ,
-                        locus-tag "AMHDIIJN_00007" } } } ,
-                dbxref {
-                  {
-                    db "COG" ,
-                    tag
-                      str "COG0336" } } } ,
-              {
-                id
-                  local
-                    id 14 ,
-                data
-                  cdregion {
-                    frame one ,
-                    code {
-                      id 11 } } ,
-                product
-                  whole
-                    local
-                      str "this_is_genome_3_2" ,
-                location
-                  int {
-                    from 861 ,
-                    to 1121 ,
-                    strand plus ,
-                    id
-                      local
-                        str "this_is_genome_3" } ,
-                qual {
-                  {
-                    qual "inference" ,
-                    val "ab initio prediction:Prodigal:002006" } } ,
-                xref {
-                  {
-                    data
-                      gene {
-                        locus-tag "AMHDIIJN_00008" } } } } ,
-              {
-                id
-                  local
-                    id 15 ,
-                data
-                  cdregion {
-                    frame one ,
-                    code {
-                      id 11 } } ,
-                product
-                  whole
-                    local
-                      str "this_is_genome_3_3" ,
-                location
-                  int {
-                    from 1169 ,
-                    to 1750 ,
-                    strand plus ,
-                    id
-                      local
-                        str "this_is_genome_3" } ,
-                qual {
-                  {
-                    qual "inference" ,
-                    val "ab initio prediction:Prodigal:002006" } } ,
-                xref {
-                  {
-                    data
-                      gene {
-                        locus-tag "AMHDIIJN_00009" } } } } ,
-              {
-                id
-                  local
-                    id 16 ,
-                data
-                  cdregion {
-                    frame one ,
-                    code {
-                      id 11 } } ,
-                product
-                  whole
-                    local
-                      str "this_is_genome_3_4" ,
-                location
-                  int {
-                    from 1894 ,
-                    to 2262 ,
-                    strand plus ,
-                    id
-                      local
-                        str "this_is_genome_3" } ,
-                qual {
-                  {
-                    qual "inference" ,
-                    val "ab initio prediction:Prodigal:002006" } } ,
-                xref {
-                  {
-                    data
-                      gene {
-                        locus-tag "AMHDIIJN_00010" } } } } } } } } ,
-    set {
-      class nuc-prot ,
-      descr {
-        source {
-          org {
-            taxname "Genus species" ,
-            orgname {
-              mod {
-                {
-                  subtype strain ,
-                  subname "strain" } } ,
-              gcode 11 } } } ,
-        comment "Annotated using prokka 1.14.5 from
- https://github.com/tseemann/prokka" ,
-        user {
-          type
-            str "NcbiCleanup" ,
-          data {
-            {
-              label
-                str "method" ,
-              data
-                str "SeriousSeqEntryCleanup" } ,
-            {
-              label
-                str "version" ,
-              data
-                int 8 } ,
-            {
-              label
-                str "month" ,
-              data
-                int 12 } ,
-            {
-              label
-                str "day" ,
-              data
-                int 9 } ,
-            {
-              label
-                str "year" ,
-              data
-                int 2019 } } } ,
-        create-date
-          std {
-            year 2019 ,
-            month 12 ,
-            day 9 } } ,
-      seq-set {
-        seq {
-          id {
-            local
-              str "this_is_genome_4" } ,
-          descr {
-            molinfo {
-              biomol genomic } } ,
-          inst {
-            repr raw ,
-            mol dna ,
-            length 2845 ,
-            seq-data
-              iupacna "ATGATTGACCCTATTTTTGCGTCCTGTACGCTAATTGCCGTCTTTGTTGTTTTAC
-TGGCCATGGGCGCGCCTATCGGGATCTGCATCGTTATCGCCTCTTTCAGCACCATGATGCTGGTACTGCCTTTCGATA
-TTTCGATGTTCGCCACCGCGCAAAAAATGTTCTCCAGCCTGGACAGTTTTGCCTTGCTGGCCGTGCCGTTCTTCGTTT
-TGTCCGGGGTGATCATGAATAGCGGGGGAATTGCCGCCCGACTGGTCAATTTTGCCAAACTGTTTACTGGCAAACTGC
-CCGGCTCGCTCTCTTACACCAACATCGTCGGCAATATGATGTTCGGTGCAATTTCCGGATCGGCGATTGCCGCCTCAA
-CCTCTATCGGCGGCGTGATGGTGCCGATGAGCGCGCGCGAAGGTTACGATCGCGGTTTTGCGGCCGCGGTGAATATCG
-CCTCCGCGCCGACGGGAATGTTAATTCCGCCCACCACGGCTTTTATCCTTTATGCGCTGGCAAGCGGGGGAACATCGA
-TTGCCGCTCTGTTCGCCGGCGGTCTGGTCGCGGGAGTGCTGTGGGGCGTTGGCTGTATGCTGGTCACGCTGGTGGTCG
-CTAAGCGTCGAAATTATCGGGTTTTCTTCACCGTCCAAAAAGGCATGGCGCTAAAAGTTGCCGTTGAGGCCATTCCCA
-GCCTGTTACTGATCGTGATTATTGTCGGCGGCATTGTGCAGGGGATTTTCACCGCCATTGAAGCCTCCGCGATTGCCG
-TGGTGTATACGTTATTGCTGACGATAGTGTTTTACCGCACGCTGAAAATTAAGGATTTGCCTTCGATTTTGCTCCAGA
-CAGTGGTAATGACCGGGGTCATCATGTTCCTGCTGGCAACCTCTTCGGCGATGTCCTTCTCGATGTCGATCACCAATA
-TTCCTGCGGCGCTGAGCGATATGATCCTCGGTATTTCCGCCAATAAACTGGTTATCCTGTTAGTCATTACCGTCTTTT
-TGTTGATTATCGGCGCATTTATGGATATCGGTCCGGCCATTCTGATTTTTACCCCGATTCTGCTGCCGATTATGACTA
-AACTGGGCGTCGATCCGGTGCATTTCGGCATTATCATGATCTATAACCTGGCGATAGGCACCATTACGCCGCCAGTTG
-GCAGTGGTTTATATGTCGGGGCGAGCGTCGGTAAGGTCAAAGTTGAGGACGTTATCAAACCGTTGATGCCTTTTTACG
-GCGCGATTATCGGCGTTCTGTTATTAATTACCTACATTCCGGAAATCACACTGTTTTTACCCCGTCTACTGGGCATCA
-TGTAAACGCTCATAGGCGGCGCGCGCGCTCTCAGGAATGAAGTTTGTTGCGCCAGAACAGGCACCGGAACAGGCGGAG
-GTCATCAAAAATACGCCGTTCTGGCCTGATGTGAACCTGTCGGAATTTCGCAGTGTGATGCGCACTGACGGCACGGTG
-ACGCAGCCGCGTTTAAAGCAGGTCGTGCTGACGGCGATCTCTGAGGTTAACGCTGAGCTGTACGACTTCCGCAACCGT
-CAGCAGATGCTGGGCTGGCGGACACTTGCTGAGGTTCCCGCAGAAATGCTGGACGGTAAAAGCGAGCGTATCCGGCAC
-TACCACAACGCTGTTTTTTGCTGGGCGCGCGCTGTGCTTAATGAGCGTTATCAGGACTATGACGCCACGGCGTCAGGC
-GTGAAGCGAGGGGAGGAGCTGGCGGAGGCCAGCGGCGATCTGTGGCGTGATGCCCGCTGGGCCATCAGCCGGGTGCAG
-GATGCACCGCACTGTACGGTGGAGCTTATCTGACGCTCATAGGCGCGCGCTCATAGCGCGATGGAAACAAATATTACC
-TGGCAACAATTGATAGATGAATATTTCTTCGCAAAACCTCTGCGCTCAGCATCTGAATGGAGTTACACCAAAGTCTTC
-AAATCATTTGTACATTATATGGGGCCGTTAAGCTGCCCTAATGATGTGACATATCACAAAGTGCTTGCCTGGCGCCGT
-TTTCTTTTAAAAGAGAAAAAGCTGTCCGGACGTACCTGGAATAACAAGGTGGCGCATATGCGGGCCATCTTTAACTAC
-GGAATACAGCGAGGGTTACTGCACTATGACGAAAATCCGTTTAACAATTCGGTAGTTAAACCGGACAAGAAGAGAAAG
-AAAACGCTCACTCAGGCACAGATTGAGTATGCCTATCAGATCATGGAGCAGTATGAAAATCAGGAGAATACAGGGCTG
-GGACTGAAATATTCCCGCTGCGCCTTATTTCCTGCATGGTTCTGGCTCACTGTCCTGGATACGCTCTATTACACAGGG
-ATACGTCAGAACCAGTTATTACATATTCGGCTGAATGATGTTGATTTGAGAGAAGGGCAGATTCGGCTGATTACGGAG
-GGGTGTAAAAATCACAAAGAACACTATGTGCCGGTGATCAGTTTTCTGCGTCCACGGCTGACCTGTTTAATGGAGAAA
-GCGCAGAGCGAAGGATTGAAAGGTAATGACCGCCTGTTCAATATTGCACTTTTTACCGGCAAAGATCCCGCCATTGGC
-GATGACATGGATTCTCCTCAGGTAAGAGCATTCTTCCGTCGTCTGTCCAAGGAGTGTCAGTTTGCGATCAGTCCTCAT
-CGTTTCAGACACACGCTGGCCACGGAGATGATGAAAATGCCGGAACAGAATCTGCATATGGCGCAAAGTGTGCTGGGT
-CATTCAAACATGAAATCCACGCTGGAGTATGTGGAGAATGATATTGCAGTGATGGGGAGGGCTCTGGAAGCGCAGTTT
-ATGCAGATTAAGGCAGCACATGCCCGAAGCATTTACAGTGGGTTGACAAAGAATAGATAA" } } ,
-        seq {
-          id {
-            local
-              str "this_is_genome_4_1" } ,
-          descr {
-            title "C4-dicarboxylate TRAP transporter large permease protein
- DctM [Genus species]" ,
-            molinfo {
-              biomol peptide ,
-              tech concept-trans } } ,
-          inst {
-            repr raw ,
-            mol aa ,
-            length 435 ,
-            seq-data
-              ncbieaa "MIDPIFASCTLIAVFVVLLAMGAPIGICIVIASFSTMMLVLPFDISMFATAQKMF
-SSLDSFALLAVPFFVLSGVIMNSGGIAARLVNFAKLFTGKLPGSLSYTNIVGNMMFGAISGSAIAASTSIGGVMVPMS
-AREGYDRGFAAAVNIASAPTGMLIPPTTAFILYALASGGTSIAALFAGGLVAGVLWGVGCMLVTLVVAKRRNYRVFFT
-VQKGMALKVAVEAIPSLLLIVIIVGGIVQGIFTAIEASAIAVVYTLLLTIVFYRTLKIKDLPSILLQTVVMTGVIMFL
-LATSSAMSFSMSITNIPAALSDMILGISANKLVILLVITVFLLIIGAFMDIGPAILIFTPILLPIMTKLGVDPVHFGI
-IMIYNLAIGTITPPVGSGLYVGASVGKVKVEDVIKPLMPFYGAIIGVLLLITYIPEITLFLPRLLGIM" } ,
-          annot {
-            {
-              data
-                ftable {
-                  {
-                    id
-                      local
-                        id 24 ,
-                    data
-                      prot {
-                        name {
-                          "C4-dicarboxylate TRAP transporter large permease
- protein DctM" } } ,
-                    location
-                      int {
-                        from 0 ,
-                        to 434 ,
-                        id
-                          local
-                            str "this_is_genome_4_1" } } } } } } ,
-        seq {
-          id {
-            local
-              str "this_is_genome_4_2" } ,
-          descr {
-            title "hypothetical protein AMHDIIJN_00012 [Genus species]" ,
-            molinfo {
-              biomol peptide ,
-              tech concept-trans } } ,
-          inst {
-            repr raw ,
-            mol aa ,
-            length 154 ,
-            seq-data
-              ncbieaa "MKFVAPEQAPEQAEVIKNTPFWPDVNLSEFRSVMRTDGTVTQPRLKQVVLTAISE
-VNAELYDFRNRQQMLGWRTLAEVPAEMLDGKSERIRHYHNAVFCWARAVLNERYQDYDATASGVKRGEELAEASGDLW
-RDARWAISRVQDAPHCTVELI" } ,
-          annot {
-            {
-              data
-                ftable {
-                  {
-                    id
-                      local
-                        id 25 ,
-                    data
-                      prot {
-                        name {
-                          "hypothetical protein" } } ,
-                    location
-                      int {
-                        from 0 ,
-                        to 153 ,
-                        id
-                          local
-                            str "this_is_genome_4_2" } } } } } } ,
-        seq {
-          id {
-            local
-              str "this_is_genome_4_3" } ,
-          descr {
-            title "Tyrosine recombinase XerC [Genus species]" ,
-            molinfo {
-              biomol peptide ,
-              tech concept-trans } } ,
-          inst {
-            repr raw ,
-            mol aa ,
-            length 337 ,
-            seq-data
-              ncbieaa "METNITWQQLIDEYFFAKPLRSASEWSYTKVFKSFVHYMGPLSCPNDVTYHKVLA
-WRRFLLKEKKLSGRTWNNKVAHMRAIFNYGIQRGLLHYDENPFNNSVVKPDKKRKKTLTQAQIEYAYQIMEQYENQEN
-TGLGLKYSRCALFPAWFWLTVLDTLYYTGIRQNQLLHIRLNDVDLREGQIRLITEGCKNHKEHYVPVISFLRPRLTCL
-MEKAQSEGLKGNDRLFNIALFTGKDPAIGDDMDSPQVRAFFRRLSKECQFAISPHRFRHTLATEMMKMPEQNLHMAQS
-VLGHSNMKSTLEYVENDIAVMGRALEAQFMQIKAAHARSIYSGLTKNR" } ,
-          annot {
-            {
-              data
-                ftable {
-                  {
-                    id
-                      local
-                        id 26 ,
-                    data
-                      prot {
-                        name {
-                          "Tyrosine recombinase XerC" } } ,
-                    location
-                      int {
-                        from 0 ,
-                        to 336 ,
-                        id
-                          local
-                            str "this_is_genome_4_3" } } } } } } } ,
-      annot {
-        {
-          data
-            ftable {
-              {
-                id
-                  local
-                    id 21 ,
-                data
-                  cdregion {
-                    frame one ,
-                    code {
-                      id 11 } } ,
-                product
-                  whole
-                    local
-                      str "this_is_genome_4_1" ,
-                location
-                  int {
-                    from 0 ,
-                    to 1307 ,
-                    strand plus ,
-                    id
-                      local
-                        str "this_is_genome_4" } ,
-                qual {
-                  {
-                    qual "inference" ,
-                    val "ab initio prediction:Prodigal:002006" } ,
-                  {
-                    qual "inference" ,
-                    val "similar to AA sequence:UniProtKB:O07838" } } ,
-                xref {
-                  {
-                    data
-                      gene {
-                        locus "dctM" ,
-                        locus-tag "AMHDIIJN_00011" } } } ,
-                dbxref {
-                  {
-                    db "COG" ,
-                    tag
-                      str "COG1593" } } } ,
-              {
-                id
-                  local
-                    id 22 ,
-                data
-                  cdregion {
-                    frame one ,
-                    code {
-                      id 11 } } ,
-                product
-                  whole
-                    local
-                      str "this_is_genome_4_2" ,
-                location
-                  int {
-                    from 1339 ,
-                    to 1803 ,
-                    strand plus ,
-                    id
-                      local
-                        str "this_is_genome_4" } ,
-                qual {
-                  {
-                    qual "inference" ,
-                    val "ab initio prediction:Prodigal:002006" } } ,
-                xref {
-                  {
-                    data
-                      gene {
-                        locus-tag "AMHDIIJN_00012" } } } } ,
-              {
-                id
-                  local
-                    id 23 ,
-                data
-                  cdregion {
-                    frame one ,
-                    code {
-                      id 11 } } ,
-                product
-                  whole
-                    local
-                      str "this_is_genome_4_3" ,
-                location
-                  int {
-                    from 1831 ,
-                    to 2844 ,
-                    strand plus ,
-                    id
-                      local
-                        str "this_is_genome_4" } ,
-                qual {
-                  {
-                    qual "inference" ,
-                    val "ab initio prediction:Prodigal:002006" } ,
-                  {
-                    qual "inference" ,
-                    val "protein motif:HAMAP:MF_01808" } } ,
-                xref {
-                  {
-                    data
-                      gene {
-                        locus "xerC" ,
-                        locus-tag "AMHDIIJN_00013" } } } } } } } } ,
-    seq {
-      id {
-        local
-          str "genome2_small_5" } ,
-      descr {
-        source {
-          org {
-            taxname "Genus species" ,
-            orgname {
-              mod {
-                {
-                  subtype strain ,
-                  subname "strain" } } ,
-              gcode 11 } } } ,
-        molinfo {
-          biomol genomic } ,
-        comment "Annotated using prokka 1.14.5 from
- https://github.com/tseemann/prokka" ,
-        user {
-          type
-            str "NcbiCleanup" ,
-          data {
-            {
-              label
-                str "method" ,
-              data
-                str "SeriousSeqEntryCleanup" } ,
-            {
-              label
-                str "version" ,
-              data
-                int 8 } ,
-            {
-              label
-                str "month" ,
-              data
-                int 12 } ,
-            {
-              label
-                str "day" ,
-              data
-                int 9 } ,
-            {
-              label
-                str "year" ,
-              data
-                int 2019 } } } ,
-        create-date
-          std {
-            year 2019 ,
-            month 12 ,
-            day 9 } } ,
-      inst {
-        repr raw ,
-        mol dna ,
-        length 6 ,
-        seq-data
-          iupacna "GATACA" } } } }
diff --git a/Examples/2-res-Annotate-prokka/tmp_files/genome2.fst_prokka-split5N.fna-prokkaRes/GEN2.1219.00001.tbl b/Examples/2-res-Annotate-prokka/tmp_files/genome2.fst_prokka-split5N.fna-prokkaRes/GEN2.1219.00001.tbl
deleted file mode 100644
index 659f93f94f9f78b9060a12d89b654aafba9790ab..0000000000000000000000000000000000000000
--- a/Examples/2-res-Annotate-prokka/tmp_files/genome2.fst_prokka-split5N.fna-prokkaRes/GEN2.1219.00001.tbl
+++ /dev/null
@@ -1,82 +0,0 @@
->Feature this_is_genome_1
-1	774	CDS
-			db_xref	COG:COG4598
-			gene	hisP
-			inference	ab initio prediction:Prodigal:002006
-			inference	similar to AA sequence:UniProtKB:P02915
-			locus_tag	AMHDIIJN_00001
-			product	Histidine transport ATP-binding protein HisP
-857	2260	CDS
-			inference	ab initio prediction:Prodigal:002006
-			locus_tag	AMHDIIJN_00002
-			product	hypothetical protein
->Feature this_is_genome_2
-28	252	CDS
-			gene	pspB
-			inference	ab initio prediction:Prodigal:002006
-			inference	similar to AA sequence:UniProtKB:P0AFM9
-			locus_tag	AMHDIIJN_00003
-			product	Phage shock protein B
-301	681	CDS
-			EC_number	5.3.3.10
-			gene	hpcD
-			inference	ab initio prediction:Prodigal:002006
-			inference	similar to AA sequence:UniProtKB:Q05354
-			locus_tag	AMHDIIJN_00004
-			product	5-carboxymethyl-2-hydroxymuconate Delta-isomerase
-764	1597	CDS
-			EC_number	3.5.1.28
-			db_xref	COG:COG3023
-			gene	amiD
-			inference	ab initio prediction:Prodigal:002006
-			inference	similar to AA sequence:UniProtKB:P75820
-			locus_tag	AMHDIIJN_00005
-			product	N-acetylmuramoyl-L-alanine amidase AmiD
-1628	3295	CDS
-			EC_number	6.1.1.18
-			db_xref	COG:COG0008
-			gene	glnS
-			inference	ab initio prediction:Prodigal:002006
-			inference	similar to AA sequence:UniProtKB:P00962
-			locus_tag	AMHDIIJN_00006
-			product	Glutamine--tRNA ligase
->Feature this_is_genome_3
-30	797	CDS
-			EC_number	2.1.1.228
-			db_xref	COG:COG0336
-			gene	trmD
-			inference	ab initio prediction:Prodigal:002006
-			inference	similar to AA sequence:UniProtKB:P0A873
-			locus_tag	AMHDIIJN_00007
-			product	tRNA (guanine-N(1)-)-methyltransferase
-862	1122	CDS
-			inference	ab initio prediction:Prodigal:002006
-			locus_tag	AMHDIIJN_00008
-			product	hypothetical protein
-1170	1751	CDS
-			inference	ab initio prediction:Prodigal:002006
-			locus_tag	AMHDIIJN_00009
-			product	hypothetical protein
-1895	2263	CDS
-			inference	ab initio prediction:Prodigal:002006
-			locus_tag	AMHDIIJN_00010
-			product	hypothetical protein
->Feature this_is_genome_4
-1	1308	CDS
-			db_xref	COG:COG1593
-			gene	dctM
-			inference	ab initio prediction:Prodigal:002006
-			inference	similar to AA sequence:UniProtKB:O07838
-			locus_tag	AMHDIIJN_00011
-			product	C4-dicarboxylate TRAP transporter large permease protein DctM
-1340	1804	CDS
-			inference	ab initio prediction:Prodigal:002006
-			locus_tag	AMHDIIJN_00012
-			product	hypothetical protein
-1832	2845	CDS
-			gene	xerC
-			inference	ab initio prediction:Prodigal:002006
-			inference	protein motif:HAMAP:MF_01808
-			locus_tag	AMHDIIJN_00013
-			product	Tyrosine recombinase XerC
->Feature genome2_small_5
diff --git a/Examples/2-res-Annotate-prokka/tmp_files/genome2.fst_prokka-split5N.fna-prokkaRes/GEN2.1219.00001.tsv b/Examples/2-res-Annotate-prokka/tmp_files/genome2.fst_prokka-split5N.fna-prokkaRes/GEN2.1219.00001.tsv
deleted file mode 100644
index 0a8b13f4be56145de4e8a6daab023c9805259274..0000000000000000000000000000000000000000
--- a/Examples/2-res-Annotate-prokka/tmp_files/genome2.fst_prokka-split5N.fna-prokkaRes/GEN2.1219.00001.tsv
+++ /dev/null
@@ -1,14 +0,0 @@
-locus_tag	ftype	length_bp	gene	EC_number	COG	product
-AMHDIIJN_00001	CDS	774	hisP		COG4598	Histidine transport ATP-binding protein HisP
-AMHDIIJN_00002	CDS	1404				hypothetical protein
-AMHDIIJN_00003	CDS	225	pspB			Phage shock protein B
-AMHDIIJN_00004	CDS	381	hpcD	5.3.3.10		5-carboxymethyl-2-hydroxymuconate Delta-isomerase
-AMHDIIJN_00005	CDS	834	amiD	3.5.1.28	COG3023	N-acetylmuramoyl-L-alanine amidase AmiD
-AMHDIIJN_00006	CDS	1668	glnS	6.1.1.18	COG0008	Glutamine--tRNA ligase
-AMHDIIJN_00007	CDS	768	trmD	2.1.1.228	COG0336	tRNA (guanine-N(1)-)-methyltransferase
-AMHDIIJN_00008	CDS	261				hypothetical protein
-AMHDIIJN_00009	CDS	582				hypothetical protein
-AMHDIIJN_00010	CDS	369				hypothetical protein
-AMHDIIJN_00011	CDS	1308	dctM		COG1593	C4-dicarboxylate TRAP transporter large permease protein DctM
-AMHDIIJN_00012	CDS	465				hypothetical protein
-AMHDIIJN_00013	CDS	1014	xerC			Tyrosine recombinase XerC
diff --git a/Examples/2-res-Annotate-prokka/tmp_files/genome2.fst_prokka-split5N.fna-prokkaRes/GEN2.1219.00001.txt b/Examples/2-res-Annotate-prokka/tmp_files/genome2.fst_prokka-split5N.fna-prokkaRes/GEN2.1219.00001.txt
deleted file mode 100644
index 6c0947164ab122fdbf2e0bd8678ddb145d70809b..0000000000000000000000000000000000000000
--- a/Examples/2-res-Annotate-prokka/tmp_files/genome2.fst_prokka-split5N.fna-prokkaRes/GEN2.1219.00001.txt
+++ /dev/null
@@ -1,4 +0,0 @@
-organism: Genus species strain 
-contigs: 5
-bases: 10717
-CDS: 13
diff --git a/Examples/2-res-Annotate-prokka/tmp_files/genome3-chromo.fst-all.fna b/Examples/2-res-Annotate-prokka/tmp_files/genome3-chromo.fst-all.fna
deleted file mode 100644
index 35d4e193748f3c3fa8abcaa61bc65ae4cae8054f..0000000000000000000000000000000000000000
--- a/Examples/2-res-Annotate-prokka/tmp_files/genome3-chromo.fst-all.fna
+++ /dev/null
@@ -1,25 +0,0 @@
->header_genome3_chromo
-ATGAGAGCGCTACTGTGGCTGGTGGGTCTTGCGTTGCTGTTAACAGGCTGCGCGAGCGAAAAAGGAATTATCGATGAAGAGGGATATCAGCTTGATACCCGACATCGGGCGCAGGCGGCCTATCCGCGCATTAAAGTCCTGGTGATTCACTATACGGCGGAAAACTTTGACGTTTCGCTGGCGACGTTAACGGGCCGCAACGTCAGTTCGCATTACCTGATTCCCGCAACCCCGCCATTATATGGCGGTAAACCGCGCATCTGGCAACTGGTGCCGGAACAGGATCAGGCCTGGCATGCGGGCGTCAGTTTCTGGCGAGGCGCCACGCGTCTCAATGATACGTCTATTGGCATTGAGCTGGAAAATCGCGGCTGGCGAATGTCCGGCGGGGTGAAATCTTTCGCGCCGTTTGAATCCGCGCAAATTCAGGCATTGATTCCGTTAGCGAAGGACATTATCGCGCGCTATGACATCAAACCGCAGAATGTGGTGGCCCATGCGGATATCGCGCCGCAGCGTAAAGACGATCCCGGCCCGCGCTTCCCGTGGCGCGAGCTGGCGGCACAGGGGATTGGCGCCTGGCCTGACGCCCAGCGTGTGGCGTTTTATCTGGCTGGACGCGCGCCGTATACGCCAGTCGATACCGCAACGGTGCTTGCGTTACTCTCGCGCTATGGCTATGAAGTCAAAGCCGATATGACGGCGCGCGAGCAACAGCGGGTGATTATGGCGTTCCAGATGCACTTCCGTCCGGCGCAATGGAACGGTATCGCAGATGCCGAAACGCAGGCGATTGCCGAAGCATTACTGGAGAAGTACGGCCAGGATTAA
-CGAGTCCGGGAGCGGCGAGATTCCGGGCAGAGGAGGCGGCTATAGCGG
-ATGAGAGCGCTACTGTGGCTGGTGGGTCTTGCGTTGCTGTTAACAGGCTGCGCGAGCGAAAAAGGAATTATCGATGAAGAGGGATATCAGCTTGATACCCGACATCGGGCGCAGGCGGCCTATCCGCGCATTAAAGTCCTGGTGATTCACTATACGGCGGAAAACTTTGACGTTTCGCTGGCGACGTTAACGGGCCGCAACGTCAGTTCGCATTACCTGATTCCCGCAACCCCGCCATTATATGGCGGTAAACCGCGCATCTGGCAACTGGTGCCGGAACAGGATCAGGCCTGGCATGCGGGCGTCAGTTTCTGGCGAGGCGCCACGCGTCTCAATGATACGTCTATTGGCATTGAGCTGGAAAATCGCGGCTGGCGAATGTCCGGCGGGGTGAAATCTTTCGCGCCGTTTGAATCCGCGCAAATTCAGGCATTGATTCCGTTAGCGAAGGACATTATCGCGCGCTATGACATCAAACCGCAGAATGTGGTGGCCCATGCGGATATCGCGCCGCAGCGTAAAGACGATCCCGGCCCGCGCTTCCCGTGGCGCGAGCTGGCGGCACAGGGGATTGGCGCCTGGCCTGACGCCCAGCGTGTGGCGTTTTATCTGGCTGGACGCGCGCCGTATACGCCAGTCGATACCGCAACGGTGCTTGCGTTACTCTCGCGCTATGGCTATGAAGTCAAAGCCGATATGACGGCGCGCGAGCAACAGCGGGTGATTATGGCGTTCCAGATGCACTTCCGTCCGGCGCAATGGAACGGTATCGCAGATGCCGAAACGCAGGCGATTGCCGAAGCATTACTGGAGAAGTACGGCCAGGATTAA
-CAGGGCGCGGTATCGCGAGGACTCTCTCTTCGAGGAC
-ATGCCGCACTTTATTGCTGAATGTACTGAAAATATTCGCGAGCAGGCTGATTTACCCGGCCTGTTCAGCAAGGTAAACGAGGCGCTGGCCGCCAGCGGGATTTTCCCCATCGGCGGTATCCGCAGTCGCGCCCACTGGCTGGATACCTGGCAGATGGCTGACGGTAAGCATGATTACGCGTTTGTGCATATGACGCTGAAAATCGGCGCCGGGCGCAGCCTGGAGAGCCGTCAGGAAGTCGGCGAAATGCTGTTCGGGCTGATTAAAGCCCACTTCGCCGACCTGATGGAGAACCGCTATCTGGCGCTGTCGTTTGAGATTGCCGAGTTACATCCAACGCTCAATTACAAACAAAACAACGTACACGCGTTATTTAAATAG
-CCCGAGTATTAGCGCGCGGCGGCGCTATAGGCGCGCTATAGGC
-ATGAGCGCGCTATTTCTGGCCATCCCGTTAACCATTTTTGTGTTGTTTGTGTTACCGATTTGGCTGTGGCTGCATTACAGCAACCGCGCCGGTCGGGGAGAACTGTCGCAAAGCGAGCAGCAACGCTTACTGCAACTCACAGACGACGCGCAACGTATGCGCGAGCGCATTCAGGCGCTGGAAGACATTCTTGATGCAGAGCATCCGAACTGGAGAGAGCGCTAA
-CGAGAGTCTCGGAGGAGCGGCGCTCTGg
-ATGCCCGCGACTAAATTCTCCCGACGTACCCTCCTGACGGCAGGTTCTGCGCTTGCTGTTCTTCCTTTCCTGCGCGCCTTGCCGGTACAGGCGCGTGAACCTCGCGAGACCGTCGATATTAAGGATTATCCGGCGGATGACGGTATCGCCTCGTTCAAACAGGCCTTCGCCGACGGACAGACCGTGGTCGTACCGCCAGGATGGGTGTGTGAAAATATCAATGCGGCGATAACGATTCCGGCGGGAAAAACGCTGCGGGTACAGGGCGCGGTGCGTGGGAATGGCCGGGGACGGTTTATTTTGCAGGACGGGTGTCAGGTGGTGGGGGAGCAGGGCGGCAGTCTGCACAATGTGACGCTGGATGTTCGCGGGTCGGACTGTGTGATTAAAGGCGTGGCGATGAGCGGCTTTGGCCCCGTCGCGCAAATTTTCATCGGTGGTAAGGAACCGCAGGTGATGCGTAATCTCATTATCGATGACATCACCGTTACCCACGCCAACTACGCCATTCTCCGCCAGGGATTTCATAACCAAATGGACGGCGCGAGGATTACGCATAGCCGCTTTAGCGATTTACAGGGGGACGCCATTGAGTGGAATGTCGCGATTCACGACCGCGATATCCTGATTTCCGATCATGTCATCGAACGCATTGATTGTACCAATGGCAAAATCAACTGGGGGATCGGCATCGGGCTGGCGGGTAGCACCTATGACAACAGTTATCCTGAAGACCAGGCAGTAAAAAACTTTGTGGTGGCCAATATTACCGGATCTGATTGCCGACAGCTTGTGCACGTAGAAAATGGCAAACATTTCGTCATTCGCAATGTCAAAGCCAAAAACATCACGCCCGATTTCAGTAAAAATGCGGGTATTGATAACGCAACGATCGCAATTTATGGCTGTGATAATTTCGTCATTGATAATATTGATATGACGAATAGTGCCGGGATGCTCATCGGCTATGGCGTCGTTAAAGGAAAATACCTGTCAATTCCGCAAAACTTTAAATTAAACGCTATTCGGTTGGATAATCGCCAGGTTGCTTATAAATTACGCGGCATTCAAATTTCCTCCGGCAACACCCCCTCTTTTGTCGCCATCACCAATGTACGGATGACGCGTGCTACGCTGGAACTGCATAATCAACCGCAGCACCTCTTCCTGCGTAATATCAACGTGATGCAAACTTCAGCGATTGGCCCGGCGTTAAAAATGCATTTCGATTTGCGTAAAGATGTCCGTGGTCAATTTATGGCCCGCCAGGACACGCTGCTTTCCCTCGCTAATGTTCATGCCATCAATGAAAACGGGCAGAGTTCCGTGGATATCGACAGGATTAATCACCAAACCGTGAATGTCGAAGCAGTGAATTTTTCGCTGCCGAAGCGGGGAGGGTAA
-CGCGTCTGCGCGCGCGGAGAGAGGCTCTCAGGAC
-ATGTCAGAAAATAAATTACACGTTATCGATTTGCACAAACGCTACGGCGGTCATGAAGTGCTGAAAGGGGTATCGCTGCAGGCCCGCGCCGGAGATGTGATTAGCATCATCGGCTCGTCCGGCTCCGGTAAAAGCACTTTTTTGCGCTGTATTAACTTCCTCGAAAAACCGAGCGAAGACGCGATTATCGTGAACGGTCAGAACATTAATCTGGTGCGCGACAAAGACGGGCAGCTCAAAGTGGCGGATAAAAATCAGCTACGCTTGTTGCGTACCCGCCTGACGATGGTGTTTCAGCACTTTAACCTCTGGAGCCACATGACGGTGCTGGAAAATGTGATGGAAGCGCCGATTCAGGTACTGGGATTAAGCAAGCACGACGCGCGCGAGCGGGCGTTGAAATATCTGGCGAAGGTGGGGATTGATGAGCGCGCTCAGGGCAAATATCCCGTTCATCTCTCCGGTGGCCAACAGCAGCGCGTTTCTATTGCGCGCGCGCTGGCGATGGAACCTGACGTTTTACTGTTCGATGAACCCACTTCGGCGCTCGATCCTGAACTGGTCGGCGAAGTGTTGCGCATCATGCAACAACTGGCGGAAGAAGGCAAAACGATGGTGGTGGTCACGCATGAAATGGGCTTCGTTCGCCATGTCTCTTCGCACGTTATTTTTCTGCATCAGGGGAAAATTGAAGAAGAGGGCGATCCGGAGCAGGTGTTCGGCAATCCGCAAAGCCCGCGTTTACAGCAATTCCTGAAAGGCTCGCTGAAATAA
-CCGGATGCGCGCGATATATCGGCGATGC
-GTGTTTATTGGCATCGTTAGCCTGTTTCCTGAAATGTTCCGCGCAATTACCGATTACGGGGTAACTGGCCGGGCAGTAAAAAATGGCCTGCTGAACATCCAAAGCTGGAGTCCTCGCGACTTCACGCATGACCGGCACCGTACCGTGGACGATCGTCCTTACGGCGGCGGACCAGGGATGTTAATGATGGTGCAACCCTTGCGGGACGCCATTCACGCAGCAAAAGCCGCGGCAGGTGAAGGCGCTAAAGTGATTTATCTGTCGCCTCAGGGACGCAAGCTTGATCAAGCGGGCGTTAGCGAGCTGGCCACGAATCAGAAGCTTATTCTGGTGTGTGGTCGCTACGAAGGCGTAGATGAGCGCGTAATTCAGACCGAAATTGACGAAGAATGGTCAATTGGCGATTACGTTCTCAGCGGTGGCGAACTACCGGCAATGACGCTGATTGACTCCGTCGCCCGGTTTATACCGGGAGTTCTGGGGCATGAAGCATCAGCAATCGAAGATTCGTTTGCTGATGGGTTGCTGGATTGTCCGCACTATACGCGCCCTGAAGTGTTAGAGGGGATGGAAGTACCGCCAGTATTGCTGTCGGGAAACCATGCTGAGATACGTCGCTGGCGTTTGAAACAGTCGCTGGGCCGAACCTGGCTTAGAAGACCTGAACTTCTGGAAAACCTGGCTCTGACTGAAGAGCAAGCAAGGTTGCTGGCGGAGTTCAAAACAGAACACGCACAACAGCAGCATAAACATGATGGGATGGCATAG
-CCGGCTCTGCGAGAGAGGAGCGCTCGC
-ATGAATAATCATTTTGGGAAAGGGTTAATGGCCGGGTTGCACGCGCCATATGCATATAGCGCGCATCATGCGGTGAATTTCTGTTCTGAGTATAAACGTGGCTTTGTATTGGGTTTTACACACCGTATGTTCGAAAAGACCGGCGATCGTCAACTTAGCGCGTGGGAGGCTGGAATTCTGACGCGTCGCTATGGTCTGGATAAAGAAATGGTGATGGATTTCTTTAAAGAGAATCATTCCGGGATGGCGGTTCGCTTCTTTATGGCCGGTTATCGACTCGAAGGTTGA
-
->genome3_plasmid
-ATGTCTACGCTTCTCTATTTGCACGGATTCAACAGTTCCCCTCGCTCGGCAAAAGCGTGCCAGCTAAAAAACTGGCTGGCGGAGCGTCATCCGCATGTTGAGATGATCGTCCCTCAACTACCGCCGTATCCTGCCGATGCGGCGGAGTTGCTGGAGTCTCTCGTGCTTGAGCATGGCGGTGCGCCATTAGGGCTGGTAGGATCGTCGCTGGGTGGTTATTACGCCACCTGGCTGTCGCAATGTTTTATGCTGCCGGCTGTGGTGGTGAATCCCGCCGTGCGGCCCTTTGAATTACTGACCGACTATCTCGGTCAGAACGAGAACCCCTACACCGGGCAGCAATATGTGCTAGAGTCTCGCCATATTTATGATCTTAAAGTCATGCAGATTGACCCGCTGGAAGCGCCGGACCTGATCTGGCTACTGCAACAGACGGGCGATGAAGTGCTGGATTACCGCCAGGCGGTGGCATATTACGCCTCCTGCCGTCAGACAGTGACCGAGGGTGGTAATCACGCATTCACGGGCTTCGAAGATTATTTCAACCAGATTGTCGATTTTCTTGGACTGCACAGTTGCTGA
-CGCGTAGCGGCCGGAATCTTCTCGGAGAGGCGCTTCTCTCTCGGAG
-ATGATTGACCCTATTTTTGCGTCCTGTACGCTAATTGCCGTCTTTGTTGTTTTACTGGCCATGGGCGCGCCTATCGGGATCTGCATCGTTATCGCCTCTTTCAGCACCATGATGCTGGTACTGCCTTTCGATATTTCGATGTTCGCCACCGCGCAAAAAATGTTCTCCAGCCTGGACAGTTTTGCCTTGCTGGCCGTGCCGTTCTTCGTTTTGTCCGGGGTGATCATGAATAGCGGGGGAATTGCCGCCCGGCTGATCAATTTTGCCAAACTGTTTACTGGCAAACTGCCCGGTTCGCTCTCTTATACCAACATCGTCGGCAATATGATGTTCGGTGCAATTTCCGGATCGGCAATTGCCGCCTCAACCTCCATCGGCGGCGTGATGGTGCCGATGAGCGCGCGCGAAGGTTACGATCGCGGCTTTGCGGCCGCGGTGAATATCGCCTCCGCGCCGACGGGAATGTTAATTCCGCCCACCACGGCTTTTATCCTTTATGCGCTGGCAAGCGGGGGAACATCGATTGCCGCTCTGTTCGCCGGCGGTCTGGTCGCGGGAGTGCTGTGGGGCGTTGGCTGTATGCTGGTCACGCTGGTAGTCGCTAAGCGTCGAAATTATCGGGTTTTCTTCACCGTCCAAAAAGGCATGGCGCTAAAAGTTGCCGTTGAGGCCATTCCCAGCCTGTTACTGATCGTGATTATCGTCGGCGGCATTGTGCAGGGGATTTTCACCGCCATTGAAGCCTCCGCGATTGCCGTGGTGTATACGTTATTGCTGACGATGGTGTTTTACCGCACGCTGAAAATTAAGGATTTGCCTTCGATTTTGCTCCAGACAGTGGTAATGACCGGGGTCATCATGTTCCTGCTGGCAACCTCTTCGGCGATGTCCTTCTCAATGTCGATCACCAATATTCCTGCGGCGCTGAGCGATATGATCCTCGGTATTTCCGCCAATAAACTGGTTATCCTGTTAGTCATTACCGTCTTTTTGTTGATTATCGGCGCATTTATGGATATCGGTCCGGCCATTCTGATTTTTACCCCGATTCTGCTGCCGATCATGGCTAAACTGGGCGTCGATCCGGTGCATTTGGGCATTATCATGATCTATAACCTGGCGATTGGCACCATTACGCCGCCAGTTGGCAGTGGTTTATATGTCGGGGCGAGCGTCGGTAAGGTCAAAGTTGAGGAAGTGATTAAACCGTTGCTGCCTTTTTACGGCGCGATTATCGGCGTTCTGTTATTAATTACCTACATTCCGGAAATCATACTGTTCTTACCCCGTCTACTGGGCATCATGTAA
-ACCCGATGGCGCGCAGAGGCGCGAGTTCTGGANNNNNNCACAGGGCTTAGAGGCGCTATGGCA
-ATGATAATTAATGGGAAATTAATTAAAGCAAAAGACTTAGCTAAGGCTGCAGGTGTATCTCGTTCAACAGTGATTAAATATTACGGCATTAGCCGTGAGAATTACGAAAGGGTAGCAACTGAAAGAAGGAAGCTTGCTTTTGAACTAAGAGCATCAGGTTTAAAATGGAAAGAAGTTGCTGAAAAAATGAACACGACAAAATATAGCGCAATTGCATATTATAGACGATATTTAGCATTAGAGAAAAACAAATAA
-CAGGCGCTAAGGCGGCGATCCTAGCGCGCGATCGCGCATGCG
-ATGGTCGAACTGCAACATCAACGGCTGATGGTGCTTGCCGAACAGCTCCAGCTGGACAGTCTTATCGGCGCAGCGCCGGCGCTGTCGCAACAGGCGGTGGATCAGGAATGGAGCTACATGGACTTCCTGGAGCACCTGTTACATGAGGAGAAACTGGCCCGGCATCAGCGTAAACAGGCGATGTACACGCGGATGGCAGCCTTCCCGGCGGTAAAGACGTTCGAGGAGTACGACTTCACCTTCGCCACCGGCGCTCCTCAGAAGCAAATCCAGTCGCTGCGATCCCTGAGCTTCATAGAGCGTAACGAAAACATCGTGTTGCTGGGGCCATCGGGCGTGGGAAAAACGCATCTGGCGATAGCCATGGGCTACGAAGCAGTACGGGCGGGCATCAAGGTTCGCTTCACAACAGCAGCGGACCTGCTGCTACAGCTGTCCACTTCACAGCGTCAGGGCCGTTACAAAACGACTCTCAATCGTGGTGTCATGGCCCCGAAGCTGCTTATCATCGATGAAATAGGTTATCTGCCGTTCAGTCAGGAGGAAGCCAAGCTGTTCTTCCAGGTCATCGCCAAACGTTACGAGAAGAGCGCGATGATCCTGACCTCCAACCTGCCGTTCGGGCAGTGGGATCAGACGTTCGCCGGTGATGCAGCGCTGACATCGGCGATGCTGGACCGGATCTTACATCACTCACACGTCGTGCAAATAAAAGGGGAAAGCTATCGACTGAAGCAGAAACGAAAGGCCGGGGTTATAGCTGAAGCTAATCCTGAGTAA
\ No newline at end of file
diff --git a/Examples/2-res-Annotate-prokka/tmp_files/genome3-chromo.fst-all.fna_prokka-split5N.fna b/Examples/2-res-Annotate-prokka/tmp_files/genome3-chromo.fst-all.fna_prokka-split5N.fna
deleted file mode 100644
index 4ac241054ac16abe79be2b7ad970cc22310cad1c..0000000000000000000000000000000000000000
--- a/Examples/2-res-Annotate-prokka/tmp_files/genome3-chromo.fst-all.fna_prokka-split5N.fna
+++ /dev/null
@@ -1,6 +0,0 @@
->header_genome3_1
-ATGAGAGCGCTACTGTGGCTGGTGGGTCTTGCGTTGCTGTTAACAGGCTGCGCGAGCGAAAAAGGAATTATCGATGAAGAGGGATATCAGCTTGATACCCGACATCGGGCGCAGGCGGCCTATCCGCGCATTAAAGTCCTGGTGATTCACTATACGGCGGAAAACTTTGACGTTTCGCTGGCGACGTTAACGGGCCGCAACGTCAGTTCGCATTACCTGATTCCCGCAACCCCGCCATTATATGGCGGTAAACCGCGCATCTGGCAACTGGTGCCGGAACAGGATCAGGCCTGGCATGCGGGCGTCAGTTTCTGGCGAGGCGCCACGCGTCTCAATGATACGTCTATTGGCATTGAGCTGGAAAATCGCGGCTGGCGAATGTCCGGCGGGGTGAAATCTTTCGCGCCGTTTGAATCCGCGCAAATTCAGGCATTGATTCCGTTAGCGAAGGACATTATCGCGCGCTATGACATCAAACCGCAGAATGTGGTGGCCCATGCGGATATCGCGCCGCAGCGTAAAGACGATCCCGGCCCGCGCTTCCCGTGGCGCGAGCTGGCGGCACAGGGGATTGGCGCCTGGCCTGACGCCCAGCGTGTGGCGTTTTATCTGGCTGGACGCGCGCCGTATACGCCAGTCGATACCGCAACGGTGCTTGCGTTACTCTCGCGCTATGGCTATGAAGTCAAAGCCGATATGACGGCGCGCGAGCAACAGCGGGTGATTATGGCGTTCCAGATGCACTTCCGTCCGGCGCAATGGAACGGTATCGCAGATGCCGAAACGCAGGCGATTGCCGAAGCATTACTGGAGAAGTACGGCCAGGATTAACGAGTCCGGGAGCGGCGAGATTCCGGGCAGAGGAGGCGGCTATAGCGGATGAGAGCGCTACTGTGGCTGGTGGGTCTTGCGTTGCTGTTAACAGGCTGCGCGAGCGAAAAAGGAATTATCGATGAAGAGGGATATCAGCTTGATACCCGACATCGGGCGCAGGCGGCCTATCCGCGCATTAAAGTCCTGGTGATTCACTATACGGCGGAAAACTTTGACGTTTCGCTGGCGACGTTAACGGGCCGCAACGTCAGTTCGCATTACCTGATTCCCGCAACCCCGCCATTATATGGCGGTAAACCGCGCATCTGGCAACTGGTGCCGGAACAGGATCAGGCCTGGCATGCGGGCGTCAGTTTCTGGCGAGGCGCCACGCGTCTCAATGATACGTCTATTGGCATTGAGCTGGAAAATCGCGGCTGGCGAATGTCCGGCGGGGTGAAATCTTTCGCGCCGTTTGAATCCGCGCAAATTCAGGCATTGATTCCGTTAGCGAAGGACATTATCGCGCGCTATGACATCAAACCGCAGAATGTGGTGGCCCATGCGGATATCGCGCCGCAGCGTAAAGACGATCCCGGCCCGCGCTTCCCGTGGCGCGAGCTGGCGGCACAGGGGATTGGCGCCTGGCCTGACGCCCAGCGTGTGGCGTTTTATCTGGCTGGACGCGCGCCGTATACGCCAGTCGATACCGCAACGGTGCTTGCGTTACTCTCGCGCTATGGCTATGAAGTCAAAGCCGATATGACGGCGCGCGAGCAACAGCGGGTGATTATGGCGTTCCAGATGCACTTCCGTCCGGCGCAATGGAACGGTATCGCAGATGCCGAAACGCAGGCGATTGCCGAAGCATTACTGGAGAAGTACGGCCAGGATTAACAGGGCGCGGTATCGCGAGGACTCTCTCTTCGAGGACATGCCGCACTTTATTGCTGAATGTACTGAAAATATTCGCGAGCAGGCTGATTTACCCGGCCTGTTCAGCAAGGTAAACGAGGCGCTGGCCGCCAGCGGGATTTTCCCCATCGGCGGTATCCGCAGTCGCGCCCACTGGCTGGATACCTGGCAGATGGCTGACGGTAAGCATGATTACGCGTTTGTGCATATGACGCTGAAAATCGGCGCCGGGCGCAGCCTGGAGAGCCGTCAGGAAGTCGGCGAAATGCTGTTCGGGCTGATTAAAGCCCACTTCGCCGACCTGATGGAGAACCGCTATCTGGCGCTGTCGTTTGAGATTGCCGAGTTACATCCAACGCTCAATTACAAACAAAACAACGTACACGCGTTATTTAAATAGCCCGAGTATTAGCGCGCGGCGGCGCTATAGGCGCGCTATAGGCATGAGCGCGCTATTTCTGGCCATCCCGTTAACCATTTTTGTGTTGTTTGTGTTACCGATTTGGCTGTGGCTGCATTACAGCAACCGCGCCGGTCGGGGAGAACTGTCGCAAAGCGAGCAGCAACGCTTACTGCAACTCACAGACGACGCGCAACGTATGCGCGAGCGCATTCAGGCGCTGGAAGACATTCTTGATGCAGAGCATCCGAACTGGAGAGAGCGCTAACGAGAGTCTCGGAGGAGCGGCGCTCTGGATGCCCGCGACTAAATTCTCCCGACGTACCCTCCTGACGGCAGGTTCTGCGCTTGCTGTTCTTCCTTTCCTGCGCGCCTTGCCGGTACAGGCGCGTGAACCTCGCGAGACCGTCGATATTAAGGATTATCCGGCGGATGACGGTATCGCCTCGTTCAAACAGGCCTTCGCCGACGGACAGACCGTGGTCGTACCGCCAGGATGGGTGTGTGAAAATATCAATGCGGCGATAACGATTCCGGCGGGAAAAACGCTGCGGGTACAGGGCGCGGTGCGTGGGAATGGCCGGGGACGGTTTATTTTGCAGGACGGGTGTCAGGTGGTGGGGGAGCAGGGCGGCAGTCTGCACAATGTGACGCTGGATGTTCGCGGGTCGGACTGTGTGATTAAAGGCGTGGCGATGAGCGGCTTTGGCCCCGTCGCGCAAATTTTCATCGGTGGTAAGGAACCGCAGGTGATGCGTAATCTCATTATCGATGACATCACCGTTACCCACGCCAACTACGCCATTCTCCGCCAGGGATTTCATAACCAAATGGACGGCGCGAGGATTACGCATAGCCGCTTTAGCGATTTACAGGGGGACGCCATTGAGTGGAATGTCGCGATTCACGACCGCGATATCCTGATTTCCGATCATGTCATCGAACGCATTGATTGTACCAATGGCAAAATCAACTGGGGGATCGGCATCGGGCTGGCGGGTAGCACCTATGACAACAGTTATCCTGAAGACCAGGCAGTAAAAAACTTTGTGGTGGCCAATATTACCGGATCTGATTGCCGACAGCTTGTGCACGTAGAAAATGGCAAACATTTCGTCATTCGCAATGTCAAAGCCAAAAACATCACGCCCGATTTCAGTAAAAATGCGGGTATTGATAACGCAACGATCGCAATTTATGGCTGTGATAATTTCGTCATTGATAATATTGATATGACGAATAGTGCCGGGATGCTCATCGGCTATGGCGTCGTTAAAGGAAAATACCTGTCAATTCCGCAAAACTTTAAATTAAACGCTATTCGGTTGGATAATCGCCAGGTTGCTTATAAATTACGCGGCATTCAAATTTCCTCCGGCAACACCCCCTCTTTTGTCGCCATCACCAATGTACGGATGACGCGTGCTACGCTGGAACTGCATAATCAACCGCAGCACCTCTTCCTGCGTAATATCAACGTGATGCAAACTTCAGCGATTGGCCCGGCGTTAAAAATGCATTTCGATTTGCGTAAAGATGTCCGTGGTCAATTTATGGCCCGCCAGGACACGCTGCTTTCCCTCGCTAATGTTCATGCCATCAATGAAAACGGGCAGAGTTCCGTGGATATCGACAGGATTAATCACCAAACCGTGAATGTCGAAGCAGTGAATTTTTCGCTGCCGAAGCGGGGAGGGTAACGCGTCTGCGCGCGCGGAGAGAGGCTCTCAGGACATGTCAGAAAATAAATTACACGTTATCGATTTGCACAAACGCTACGGCGGTCATGAAGTGCTGAAAGGGGTATCGCTGCAGGCCCGCGCCGGAGATGTGATTAGCATCATCGGCTCGTCCGGCTCCGGTAAAAGCACTTTTTTGCGCTGTATTAACTTCCTCGAAAAACCGAGCGAAGACGCGATTATCGTGAACGGTCAGAACATTAATCTGGTGCGCGACAAAGACGGGCAGCTCAAAGTGGCGGATAAAAATCAGCTACGCTTGTTGCGTACCCGCCTGACGATGGTGTTTCAGCACTTTAACCTCTGGAGCCACATGACGGTGCTGGAAAATGTGATGGAAGCGCCGATTCAGGTACTGGGATTAAGCAAGCACGACGCGCGCGAGCGGGCGTTGAAATATCTGGCGAAGGTGGGGATTGATGAGCGCGCTCAGGGCAAATATCCCGTTCATCTCTCCGGTGGCCAACAGCAGCGCGTTTCTATTGCGCGCGCGCTGGCGATGGAACCTGACGTTTTACTGTTCGATGAACCCACTTCGGCGCTCGATCCTGAACTGGTCGGCGAAGTGTTGCGCATCATGCAACAACTGGCGGAAGAAGGCAAAACGATGGTGGTGGTCACGCATGAAATGGGCTTCGTTCGCCATGTCTCTTCGCACGTTATTTTTCTGCATCAGGGGAAAATTGAAGAAGAGGGCGATCCGGAGCAGGTGTTCGGCAATCCGCAAAGCCCGCGTTTACAGCAATTCCTGAAAGGCTCGCTGAAATAACCGGATGCGCGCGATATATCGGCGATGCGTGTTTATTGGCATCGTTAGCCTGTTTCCTGAAATGTTCCGCGCAATTACCGATTACGGGGTAACTGGCCGGGCAGTAAAAAATGGCCTGCTGAACATCCAAAGCTGGAGTCCTCGCGACTTCACGCATGACCGGCACCGTACCGTGGACGATCGTCCTTACGGCGGCGGACCAGGGATGTTAATGATGGTGCAACCCTTGCGGGACGCCATTCACGCAGCAAAAGCCGCGGCAGGTGAAGGCGCTAAAGTGATTTATCTGTCGCCTCAGGGACGCAAGCTTGATCAAGCGGGCGTTAGCGAGCTGGCCACGAATCAGAAGCTTATTCTGGTGTGTGGTCGCTACGAAGGCGTAGATGAGCGCGTAATTCAGACCGAAATTGACGAAGAATGGTCAATTGGCGATTACGTTCTCAGCGGTGGCGAACTACCGGCAATGACGCTGATTGACTCCGTCGCCCGGTTTATACCGGGAGTTCTGGGGCATGAAGCATCAGCAATCGAAGATTCGTTTGCTGATGGGTTGCTGGATTGTCCGCACTATACGCGCCCTGAAGTGTTAGAGGGGATGGAAGTACCGCCAGTATTGCTGTCGGGAAACCATGCTGAGATACGTCGCTGGCGTTTGAAACAGTCGCTGGGCCGAACCTGGCTTAGAAGACCTGAACTTCTGGAAAACCTGGCTCTGACTGAAGAGCAAGCAAGGTTGCTGGCGGAGTTCAAAACAGAACACGCACAACAGCAGCATAAACATGATGGGATGGCATAGCCGGCTCTGCGAGAGAGGAGCGCTCGCATGAATAATCATTTTGGGAAAGGGTTAATGGCCGGGTTGCACGCGCCATATGCATATAGCGCGCATCATGCGGTGAATTTCTGTTCTGAGTATAAACGTGGCTTTGTATTGGGTTTTACACACCGTATGTTCGAAAAGACCGGCGATCGTCAACTTAGCGCGTGGGAGGCTGGAATTCTGACGCGTCGCTATGGTCTGGATAAAGAAATGGTGATGGATTTCTTTAAAGAGAATCATTCCGGGATGGCGGTTCGCTTCTTTATGGCCGGTTATCGACTCGAAGGTTGA
->genome3_plasmi_2
-ATGTCTACGCTTCTCTATTTGCACGGATTCAACAGTTCCCCTCGCTCGGCAAAAGCGTGCCAGCTAAAAAACTGGCTGGCGGAGCGTCATCCGCATGTTGAGATGATCGTCCCTCAACTACCGCCGTATCCTGCCGATGCGGCGGAGTTGCTGGAGTCTCTCGTGCTTGAGCATGGCGGTGCGCCATTAGGGCTGGTAGGATCGTCGCTGGGTGGTTATTACGCCACCTGGCTGTCGCAATGTTTTATGCTGCCGGCTGTGGTGGTGAATCCCGCCGTGCGGCCCTTTGAATTACTGACCGACTATCTCGGTCAGAACGAGAACCCCTACACCGGGCAGCAATATGTGCTAGAGTCTCGCCATATTTATGATCTTAAAGTCATGCAGATTGACCCGCTGGAAGCGCCGGACCTGATCTGGCTACTGCAACAGACGGGCGATGAAGTGCTGGATTACCGCCAGGCGGTGGCATATTACGCCTCCTGCCGTCAGACAGTGACCGAGGGTGGTAATCACGCATTCACGGGCTTCGAAGATTATTTCAACCAGATTGTCGATTTTCTTGGACTGCACAGTTGCTGACGCGTAGCGGCCGGAATCTTCTCGGAGAGGCGCTTCTCTCTCGGAGATGATTGACCCTATTTTTGCGTCCTGTACGCTAATTGCCGTCTTTGTTGTTTTACTGGCCATGGGCGCGCCTATCGGGATCTGCATCGTTATCGCCTCTTTCAGCACCATGATGCTGGTACTGCCTTTCGATATTTCGATGTTCGCCACCGCGCAAAAAATGTTCTCCAGCCTGGACAGTTTTGCCTTGCTGGCCGTGCCGTTCTTCGTTTTGTCCGGGGTGATCATGAATAGCGGGGGAATTGCCGCCCGGCTGATCAATTTTGCCAAACTGTTTACTGGCAAACTGCCCGGTTCGCTCTCTTATACCAACATCGTCGGCAATATGATGTTCGGTGCAATTTCCGGATCGGCAATTGCCGCCTCAACCTCCATCGGCGGCGTGATGGTGCCGATGAGCGCGCGCGAAGGTTACGATCGCGGCTTTGCGGCCGCGGTGAATATCGCCTCCGCGCCGACGGGAATGTTAATTCCGCCCACCACGGCTTTTATCCTTTATGCGCTGGCAAGCGGGGGAACATCGATTGCCGCTCTGTTCGCCGGCGGTCTGGTCGCGGGAGTGCTGTGGGGCGTTGGCTGTATGCTGGTCACGCTGGTAGTCGCTAAGCGTCGAAATTATCGGGTTTTCTTCACCGTCCAAAAAGGCATGGCGCTAAAAGTTGCCGTTGAGGCCATTCCCAGCCTGTTACTGATCGTGATTATCGTCGGCGGCATTGTGCAGGGGATTTTCACCGCCATTGAAGCCTCCGCGATTGCCGTGGTGTATACGTTATTGCTGACGATGGTGTTTTACCGCACGCTGAAAATTAAGGATTTGCCTTCGATTTTGCTCCAGACAGTGGTAATGACCGGGGTCATCATGTTCCTGCTGGCAACCTCTTCGGCGATGTCCTTCTCAATGTCGATCACCAATATTCCTGCGGCGCTGAGCGATATGATCCTCGGTATTTCCGCCAATAAACTGGTTATCCTGTTAGTCATTACCGTCTTTTTGTTGATTATCGGCGCATTTATGGATATCGGTCCGGCCATTCTGATTTTTACCCCGATTCTGCTGCCGATCATGGCTAAACTGGGCGTCGATCCGGTGCATTTGGGCATTATCATGATCTATAACCTGGCGATTGGCACCATTACGCCGCCAGTTGGCAGTGGTTTATATGTCGGGGCGAGCGTCGGTAAGGTCAAAGTTGAGGAAGTGATTAAACCGTTGCTGCCTTTTTACGGCGCGATTATCGGCGTTCTGTTATTAATTACCTACATTCCGGAAATCATACTGTTCTTACCCCGTCTACTGGGCATCATGTAAACCCGATGGCGCGCAGAGGCGCGAGTTCTGGA
->genome3_plasmi_3
-CACAGGGCTTAGAGGCGCTATGGCAATGATAATTAATGGGAAATTAATTAAAGCAAAAGACTTAGCTAAGGCTGCAGGTGTATCTCGTTCAACAGTGATTAAATATTACGGCATTAGCCGTGAGAATTACGAAAGGGTAGCAACTGAAAGAAGGAAGCTTGCTTTTGAACTAAGAGCATCAGGTTTAAAATGGAAAGAAGTTGCTGAAAAAATGAACACGACAAAATATAGCGCAATTGCATATTATAGACGATATTTAGCATTAGAGAAAAACAAATAACAGGCGCTAAGGCGGCGATCCTAGCGCGCGATCGCGCATGCGATGGTCGAACTGCAACATCAACGGCTGATGGTGCTTGCCGAACAGCTCCAGCTGGACAGTCTTATCGGCGCAGCGCCGGCGCTGTCGCAACAGGCGGTGGATCAGGAATGGAGCTACATGGACTTCCTGGAGCACCTGTTACATGAGGAGAAACTGGCCCGGCATCAGCGTAAACAGGCGATGTACACGCGGATGGCAGCCTTCCCGGCGGTAAAGACGTTCGAGGAGTACGACTTCACCTTCGCCACCGGCGCTCCTCAGAAGCAAATCCAGTCGCTGCGATCCCTGAGCTTCATAGAGCGTAACGAAAACATCGTGTTGCTGGGGCCATCGGGCGTGGGAAAAACGCATCTGGCGATAGCCATGGGCTACGAAGCAGTACGGGCGGGCATCAAGGTTCGCTTCACAACAGCAGCGGACCTGCTGCTACAGCTGTCCACTTCACAGCGTCAGGGCCGTTACAAAACGACTCTCAATCGTGGTGTCATGGCCCCGAAGCTGCTTATCATCGATGAAATAGGTTATCTGCCGTTCAGTCAGGAGGAAGCCAAGCTGTTCTTCCAGGTCATCGCCAAACGTTACGAGAAGAGCGCGATGATCCTGACCTCCAACCTGCCGTTCGGGCAGTGGGATCAGACGTTCGCCGGTGATGCAGCGCTGACATCGGCGATGCTGGACCGGATCTTACATCACTCACACGTCGTGCAAATAAAAGGGGAAAGCTATCGACTGAAGCAGAAACGAAAGGCCGGGGTTATAGCTGAAGCTAATCCTGAGTAA
diff --git a/Examples/2-res-Annotate-prokka/tmp_files/genome3-chromo.fst-all.fna_prokka-split5N.fna-prokka.log b/Examples/2-res-Annotate-prokka/tmp_files/genome3-chromo.fst-all.fna_prokka-split5N.fna-prokka.log
deleted file mode 100644
index 2f4b4ec62dc78ead58ae6e955c576069f4ec45ea..0000000000000000000000000000000000000000
--- a/Examples/2-res-Annotate-prokka/tmp_files/genome3-chromo.fst-all.fna_prokka-split5N.fna-prokka.log
+++ /dev/null
@@ -1,130 +0,0 @@
-[13:15:30] This is prokka 1.14.5
-[13:15:30] Written by Torsten Seemann <torsten.seemann@gmail.com>
-[13:15:30] Homepage is https://github.com/tseemann/prokka
-[13:15:30] Local time is Mon Dec  9 13:15:30 2019
-[13:15:30] You are aperrin
-[13:15:30] Operating system is darwin
-[13:15:30] You have BioPerl 1.007002
-[13:15:30] System has 8 cores.
-[13:15:30] Will use maximum of 1 cores.
-[13:15:30] Annotating as >>> Bacteria <<<
-[13:15:30] Generating locus_tag from 'Examples/2-res-Annotate-prokka/tmp_files/genome3-chromo.fst-all.fna_prokka-split5N.fna' contents.
-[13:15:30] Setting --locustag PFKCIMHH from MD5 9f4c2611ce3f44c6b2e6fb97579c5725
-[13:15:30] Creating new output folder: Examples/2-res-Annotate-prokka/tmp_files/genome3-chromo.fst-all.fna_prokka-split5N.fna-prokkaRes
-[13:15:30] Running: mkdir -p Examples\/2\-res\-Annotate\-prokka\/tmp_files\/genome3\-chromo\.fst\-all\.fna_prokka\-split5N\.fna\-prokkaRes
-[13:15:30] Using filename prefix: EXAM.1216.00002.XXX
-[13:15:30] Setting HMMER_NCPU=1
-[13:15:30] Writing log to: Examples/2-res-Annotate-prokka/tmp_files/genome3-chromo.fst-all.fna_prokka-split5N.fna-prokkaRes/EXAM.1216.00002.log
-[13:15:30] Command: /usr/local/bin/prokka --outdir Examples/2-res-Annotate-prokka/tmp_files/genome3-chromo.fst-all.fna_prokka-split5N.fna-prokkaRes --cpus 1 --prefix EXAM.1216.00002 Examples/2-res-Annotate-prokka/tmp_files/genome3-chromo.fst-all.fna_prokka-split5N.fna
-[13:15:30] Appending to PATH: /Users/aperrin/Softwares/src/prokka-dec.19/bin/../binaries/darwin
-[13:15:30] Appending to PATH: /Users/aperrin/Softwares/src/prokka-dec.19/bin/../binaries/darwin/../common
-[13:15:30] Appending to PATH: /Users/aperrin/Softwares/src/prokka-dec.19/bin
-[13:15:30] Looking for 'aragorn' - found /usr/local/bin/aragorn
-[13:15:30] Determined aragorn version is 001002 from 'ARAGORN v1.2.38 Dean Laslett'
-[13:15:30] Looking for 'barrnap' - found /usr/local/bin/barrnap
-[13:15:31] Determined barrnap version is 000008 from 'barrnap 0.8'
-[13:15:31] Looking for 'blastp' - found /Users/aperrin/Softwares/bin/blastp
-[13:15:31] Determined blastp version is 002009 from 'blastp: 2.9.0+'
-[13:15:31] Looking for 'cmpress' - found /usr/local/bin/cmpress
-[13:15:31] Determined cmpress version is 001001 from '# INFERNAL 1.1.2 (July 2016)'
-[13:15:31] Looking for 'cmscan' - found /usr/local/bin/cmscan
-[13:15:31] Determined cmscan version is 001001 from '# INFERNAL 1.1.2 (July 2016)'
-[13:15:31] Looking for 'egrep' - found /usr/bin/egrep
-[13:15:31] Looking for 'find' - found /usr/bin/find
-[13:15:31] Looking for 'grep' - found /usr/bin/grep
-[13:15:31] Looking for 'hmmpress' - found /Users/aperrin/Softwares/src/prokka-dec.19/bin/../binaries/darwin/hmmpress
-[13:15:31] Determined hmmpress version is 003001 from '# HMMER 3.1b1 (May 2013); http://hmmer.org/'
-[13:15:31] Looking for 'hmmscan' - found /usr/local/bin/hmmscan
-[13:15:31] Determined hmmscan version is 003001 from '# HMMER 3.1b2 (February 2015); http://hmmer.org/'
-[13:15:31] Looking for 'java' - found /usr/bin/java
-[13:15:31] Looking for 'makeblastdb' - found /Users/aperrin/Softwares/bin/makeblastdb
-[13:15:31] Determined makeblastdb version is 002009 from 'makeblastdb: 2.9.0+'
-[13:15:31] Looking for 'minced' - found /Users/aperrin/Softwares/src/prokka-dec.19/bin/../binaries/darwin/../common/minced
-[13:15:31] Determined minced version is 002000 from 'minced 0.2.0'
-[13:15:31] Looking for 'parallel' - found /usr/local/bin/parallel
-[13:15:31] Determined parallel version is 20181022 from 'GNU parallel 20181022'
-[13:15:31] Looking for 'prodigal' - found /usr/local/bin/prodigal
-[13:15:31] Determined prodigal version is 002006 from 'Prodigal V2.6.3: February, 2016'
-[13:15:31] Looking for 'prokka-genbank_to_fasta_db' - found /Users/aperrin/Softwares/src/prokka-dec.19/bin/prokka-genbank_to_fasta_db
-[13:15:31] Looking for 'sed' - found /usr/bin/sed
-[13:15:31] Looking for 'tbl2asn' - found /Users/aperrin/Softwares/src/prokka-dec.19/bin/../binaries/darwin/tbl2asn
-[13:15:31] Determined tbl2asn version is 025007 from 'tbl2asn 25.7   arguments:'
-[13:15:31] Using genetic code table 11.
-[13:15:31] Loading and checking input file: Examples/2-res-Annotate-prokka/tmp_files/genome3-chromo.fst-all.fna_prokka-split5N.fna
-[13:15:31] Wrote 3 contigs totalling 8817 bp.
-[13:15:31] Predicting tRNAs and tmRNAs
-[13:15:31] Running: aragorn -l -gc11  -w Examples\/2\-res\-Annotate\-prokka\/tmp_files\/genome3\-chromo\.fst\-all\.fna_prokka\-split5N\.fna\-prokkaRes\/EXAM\.1216\.00002\.fna
-[13:15:31] Found 0 tRNAs
-[13:15:31] Predicting Ribosomal RNAs
-[13:15:31] Running Barrnap with 1 threads
-[13:15:31] Found 0 rRNAs
-[13:15:31] Skipping ncRNA search, enable with --rfam if desired.
-[13:15:31] Total of 0 tRNA + rRNA features
-[13:15:31] Searching for CRISPR repeats
-[13:15:31] Found 0 CRISPRs
-[13:15:31] Predicting coding sequences
-[13:15:31] Contigs total 8817 bp, so using meta mode
-[13:15:31] Running: prodigal -i Examples\/2\-res\-Annotate\-prokka\/tmp_files\/genome3\-chromo\.fst\-all\.fna_prokka\-split5N\.fna\-prokkaRes\/EXAM\.1216\.00002\.fna -c -m -g 11 -p meta -f sco -q
-[13:15:31] Found 12 CDS
-[13:15:31] Connecting features back to sequences
-[13:15:31] Not using genus-specific database. Try --usegenus to enable it.
-[13:15:31] Annotating CDS, please be patient.
-[13:15:31] Will use 1 CPUs for similarity searching.
-[13:15:31] There are still 12 unannotated CDS left (started with 12)
-[13:15:31] Will use blast to search against /Users/aperrin/Softwares/src/prokka-dec.19/db/kingdom/Bacteria/IS with 1 CPUs
-[13:15:31] Running: cat Examples\/2\-res\-Annotate\-prokka\/tmp_files\/genome3\-chromo\.fst\-all\.fna_prokka\-split5N\.fna\-prokkaRes\/EXAM\.1216\.00002\.IS\.tmp\.95230\.faa | parallel --gnu --plain -j 1 --block 1443 --recstart '>' --pipe blastp -query - -db /Users/aperrin/Softwares/src/prokka-dec.19/db/kingdom/Bacteria/IS -evalue 1e-30 -qcov_hsp_perc 90 -num_threads 1 -num_descriptions 1 -num_alignments 1 -seg no > Examples\/2\-res\-Annotate\-prokka\/tmp_files\/genome3\-chromo\.fst\-all\.fna_prokka\-split5N\.fna\-prokkaRes\/EXAM\.1216\.00002\.IS\.tmp\.95230\.blast 2> /dev/null
-[13:15:32] Deleting unwanted file: Examples/2-res-Annotate-prokka/tmp_files/genome3-chromo.fst-all.fna_prokka-split5N.fna-prokkaRes/EXAM.1216.00002.IS.tmp.95230.faa
-[13:15:32] Deleting unwanted file: Examples/2-res-Annotate-prokka/tmp_files/genome3-chromo.fst-all.fna_prokka-split5N.fna-prokkaRes/EXAM.1216.00002.IS.tmp.95230.blast
-[13:15:32] There are still 11 unannotated CDS left (started with 12)
-[13:15:32] Will use blast to search against /Users/aperrin/Softwares/src/prokka-dec.19/db/kingdom/Bacteria/AMR with 1 CPUs
-[13:15:32] Running: cat Examples\/2\-res\-Annotate\-prokka\/tmp_files\/genome3\-chromo\.fst\-all\.fna_prokka\-split5N\.fna\-prokkaRes\/EXAM\.1216\.00002\.AMR\.tmp\.95230\.faa | parallel --gnu --plain -j 1 --block 1311 --recstart '>' --pipe blastp -query - -db /Users/aperrin/Softwares/src/prokka-dec.19/db/kingdom/Bacteria/AMR -evalue 1e-300 -qcov_hsp_perc 90 -num_threads 1 -num_descriptions 1 -num_alignments 1 -seg no > Examples\/2\-res\-Annotate\-prokka\/tmp_files\/genome3\-chromo\.fst\-all\.fna_prokka\-split5N\.fna\-prokkaRes\/EXAM\.1216\.00002\.AMR\.tmp\.95230\.blast 2> /dev/null
-[13:15:32] Deleting unwanted file: Examples/2-res-Annotate-prokka/tmp_files/genome3-chromo.fst-all.fna_prokka-split5N.fna-prokkaRes/EXAM.1216.00002.AMR.tmp.95230.faa
-[13:15:32] Deleting unwanted file: Examples/2-res-Annotate-prokka/tmp_files/genome3-chromo.fst-all.fna_prokka-split5N.fna-prokkaRes/EXAM.1216.00002.AMR.tmp.95230.blast
-[13:15:32] There are still 11 unannotated CDS left (started with 12)
-[13:15:32] Will use blast to search against /Users/aperrin/Softwares/src/prokka-dec.19/db/kingdom/Bacteria/sprot with 1 CPUs
-[13:15:32] Running: cat Examples\/2\-res\-Annotate\-prokka\/tmp_files\/genome3\-chromo\.fst\-all\.fna_prokka\-split5N\.fna\-prokkaRes\/EXAM\.1216\.00002\.sprot\.tmp\.95230\.faa | parallel --gnu --plain -j 1 --block 1311 --recstart '>' --pipe blastp -query - -db /Users/aperrin/Softwares/src/prokka-dec.19/db/kingdom/Bacteria/sprot -evalue 1e-09 -qcov_hsp_perc 80 -num_threads 1 -num_descriptions 1 -num_alignments 1 -seg no > Examples\/2\-res\-Annotate\-prokka\/tmp_files\/genome3\-chromo\.fst\-all\.fna_prokka\-split5N\.fna\-prokkaRes\/EXAM\.1216\.00002\.sprot\.tmp\.95230\.blast 2> /dev/null
-[13:15:33] Deleting unwanted file: Examples/2-res-Annotate-prokka/tmp_files/genome3-chromo.fst-all.fna_prokka-split5N.fna-prokkaRes/EXAM.1216.00002.sprot.tmp.95230.faa
-[13:15:33] Deleting unwanted file: Examples/2-res-Annotate-prokka/tmp_files/genome3-chromo.fst-all.fna_prokka-split5N.fna-prokkaRes/EXAM.1216.00002.sprot.tmp.95230.blast
-[13:15:33] There are still 4 unannotated CDS left (started with 12)
-[13:15:33] Will use hmmer3 to search against /Users/aperrin/Softwares/src/prokka-dec.19/db/hmm/HAMAP.hmm with 1 CPUs
-[13:15:33] Running: cat Examples\/2\-res\-Annotate\-prokka\/tmp_files\/genome3\-chromo\.fst\-all\.fna_prokka\-split5N\.fna\-prokkaRes\/EXAM\.1216\.00002\.HAMAP\.hmm\.tmp\.95230\.faa | parallel --gnu --plain -j 1 --block 427 --recstart '>' --pipe hmmscan --noali --notextw --acc -E 1e-09 --cpu 1 /Users/aperrin/Softwares/src/prokka-dec.19/db/hmm/HAMAP.hmm /dev/stdin > Examples\/2\-res\-Annotate\-prokka\/tmp_files\/genome3\-chromo\.fst\-all\.fna_prokka\-split5N\.fna\-prokkaRes\/EXAM\.1216\.00002\.HAMAP\.hmm\.tmp\.95230\.hmmer3 2> /dev/null
-[13:15:34] Deleting unwanted file: Examples/2-res-Annotate-prokka/tmp_files/genome3-chromo.fst-all.fna_prokka-split5N.fna-prokkaRes/EXAM.1216.00002.HAMAP.hmm.tmp.95230.faa
-[13:15:34] Deleting unwanted file: Examples/2-res-Annotate-prokka/tmp_files/genome3-chromo.fst-all.fna_prokka-split5N.fna-prokkaRes/EXAM.1216.00002.HAMAP.hmm.tmp.95230.hmmer3
-[13:15:34] Labelling remaining 4 proteins as 'hypothetical protein'
-[13:15:34] Possible /pseudo 'N-acetylmuramoyl-L-alanine amidase AmiD' at header_genome3_1 position 880
-[13:15:34] Found 6 unique /gene codes.
-[13:15:34] Fixed 2 duplicate /gene - amiD_1 amiD_2
-[13:15:34] Fixed 1 colliding /gene names.
-[13:15:34] Adding /locus_tag identifiers
-[13:15:34] Assigned 12 locus_tags to CDS and RNA features.
-[13:15:34] Writing outputs to Examples/2-res-Annotate-prokka/tmp_files/genome3-chromo.fst-all.fna_prokka-split5N.fna-prokkaRes/
-[13:15:34] Generating annotation statistics file
-[13:15:34] Generating Genbank and Sequin files
-[13:15:34] Running: tbl2asn -V b -a r10k -l paired-ends -M n -N 1 -y 'Annotated using prokka 1.14.5 from https://github.com/tseemann/prokka' -Z Examples\/2\-res\-Annotate\-prokka\/tmp_files\/genome3\-chromo\.fst\-all\.fna_prokka\-split5N\.fna\-prokkaRes\/EXAM\.1216\.00002\.err -i Examples\/2\-res\-Annotate\-prokka\/tmp_files\/genome3\-chromo\.fst\-all\.fna_prokka\-split5N\.fna\-prokkaRes\/EXAM\.1216\.00002\.fsa 2> /dev/null
-[13:15:34] Deleting unwanted file: Examples/2-res-Annotate-prokka/tmp_files/genome3-chromo.fst-all.fna_prokka-split5N.fna-prokkaRes/errorsummary.val
-[13:15:34] Deleting unwanted file: Examples/2-res-Annotate-prokka/tmp_files/genome3-chromo.fst-all.fna_prokka-split5N.fna-prokkaRes/EXAM.1216.00002.dr
-[13:15:34] Deleting unwanted file: Examples/2-res-Annotate-prokka/tmp_files/genome3-chromo.fst-all.fna_prokka-split5N.fna-prokkaRes/EXAM.1216.00002.fixedproducts
-[13:15:34] Deleting unwanted file: Examples/2-res-Annotate-prokka/tmp_files/genome3-chromo.fst-all.fna_prokka-split5N.fna-prokkaRes/EXAM.1216.00002.ecn
-[13:15:34] Deleting unwanted file: Examples/2-res-Annotate-prokka/tmp_files/genome3-chromo.fst-all.fna_prokka-split5N.fna-prokkaRes/EXAM.1216.00002.val
-[13:15:34] Repairing broken .GBK output that tbl2asn produces...
-[13:15:34] Running: sed 's/COORDINATES: profile/COORDINATES:profile/' < Examples\/2\-res\-Annotate\-prokka\/tmp_files\/genome3\-chromo\.fst\-all\.fna_prokka\-split5N\.fna\-prokkaRes\/EXAM\.1216\.00002\.gbf > Examples\/2\-res\-Annotate\-prokka\/tmp_files\/genome3\-chromo\.fst\-all\.fna_prokka\-split5N\.fna\-prokkaRes\/EXAM\.1216\.00002\.gbk
-[13:15:34] Deleting unwanted file: Examples/2-res-Annotate-prokka/tmp_files/genome3-chromo.fst-all.fna_prokka-split5N.fna-prokkaRes/EXAM.1216.00002.gbf
-[13:15:34] Output files:
-[13:15:34] Examples/2-res-Annotate-prokka/tmp_files/genome3-chromo.fst-all.fna_prokka-split5N.fna-prokkaRes/EXAM.1216.00002.log
-[13:15:34] Examples/2-res-Annotate-prokka/tmp_files/genome3-chromo.fst-all.fna_prokka-split5N.fna-prokkaRes/EXAM.1216.00002.ffn
-[13:15:34] Examples/2-res-Annotate-prokka/tmp_files/genome3-chromo.fst-all.fna_prokka-split5N.fna-prokkaRes/EXAM.1216.00002.gbk
-[13:15:34] Examples/2-res-Annotate-prokka/tmp_files/genome3-chromo.fst-all.fna_prokka-split5N.fna-prokkaRes/EXAM.1216.00002.fsa
-[13:15:34] Examples/2-res-Annotate-prokka/tmp_files/genome3-chromo.fst-all.fna_prokka-split5N.fna-prokkaRes/EXAM.1216.00002.faa
-[13:15:34] Examples/2-res-Annotate-prokka/tmp_files/genome3-chromo.fst-all.fna_prokka-split5N.fna-prokkaRes/EXAM.1216.00002.txt
-[13:15:34] Examples/2-res-Annotate-prokka/tmp_files/genome3-chromo.fst-all.fna_prokka-split5N.fna-prokkaRes/EXAM.1216.00002.gff
-[13:15:34] Examples/2-res-Annotate-prokka/tmp_files/genome3-chromo.fst-all.fna_prokka-split5N.fna-prokkaRes/EXAM.1216.00002.tbl
-[13:15:34] Examples/2-res-Annotate-prokka/tmp_files/genome3-chromo.fst-all.fna_prokka-split5N.fna-prokkaRes/EXAM.1216.00002.sqn
-[13:15:34] Examples/2-res-Annotate-prokka/tmp_files/genome3-chromo.fst-all.fna_prokka-split5N.fna-prokkaRes/EXAM.1216.00002.tsv
-[13:15:34] Examples/2-res-Annotate-prokka/tmp_files/genome3-chromo.fst-all.fna_prokka-split5N.fna-prokkaRes/EXAM.1216.00002.fna
-[13:15:34] Examples/2-res-Annotate-prokka/tmp_files/genome3-chromo.fst-all.fna_prokka-split5N.fna-prokkaRes/EXAM.1216.00002.err
-[13:15:34] Annotation finished successfully.
-[13:15:34] Walltime used: 0.07 minutes
-[13:15:34] If you use this result please cite the Prokka paper:
-[13:15:34] Seemann T (2014) Prokka: rapid prokaryotic genome annotation. Bioinformatics. 30(14):2068-9.
-[13:15:34] Type 'prokka --citation' for more details.
-[13:15:34] Thank you, come again.
diff --git a/Examples/2-res-Annotate-prokka/tmp_files/genome3-chromo.fst-all.fna_prokka-split5N.fna-prokkaRes/EXAM.1216.00002.err b/Examples/2-res-Annotate-prokka/tmp_files/genome3-chromo.fst-all.fna_prokka-split5N.fna-prokkaRes/EXAM.1216.00002.err
deleted file mode 100644
index f00ebd9ac9accff2f75910c97e5b7e58d4d07828..0000000000000000000000000000000000000000
--- a/Examples/2-res-Annotate-prokka/tmp_files/genome3-chromo.fst-all.fna_prokka-split5N.fna-prokkaRes/EXAM.1216.00002.err
+++ /dev/null
@@ -1,133 +0,0 @@
-Discrepancy Report Results
-
-Summary
-FATAL: MISSING_PROTEIN_ID:12 proteins have invalid IDs.
-DISC_SOURCE_QUALS_ASNDISC:strain (all present, all same)
-DISC_SOURCE_QUALS_ASNDISC:taxname (all present, all same)
-DISC_FEATURE_COUNT:CDS: 12 present
-DISC_COUNT_NUCLEOTIDES:3 nucleotide Bioseqs are present
-FEATURE_LOCATION_CONFLICT:12 features have inconsistent gene locations.
-DISC_QUALITY_SCORES:Quality scores are missing on all sequences.
-ONCALLER_COMMENT_PRESENT:3 comment descriptors were found (all same)
-MISSING_GENOMEASSEMBLY_COMMENTS:3 bioseqs are missing GenomeAssembly structured comments
-MOLTYPE_NOT_MRNA:3 molecule types are not set as mRNA.
-TECHNIQUE_NOT_TSA:3 technique are not set as TSA
-MISSING_STRUCTURED_COMMENT:3 sequences do not include structured comments.
-MISSING_PROJECT:15 sequences do not include project.
-DISC_INCONSISTENT_MOLINFO_TECH:Molinfo Technique Report (some missing, all same)
-
-
-Detailed Report
-
-FATAL: DiscRep_ALL:MISSING_PROTEIN_ID::12 proteins halid nvalid IDs.
-Examples/2-res-Annotate-prokka/tmp_files/genome3-chromo.fst-all.fna_prokka-split5N.fna-prokkaRes/EXAM.1216.00002:header_genome3_1_1 (length 276)
-Examples/2-res-Annotate-prokka/tmp_files/genome3-chromo.fst-all.fna_prokka-split5N.fna-prokkaRes/EXAM.1216.00002:header_genome3_1_2 (length 276)
-Examples/2-res-Annotate-prokka/tmp_files/genome3-chromo.fst-all.fna_prokka-split5N.fna-prokkaRes/EXAM.1216.00002:header_genome3_1_3 (length 157)
-Examples/2-res-Annotate-prokka/tmp_files/genome3-chromo.fst-all.fna_prokka-split5N.fna-prokkaRes/EXAM.1216.00002:header_genome3_1_4 (length 74)
-Examples/2-res-Annotate-prokka/tmp_files/genome3-chromo.fst-all.fna_prokka-split5N.fna-prokkaRes/EXAM.1216.00002:header_genome3_1_5 (length 467)
-Examples/2-res-Annotate-prokka/tmp_files/genome3-chromo.fst-all.fna_prokka-split5N.fna-prokkaRes/EXAM.1216.00002:header_genome3_1_6 (length 257)
-Examples/2-res-Annotate-prokka/tmp_files/genome3-chromo.fst-all.fna_prokka-split5N.fna-prokkaRes/EXAM.1216.00002:header_genome3_1_7 (length 263)
-Examples/2-res-Annotate-prokka/tmp_files/genome3-chromo.fst-all.fna_prokka-split5N.fna-prokkaRes/EXAM.1216.00002:header_genome3_1_8 (length 95)
-Examples/2-res-Annotate-prokka/tmp_files/genome3-chromo.fst-all.fna_prokka-split5N.fna-prokkaRes/EXAM.1216.00002:genome3_plasmi_2_1 (length 193)
-Examples/2-res-Annotate-prokka/tmp_files/genome3-chromo.fst-all.fna_prokka-split5N.fna-prokkaRes/EXAM.1216.00002:genome3_plasmi_2_2 (length 435)
-Examples/2-res-Annotate-prokka/tmp_files/genome3-chromo.fst-all.fna_prokka-split5N.fna-prokkaRes/EXAM.1216.00002:genome3_plasmi_3_1 (length 84)
-Examples/2-res-Annotate-prokka/tmp_files/genome3-chromo.fst-all.fna_prokka-split5N.fna-prokkaRes/EXAM.1216.00002:genome3_plasmi_3_2 (length 259)
-
-DiscRep_ALL:DISC_SOURCE_QUALS_ASNDISC::strain (all present, all same)
-DiscRep_SUB:DISC_SOURCE_QUALS_ASNDISC::3 sources have 'strain' for strain
-DiscRep_ALL:DISC_SOURCE_QUALS_ASNDISC::taxname (all present, all same)
-DiscRep_SUB:DISC_SOURCE_QUALS_ASNDISC::3 sources have 'Genus species' for taxname
-DiscRep_ALL:DISC_FEATURE_COUNT::CDS: 12 present
-DiscRep_ALL:DISC_COUNT_NUCLEOTIDES::3 nucleotide Bioseqs are present
-Examples/2-res-Annotate-prokka/tmp_files/genome3-chromo.fst-all.fna_prokka-split5N.fna-prokkaRes/EXAM.1216.00002:header_genome3_1 (length 5747)
-Examples/2-res-Annotate-prokka/tmp_files/genome3-chromo.fst-all.fna_prokka-split5N.fna-prokkaRes/EXAM.1216.00002:genome3_plasmi_2 (length 1968)
-Examples/2-res-Annotate-prokka/tmp_files/genome3-chromo.fst-all.fna_prokka-split5N.fna-prokkaRes/EXAM.1216.00002:genome3_plasmi_3 (length 1102)
-
-DiscRep_ALL:FEATURE_LOCATION_CONFLICT::12 features have inconsistent gene locations.
-DiscRep_SUB:FEATURE_LOCATION_CONFLICT::Coding region xref gene does not exist
-Examples/2-res-Annotate-prokka/tmp_files/genome3-chromo.fst-all.fna_prokka-split5N.fna-prokkaRes/EXAM.1216.00002:CDS	N-acetylmuramoyl-L-alanine amidase AmiD	header_genome3_1:1-831	PFKCIMHH_00001
-
-DiscRep_SUB:FEATURE_LOCATION_CONFLICT::Coding region xref gene does not exist
-Examples/2-res-Annotate-prokka/tmp_files/genome3-chromo.fst-all.fna_prokka-split5N.fna-prokkaRes/EXAM.1216.00002:CDS	N-acetylmuramoyl-L-alanine amidase AmiD	header_genome3_1:880-1710	PFKCIMHH_00002
-
-DiscRep_SUB:FEATURE_LOCATION_CONFLICT::Coding region xref gene does not exist
-Examples/2-res-Annotate-prokka/tmp_files/genome3-chromo.fst-all.fna_prokka-split5N.fna-prokkaRes/EXAM.1216.00002:CDS	5-carboxymethyl-2-hydroxymuconate Delta-isomerase	header_genome3_1:1655-2128	PFKCIMHH_00003
-
-DiscRep_SUB:FEATURE_LOCATION_CONFLICT::Coding region xref gene does not exist
-Examples/2-res-Annotate-prokka/tmp_files/genome3-chromo.fst-all.fna_prokka-split5N.fna-prokkaRes/EXAM.1216.00002:CDS	Phage shock protein B	header_genome3_1:2172-2396	PFKCIMHH_00004
-
-DiscRep_SUB:FEATURE_LOCATION_CONFLICT::Coding region xref gene does not exist
-Examples/2-res-Annotate-prokka/tmp_files/genome3-chromo.fst-all.fna_prokka-split5N.fna-prokkaRes/EXAM.1216.00002:CDS	hypothetical protein	header_genome3_1:2425-3828	PFKCIMHH_00005
-
-DiscRep_SUB:FEATURE_LOCATION_CONFLICT::Coding region xref gene does not exist
-Examples/2-res-Annotate-prokka/tmp_files/genome3-chromo.fst-all.fna_prokka-split5N.fna-prokkaRes/EXAM.1216.00002:CDS	Histidine transport ATP-binding protein HisP	header_genome3_1:3863-4636	PFKCIMHH_00006
-
-DiscRep_SUB:FEATURE_LOCATION_CONFLICT::Coding region xref gene does not exist
-Examples/2-res-Annotate-prokka/tmp_files/genome3-chromo.fst-all.fna_prokka-split5N.fna-prokkaRes/EXAM.1216.00002:CDS	tRNA (guanine-N(1)-)-methyltransferase	header_genome3_1:4641-5432	PFKCIMHH_00007
-
-DiscRep_SUB:FEATURE_LOCATION_CONFLICT::Coding region xref gene does not exist
-Examples/2-res-Annotate-prokka/tmp_files/genome3-chromo.fst-all.fna_prokka-split5N.fna-prokkaRes/EXAM.1216.00002:CDS	hypothetical protein	header_genome3_1:5460-5747	PFKCIMHH_00008
-
-DiscRep_SUB:FEATURE_LOCATION_CONFLICT::Coding region xref gene does not exist
-Examples/2-res-Annotate-prokka/tmp_files/genome3-chromo.fst-all.fna_prokka-split5N.fna-prokkaRes/EXAM.1216.00002:CDS	hypothetical protein	genome3_plasmi_2:1-582	PFKCIMHH_00009
-
-DiscRep_SUB:FEATURE_LOCATION_CONFLICT::Coding region xref gene does not exist
-Examples/2-res-Annotate-prokka/tmp_files/genome3-chromo.fst-all.fna_prokka-split5N.fna-prokkaRes/EXAM.1216.00002:CDS	C4-dicarboxylate TRAP transporter large permease protein DctM	genome3_plasmi_2:629-1936	PFKCIMHH_00010
-
-DiscRep_SUB:FEATURE_LOCATION_CONFLICT::Coding region xref gene does not exist
-Examples/2-res-Annotate-prokka/tmp_files/genome3-chromo.fst-all.fna_prokka-split5N.fna-prokkaRes/EXAM.1216.00002:CDS	hypothetical protein	genome3_plasmi_3:26-280	PFKCIMHH_00011
-
-DiscRep_SUB:FEATURE_LOCATION_CONFLICT::Coding region xref gene does not exist
-Examples/2-res-Annotate-prokka/tmp_files/genome3-chromo.fst-all.fna_prokka-split5N.fna-prokkaRes/EXAM.1216.00002:CDS	IS21 family transposase ISSen3	genome3_plasmi_3:323-1102	PFKCIMHH_00012
-
-DiscRep_ALL:DISC_QUALITY_SCORES::Quality scores are missing on all sequences.
-
-DiscRep_ALL:ONCALLER_COMMENT_PRESENT::3 comment descriptors were found (all same)
-Examples/2-res-Annotate-prokka/tmp_files/genome3-chromo.fst-all.fna_prokka-split5N.fna-prokkaRes/EXAM.1216.00002:header_genome3_1:Annotated using prokka 1.14.5 from https://github.com/tseemann/prokka
-Examples/2-res-Annotate-prokka/tmp_files/genome3-chromo.fst-all.fna_prokka-split5N.fna-prokkaRes/EXAM.1216.00002:genome3_plasmi_2:Annotated using prokka 1.14.5 from https://github.com/tseemann/prokka
-Examples/2-res-Annotate-prokka/tmp_files/genome3-chromo.fst-all.fna_prokka-split5N.fna-prokkaRes/EXAM.1216.00002:genome3_plasmi_3:Annotated using prokka 1.14.5 from https://github.com/tseemann/prokka
-
-DiscRep_ALL:MISSING_GENOMEASSEMBLY_COMMENTS::3 bioseqs are missing GenomeAssembly structured comments
-Examples/2-res-Annotate-prokka/tmp_files/genome3-chromo.fst-all.fna_prokka-split5N.fna-prokkaRes/EXAM.1216.00002:header_genome3_1 (length 5747)
-Examples/2-res-Annotate-prokka/tmp_files/genome3-chromo.fst-all.fna_prokka-split5N.fna-prokkaRes/EXAM.1216.00002:genome3_plasmi_2 (length 1968)
-Examples/2-res-Annotate-prokka/tmp_files/genome3-chromo.fst-all.fna_prokka-split5N.fna-prokkaRes/EXAM.1216.00002:genome3_plasmi_3 (length 1102)
-
-DiscRep_ALL:MOLTYPE_NOT_MRNA::3 molecule types are not set as mRNA.
-Examples/2-res-Annotate-prokka/tmp_files/genome3-chromo.fst-all.fna_prokka-split5N.fna-prokkaRes/EXAM.1216.00002:header_genome3_1 (length 5747)
-Examples/2-res-Annotate-prokka/tmp_files/genome3-chromo.fst-all.fna_prokka-split5N.fna-prokkaRes/EXAM.1216.00002:genome3_plasmi_2 (length 1968)
-Examples/2-res-Annotate-prokka/tmp_files/genome3-chromo.fst-all.fna_prokka-split5N.fna-prokkaRes/EXAM.1216.00002:genome3_plasmi_3 (length 1102)
-
-DiscRep_ALL:TECHNIQUE_NOT_TSA::3 technique are not set as TSA
-Examples/2-res-Annotate-prokka/tmp_files/genome3-chromo.fst-all.fna_prokka-split5N.fna-prokkaRes/EXAM.1216.00002:header_genome3_1 (length 5747)
-Examples/2-res-Annotate-prokka/tmp_files/genome3-chromo.fst-all.fna_prokka-split5N.fna-prokkaRes/EXAM.1216.00002:genome3_plasmi_2 (length 1968)
-Examples/2-res-Annotate-prokka/tmp_files/genome3-chromo.fst-all.fna_prokka-split5N.fna-prokkaRes/EXAM.1216.00002:genome3_plasmi_3 (length 1102)
-
-DiscRep_ALL:MISSING_STRUCTURED_COMMENT::3 sequences do not include structured comments.
-Examples/2-res-Annotate-prokka/tmp_files/genome3-chromo.fst-all.fna_prokka-split5N.fna-prokkaRes/EXAM.1216.00002:header_genome3_1 (length 5747)
-Examples/2-res-Annotate-prokka/tmp_files/genome3-chromo.fst-all.fna_prokka-split5N.fna-prokkaRes/EXAM.1216.00002:genome3_plasmi_2 (length 1968)
-Examples/2-res-Annotate-prokka/tmp_files/genome3-chromo.fst-all.fna_prokka-split5N.fna-prokkaRes/EXAM.1216.00002:genome3_plasmi_3 (length 1102)
-
-DiscRep_ALL:MISSING_PROJECT::15 sequences do not include project.
-Examples/2-res-Annotate-prokka/tmp_files/genome3-chromo.fst-all.fna_prokka-split5N.fna-prokkaRes/EXAM.1216.00002:header_genome3_1 (length 5747)
-Examples/2-res-Annotate-prokka/tmp_files/genome3-chromo.fst-all.fna_prokka-split5N.fna-prokkaRes/EXAM.1216.00002:header_genome3_1_1 (length 276)
-Examples/2-res-Annotate-prokka/tmp_files/genome3-chromo.fst-all.fna_prokka-split5N.fna-prokkaRes/EXAM.1216.00002:header_genome3_1_2 (length 276)
-Examples/2-res-Annotate-prokka/tmp_files/genome3-chromo.fst-all.fna_prokka-split5N.fna-prokkaRes/EXAM.1216.00002:header_genome3_1_3 (length 157)
-Examples/2-res-Annotate-prokka/tmp_files/genome3-chromo.fst-all.fna_prokka-split5N.fna-prokkaRes/EXAM.1216.00002:header_genome3_1_4 (length 74)
-Examples/2-res-Annotate-prokka/tmp_files/genome3-chromo.fst-all.fna_prokka-split5N.fna-prokkaRes/EXAM.1216.00002:header_genome3_1_5 (length 467)
-Examples/2-res-Annotate-prokka/tmp_files/genome3-chromo.fst-all.fna_prokka-split5N.fna-prokkaRes/EXAM.1216.00002:header_genome3_1_6 (length 257)
-Examples/2-res-Annotate-prokka/tmp_files/genome3-chromo.fst-all.fna_prokka-split5N.fna-prokkaRes/EXAM.1216.00002:header_genome3_1_7 (length 263)
-Examples/2-res-Annotate-prokka/tmp_files/genome3-chromo.fst-all.fna_prokka-split5N.fna-prokkaRes/EXAM.1216.00002:header_genome3_1_8 (length 95)
-Examples/2-res-Annotate-prokka/tmp_files/genome3-chromo.fst-all.fna_prokka-split5N.fna-prokkaRes/EXAM.1216.00002:genome3_plasmi_2 (length 1968)
-Examples/2-res-Annotate-prokka/tmp_files/genome3-chromo.fst-all.fna_prokka-split5N.fna-prokkaRes/EXAM.1216.00002:genome3_plasmi_2_1 (length 193)
-Examples/2-res-Annotate-prokka/tmp_files/genome3-chromo.fst-all.fna_prokka-split5N.fna-prokkaRes/EXAM.1216.00002:genome3_plasmi_2_2 (length 435)
-Examples/2-res-Annotate-prokka/tmp_files/genome3-chromo.fst-all.fna_prokka-split5N.fna-prokkaRes/EXAM.1216.00002:genome3_plasmi_3 (length 1102)
-Examples/2-res-Annotate-prokka/tmp_files/genome3-chromo.fst-all.fna_prokka-split5N.fna-prokkaRes/EXAM.1216.00002:genome3_plasmi_3_1 (length 84)
-Examples/2-res-Annotate-prokka/tmp_files/genome3-chromo.fst-all.fna_prokka-split5N.fna-prokkaRes/EXAM.1216.00002:genome3_plasmi_3_2 (length 259)
-
-DiscRep_ALL:DISC_INCONSISTENT_MOLINFO_TECH::Molinfo Technique Report (some missing, all same)
-DiscRep_SUB:DISC_INCONSISTENT_MOLINFO_TECH::technique (all missing)
-DiscRep_SUB:DISC_INCONSISTENT_MOLINFO_TECH::3 Molinfos are missing field technique
-Examples/2-res-Annotate-prokka/tmp_files/genome3-chromo.fst-all.fna_prokka-split5N.fna-prokkaRes/EXAM.1216.00002:genome3_plasmi_2 (length 1968)
-Examples/2-res-Annotate-prokka/tmp_files/genome3-chromo.fst-all.fna_prokka-split5N.fna-prokkaRes/EXAM.1216.00002:genome3_plasmi_3 (length 1102)
-Examples/2-res-Annotate-prokka/tmp_files/genome3-chromo.fst-all.fna_prokka-split5N.fna-prokkaRes/EXAM.1216.00002:header_genome3_1 (length 5747)
-
diff --git a/Examples/2-res-Annotate-prokka/tmp_files/genome3-chromo.fst-all.fna_prokka-split5N.fna-prokkaRes/EXAM.1216.00002.faa b/Examples/2-res-Annotate-prokka/tmp_files/genome3-chromo.fst-all.fna_prokka-split5N.fna-prokkaRes/EXAM.1216.00002.faa
deleted file mode 100644
index 12e3ed23e75ae8861a35beea8d1292b1c14faa03..0000000000000000000000000000000000000000
--- a/Examples/2-res-Annotate-prokka/tmp_files/genome3-chromo.fst-all.fna_prokka-split5N.fna-prokkaRes/EXAM.1216.00002.faa
+++ /dev/null
@@ -1,66 +0,0 @@
->PFKCIMHH_00001 N-acetylmuramoyl-L-alanine amidase AmiD
-MRALLWLVGLALLLTGCASEKGIIDEEGYQLDTRHRAQAAYPRIKVLVIHYTAENFDVSL
-ATLTGRNVSSHYLIPATPPLYGGKPRIWQLVPEQDQAWHAGVSFWRGATRLNDTSIGIEL
-ENRGWRMSGGVKSFAPFESAQIQALIPLAKDIIARYDIKPQNVVAHADIAPQRKDDPGPR
-FPWRELAAQGIGAWPDAQRVAFYLAGRAPYTPVDTATVLALLSRYGYEVKADMTAREQQR
-VIMAFQMHFRPAQWNGIADAETQAIAEALLEKYGQD
->PFKCIMHH_00002 N-acetylmuramoyl-L-alanine amidase AmiD
-MRALLWLVGLALLLTGCASEKGIIDEEGYQLDTRHRAQAAYPRIKVLVIHYTAENFDVSL
-ATLTGRNVSSHYLIPATPPLYGGKPRIWQLVPEQDQAWHAGVSFWRGATRLNDTSIGIEL
-ENRGWRMSGGVKSFAPFESAQIQALIPLAKDIIARYDIKPQNVVAHADIAPQRKDDPGPR
-FPWRELAAQGIGAWPDAQRVAFYLAGRAPYTPVDTATVLALLSRYGYEVKADMTAREQQR
-VIMAFQMHFRPAQWNGIADAETQAIAEALLEKYGQD
->PFKCIMHH_00003 5-carboxymethyl-2-hydroxymuconate Delta-isomerase
-MPKRRRLPKHYWRSTARINRARYREDSLFEDMPHFIAECTENIREQADLPGLFSKVNEAL
-AASGIFPIGGIRSRAHWLDTWQMADGKHDYAFVHMTLKIGAGRSLESRQEVGEMLFGLIK
-AHFADLMENRYLALSFEIAELHPTLNYKQNNVHALFK
->PFKCIMHH_00004 Phage shock protein B
-MSALFLAIPLTIFVLFVLPIWLWLHYSNRAGRGELSQSEQQRLLQLTDDAQRMRERIQAL
-EDILDAEHPNWRER
->PFKCIMHH_00005 hypothetical protein
-MPATKFSRRTLLTAGSALAVLPFLRALPVQAREPRETVDIKDYPADDGIASFKQAFADGQ
-TVVVPPGWVCENINAAITIPAGKTLRVQGAVRGNGRGRFILQDGCQVVGEQGGSLHNVTL
-DVRGSDCVIKGVAMSGFGPVAQIFIGGKEPQVMRNLIIDDITVTHANYAILRQGFHNQMD
-GARITHSRFSDLQGDAIEWNVAIHDRDILISDHVIERIDCTNGKINWGIGIGLAGSTYDN
-SYPEDQAVKNFVVANITGSDCRQLVHVENGKHFVIRNVKAKNITPDFSKNAGIDNATIAI
-YGCDNFVIDNIDMTNSAGMLIGYGVVKGKYLSIPQNFKLNAIRLDNRQVAYKLRGIQISS
-GNTPSFVAITNVRMTRATLELHNQPQHLFLRNINVMQTSAIGPALKMHFDLRKDVRGQFM
-ARQDTLLSLANVHAINENGQSSVDIDRINHQTVNVEAVNFSLPKRGG
->PFKCIMHH_00006 Histidine transport ATP-binding protein HisP
-MSENKLHVIDLHKRYGGHEVLKGVSLQARAGDVISIIGSSGSGKSTFLRCINFLEKPSED
-AIIVNGQNINLVRDKDGQLKVADKNQLRLLRTRLTMVFQHFNLWSHMTVLENVMEAPIQV
-LGLSKHDARERALKYLAKVGIDERAQGKYPVHLSGGQQQRVSIARALAMEPDVLLFDEPT
-SALDPELVGEVLRIMQQLAEEGKTMVVVTHEMGFVRHVSSHVIFLHQGKIEEEGDPEQVF
-GNPQSPRLQQFLKGSLK
->PFKCIMHH_00007 tRNA (guanine-N(1)-)-methyltransferase
-MRAIYRRCVFIGIVSLFPEMFRAITDYGVTGRAVKNGLLNIQSWSPRDFTHDRHRTVDDR
-PYGGGPGMLMMVQPLRDAIHAAKAAAGEGAKVIYLSPQGRKLDQAGVSELATNQKLILVC
-GRYEGVDERVIQTEIDEEWSIGDYVLSGGELPAMTLIDSVARFIPGVLGHEASAIEDSFA
-DGLLDCPHYTRPEVLEGMEVPPVLLSGNHAEIRRWRLKQSLGRTWLRRPELLENLALTEE
-QARLLAEFKTEHAQQQHKHDGMA
->PFKCIMHH_00008 hypothetical protein
-MNNHFGKGLMAGLHAPYAYSAHHAVNFCSEYKRGFVLGFTHRMFEKTGDRQLSAWEAGIL
-TRRYGLDKEMVMDFFKENHSGMAVRFFMAGYRLEG
->PFKCIMHH_00009 hypothetical protein
-MSTLLYLHGFNSSPRSAKACQLKNWLAERHPHVEMIVPQLPPYPADAAELLESLVLEHGG
-APLGLVGSSLGGYYATWLSQCFMLPAVVVNPAVRPFELLTDYLGQNENPYTGQQYVLESR
-HIYDLKVMQIDPLEAPDLIWLLQQTGDEVLDYRQAVAYYASCRQTVTEGGNHAFTGFEDY
-FNQIVDFLGLHSC
->PFKCIMHH_00010 C4-dicarboxylate TRAP transporter large permease protein DctM
-MIDPIFASCTLIAVFVVLLAMGAPIGICIVIASFSTMMLVLPFDISMFATAQKMFSSLDS
-FALLAVPFFVLSGVIMNSGGIAARLINFAKLFTGKLPGSLSYTNIVGNMMFGAISGSAIA
-ASTSIGGVMVPMSAREGYDRGFAAAVNIASAPTGMLIPPTTAFILYALASGGTSIAALFA
-GGLVAGVLWGVGCMLVTLVVAKRRNYRVFFTVQKGMALKVAVEAIPSLLLIVIIVGGIVQ
-GIFTAIEASAIAVVYTLLLTMVFYRTLKIKDLPSILLQTVVMTGVIMFLLATSSAMSFSM
-SITNIPAALSDMILGISANKLVILLVITVFLLIIGAFMDIGPAILIFTPILLPIMAKLGV
-DPVHLGIIMIYNLAIGTITPPVGSGLYVGASVGKVKVEEVIKPLLPFYGAIIGVLLLITY
-IPEIILFLPRLLGIM
->PFKCIMHH_00011 hypothetical protein
-MIINGKLIKAKDLAKAAGVSRSTVIKYYGISRENYERVATERRKLAFELRASGLKWKEVA
-EKMNTTKYSAIAYYRRYLALEKNK
->PFKCIMHH_00012 IS21 family transposase ISSen3
-MVELQHQRLMVLAEQLQLDSLIGAAPALSQQAVDQEWSYMDFLEHLLHEEKLARHQRKQA
-MYTRMAAFPAVKTFEEYDFTFATGAPQKQIQSLRSLSFIERNENIVLLGPSGVGKTHLAI
-AMGYEAVRAGIKVRFTTAADLLLQLSTSQRQGRYKTTLNRGVMAPKLLIIDEIGYLPFSQ
-EEAKLFFQVIAKRYEKSAMILTSNLPFGQWDQTFAGDAALTSAMLDRILHHSHVVQIKGE
-SYRLKQKRKAGVIAEANPE
diff --git a/Examples/2-res-Annotate-prokka/tmp_files/genome3-chromo.fst-all.fna_prokka-split5N.fna-prokkaRes/EXAM.1216.00002.ffn b/Examples/2-res-Annotate-prokka/tmp_files/genome3-chromo.fst-all.fna_prokka-split5N.fna-prokkaRes/EXAM.1216.00002.ffn
deleted file mode 100644
index a384b2732604b5565c934528801854be54c1580e..0000000000000000000000000000000000000000
--- a/Examples/2-res-Annotate-prokka/tmp_files/genome3-chromo.fst-all.fna_prokka-split5N.fna-prokkaRes/EXAM.1216.00002.ffn
+++ /dev/null
@@ -1,158 +0,0 @@
->PFKCIMHH_00001 N-acetylmuramoyl-L-alanine amidase AmiD
-ATGAGAGCGCTACTGTGGCTGGTGGGTCTTGCGTTGCTGTTAACAGGCTGCGCGAGCGAA
-AAAGGAATTATCGATGAAGAGGGATATCAGCTTGATACCCGACATCGGGCGCAGGCGGCC
-TATCCGCGCATTAAAGTCCTGGTGATTCACTATACGGCGGAAAACTTTGACGTTTCGCTG
-GCGACGTTAACGGGCCGCAACGTCAGTTCGCATTACCTGATTCCCGCAACCCCGCCATTA
-TATGGCGGTAAACCGCGCATCTGGCAACTGGTGCCGGAACAGGATCAGGCCTGGCATGCG
-GGCGTCAGTTTCTGGCGAGGCGCCACGCGTCTCAATGATACGTCTATTGGCATTGAGCTG
-GAAAATCGCGGCTGGCGAATGTCCGGCGGGGTGAAATCTTTCGCGCCGTTTGAATCCGCG
-CAAATTCAGGCATTGATTCCGTTAGCGAAGGACATTATCGCGCGCTATGACATCAAACCG
-CAGAATGTGGTGGCCCATGCGGATATCGCGCCGCAGCGTAAAGACGATCCCGGCCCGCGC
-TTCCCGTGGCGCGAGCTGGCGGCACAGGGGATTGGCGCCTGGCCTGACGCCCAGCGTGTG
-GCGTTTTATCTGGCTGGACGCGCGCCGTATACGCCAGTCGATACCGCAACGGTGCTTGCG
-TTACTCTCGCGCTATGGCTATGAAGTCAAAGCCGATATGACGGCGCGCGAGCAACAGCGG
-GTGATTATGGCGTTCCAGATGCACTTCCGTCCGGCGCAATGGAACGGTATCGCAGATGCC
-GAAACGCAGGCGATTGCCGAAGCATTACTGGAGAAGTACGGCCAGGATTAA
->PFKCIMHH_00002 N-acetylmuramoyl-L-alanine amidase AmiD
-ATGAGAGCGCTACTGTGGCTGGTGGGTCTTGCGTTGCTGTTAACAGGCTGCGCGAGCGAA
-AAAGGAATTATCGATGAAGAGGGATATCAGCTTGATACCCGACATCGGGCGCAGGCGGCC
-TATCCGCGCATTAAAGTCCTGGTGATTCACTATACGGCGGAAAACTTTGACGTTTCGCTG
-GCGACGTTAACGGGCCGCAACGTCAGTTCGCATTACCTGATTCCCGCAACCCCGCCATTA
-TATGGCGGTAAACCGCGCATCTGGCAACTGGTGCCGGAACAGGATCAGGCCTGGCATGCG
-GGCGTCAGTTTCTGGCGAGGCGCCACGCGTCTCAATGATACGTCTATTGGCATTGAGCTG
-GAAAATCGCGGCTGGCGAATGTCCGGCGGGGTGAAATCTTTCGCGCCGTTTGAATCCGCG
-CAAATTCAGGCATTGATTCCGTTAGCGAAGGACATTATCGCGCGCTATGACATCAAACCG
-CAGAATGTGGTGGCCCATGCGGATATCGCGCCGCAGCGTAAAGACGATCCCGGCCCGCGC
-TTCCCGTGGCGCGAGCTGGCGGCACAGGGGATTGGCGCCTGGCCTGACGCCCAGCGTGTG
-GCGTTTTATCTGGCTGGACGCGCGCCGTATACGCCAGTCGATACCGCAACGGTGCTTGCG
-TTACTCTCGCGCTATGGCTATGAAGTCAAAGCCGATATGACGGCGCGCGAGCAACAGCGG
-GTGATTATGGCGTTCCAGATGCACTTCCGTCCGGCGCAATGGAACGGTATCGCAGATGCC
-GAAACGCAGGCGATTGCCGAAGCATTACTGGAGAAGTACGGCCAGGATTAA
->PFKCIMHH_00003 5-carboxymethyl-2-hydroxymuconate Delta-isomerase
-ATGCCGAAACGCAGGCGATTGCCGAAGCATTACTGGAGAAGTACGGCCAGGATTAACAGG
-GCGCGGTATCGCGAGGACTCTCTCTTCGAGGACATGCCGCACTTTATTGCTGAATGTACT
-GAAAATATTCGCGAGCAGGCTGATTTACCCGGCCTGTTCAGCAAGGTAAACGAGGCGCTG
-GCCGCCAGCGGGATTTTCCCCATCGGCGGTATCCGCAGTCGCGCCCACTGGCTGGATACC
-TGGCAGATGGCTGACGGTAAGCATGATTACGCGTTTGTGCATATGACGCTGAAAATCGGC
-GCCGGGCGCAGCCTGGAGAGCCGTCAGGAAGTCGGCGAAATGCTGTTCGGGCTGATTAAA
-GCCCACTTCGCCGACCTGATGGAGAACCGCTATCTGGCGCTGTCGTTTGAGATTGCCGAG
-TTACATCCAACGCTCAATTACAAACAAAACAACGTACACGCGTTATTTAAATAG
->PFKCIMHH_00004 Phage shock protein B
-ATGAGCGCGCTATTTCTGGCCATCCCGTTAACCATTTTTGTGTTGTTTGTGTTACCGATT
-TGGCTGTGGCTGCATTACAGCAACCGCGCCGGTCGGGGAGAACTGTCGCAAAGCGAGCAG
-CAACGCTTACTGCAACTCACAGACGACGCGCAACGTATGCGCGAGCGCATTCAGGCGCTG
-GAAGACATTCTTGATGCAGAGCATCCGAACTGGAGAGAGCGCTAA
->PFKCIMHH_00005 hypothetical protein
-ATGCCCGCGACTAAATTCTCCCGACGTACCCTCCTGACGGCAGGTTCTGCGCTTGCTGTT
-CTTCCTTTCCTGCGCGCCTTGCCGGTACAGGCGCGTGAACCTCGCGAGACCGTCGATATT
-AAGGATTATCCGGCGGATGACGGTATCGCCTCGTTCAAACAGGCCTTCGCCGACGGACAG
-ACCGTGGTCGTACCGCCAGGATGGGTGTGTGAAAATATCAATGCGGCGATAACGATTCCG
-GCGGGAAAAACGCTGCGGGTACAGGGCGCGGTGCGTGGGAATGGCCGGGGACGGTTTATT
-TTGCAGGACGGGTGTCAGGTGGTGGGGGAGCAGGGCGGCAGTCTGCACAATGTGACGCTG
-GATGTTCGCGGGTCGGACTGTGTGATTAAAGGCGTGGCGATGAGCGGCTTTGGCCCCGTC
-GCGCAAATTTTCATCGGTGGTAAGGAACCGCAGGTGATGCGTAATCTCATTATCGATGAC
-ATCACCGTTACCCACGCCAACTACGCCATTCTCCGCCAGGGATTTCATAACCAAATGGAC
-GGCGCGAGGATTACGCATAGCCGCTTTAGCGATTTACAGGGGGACGCCATTGAGTGGAAT
-GTCGCGATTCACGACCGCGATATCCTGATTTCCGATCATGTCATCGAACGCATTGATTGT
-ACCAATGGCAAAATCAACTGGGGGATCGGCATCGGGCTGGCGGGTAGCACCTATGACAAC
-AGTTATCCTGAAGACCAGGCAGTAAAAAACTTTGTGGTGGCCAATATTACCGGATCTGAT
-TGCCGACAGCTTGTGCACGTAGAAAATGGCAAACATTTCGTCATTCGCAATGTCAAAGCC
-AAAAACATCACGCCCGATTTCAGTAAAAATGCGGGTATTGATAACGCAACGATCGCAATT
-TATGGCTGTGATAATTTCGTCATTGATAATATTGATATGACGAATAGTGCCGGGATGCTC
-ATCGGCTATGGCGTCGTTAAAGGAAAATACCTGTCAATTCCGCAAAACTTTAAATTAAAC
-GCTATTCGGTTGGATAATCGCCAGGTTGCTTATAAATTACGCGGCATTCAAATTTCCTCC
-GGCAACACCCCCTCTTTTGTCGCCATCACCAATGTACGGATGACGCGTGCTACGCTGGAA
-CTGCATAATCAACCGCAGCACCTCTTCCTGCGTAATATCAACGTGATGCAAACTTCAGCG
-ATTGGCCCGGCGTTAAAAATGCATTTCGATTTGCGTAAAGATGTCCGTGGTCAATTTATG
-GCCCGCCAGGACACGCTGCTTTCCCTCGCTAATGTTCATGCCATCAATGAAAACGGGCAG
-AGTTCCGTGGATATCGACAGGATTAATCACCAAACCGTGAATGTCGAAGCAGTGAATTTT
-TCGCTGCCGAAGCGGGGAGGGTAA
->PFKCIMHH_00006 Histidine transport ATP-binding protein HisP
-ATGTCAGAAAATAAATTACACGTTATCGATTTGCACAAACGCTACGGCGGTCATGAAGTG
-CTGAAAGGGGTATCGCTGCAGGCCCGCGCCGGAGATGTGATTAGCATCATCGGCTCGTCC
-GGCTCCGGTAAAAGCACTTTTTTGCGCTGTATTAACTTCCTCGAAAAACCGAGCGAAGAC
-GCGATTATCGTGAACGGTCAGAACATTAATCTGGTGCGCGACAAAGACGGGCAGCTCAAA
-GTGGCGGATAAAAATCAGCTACGCTTGTTGCGTACCCGCCTGACGATGGTGTTTCAGCAC
-TTTAACCTCTGGAGCCACATGACGGTGCTGGAAAATGTGATGGAAGCGCCGATTCAGGTA
-CTGGGATTAAGCAAGCACGACGCGCGCGAGCGGGCGTTGAAATATCTGGCGAAGGTGGGG
-ATTGATGAGCGCGCTCAGGGCAAATATCCCGTTCATCTCTCCGGTGGCCAACAGCAGCGC
-GTTTCTATTGCGCGCGCGCTGGCGATGGAACCTGACGTTTTACTGTTCGATGAACCCACT
-TCGGCGCTCGATCCTGAACTGGTCGGCGAAGTGTTGCGCATCATGCAACAACTGGCGGAA
-GAAGGCAAAACGATGGTGGTGGTCACGCATGAAATGGGCTTCGTTCGCCATGTCTCTTCG
-CACGTTATTTTTCTGCATCAGGGGAAAATTGAAGAAGAGGGCGATCCGGAGCAGGTGTTC
-GGCAATCCGCAAAGCCCGCGTTTACAGCAATTCCTGAAAGGCTCGCTGAAATAA
->PFKCIMHH_00007 tRNA (guanine-N(1)-)-methyltransferase
-ATGCGCGCGATATATCGGCGATGCGTGTTTATTGGCATCGTTAGCCTGTTTCCTGAAATG
-TTCCGCGCAATTACCGATTACGGGGTAACTGGCCGGGCAGTAAAAAATGGCCTGCTGAAC
-ATCCAAAGCTGGAGTCCTCGCGACTTCACGCATGACCGGCACCGTACCGTGGACGATCGT
-CCTTACGGCGGCGGACCAGGGATGTTAATGATGGTGCAACCCTTGCGGGACGCCATTCAC
-GCAGCAAAAGCCGCGGCAGGTGAAGGCGCTAAAGTGATTTATCTGTCGCCTCAGGGACGC
-AAGCTTGATCAAGCGGGCGTTAGCGAGCTGGCCACGAATCAGAAGCTTATTCTGGTGTGT
-GGTCGCTACGAAGGCGTAGATGAGCGCGTAATTCAGACCGAAATTGACGAAGAATGGTCA
-ATTGGCGATTACGTTCTCAGCGGTGGCGAACTACCGGCAATGACGCTGATTGACTCCGTC
-GCCCGGTTTATACCGGGAGTTCTGGGGCATGAAGCATCAGCAATCGAAGATTCGTTTGCT
-GATGGGTTGCTGGATTGTCCGCACTATACGCGCCCTGAAGTGTTAGAGGGGATGGAAGTA
-CCGCCAGTATTGCTGTCGGGAAACCATGCTGAGATACGTCGCTGGCGTTTGAAACAGTCG
-CTGGGCCGAACCTGGCTTAGAAGACCTGAACTTCTGGAAAACCTGGCTCTGACTGAAGAG
-CAAGCAAGGTTGCTGGCGGAGTTCAAAACAGAACACGCACAACAGCAGCATAAACATGAT
-GGGATGGCATAG
->PFKCIMHH_00008 hypothetical protein
-ATGAATAATCATTTTGGGAAAGGGTTAATGGCCGGGTTGCACGCGCCATATGCATATAGC
-GCGCATCATGCGGTGAATTTCTGTTCTGAGTATAAACGTGGCTTTGTATTGGGTTTTACA
-CACCGTATGTTCGAAAAGACCGGCGATCGTCAACTTAGCGCGTGGGAGGCTGGAATTCTG
-ACGCGTCGCTATGGTCTGGATAAAGAAATGGTGATGGATTTCTTTAAAGAGAATCATTCC
-GGGATGGCGGTTCGCTTCTTTATGGCCGGTTATCGACTCGAAGGTTGA
->PFKCIMHH_00009 hypothetical protein
-ATGTCTACGCTTCTCTATTTGCACGGATTCAACAGTTCCCCTCGCTCGGCAAAAGCGTGC
-CAGCTAAAAAACTGGCTGGCGGAGCGTCATCCGCATGTTGAGATGATCGTCCCTCAACTA
-CCGCCGTATCCTGCCGATGCGGCGGAGTTGCTGGAGTCTCTCGTGCTTGAGCATGGCGGT
-GCGCCATTAGGGCTGGTAGGATCGTCGCTGGGTGGTTATTACGCCACCTGGCTGTCGCAA
-TGTTTTATGCTGCCGGCTGTGGTGGTGAATCCCGCCGTGCGGCCCTTTGAATTACTGACC
-GACTATCTCGGTCAGAACGAGAACCCCTACACCGGGCAGCAATATGTGCTAGAGTCTCGC
-CATATTTATGATCTTAAAGTCATGCAGATTGACCCGCTGGAAGCGCCGGACCTGATCTGG
-CTACTGCAACAGACGGGCGATGAAGTGCTGGATTACCGCCAGGCGGTGGCATATTACGCC
-TCCTGCCGTCAGACAGTGACCGAGGGTGGTAATCACGCATTCACGGGCTTCGAAGATTAT
-TTCAACCAGATTGTCGATTTTCTTGGACTGCACAGTTGCTGA
->PFKCIMHH_00010 C4-dicarboxylate TRAP transporter large permease protein DctM
-ATGATTGACCCTATTTTTGCGTCCTGTACGCTAATTGCCGTCTTTGTTGTTTTACTGGCC
-ATGGGCGCGCCTATCGGGATCTGCATCGTTATCGCCTCTTTCAGCACCATGATGCTGGTA
-CTGCCTTTCGATATTTCGATGTTCGCCACCGCGCAAAAAATGTTCTCCAGCCTGGACAGT
-TTTGCCTTGCTGGCCGTGCCGTTCTTCGTTTTGTCCGGGGTGATCATGAATAGCGGGGGA
-ATTGCCGCCCGGCTGATCAATTTTGCCAAACTGTTTACTGGCAAACTGCCCGGTTCGCTC
-TCTTATACCAACATCGTCGGCAATATGATGTTCGGTGCAATTTCCGGATCGGCAATTGCC
-GCCTCAACCTCCATCGGCGGCGTGATGGTGCCGATGAGCGCGCGCGAAGGTTACGATCGC
-GGCTTTGCGGCCGCGGTGAATATCGCCTCCGCGCCGACGGGAATGTTAATTCCGCCCACC
-ACGGCTTTTATCCTTTATGCGCTGGCAAGCGGGGGAACATCGATTGCCGCTCTGTTCGCC
-GGCGGTCTGGTCGCGGGAGTGCTGTGGGGCGTTGGCTGTATGCTGGTCACGCTGGTAGTC
-GCTAAGCGTCGAAATTATCGGGTTTTCTTCACCGTCCAAAAAGGCATGGCGCTAAAAGTT
-GCCGTTGAGGCCATTCCCAGCCTGTTACTGATCGTGATTATCGTCGGCGGCATTGTGCAG
-GGGATTTTCACCGCCATTGAAGCCTCCGCGATTGCCGTGGTGTATACGTTATTGCTGACG
-ATGGTGTTTTACCGCACGCTGAAAATTAAGGATTTGCCTTCGATTTTGCTCCAGACAGTG
-GTAATGACCGGGGTCATCATGTTCCTGCTGGCAACCTCTTCGGCGATGTCCTTCTCAATG
-TCGATCACCAATATTCCTGCGGCGCTGAGCGATATGATCCTCGGTATTTCCGCCAATAAA
-CTGGTTATCCTGTTAGTCATTACCGTCTTTTTGTTGATTATCGGCGCATTTATGGATATC
-GGTCCGGCCATTCTGATTTTTACCCCGATTCTGCTGCCGATCATGGCTAAACTGGGCGTC
-GATCCGGTGCATTTGGGCATTATCATGATCTATAACCTGGCGATTGGCACCATTACGCCG
-CCAGTTGGCAGTGGTTTATATGTCGGGGCGAGCGTCGGTAAGGTCAAAGTTGAGGAAGTG
-ATTAAACCGTTGCTGCCTTTTTACGGCGCGATTATCGGCGTTCTGTTATTAATTACCTAC
-ATTCCGGAAATCATACTGTTCTTACCCCGTCTACTGGGCATCATGTAA
->PFKCIMHH_00011 hypothetical protein
-ATGATAATTAATGGGAAATTAATTAAAGCAAAAGACTTAGCTAAGGCTGCAGGTGTATCT
-CGTTCAACAGTGATTAAATATTACGGCATTAGCCGTGAGAATTACGAAAGGGTAGCAACT
-GAAAGAAGGAAGCTTGCTTTTGAACTAAGAGCATCAGGTTTAAAATGGAAAGAAGTTGCT
-GAAAAAATGAACACGACAAAATATAGCGCAATTGCATATTATAGACGATATTTAGCATTA
-GAGAAAAACAAATAA
->PFKCIMHH_00012 IS21 family transposase ISSen3
-ATGGTCGAACTGCAACATCAACGGCTGATGGTGCTTGCCGAACAGCTCCAGCTGGACAGT
-CTTATCGGCGCAGCGCCGGCGCTGTCGCAACAGGCGGTGGATCAGGAATGGAGCTACATG
-GACTTCCTGGAGCACCTGTTACATGAGGAGAAACTGGCCCGGCATCAGCGTAAACAGGCG
-ATGTACACGCGGATGGCAGCCTTCCCGGCGGTAAAGACGTTCGAGGAGTACGACTTCACC
-TTCGCCACCGGCGCTCCTCAGAAGCAAATCCAGTCGCTGCGATCCCTGAGCTTCATAGAG
-CGTAACGAAAACATCGTGTTGCTGGGGCCATCGGGCGTGGGAAAAACGCATCTGGCGATA
-GCCATGGGCTACGAAGCAGTACGGGCGGGCATCAAGGTTCGCTTCACAACAGCAGCGGAC
-CTGCTGCTACAGCTGTCCACTTCACAGCGTCAGGGCCGTTACAAAACGACTCTCAATCGT
-GGTGTCATGGCCCCGAAGCTGCTTATCATCGATGAAATAGGTTATCTGCCGTTCAGTCAG
-GAGGAAGCCAAGCTGTTCTTCCAGGTCATCGCCAAACGTTACGAGAAGAGCGCGATGATC
-CTGACCTCCAACCTGCCGTTCGGGCAGTGGGATCAGACGTTCGCCGGTGATGCAGCGCTG
-ACATCGGCGATGCTGGACCGGATCTTACATCACTCACACGTCGTGCAAATAAAAGGGGAA
-AGCTATCGACTGAAGCAGAAACGAAAGGCCGGGGTTATAGCTGAAGCTAATCCTGAGTAA
diff --git a/Examples/2-res-Annotate-prokka/tmp_files/genome3-chromo.fst-all.fna_prokka-split5N.fna-prokkaRes/EXAM.1216.00002.fna b/Examples/2-res-Annotate-prokka/tmp_files/genome3-chromo.fst-all.fna_prokka-split5N.fna-prokkaRes/EXAM.1216.00002.fna
deleted file mode 100644
index 07bd5c4b160a7dc19f4e7c640e3813aeff601694..0000000000000000000000000000000000000000
--- a/Examples/2-res-Annotate-prokka/tmp_files/genome3-chromo.fst-all.fna_prokka-split5N.fna-prokkaRes/EXAM.1216.00002.fna
+++ /dev/null
@@ -1,151 +0,0 @@
->header_genome3_1
-ATGAGAGCGCTACTGTGGCTGGTGGGTCTTGCGTTGCTGTTAACAGGCTGCGCGAGCGAA
-AAAGGAATTATCGATGAAGAGGGATATCAGCTTGATACCCGACATCGGGCGCAGGCGGCC
-TATCCGCGCATTAAAGTCCTGGTGATTCACTATACGGCGGAAAACTTTGACGTTTCGCTG
-GCGACGTTAACGGGCCGCAACGTCAGTTCGCATTACCTGATTCCCGCAACCCCGCCATTA
-TATGGCGGTAAACCGCGCATCTGGCAACTGGTGCCGGAACAGGATCAGGCCTGGCATGCG
-GGCGTCAGTTTCTGGCGAGGCGCCACGCGTCTCAATGATACGTCTATTGGCATTGAGCTG
-GAAAATCGCGGCTGGCGAATGTCCGGCGGGGTGAAATCTTTCGCGCCGTTTGAATCCGCG
-CAAATTCAGGCATTGATTCCGTTAGCGAAGGACATTATCGCGCGCTATGACATCAAACCG
-CAGAATGTGGTGGCCCATGCGGATATCGCGCCGCAGCGTAAAGACGATCCCGGCCCGCGC
-TTCCCGTGGCGCGAGCTGGCGGCACAGGGGATTGGCGCCTGGCCTGACGCCCAGCGTGTG
-GCGTTTTATCTGGCTGGACGCGCGCCGTATACGCCAGTCGATACCGCAACGGTGCTTGCG
-TTACTCTCGCGCTATGGCTATGAAGTCAAAGCCGATATGACGGCGCGCGAGCAACAGCGG
-GTGATTATGGCGTTCCAGATGCACTTCCGTCCGGCGCAATGGAACGGTATCGCAGATGCC
-GAAACGCAGGCGATTGCCGAAGCATTACTGGAGAAGTACGGCCAGGATTAACGAGTCCGG
-GAGCGGCGAGATTCCGGGCAGAGGAGGCGGCTATAGCGGATGAGAGCGCTACTGTGGCTG
-GTGGGTCTTGCGTTGCTGTTAACAGGCTGCGCGAGCGAAAAAGGAATTATCGATGAAGAG
-GGATATCAGCTTGATACCCGACATCGGGCGCAGGCGGCCTATCCGCGCATTAAAGTCCTG
-GTGATTCACTATACGGCGGAAAACTTTGACGTTTCGCTGGCGACGTTAACGGGCCGCAAC
-GTCAGTTCGCATTACCTGATTCCCGCAACCCCGCCATTATATGGCGGTAAACCGCGCATC
-TGGCAACTGGTGCCGGAACAGGATCAGGCCTGGCATGCGGGCGTCAGTTTCTGGCGAGGC
-GCCACGCGTCTCAATGATACGTCTATTGGCATTGAGCTGGAAAATCGCGGCTGGCGAATG
-TCCGGCGGGGTGAAATCTTTCGCGCCGTTTGAATCCGCGCAAATTCAGGCATTGATTCCG
-TTAGCGAAGGACATTATCGCGCGCTATGACATCAAACCGCAGAATGTGGTGGCCCATGCG
-GATATCGCGCCGCAGCGTAAAGACGATCCCGGCCCGCGCTTCCCGTGGCGCGAGCTGGCG
-GCACAGGGGATTGGCGCCTGGCCTGACGCCCAGCGTGTGGCGTTTTATCTGGCTGGACGC
-GCGCCGTATACGCCAGTCGATACCGCAACGGTGCTTGCGTTACTCTCGCGCTATGGCTAT
-GAAGTCAAAGCCGATATGACGGCGCGCGAGCAACAGCGGGTGATTATGGCGTTCCAGATG
-CACTTCCGTCCGGCGCAATGGAACGGTATCGCAGATGCCGAAACGCAGGCGATTGCCGAA
-GCATTACTGGAGAAGTACGGCCAGGATTAACAGGGCGCGGTATCGCGAGGACTCTCTCTT
-CGAGGACATGCCGCACTTTATTGCTGAATGTACTGAAAATATTCGCGAGCAGGCTGATTT
-ACCCGGCCTGTTCAGCAAGGTAAACGAGGCGCTGGCCGCCAGCGGGATTTTCCCCATCGG
-CGGTATCCGCAGTCGCGCCCACTGGCTGGATACCTGGCAGATGGCTGACGGTAAGCATGA
-TTACGCGTTTGTGCATATGACGCTGAAAATCGGCGCCGGGCGCAGCCTGGAGAGCCGTCA
-GGAAGTCGGCGAAATGCTGTTCGGGCTGATTAAAGCCCACTTCGCCGACCTGATGGAGAA
-CCGCTATCTGGCGCTGTCGTTTGAGATTGCCGAGTTACATCCAACGCTCAATTACAAACA
-AAACAACGTACACGCGTTATTTAAATAGCCCGAGTATTAGCGCGCGGCGGCGCTATAGGC
-GCGCTATAGGCATGAGCGCGCTATTTCTGGCCATCCCGTTAACCATTTTTGTGTTGTTTG
-TGTTACCGATTTGGCTGTGGCTGCATTACAGCAACCGCGCCGGTCGGGGAGAACTGTCGC
-AAAGCGAGCAGCAACGCTTACTGCAACTCACAGACGACGCGCAACGTATGCGCGAGCGCA
-TTCAGGCGCTGGAAGACATTCTTGATGCAGAGCATCCGAACTGGAGAGAGCGCTAACGAG
-AGTCTCGGAGGAGCGGCGCTCTGGATGCCCGCGACTAAATTCTCCCGACGTACCCTCCTG
-ACGGCAGGTTCTGCGCTTGCTGTTCTTCCTTTCCTGCGCGCCTTGCCGGTACAGGCGCGT
-GAACCTCGCGAGACCGTCGATATTAAGGATTATCCGGCGGATGACGGTATCGCCTCGTTC
-AAACAGGCCTTCGCCGACGGACAGACCGTGGTCGTACCGCCAGGATGGGTGTGTGAAAAT
-ATCAATGCGGCGATAACGATTCCGGCGGGAAAAACGCTGCGGGTACAGGGCGCGGTGCGT
-GGGAATGGCCGGGGACGGTTTATTTTGCAGGACGGGTGTCAGGTGGTGGGGGAGCAGGGC
-GGCAGTCTGCACAATGTGACGCTGGATGTTCGCGGGTCGGACTGTGTGATTAAAGGCGTG
-GCGATGAGCGGCTTTGGCCCCGTCGCGCAAATTTTCATCGGTGGTAAGGAACCGCAGGTG
-ATGCGTAATCTCATTATCGATGACATCACCGTTACCCACGCCAACTACGCCATTCTCCGC
-CAGGGATTTCATAACCAAATGGACGGCGCGAGGATTACGCATAGCCGCTTTAGCGATTTA
-CAGGGGGACGCCATTGAGTGGAATGTCGCGATTCACGACCGCGATATCCTGATTTCCGAT
-CATGTCATCGAACGCATTGATTGTACCAATGGCAAAATCAACTGGGGGATCGGCATCGGG
-CTGGCGGGTAGCACCTATGACAACAGTTATCCTGAAGACCAGGCAGTAAAAAACTTTGTG
-GTGGCCAATATTACCGGATCTGATTGCCGACAGCTTGTGCACGTAGAAAATGGCAAACAT
-TTCGTCATTCGCAATGTCAAAGCCAAAAACATCACGCCCGATTTCAGTAAAAATGCGGGT
-ATTGATAACGCAACGATCGCAATTTATGGCTGTGATAATTTCGTCATTGATAATATTGAT
-ATGACGAATAGTGCCGGGATGCTCATCGGCTATGGCGTCGTTAAAGGAAAATACCTGTCA
-ATTCCGCAAAACTTTAAATTAAACGCTATTCGGTTGGATAATCGCCAGGTTGCTTATAAA
-TTACGCGGCATTCAAATTTCCTCCGGCAACACCCCCTCTTTTGTCGCCATCACCAATGTA
-CGGATGACGCGTGCTACGCTGGAACTGCATAATCAACCGCAGCACCTCTTCCTGCGTAAT
-ATCAACGTGATGCAAACTTCAGCGATTGGCCCGGCGTTAAAAATGCATTTCGATTTGCGT
-AAAGATGTCCGTGGTCAATTTATGGCCCGCCAGGACACGCTGCTTTCCCTCGCTAATGTT
-CATGCCATCAATGAAAACGGGCAGAGTTCCGTGGATATCGACAGGATTAATCACCAAACC
-GTGAATGTCGAAGCAGTGAATTTTTCGCTGCCGAAGCGGGGAGGGTAACGCGTCTGCGCG
-CGCGGAGAGAGGCTCTCAGGACATGTCAGAAAATAAATTACACGTTATCGATTTGCACAA
-ACGCTACGGCGGTCATGAAGTGCTGAAAGGGGTATCGCTGCAGGCCCGCGCCGGAGATGT
-GATTAGCATCATCGGCTCGTCCGGCTCCGGTAAAAGCACTTTTTTGCGCTGTATTAACTT
-CCTCGAAAAACCGAGCGAAGACGCGATTATCGTGAACGGTCAGAACATTAATCTGGTGCG
-CGACAAAGACGGGCAGCTCAAAGTGGCGGATAAAAATCAGCTACGCTTGTTGCGTACCCG
-CCTGACGATGGTGTTTCAGCACTTTAACCTCTGGAGCCACATGACGGTGCTGGAAAATGT
-GATGGAAGCGCCGATTCAGGTACTGGGATTAAGCAAGCACGACGCGCGCGAGCGGGCGTT
-GAAATATCTGGCGAAGGTGGGGATTGATGAGCGCGCTCAGGGCAAATATCCCGTTCATCT
-CTCCGGTGGCCAACAGCAGCGCGTTTCTATTGCGCGCGCGCTGGCGATGGAACCTGACGT
-TTTACTGTTCGATGAACCCACTTCGGCGCTCGATCCTGAACTGGTCGGCGAAGTGTTGCG
-CATCATGCAACAACTGGCGGAAGAAGGCAAAACGATGGTGGTGGTCACGCATGAAATGGG
-CTTCGTTCGCCATGTCTCTTCGCACGTTATTTTTCTGCATCAGGGGAAAATTGAAGAAGA
-GGGCGATCCGGAGCAGGTGTTCGGCAATCCGCAAAGCCCGCGTTTACAGCAATTCCTGAA
-AGGCTCGCTGAAATAACCGGATGCGCGCGATATATCGGCGATGCGTGTTTATTGGCATCG
-TTAGCCTGTTTCCTGAAATGTTCCGCGCAATTACCGATTACGGGGTAACTGGCCGGGCAG
-TAAAAAATGGCCTGCTGAACATCCAAAGCTGGAGTCCTCGCGACTTCACGCATGACCGGC
-ACCGTACCGTGGACGATCGTCCTTACGGCGGCGGACCAGGGATGTTAATGATGGTGCAAC
-CCTTGCGGGACGCCATTCACGCAGCAAAAGCCGCGGCAGGTGAAGGCGCTAAAGTGATTT
-ATCTGTCGCCTCAGGGACGCAAGCTTGATCAAGCGGGCGTTAGCGAGCTGGCCACGAATC
-AGAAGCTTATTCTGGTGTGTGGTCGCTACGAAGGCGTAGATGAGCGCGTAATTCAGACCG
-AAATTGACGAAGAATGGTCAATTGGCGATTACGTTCTCAGCGGTGGCGAACTACCGGCAA
-TGACGCTGATTGACTCCGTCGCCCGGTTTATACCGGGAGTTCTGGGGCATGAAGCATCAG
-CAATCGAAGATTCGTTTGCTGATGGGTTGCTGGATTGTCCGCACTATACGCGCCCTGAAG
-TGTTAGAGGGGATGGAAGTACCGCCAGTATTGCTGTCGGGAAACCATGCTGAGATACGTC
-GCTGGCGTTTGAAACAGTCGCTGGGCCGAACCTGGCTTAGAAGACCTGAACTTCTGGAAA
-ACCTGGCTCTGACTGAAGAGCAAGCAAGGTTGCTGGCGGAGTTCAAAACAGAACACGCAC
-AACAGCAGCATAAACATGATGGGATGGCATAGCCGGCTCTGCGAGAGAGGAGCGCTCGCA
-TGAATAATCATTTTGGGAAAGGGTTAATGGCCGGGTTGCACGCGCCATATGCATATAGCG
-CGCATCATGCGGTGAATTTCTGTTCTGAGTATAAACGTGGCTTTGTATTGGGTTTTACAC
-ACCGTATGTTCGAAAAGACCGGCGATCGTCAACTTAGCGCGTGGGAGGCTGGAATTCTGA
-CGCGTCGCTATGGTCTGGATAAAGAAATGGTGATGGATTTCTTTAAAGAGAATCATTCCG
-GGATGGCGGTTCGCTTCTTTATGGCCGGTTATCGACTCGAAGGTTGA
->genome3_plasmi_2
-ATGTCTACGCTTCTCTATTTGCACGGATTCAACAGTTCCCCTCGCTCGGCAAAAGCGTGC
-CAGCTAAAAAACTGGCTGGCGGAGCGTCATCCGCATGTTGAGATGATCGTCCCTCAACTA
-CCGCCGTATCCTGCCGATGCGGCGGAGTTGCTGGAGTCTCTCGTGCTTGAGCATGGCGGT
-GCGCCATTAGGGCTGGTAGGATCGTCGCTGGGTGGTTATTACGCCACCTGGCTGTCGCAA
-TGTTTTATGCTGCCGGCTGTGGTGGTGAATCCCGCCGTGCGGCCCTTTGAATTACTGACC
-GACTATCTCGGTCAGAACGAGAACCCCTACACCGGGCAGCAATATGTGCTAGAGTCTCGC
-CATATTTATGATCTTAAAGTCATGCAGATTGACCCGCTGGAAGCGCCGGACCTGATCTGG
-CTACTGCAACAGACGGGCGATGAAGTGCTGGATTACCGCCAGGCGGTGGCATATTACGCC
-TCCTGCCGTCAGACAGTGACCGAGGGTGGTAATCACGCATTCACGGGCTTCGAAGATTAT
-TTCAACCAGATTGTCGATTTTCTTGGACTGCACAGTTGCTGACGCGTAGCGGCCGGAATC
-TTCTCGGAGAGGCGCTTCTCTCTCGGAGATGATTGACCCTATTTTTGCGTCCTGTACGCT
-AATTGCCGTCTTTGTTGTTTTACTGGCCATGGGCGCGCCTATCGGGATCTGCATCGTTAT
-CGCCTCTTTCAGCACCATGATGCTGGTACTGCCTTTCGATATTTCGATGTTCGCCACCGC
-GCAAAAAATGTTCTCCAGCCTGGACAGTTTTGCCTTGCTGGCCGTGCCGTTCTTCGTTTT
-GTCCGGGGTGATCATGAATAGCGGGGGAATTGCCGCCCGGCTGATCAATTTTGCCAAACT
-GTTTACTGGCAAACTGCCCGGTTCGCTCTCTTATACCAACATCGTCGGCAATATGATGTT
-CGGTGCAATTTCCGGATCGGCAATTGCCGCCTCAACCTCCATCGGCGGCGTGATGGTGCC
-GATGAGCGCGCGCGAAGGTTACGATCGCGGCTTTGCGGCCGCGGTGAATATCGCCTCCGC
-GCCGACGGGAATGTTAATTCCGCCCACCACGGCTTTTATCCTTTATGCGCTGGCAAGCGG
-GGGAACATCGATTGCCGCTCTGTTCGCCGGCGGTCTGGTCGCGGGAGTGCTGTGGGGCGT
-TGGCTGTATGCTGGTCACGCTGGTAGTCGCTAAGCGTCGAAATTATCGGGTTTTCTTCAC
-CGTCCAAAAAGGCATGGCGCTAAAAGTTGCCGTTGAGGCCATTCCCAGCCTGTTACTGAT
-CGTGATTATCGTCGGCGGCATTGTGCAGGGGATTTTCACCGCCATTGAAGCCTCCGCGAT
-TGCCGTGGTGTATACGTTATTGCTGACGATGGTGTTTTACCGCACGCTGAAAATTAAGGA
-TTTGCCTTCGATTTTGCTCCAGACAGTGGTAATGACCGGGGTCATCATGTTCCTGCTGGC
-AACCTCTTCGGCGATGTCCTTCTCAATGTCGATCACCAATATTCCTGCGGCGCTGAGCGA
-TATGATCCTCGGTATTTCCGCCAATAAACTGGTTATCCTGTTAGTCATTACCGTCTTTTT
-GTTGATTATCGGCGCATTTATGGATATCGGTCCGGCCATTCTGATTTTTACCCCGATTCT
-GCTGCCGATCATGGCTAAACTGGGCGTCGATCCGGTGCATTTGGGCATTATCATGATCTA
-TAACCTGGCGATTGGCACCATTACGCCGCCAGTTGGCAGTGGTTTATATGTCGGGGCGAG
-CGTCGGTAAGGTCAAAGTTGAGGAAGTGATTAAACCGTTGCTGCCTTTTTACGGCGCGAT
-TATCGGCGTTCTGTTATTAATTACCTACATTCCGGAAATCATACTGTTCTTACCCCGTCT
-ACTGGGCATCATGTAAACCCGATGGCGCGCAGAGGCGCGAGTTCTGGA
->genome3_plasmi_3
-CACAGGGCTTAGAGGCGCTATGGCAATGATAATTAATGGGAAATTAATTAAAGCAAAAGA
-CTTAGCTAAGGCTGCAGGTGTATCTCGTTCAACAGTGATTAAATATTACGGCATTAGCCG
-TGAGAATTACGAAAGGGTAGCAACTGAAAGAAGGAAGCTTGCTTTTGAACTAAGAGCATC
-AGGTTTAAAATGGAAAGAAGTTGCTGAAAAAATGAACACGACAAAATATAGCGCAATTGC
-ATATTATAGACGATATTTAGCATTAGAGAAAAACAAATAACAGGCGCTAAGGCGGCGATC
-CTAGCGCGCGATCGCGCATGCGATGGTCGAACTGCAACATCAACGGCTGATGGTGCTTGC
-CGAACAGCTCCAGCTGGACAGTCTTATCGGCGCAGCGCCGGCGCTGTCGCAACAGGCGGT
-GGATCAGGAATGGAGCTACATGGACTTCCTGGAGCACCTGTTACATGAGGAGAAACTGGC
-CCGGCATCAGCGTAAACAGGCGATGTACACGCGGATGGCAGCCTTCCCGGCGGTAAAGAC
-GTTCGAGGAGTACGACTTCACCTTCGCCACCGGCGCTCCTCAGAAGCAAATCCAGTCGCT
-GCGATCCCTGAGCTTCATAGAGCGTAACGAAAACATCGTGTTGCTGGGGCCATCGGGCGT
-GGGAAAAACGCATCTGGCGATAGCCATGGGCTACGAAGCAGTACGGGCGGGCATCAAGGT
-TCGCTTCACAACAGCAGCGGACCTGCTGCTACAGCTGTCCACTTCACAGCGTCAGGGCCG
-TTACAAAACGACTCTCAATCGTGGTGTCATGGCCCCGAAGCTGCTTATCATCGATGAAAT
-AGGTTATCTGCCGTTCAGTCAGGAGGAAGCCAAGCTGTTCTTCCAGGTCATCGCCAAACG
-TTACGAGAAGAGCGCGATGATCCTGACCTCCAACCTGCCGTTCGGGCAGTGGGATCAGAC
-GTTCGCCGGTGATGCAGCGCTGACATCGGCGATGCTGGACCGGATCTTACATCACTCACA
-CGTCGTGCAAATAAAAGGGGAAAGCTATCGACTGAAGCAGAAACGAAAGGCCGGGGTTAT
-AGCTGAAGCTAATCCTGAGTAA
diff --git a/Examples/2-res-Annotate-prokka/tmp_files/genome3-chromo.fst-all.fna_prokka-split5N.fna-prokkaRes/EXAM.1216.00002.fsa b/Examples/2-res-Annotate-prokka/tmp_files/genome3-chromo.fst-all.fna_prokka-split5N.fna-prokkaRes/EXAM.1216.00002.fsa
deleted file mode 100644
index b25cc5564aa6b94e47594a34e65b0524a5bcda96..0000000000000000000000000000000000000000
--- a/Examples/2-res-Annotate-prokka/tmp_files/genome3-chromo.fst-all.fna_prokka-split5N.fna-prokkaRes/EXAM.1216.00002.fsa
+++ /dev/null
@@ -1,151 +0,0 @@
->header_genome3_1 [gcode=11] [organism=Genus species] [strain=strain]
-ATGAGAGCGCTACTGTGGCTGGTGGGTCTTGCGTTGCTGTTAACAGGCTGCGCGAGCGAA
-AAAGGAATTATCGATGAAGAGGGATATCAGCTTGATACCCGACATCGGGCGCAGGCGGCC
-TATCCGCGCATTAAAGTCCTGGTGATTCACTATACGGCGGAAAACTTTGACGTTTCGCTG
-GCGACGTTAACGGGCCGCAACGTCAGTTCGCATTACCTGATTCCCGCAACCCCGCCATTA
-TATGGCGGTAAACCGCGCATCTGGCAACTGGTGCCGGAACAGGATCAGGCCTGGCATGCG
-GGCGTCAGTTTCTGGCGAGGCGCCACGCGTCTCAATGATACGTCTATTGGCATTGAGCTG
-GAAAATCGCGGCTGGCGAATGTCCGGCGGGGTGAAATCTTTCGCGCCGTTTGAATCCGCG
-CAAATTCAGGCATTGATTCCGTTAGCGAAGGACATTATCGCGCGCTATGACATCAAACCG
-CAGAATGTGGTGGCCCATGCGGATATCGCGCCGCAGCGTAAAGACGATCCCGGCCCGCGC
-TTCCCGTGGCGCGAGCTGGCGGCACAGGGGATTGGCGCCTGGCCTGACGCCCAGCGTGTG
-GCGTTTTATCTGGCTGGACGCGCGCCGTATACGCCAGTCGATACCGCAACGGTGCTTGCG
-TTACTCTCGCGCTATGGCTATGAAGTCAAAGCCGATATGACGGCGCGCGAGCAACAGCGG
-GTGATTATGGCGTTCCAGATGCACTTCCGTCCGGCGCAATGGAACGGTATCGCAGATGCC
-GAAACGCAGGCGATTGCCGAAGCATTACTGGAGAAGTACGGCCAGGATTAACGAGTCCGG
-GAGCGGCGAGATTCCGGGCAGAGGAGGCGGCTATAGCGGATGAGAGCGCTACTGTGGCTG
-GTGGGTCTTGCGTTGCTGTTAACAGGCTGCGCGAGCGAAAAAGGAATTATCGATGAAGAG
-GGATATCAGCTTGATACCCGACATCGGGCGCAGGCGGCCTATCCGCGCATTAAAGTCCTG
-GTGATTCACTATACGGCGGAAAACTTTGACGTTTCGCTGGCGACGTTAACGGGCCGCAAC
-GTCAGTTCGCATTACCTGATTCCCGCAACCCCGCCATTATATGGCGGTAAACCGCGCATC
-TGGCAACTGGTGCCGGAACAGGATCAGGCCTGGCATGCGGGCGTCAGTTTCTGGCGAGGC
-GCCACGCGTCTCAATGATACGTCTATTGGCATTGAGCTGGAAAATCGCGGCTGGCGAATG
-TCCGGCGGGGTGAAATCTTTCGCGCCGTTTGAATCCGCGCAAATTCAGGCATTGATTCCG
-TTAGCGAAGGACATTATCGCGCGCTATGACATCAAACCGCAGAATGTGGTGGCCCATGCG
-GATATCGCGCCGCAGCGTAAAGACGATCCCGGCCCGCGCTTCCCGTGGCGCGAGCTGGCG
-GCACAGGGGATTGGCGCCTGGCCTGACGCCCAGCGTGTGGCGTTTTATCTGGCTGGACGC
-GCGCCGTATACGCCAGTCGATACCGCAACGGTGCTTGCGTTACTCTCGCGCTATGGCTAT
-GAAGTCAAAGCCGATATGACGGCGCGCGAGCAACAGCGGGTGATTATGGCGTTCCAGATG
-CACTTCCGTCCGGCGCAATGGAACGGTATCGCAGATGCCGAAACGCAGGCGATTGCCGAA
-GCATTACTGGAGAAGTACGGCCAGGATTAACAGGGCGCGGTATCGCGAGGACTCTCTCTT
-CGAGGACATGCCGCACTTTATTGCTGAATGTACTGAAAATATTCGCGAGCAGGCTGATTT
-ACCCGGCCTGTTCAGCAAGGTAAACGAGGCGCTGGCCGCCAGCGGGATTTTCCCCATCGG
-CGGTATCCGCAGTCGCGCCCACTGGCTGGATACCTGGCAGATGGCTGACGGTAAGCATGA
-TTACGCGTTTGTGCATATGACGCTGAAAATCGGCGCCGGGCGCAGCCTGGAGAGCCGTCA
-GGAAGTCGGCGAAATGCTGTTCGGGCTGATTAAAGCCCACTTCGCCGACCTGATGGAGAA
-CCGCTATCTGGCGCTGTCGTTTGAGATTGCCGAGTTACATCCAACGCTCAATTACAAACA
-AAACAACGTACACGCGTTATTTAAATAGCCCGAGTATTAGCGCGCGGCGGCGCTATAGGC
-GCGCTATAGGCATGAGCGCGCTATTTCTGGCCATCCCGTTAACCATTTTTGTGTTGTTTG
-TGTTACCGATTTGGCTGTGGCTGCATTACAGCAACCGCGCCGGTCGGGGAGAACTGTCGC
-AAAGCGAGCAGCAACGCTTACTGCAACTCACAGACGACGCGCAACGTATGCGCGAGCGCA
-TTCAGGCGCTGGAAGACATTCTTGATGCAGAGCATCCGAACTGGAGAGAGCGCTAACGAG
-AGTCTCGGAGGAGCGGCGCTCTGGATGCCCGCGACTAAATTCTCCCGACGTACCCTCCTG
-ACGGCAGGTTCTGCGCTTGCTGTTCTTCCTTTCCTGCGCGCCTTGCCGGTACAGGCGCGT
-GAACCTCGCGAGACCGTCGATATTAAGGATTATCCGGCGGATGACGGTATCGCCTCGTTC
-AAACAGGCCTTCGCCGACGGACAGACCGTGGTCGTACCGCCAGGATGGGTGTGTGAAAAT
-ATCAATGCGGCGATAACGATTCCGGCGGGAAAAACGCTGCGGGTACAGGGCGCGGTGCGT
-GGGAATGGCCGGGGACGGTTTATTTTGCAGGACGGGTGTCAGGTGGTGGGGGAGCAGGGC
-GGCAGTCTGCACAATGTGACGCTGGATGTTCGCGGGTCGGACTGTGTGATTAAAGGCGTG
-GCGATGAGCGGCTTTGGCCCCGTCGCGCAAATTTTCATCGGTGGTAAGGAACCGCAGGTG
-ATGCGTAATCTCATTATCGATGACATCACCGTTACCCACGCCAACTACGCCATTCTCCGC
-CAGGGATTTCATAACCAAATGGACGGCGCGAGGATTACGCATAGCCGCTTTAGCGATTTA
-CAGGGGGACGCCATTGAGTGGAATGTCGCGATTCACGACCGCGATATCCTGATTTCCGAT
-CATGTCATCGAACGCATTGATTGTACCAATGGCAAAATCAACTGGGGGATCGGCATCGGG
-CTGGCGGGTAGCACCTATGACAACAGTTATCCTGAAGACCAGGCAGTAAAAAACTTTGTG
-GTGGCCAATATTACCGGATCTGATTGCCGACAGCTTGTGCACGTAGAAAATGGCAAACAT
-TTCGTCATTCGCAATGTCAAAGCCAAAAACATCACGCCCGATTTCAGTAAAAATGCGGGT
-ATTGATAACGCAACGATCGCAATTTATGGCTGTGATAATTTCGTCATTGATAATATTGAT
-ATGACGAATAGTGCCGGGATGCTCATCGGCTATGGCGTCGTTAAAGGAAAATACCTGTCA
-ATTCCGCAAAACTTTAAATTAAACGCTATTCGGTTGGATAATCGCCAGGTTGCTTATAAA
-TTACGCGGCATTCAAATTTCCTCCGGCAACACCCCCTCTTTTGTCGCCATCACCAATGTA
-CGGATGACGCGTGCTACGCTGGAACTGCATAATCAACCGCAGCACCTCTTCCTGCGTAAT
-ATCAACGTGATGCAAACTTCAGCGATTGGCCCGGCGTTAAAAATGCATTTCGATTTGCGT
-AAAGATGTCCGTGGTCAATTTATGGCCCGCCAGGACACGCTGCTTTCCCTCGCTAATGTT
-CATGCCATCAATGAAAACGGGCAGAGTTCCGTGGATATCGACAGGATTAATCACCAAACC
-GTGAATGTCGAAGCAGTGAATTTTTCGCTGCCGAAGCGGGGAGGGTAACGCGTCTGCGCG
-CGCGGAGAGAGGCTCTCAGGACATGTCAGAAAATAAATTACACGTTATCGATTTGCACAA
-ACGCTACGGCGGTCATGAAGTGCTGAAAGGGGTATCGCTGCAGGCCCGCGCCGGAGATGT
-GATTAGCATCATCGGCTCGTCCGGCTCCGGTAAAAGCACTTTTTTGCGCTGTATTAACTT
-CCTCGAAAAACCGAGCGAAGACGCGATTATCGTGAACGGTCAGAACATTAATCTGGTGCG
-CGACAAAGACGGGCAGCTCAAAGTGGCGGATAAAAATCAGCTACGCTTGTTGCGTACCCG
-CCTGACGATGGTGTTTCAGCACTTTAACCTCTGGAGCCACATGACGGTGCTGGAAAATGT
-GATGGAAGCGCCGATTCAGGTACTGGGATTAAGCAAGCACGACGCGCGCGAGCGGGCGTT
-GAAATATCTGGCGAAGGTGGGGATTGATGAGCGCGCTCAGGGCAAATATCCCGTTCATCT
-CTCCGGTGGCCAACAGCAGCGCGTTTCTATTGCGCGCGCGCTGGCGATGGAACCTGACGT
-TTTACTGTTCGATGAACCCACTTCGGCGCTCGATCCTGAACTGGTCGGCGAAGTGTTGCG
-CATCATGCAACAACTGGCGGAAGAAGGCAAAACGATGGTGGTGGTCACGCATGAAATGGG
-CTTCGTTCGCCATGTCTCTTCGCACGTTATTTTTCTGCATCAGGGGAAAATTGAAGAAGA
-GGGCGATCCGGAGCAGGTGTTCGGCAATCCGCAAAGCCCGCGTTTACAGCAATTCCTGAA
-AGGCTCGCTGAAATAACCGGATGCGCGCGATATATCGGCGATGCGTGTTTATTGGCATCG
-TTAGCCTGTTTCCTGAAATGTTCCGCGCAATTACCGATTACGGGGTAACTGGCCGGGCAG
-TAAAAAATGGCCTGCTGAACATCCAAAGCTGGAGTCCTCGCGACTTCACGCATGACCGGC
-ACCGTACCGTGGACGATCGTCCTTACGGCGGCGGACCAGGGATGTTAATGATGGTGCAAC
-CCTTGCGGGACGCCATTCACGCAGCAAAAGCCGCGGCAGGTGAAGGCGCTAAAGTGATTT
-ATCTGTCGCCTCAGGGACGCAAGCTTGATCAAGCGGGCGTTAGCGAGCTGGCCACGAATC
-AGAAGCTTATTCTGGTGTGTGGTCGCTACGAAGGCGTAGATGAGCGCGTAATTCAGACCG
-AAATTGACGAAGAATGGTCAATTGGCGATTACGTTCTCAGCGGTGGCGAACTACCGGCAA
-TGACGCTGATTGACTCCGTCGCCCGGTTTATACCGGGAGTTCTGGGGCATGAAGCATCAG
-CAATCGAAGATTCGTTTGCTGATGGGTTGCTGGATTGTCCGCACTATACGCGCCCTGAAG
-TGTTAGAGGGGATGGAAGTACCGCCAGTATTGCTGTCGGGAAACCATGCTGAGATACGTC
-GCTGGCGTTTGAAACAGTCGCTGGGCCGAACCTGGCTTAGAAGACCTGAACTTCTGGAAA
-ACCTGGCTCTGACTGAAGAGCAAGCAAGGTTGCTGGCGGAGTTCAAAACAGAACACGCAC
-AACAGCAGCATAAACATGATGGGATGGCATAGCCGGCTCTGCGAGAGAGGAGCGCTCGCA
-TGAATAATCATTTTGGGAAAGGGTTAATGGCCGGGTTGCACGCGCCATATGCATATAGCG
-CGCATCATGCGGTGAATTTCTGTTCTGAGTATAAACGTGGCTTTGTATTGGGTTTTACAC
-ACCGTATGTTCGAAAAGACCGGCGATCGTCAACTTAGCGCGTGGGAGGCTGGAATTCTGA
-CGCGTCGCTATGGTCTGGATAAAGAAATGGTGATGGATTTCTTTAAAGAGAATCATTCCG
-GGATGGCGGTTCGCTTCTTTATGGCCGGTTATCGACTCGAAGGTTGA
->genome3_plasmi_2 [gcode=11] [organism=Genus species] [strain=strain]
-ATGTCTACGCTTCTCTATTTGCACGGATTCAACAGTTCCCCTCGCTCGGCAAAAGCGTGC
-CAGCTAAAAAACTGGCTGGCGGAGCGTCATCCGCATGTTGAGATGATCGTCCCTCAACTA
-CCGCCGTATCCTGCCGATGCGGCGGAGTTGCTGGAGTCTCTCGTGCTTGAGCATGGCGGT
-GCGCCATTAGGGCTGGTAGGATCGTCGCTGGGTGGTTATTACGCCACCTGGCTGTCGCAA
-TGTTTTATGCTGCCGGCTGTGGTGGTGAATCCCGCCGTGCGGCCCTTTGAATTACTGACC
-GACTATCTCGGTCAGAACGAGAACCCCTACACCGGGCAGCAATATGTGCTAGAGTCTCGC
-CATATTTATGATCTTAAAGTCATGCAGATTGACCCGCTGGAAGCGCCGGACCTGATCTGG
-CTACTGCAACAGACGGGCGATGAAGTGCTGGATTACCGCCAGGCGGTGGCATATTACGCC
-TCCTGCCGTCAGACAGTGACCGAGGGTGGTAATCACGCATTCACGGGCTTCGAAGATTAT
-TTCAACCAGATTGTCGATTTTCTTGGACTGCACAGTTGCTGACGCGTAGCGGCCGGAATC
-TTCTCGGAGAGGCGCTTCTCTCTCGGAGATGATTGACCCTATTTTTGCGTCCTGTACGCT
-AATTGCCGTCTTTGTTGTTTTACTGGCCATGGGCGCGCCTATCGGGATCTGCATCGTTAT
-CGCCTCTTTCAGCACCATGATGCTGGTACTGCCTTTCGATATTTCGATGTTCGCCACCGC
-GCAAAAAATGTTCTCCAGCCTGGACAGTTTTGCCTTGCTGGCCGTGCCGTTCTTCGTTTT
-GTCCGGGGTGATCATGAATAGCGGGGGAATTGCCGCCCGGCTGATCAATTTTGCCAAACT
-GTTTACTGGCAAACTGCCCGGTTCGCTCTCTTATACCAACATCGTCGGCAATATGATGTT
-CGGTGCAATTTCCGGATCGGCAATTGCCGCCTCAACCTCCATCGGCGGCGTGATGGTGCC
-GATGAGCGCGCGCGAAGGTTACGATCGCGGCTTTGCGGCCGCGGTGAATATCGCCTCCGC
-GCCGACGGGAATGTTAATTCCGCCCACCACGGCTTTTATCCTTTATGCGCTGGCAAGCGG
-GGGAACATCGATTGCCGCTCTGTTCGCCGGCGGTCTGGTCGCGGGAGTGCTGTGGGGCGT
-TGGCTGTATGCTGGTCACGCTGGTAGTCGCTAAGCGTCGAAATTATCGGGTTTTCTTCAC
-CGTCCAAAAAGGCATGGCGCTAAAAGTTGCCGTTGAGGCCATTCCCAGCCTGTTACTGAT
-CGTGATTATCGTCGGCGGCATTGTGCAGGGGATTTTCACCGCCATTGAAGCCTCCGCGAT
-TGCCGTGGTGTATACGTTATTGCTGACGATGGTGTTTTACCGCACGCTGAAAATTAAGGA
-TTTGCCTTCGATTTTGCTCCAGACAGTGGTAATGACCGGGGTCATCATGTTCCTGCTGGC
-AACCTCTTCGGCGATGTCCTTCTCAATGTCGATCACCAATATTCCTGCGGCGCTGAGCGA
-TATGATCCTCGGTATTTCCGCCAATAAACTGGTTATCCTGTTAGTCATTACCGTCTTTTT
-GTTGATTATCGGCGCATTTATGGATATCGGTCCGGCCATTCTGATTTTTACCCCGATTCT
-GCTGCCGATCATGGCTAAACTGGGCGTCGATCCGGTGCATTTGGGCATTATCATGATCTA
-TAACCTGGCGATTGGCACCATTACGCCGCCAGTTGGCAGTGGTTTATATGTCGGGGCGAG
-CGTCGGTAAGGTCAAAGTTGAGGAAGTGATTAAACCGTTGCTGCCTTTTTACGGCGCGAT
-TATCGGCGTTCTGTTATTAATTACCTACATTCCGGAAATCATACTGTTCTTACCCCGTCT
-ACTGGGCATCATGTAAACCCGATGGCGCGCAGAGGCGCGAGTTCTGGA
->genome3_plasmi_3 [gcode=11] [organism=Genus species] [strain=strain]
-CACAGGGCTTAGAGGCGCTATGGCAATGATAATTAATGGGAAATTAATTAAAGCAAAAGA
-CTTAGCTAAGGCTGCAGGTGTATCTCGTTCAACAGTGATTAAATATTACGGCATTAGCCG
-TGAGAATTACGAAAGGGTAGCAACTGAAAGAAGGAAGCTTGCTTTTGAACTAAGAGCATC
-AGGTTTAAAATGGAAAGAAGTTGCTGAAAAAATGAACACGACAAAATATAGCGCAATTGC
-ATATTATAGACGATATTTAGCATTAGAGAAAAACAAATAACAGGCGCTAAGGCGGCGATC
-CTAGCGCGCGATCGCGCATGCGATGGTCGAACTGCAACATCAACGGCTGATGGTGCTTGC
-CGAACAGCTCCAGCTGGACAGTCTTATCGGCGCAGCGCCGGCGCTGTCGCAACAGGCGGT
-GGATCAGGAATGGAGCTACATGGACTTCCTGGAGCACCTGTTACATGAGGAGAAACTGGC
-CCGGCATCAGCGTAAACAGGCGATGTACACGCGGATGGCAGCCTTCCCGGCGGTAAAGAC
-GTTCGAGGAGTACGACTTCACCTTCGCCACCGGCGCTCCTCAGAAGCAAATCCAGTCGCT
-GCGATCCCTGAGCTTCATAGAGCGTAACGAAAACATCGTGTTGCTGGGGCCATCGGGCGT
-GGGAAAAACGCATCTGGCGATAGCCATGGGCTACGAAGCAGTACGGGCGGGCATCAAGGT
-TCGCTTCACAACAGCAGCGGACCTGCTGCTACAGCTGTCCACTTCACAGCGTCAGGGCCG
-TTACAAAACGACTCTCAATCGTGGTGTCATGGCCCCGAAGCTGCTTATCATCGATGAAAT
-AGGTTATCTGCCGTTCAGTCAGGAGGAAGCCAAGCTGTTCTTCCAGGTCATCGCCAAACG
-TTACGAGAAGAGCGCGATGATCCTGACCTCCAACCTGCCGTTCGGGCAGTGGGATCAGAC
-GTTCGCCGGTGATGCAGCGCTGACATCGGCGATGCTGGACCGGATCTTACATCACTCACA
-CGTCGTGCAAATAAAAGGGGAAAGCTATCGACTGAAGCAGAAACGAAAGGCCGGGGTTAT
-AGCTGAAGCTAATCCTGAGTAA
diff --git a/Examples/2-res-Annotate-prokka/tmp_files/genome3-chromo.fst-all.fna_prokka-split5N.fna-prokkaRes/EXAM.1216.00002.gbk b/Examples/2-res-Annotate-prokka/tmp_files/genome3-chromo.fst-all.fna_prokka-split5N.fna-prokkaRes/EXAM.1216.00002.gbk
deleted file mode 100644
index e184f33cecc6f9e4108cb6b22acb54d182526686..0000000000000000000000000000000000000000
--- a/Examples/2-res-Annotate-prokka/tmp_files/genome3-chromo.fst-all.fna_prokka-split5N.fna-prokkaRes/EXAM.1216.00002.gbk
+++ /dev/null
@@ -1,354 +0,0 @@
-LOCUS       header_genome3_1        5747 bp    DNA     linear       09-DEC-2019
-DEFINITION  Genus species strain strain.
-ACCESSION   
-VERSION
-KEYWORDS    .
-SOURCE      Genus species
-  ORGANISM  Genus species
-            Unclassified.
-COMMENT     Annotated using prokka 1.14.5 from
-            https://github.com/tseemann/prokka.
-FEATURES             Location/Qualifiers
-     source          1..5747
-                     /organism="Genus species"
-                     /mol_type="genomic DNA"
-                     /strain="strain"
-     CDS             1..831
-                     /gene="amiD_1"
-                     /locus_tag="PFKCIMHH_00001"
-                     /EC_number="3.5.1.28"
-                     /inference="ab initio prediction:Prodigal:002006"
-                     /inference="similar to AA sequence:UniProtKB:P75820"
-                     /codon_start=1
-                     /transl_table=11
-                     /product="N-acetylmuramoyl-L-alanine amidase AmiD"
-                     /db_xref="COG:COG3023"
-                     /translation="MRALLWLVGLALLLTGCASEKGIIDEEGYQLDTRHRAQAAYPRI
-                     KVLVIHYTAENFDVSLATLTGRNVSSHYLIPATPPLYGGKPRIWQLVPEQDQAWHAGV
-                     SFWRGATRLNDTSIGIELENRGWRMSGGVKSFAPFESAQIQALIPLAKDIIARYDIKP
-                     QNVVAHADIAPQRKDDPGPRFPWRELAAQGIGAWPDAQRVAFYLAGRAPYTPVDTATV
-                     LALLSRYGYEVKADMTAREQQRVIMAFQMHFRPAQWNGIADAETQAIAEALLEKYGQD
-                     "
-     CDS             880..1710
-                     /gene="amiD_2"
-                     /locus_tag="PFKCIMHH_00002"
-                     /EC_number="3.5.1.28"
-                     /inference="ab initio prediction:Prodigal:002006"
-                     /inference="similar to AA sequence:UniProtKB:P75820"
-                     /codon_start=1
-                     /transl_table=11
-                     /product="N-acetylmuramoyl-L-alanine amidase AmiD"
-                     /db_xref="COG:COG3023"
-                     /translation="MRALLWLVGLALLLTGCASEKGIIDEEGYQLDTRHRAQAAYPRI
-                     KVLVIHYTAENFDVSLATLTGRNVSSHYLIPATPPLYGGKPRIWQLVPEQDQAWHAGV
-                     SFWRGATRLNDTSIGIELENRGWRMSGGVKSFAPFESAQIQALIPLAKDIIARYDIKP
-                     QNVVAHADIAPQRKDDPGPRFPWRELAAQGIGAWPDAQRVAFYLAGRAPYTPVDTATV
-                     LALLSRYGYEVKADMTAREQQRVIMAFQMHFRPAQWNGIADAETQAIAEALLEKYGQD
-                     "
-     CDS             1655..2128
-                     /gene="hpcD"
-                     /locus_tag="PFKCIMHH_00003"
-                     /EC_number="5.3.3.10"
-                     /inference="ab initio prediction:Prodigal:002006"
-                     /inference="similar to AA sequence:UniProtKB:Q05354"
-                     /codon_start=1
-                     /transl_table=11
-                     /product="5-carboxymethyl-2-hydroxymuconate
-                     Delta-isomerase"
-                     /translation="MPKRRRLPKHYWRSTARINRARYREDSLFEDMPHFIAECTENIR
-                     EQADLPGLFSKVNEALAASGIFPIGGIRSRAHWLDTWQMADGKHDYAFVHMTLKIGAG
-                     RSLESRQEVGEMLFGLIKAHFADLMENRYLALSFEIAELHPTLNYKQNNVHALFK"
-     CDS             2172..2396
-                     /gene="pspB"
-                     /locus_tag="PFKCIMHH_00004"
-                     /inference="ab initio prediction:Prodigal:002006"
-                     /inference="similar to AA sequence:UniProtKB:P0AFM9"
-                     /codon_start=1
-                     /transl_table=11
-                     /product="Phage shock protein B"
-                     /translation="MSALFLAIPLTIFVLFVLPIWLWLHYSNRAGRGELSQSEQQRLL
-                     QLTDDAQRMRERIQALEDILDAEHPNWRER"
-     CDS             2425..3828
-                     /locus_tag="PFKCIMHH_00005"
-                     /inference="ab initio prediction:Prodigal:002006"
-                     /codon_start=1
-                     /transl_table=11
-                     /product="hypothetical protein"
-                     /translation="MPATKFSRRTLLTAGSALAVLPFLRALPVQAREPRETVDIKDYP
-                     ADDGIASFKQAFADGQTVVVPPGWVCENINAAITIPAGKTLRVQGAVRGNGRGRFILQ
-                     DGCQVVGEQGGSLHNVTLDVRGSDCVIKGVAMSGFGPVAQIFIGGKEPQVMRNLIIDD
-                     ITVTHANYAILRQGFHNQMDGARITHSRFSDLQGDAIEWNVAIHDRDILISDHVIERI
-                     DCTNGKINWGIGIGLAGSTYDNSYPEDQAVKNFVVANITGSDCRQLVHVENGKHFVIR
-                     NVKAKNITPDFSKNAGIDNATIAIYGCDNFVIDNIDMTNSAGMLIGYGVVKGKYLSIP
-                     QNFKLNAIRLDNRQVAYKLRGIQISSGNTPSFVAITNVRMTRATLELHNQPQHLFLRN
-                     INVMQTSAIGPALKMHFDLRKDVRGQFMARQDTLLSLANVHAINENGQSSVDIDRINH
-                     QTVNVEAVNFSLPKRGG"
-     CDS             3863..4636
-                     /gene="hisP"
-                     /locus_tag="PFKCIMHH_00006"
-                     /inference="ab initio prediction:Prodigal:002006"
-                     /inference="similar to AA sequence:UniProtKB:P02915"
-                     /codon_start=1
-                     /transl_table=11
-                     /product="Histidine transport ATP-binding protein HisP"
-                     /db_xref="COG:COG4598"
-                     /translation="MSENKLHVIDLHKRYGGHEVLKGVSLQARAGDVISIIGSSGSGK
-                     STFLRCINFLEKPSEDAIIVNGQNINLVRDKDGQLKVADKNQLRLLRTRLTMVFQHFN
-                     LWSHMTVLENVMEAPIQVLGLSKHDARERALKYLAKVGIDERAQGKYPVHLSGGQQQR
-                     VSIARALAMEPDVLLFDEPTSALDPELVGEVLRIMQQLAEEGKTMVVVTHEMGFVRHV
-                     SSHVIFLHQGKIEEEGDPEQVFGNPQSPRLQQFLKGSLK"
-     CDS             4641..5432
-                     /gene="trmD"
-                     /locus_tag="PFKCIMHH_00007"
-                     /EC_number="2.1.1.228"
-                     /inference="ab initio prediction:Prodigal:002006"
-                     /inference="similar to AA sequence:UniProtKB:P0A873"
-                     /codon_start=1
-                     /transl_table=11
-                     /product="tRNA (guanine-N(1)-)-methyltransferase"
-                     /db_xref="COG:COG0336"
-                     /translation="MRAIYRRCVFIGIVSLFPEMFRAITDYGVTGRAVKNGLLNIQSW
-                     SPRDFTHDRHRTVDDRPYGGGPGMLMMVQPLRDAIHAAKAAAGEGAKVIYLSPQGRKL
-                     DQAGVSELATNQKLILVCGRYEGVDERVIQTEIDEEWSIGDYVLSGGELPAMTLIDSV
-                     ARFIPGVLGHEASAIEDSFADGLLDCPHYTRPEVLEGMEVPPVLLSGNHAEIRRWRLK
-                     QSLGRTWLRRPELLENLALTEEQARLLAEFKTEHAQQQHKHDGMA"
-     CDS             5460..5747
-                     /locus_tag="PFKCIMHH_00008"
-                     /inference="ab initio prediction:Prodigal:002006"
-                     /codon_start=1
-                     /transl_table=11
-                     /product="hypothetical protein"
-                     /translation="MNNHFGKGLMAGLHAPYAYSAHHAVNFCSEYKRGFVLGFTHRMF
-                     EKTGDRQLSAWEAGILTRRYGLDKEMVMDFFKENHSGMAVRFFMAGYRLEG"
-ORIGIN      
-        1 atgagagcgc tactgtggct ggtgggtctt gcgttgctgt taacaggctg cgcgagcgaa
-       61 aaaggaatta tcgatgaaga gggatatcag cttgataccc gacatcgggc gcaggcggcc
-      121 tatccgcgca ttaaagtcct ggtgattcac tatacggcgg aaaactttga cgtttcgctg
-      181 gcgacgttaa cgggccgcaa cgtcagttcg cattacctga ttcccgcaac cccgccatta
-      241 tatggcggta aaccgcgcat ctggcaactg gtgccggaac aggatcaggc ctggcatgcg
-      301 ggcgtcagtt tctggcgagg cgccacgcgt ctcaatgata cgtctattgg cattgagctg
-      361 gaaaatcgcg gctggcgaat gtccggcggg gtgaaatctt tcgcgccgtt tgaatccgcg
-      421 caaattcagg cattgattcc gttagcgaag gacattatcg cgcgctatga catcaaaccg
-      481 cagaatgtgg tggcccatgc ggatatcgcg ccgcagcgta aagacgatcc cggcccgcgc
-      541 ttcccgtggc gcgagctggc ggcacagggg attggcgcct ggcctgacgc ccagcgtgtg
-      601 gcgttttatc tggctggacg cgcgccgtat acgccagtcg ataccgcaac ggtgcttgcg
-      661 ttactctcgc gctatggcta tgaagtcaaa gccgatatga cggcgcgcga gcaacagcgg
-      721 gtgattatgg cgttccagat gcacttccgt ccggcgcaat ggaacggtat cgcagatgcc
-      781 gaaacgcagg cgattgccga agcattactg gagaagtacg gccaggatta acgagtccgg
-      841 gagcggcgag attccgggca gaggaggcgg ctatagcgga tgagagcgct actgtggctg
-      901 gtgggtcttg cgttgctgtt aacaggctgc gcgagcgaaa aaggaattat cgatgaagag
-      961 ggatatcagc ttgatacccg acatcgggcg caggcggcct atccgcgcat taaagtcctg
-     1021 gtgattcact atacggcgga aaactttgac gtttcgctgg cgacgttaac gggccgcaac
-     1081 gtcagttcgc attacctgat tcccgcaacc ccgccattat atggcggtaa accgcgcatc
-     1141 tggcaactgg tgccggaaca ggatcaggcc tggcatgcgg gcgtcagttt ctggcgaggc
-     1201 gccacgcgtc tcaatgatac gtctattggc attgagctgg aaaatcgcgg ctggcgaatg
-     1261 tccggcgggg tgaaatcttt cgcgccgttt gaatccgcgc aaattcaggc attgattccg
-     1321 ttagcgaagg acattatcgc gcgctatgac atcaaaccgc agaatgtggt ggcccatgcg
-     1381 gatatcgcgc cgcagcgtaa agacgatccc ggcccgcgct tcccgtggcg cgagctggcg
-     1441 gcacagggga ttggcgcctg gcctgacgcc cagcgtgtgg cgttttatct ggctggacgc
-     1501 gcgccgtata cgccagtcga taccgcaacg gtgcttgcgt tactctcgcg ctatggctat
-     1561 gaagtcaaag ccgatatgac ggcgcgcgag caacagcggg tgattatggc gttccagatg
-     1621 cacttccgtc cggcgcaatg gaacggtatc gcagatgccg aaacgcaggc gattgccgaa
-     1681 gcattactgg agaagtacgg ccaggattaa cagggcgcgg tatcgcgagg actctctctt
-     1741 cgaggacatg ccgcacttta ttgctgaatg tactgaaaat attcgcgagc aggctgattt
-     1801 acccggcctg ttcagcaagg taaacgaggc gctggccgcc agcgggattt tccccatcgg
-     1861 cggtatccgc agtcgcgccc actggctgga tacctggcag atggctgacg gtaagcatga
-     1921 ttacgcgttt gtgcatatga cgctgaaaat cggcgccggg cgcagcctgg agagccgtca
-     1981 ggaagtcggc gaaatgctgt tcgggctgat taaagcccac ttcgccgacc tgatggagaa
-     2041 ccgctatctg gcgctgtcgt ttgagattgc cgagttacat ccaacgctca attacaaaca
-     2101 aaacaacgta cacgcgttat ttaaatagcc cgagtattag cgcgcggcgg cgctataggc
-     2161 gcgctatagg catgagcgcg ctatttctgg ccatcccgtt aaccattttt gtgttgtttg
-     2221 tgttaccgat ttggctgtgg ctgcattaca gcaaccgcgc cggtcgggga gaactgtcgc
-     2281 aaagcgagca gcaacgctta ctgcaactca cagacgacgc gcaacgtatg cgcgagcgca
-     2341 ttcaggcgct ggaagacatt cttgatgcag agcatccgaa ctggagagag cgctaacgag
-     2401 agtctcggag gagcggcgct ctggatgccc gcgactaaat tctcccgacg taccctcctg
-     2461 acggcaggtt ctgcgcttgc tgttcttcct ttcctgcgcg ccttgccggt acaggcgcgt
-     2521 gaacctcgcg agaccgtcga tattaaggat tatccggcgg atgacggtat cgcctcgttc
-     2581 aaacaggcct tcgccgacgg acagaccgtg gtcgtaccgc caggatgggt gtgtgaaaat
-     2641 atcaatgcgg cgataacgat tccggcggga aaaacgctgc gggtacaggg cgcggtgcgt
-     2701 gggaatggcc ggggacggtt tattttgcag gacgggtgtc aggtggtggg ggagcagggc
-     2761 ggcagtctgc acaatgtgac gctggatgtt cgcgggtcgg actgtgtgat taaaggcgtg
-     2821 gcgatgagcg gctttggccc cgtcgcgcaa attttcatcg gtggtaagga accgcaggtg
-     2881 atgcgtaatc tcattatcga tgacatcacc gttacccacg ccaactacgc cattctccgc
-     2941 cagggatttc ataaccaaat ggacggcgcg aggattacgc atagccgctt tagcgattta
-     3001 cagggggacg ccattgagtg gaatgtcgcg attcacgacc gcgatatcct gatttccgat
-     3061 catgtcatcg aacgcattga ttgtaccaat ggcaaaatca actgggggat cggcatcggg
-     3121 ctggcgggta gcacctatga caacagttat cctgaagacc aggcagtaaa aaactttgtg
-     3181 gtggccaata ttaccggatc tgattgccga cagcttgtgc acgtagaaaa tggcaaacat
-     3241 ttcgtcattc gcaatgtcaa agccaaaaac atcacgcccg atttcagtaa aaatgcgggt
-     3301 attgataacg caacgatcgc aatttatggc tgtgataatt tcgtcattga taatattgat
-     3361 atgacgaata gtgccgggat gctcatcggc tatggcgtcg ttaaaggaaa atacctgtca
-     3421 attccgcaaa actttaaatt aaacgctatt cggttggata atcgccaggt tgcttataaa
-     3481 ttacgcggca ttcaaatttc ctccggcaac accccctctt ttgtcgccat caccaatgta
-     3541 cggatgacgc gtgctacgct ggaactgcat aatcaaccgc agcacctctt cctgcgtaat
-     3601 atcaacgtga tgcaaacttc agcgattggc ccggcgttaa aaatgcattt cgatttgcgt
-     3661 aaagatgtcc gtggtcaatt tatggcccgc caggacacgc tgctttccct cgctaatgtt
-     3721 catgccatca atgaaaacgg gcagagttcc gtggatatcg acaggattaa tcaccaaacc
-     3781 gtgaatgtcg aagcagtgaa tttttcgctg ccgaagcggg gagggtaacg cgtctgcgcg
-     3841 cgcggagaga ggctctcagg acatgtcaga aaataaatta cacgttatcg atttgcacaa
-     3901 acgctacggc ggtcatgaag tgctgaaagg ggtatcgctg caggcccgcg ccggagatgt
-     3961 gattagcatc atcggctcgt ccggctccgg taaaagcact tttttgcgct gtattaactt
-     4021 cctcgaaaaa ccgagcgaag acgcgattat cgtgaacggt cagaacatta atctggtgcg
-     4081 cgacaaagac gggcagctca aagtggcgga taaaaatcag ctacgcttgt tgcgtacccg
-     4141 cctgacgatg gtgtttcagc actttaacct ctggagccac atgacggtgc tggaaaatgt
-     4201 gatggaagcg ccgattcagg tactgggatt aagcaagcac gacgcgcgcg agcgggcgtt
-     4261 gaaatatctg gcgaaggtgg ggattgatga gcgcgctcag ggcaaatatc ccgttcatct
-     4321 ctccggtggc caacagcagc gcgtttctat tgcgcgcgcg ctggcgatgg aacctgacgt
-     4381 tttactgttc gatgaaccca cttcggcgct cgatcctgaa ctggtcggcg aagtgttgcg
-     4441 catcatgcaa caactggcgg aagaaggcaa aacgatggtg gtggtcacgc atgaaatggg
-     4501 cttcgttcgc catgtctctt cgcacgttat ttttctgcat caggggaaaa ttgaagaaga
-     4561 gggcgatccg gagcaggtgt tcggcaatcc gcaaagcccg cgtttacagc aattcctgaa
-     4621 aggctcgctg aaataaccgg atgcgcgcga tatatcggcg atgcgtgttt attggcatcg
-     4681 ttagcctgtt tcctgaaatg ttccgcgcaa ttaccgatta cggggtaact ggccgggcag
-     4741 taaaaaatgg cctgctgaac atccaaagct ggagtcctcg cgacttcacg catgaccggc
-     4801 accgtaccgt ggacgatcgt ccttacggcg gcggaccagg gatgttaatg atggtgcaac
-     4861 ccttgcggga cgccattcac gcagcaaaag ccgcggcagg tgaaggcgct aaagtgattt
-     4921 atctgtcgcc tcagggacgc aagcttgatc aagcgggcgt tagcgagctg gccacgaatc
-     4981 agaagcttat tctggtgtgt ggtcgctacg aaggcgtaga tgagcgcgta attcagaccg
-     5041 aaattgacga agaatggtca attggcgatt acgttctcag cggtggcgaa ctaccggcaa
-     5101 tgacgctgat tgactccgtc gcccggttta taccgggagt tctggggcat gaagcatcag
-     5161 caatcgaaga ttcgtttgct gatgggttgc tggattgtcc gcactatacg cgccctgaag
-     5221 tgttagaggg gatggaagta ccgccagtat tgctgtcggg aaaccatgct gagatacgtc
-     5281 gctggcgttt gaaacagtcg ctgggccgaa cctggcttag aagacctgaa cttctggaaa
-     5341 acctggctct gactgaagag caagcaaggt tgctggcgga gttcaaaaca gaacacgcac
-     5401 aacagcagca taaacatgat gggatggcat agccggctct gcgagagagg agcgctcgca
-     5461 tgaataatca ttttgggaaa gggttaatgg ccgggttgca cgcgccatat gcatatagcg
-     5521 cgcatcatgc ggtgaatttc tgttctgagt ataaacgtgg ctttgtattg ggttttacac
-     5581 accgtatgtt cgaaaagacc ggcgatcgtc aacttagcgc gtgggaggct ggaattctga
-     5641 cgcgtcgcta tggtctggat aaagaaatgg tgatggattt ctttaaagag aatcattccg
-     5701 ggatggcggt tcgcttcttt atggccggtt atcgactcga aggttga
-//
-LOCUS       genome3_plasmi_2        1968 bp    DNA     linear       09-DEC-2019
-DEFINITION  Genus species strain strain.
-ACCESSION   
-VERSION
-KEYWORDS    .
-SOURCE      Genus species
-  ORGANISM  Genus species
-            Unclassified.
-COMMENT     Annotated using prokka 1.14.5 from
-            https://github.com/tseemann/prokka.
-FEATURES             Location/Qualifiers
-     source          1..1968
-                     /organism="Genus species"
-                     /mol_type="genomic DNA"
-                     /strain="strain"
-     CDS             1..582
-                     /locus_tag="PFKCIMHH_00009"
-                     /inference="ab initio prediction:Prodigal:002006"
-                     /codon_start=1
-                     /transl_table=11
-                     /product="hypothetical protein"
-                     /translation="MSTLLYLHGFNSSPRSAKACQLKNWLAERHPHVEMIVPQLPPYP
-                     ADAAELLESLVLEHGGAPLGLVGSSLGGYYATWLSQCFMLPAVVVNPAVRPFELLTDY
-                     LGQNENPYTGQQYVLESRHIYDLKVMQIDPLEAPDLIWLLQQTGDEVLDYRQAVAYYA
-                     SCRQTVTEGGNHAFTGFEDYFNQIVDFLGLHSC"
-     CDS             629..1936
-                     /gene="dctM"
-                     /locus_tag="PFKCIMHH_00010"
-                     /inference="ab initio prediction:Prodigal:002006"
-                     /inference="similar to AA sequence:UniProtKB:O07838"
-                     /codon_start=1
-                     /transl_table=11
-                     /product="C4-dicarboxylate TRAP transporter large permease
-                     protein DctM"
-                     /db_xref="COG:COG1593"
-                     /translation="MIDPIFASCTLIAVFVVLLAMGAPIGICIVIASFSTMMLVLPFD
-                     ISMFATAQKMFSSLDSFALLAVPFFVLSGVIMNSGGIAARLINFAKLFTGKLPGSLSY
-                     TNIVGNMMFGAISGSAIAASTSIGGVMVPMSAREGYDRGFAAAVNIASAPTGMLIPPT
-                     TAFILYALASGGTSIAALFAGGLVAGVLWGVGCMLVTLVVAKRRNYRVFFTVQKGMAL
-                     KVAVEAIPSLLLIVIIVGGIVQGIFTAIEASAIAVVYTLLLTMVFYRTLKIKDLPSIL
-                     LQTVVMTGVIMFLLATSSAMSFSMSITNIPAALSDMILGISANKLVILLVITVFLLII
-                     GAFMDIGPAILIFTPILLPIMAKLGVDPVHLGIIMIYNLAIGTITPPVGSGLYVGASV
-                     GKVKVEEVIKPLLPFYGAIIGVLLLITYIPEIILFLPRLLGIM"
-ORIGIN      
-        1 atgtctacgc ttctctattt gcacggattc aacagttccc ctcgctcggc aaaagcgtgc
-       61 cagctaaaaa actggctggc ggagcgtcat ccgcatgttg agatgatcgt ccctcaacta
-      121 ccgccgtatc ctgccgatgc ggcggagttg ctggagtctc tcgtgcttga gcatggcggt
-      181 gcgccattag ggctggtagg atcgtcgctg ggtggttatt acgccacctg gctgtcgcaa
-      241 tgttttatgc tgccggctgt ggtggtgaat cccgccgtgc ggccctttga attactgacc
-      301 gactatctcg gtcagaacga gaacccctac accgggcagc aatatgtgct agagtctcgc
-      361 catatttatg atcttaaagt catgcagatt gacccgctgg aagcgccgga cctgatctgg
-      421 ctactgcaac agacgggcga tgaagtgctg gattaccgcc aggcggtggc atattacgcc
-      481 tcctgccgtc agacagtgac cgagggtggt aatcacgcat tcacgggctt cgaagattat
-      541 ttcaaccaga ttgtcgattt tcttggactg cacagttgct gacgcgtagc ggccggaatc
-      601 ttctcggaga ggcgcttctc tctcggagat gattgaccct atttttgcgt cctgtacgct
-      661 aattgccgtc tttgttgttt tactggccat gggcgcgcct atcgggatct gcatcgttat
-      721 cgcctctttc agcaccatga tgctggtact gcctttcgat atttcgatgt tcgccaccgc
-      781 gcaaaaaatg ttctccagcc tggacagttt tgccttgctg gccgtgccgt tcttcgtttt
-      841 gtccggggtg atcatgaata gcgggggaat tgccgcccgg ctgatcaatt ttgccaaact
-      901 gtttactggc aaactgcccg gttcgctctc ttataccaac atcgtcggca atatgatgtt
-      961 cggtgcaatt tccggatcgg caattgccgc ctcaacctcc atcggcggcg tgatggtgcc
-     1021 gatgagcgcg cgcgaaggtt acgatcgcgg ctttgcggcc gcggtgaata tcgcctccgc
-     1081 gccgacggga atgttaattc cgcccaccac ggcttttatc ctttatgcgc tggcaagcgg
-     1141 gggaacatcg attgccgctc tgttcgccgg cggtctggtc gcgggagtgc tgtggggcgt
-     1201 tggctgtatg ctggtcacgc tggtagtcgc taagcgtcga aattatcggg ttttcttcac
-     1261 cgtccaaaaa ggcatggcgc taaaagttgc cgttgaggcc attcccagcc tgttactgat
-     1321 cgtgattatc gtcggcggca ttgtgcaggg gattttcacc gccattgaag cctccgcgat
-     1381 tgccgtggtg tatacgttat tgctgacgat ggtgttttac cgcacgctga aaattaagga
-     1441 tttgccttcg attttgctcc agacagtggt aatgaccggg gtcatcatgt tcctgctggc
-     1501 aacctcttcg gcgatgtcct tctcaatgtc gatcaccaat attcctgcgg cgctgagcga
-     1561 tatgatcctc ggtatttccg ccaataaact ggttatcctg ttagtcatta ccgtcttttt
-     1621 gttgattatc ggcgcattta tggatatcgg tccggccatt ctgattttta ccccgattct
-     1681 gctgccgatc atggctaaac tgggcgtcga tccggtgcat ttgggcatta tcatgatcta
-     1741 taacctggcg attggcacca ttacgccgcc agttggcagt ggtttatatg tcggggcgag
-     1801 cgtcggtaag gtcaaagttg aggaagtgat taaaccgttg ctgccttttt acggcgcgat
-     1861 tatcggcgtt ctgttattaa ttacctacat tccggaaatc atactgttct taccccgtct
-     1921 actgggcatc atgtaaaccc gatggcgcgc agaggcgcga gttctgga
-//
-LOCUS       genome3_plasmi_3        1102 bp    DNA     linear       09-DEC-2019
-DEFINITION  Genus species strain strain.
-ACCESSION   
-VERSION
-KEYWORDS    .
-SOURCE      Genus species
-  ORGANISM  Genus species
-            Unclassified.
-COMMENT     Annotated using prokka 1.14.5 from
-            https://github.com/tseemann/prokka.
-FEATURES             Location/Qualifiers
-     source          1..1102
-                     /organism="Genus species"
-                     /mol_type="genomic DNA"
-                     /strain="strain"
-     CDS             26..280
-                     /locus_tag="PFKCIMHH_00011"
-                     /inference="ab initio prediction:Prodigal:002006"
-                     /codon_start=1
-                     /transl_table=11
-                     /product="hypothetical protein"
-                     /translation="MIINGKLIKAKDLAKAAGVSRSTVIKYYGISRENYERVATERRK
-                     LAFELRASGLKWKEVAEKMNTTKYSAIAYYRRYLALEKNK"
-     CDS             323..1102
-                     /locus_tag="PFKCIMHH_00012"
-                     /inference="ab initio prediction:Prodigal:002006"
-                     /inference="similar to AA sequence:ISfinder:ISSen3"
-                     /codon_start=1
-                     /transl_table=11
-                     /product="IS21 family transposase ISSen3"
-                     /translation="MVELQHQRLMVLAEQLQLDSLIGAAPALSQQAVDQEWSYMDFLE
-                     HLLHEEKLARHQRKQAMYTRMAAFPAVKTFEEYDFTFATGAPQKQIQSLRSLSFIERN
-                     ENIVLLGPSGVGKTHLAIAMGYEAVRAGIKVRFTTAADLLLQLSTSQRQGRYKTTLNR
-                     GVMAPKLLIIDEIGYLPFSQEEAKLFFQVIAKRYEKSAMILTSNLPFGQWDQTFAGDA
-                     ALTSAMLDRILHHSHVVQIKGESYRLKQKRKAGVIAEANPE"
-ORIGIN      
-        1 cacagggctt agaggcgcta tggcaatgat aattaatggg aaattaatta aagcaaaaga
-       61 cttagctaag gctgcaggtg tatctcgttc aacagtgatt aaatattacg gcattagccg
-      121 tgagaattac gaaagggtag caactgaaag aaggaagctt gcttttgaac taagagcatc
-      181 aggtttaaaa tggaaagaag ttgctgaaaa aatgaacacg acaaaatata gcgcaattgc
-      241 atattataga cgatatttag cattagagaa aaacaaataa caggcgctaa ggcggcgatc
-      301 ctagcgcgcg atcgcgcatg cgatggtcga actgcaacat caacggctga tggtgcttgc
-      361 cgaacagctc cagctggaca gtcttatcgg cgcagcgccg gcgctgtcgc aacaggcggt
-      421 ggatcaggaa tggagctaca tggacttcct ggagcacctg ttacatgagg agaaactggc
-      481 ccggcatcag cgtaaacagg cgatgtacac gcggatggca gccttcccgg cggtaaagac
-      541 gttcgaggag tacgacttca ccttcgccac cggcgctcct cagaagcaaa tccagtcgct
-      601 gcgatccctg agcttcatag agcgtaacga aaacatcgtg ttgctggggc catcgggcgt
-      661 gggaaaaacg catctggcga tagccatggg ctacgaagca gtacgggcgg gcatcaaggt
-      721 tcgcttcaca acagcagcgg acctgctgct acagctgtcc acttcacagc gtcagggccg
-      781 ttacaaaacg actctcaatc gtggtgtcat ggccccgaag ctgcttatca tcgatgaaat
-      841 aggttatctg ccgttcagtc aggaggaagc caagctgttc ttccaggtca tcgccaaacg
-      901 ttacgagaag agcgcgatga tcctgacctc caacctgccg ttcgggcagt gggatcagac
-      961 gttcgccggt gatgcagcgc tgacatcggc gatgctggac cggatcttac atcactcaca
-     1021 cgtcgtgcaa ataaaagggg aaagctatcg actgaagcag aaacgaaagg ccggggttat
-     1081 agctgaagct aatcctgagt aa
-//
diff --git a/Examples/2-res-Annotate-prokka/tmp_files/genome3-chromo.fst-all.fna_prokka-split5N.fna-prokkaRes/EXAM.1216.00002.gff b/Examples/2-res-Annotate-prokka/tmp_files/genome3-chromo.fst-all.fna_prokka-split5N.fna-prokkaRes/EXAM.1216.00002.gff
deleted file mode 100644
index 3220735af9ae09cb1a1628146c5ba6388c7a8849..0000000000000000000000000000000000000000
--- a/Examples/2-res-Annotate-prokka/tmp_files/genome3-chromo.fst-all.fna_prokka-split5N.fna-prokkaRes/EXAM.1216.00002.gff
+++ /dev/null
@@ -1,168 +0,0 @@
-##gff-version 3
-##sequence-region header_genome3_1 1 5747
-##sequence-region genome3_plasmi_2 1 1968
-##sequence-region genome3_plasmi_3 1 1102
-header_genome3_1	Prodigal:002006	CDS	1	831	.	+	0	ID=PFKCIMHH_00001;eC_number=3.5.1.28;Name=amiD_1;db_xref=COG:COG3023;gene=amiD_1;inference=ab initio prediction:Prodigal:002006,similar to AA sequence:UniProtKB:P75820;locus_tag=PFKCIMHH_00001;product=N-acetylmuramoyl-L-alanine amidase AmiD
-header_genome3_1	Prodigal:002006	CDS	880	1710	.	+	0	ID=PFKCIMHH_00002;eC_number=3.5.1.28;Name=amiD_2;db_xref=COG:COG3023;gene=amiD_2;inference=ab initio prediction:Prodigal:002006,similar to AA sequence:UniProtKB:P75820;locus_tag=PFKCIMHH_00002;product=N-acetylmuramoyl-L-alanine amidase AmiD
-header_genome3_1	Prodigal:002006	CDS	1655	2128	.	+	0	ID=PFKCIMHH_00003;eC_number=5.3.3.10;Name=hpcD;gene=hpcD;inference=ab initio prediction:Prodigal:002006,similar to AA sequence:UniProtKB:Q05354;locus_tag=PFKCIMHH_00003;product=5-carboxymethyl-2-hydroxymuconate Delta-isomerase
-header_genome3_1	Prodigal:002006	CDS	2172	2396	.	+	0	ID=PFKCIMHH_00004;Name=pspB;gene=pspB;inference=ab initio prediction:Prodigal:002006,similar to AA sequence:UniProtKB:P0AFM9;locus_tag=PFKCIMHH_00004;product=Phage shock protein B
-header_genome3_1	Prodigal:002006	CDS	2425	3828	.	+	0	ID=PFKCIMHH_00005;inference=ab initio prediction:Prodigal:002006;locus_tag=PFKCIMHH_00005;product=hypothetical protein
-header_genome3_1	Prodigal:002006	CDS	3863	4636	.	+	0	ID=PFKCIMHH_00006;Name=hisP;db_xref=COG:COG4598;gene=hisP;inference=ab initio prediction:Prodigal:002006,similar to AA sequence:UniProtKB:P02915;locus_tag=PFKCIMHH_00006;product=Histidine transport ATP-binding protein HisP
-header_genome3_1	Prodigal:002006	CDS	4641	5432	.	+	0	ID=PFKCIMHH_00007;eC_number=2.1.1.228;Name=trmD;db_xref=COG:COG0336;gene=trmD;inference=ab initio prediction:Prodigal:002006,similar to AA sequence:UniProtKB:P0A873;locus_tag=PFKCIMHH_00007;product=tRNA (guanine-N(1)-)-methyltransferase
-header_genome3_1	Prodigal:002006	CDS	5460	5747	.	+	0	ID=PFKCIMHH_00008;inference=ab initio prediction:Prodigal:002006;locus_tag=PFKCIMHH_00008;product=hypothetical protein
-genome3_plasmi_2	Prodigal:002006	CDS	1	582	.	+	0	ID=PFKCIMHH_00009;inference=ab initio prediction:Prodigal:002006;locus_tag=PFKCIMHH_00009;product=hypothetical protein
-genome3_plasmi_2	Prodigal:002006	CDS	629	1936	.	+	0	ID=PFKCIMHH_00010;Name=dctM;db_xref=COG:COG1593;gene=dctM;inference=ab initio prediction:Prodigal:002006,similar to AA sequence:UniProtKB:O07838;locus_tag=PFKCIMHH_00010;product=C4-dicarboxylate TRAP transporter large permease protein DctM
-genome3_plasmi_3	Prodigal:002006	CDS	26	280	.	+	0	ID=PFKCIMHH_00011;inference=ab initio prediction:Prodigal:002006;locus_tag=PFKCIMHH_00011;product=hypothetical protein
-genome3_plasmi_3	Prodigal:002006	CDS	323	1102	.	+	0	ID=PFKCIMHH_00012;inference=ab initio prediction:Prodigal:002006,similar to AA sequence:ISfinder:ISSen3;locus_tag=PFKCIMHH_00012;product=IS21 family transposase ISSen3
-##FASTA
->header_genome3_1
-ATGAGAGCGCTACTGTGGCTGGTGGGTCTTGCGTTGCTGTTAACAGGCTGCGCGAGCGAA
-AAAGGAATTATCGATGAAGAGGGATATCAGCTTGATACCCGACATCGGGCGCAGGCGGCC
-TATCCGCGCATTAAAGTCCTGGTGATTCACTATACGGCGGAAAACTTTGACGTTTCGCTG
-GCGACGTTAACGGGCCGCAACGTCAGTTCGCATTACCTGATTCCCGCAACCCCGCCATTA
-TATGGCGGTAAACCGCGCATCTGGCAACTGGTGCCGGAACAGGATCAGGCCTGGCATGCG
-GGCGTCAGTTTCTGGCGAGGCGCCACGCGTCTCAATGATACGTCTATTGGCATTGAGCTG
-GAAAATCGCGGCTGGCGAATGTCCGGCGGGGTGAAATCTTTCGCGCCGTTTGAATCCGCG
-CAAATTCAGGCATTGATTCCGTTAGCGAAGGACATTATCGCGCGCTATGACATCAAACCG
-CAGAATGTGGTGGCCCATGCGGATATCGCGCCGCAGCGTAAAGACGATCCCGGCCCGCGC
-TTCCCGTGGCGCGAGCTGGCGGCACAGGGGATTGGCGCCTGGCCTGACGCCCAGCGTGTG
-GCGTTTTATCTGGCTGGACGCGCGCCGTATACGCCAGTCGATACCGCAACGGTGCTTGCG
-TTACTCTCGCGCTATGGCTATGAAGTCAAAGCCGATATGACGGCGCGCGAGCAACAGCGG
-GTGATTATGGCGTTCCAGATGCACTTCCGTCCGGCGCAATGGAACGGTATCGCAGATGCC
-GAAACGCAGGCGATTGCCGAAGCATTACTGGAGAAGTACGGCCAGGATTAACGAGTCCGG
-GAGCGGCGAGATTCCGGGCAGAGGAGGCGGCTATAGCGGATGAGAGCGCTACTGTGGCTG
-GTGGGTCTTGCGTTGCTGTTAACAGGCTGCGCGAGCGAAAAAGGAATTATCGATGAAGAG
-GGATATCAGCTTGATACCCGACATCGGGCGCAGGCGGCCTATCCGCGCATTAAAGTCCTG
-GTGATTCACTATACGGCGGAAAACTTTGACGTTTCGCTGGCGACGTTAACGGGCCGCAAC
-GTCAGTTCGCATTACCTGATTCCCGCAACCCCGCCATTATATGGCGGTAAACCGCGCATC
-TGGCAACTGGTGCCGGAACAGGATCAGGCCTGGCATGCGGGCGTCAGTTTCTGGCGAGGC
-GCCACGCGTCTCAATGATACGTCTATTGGCATTGAGCTGGAAAATCGCGGCTGGCGAATG
-TCCGGCGGGGTGAAATCTTTCGCGCCGTTTGAATCCGCGCAAATTCAGGCATTGATTCCG
-TTAGCGAAGGACATTATCGCGCGCTATGACATCAAACCGCAGAATGTGGTGGCCCATGCG
-GATATCGCGCCGCAGCGTAAAGACGATCCCGGCCCGCGCTTCCCGTGGCGCGAGCTGGCG
-GCACAGGGGATTGGCGCCTGGCCTGACGCCCAGCGTGTGGCGTTTTATCTGGCTGGACGC
-GCGCCGTATACGCCAGTCGATACCGCAACGGTGCTTGCGTTACTCTCGCGCTATGGCTAT
-GAAGTCAAAGCCGATATGACGGCGCGCGAGCAACAGCGGGTGATTATGGCGTTCCAGATG
-CACTTCCGTCCGGCGCAATGGAACGGTATCGCAGATGCCGAAACGCAGGCGATTGCCGAA
-GCATTACTGGAGAAGTACGGCCAGGATTAACAGGGCGCGGTATCGCGAGGACTCTCTCTT
-CGAGGACATGCCGCACTTTATTGCTGAATGTACTGAAAATATTCGCGAGCAGGCTGATTT
-ACCCGGCCTGTTCAGCAAGGTAAACGAGGCGCTGGCCGCCAGCGGGATTTTCCCCATCGG
-CGGTATCCGCAGTCGCGCCCACTGGCTGGATACCTGGCAGATGGCTGACGGTAAGCATGA
-TTACGCGTTTGTGCATATGACGCTGAAAATCGGCGCCGGGCGCAGCCTGGAGAGCCGTCA
-GGAAGTCGGCGAAATGCTGTTCGGGCTGATTAAAGCCCACTTCGCCGACCTGATGGAGAA
-CCGCTATCTGGCGCTGTCGTTTGAGATTGCCGAGTTACATCCAACGCTCAATTACAAACA
-AAACAACGTACACGCGTTATTTAAATAGCCCGAGTATTAGCGCGCGGCGGCGCTATAGGC
-GCGCTATAGGCATGAGCGCGCTATTTCTGGCCATCCCGTTAACCATTTTTGTGTTGTTTG
-TGTTACCGATTTGGCTGTGGCTGCATTACAGCAACCGCGCCGGTCGGGGAGAACTGTCGC
-AAAGCGAGCAGCAACGCTTACTGCAACTCACAGACGACGCGCAACGTATGCGCGAGCGCA
-TTCAGGCGCTGGAAGACATTCTTGATGCAGAGCATCCGAACTGGAGAGAGCGCTAACGAG
-AGTCTCGGAGGAGCGGCGCTCTGGATGCCCGCGACTAAATTCTCCCGACGTACCCTCCTG
-ACGGCAGGTTCTGCGCTTGCTGTTCTTCCTTTCCTGCGCGCCTTGCCGGTACAGGCGCGT
-GAACCTCGCGAGACCGTCGATATTAAGGATTATCCGGCGGATGACGGTATCGCCTCGTTC
-AAACAGGCCTTCGCCGACGGACAGACCGTGGTCGTACCGCCAGGATGGGTGTGTGAAAAT
-ATCAATGCGGCGATAACGATTCCGGCGGGAAAAACGCTGCGGGTACAGGGCGCGGTGCGT
-GGGAATGGCCGGGGACGGTTTATTTTGCAGGACGGGTGTCAGGTGGTGGGGGAGCAGGGC
-GGCAGTCTGCACAATGTGACGCTGGATGTTCGCGGGTCGGACTGTGTGATTAAAGGCGTG
-GCGATGAGCGGCTTTGGCCCCGTCGCGCAAATTTTCATCGGTGGTAAGGAACCGCAGGTG
-ATGCGTAATCTCATTATCGATGACATCACCGTTACCCACGCCAACTACGCCATTCTCCGC
-CAGGGATTTCATAACCAAATGGACGGCGCGAGGATTACGCATAGCCGCTTTAGCGATTTA
-CAGGGGGACGCCATTGAGTGGAATGTCGCGATTCACGACCGCGATATCCTGATTTCCGAT
-CATGTCATCGAACGCATTGATTGTACCAATGGCAAAATCAACTGGGGGATCGGCATCGGG
-CTGGCGGGTAGCACCTATGACAACAGTTATCCTGAAGACCAGGCAGTAAAAAACTTTGTG
-GTGGCCAATATTACCGGATCTGATTGCCGACAGCTTGTGCACGTAGAAAATGGCAAACAT
-TTCGTCATTCGCAATGTCAAAGCCAAAAACATCACGCCCGATTTCAGTAAAAATGCGGGT
-ATTGATAACGCAACGATCGCAATTTATGGCTGTGATAATTTCGTCATTGATAATATTGAT
-ATGACGAATAGTGCCGGGATGCTCATCGGCTATGGCGTCGTTAAAGGAAAATACCTGTCA
-ATTCCGCAAAACTTTAAATTAAACGCTATTCGGTTGGATAATCGCCAGGTTGCTTATAAA
-TTACGCGGCATTCAAATTTCCTCCGGCAACACCCCCTCTTTTGTCGCCATCACCAATGTA
-CGGATGACGCGTGCTACGCTGGAACTGCATAATCAACCGCAGCACCTCTTCCTGCGTAAT
-ATCAACGTGATGCAAACTTCAGCGATTGGCCCGGCGTTAAAAATGCATTTCGATTTGCGT
-AAAGATGTCCGTGGTCAATTTATGGCCCGCCAGGACACGCTGCTTTCCCTCGCTAATGTT
-CATGCCATCAATGAAAACGGGCAGAGTTCCGTGGATATCGACAGGATTAATCACCAAACC
-GTGAATGTCGAAGCAGTGAATTTTTCGCTGCCGAAGCGGGGAGGGTAACGCGTCTGCGCG
-CGCGGAGAGAGGCTCTCAGGACATGTCAGAAAATAAATTACACGTTATCGATTTGCACAA
-ACGCTACGGCGGTCATGAAGTGCTGAAAGGGGTATCGCTGCAGGCCCGCGCCGGAGATGT
-GATTAGCATCATCGGCTCGTCCGGCTCCGGTAAAAGCACTTTTTTGCGCTGTATTAACTT
-CCTCGAAAAACCGAGCGAAGACGCGATTATCGTGAACGGTCAGAACATTAATCTGGTGCG
-CGACAAAGACGGGCAGCTCAAAGTGGCGGATAAAAATCAGCTACGCTTGTTGCGTACCCG
-CCTGACGATGGTGTTTCAGCACTTTAACCTCTGGAGCCACATGACGGTGCTGGAAAATGT
-GATGGAAGCGCCGATTCAGGTACTGGGATTAAGCAAGCACGACGCGCGCGAGCGGGCGTT
-GAAATATCTGGCGAAGGTGGGGATTGATGAGCGCGCTCAGGGCAAATATCCCGTTCATCT
-CTCCGGTGGCCAACAGCAGCGCGTTTCTATTGCGCGCGCGCTGGCGATGGAACCTGACGT
-TTTACTGTTCGATGAACCCACTTCGGCGCTCGATCCTGAACTGGTCGGCGAAGTGTTGCG
-CATCATGCAACAACTGGCGGAAGAAGGCAAAACGATGGTGGTGGTCACGCATGAAATGGG
-CTTCGTTCGCCATGTCTCTTCGCACGTTATTTTTCTGCATCAGGGGAAAATTGAAGAAGA
-GGGCGATCCGGAGCAGGTGTTCGGCAATCCGCAAAGCCCGCGTTTACAGCAATTCCTGAA
-AGGCTCGCTGAAATAACCGGATGCGCGCGATATATCGGCGATGCGTGTTTATTGGCATCG
-TTAGCCTGTTTCCTGAAATGTTCCGCGCAATTACCGATTACGGGGTAACTGGCCGGGCAG
-TAAAAAATGGCCTGCTGAACATCCAAAGCTGGAGTCCTCGCGACTTCACGCATGACCGGC
-ACCGTACCGTGGACGATCGTCCTTACGGCGGCGGACCAGGGATGTTAATGATGGTGCAAC
-CCTTGCGGGACGCCATTCACGCAGCAAAAGCCGCGGCAGGTGAAGGCGCTAAAGTGATTT
-ATCTGTCGCCTCAGGGACGCAAGCTTGATCAAGCGGGCGTTAGCGAGCTGGCCACGAATC
-AGAAGCTTATTCTGGTGTGTGGTCGCTACGAAGGCGTAGATGAGCGCGTAATTCAGACCG
-AAATTGACGAAGAATGGTCAATTGGCGATTACGTTCTCAGCGGTGGCGAACTACCGGCAA
-TGACGCTGATTGACTCCGTCGCCCGGTTTATACCGGGAGTTCTGGGGCATGAAGCATCAG
-CAATCGAAGATTCGTTTGCTGATGGGTTGCTGGATTGTCCGCACTATACGCGCCCTGAAG
-TGTTAGAGGGGATGGAAGTACCGCCAGTATTGCTGTCGGGAAACCATGCTGAGATACGTC
-GCTGGCGTTTGAAACAGTCGCTGGGCCGAACCTGGCTTAGAAGACCTGAACTTCTGGAAA
-ACCTGGCTCTGACTGAAGAGCAAGCAAGGTTGCTGGCGGAGTTCAAAACAGAACACGCAC
-AACAGCAGCATAAACATGATGGGATGGCATAGCCGGCTCTGCGAGAGAGGAGCGCTCGCA
-TGAATAATCATTTTGGGAAAGGGTTAATGGCCGGGTTGCACGCGCCATATGCATATAGCG
-CGCATCATGCGGTGAATTTCTGTTCTGAGTATAAACGTGGCTTTGTATTGGGTTTTACAC
-ACCGTATGTTCGAAAAGACCGGCGATCGTCAACTTAGCGCGTGGGAGGCTGGAATTCTGA
-CGCGTCGCTATGGTCTGGATAAAGAAATGGTGATGGATTTCTTTAAAGAGAATCATTCCG
-GGATGGCGGTTCGCTTCTTTATGGCCGGTTATCGACTCGAAGGTTGA
->genome3_plasmi_2
-ATGTCTACGCTTCTCTATTTGCACGGATTCAACAGTTCCCCTCGCTCGGCAAAAGCGTGC
-CAGCTAAAAAACTGGCTGGCGGAGCGTCATCCGCATGTTGAGATGATCGTCCCTCAACTA
-CCGCCGTATCCTGCCGATGCGGCGGAGTTGCTGGAGTCTCTCGTGCTTGAGCATGGCGGT
-GCGCCATTAGGGCTGGTAGGATCGTCGCTGGGTGGTTATTACGCCACCTGGCTGTCGCAA
-TGTTTTATGCTGCCGGCTGTGGTGGTGAATCCCGCCGTGCGGCCCTTTGAATTACTGACC
-GACTATCTCGGTCAGAACGAGAACCCCTACACCGGGCAGCAATATGTGCTAGAGTCTCGC
-CATATTTATGATCTTAAAGTCATGCAGATTGACCCGCTGGAAGCGCCGGACCTGATCTGG
-CTACTGCAACAGACGGGCGATGAAGTGCTGGATTACCGCCAGGCGGTGGCATATTACGCC
-TCCTGCCGTCAGACAGTGACCGAGGGTGGTAATCACGCATTCACGGGCTTCGAAGATTAT
-TTCAACCAGATTGTCGATTTTCTTGGACTGCACAGTTGCTGACGCGTAGCGGCCGGAATC
-TTCTCGGAGAGGCGCTTCTCTCTCGGAGATGATTGACCCTATTTTTGCGTCCTGTACGCT
-AATTGCCGTCTTTGTTGTTTTACTGGCCATGGGCGCGCCTATCGGGATCTGCATCGTTAT
-CGCCTCTTTCAGCACCATGATGCTGGTACTGCCTTTCGATATTTCGATGTTCGCCACCGC
-GCAAAAAATGTTCTCCAGCCTGGACAGTTTTGCCTTGCTGGCCGTGCCGTTCTTCGTTTT
-GTCCGGGGTGATCATGAATAGCGGGGGAATTGCCGCCCGGCTGATCAATTTTGCCAAACT
-GTTTACTGGCAAACTGCCCGGTTCGCTCTCTTATACCAACATCGTCGGCAATATGATGTT
-CGGTGCAATTTCCGGATCGGCAATTGCCGCCTCAACCTCCATCGGCGGCGTGATGGTGCC
-GATGAGCGCGCGCGAAGGTTACGATCGCGGCTTTGCGGCCGCGGTGAATATCGCCTCCGC
-GCCGACGGGAATGTTAATTCCGCCCACCACGGCTTTTATCCTTTATGCGCTGGCAAGCGG
-GGGAACATCGATTGCCGCTCTGTTCGCCGGCGGTCTGGTCGCGGGAGTGCTGTGGGGCGT
-TGGCTGTATGCTGGTCACGCTGGTAGTCGCTAAGCGTCGAAATTATCGGGTTTTCTTCAC
-CGTCCAAAAAGGCATGGCGCTAAAAGTTGCCGTTGAGGCCATTCCCAGCCTGTTACTGAT
-CGTGATTATCGTCGGCGGCATTGTGCAGGGGATTTTCACCGCCATTGAAGCCTCCGCGAT
-TGCCGTGGTGTATACGTTATTGCTGACGATGGTGTTTTACCGCACGCTGAAAATTAAGGA
-TTTGCCTTCGATTTTGCTCCAGACAGTGGTAATGACCGGGGTCATCATGTTCCTGCTGGC
-AACCTCTTCGGCGATGTCCTTCTCAATGTCGATCACCAATATTCCTGCGGCGCTGAGCGA
-TATGATCCTCGGTATTTCCGCCAATAAACTGGTTATCCTGTTAGTCATTACCGTCTTTTT
-GTTGATTATCGGCGCATTTATGGATATCGGTCCGGCCATTCTGATTTTTACCCCGATTCT
-GCTGCCGATCATGGCTAAACTGGGCGTCGATCCGGTGCATTTGGGCATTATCATGATCTA
-TAACCTGGCGATTGGCACCATTACGCCGCCAGTTGGCAGTGGTTTATATGTCGGGGCGAG
-CGTCGGTAAGGTCAAAGTTGAGGAAGTGATTAAACCGTTGCTGCCTTTTTACGGCGCGAT
-TATCGGCGTTCTGTTATTAATTACCTACATTCCGGAAATCATACTGTTCTTACCCCGTCT
-ACTGGGCATCATGTAAACCCGATGGCGCGCAGAGGCGCGAGTTCTGGA
->genome3_plasmi_3
-CACAGGGCTTAGAGGCGCTATGGCAATGATAATTAATGGGAAATTAATTAAAGCAAAAGA
-CTTAGCTAAGGCTGCAGGTGTATCTCGTTCAACAGTGATTAAATATTACGGCATTAGCCG
-TGAGAATTACGAAAGGGTAGCAACTGAAAGAAGGAAGCTTGCTTTTGAACTAAGAGCATC
-AGGTTTAAAATGGAAAGAAGTTGCTGAAAAAATGAACACGACAAAATATAGCGCAATTGC
-ATATTATAGACGATATTTAGCATTAGAGAAAAACAAATAACAGGCGCTAAGGCGGCGATC
-CTAGCGCGCGATCGCGCATGCGATGGTCGAACTGCAACATCAACGGCTGATGGTGCTTGC
-CGAACAGCTCCAGCTGGACAGTCTTATCGGCGCAGCGCCGGCGCTGTCGCAACAGGCGGT
-GGATCAGGAATGGAGCTACATGGACTTCCTGGAGCACCTGTTACATGAGGAGAAACTGGC
-CCGGCATCAGCGTAAACAGGCGATGTACACGCGGATGGCAGCCTTCCCGGCGGTAAAGAC
-GTTCGAGGAGTACGACTTCACCTTCGCCACCGGCGCTCCTCAGAAGCAAATCCAGTCGCT
-GCGATCCCTGAGCTTCATAGAGCGTAACGAAAACATCGTGTTGCTGGGGCCATCGGGCGT
-GGGAAAAACGCATCTGGCGATAGCCATGGGCTACGAAGCAGTACGGGCGGGCATCAAGGT
-TCGCTTCACAACAGCAGCGGACCTGCTGCTACAGCTGTCCACTTCACAGCGTCAGGGCCG
-TTACAAAACGACTCTCAATCGTGGTGTCATGGCCCCGAAGCTGCTTATCATCGATGAAAT
-AGGTTATCTGCCGTTCAGTCAGGAGGAAGCCAAGCTGTTCTTCCAGGTCATCGCCAAACG
-TTACGAGAAGAGCGCGATGATCCTGACCTCCAACCTGCCGTTCGGGCAGTGGGATCAGAC
-GTTCGCCGGTGATGCAGCGCTGACATCGGCGATGCTGGACCGGATCTTACATCACTCACA
-CGTCGTGCAAATAAAAGGGGAAAGCTATCGACTGAAGCAGAAACGAAAGGCCGGGGTTAT
-AGCTGAAGCTAATCCTGAGTAA
diff --git a/Examples/2-res-Annotate-prokka/tmp_files/genome3-chromo.fst-all.fna_prokka-split5N.fna-prokkaRes/EXAM.1216.00002.log b/Examples/2-res-Annotate-prokka/tmp_files/genome3-chromo.fst-all.fna_prokka-split5N.fna-prokkaRes/EXAM.1216.00002.log
deleted file mode 100644
index 2f4b4ec62dc78ead58ae6e955c576069f4ec45ea..0000000000000000000000000000000000000000
--- a/Examples/2-res-Annotate-prokka/tmp_files/genome3-chromo.fst-all.fna_prokka-split5N.fna-prokkaRes/EXAM.1216.00002.log
+++ /dev/null
@@ -1,130 +0,0 @@
-[13:15:30] This is prokka 1.14.5
-[13:15:30] Written by Torsten Seemann <torsten.seemann@gmail.com>
-[13:15:30] Homepage is https://github.com/tseemann/prokka
-[13:15:30] Local time is Mon Dec  9 13:15:30 2019
-[13:15:30] You are aperrin
-[13:15:30] Operating system is darwin
-[13:15:30] You have BioPerl 1.007002
-[13:15:30] System has 8 cores.
-[13:15:30] Will use maximum of 1 cores.
-[13:15:30] Annotating as >>> Bacteria <<<
-[13:15:30] Generating locus_tag from 'Examples/2-res-Annotate-prokka/tmp_files/genome3-chromo.fst-all.fna_prokka-split5N.fna' contents.
-[13:15:30] Setting --locustag PFKCIMHH from MD5 9f4c2611ce3f44c6b2e6fb97579c5725
-[13:15:30] Creating new output folder: Examples/2-res-Annotate-prokka/tmp_files/genome3-chromo.fst-all.fna_prokka-split5N.fna-prokkaRes
-[13:15:30] Running: mkdir -p Examples\/2\-res\-Annotate\-prokka\/tmp_files\/genome3\-chromo\.fst\-all\.fna_prokka\-split5N\.fna\-prokkaRes
-[13:15:30] Using filename prefix: EXAM.1216.00002.XXX
-[13:15:30] Setting HMMER_NCPU=1
-[13:15:30] Writing log to: Examples/2-res-Annotate-prokka/tmp_files/genome3-chromo.fst-all.fna_prokka-split5N.fna-prokkaRes/EXAM.1216.00002.log
-[13:15:30] Command: /usr/local/bin/prokka --outdir Examples/2-res-Annotate-prokka/tmp_files/genome3-chromo.fst-all.fna_prokka-split5N.fna-prokkaRes --cpus 1 --prefix EXAM.1216.00002 Examples/2-res-Annotate-prokka/tmp_files/genome3-chromo.fst-all.fna_prokka-split5N.fna
-[13:15:30] Appending to PATH: /Users/aperrin/Softwares/src/prokka-dec.19/bin/../binaries/darwin
-[13:15:30] Appending to PATH: /Users/aperrin/Softwares/src/prokka-dec.19/bin/../binaries/darwin/../common
-[13:15:30] Appending to PATH: /Users/aperrin/Softwares/src/prokka-dec.19/bin
-[13:15:30] Looking for 'aragorn' - found /usr/local/bin/aragorn
-[13:15:30] Determined aragorn version is 001002 from 'ARAGORN v1.2.38 Dean Laslett'
-[13:15:30] Looking for 'barrnap' - found /usr/local/bin/barrnap
-[13:15:31] Determined barrnap version is 000008 from 'barrnap 0.8'
-[13:15:31] Looking for 'blastp' - found /Users/aperrin/Softwares/bin/blastp
-[13:15:31] Determined blastp version is 002009 from 'blastp: 2.9.0+'
-[13:15:31] Looking for 'cmpress' - found /usr/local/bin/cmpress
-[13:15:31] Determined cmpress version is 001001 from '# INFERNAL 1.1.2 (July 2016)'
-[13:15:31] Looking for 'cmscan' - found /usr/local/bin/cmscan
-[13:15:31] Determined cmscan version is 001001 from '# INFERNAL 1.1.2 (July 2016)'
-[13:15:31] Looking for 'egrep' - found /usr/bin/egrep
-[13:15:31] Looking for 'find' - found /usr/bin/find
-[13:15:31] Looking for 'grep' - found /usr/bin/grep
-[13:15:31] Looking for 'hmmpress' - found /Users/aperrin/Softwares/src/prokka-dec.19/bin/../binaries/darwin/hmmpress
-[13:15:31] Determined hmmpress version is 003001 from '# HMMER 3.1b1 (May 2013); http://hmmer.org/'
-[13:15:31] Looking for 'hmmscan' - found /usr/local/bin/hmmscan
-[13:15:31] Determined hmmscan version is 003001 from '# HMMER 3.1b2 (February 2015); http://hmmer.org/'
-[13:15:31] Looking for 'java' - found /usr/bin/java
-[13:15:31] Looking for 'makeblastdb' - found /Users/aperrin/Softwares/bin/makeblastdb
-[13:15:31] Determined makeblastdb version is 002009 from 'makeblastdb: 2.9.0+'
-[13:15:31] Looking for 'minced' - found /Users/aperrin/Softwares/src/prokka-dec.19/bin/../binaries/darwin/../common/minced
-[13:15:31] Determined minced version is 002000 from 'minced 0.2.0'
-[13:15:31] Looking for 'parallel' - found /usr/local/bin/parallel
-[13:15:31] Determined parallel version is 20181022 from 'GNU parallel 20181022'
-[13:15:31] Looking for 'prodigal' - found /usr/local/bin/prodigal
-[13:15:31] Determined prodigal version is 002006 from 'Prodigal V2.6.3: February, 2016'
-[13:15:31] Looking for 'prokka-genbank_to_fasta_db' - found /Users/aperrin/Softwares/src/prokka-dec.19/bin/prokka-genbank_to_fasta_db
-[13:15:31] Looking for 'sed' - found /usr/bin/sed
-[13:15:31] Looking for 'tbl2asn' - found /Users/aperrin/Softwares/src/prokka-dec.19/bin/../binaries/darwin/tbl2asn
-[13:15:31] Determined tbl2asn version is 025007 from 'tbl2asn 25.7   arguments:'
-[13:15:31] Using genetic code table 11.
-[13:15:31] Loading and checking input file: Examples/2-res-Annotate-prokka/tmp_files/genome3-chromo.fst-all.fna_prokka-split5N.fna
-[13:15:31] Wrote 3 contigs totalling 8817 bp.
-[13:15:31] Predicting tRNAs and tmRNAs
-[13:15:31] Running: aragorn -l -gc11  -w Examples\/2\-res\-Annotate\-prokka\/tmp_files\/genome3\-chromo\.fst\-all\.fna_prokka\-split5N\.fna\-prokkaRes\/EXAM\.1216\.00002\.fna
-[13:15:31] Found 0 tRNAs
-[13:15:31] Predicting Ribosomal RNAs
-[13:15:31] Running Barrnap with 1 threads
-[13:15:31] Found 0 rRNAs
-[13:15:31] Skipping ncRNA search, enable with --rfam if desired.
-[13:15:31] Total of 0 tRNA + rRNA features
-[13:15:31] Searching for CRISPR repeats
-[13:15:31] Found 0 CRISPRs
-[13:15:31] Predicting coding sequences
-[13:15:31] Contigs total 8817 bp, so using meta mode
-[13:15:31] Running: prodigal -i Examples\/2\-res\-Annotate\-prokka\/tmp_files\/genome3\-chromo\.fst\-all\.fna_prokka\-split5N\.fna\-prokkaRes\/EXAM\.1216\.00002\.fna -c -m -g 11 -p meta -f sco -q
-[13:15:31] Found 12 CDS
-[13:15:31] Connecting features back to sequences
-[13:15:31] Not using genus-specific database. Try --usegenus to enable it.
-[13:15:31] Annotating CDS, please be patient.
-[13:15:31] Will use 1 CPUs for similarity searching.
-[13:15:31] There are still 12 unannotated CDS left (started with 12)
-[13:15:31] Will use blast to search against /Users/aperrin/Softwares/src/prokka-dec.19/db/kingdom/Bacteria/IS with 1 CPUs
-[13:15:31] Running: cat Examples\/2\-res\-Annotate\-prokka\/tmp_files\/genome3\-chromo\.fst\-all\.fna_prokka\-split5N\.fna\-prokkaRes\/EXAM\.1216\.00002\.IS\.tmp\.95230\.faa | parallel --gnu --plain -j 1 --block 1443 --recstart '>' --pipe blastp -query - -db /Users/aperrin/Softwares/src/prokka-dec.19/db/kingdom/Bacteria/IS -evalue 1e-30 -qcov_hsp_perc 90 -num_threads 1 -num_descriptions 1 -num_alignments 1 -seg no > Examples\/2\-res\-Annotate\-prokka\/tmp_files\/genome3\-chromo\.fst\-all\.fna_prokka\-split5N\.fna\-prokkaRes\/EXAM\.1216\.00002\.IS\.tmp\.95230\.blast 2> /dev/null
-[13:15:32] Deleting unwanted file: Examples/2-res-Annotate-prokka/tmp_files/genome3-chromo.fst-all.fna_prokka-split5N.fna-prokkaRes/EXAM.1216.00002.IS.tmp.95230.faa
-[13:15:32] Deleting unwanted file: Examples/2-res-Annotate-prokka/tmp_files/genome3-chromo.fst-all.fna_prokka-split5N.fna-prokkaRes/EXAM.1216.00002.IS.tmp.95230.blast
-[13:15:32] There are still 11 unannotated CDS left (started with 12)
-[13:15:32] Will use blast to search against /Users/aperrin/Softwares/src/prokka-dec.19/db/kingdom/Bacteria/AMR with 1 CPUs
-[13:15:32] Running: cat Examples\/2\-res\-Annotate\-prokka\/tmp_files\/genome3\-chromo\.fst\-all\.fna_prokka\-split5N\.fna\-prokkaRes\/EXAM\.1216\.00002\.AMR\.tmp\.95230\.faa | parallel --gnu --plain -j 1 --block 1311 --recstart '>' --pipe blastp -query - -db /Users/aperrin/Softwares/src/prokka-dec.19/db/kingdom/Bacteria/AMR -evalue 1e-300 -qcov_hsp_perc 90 -num_threads 1 -num_descriptions 1 -num_alignments 1 -seg no > Examples\/2\-res\-Annotate\-prokka\/tmp_files\/genome3\-chromo\.fst\-all\.fna_prokka\-split5N\.fna\-prokkaRes\/EXAM\.1216\.00002\.AMR\.tmp\.95230\.blast 2> /dev/null
-[13:15:32] Deleting unwanted file: Examples/2-res-Annotate-prokka/tmp_files/genome3-chromo.fst-all.fna_prokka-split5N.fna-prokkaRes/EXAM.1216.00002.AMR.tmp.95230.faa
-[13:15:32] Deleting unwanted file: Examples/2-res-Annotate-prokka/tmp_files/genome3-chromo.fst-all.fna_prokka-split5N.fna-prokkaRes/EXAM.1216.00002.AMR.tmp.95230.blast
-[13:15:32] There are still 11 unannotated CDS left (started with 12)
-[13:15:32] Will use blast to search against /Users/aperrin/Softwares/src/prokka-dec.19/db/kingdom/Bacteria/sprot with 1 CPUs
-[13:15:32] Running: cat Examples\/2\-res\-Annotate\-prokka\/tmp_files\/genome3\-chromo\.fst\-all\.fna_prokka\-split5N\.fna\-prokkaRes\/EXAM\.1216\.00002\.sprot\.tmp\.95230\.faa | parallel --gnu --plain -j 1 --block 1311 --recstart '>' --pipe blastp -query - -db /Users/aperrin/Softwares/src/prokka-dec.19/db/kingdom/Bacteria/sprot -evalue 1e-09 -qcov_hsp_perc 80 -num_threads 1 -num_descriptions 1 -num_alignments 1 -seg no > Examples\/2\-res\-Annotate\-prokka\/tmp_files\/genome3\-chromo\.fst\-all\.fna_prokka\-split5N\.fna\-prokkaRes\/EXAM\.1216\.00002\.sprot\.tmp\.95230\.blast 2> /dev/null
-[13:15:33] Deleting unwanted file: Examples/2-res-Annotate-prokka/tmp_files/genome3-chromo.fst-all.fna_prokka-split5N.fna-prokkaRes/EXAM.1216.00002.sprot.tmp.95230.faa
-[13:15:33] Deleting unwanted file: Examples/2-res-Annotate-prokka/tmp_files/genome3-chromo.fst-all.fna_prokka-split5N.fna-prokkaRes/EXAM.1216.00002.sprot.tmp.95230.blast
-[13:15:33] There are still 4 unannotated CDS left (started with 12)
-[13:15:33] Will use hmmer3 to search against /Users/aperrin/Softwares/src/prokka-dec.19/db/hmm/HAMAP.hmm with 1 CPUs
-[13:15:33] Running: cat Examples\/2\-res\-Annotate\-prokka\/tmp_files\/genome3\-chromo\.fst\-all\.fna_prokka\-split5N\.fna\-prokkaRes\/EXAM\.1216\.00002\.HAMAP\.hmm\.tmp\.95230\.faa | parallel --gnu --plain -j 1 --block 427 --recstart '>' --pipe hmmscan --noali --notextw --acc -E 1e-09 --cpu 1 /Users/aperrin/Softwares/src/prokka-dec.19/db/hmm/HAMAP.hmm /dev/stdin > Examples\/2\-res\-Annotate\-prokka\/tmp_files\/genome3\-chromo\.fst\-all\.fna_prokka\-split5N\.fna\-prokkaRes\/EXAM\.1216\.00002\.HAMAP\.hmm\.tmp\.95230\.hmmer3 2> /dev/null
-[13:15:34] Deleting unwanted file: Examples/2-res-Annotate-prokka/tmp_files/genome3-chromo.fst-all.fna_prokka-split5N.fna-prokkaRes/EXAM.1216.00002.HAMAP.hmm.tmp.95230.faa
-[13:15:34] Deleting unwanted file: Examples/2-res-Annotate-prokka/tmp_files/genome3-chromo.fst-all.fna_prokka-split5N.fna-prokkaRes/EXAM.1216.00002.HAMAP.hmm.tmp.95230.hmmer3
-[13:15:34] Labelling remaining 4 proteins as 'hypothetical protein'
-[13:15:34] Possible /pseudo 'N-acetylmuramoyl-L-alanine amidase AmiD' at header_genome3_1 position 880
-[13:15:34] Found 6 unique /gene codes.
-[13:15:34] Fixed 2 duplicate /gene - amiD_1 amiD_2
-[13:15:34] Fixed 1 colliding /gene names.
-[13:15:34] Adding /locus_tag identifiers
-[13:15:34] Assigned 12 locus_tags to CDS and RNA features.
-[13:15:34] Writing outputs to Examples/2-res-Annotate-prokka/tmp_files/genome3-chromo.fst-all.fna_prokka-split5N.fna-prokkaRes/
-[13:15:34] Generating annotation statistics file
-[13:15:34] Generating Genbank and Sequin files
-[13:15:34] Running: tbl2asn -V b -a r10k -l paired-ends -M n -N 1 -y 'Annotated using prokka 1.14.5 from https://github.com/tseemann/prokka' -Z Examples\/2\-res\-Annotate\-prokka\/tmp_files\/genome3\-chromo\.fst\-all\.fna_prokka\-split5N\.fna\-prokkaRes\/EXAM\.1216\.00002\.err -i Examples\/2\-res\-Annotate\-prokka\/tmp_files\/genome3\-chromo\.fst\-all\.fna_prokka\-split5N\.fna\-prokkaRes\/EXAM\.1216\.00002\.fsa 2> /dev/null
-[13:15:34] Deleting unwanted file: Examples/2-res-Annotate-prokka/tmp_files/genome3-chromo.fst-all.fna_prokka-split5N.fna-prokkaRes/errorsummary.val
-[13:15:34] Deleting unwanted file: Examples/2-res-Annotate-prokka/tmp_files/genome3-chromo.fst-all.fna_prokka-split5N.fna-prokkaRes/EXAM.1216.00002.dr
-[13:15:34] Deleting unwanted file: Examples/2-res-Annotate-prokka/tmp_files/genome3-chromo.fst-all.fna_prokka-split5N.fna-prokkaRes/EXAM.1216.00002.fixedproducts
-[13:15:34] Deleting unwanted file: Examples/2-res-Annotate-prokka/tmp_files/genome3-chromo.fst-all.fna_prokka-split5N.fna-prokkaRes/EXAM.1216.00002.ecn
-[13:15:34] Deleting unwanted file: Examples/2-res-Annotate-prokka/tmp_files/genome3-chromo.fst-all.fna_prokka-split5N.fna-prokkaRes/EXAM.1216.00002.val
-[13:15:34] Repairing broken .GBK output that tbl2asn produces...
-[13:15:34] Running: sed 's/COORDINATES: profile/COORDINATES:profile/' < Examples\/2\-res\-Annotate\-prokka\/tmp_files\/genome3\-chromo\.fst\-all\.fna_prokka\-split5N\.fna\-prokkaRes\/EXAM\.1216\.00002\.gbf > Examples\/2\-res\-Annotate\-prokka\/tmp_files\/genome3\-chromo\.fst\-all\.fna_prokka\-split5N\.fna\-prokkaRes\/EXAM\.1216\.00002\.gbk
-[13:15:34] Deleting unwanted file: Examples/2-res-Annotate-prokka/tmp_files/genome3-chromo.fst-all.fna_prokka-split5N.fna-prokkaRes/EXAM.1216.00002.gbf
-[13:15:34] Output files:
-[13:15:34] Examples/2-res-Annotate-prokka/tmp_files/genome3-chromo.fst-all.fna_prokka-split5N.fna-prokkaRes/EXAM.1216.00002.log
-[13:15:34] Examples/2-res-Annotate-prokka/tmp_files/genome3-chromo.fst-all.fna_prokka-split5N.fna-prokkaRes/EXAM.1216.00002.ffn
-[13:15:34] Examples/2-res-Annotate-prokka/tmp_files/genome3-chromo.fst-all.fna_prokka-split5N.fna-prokkaRes/EXAM.1216.00002.gbk
-[13:15:34] Examples/2-res-Annotate-prokka/tmp_files/genome3-chromo.fst-all.fna_prokka-split5N.fna-prokkaRes/EXAM.1216.00002.fsa
-[13:15:34] Examples/2-res-Annotate-prokka/tmp_files/genome3-chromo.fst-all.fna_prokka-split5N.fna-prokkaRes/EXAM.1216.00002.faa
-[13:15:34] Examples/2-res-Annotate-prokka/tmp_files/genome3-chromo.fst-all.fna_prokka-split5N.fna-prokkaRes/EXAM.1216.00002.txt
-[13:15:34] Examples/2-res-Annotate-prokka/tmp_files/genome3-chromo.fst-all.fna_prokka-split5N.fna-prokkaRes/EXAM.1216.00002.gff
-[13:15:34] Examples/2-res-Annotate-prokka/tmp_files/genome3-chromo.fst-all.fna_prokka-split5N.fna-prokkaRes/EXAM.1216.00002.tbl
-[13:15:34] Examples/2-res-Annotate-prokka/tmp_files/genome3-chromo.fst-all.fna_prokka-split5N.fna-prokkaRes/EXAM.1216.00002.sqn
-[13:15:34] Examples/2-res-Annotate-prokka/tmp_files/genome3-chromo.fst-all.fna_prokka-split5N.fna-prokkaRes/EXAM.1216.00002.tsv
-[13:15:34] Examples/2-res-Annotate-prokka/tmp_files/genome3-chromo.fst-all.fna_prokka-split5N.fna-prokkaRes/EXAM.1216.00002.fna
-[13:15:34] Examples/2-res-Annotate-prokka/tmp_files/genome3-chromo.fst-all.fna_prokka-split5N.fna-prokkaRes/EXAM.1216.00002.err
-[13:15:34] Annotation finished successfully.
-[13:15:34] Walltime used: 0.07 minutes
-[13:15:34] If you use this result please cite the Prokka paper:
-[13:15:34] Seemann T (2014) Prokka: rapid prokaryotic genome annotation. Bioinformatics. 30(14):2068-9.
-[13:15:34] Type 'prokka --citation' for more details.
-[13:15:34] Thank you, come again.
diff --git a/Examples/2-res-Annotate-prokka/tmp_files/genome3-chromo.fst-all.fna_prokka-split5N.fna-prokkaRes/EXAM.1216.00002.sqn b/Examples/2-res-Annotate-prokka/tmp_files/genome3-chromo.fst-all.fna_prokka-split5N.fna-prokkaRes/EXAM.1216.00002.sqn
deleted file mode 100644
index 512f187d3bec9b7bb52fae68ea6217b9202dab1f..0000000000000000000000000000000000000000
--- a/Examples/2-res-Annotate-prokka/tmp_files/genome3-chromo.fst-all.fna_prokka-split5N.fna-prokkaRes/EXAM.1216.00002.sqn
+++ /dev/null
@@ -1,1182 +0,0 @@
-Seq-entry ::= set {
-  class genbank ,
-  seq-set {
-    set {
-      class nuc-prot ,
-      descr {
-        source {
-          org {
-            taxname "Genus species" ,
-            orgname {
-              mod {
-                {
-                  subtype strain ,
-                  subname "strain" } } ,
-              gcode 11 } } } ,
-        comment "Annotated using prokka 1.14.5 from
- https://github.com/tseemann/prokka" ,
-        user {
-          type
-            str "NcbiCleanup" ,
-          data {
-            {
-              label
-                str "method" ,
-              data
-                str "SeriousSeqEntryCleanup" } ,
-            {
-              label
-                str "version" ,
-              data
-                int 8 } ,
-            {
-              label
-                str "month" ,
-              data
-                int 12 } ,
-            {
-              label
-                str "day" ,
-              data
-                int 9 } ,
-            {
-              label
-                str "year" ,
-              data
-                int 2019 } } } ,
-        create-date
-          std {
-            year 2019 ,
-            month 12 ,
-            day 9 } } ,
-      seq-set {
-        seq {
-          id {
-            local
-              str "header_genome3_1" } ,
-          descr {
-            molinfo {
-              biomol genomic } } ,
-          inst {
-            repr raw ,
-            mol dna ,
-            length 5747 ,
-            seq-data
-              iupacna "ATGAGAGCGCTACTGTGGCTGGTGGGTCTTGCGTTGCTGTTAACAGGCTGCGCGA
-GCGAAAAAGGAATTATCGATGAAGAGGGATATCAGCTTGATACCCGACATCGGGCGCAGGCGGCCTATCCGCGCATTA
-AAGTCCTGGTGATTCACTATACGGCGGAAAACTTTGACGTTTCGCTGGCGACGTTAACGGGCCGCAACGTCAGTTCGC
-ATTACCTGATTCCCGCAACCCCGCCATTATATGGCGGTAAACCGCGCATCTGGCAACTGGTGCCGGAACAGGATCAGG
-CCTGGCATGCGGGCGTCAGTTTCTGGCGAGGCGCCACGCGTCTCAATGATACGTCTATTGGCATTGAGCTGGAAAATC
-GCGGCTGGCGAATGTCCGGCGGGGTGAAATCTTTCGCGCCGTTTGAATCCGCGCAAATTCAGGCATTGATTCCGTTAG
-CGAAGGACATTATCGCGCGCTATGACATCAAACCGCAGAATGTGGTGGCCCATGCGGATATCGCGCCGCAGCGTAAAG
-ACGATCCCGGCCCGCGCTTCCCGTGGCGCGAGCTGGCGGCACAGGGGATTGGCGCCTGGCCTGACGCCCAGCGTGTGG
-CGTTTTATCTGGCTGGACGCGCGCCGTATACGCCAGTCGATACCGCAACGGTGCTTGCGTTACTCTCGCGCTATGGCT
-ATGAAGTCAAAGCCGATATGACGGCGCGCGAGCAACAGCGGGTGATTATGGCGTTCCAGATGCACTTCCGTCCGGCGC
-AATGGAACGGTATCGCAGATGCCGAAACGCAGGCGATTGCCGAAGCATTACTGGAGAAGTACGGCCAGGATTAACGAG
-TCCGGGAGCGGCGAGATTCCGGGCAGAGGAGGCGGCTATAGCGGATGAGAGCGCTACTGTGGCTGGTGGGTCTTGCGT
-TGCTGTTAACAGGCTGCGCGAGCGAAAAAGGAATTATCGATGAAGAGGGATATCAGCTTGATACCCGACATCGGGCGC
-AGGCGGCCTATCCGCGCATTAAAGTCCTGGTGATTCACTATACGGCGGAAAACTTTGACGTTTCGCTGGCGACGTTAA
-CGGGCCGCAACGTCAGTTCGCATTACCTGATTCCCGCAACCCCGCCATTATATGGCGGTAAACCGCGCATCTGGCAAC
-TGGTGCCGGAACAGGATCAGGCCTGGCATGCGGGCGTCAGTTTCTGGCGAGGCGCCACGCGTCTCAATGATACGTCTA
-TTGGCATTGAGCTGGAAAATCGCGGCTGGCGAATGTCCGGCGGGGTGAAATCTTTCGCGCCGTTTGAATCCGCGCAAA
-TTCAGGCATTGATTCCGTTAGCGAAGGACATTATCGCGCGCTATGACATCAAACCGCAGAATGTGGTGGCCCATGCGG
-ATATCGCGCCGCAGCGTAAAGACGATCCCGGCCCGCGCTTCCCGTGGCGCGAGCTGGCGGCACAGGGGATTGGCGCCT
-GGCCTGACGCCCAGCGTGTGGCGTTTTATCTGGCTGGACGCGCGCCGTATACGCCAGTCGATACCGCAACGGTGCTTG
-CGTTACTCTCGCGCTATGGCTATGAAGTCAAAGCCGATATGACGGCGCGCGAGCAACAGCGGGTGATTATGGCGTTCC
-AGATGCACTTCCGTCCGGCGCAATGGAACGGTATCGCAGATGCCGAAACGCAGGCGATTGCCGAAGCATTACTGGAGA
-AGTACGGCCAGGATTAACAGGGCGCGGTATCGCGAGGACTCTCTCTTCGAGGACATGCCGCACTTTATTGCTGAATGT
-ACTGAAAATATTCGCGAGCAGGCTGATTTACCCGGCCTGTTCAGCAAGGTAAACGAGGCGCTGGCCGCCAGCGGGATT
-TTCCCCATCGGCGGTATCCGCAGTCGCGCCCACTGGCTGGATACCTGGCAGATGGCTGACGGTAAGCATGATTACGCG
-TTTGTGCATATGACGCTGAAAATCGGCGCCGGGCGCAGCCTGGAGAGCCGTCAGGAAGTCGGCGAAATGCTGTTCGGG
-CTGATTAAAGCCCACTTCGCCGACCTGATGGAGAACCGCTATCTGGCGCTGTCGTTTGAGATTGCCGAGTTACATCCA
-ACGCTCAATTACAAACAAAACAACGTACACGCGTTATTTAAATAGCCCGAGTATTAGCGCGCGGCGGCGCTATAGGCG
-CGCTATAGGCATGAGCGCGCTATTTCTGGCCATCCCGTTAACCATTTTTGTGTTGTTTGTGTTACCGATTTGGCTGTG
-GCTGCATTACAGCAACCGCGCCGGTCGGGGAGAACTGTCGCAAAGCGAGCAGCAACGCTTACTGCAACTCACAGACGA
-CGCGCAACGTATGCGCGAGCGCATTCAGGCGCTGGAAGACATTCTTGATGCAGAGCATCCGAACTGGAGAGAGCGCTA
-ACGAGAGTCTCGGAGGAGCGGCGCTCTGGATGCCCGCGACTAAATTCTCCCGACGTACCCTCCTGACGGCAGGTTCTG
-CGCTTGCTGTTCTTCCTTTCCTGCGCGCCTTGCCGGTACAGGCGCGTGAACCTCGCGAGACCGTCGATATTAAGGATT
-ATCCGGCGGATGACGGTATCGCCTCGTTCAAACAGGCCTTCGCCGACGGACAGACCGTGGTCGTACCGCCAGGATGGG
-TGTGTGAAAATATCAATGCGGCGATAACGATTCCGGCGGGAAAAACGCTGCGGGTACAGGGCGCGGTGCGTGGGAATG
-GCCGGGGACGGTTTATTTTGCAGGACGGGTGTCAGGTGGTGGGGGAGCAGGGCGGCAGTCTGCACAATGTGACGCTGG
-ATGTTCGCGGGTCGGACTGTGTGATTAAAGGCGTGGCGATGAGCGGCTTTGGCCCCGTCGCGCAAATTTTCATCGGTG
-GTAAGGAACCGCAGGTGATGCGTAATCTCATTATCGATGACATCACCGTTACCCACGCCAACTACGCCATTCTCCGCC
-AGGGATTTCATAACCAAATGGACGGCGCGAGGATTACGCATAGCCGCTTTAGCGATTTACAGGGGGACGCCATTGAGT
-GGAATGTCGCGATTCACGACCGCGATATCCTGATTTCCGATCATGTCATCGAACGCATTGATTGTACCAATGGCAAAA
-TCAACTGGGGGATCGGCATCGGGCTGGCGGGTAGCACCTATGACAACAGTTATCCTGAAGACCAGGCAGTAAAAAACT
-TTGTGGTGGCCAATATTACCGGATCTGATTGCCGACAGCTTGTGCACGTAGAAAATGGCAAACATTTCGTCATTCGCA
-ATGTCAAAGCCAAAAACATCACGCCCGATTTCAGTAAAAATGCGGGTATTGATAACGCAACGATCGCAATTTATGGCT
-GTGATAATTTCGTCATTGATAATATTGATATGACGAATAGTGCCGGGATGCTCATCGGCTATGGCGTCGTTAAAGGAA
-AATACCTGTCAATTCCGCAAAACTTTAAATTAAACGCTATTCGGTTGGATAATCGCCAGGTTGCTTATAAATTACGCG
-GCATTCAAATTTCCTCCGGCAACACCCCCTCTTTTGTCGCCATCACCAATGTACGGATGACGCGTGCTACGCTGGAAC
-TGCATAATCAACCGCAGCACCTCTTCCTGCGTAATATCAACGTGATGCAAACTTCAGCGATTGGCCCGGCGTTAAAAA
-TGCATTTCGATTTGCGTAAAGATGTCCGTGGTCAATTTATGGCCCGCCAGGACACGCTGCTTTCCCTCGCTAATGTTC
-ATGCCATCAATGAAAACGGGCAGAGTTCCGTGGATATCGACAGGATTAATCACCAAACCGTGAATGTCGAAGCAGTGA
-ATTTTTCGCTGCCGAAGCGGGGAGGGTAACGCGTCTGCGCGCGCGGAGAGAGGCTCTCAGGACATGTCAGAAAATAAA
-TTACACGTTATCGATTTGCACAAACGCTACGGCGGTCATGAAGTGCTGAAAGGGGTATCGCTGCAGGCCCGCGCCGGA
-GATGTGATTAGCATCATCGGCTCGTCCGGCTCCGGTAAAAGCACTTTTTTGCGCTGTATTAACTTCCTCGAAAAACCG
-AGCGAAGACGCGATTATCGTGAACGGTCAGAACATTAATCTGGTGCGCGACAAAGACGGGCAGCTCAAAGTGGCGGAT
-AAAAATCAGCTACGCTTGTTGCGTACCCGCCTGACGATGGTGTTTCAGCACTTTAACCTCTGGAGCCACATGACGGTG
-CTGGAAAATGTGATGGAAGCGCCGATTCAGGTACTGGGATTAAGCAAGCACGACGCGCGCGAGCGGGCGTTGAAATAT
-CTGGCGAAGGTGGGGATTGATGAGCGCGCTCAGGGCAAATATCCCGTTCATCTCTCCGGTGGCCAACAGCAGCGCGTT
-TCTATTGCGCGCGCGCTGGCGATGGAACCTGACGTTTTACTGTTCGATGAACCCACTTCGGCGCTCGATCCTGAACTG
-GTCGGCGAAGTGTTGCGCATCATGCAACAACTGGCGGAAGAAGGCAAAACGATGGTGGTGGTCACGCATGAAATGGGC
-TTCGTTCGCCATGTCTCTTCGCACGTTATTTTTCTGCATCAGGGGAAAATTGAAGAAGAGGGCGATCCGGAGCAGGTG
-TTCGGCAATCCGCAAAGCCCGCGTTTACAGCAATTCCTGAAAGGCTCGCTGAAATAACCGGATGCGCGCGATATATCG
-GCGATGCGTGTTTATTGGCATCGTTAGCCTGTTTCCTGAAATGTTCCGCGCAATTACCGATTACGGGGTAACTGGCCG
-GGCAGTAAAAAATGGCCTGCTGAACATCCAAAGCTGGAGTCCTCGCGACTTCACGCATGACCGGCACCGTACCGTGGA
-CGATCGTCCTTACGGCGGCGGACCAGGGATGTTAATGATGGTGCAACCCTTGCGGGACGCCATTCACGCAGCAAAAGC
-CGCGGCAGGTGAAGGCGCTAAAGTGATTTATCTGTCGCCTCAGGGACGCAAGCTTGATCAAGCGGGCGTTAGCGAGCT
-GGCCACGAATCAGAAGCTTATTCTGGTGTGTGGTCGCTACGAAGGCGTAGATGAGCGCGTAATTCAGACCGAAATTGA
-CGAAGAATGGTCAATTGGCGATTACGTTCTCAGCGGTGGCGAACTACCGGCAATGACGCTGATTGACTCCGTCGCCCG
-GTTTATACCGGGAGTTCTGGGGCATGAAGCATCAGCAATCGAAGATTCGTTTGCTGATGGGTTGCTGGATTGTCCGCA
-CTATACGCGCCCTGAAGTGTTAGAGGGGATGGAAGTACCGCCAGTATTGCTGTCGGGAAACCATGCTGAGATACGTCG
-CTGGCGTTTGAAACAGTCGCTGGGCCGAACCTGGCTTAGAAGACCTGAACTTCTGGAAAACCTGGCTCTGACTGAAGA
-GCAAGCAAGGTTGCTGGCGGAGTTCAAAACAGAACACGCACAACAGCAGCATAAACATGATGGGATGGCATAGCCGGC
-TCTGCGAGAGAGGAGCGCTCGCATGAATAATCATTTTGGGAAAGGGTTAATGGCCGGGTTGCACGCGCCATATGCATA
-TAGCGCGCATCATGCGGTGAATTTCTGTTCTGAGTATAAACGTGGCTTTGTATTGGGTTTTACACACCGTATGTTCGA
-AAAGACCGGCGATCGTCAACTTAGCGCGTGGGAGGCTGGAATTCTGACGCGTCGCTATGGTCTGGATAAAGAAATGGT
-GATGGATTTCTTTAAAGAGAATCATTCCGGGATGGCGGTTCGCTTCTTTATGGCCGGTTATCGACTCGAAGGTTGA" } } ,
-        seq {
-          id {
-            local
-              str "header_genome3_1_1" } ,
-          descr {
-            title "N-acetylmuramoyl-L-alanine amidase AmiD [Genus species]" ,
-            molinfo {
-              biomol peptide ,
-              tech concept-trans } } ,
-          inst {
-            repr raw ,
-            mol aa ,
-            length 276 ,
-            seq-data
-              ncbieaa "MRALLWLVGLALLLTGCASEKGIIDEEGYQLDTRHRAQAAYPRIKVLVIHYTAEN
-FDVSLATLTGRNVSSHYLIPATPPLYGGKPRIWQLVPEQDQAWHAGVSFWRGATRLNDTSIGIELENRGWRMSGGVKS
-FAPFESAQIQALIPLAKDIIARYDIKPQNVVAHADIAPQRKDDPGPRFPWRELAAQGIGAWPDAQRVAFYLAGRAPYT
-PVDTATVLALLSRYGYEVKADMTAREQQRVIMAFQMHFRPAQWNGIADAETQAIAEALLEKYGQD" } ,
-          annot {
-            {
-              data
-                ftable {
-                  {
-                    id
-                      local
-                        id 9 ,
-                    data
-                      prot {
-                        name {
-                          "N-acetylmuramoyl-L-alanine amidase AmiD" } ,
-                        ec {
-                          "3.5.1.28" } } ,
-                    location
-                      int {
-                        from 0 ,
-                        to 275 ,
-                        id
-                          local
-                            str "header_genome3_1_1" } } } } } } ,
-        seq {
-          id {
-            local
-              str "header_genome3_1_2" } ,
-          descr {
-            title "N-acetylmuramoyl-L-alanine amidase AmiD [Genus species]" ,
-            molinfo {
-              biomol peptide ,
-              tech concept-trans } } ,
-          inst {
-            repr raw ,
-            mol aa ,
-            length 276 ,
-            seq-data
-              ncbieaa "MRALLWLVGLALLLTGCASEKGIIDEEGYQLDTRHRAQAAYPRIKVLVIHYTAEN
-FDVSLATLTGRNVSSHYLIPATPPLYGGKPRIWQLVPEQDQAWHAGVSFWRGATRLNDTSIGIELENRGWRMSGGVKS
-FAPFESAQIQALIPLAKDIIARYDIKPQNVVAHADIAPQRKDDPGPRFPWRELAAQGIGAWPDAQRVAFYLAGRAPYT
-PVDTATVLALLSRYGYEVKADMTAREQQRVIMAFQMHFRPAQWNGIADAETQAIAEALLEKYGQD" } ,
-          annot {
-            {
-              data
-                ftable {
-                  {
-                    id
-                      local
-                        id 10 ,
-                    data
-                      prot {
-                        name {
-                          "N-acetylmuramoyl-L-alanine amidase AmiD" } ,
-                        ec {
-                          "3.5.1.28" } } ,
-                    location
-                      int {
-                        from 0 ,
-                        to 275 ,
-                        id
-                          local
-                            str "header_genome3_1_2" } } } } } } ,
-        seq {
-          id {
-            local
-              str "header_genome3_1_3" } ,
-          descr {
-            title "5-carboxymethyl-2-hydroxymuconate Delta-isomerase [Genus
- species]" ,
-            molinfo {
-              biomol peptide ,
-              tech concept-trans } } ,
-          inst {
-            repr raw ,
-            mol aa ,
-            length 157 ,
-            seq-data
-              ncbieaa "MPKRRRLPKHYWRSTARINRARYREDSLFEDMPHFIAECTENIREQADLPGLFSK
-VNEALAASGIFPIGGIRSRAHWLDTWQMADGKHDYAFVHMTLKIGAGRSLESRQEVGEMLFGLIKAHFADLMENRYLA
-LSFEIAELHPTLNYKQNNVHALFK" } ,
-          annot {
-            {
-              data
-                ftable {
-                  {
-                    id
-                      local
-                        id 11 ,
-                    data
-                      prot {
-                        name {
-                          "5-carboxymethyl-2-hydroxymuconate Delta-isomerase" } ,
-                        ec {
-                          "5.3.3.10" } } ,
-                    location
-                      int {
-                        from 0 ,
-                        to 156 ,
-                        id
-                          local
-                            str "header_genome3_1_3" } } } } } } ,
-        seq {
-          id {
-            local
-              str "header_genome3_1_4" } ,
-          descr {
-            title "Phage shock protein B [Genus species]" ,
-            molinfo {
-              biomol peptide ,
-              tech concept-trans } } ,
-          inst {
-            repr raw ,
-            mol aa ,
-            length 74 ,
-            seq-data
-              ncbieaa "MSALFLAIPLTIFVLFVLPIWLWLHYSNRAGRGELSQSEQQRLLQLTDDAQRMRE
-RIQALEDILDAEHPNWRER" } ,
-          annot {
-            {
-              data
-                ftable {
-                  {
-                    id
-                      local
-                        id 12 ,
-                    data
-                      prot {
-                        name {
-                          "Phage shock protein B" } } ,
-                    location
-                      int {
-                        from 0 ,
-                        to 73 ,
-                        id
-                          local
-                            str "header_genome3_1_4" } } } } } } ,
-        seq {
-          id {
-            local
-              str "header_genome3_1_5" } ,
-          descr {
-            title "hypothetical protein PFKCIMHH_00005 [Genus species]" ,
-            molinfo {
-              biomol peptide ,
-              tech concept-trans } } ,
-          inst {
-            repr raw ,
-            mol aa ,
-            length 467 ,
-            seq-data
-              ncbieaa "MPATKFSRRTLLTAGSALAVLPFLRALPVQAREPRETVDIKDYPADDGIASFKQA
-FADGQTVVVPPGWVCENINAAITIPAGKTLRVQGAVRGNGRGRFILQDGCQVVGEQGGSLHNVTLDVRGSDCVIKGVA
-MSGFGPVAQIFIGGKEPQVMRNLIIDDITVTHANYAILRQGFHNQMDGARITHSRFSDLQGDAIEWNVAIHDRDILIS
-DHVIERIDCTNGKINWGIGIGLAGSTYDNSYPEDQAVKNFVVANITGSDCRQLVHVENGKHFVIRNVKAKNITPDFSK
-NAGIDNATIAIYGCDNFVIDNIDMTNSAGMLIGYGVVKGKYLSIPQNFKLNAIRLDNRQVAYKLRGIQISSGNTPSFV
-AITNVRMTRATLELHNQPQHLFLRNINVMQTSAIGPALKMHFDLRKDVRGQFMARQDTLLSLANVHAINENGQSSVDI
-DRINHQTVNVEAVNFSLPKRGG" } ,
-          annot {
-            {
-              data
-                ftable {
-                  {
-                    id
-                      local
-                        id 13 ,
-                    data
-                      prot {
-                        name {
-                          "hypothetical protein" } } ,
-                    location
-                      int {
-                        from 0 ,
-                        to 466 ,
-                        id
-                          local
-                            str "header_genome3_1_5" } } } } } } ,
-        seq {
-          id {
-            local
-              str "header_genome3_1_6" } ,
-          descr {
-            title "Histidine transport ATP-binding protein HisP [Genus
- species]" ,
-            molinfo {
-              biomol peptide ,
-              tech concept-trans } } ,
-          inst {
-            repr raw ,
-            mol aa ,
-            length 257 ,
-            seq-data
-              ncbieaa "MSENKLHVIDLHKRYGGHEVLKGVSLQARAGDVISIIGSSGSGKSTFLRCINFLE
-KPSEDAIIVNGQNINLVRDKDGQLKVADKNQLRLLRTRLTMVFQHFNLWSHMTVLENVMEAPIQVLGLSKHDARERAL
-KYLAKVGIDERAQGKYPVHLSGGQQQRVSIARALAMEPDVLLFDEPTSALDPELVGEVLRIMQQLAEEGKTMVVVTHE
-MGFVRHVSSHVIFLHQGKIEEEGDPEQVFGNPQSPRLQQFLKGSLK" } ,
-          annot {
-            {
-              data
-                ftable {
-                  {
-                    id
-                      local
-                        id 14 ,
-                    data
-                      prot {
-                        name {
-                          "Histidine transport ATP-binding protein HisP" } } ,
-                    location
-                      int {
-                        from 0 ,
-                        to 256 ,
-                        id
-                          local
-                            str "header_genome3_1_6" } } } } } } ,
-        seq {
-          id {
-            local
-              str "header_genome3_1_7" } ,
-          descr {
-            title "tRNA (guanine-N(1)-)-methyltransferase [Genus species]" ,
-            molinfo {
-              biomol peptide ,
-              tech concept-trans } } ,
-          inst {
-            repr raw ,
-            mol aa ,
-            length 263 ,
-            seq-data
-              ncbieaa "MRAIYRRCVFIGIVSLFPEMFRAITDYGVTGRAVKNGLLNIQSWSPRDFTHDRHR
-TVDDRPYGGGPGMLMMVQPLRDAIHAAKAAAGEGAKVIYLSPQGRKLDQAGVSELATNQKLILVCGRYEGVDERVIQT
-EIDEEWSIGDYVLSGGELPAMTLIDSVARFIPGVLGHEASAIEDSFADGLLDCPHYTRPEVLEGMEVPPVLLSGNHAE
-IRRWRLKQSLGRTWLRRPELLENLALTEEQARLLAEFKTEHAQQQHKHDGMA" } ,
-          annot {
-            {
-              data
-                ftable {
-                  {
-                    id
-                      local
-                        id 15 ,
-                    data
-                      prot {
-                        name {
-                          "tRNA (guanine-N(1)-)-methyltransferase" } ,
-                        ec {
-                          "2.1.1.228" } } ,
-                    location
-                      int {
-                        from 0 ,
-                        to 262 ,
-                        id
-                          local
-                            str "header_genome3_1_7" } } } } } } ,
-        seq {
-          id {
-            local
-              str "header_genome3_1_8" } ,
-          descr {
-            title "hypothetical protein PFKCIMHH_00008 [Genus species]" ,
-            molinfo {
-              biomol peptide ,
-              tech concept-trans } } ,
-          inst {
-            repr raw ,
-            mol aa ,
-            length 95 ,
-            seq-data
-              ncbieaa "MNNHFGKGLMAGLHAPYAYSAHHAVNFCSEYKRGFVLGFTHRMFEKTGDRQLSAW
-EAGILTRRYGLDKEMVMDFFKENHSGMAVRFFMAGYRLEG" } ,
-          annot {
-            {
-              data
-                ftable {
-                  {
-                    id
-                      local
-                        id 16 ,
-                    data
-                      prot {
-                        name {
-                          "hypothetical protein" } } ,
-                    location
-                      int {
-                        from 0 ,
-                        to 94 ,
-                        id
-                          local
-                            str "header_genome3_1_8" } } } } } } } ,
-      annot {
-        {
-          data
-            ftable {
-              {
-                id
-                  local
-                    id 1 ,
-                data
-                  cdregion {
-                    frame one ,
-                    code {
-                      id 11 } } ,
-                product
-                  whole
-                    local
-                      str "header_genome3_1_1" ,
-                location
-                  int {
-                    from 0 ,
-                    to 830 ,
-                    strand plus ,
-                    id
-                      local
-                        str "header_genome3_1" } ,
-                qual {
-                  {
-                    qual "inference" ,
-                    val "ab initio prediction:Prodigal:002006" } ,
-                  {
-                    qual "inference" ,
-                    val "similar to AA sequence:UniProtKB:P75820" } } ,
-                xref {
-                  {
-                    data
-                      gene {
-                        locus "amiD_1" ,
-                        locus-tag "PFKCIMHH_00001" } } } ,
-                dbxref {
-                  {
-                    db "COG" ,
-                    tag
-                      str "COG3023" } } } ,
-              {
-                id
-                  local
-                    id 2 ,
-                data
-                  cdregion {
-                    frame one ,
-                    code {
-                      id 11 } } ,
-                product
-                  whole
-                    local
-                      str "header_genome3_1_2" ,
-                location
-                  int {
-                    from 879 ,
-                    to 1709 ,
-                    strand plus ,
-                    id
-                      local
-                        str "header_genome3_1" } ,
-                qual {
-                  {
-                    qual "inference" ,
-                    val "ab initio prediction:Prodigal:002006" } ,
-                  {
-                    qual "inference" ,
-                    val "similar to AA sequence:UniProtKB:P75820" } } ,
-                xref {
-                  {
-                    data
-                      gene {
-                        locus "amiD_2" ,
-                        locus-tag "PFKCIMHH_00002" } } } ,
-                dbxref {
-                  {
-                    db "COG" ,
-                    tag
-                      str "COG3023" } } } ,
-              {
-                id
-                  local
-                    id 3 ,
-                data
-                  cdregion {
-                    frame one ,
-                    code {
-                      id 11 } } ,
-                product
-                  whole
-                    local
-                      str "header_genome3_1_3" ,
-                location
-                  int {
-                    from 1654 ,
-                    to 2127 ,
-                    strand plus ,
-                    id
-                      local
-                        str "header_genome3_1" } ,
-                qual {
-                  {
-                    qual "inference" ,
-                    val "ab initio prediction:Prodigal:002006" } ,
-                  {
-                    qual "inference" ,
-                    val "similar to AA sequence:UniProtKB:Q05354" } } ,
-                xref {
-                  {
-                    data
-                      gene {
-                        locus "hpcD" ,
-                        locus-tag "PFKCIMHH_00003" } } } } ,
-              {
-                id
-                  local
-                    id 4 ,
-                data
-                  cdregion {
-                    frame one ,
-                    code {
-                      id 11 } } ,
-                product
-                  whole
-                    local
-                      str "header_genome3_1_4" ,
-                location
-                  int {
-                    from 2171 ,
-                    to 2395 ,
-                    strand plus ,
-                    id
-                      local
-                        str "header_genome3_1" } ,
-                qual {
-                  {
-                    qual "inference" ,
-                    val "ab initio prediction:Prodigal:002006" } ,
-                  {
-                    qual "inference" ,
-                    val "similar to AA sequence:UniProtKB:P0AFM9" } } ,
-                xref {
-                  {
-                    data
-                      gene {
-                        locus "pspB" ,
-                        locus-tag "PFKCIMHH_00004" } } } } ,
-              {
-                id
-                  local
-                    id 5 ,
-                data
-                  cdregion {
-                    frame one ,
-                    code {
-                      id 11 } } ,
-                product
-                  whole
-                    local
-                      str "header_genome3_1_5" ,
-                location
-                  int {
-                    from 2424 ,
-                    to 3827 ,
-                    strand plus ,
-                    id
-                      local
-                        str "header_genome3_1" } ,
-                qual {
-                  {
-                    qual "inference" ,
-                    val "ab initio prediction:Prodigal:002006" } } ,
-                xref {
-                  {
-                    data
-                      gene {
-                        locus-tag "PFKCIMHH_00005" } } } } ,
-              {
-                id
-                  local
-                    id 6 ,
-                data
-                  cdregion {
-                    frame one ,
-                    code {
-                      id 11 } } ,
-                product
-                  whole
-                    local
-                      str "header_genome3_1_6" ,
-                location
-                  int {
-                    from 3862 ,
-                    to 4635 ,
-                    strand plus ,
-                    id
-                      local
-                        str "header_genome3_1" } ,
-                qual {
-                  {
-                    qual "inference" ,
-                    val "ab initio prediction:Prodigal:002006" } ,
-                  {
-                    qual "inference" ,
-                    val "similar to AA sequence:UniProtKB:P02915" } } ,
-                xref {
-                  {
-                    data
-                      gene {
-                        locus "hisP" ,
-                        locus-tag "PFKCIMHH_00006" } } } ,
-                dbxref {
-                  {
-                    db "COG" ,
-                    tag
-                      str "COG4598" } } } ,
-              {
-                id
-                  local
-                    id 7 ,
-                data
-                  cdregion {
-                    frame one ,
-                    code {
-                      id 11 } } ,
-                product
-                  whole
-                    local
-                      str "header_genome3_1_7" ,
-                location
-                  int {
-                    from 4640 ,
-                    to 5431 ,
-                    strand plus ,
-                    id
-                      local
-                        str "header_genome3_1" } ,
-                qual {
-                  {
-                    qual "inference" ,
-                    val "ab initio prediction:Prodigal:002006" } ,
-                  {
-                    qual "inference" ,
-                    val "similar to AA sequence:UniProtKB:P0A873" } } ,
-                xref {
-                  {
-                    data
-                      gene {
-                        locus "trmD" ,
-                        locus-tag "PFKCIMHH_00007" } } } ,
-                dbxref {
-                  {
-                    db "COG" ,
-                    tag
-                      str "COG0336" } } } ,
-              {
-                id
-                  local
-                    id 8 ,
-                data
-                  cdregion {
-                    frame one ,
-                    code {
-                      id 11 } } ,
-                product
-                  whole
-                    local
-                      str "header_genome3_1_8" ,
-                location
-                  int {
-                    from 5459 ,
-                    to 5746 ,
-                    strand plus ,
-                    id
-                      local
-                        str "header_genome3_1" } ,
-                qual {
-                  {
-                    qual "inference" ,
-                    val "ab initio prediction:Prodigal:002006" } } ,
-                xref {
-                  {
-                    data
-                      gene {
-                        locus-tag "PFKCIMHH_00008" } } } } } } } } ,
-    set {
-      class nuc-prot ,
-      descr {
-        source {
-          org {
-            taxname "Genus species" ,
-            orgname {
-              mod {
-                {
-                  subtype strain ,
-                  subname "strain" } } ,
-              gcode 11 } } } ,
-        comment "Annotated using prokka 1.14.5 from
- https://github.com/tseemann/prokka" ,
-        user {
-          type
-            str "NcbiCleanup" ,
-          data {
-            {
-              label
-                str "method" ,
-              data
-                str "SeriousSeqEntryCleanup" } ,
-            {
-              label
-                str "version" ,
-              data
-                int 8 } ,
-            {
-              label
-                str "month" ,
-              data
-                int 12 } ,
-            {
-              label
-                str "day" ,
-              data
-                int 9 } ,
-            {
-              label
-                str "year" ,
-              data
-                int 2019 } } } ,
-        create-date
-          std {
-            year 2019 ,
-            month 12 ,
-            day 9 } } ,
-      seq-set {
-        seq {
-          id {
-            local
-              str "genome3_plasmi_2" } ,
-          descr {
-            molinfo {
-              biomol genomic } } ,
-          inst {
-            repr raw ,
-            mol dna ,
-            length 1968 ,
-            seq-data
-              iupacna "ATGTCTACGCTTCTCTATTTGCACGGATTCAACAGTTCCCCTCGCTCGGCAAAAG
-CGTGCCAGCTAAAAAACTGGCTGGCGGAGCGTCATCCGCATGTTGAGATGATCGTCCCTCAACTACCGCCGTATCCTG
-CCGATGCGGCGGAGTTGCTGGAGTCTCTCGTGCTTGAGCATGGCGGTGCGCCATTAGGGCTGGTAGGATCGTCGCTGG
-GTGGTTATTACGCCACCTGGCTGTCGCAATGTTTTATGCTGCCGGCTGTGGTGGTGAATCCCGCCGTGCGGCCCTTTG
-AATTACTGACCGACTATCTCGGTCAGAACGAGAACCCCTACACCGGGCAGCAATATGTGCTAGAGTCTCGCCATATTT
-ATGATCTTAAAGTCATGCAGATTGACCCGCTGGAAGCGCCGGACCTGATCTGGCTACTGCAACAGACGGGCGATGAAG
-TGCTGGATTACCGCCAGGCGGTGGCATATTACGCCTCCTGCCGTCAGACAGTGACCGAGGGTGGTAATCACGCATTCA
-CGGGCTTCGAAGATTATTTCAACCAGATTGTCGATTTTCTTGGACTGCACAGTTGCTGACGCGTAGCGGCCGGAATCT
-TCTCGGAGAGGCGCTTCTCTCTCGGAGATGATTGACCCTATTTTTGCGTCCTGTACGCTAATTGCCGTCTTTGTTGTT
-TTACTGGCCATGGGCGCGCCTATCGGGATCTGCATCGTTATCGCCTCTTTCAGCACCATGATGCTGGTACTGCCTTTC
-GATATTTCGATGTTCGCCACCGCGCAAAAAATGTTCTCCAGCCTGGACAGTTTTGCCTTGCTGGCCGTGCCGTTCTTC
-GTTTTGTCCGGGGTGATCATGAATAGCGGGGGAATTGCCGCCCGGCTGATCAATTTTGCCAAACTGTTTACTGGCAAA
-CTGCCCGGTTCGCTCTCTTATACCAACATCGTCGGCAATATGATGTTCGGTGCAATTTCCGGATCGGCAATTGCCGCC
-TCAACCTCCATCGGCGGCGTGATGGTGCCGATGAGCGCGCGCGAAGGTTACGATCGCGGCTTTGCGGCCGCGGTGAAT
-ATCGCCTCCGCGCCGACGGGAATGTTAATTCCGCCCACCACGGCTTTTATCCTTTATGCGCTGGCAAGCGGGGGAACA
-TCGATTGCCGCTCTGTTCGCCGGCGGTCTGGTCGCGGGAGTGCTGTGGGGCGTTGGCTGTATGCTGGTCACGCTGGTA
-GTCGCTAAGCGTCGAAATTATCGGGTTTTCTTCACCGTCCAAAAAGGCATGGCGCTAAAAGTTGCCGTTGAGGCCATT
-CCCAGCCTGTTACTGATCGTGATTATCGTCGGCGGCATTGTGCAGGGGATTTTCACCGCCATTGAAGCCTCCGCGATT
-GCCGTGGTGTATACGTTATTGCTGACGATGGTGTTTTACCGCACGCTGAAAATTAAGGATTTGCCTTCGATTTTGCTC
-CAGACAGTGGTAATGACCGGGGTCATCATGTTCCTGCTGGCAACCTCTTCGGCGATGTCCTTCTCAATGTCGATCACC
-AATATTCCTGCGGCGCTGAGCGATATGATCCTCGGTATTTCCGCCAATAAACTGGTTATCCTGTTAGTCATTACCGTC
-TTTTTGTTGATTATCGGCGCATTTATGGATATCGGTCCGGCCATTCTGATTTTTACCCCGATTCTGCTGCCGATCATG
-GCTAAACTGGGCGTCGATCCGGTGCATTTGGGCATTATCATGATCTATAACCTGGCGATTGGCACCATTACGCCGCCA
-GTTGGCAGTGGTTTATATGTCGGGGCGAGCGTCGGTAAGGTCAAAGTTGAGGAAGTGATTAAACCGTTGCTGCCTTTT
-TACGGCGCGATTATCGGCGTTCTGTTATTAATTACCTACATTCCGGAAATCATACTGTTCTTACCCCGTCTACTGGGC
-ATCATGTAAACCCGATGGCGCGCAGAGGCGCGAGTTCTGGA" } } ,
-        seq {
-          id {
-            local
-              str "genome3_plasmi_2_1" } ,
-          descr {
-            title "hypothetical protein PFKCIMHH_00009 [Genus species]" ,
-            molinfo {
-              biomol peptide ,
-              tech concept-trans } } ,
-          inst {
-            repr raw ,
-            mol aa ,
-            length 193 ,
-            seq-data
-              ncbieaa "MSTLLYLHGFNSSPRSAKACQLKNWLAERHPHVEMIVPQLPPYPADAAELLESLV
-LEHGGAPLGLVGSSLGGYYATWLSQCFMLPAVVVNPAVRPFELLTDYLGQNENPYTGQQYVLESRHIYDLKVMQIDPL
-EAPDLIWLLQQTGDEVLDYRQAVAYYASCRQTVTEGGNHAFTGFEDYFNQIVDFLGLHSC" } ,
-          annot {
-            {
-              data
-                ftable {
-                  {
-                    id
-                      local
-                        id 19 ,
-                    data
-                      prot {
-                        name {
-                          "hypothetical protein" } } ,
-                    location
-                      int {
-                        from 0 ,
-                        to 192 ,
-                        id
-                          local
-                            str "genome3_plasmi_2_1" } } } } } } ,
-        seq {
-          id {
-            local
-              str "genome3_plasmi_2_2" } ,
-          descr {
-            title "C4-dicarboxylate TRAP transporter large permease protein
- DctM [Genus species]" ,
-            molinfo {
-              biomol peptide ,
-              tech concept-trans } } ,
-          inst {
-            repr raw ,
-            mol aa ,
-            length 435 ,
-            seq-data
-              ncbieaa "MIDPIFASCTLIAVFVVLLAMGAPIGICIVIASFSTMMLVLPFDISMFATAQKMF
-SSLDSFALLAVPFFVLSGVIMNSGGIAARLINFAKLFTGKLPGSLSYTNIVGNMMFGAISGSAIAASTSIGGVMVPMS
-AREGYDRGFAAAVNIASAPTGMLIPPTTAFILYALASGGTSIAALFAGGLVAGVLWGVGCMLVTLVVAKRRNYRVFFT
-VQKGMALKVAVEAIPSLLLIVIIVGGIVQGIFTAIEASAIAVVYTLLLTMVFYRTLKIKDLPSILLQTVVMTGVIMFL
-LATSSAMSFSMSITNIPAALSDMILGISANKLVILLVITVFLLIIGAFMDIGPAILIFTPILLPIMAKLGVDPVHLGI
-IMIYNLAIGTITPPVGSGLYVGASVGKVKVEEVIKPLLPFYGAIIGVLLLITYIPEIILFLPRLLGIM" } ,
-          annot {
-            {
-              data
-                ftable {
-                  {
-                    id
-                      local
-                        id 20 ,
-                    data
-                      prot {
-                        name {
-                          "C4-dicarboxylate TRAP transporter large permease
- protein DctM" } } ,
-                    location
-                      int {
-                        from 0 ,
-                        to 434 ,
-                        id
-                          local
-                            str "genome3_plasmi_2_2" } } } } } } } ,
-      annot {
-        {
-          data
-            ftable {
-              {
-                id
-                  local
-                    id 17 ,
-                data
-                  cdregion {
-                    frame one ,
-                    code {
-                      id 11 } } ,
-                product
-                  whole
-                    local
-                      str "genome3_plasmi_2_1" ,
-                location
-                  int {
-                    from 0 ,
-                    to 581 ,
-                    strand plus ,
-                    id
-                      local
-                        str "genome3_plasmi_2" } ,
-                qual {
-                  {
-                    qual "inference" ,
-                    val "ab initio prediction:Prodigal:002006" } } ,
-                xref {
-                  {
-                    data
-                      gene {
-                        locus-tag "PFKCIMHH_00009" } } } } ,
-              {
-                id
-                  local
-                    id 18 ,
-                data
-                  cdregion {
-                    frame one ,
-                    code {
-                      id 11 } } ,
-                product
-                  whole
-                    local
-                      str "genome3_plasmi_2_2" ,
-                location
-                  int {
-                    from 628 ,
-                    to 1935 ,
-                    strand plus ,
-                    id
-                      local
-                        str "genome3_plasmi_2" } ,
-                qual {
-                  {
-                    qual "inference" ,
-                    val "ab initio prediction:Prodigal:002006" } ,
-                  {
-                    qual "inference" ,
-                    val "similar to AA sequence:UniProtKB:O07838" } } ,
-                xref {
-                  {
-                    data
-                      gene {
-                        locus "dctM" ,
-                        locus-tag "PFKCIMHH_00010" } } } ,
-                dbxref {
-                  {
-                    db "COG" ,
-                    tag
-                      str "COG1593" } } } } } } } ,
-    set {
-      class nuc-prot ,
-      descr {
-        source {
-          org {
-            taxname "Genus species" ,
-            orgname {
-              mod {
-                {
-                  subtype strain ,
-                  subname "strain" } } ,
-              gcode 11 } } } ,
-        comment "Annotated using prokka 1.14.5 from
- https://github.com/tseemann/prokka" ,
-        user {
-          type
-            str "NcbiCleanup" ,
-          data {
-            {
-              label
-                str "method" ,
-              data
-                str "SeriousSeqEntryCleanup" } ,
-            {
-              label
-                str "version" ,
-              data
-                int 8 } ,
-            {
-              label
-                str "month" ,
-              data
-                int 12 } ,
-            {
-              label
-                str "day" ,
-              data
-                int 9 } ,
-            {
-              label
-                str "year" ,
-              data
-                int 2019 } } } ,
-        create-date
-          std {
-            year 2019 ,
-            month 12 ,
-            day 9 } } ,
-      seq-set {
-        seq {
-          id {
-            local
-              str "genome3_plasmi_3" } ,
-          descr {
-            molinfo {
-              biomol genomic } } ,
-          inst {
-            repr raw ,
-            mol dna ,
-            length 1102 ,
-            seq-data
-              iupacna "CACAGGGCTTAGAGGCGCTATGGCAATGATAATTAATGGGAAATTAATTAAAGCA
-AAAGACTTAGCTAAGGCTGCAGGTGTATCTCGTTCAACAGTGATTAAATATTACGGCATTAGCCGTGAGAATTACGAA
-AGGGTAGCAACTGAAAGAAGGAAGCTTGCTTTTGAACTAAGAGCATCAGGTTTAAAATGGAAAGAAGTTGCTGAAAAA
-ATGAACACGACAAAATATAGCGCAATTGCATATTATAGACGATATTTAGCATTAGAGAAAAACAAATAACAGGCGCTA
-AGGCGGCGATCCTAGCGCGCGATCGCGCATGCGATGGTCGAACTGCAACATCAACGGCTGATGGTGCTTGCCGAACAG
-CTCCAGCTGGACAGTCTTATCGGCGCAGCGCCGGCGCTGTCGCAACAGGCGGTGGATCAGGAATGGAGCTACATGGAC
-TTCCTGGAGCACCTGTTACATGAGGAGAAACTGGCCCGGCATCAGCGTAAACAGGCGATGTACACGCGGATGGCAGCC
-TTCCCGGCGGTAAAGACGTTCGAGGAGTACGACTTCACCTTCGCCACCGGCGCTCCTCAGAAGCAAATCCAGTCGCTG
-CGATCCCTGAGCTTCATAGAGCGTAACGAAAACATCGTGTTGCTGGGGCCATCGGGCGTGGGAAAAACGCATCTGGCG
-ATAGCCATGGGCTACGAAGCAGTACGGGCGGGCATCAAGGTTCGCTTCACAACAGCAGCGGACCTGCTGCTACAGCTG
-TCCACTTCACAGCGTCAGGGCCGTTACAAAACGACTCTCAATCGTGGTGTCATGGCCCCGAAGCTGCTTATCATCGAT
-GAAATAGGTTATCTGCCGTTCAGTCAGGAGGAAGCCAAGCTGTTCTTCCAGGTCATCGCCAAACGTTACGAGAAGAGC
-GCGATGATCCTGACCTCCAACCTGCCGTTCGGGCAGTGGGATCAGACGTTCGCCGGTGATGCAGCGCTGACATCGGCG
-ATGCTGGACCGGATCTTACATCACTCACACGTCGTGCAAATAAAAGGGGAAAGCTATCGACTGAAGCAGAAACGAAAG
-GCCGGGGTTATAGCTGAAGCTAATCCTGAGTAA" } } ,
-        seq {
-          id {
-            local
-              str "genome3_plasmi_3_1" } ,
-          descr {
-            title "hypothetical protein PFKCIMHH_00011 [Genus species]" ,
-            molinfo {
-              biomol peptide ,
-              tech concept-trans } } ,
-          inst {
-            repr raw ,
-            mol aa ,
-            length 84 ,
-            seq-data
-              ncbieaa "MIINGKLIKAKDLAKAAGVSRSTVIKYYGISRENYERVATERRKLAFELRASGLK
-WKEVAEKMNTTKYSAIAYYRRYLALEKNK" } ,
-          annot {
-            {
-              data
-                ftable {
-                  {
-                    id
-                      local
-                        id 23 ,
-                    data
-                      prot {
-                        name {
-                          "hypothetical protein" } } ,
-                    location
-                      int {
-                        from 0 ,
-                        to 83 ,
-                        id
-                          local
-                            str "genome3_plasmi_3_1" } } } } } } ,
-        seq {
-          id {
-            local
-              str "genome3_plasmi_3_2" } ,
-          descr {
-            title "IS21 family transposase ISSen3 [Genus species]" ,
-            molinfo {
-              biomol peptide ,
-              tech concept-trans } } ,
-          inst {
-            repr raw ,
-            mol aa ,
-            length 259 ,
-            seq-data
-              ncbieaa "MVELQHQRLMVLAEQLQLDSLIGAAPALSQQAVDQEWSYMDFLEHLLHEEKLARH
-QRKQAMYTRMAAFPAVKTFEEYDFTFATGAPQKQIQSLRSLSFIERNENIVLLGPSGVGKTHLAIAMGYEAVRAGIKV
-RFTTAADLLLQLSTSQRQGRYKTTLNRGVMAPKLLIIDEIGYLPFSQEEAKLFFQVIAKRYEKSAMILTSNLPFGQWD
-QTFAGDAALTSAMLDRILHHSHVVQIKGESYRLKQKRKAGVIAEANPE" } ,
-          annot {
-            {
-              data
-                ftable {
-                  {
-                    id
-                      local
-                        id 24 ,
-                    data
-                      prot {
-                        name {
-                          "IS21 family transposase ISSen3" } } ,
-                    location
-                      int {
-                        from 0 ,
-                        to 258 ,
-                        id
-                          local
-                            str "genome3_plasmi_3_2" } } } } } } } ,
-      annot {
-        {
-          data
-            ftable {
-              {
-                id
-                  local
-                    id 21 ,
-                data
-                  cdregion {
-                    frame one ,
-                    code {
-                      id 11 } } ,
-                product
-                  whole
-                    local
-                      str "genome3_plasmi_3_1" ,
-                location
-                  int {
-                    from 25 ,
-                    to 279 ,
-                    strand plus ,
-                    id
-                      local
-                        str "genome3_plasmi_3" } ,
-                qual {
-                  {
-                    qual "inference" ,
-                    val "ab initio prediction:Prodigal:002006" } } ,
-                xref {
-                  {
-                    data
-                      gene {
-                        locus-tag "PFKCIMHH_00011" } } } } ,
-              {
-                id
-                  local
-                    id 22 ,
-                data
-                  cdregion {
-                    frame one ,
-                    code {
-                      id 11 } } ,
-                product
-                  whole
-                    local
-                      str "genome3_plasmi_3_2" ,
-                location
-                  int {
-                    from 322 ,
-                    to 1101 ,
-                    strand plus ,
-                    id
-                      local
-                        str "genome3_plasmi_3" } ,
-                qual {
-                  {
-                    qual "inference" ,
-                    val "ab initio prediction:Prodigal:002006" } ,
-                  {
-                    qual "inference" ,
-                    val "similar to AA sequence:ISfinder:ISSen3" } } ,
-                xref {
-                  {
-                    data
-                      gene {
-                        locus-tag "PFKCIMHH_00012" } } } } } } } } } }
diff --git a/Examples/2-res-Annotate-prokka/tmp_files/genome3-chromo.fst-all.fna_prokka-split5N.fna-prokkaRes/EXAM.1216.00002.tbl b/Examples/2-res-Annotate-prokka/tmp_files/genome3-chromo.fst-all.fna_prokka-split5N.fna-prokkaRes/EXAM.1216.00002.tbl
deleted file mode 100644
index b267e3bdae451266fbb42bcdbcd84491f326ac6f..0000000000000000000000000000000000000000
--- a/Examples/2-res-Annotate-prokka/tmp_files/genome3-chromo.fst-all.fna_prokka-split5N.fna-prokkaRes/EXAM.1216.00002.tbl
+++ /dev/null
@@ -1,75 +0,0 @@
->Feature header_genome3_1
-1	831	CDS
-			EC_number	3.5.1.28
-			db_xref	COG:COG3023
-			gene	amiD_1
-			inference	ab initio prediction:Prodigal:002006
-			inference	similar to AA sequence:UniProtKB:P75820
-			locus_tag	PFKCIMHH_00001
-			product	N-acetylmuramoyl-L-alanine amidase AmiD
-880	1710	CDS
-			EC_number	3.5.1.28
-			db_xref	COG:COG3023
-			gene	amiD_2
-			inference	ab initio prediction:Prodigal:002006
-			inference	similar to AA sequence:UniProtKB:P75820
-			locus_tag	PFKCIMHH_00002
-			product	N-acetylmuramoyl-L-alanine amidase AmiD
-1655	2128	CDS
-			EC_number	5.3.3.10
-			gene	hpcD
-			inference	ab initio prediction:Prodigal:002006
-			inference	similar to AA sequence:UniProtKB:Q05354
-			locus_tag	PFKCIMHH_00003
-			product	5-carboxymethyl-2-hydroxymuconate Delta-isomerase
-2172	2396	CDS
-			gene	pspB
-			inference	ab initio prediction:Prodigal:002006
-			inference	similar to AA sequence:UniProtKB:P0AFM9
-			locus_tag	PFKCIMHH_00004
-			product	Phage shock protein B
-2425	3828	CDS
-			inference	ab initio prediction:Prodigal:002006
-			locus_tag	PFKCIMHH_00005
-			product	hypothetical protein
-3863	4636	CDS
-			db_xref	COG:COG4598
-			gene	hisP
-			inference	ab initio prediction:Prodigal:002006
-			inference	similar to AA sequence:UniProtKB:P02915
-			locus_tag	PFKCIMHH_00006
-			product	Histidine transport ATP-binding protein HisP
-4641	5432	CDS
-			EC_number	2.1.1.228
-			db_xref	COG:COG0336
-			gene	trmD
-			inference	ab initio prediction:Prodigal:002006
-			inference	similar to AA sequence:UniProtKB:P0A873
-			locus_tag	PFKCIMHH_00007
-			product	tRNA (guanine-N(1)-)-methyltransferase
-5460	5747	CDS
-			inference	ab initio prediction:Prodigal:002006
-			locus_tag	PFKCIMHH_00008
-			product	hypothetical protein
->Feature genome3_plasmi_2
-1	582	CDS
-			inference	ab initio prediction:Prodigal:002006
-			locus_tag	PFKCIMHH_00009
-			product	hypothetical protein
-629	1936	CDS
-			db_xref	COG:COG1593
-			gene	dctM
-			inference	ab initio prediction:Prodigal:002006
-			inference	similar to AA sequence:UniProtKB:O07838
-			locus_tag	PFKCIMHH_00010
-			product	C4-dicarboxylate TRAP transporter large permease protein DctM
->Feature genome3_plasmi_3
-26	280	CDS
-			inference	ab initio prediction:Prodigal:002006
-			locus_tag	PFKCIMHH_00011
-			product	hypothetical protein
-323	1102	CDS
-			inference	ab initio prediction:Prodigal:002006
-			inference	similar to AA sequence:ISfinder:ISSen3
-			locus_tag	PFKCIMHH_00012
-			product	IS21 family transposase ISSen3
diff --git a/Examples/2-res-Annotate-prokka/tmp_files/genome3-chromo.fst-all.fna_prokka-split5N.fna-prokkaRes/EXAM.1216.00002.tsv b/Examples/2-res-Annotate-prokka/tmp_files/genome3-chromo.fst-all.fna_prokka-split5N.fna-prokkaRes/EXAM.1216.00002.tsv
deleted file mode 100644
index b330ee1260946ebd5b0e367a249902887444c973..0000000000000000000000000000000000000000
--- a/Examples/2-res-Annotate-prokka/tmp_files/genome3-chromo.fst-all.fna_prokka-split5N.fna-prokkaRes/EXAM.1216.00002.tsv
+++ /dev/null
@@ -1,13 +0,0 @@
-locus_tag	ftype	length_bp	gene	EC_number	COG	product
-PFKCIMHH_00001	CDS	831	amiD_1	3.5.1.28	COG3023	N-acetylmuramoyl-L-alanine amidase AmiD
-PFKCIMHH_00002	CDS	831	amiD_2	3.5.1.28	COG3023	N-acetylmuramoyl-L-alanine amidase AmiD
-PFKCIMHH_00003	CDS	474	hpcD	5.3.3.10		5-carboxymethyl-2-hydroxymuconate Delta-isomerase
-PFKCIMHH_00004	CDS	225	pspB			Phage shock protein B
-PFKCIMHH_00005	CDS	1404				hypothetical protein
-PFKCIMHH_00006	CDS	774	hisP		COG4598	Histidine transport ATP-binding protein HisP
-PFKCIMHH_00007	CDS	792	trmD	2.1.1.228	COG0336	tRNA (guanine-N(1)-)-methyltransferase
-PFKCIMHH_00008	CDS	288				hypothetical protein
-PFKCIMHH_00009	CDS	582				hypothetical protein
-PFKCIMHH_00010	CDS	1308	dctM		COG1593	C4-dicarboxylate TRAP transporter large permease protein DctM
-PFKCIMHH_00011	CDS	255				hypothetical protein
-PFKCIMHH_00012	CDS	780				IS21 family transposase ISSen3
diff --git a/Examples/2-res-Annotate-prokka/tmp_files/genome3-chromo.fst-all.fna_prokka-split5N.fna-prokkaRes/EXAM.1216.00002.txt b/Examples/2-res-Annotate-prokka/tmp_files/genome3-chromo.fst-all.fna_prokka-split5N.fna-prokkaRes/EXAM.1216.00002.txt
deleted file mode 100644
index 89b53831ab4386399ff71a68e8a46275f9d39114..0000000000000000000000000000000000000000
--- a/Examples/2-res-Annotate-prokka/tmp_files/genome3-chromo.fst-all.fna_prokka-split5N.fna-prokkaRes/EXAM.1216.00002.txt
+++ /dev/null
@@ -1,4 +0,0 @@
-organism: Genus species strain 
-contigs: 3
-bases: 8817
-CDS: 12
diff --git a/Examples/2-res-Annotate-prokka/tmp_files/genome4.fst_prokka-split5N.fna b/Examples/2-res-Annotate-prokka/tmp_files/genome4.fst_prokka-split5N.fna
deleted file mode 100644
index 85013c024cf3d318b654b2e8b07613ef6052c0ae..0000000000000000000000000000000000000000
--- a/Examples/2-res-Annotate-prokka/tmp_files/genome4.fst_prokka-split5N.fna
+++ /dev/null
@@ -1,2 +0,0 @@
->g4_1
-ATGAAAGCGCTACTGTGGCTGGTGGGTCTCGCGTTGCTGTTAACAGGCTGCGCGAGCGAAAAAGGAATTATCGATAAAGAGGGATATCAGCTTGATACCCGACATCGGGCGCAGGCGGCCTATCCGCGCATTAAAGTCCTGGTGATTCACTATACGGCGGAAAACTTTGACGTTTCGCTGGCGACGTTAACGGGCCGCAACGTCAGTTCGCATTACCTGATTCCCGCAACCCCGCCATTATATGGCGGTAAACCGCGCATCTGGCAACTGGTGCCGGAACAGGATCAGGCCTGGCATGCGGGCGTCAGTTTCTGGCGAGGCGCCACGCGTCTCAATGATACGTCTATTGGCATTGAGCTGGAAAATCGCGGCTGGCGAATGTCCGGCGGGGTGAAATCTTTCGCGCCGTTTGAATCCGCGCAAATTCAGGCATTGATTCCGTTAGCGAAGGACATTATCGCGCGCTATGACATCAAACCGCAGAATGTGGTGGCCCATGCGGATATCGCGCCGCAGCGTAAAGACGATCCCGGCCCGCGCTTCCCGTGGCGCGAGCTGGCGGCGCAGGGGATTGGCGCCTGGCCTGACGCCCAGCGTGTGGCGTTTTATCTGGCTGGACGCGCGCCGTATACGCCAGTCGATACCGCAACGGTGCTTGCGTTACTCTCGCGCTATGGCTATGAAGTCAAAGCCGATATGACGGCGCGCGAGCAGCAGCGGGTGATTATGGCGTTCCAGATGCACTTCCGTCCGGCGCAATGGAACGGTATCGCAGATGCCGAAACGCAGGCGATTGCCGAAGCATTACTGGAGAAGTACGGCCAGGATTAACGCGATCGCGCGCATATCGCGCGCGATAGATGCCGCACTTTATTGCTGAATGTACTGAAAATATTCGCGAGCAGGCTGATTTACCCGGCCTGTTCAGCAAGGTAAACGAGGCGCTGGCCGCCAGCGGGATTTTCCCCATCGGCGGTATCCGCAGTCGCGCCCACTGGCTGGATACCTGGCAGATGGCTGACGGTAAGCATGATTATGCGTTTGTGCATATGACGCTGAAAATCGGTACCGGGCGCAGCCTGGAGAGCCGTCAGGAAGTCGGCGAAATGCTGTTTGGGCTGATTAAAGCCCACTTCGCCGACCTGATGGAGAACCGCTATCTGGCGCTGTCGTTTGAGATTGCCGAGCTACATCCGACGCTCAATTACAAACAAAACAACGTACACGCGTTATTTAAATAGCCGCATATGCGGCGCTCAGGAGCGCTAGCATGCTCGATAAACAGACCCATACCCTGATCGCCCAGCGACTTAATCAGGCTGAAAAACAGCGTGAACAAATTCGCGCAGTGTCGCTGGATTATCCCAACATCACTATTGAAGATGCCTATGCCGTACAGCGTGAATGGGTCAATATCAAGATCGCCGAAGGGCGCACGCTCAAAGGCCACAAAATCGGCCTGACCTCAAAAGCGATGCAGGCCAGCTCGCAAATCAGCGAACCGGATTACGGCGCGCTGCTTGACGATATGTTCTTCCATGACGGCGGCGATATCCCCACCGACCGTTTTATCGTCCCGCGTATTGAAGTGGAGCTGGCGTTCGTGCTGGCGAAACCGCTGCGCGGCCCTCACTGCACGCTGTTCGACGTCTACAACGCCACGGATTATGTGATTCCGGCGCTGGAACTGATTGACGCCCGCAGCCACAACATCGACCCGGAAACCCAGCGCCCGCGCAAAGTGTTCGACACCATTTCCGACAACGCCGCCAACGCCGGGGTGATCCTCGGTGGTCGCCCCATCAAACCAGACGAGCTGGATCTGCGCTGGATCTCCGCGCTGCTCTATCGCAACGGCGTGATCGAAGAAACCGGCGTCGCCGCAGGCGTGCTGAATCATCCGGCCAACGGCGTGGCGTGGCTGGCGAACAAGCTTGCCCCCTACGATGTCCAGCTTGAAGCCGGGCAGATCATCCTCGGCGGCTCGTTCACCCGCCCGGTGCCGGCGAGCAAGGGCGACACCTTCCATGTCGATTACGGCAACATGGGCGCGATCAGTTGCCGGTTTGTGTAACCAGATCCGCGCGCGCATATATATCGCGCGCATACGATGCCCGTGAATAAGTTCTCCCGACGTACCCTCCTGACGGCAGGTTCCGCGCTTGCTGTTCTTCCTTTTCTGCGCGCCTTGCCGGTACAGGCGCGTGAACCTCGCGAGACCGTCGATATTAAGGATTATCCGGCGGATGACGGTATCGCCTCGTTCAAACAGGCCTTCGCCGACGGACAGACCGTGGTCTTACCGCCAGGATGGGTGTGTGAAAATATCAATGCGGCGATAACGATTCCGGCGGGAAAAACGCTGCGGGTACAGGGCGCGGTGCGTGGGAATGGCCGGGGACGGTTTATTTTGCAGGACGGGTGTCAGGTGGTGGGGGAGCAGGGCGGCAGTCTGCACAATGTGACGCTGGATGTTCGCGGGTCGGACTGTGTGATTAAAGGCGTGACGATGAGCGGCTTTGGCCCCGTCGCGCAAATTTTCATCGGCGGTAAGGAACCGCAGGTGATGCGTAATCTCATTATCGATGACATCACCGTTACCCACGCCAACTACGCCATTCTCCGCCAGGGATTTCATAACCAAATGGACGGCGCGCGGATTACGCATAGCCGCTTTAGCGATTTGCAGGGGGACGCCATTGAGTGGAATGTCGCGATTCACGACCGCGACATCCTGATTTCCGATCATGTCATCGAACGCATTGATTGTACCAATGGCAAAATCAACTGGGGGATCGGCATCGGGCTGGCGGGTAGCACCTATGACAACAGTTATCCTGAAGATCAGGCAGTAAAAAACTTTGTGGTGGCCAATATTACCGGATCTGATTGCCGACAGCTGGTGCACGTAGAAAATGGCAAACATTTCGTCATTCGCAATGTCAAAGCCAAAAACATCACGCCCGATTTCAGTAAAAATGCGGGTATTGATAACGCAACGATCGCCATTTATGGCTGTGATAATTTCGTCATTGATAATATTGATATGACGAATAGTGCTGGGATGCTCATCGGCTATGGCGTCGTTAAAGGAAAATACCTGTCAATTCCGCAAAACTTTAAATTAAACGCTATTCGGTTGGATAATCGCCAGGTTGCTTATAAATTACGCGGCATTCAAATTTCCTCCGGCAACATCCCCTCTTTTGTCGCCATCACCAATGTACGGATGACGCGTGCTACGCTGGAACTGCATAATCAACCGCAGCACCTCTTTCTGCGTAATATCAACGTGATGCAAACTTCAGCGATTGGCCCGGCGTTAAAAATGCATTTCGATTTGCGTAAAGATGTCCGTGGTCAATTTATGGCCCGCCAGGACACGCTGCTTTCCCTCGCTAATGTTCATGCCATCAATGAAAACGGGCAGAGTTCCGTGGATATCGACAGGATTAATCACCAAACCGTGAATGTCGAAGCAGTGAATTTTTCGCTGCCGAAGCGGGGAGGGTAACAGAGCTCGCGCGATCGCGAATGTCAGAAAATAAATTACACGTTATCGATTTGCACAAACGCTACGGCGGTCATGAAGTGCTGAAAGGGGTATCGTTGCAGGCCCGCGCCGGAGATGTGATTAGCATCATCGGCTCGTCCGGCTCCGGTAAAAGCACTTTTTTGCGCTGTATTAACTTCCTCGAAAAACCGAGCGAAGGCGCGATTATCGTGAACGGTCAGAACATTAATCTGGTGCGCGACAAAGACGGGCAGCTCAAAGTGGCGGATAAAAATCAGCTACGCTTGTTGCGTACCCGCCTGACGATGGTGTTTCAGCACTTTAACCTCTGGAGCCACATGACGGTGCTGGAAAATGTGATGGAAGCGCCGATTCAGGTACTGGGATTAAGCAAGCACGACGCGCGCGAGCGGGCGTTGAAATATCTGGCGAAGGTGGGGATTGATGAGCGCGCTCAGGGCAAATATCCCGTCCATCTCTCCGGCGGCCAACAGCAGCGCGTTTCTATTGCGCGCGCGCTGGCGATGGAACCTGACGTTTTACTGTTCGATGAACCCACATCGGCGCTCGATCCTGAACTGGTCGGCGAAGTGTTGCGCATCATGCAACAACTGGCGGAAGAAGGCAAAACGATGGTGGTGGTCACGCATGAAATGGGCTTCGCCCGCCATGTCTCTTCGCACGTTATTTTTCTGCATCAGGGGAAAATTGAAGAAGAGGGCGATCCGGAGCAGGTGTTCGGCAATCCGCAAAGCCCGCGTTTACAGCAATTCCTGAAAGGCTCGCTGAAATAACAGATACGCGCATGGCGAGTGTTTATTGGCATCGTTAGCCTGTTTCCTGAAATGTTCCGCGCAATTACCGATTACGGGGTAACTGGCCGGGCAGTAAAAAAAGGCCTGCTGAACATCCAAAGCTGGAGTCCTCGCGACTTCGCGCATGACCGGCACCGTACCGTGGACGACCGTCCTTACGGCGGCGGACCGGGGATGTTAATGATGGTGCAACCCTTGCGGGACGCCATTCACGCAGCAAAAGCCGCGGCAGGTGAAGGCGCTAAAGTGATTTATCTGTCGCCTCAGGGACGCAAGCTTGATCAAGCGGGCGTTAGCGAGCTGGCCACGAATCAGAAGCTTATTCTGGTGTGTGGTCGCTACGAAGGCGTAGATGAGCGCGTAATTCAGACCGAAATTGACGAAGAATGGTCAATTGGCGATTACGTTCTCAGCGGTGGCGAACTACCGGCAATGACGCTGATTGACTCCGTCGCCCGGTTTATACCGGGGGTTCTGGGGCATGAGGCATCAGCAATCGAAGATTCGTTTGCTGATGGGTTGCTGGATTGTCCGCACTATACGCGCCCTGAAGTGTTAGAGGGGATGGAAGTACCGCCAGTATTGCTGTCGGGAAACCATGCCGAGATACGTCGCTGGCGCTTGAAACAGTCGCTGGGCCGAACCTGGCTTAGAAGACCTGAACTTCTGGAAAACCTGGCTCTGACTGAAGAGCAAGCAAGGTTGCTGGCGGAGTTCAAAACAGAACACGCACAACAGCAGCATAAACATGATGGGATGGCATAGCGATAGCGCTAGAGCGATGAATAATCATTTTGGGAAAGGGTTAATGGCTGGGTTGCACGCGCCATATGCATATAGCGCGCATCATGCGGTGAATTTCTGTTCTGAGTATAAACGTGGCTTTGTATTGGGTTTTACACACCGTATGTTCGAAAAGACCGGCGATCGTCAACTTAGCGCGTGGGAGGCCGGAATTCTGACGCGTCGCTATGGTCTGGATAAAGAAATGGTGATGGATTTCTTTAAAGAGAATCATTCCGGGATGGCGGTTCGCTTCTTTATGGTCGGTTATCGACTCGAAGGTTGACAGATGCGCGATCGATGTCTACGCTTCTCTATTTGCACGGATTCAACAGTTCCCCTCGCTCGGCAAAAGCGTGCCAGCTAAAAAACTGGCTGGCGGAGCGTCATCCGCATGTCGAGATGATCGTCCCTCAACTACCGCCGTATCCTGCCGATGCGGCGGAGTTGCTGGAATCTCTCGTGCTTGAGCATGGCGGTGCGCCATTAGGGCTGGTAGGATCGTCGCTGGGTGGTTATTACGCCACCTGGCTGTCGCAATGTTTTATGCTGCCGGCTGTGGTGGTGAATCCCGCCGTGCGGCCCTTTGAATTACTGACCGACTATCTCGGTCAGAACGAGAACCCCTACACCGGGCAGCAATATGTGCTAGAGTCTCGCCATATTTATGATCTTAAAGTCATGCAGATTGACCCGCTGGAAGCGCCGGACCTGATCTGGCTACTGCAACAGACGGGCGATGAAGTGCTGGATTACCGCCAGGCGGTGGCATATTACGCCTCCTGCCGTCAGACAGTGACCGAGGGTGGTAATCACGCATTCACGGGCTTCGAAGATTATTTCAACCAGATTGTCGATTTTCTTGGACTGCACAGTTGCTGACACGGATGCGCCATCGGCTTGCTGGCCGTGCCGTTCTTCGTTTTGTCCGGGGTGATCATGAATAGCGGGGGAATTGCCGCCCGGCTGGTCAATTTTGCCAAACTGTTTACTGGCAAACTGCCCGGCTCGCTCTCTTATACCAACATCGTCGGCAATATGATGTTCGGTGCAATTTCCGGATCGGCAATTGCCGCCTCAACCTCCATCGGCGGCGTGATGGTGCCGATGAGCGCGCGCGAAGGTTACGATCGCGGCTTTGCGGCCGCGGTGAATATCGCCTCCGCGCCGACGGGAATGTTAATTCCGCCCACCACGGCTTTTATCCTTTATGCGCTGGCAAGCGGGGGAACATCGATTGCCGCTCTGTTCGCCGGCGGTCTGGTCGCGGGAGTGCTGTGGGGCGTTGGCTGTATGCTGGTCACGCTGGTGGTCGCTAAGCGTCGAAATTATCGGGTTTTCTTCACCGTCCAAAAAGGCATGGCGCTAAAAGTTGCCGTTGAGGCCATTCCCAGCCTGCTGCTGATCGTGATTATCGTCGGCGGCATTGTGCAGGGGATTTTCACCGCCATTGAAGCCTCCGCGATTGCCGTGGTGTATACATTATTGTTGACGATGGTGTTTTACCGCACGCTGAAAATTAAGGATTTGCCTTCGATTTTGCTCCAGACAGTGGTAATGACCGGGGTCATCATGTTCCTGCTGGCAACCTCTTCGGCGATGTCCTTCTCGATGTCGATCACCAATATTCCTGCGGCGCTGAGCGATATGATCCTCGGTATTTCCGCCAATAAACTGGTTATCCTGTTAGTCATTACCGTCTTTTTGTTGATTATCGGCGCATTTATGGATATCGGTCCGGCCATTCTGATTTTTACCCCGATTCTGCTGCCGATCATGGCTAAACTGGGCGTCGATCCGGTGCATTTTGGCATTATCATGATCTATAACCTGGCGATTGGCACCATTACGCCGCCAGTTGGCAGTGGTTTATATGTCGGGGCGAGCGTCGGTAAGGTCAAAGTTGAGGAAGTGATTAAACCGTTGCTGCCTTTTTACGGCGCGATTATCGGCGTTCTGTTATTAATTACCTACATTCCGGAAATCACACTGTTCTTACCCCGTCTACTGGGCATCATGTAA
diff --git a/Examples/2-res-Annotate-prokka/tmp_files/genome4.fst_prokka-split5N.fna-prokka.log b/Examples/2-res-Annotate-prokka/tmp_files/genome4.fst_prokka-split5N.fna-prokka.log
deleted file mode 100644
index db5cc442dc4f7834bc5164f48c66b3c1b87d3faf..0000000000000000000000000000000000000000
--- a/Examples/2-res-Annotate-prokka/tmp_files/genome4.fst_prokka-split5N.fna-prokka.log
+++ /dev/null
@@ -1,128 +0,0 @@
-[13:15:34] This is prokka 1.14.5
-[13:15:34] Written by Torsten Seemann <torsten.seemann@gmail.com>
-[13:15:34] Homepage is https://github.com/tseemann/prokka
-[13:15:34] Local time is Mon Dec  9 13:15:34 2019
-[13:15:34] You are aperrin
-[13:15:34] Operating system is darwin
-[13:15:34] You have BioPerl 1.007002
-[13:15:35] System has 8 cores.
-[13:15:35] Will use maximum of 1 cores.
-[13:15:35] Annotating as >>> Bacteria <<<
-[13:15:35] Generating locus_tag from 'Examples/2-res-Annotate-prokka/tmp_files/genome4.fst_prokka-split5N.fna' contents.
-[13:15:35] Setting --locustag LIKMDGFN from MD5 5246d0f7b5f59e1da550241263d19049
-[13:15:35] Creating new output folder: Examples/2-res-Annotate-prokka/tmp_files/genome4.fst_prokka-split5N.fna-prokkaRes
-[13:15:35] Running: mkdir -p Examples\/2\-res\-Annotate\-prokka\/tmp_files\/genome4\.fst_prokka\-split5N\.fna\-prokkaRes
-[13:15:35] Using filename prefix: GEN4.1111.00001.XXX
-[13:15:35] Setting HMMER_NCPU=1
-[13:15:35] Writing log to: Examples/2-res-Annotate-prokka/tmp_files/genome4.fst_prokka-split5N.fna-prokkaRes/GEN4.1111.00001.log
-[13:15:35] Command: /usr/local/bin/prokka --outdir Examples/2-res-Annotate-prokka/tmp_files/genome4.fst_prokka-split5N.fna-prokkaRes --cpus 1 --prefix GEN4.1111.00001 Examples/2-res-Annotate-prokka/tmp_files/genome4.fst_prokka-split5N.fna
-[13:15:35] Appending to PATH: /Users/aperrin/Softwares/src/prokka-dec.19/bin/../binaries/darwin
-[13:15:35] Appending to PATH: /Users/aperrin/Softwares/src/prokka-dec.19/bin/../binaries/darwin/../common
-[13:15:35] Appending to PATH: /Users/aperrin/Softwares/src/prokka-dec.19/bin
-[13:15:35] Looking for 'aragorn' - found /usr/local/bin/aragorn
-[13:15:35] Determined aragorn version is 001002 from 'ARAGORN v1.2.38 Dean Laslett'
-[13:15:35] Looking for 'barrnap' - found /usr/local/bin/barrnap
-[13:15:35] Determined barrnap version is 000008 from 'barrnap 0.8'
-[13:15:35] Looking for 'blastp' - found /Users/aperrin/Softwares/bin/blastp
-[13:15:35] Determined blastp version is 002009 from 'blastp: 2.9.0+'
-[13:15:35] Looking for 'cmpress' - found /usr/local/bin/cmpress
-[13:15:35] Determined cmpress version is 001001 from '# INFERNAL 1.1.2 (July 2016)'
-[13:15:35] Looking for 'cmscan' - found /usr/local/bin/cmscan
-[13:15:35] Determined cmscan version is 001001 from '# INFERNAL 1.1.2 (July 2016)'
-[13:15:35] Looking for 'egrep' - found /usr/bin/egrep
-[13:15:35] Looking for 'find' - found /usr/bin/find
-[13:15:35] Looking for 'grep' - found /usr/bin/grep
-[13:15:35] Looking for 'hmmpress' - found /Users/aperrin/Softwares/src/prokka-dec.19/bin/../binaries/darwin/hmmpress
-[13:15:35] Determined hmmpress version is 003001 from '# HMMER 3.1b1 (May 2013); http://hmmer.org/'
-[13:15:35] Looking for 'hmmscan' - found /usr/local/bin/hmmscan
-[13:15:35] Determined hmmscan version is 003001 from '# HMMER 3.1b2 (February 2015); http://hmmer.org/'
-[13:15:35] Looking for 'java' - found /usr/bin/java
-[13:15:35] Looking for 'makeblastdb' - found /Users/aperrin/Softwares/bin/makeblastdb
-[13:15:35] Determined makeblastdb version is 002009 from 'makeblastdb: 2.9.0+'
-[13:15:35] Looking for 'minced' - found /Users/aperrin/Softwares/src/prokka-dec.19/bin/../binaries/darwin/../common/minced
-[13:15:35] Determined minced version is 002000 from 'minced 0.2.0'
-[13:15:35] Looking for 'parallel' - found /usr/local/bin/parallel
-[13:15:35] Determined parallel version is 20181022 from 'GNU parallel 20181022'
-[13:15:35] Looking for 'prodigal' - found /usr/local/bin/prodigal
-[13:15:35] Determined prodigal version is 002006 from 'Prodigal V2.6.3: February, 2016'
-[13:15:35] Looking for 'prokka-genbank_to_fasta_db' - found /Users/aperrin/Softwares/src/prokka-dec.19/bin/prokka-genbank_to_fasta_db
-[13:15:35] Looking for 'sed' - found /usr/bin/sed
-[13:15:35] Looking for 'tbl2asn' - found /Users/aperrin/Softwares/src/prokka-dec.19/bin/../binaries/darwin/tbl2asn
-[13:15:35] Determined tbl2asn version is 025007 from 'tbl2asn 25.7   arguments:'
-[13:15:35] Using genetic code table 11.
-[13:15:35] Loading and checking input file: Examples/2-res-Annotate-prokka/tmp_files/genome4.fst_prokka-split5N.fna
-[13:15:35] Wrote 1 contigs totalling 7134 bp.
-[13:15:35] Predicting tRNAs and tmRNAs
-[13:15:35] Running: aragorn -l -gc11  -w Examples\/2\-res\-Annotate\-prokka\/tmp_files\/genome4\.fst_prokka\-split5N\.fna\-prokkaRes\/GEN4\.1111\.00001\.fna
-[13:15:35] Found 0 tRNAs
-[13:15:35] Predicting Ribosomal RNAs
-[13:15:35] Running Barrnap with 1 threads
-[13:15:35] Found 0 rRNAs
-[13:15:35] Skipping ncRNA search, enable with --rfam if desired.
-[13:15:35] Total of 0 tRNA + rRNA features
-[13:15:35] Searching for CRISPR repeats
-[13:15:35] Found 0 CRISPRs
-[13:15:35] Predicting coding sequences
-[13:15:35] Contigs total 7134 bp, so using meta mode
-[13:15:35] Running: prodigal -i Examples\/2\-res\-Annotate\-prokka\/tmp_files\/genome4\.fst_prokka\-split5N\.fna\-prokkaRes\/GEN4\.1111\.00001\.fna -c -m -g 11 -p meta -f sco -q
-[13:15:35] Found 9 CDS
-[13:15:35] Connecting features back to sequences
-[13:15:35] Not using genus-specific database. Try --usegenus to enable it.
-[13:15:35] Annotating CDS, please be patient.
-[13:15:35] Will use 1 CPUs for similarity searching.
-[13:15:35] There are still 9 unannotated CDS left (started with 9)
-[13:15:35] Will use blast to search against /Users/aperrin/Softwares/src/prokka-dec.19/db/kingdom/Bacteria/IS with 1 CPUs
-[13:15:35] Running: cat Examples\/2\-res\-Annotate\-prokka\/tmp_files\/genome4\.fst_prokka\-split5N\.fna\-prokkaRes\/GEN4\.1111\.00001\.IS\.tmp\.95380\.faa | parallel --gnu --plain -j 1 --block 1161 --recstart '>' --pipe blastp -query - -db /Users/aperrin/Softwares/src/prokka-dec.19/db/kingdom/Bacteria/IS -evalue 1e-30 -qcov_hsp_perc 90 -num_threads 1 -num_descriptions 1 -num_alignments 1 -seg no > Examples\/2\-res\-Annotate\-prokka\/tmp_files\/genome4\.fst_prokka\-split5N\.fna\-prokkaRes\/GEN4\.1111\.00001\.IS\.tmp\.95380\.blast 2> /dev/null
-[13:15:36] Deleting unwanted file: Examples/2-res-Annotate-prokka/tmp_files/genome4.fst_prokka-split5N.fna-prokkaRes/GEN4.1111.00001.IS.tmp.95380.faa
-[13:15:36] Deleting unwanted file: Examples/2-res-Annotate-prokka/tmp_files/genome4.fst_prokka-split5N.fna-prokkaRes/GEN4.1111.00001.IS.tmp.95380.blast
-[13:15:36] There are still 9 unannotated CDS left (started with 9)
-[13:15:36] Will use blast to search against /Users/aperrin/Softwares/src/prokka-dec.19/db/kingdom/Bacteria/AMR with 1 CPUs
-[13:15:36] Running: cat Examples\/2\-res\-Annotate\-prokka\/tmp_files\/genome4\.fst_prokka\-split5N\.fna\-prokkaRes\/GEN4\.1111\.00001\.AMR\.tmp\.95380\.faa | parallel --gnu --plain -j 1 --block 1161 --recstart '>' --pipe blastp -query - -db /Users/aperrin/Softwares/src/prokka-dec.19/db/kingdom/Bacteria/AMR -evalue 1e-300 -qcov_hsp_perc 90 -num_threads 1 -num_descriptions 1 -num_alignments 1 -seg no > Examples\/2\-res\-Annotate\-prokka\/tmp_files\/genome4\.fst_prokka\-split5N\.fna\-prokkaRes\/GEN4\.1111\.00001\.AMR\.tmp\.95380\.blast 2> /dev/null
-[13:15:36] Deleting unwanted file: Examples/2-res-Annotate-prokka/tmp_files/genome4.fst_prokka-split5N.fna-prokkaRes/GEN4.1111.00001.AMR.tmp.95380.faa
-[13:15:36] Deleting unwanted file: Examples/2-res-Annotate-prokka/tmp_files/genome4.fst_prokka-split5N.fna-prokkaRes/GEN4.1111.00001.AMR.tmp.95380.blast
-[13:15:36] There are still 9 unannotated CDS left (started with 9)
-[13:15:36] Will use blast to search against /Users/aperrin/Softwares/src/prokka-dec.19/db/kingdom/Bacteria/sprot with 1 CPUs
-[13:15:36] Running: cat Examples\/2\-res\-Annotate\-prokka\/tmp_files\/genome4\.fst_prokka\-split5N\.fna\-prokkaRes\/GEN4\.1111\.00001\.sprot\.tmp\.95380\.faa | parallel --gnu --plain -j 1 --block 1161 --recstart '>' --pipe blastp -query - -db /Users/aperrin/Softwares/src/prokka-dec.19/db/kingdom/Bacteria/sprot -evalue 1e-09 -qcov_hsp_perc 80 -num_threads 1 -num_descriptions 1 -num_alignments 1 -seg no > Examples\/2\-res\-Annotate\-prokka\/tmp_files\/genome4\.fst_prokka\-split5N\.fna\-prokkaRes\/GEN4\.1111\.00001\.sprot\.tmp\.95380\.blast 2> /dev/null
-[13:15:37] Deleting unwanted file: Examples/2-res-Annotate-prokka/tmp_files/genome4.fst_prokka-split5N.fna-prokkaRes/GEN4.1111.00001.sprot.tmp.95380.faa
-[13:15:37] Deleting unwanted file: Examples/2-res-Annotate-prokka/tmp_files/genome4.fst_prokka-split5N.fna-prokkaRes/GEN4.1111.00001.sprot.tmp.95380.blast
-[13:15:37] There are still 3 unannotated CDS left (started with 9)
-[13:15:37] Will use hmmer3 to search against /Users/aperrin/Softwares/src/prokka-dec.19/db/hmm/HAMAP.hmm with 1 CPUs
-[13:15:37] Running: cat Examples\/2\-res\-Annotate\-prokka\/tmp_files\/genome4\.fst_prokka\-split5N\.fna\-prokkaRes\/GEN4\.1111\.00001\.HAMAP\.hmm\.tmp\.95380\.faa | parallel --gnu --plain -j 1 --block 379 --recstart '>' --pipe hmmscan --noali --notextw --acc -E 1e-09 --cpu 1 /Users/aperrin/Softwares/src/prokka-dec.19/db/hmm/HAMAP.hmm /dev/stdin > Examples\/2\-res\-Annotate\-prokka\/tmp_files\/genome4\.fst_prokka\-split5N\.fna\-prokkaRes\/GEN4\.1111\.00001\.HAMAP\.hmm\.tmp\.95380\.hmmer3 2> /dev/null
-[13:15:38] Deleting unwanted file: Examples/2-res-Annotate-prokka/tmp_files/genome4.fst_prokka-split5N.fna-prokkaRes/GEN4.1111.00001.HAMAP.hmm.tmp.95380.faa
-[13:15:38] Deleting unwanted file: Examples/2-res-Annotate-prokka/tmp_files/genome4.fst_prokka-split5N.fna-prokkaRes/GEN4.1111.00001.HAMAP.hmm.tmp.95380.hmmer3
-[13:15:38] Labelling remaining 3 proteins as 'hypothetical protein'
-[13:15:38] Found 6 unique /gene codes.
-[13:15:38] Fixed 0 colliding /gene names.
-[13:15:38] Adding /locus_tag identifiers
-[13:15:38] Assigned 9 locus_tags to CDS and RNA features.
-[13:15:38] Writing outputs to Examples/2-res-Annotate-prokka/tmp_files/genome4.fst_prokka-split5N.fna-prokkaRes/
-[13:15:38] Generating annotation statistics file
-[13:15:38] Generating Genbank and Sequin files
-[13:15:38] Running: tbl2asn -V b -a r10k -l paired-ends -M n -N 1 -y 'Annotated using prokka 1.14.5 from https://github.com/tseemann/prokka' -Z Examples\/2\-res\-Annotate\-prokka\/tmp_files\/genome4\.fst_prokka\-split5N\.fna\-prokkaRes\/GEN4\.1111\.00001\.err -i Examples\/2\-res\-Annotate\-prokka\/tmp_files\/genome4\.fst_prokka\-split5N\.fna\-prokkaRes\/GEN4\.1111\.00001\.fsa 2> /dev/null
-[13:15:38] Deleting unwanted file: Examples/2-res-Annotate-prokka/tmp_files/genome4.fst_prokka-split5N.fna-prokkaRes/errorsummary.val
-[13:15:38] Deleting unwanted file: Examples/2-res-Annotate-prokka/tmp_files/genome4.fst_prokka-split5N.fna-prokkaRes/GEN4.1111.00001.dr
-[13:15:38] Deleting unwanted file: Examples/2-res-Annotate-prokka/tmp_files/genome4.fst_prokka-split5N.fna-prokkaRes/GEN4.1111.00001.fixedproducts
-[13:15:38] Deleting unwanted file: Examples/2-res-Annotate-prokka/tmp_files/genome4.fst_prokka-split5N.fna-prokkaRes/GEN4.1111.00001.ecn
-[13:15:38] Deleting unwanted file: Examples/2-res-Annotate-prokka/tmp_files/genome4.fst_prokka-split5N.fna-prokkaRes/GEN4.1111.00001.val
-[13:15:38] Repairing broken .GBK output that tbl2asn produces...
-[13:15:38] Running: sed 's/COORDINATES: profile/COORDINATES:profile/' < Examples\/2\-res\-Annotate\-prokka\/tmp_files\/genome4\.fst_prokka\-split5N\.fna\-prokkaRes\/GEN4\.1111\.00001\.gbf > Examples\/2\-res\-Annotate\-prokka\/tmp_files\/genome4\.fst_prokka\-split5N\.fna\-prokkaRes\/GEN4\.1111\.00001\.gbk
-[13:15:38] Deleting unwanted file: Examples/2-res-Annotate-prokka/tmp_files/genome4.fst_prokka-split5N.fna-prokkaRes/GEN4.1111.00001.gbf
-[13:15:38] Output files:
-[13:15:38] Examples/2-res-Annotate-prokka/tmp_files/genome4.fst_prokka-split5N.fna-prokkaRes/GEN4.1111.00001.fsa
-[13:15:38] Examples/2-res-Annotate-prokka/tmp_files/genome4.fst_prokka-split5N.fna-prokkaRes/GEN4.1111.00001.faa
-[13:15:38] Examples/2-res-Annotate-prokka/tmp_files/genome4.fst_prokka-split5N.fna-prokkaRes/GEN4.1111.00001.log
-[13:15:38] Examples/2-res-Annotate-prokka/tmp_files/genome4.fst_prokka-split5N.fna-prokkaRes/GEN4.1111.00001.ffn
-[13:15:38] Examples/2-res-Annotate-prokka/tmp_files/genome4.fst_prokka-split5N.fna-prokkaRes/GEN4.1111.00001.gbk
-[13:15:38] Examples/2-res-Annotate-prokka/tmp_files/genome4.fst_prokka-split5N.fna-prokkaRes/GEN4.1111.00001.gff
-[13:15:38] Examples/2-res-Annotate-prokka/tmp_files/genome4.fst_prokka-split5N.fna-prokkaRes/GEN4.1111.00001.tbl
-[13:15:38] Examples/2-res-Annotate-prokka/tmp_files/genome4.fst_prokka-split5N.fna-prokkaRes/GEN4.1111.00001.sqn
-[13:15:38] Examples/2-res-Annotate-prokka/tmp_files/genome4.fst_prokka-split5N.fna-prokkaRes/GEN4.1111.00001.tsv
-[13:15:38] Examples/2-res-Annotate-prokka/tmp_files/genome4.fst_prokka-split5N.fna-prokkaRes/GEN4.1111.00001.fna
-[13:15:38] Examples/2-res-Annotate-prokka/tmp_files/genome4.fst_prokka-split5N.fna-prokkaRes/GEN4.1111.00001.err
-[13:15:38] Examples/2-res-Annotate-prokka/tmp_files/genome4.fst_prokka-split5N.fna-prokkaRes/GEN4.1111.00001.txt
-[13:15:38] Annotation finished successfully.
-[13:15:38] Walltime used: 0.07 minutes
-[13:15:38] If you use this result please cite the Prokka paper:
-[13:15:38] Seemann T (2014) Prokka: rapid prokaryotic genome annotation. Bioinformatics. 30(14):2068-9.
-[13:15:38] Type 'prokka --citation' for more details.
-[13:15:38] Thank you, come again.
diff --git a/Examples/2-res-Annotate-prokka/tmp_files/genome4.fst_prokka-split5N.fna-prokkaRes/GEN4.1111.00001.err b/Examples/2-res-Annotate-prokka/tmp_files/genome4.fst_prokka-split5N.fna-prokkaRes/GEN4.1111.00001.err
deleted file mode 100644
index 1651fa9126a27e447e61ffe2653e5eced5d5a51c..0000000000000000000000000000000000000000
--- a/Examples/2-res-Annotate-prokka/tmp_files/genome4.fst_prokka-split5N.fna-prokkaRes/GEN4.1111.00001.err
+++ /dev/null
@@ -1,102 +0,0 @@
-Discrepancy Report Results
-
-Summary
-FATAL: MISSING_PROTEIN_ID:9 proteins have invalid IDs.
-DISC_SOURCE_QUALS_ASNDISC:strain (all present, all unique)
-DISC_SOURCE_QUALS_ASNDISC:taxname (all present, all unique)
-DISC_FEATURE_COUNT:CDS: 9 present
-DISC_COUNT_NUCLEOTIDES:1 nucleotide Bioseqs are present
-FEATURE_LOCATION_CONFLICT:9 features have inconsistent gene locations.
-DISC_QUALITY_SCORES:Quality scores are missing on all sequences.
-ONCALLER_COMMENT_PRESENT:1 comment descriptors were found (all same)
-MISSING_GENOMEASSEMBLY_COMMENTS:1 bioseqs are missing GenomeAssembly structured comments
-MOLTYPE_NOT_MRNA:1 molecule types are not set as mRNA.
-TECHNIQUE_NOT_TSA:1 technique are not set as TSA
-MISSING_STRUCTURED_COMMENT:1 sequences do not include structured comments.
-MISSING_PROJECT:10 sequences do not include project.
-DISC_INCONSISTENT_MOLINFO_TECH:Molinfo Technique Report (some missing, all same)
-
-
-Detailed Report
-
-FATAL: DiscRep_ALL:MISSING_PROTEIN_ID::9 proteins halid Ivalid IDs.
-Examples/2-res-Annotate-prokka/tmp_files/genome4.fst_prokka-split5N.fna-prokkaRes/GEN4.1111.00001:g4_1_1 (length 276)
-Examples/2-res-Annotate-prokka/tmp_files/genome4.fst_prokka-split5N.fna-prokkaRes/GEN4.1111.00001:g4_1_2 (length 126)
-Examples/2-res-Annotate-prokka/tmp_files/genome4.fst_prokka-split5N.fna-prokkaRes/GEN4.1111.00001:g4_1_3 (length 267)
-Examples/2-res-Annotate-prokka/tmp_files/genome4.fst_prokka-split5N.fna-prokkaRes/GEN4.1111.00001:g4_1_4 (length 467)
-Examples/2-res-Annotate-prokka/tmp_files/genome4.fst_prokka-split5N.fna-prokkaRes/GEN4.1111.00001:g4_1_5 (length 257)
-Examples/2-res-Annotate-prokka/tmp_files/genome4.fst_prokka-split5N.fna-prokkaRes/GEN4.1111.00001:g4_1_6 (length 255)
-Examples/2-res-Annotate-prokka/tmp_files/genome4.fst_prokka-split5N.fna-prokkaRes/GEN4.1111.00001:g4_1_7 (length 86)
-Examples/2-res-Annotate-prokka/tmp_files/genome4.fst_prokka-split5N.fna-prokkaRes/GEN4.1111.00001:g4_1_8 (length 193)
-Examples/2-res-Annotate-prokka/tmp_files/genome4.fst_prokka-split5N.fna-prokkaRes/GEN4.1111.00001:g4_1_9 (length 360)
-
-DiscRep_ALL:DISC_SOURCE_QUALS_ASNDISC::strain (all present, all unique)
-DiscRep_SUB:DISC_SOURCE_QUALS_ASNDISC::1 sources have unique values for strain
-DiscRep_ALL:DISC_SOURCE_QUALS_ASNDISC::taxname (all present, all unique)
-DiscRep_SUB:DISC_SOURCE_QUALS_ASNDISC::1 sources have unique values for taxname
-DiscRep_ALL:DISC_FEATURE_COUNT::CDS: 9 present
-DiscRep_ALL:DISC_COUNT_NUCLEOTIDES::1 nucleotide Bioseqs are present
-Examples/2-res-Annotate-prokka/tmp_files/genome4.fst_prokka-split5N.fna-prokkaRes/GEN4.1111.00001:g4_1 (length 7134)
-
-DiscRep_ALL:FEATURE_LOCATION_CONFLICT::9 features have inconsistent gene locations.
-DiscRep_SUB:FEATURE_LOCATION_CONFLICT::Coding region xref gene does not exist
-Examples/2-res-Annotate-prokka/tmp_files/genome4.fst_prokka-split5N.fna-prokkaRes/GEN4.1111.00001:CDS	N-acetylmuramoyl-L-alanine amidase AmiD	g4_1:1-831	LIKMDGFN_00001
-
-DiscRep_SUB:FEATURE_LOCATION_CONFLICT::Coding region xref gene does not exist
-Examples/2-res-Annotate-prokka/tmp_files/genome4.fst_prokka-split5N.fna-prokkaRes/GEN4.1111.00001:CDS	5-carboxymethyl-2-hydroxymuconate Delta-isomerase	g4_1:861-1241	LIKMDGFN_00002
-
-DiscRep_SUB:FEATURE_LOCATION_CONFLICT::Coding region xref gene does not exist
-Examples/2-res-Annotate-prokka/tmp_files/genome4.fst_prokka-split5N.fna-prokkaRes/GEN4.1111.00001:CDS	2-oxo-hept-4-ene-1,7-dioate hydratase	g4_1:1271-2074	LIKMDGFN_00003
-
-DiscRep_SUB:FEATURE_LOCATION_CONFLICT::Coding region xref gene does not exist
-Examples/2-res-Annotate-prokka/tmp_files/genome4.fst_prokka-split5N.fna-prokkaRes/GEN4.1111.00001:CDS	hypothetical protein	g4_1:2111-3514	LIKMDGFN_00004
-
-DiscRep_SUB:FEATURE_LOCATION_CONFLICT::Coding region xref gene does not exist
-Examples/2-res-Annotate-prokka/tmp_files/genome4.fst_prokka-split5N.fna-prokkaRes/GEN4.1111.00001:CDS	Histidine transport ATP-binding protein HisP	g4_1:3535-4308	LIKMDGFN_00005
-
-DiscRep_SUB:FEATURE_LOCATION_CONFLICT::Coding region xref gene does not exist
-Examples/2-res-Annotate-prokka/tmp_files/genome4.fst_prokka-split5N.fna-prokkaRes/GEN4.1111.00001:CDS	tRNA (guanine-N(1)-)-methyltransferase	g4_1:4327-5094	LIKMDGFN_00006
-
-DiscRep_SUB:FEATURE_LOCATION_CONFLICT::Coding region xref gene does not exist
-Examples/2-res-Annotate-prokka/tmp_files/genome4.fst_prokka-split5N.fna-prokkaRes/GEN4.1111.00001:CDS	hypothetical protein	g4_1:5138-5398	LIKMDGFN_00007
-
-DiscRep_SUB:FEATURE_LOCATION_CONFLICT::Coding region xref gene does not exist
-Examples/2-res-Annotate-prokka/tmp_files/genome4.fst_prokka-split5N.fna-prokkaRes/GEN4.1111.00001:CDS	hypothetical protein	g4_1:5413-5994	LIKMDGFN_00008
-
-DiscRep_SUB:FEATURE_LOCATION_CONFLICT::Coding region xref gene does not exist
-Examples/2-res-Annotate-prokka/tmp_files/genome4.fst_prokka-split5N.fna-prokkaRes/GEN4.1111.00001:CDS	C4-dicarboxylate TRAP transporter large permease protein DctM	g4_1:6052-7134	LIKMDGFN_00009
-
-DiscRep_ALL:DISC_QUALITY_SCORES::Quality scores are missing on all sequences.
-
-DiscRep_ALL:ONCALLER_COMMENT_PRESENT::1 comment descriptors were found (all same)
-Examples/2-res-Annotate-prokka/tmp_files/genome4.fst_prokka-split5N.fna-prokkaRes/GEN4.1111.00001:g4_1:Annotated using prokka 1.14.5 from https://github.com/tseemann/prokka
-
-DiscRep_ALL:MISSING_GENOMEASSEMBLY_COMMENTS::1 bioseqs are missing GenomeAssembly structured comments
-Examples/2-res-Annotate-prokka/tmp_files/genome4.fst_prokka-split5N.fna-prokkaRes/GEN4.1111.00001:g4_1 (length 7134)
-
-DiscRep_ALL:MOLTYPE_NOT_MRNA::1 molecule types are not set as mRNA.
-Examples/2-res-Annotate-prokka/tmp_files/genome4.fst_prokka-split5N.fna-prokkaRes/GEN4.1111.00001:g4_1 (length 7134)
-
-DiscRep_ALL:TECHNIQUE_NOT_TSA::1 technique are not set as TSA
-Examples/2-res-Annotate-prokka/tmp_files/genome4.fst_prokka-split5N.fna-prokkaRes/GEN4.1111.00001:g4_1 (length 7134)
-
-DiscRep_ALL:MISSING_STRUCTURED_COMMENT::1 sequences do not include structured comments.
-Examples/2-res-Annotate-prokka/tmp_files/genome4.fst_prokka-split5N.fna-prokkaRes/GEN4.1111.00001:g4_1 (length 7134)
-
-DiscRep_ALL:MISSING_PROJECT::10 sequences do not include project.
-Examples/2-res-Annotate-prokka/tmp_files/genome4.fst_prokka-split5N.fna-prokkaRes/GEN4.1111.00001:g4_1 (length 7134)
-Examples/2-res-Annotate-prokka/tmp_files/genome4.fst_prokka-split5N.fna-prokkaRes/GEN4.1111.00001:g4_1_1 (length 276)
-Examples/2-res-Annotate-prokka/tmp_files/genome4.fst_prokka-split5N.fna-prokkaRes/GEN4.1111.00001:g4_1_2 (length 126)
-Examples/2-res-Annotate-prokka/tmp_files/genome4.fst_prokka-split5N.fna-prokkaRes/GEN4.1111.00001:g4_1_3 (length 267)
-Examples/2-res-Annotate-prokka/tmp_files/genome4.fst_prokka-split5N.fna-prokkaRes/GEN4.1111.00001:g4_1_4 (length 467)
-Examples/2-res-Annotate-prokka/tmp_files/genome4.fst_prokka-split5N.fna-prokkaRes/GEN4.1111.00001:g4_1_5 (length 257)
-Examples/2-res-Annotate-prokka/tmp_files/genome4.fst_prokka-split5N.fna-prokkaRes/GEN4.1111.00001:g4_1_6 (length 255)
-Examples/2-res-Annotate-prokka/tmp_files/genome4.fst_prokka-split5N.fna-prokkaRes/GEN4.1111.00001:g4_1_7 (length 86)
-Examples/2-res-Annotate-prokka/tmp_files/genome4.fst_prokka-split5N.fna-prokkaRes/GEN4.1111.00001:g4_1_8 (length 193)
-Examples/2-res-Annotate-prokka/tmp_files/genome4.fst_prokka-split5N.fna-prokkaRes/GEN4.1111.00001:g4_1_9 (length 360)
-
-DiscRep_ALL:DISC_INCONSISTENT_MOLINFO_TECH::Molinfo Technique Report (some missing, all same)
-DiscRep_SUB:DISC_INCONSISTENT_MOLINFO_TECH::technique (all missing)
-DiscRep_SUB:DISC_INCONSISTENT_MOLINFO_TECH::1 Molinfos are missing field technique
-Examples/2-res-Annotate-prokka/tmp_files/genome4.fst_prokka-split5N.fna-prokkaRes/GEN4.1111.00001:g4_1 (length 7134)
-
diff --git a/Examples/2-res-Annotate-prokka/tmp_files/genome4.fst_prokka-split5N.fna-prokkaRes/GEN4.1111.00001.faa b/Examples/2-res-Annotate-prokka/tmp_files/genome4.fst_prokka-split5N.fna-prokkaRes/GEN4.1111.00001.faa
deleted file mode 100644
index a9dac9220a5843883e83e742358b8227b5d843ff..0000000000000000000000000000000000000000
--- a/Examples/2-res-Annotate-prokka/tmp_files/genome4.fst_prokka-split5N.fna-prokkaRes/GEN4.1111.00001.faa
+++ /dev/null
@@ -1,52 +0,0 @@
->LIKMDGFN_00001 N-acetylmuramoyl-L-alanine amidase AmiD
-MKALLWLVGLALLLTGCASEKGIIDKEGYQLDTRHRAQAAYPRIKVLVIHYTAENFDVSL
-ATLTGRNVSSHYLIPATPPLYGGKPRIWQLVPEQDQAWHAGVSFWRGATRLNDTSIGIEL
-ENRGWRMSGGVKSFAPFESAQIQALIPLAKDIIARYDIKPQNVVAHADIAPQRKDDPGPR
-FPWRELAAQGIGAWPDAQRVAFYLAGRAPYTPVDTATVLALLSRYGYEVKADMTAREQQR
-VIMAFQMHFRPAQWNGIADAETQAIAEALLEKYGQD
->LIKMDGFN_00002 5-carboxymethyl-2-hydroxymuconate Delta-isomerase
-MPHFIAECTENIREQADLPGLFSKVNEALAASGIFPIGGIRSRAHWLDTWQMADGKHDYA
-FVHMTLKIGTGRSLESRQEVGEMLFGLIKAHFADLMENRYLALSFEIAELHPTLNYKQNN
-VHALFK
->LIKMDGFN_00003 2-oxo-hept-4-ene-1,7-dioate hydratase
-MLDKQTHTLIAQRLNQAEKQREQIRAVSLDYPNITIEDAYAVQREWVNIKIAEGRTLKGH
-KIGLTSKAMQASSQISEPDYGALLDDMFFHDGGDIPTDRFIVPRIEVELAFVLAKPLRGP
-HCTLFDVYNATDYVIPALELIDARSHNIDPETQRPRKVFDTISDNAANAGVILGGRPIKP
-DELDLRWISALLYRNGVIEETGVAAGVLNHPANGVAWLANKLAPYDVQLEAGQIILGGSF
-TRPVPASKGDTFHVDYGNMGAISCRFV
->LIKMDGFN_00004 hypothetical protein
-MPVNKFSRRTLLTAGSALAVLPFLRALPVQAREPRETVDIKDYPADDGIASFKQAFADGQ
-TVVLPPGWVCENINAAITIPAGKTLRVQGAVRGNGRGRFILQDGCQVVGEQGGSLHNVTL
-DVRGSDCVIKGVTMSGFGPVAQIFIGGKEPQVMRNLIIDDITVTHANYAILRQGFHNQMD
-GARITHSRFSDLQGDAIEWNVAIHDRDILISDHVIERIDCTNGKINWGIGIGLAGSTYDN
-SYPEDQAVKNFVVANITGSDCRQLVHVENGKHFVIRNVKAKNITPDFSKNAGIDNATIAI
-YGCDNFVIDNIDMTNSAGMLIGYGVVKGKYLSIPQNFKLNAIRLDNRQVAYKLRGIQISS
-GNIPSFVAITNVRMTRATLELHNQPQHLFLRNINVMQTSAIGPALKMHFDLRKDVRGQFM
-ARQDTLLSLANVHAINENGQSSVDIDRINHQTVNVEAVNFSLPKRGG
->LIKMDGFN_00005 Histidine transport ATP-binding protein HisP
-MSENKLHVIDLHKRYGGHEVLKGVSLQARAGDVISIIGSSGSGKSTFLRCINFLEKPSEG
-AIIVNGQNINLVRDKDGQLKVADKNQLRLLRTRLTMVFQHFNLWSHMTVLENVMEAPIQV
-LGLSKHDARERALKYLAKVGIDERAQGKYPVHLSGGQQQRVSIARALAMEPDVLLFDEPT
-SALDPELVGEVLRIMQQLAEEGKTMVVVTHEMGFARHVSSHVIFLHQGKIEEEGDPEQVF
-GNPQSPRLQQFLKGSLK
->LIKMDGFN_00006 tRNA (guanine-N(1)-)-methyltransferase
-MFIGIVSLFPEMFRAITDYGVTGRAVKKGLLNIQSWSPRDFAHDRHRTVDDRPYGGGPGM
-LMMVQPLRDAIHAAKAAAGEGAKVIYLSPQGRKLDQAGVSELATNQKLILVCGRYEGVDE
-RVIQTEIDEEWSIGDYVLSGGELPAMTLIDSVARFIPGVLGHEASAIEDSFADGLLDCPH
-YTRPEVLEGMEVPPVLLSGNHAEIRRWRLKQSLGRTWLRRPELLENLALTEEQARLLAEF
-KTEHAQQQHKHDGMA
->LIKMDGFN_00007 hypothetical protein
-MAGLHAPYAYSAHHAVNFCSEYKRGFVLGFTHRMFEKTGDRQLSAWEAGILTRRYGLDKE
-MVMDFFKENHSGMAVRFFMVGYRLEG
->LIKMDGFN_00008 hypothetical protein
-MSTLLYLHGFNSSPRSAKACQLKNWLAERHPHVEMIVPQLPPYPADAAELLESLVLEHGG
-APLGLVGSSLGGYYATWLSQCFMLPAVVVNPAVRPFELLTDYLGQNENPYTGQQYVLESR
-HIYDLKVMQIDPLEAPDLIWLLQQTGDEVLDYRQAVAYYASCRQTVTEGGNHAFTGFEDY
-FNQIVDFLGLHSC
->LIKMDGFN_00009 C4-dicarboxylate TRAP transporter large permease protein DctM
-MNSGGIAARLVNFAKLFTGKLPGSLSYTNIVGNMMFGAISGSAIAASTSIGGVMVPMSAR
-EGYDRGFAAAVNIASAPTGMLIPPTTAFILYALASGGTSIAALFAGGLVAGVLWGVGCML
-VTLVVAKRRNYRVFFTVQKGMALKVAVEAIPSLLLIVIIVGGIVQGIFTAIEASAIAVVY
-TLLLTMVFYRTLKIKDLPSILLQTVVMTGVIMFLLATSSAMSFSMSITNIPAALSDMILG
-ISANKLVILLVITVFLLIIGAFMDIGPAILIFTPILLPIMAKLGVDPVHFGIIMIYNLAI
-GTITPPVGSGLYVGASVGKVKVEEVIKPLLPFYGAIIGVLLLITYIPEITLFLPRLLGIM
diff --git a/Examples/2-res-Annotate-prokka/tmp_files/genome4.fst_prokka-split5N.fna-prokkaRes/GEN4.1111.00001.ffn b/Examples/2-res-Annotate-prokka/tmp_files/genome4.fst_prokka-split5N.fna-prokkaRes/GEN4.1111.00001.ffn
deleted file mode 100644
index 40721d61f9f565ea758dd19633045b3da0e82ace..0000000000000000000000000000000000000000
--- a/Examples/2-res-Annotate-prokka/tmp_files/genome4.fst_prokka-split5N.fna-prokkaRes/GEN4.1111.00001.ffn
+++ /dev/null
@@ -1,128 +0,0 @@
->LIKMDGFN_00001 N-acetylmuramoyl-L-alanine amidase AmiD
-ATGAAAGCGCTACTGTGGCTGGTGGGTCTCGCGTTGCTGTTAACAGGCTGCGCGAGCGAA
-AAAGGAATTATCGATAAAGAGGGATATCAGCTTGATACCCGACATCGGGCGCAGGCGGCC
-TATCCGCGCATTAAAGTCCTGGTGATTCACTATACGGCGGAAAACTTTGACGTTTCGCTG
-GCGACGTTAACGGGCCGCAACGTCAGTTCGCATTACCTGATTCCCGCAACCCCGCCATTA
-TATGGCGGTAAACCGCGCATCTGGCAACTGGTGCCGGAACAGGATCAGGCCTGGCATGCG
-GGCGTCAGTTTCTGGCGAGGCGCCACGCGTCTCAATGATACGTCTATTGGCATTGAGCTG
-GAAAATCGCGGCTGGCGAATGTCCGGCGGGGTGAAATCTTTCGCGCCGTTTGAATCCGCG
-CAAATTCAGGCATTGATTCCGTTAGCGAAGGACATTATCGCGCGCTATGACATCAAACCG
-CAGAATGTGGTGGCCCATGCGGATATCGCGCCGCAGCGTAAAGACGATCCCGGCCCGCGC
-TTCCCGTGGCGCGAGCTGGCGGCGCAGGGGATTGGCGCCTGGCCTGACGCCCAGCGTGTG
-GCGTTTTATCTGGCTGGACGCGCGCCGTATACGCCAGTCGATACCGCAACGGTGCTTGCG
-TTACTCTCGCGCTATGGCTATGAAGTCAAAGCCGATATGACGGCGCGCGAGCAGCAGCGG
-GTGATTATGGCGTTCCAGATGCACTTCCGTCCGGCGCAATGGAACGGTATCGCAGATGCC
-GAAACGCAGGCGATTGCCGAAGCATTACTGGAGAAGTACGGCCAGGATTAA
->LIKMDGFN_00002 5-carboxymethyl-2-hydroxymuconate Delta-isomerase
-ATGCCGCACTTTATTGCTGAATGTACTGAAAATATTCGCGAGCAGGCTGATTTACCCGGC
-CTGTTCAGCAAGGTAAACGAGGCGCTGGCCGCCAGCGGGATTTTCCCCATCGGCGGTATC
-CGCAGTCGCGCCCACTGGCTGGATACCTGGCAGATGGCTGACGGTAAGCATGATTATGCG
-TTTGTGCATATGACGCTGAAAATCGGTACCGGGCGCAGCCTGGAGAGCCGTCAGGAAGTC
-GGCGAAATGCTGTTTGGGCTGATTAAAGCCCACTTCGCCGACCTGATGGAGAACCGCTAT
-CTGGCGCTGTCGTTTGAGATTGCCGAGCTACATCCGACGCTCAATTACAAACAAAACAAC
-GTACACGCGTTATTTAAATAG
->LIKMDGFN_00003 2-oxo-hept-4-ene-1,7-dioate hydratase
-ATGCTCGATAAACAGACCCATACCCTGATCGCCCAGCGACTTAATCAGGCTGAAAAACAG
-CGTGAACAAATTCGCGCAGTGTCGCTGGATTATCCCAACATCACTATTGAAGATGCCTAT
-GCCGTACAGCGTGAATGGGTCAATATCAAGATCGCCGAAGGGCGCACGCTCAAAGGCCAC
-AAAATCGGCCTGACCTCAAAAGCGATGCAGGCCAGCTCGCAAATCAGCGAACCGGATTAC
-GGCGCGCTGCTTGACGATATGTTCTTCCATGACGGCGGCGATATCCCCACCGACCGTTTT
-ATCGTCCCGCGTATTGAAGTGGAGCTGGCGTTCGTGCTGGCGAAACCGCTGCGCGGCCCT
-CACTGCACGCTGTTCGACGTCTACAACGCCACGGATTATGTGATTCCGGCGCTGGAACTG
-ATTGACGCCCGCAGCCACAACATCGACCCGGAAACCCAGCGCCCGCGCAAAGTGTTCGAC
-ACCATTTCCGACAACGCCGCCAACGCCGGGGTGATCCTCGGTGGTCGCCCCATCAAACCA
-GACGAGCTGGATCTGCGCTGGATCTCCGCGCTGCTCTATCGCAACGGCGTGATCGAAGAA
-ACCGGCGTCGCCGCAGGCGTGCTGAATCATCCGGCCAACGGCGTGGCGTGGCTGGCGAAC
-AAGCTTGCCCCCTACGATGTCCAGCTTGAAGCCGGGCAGATCATCCTCGGCGGCTCGTTC
-ACCCGCCCGGTGCCGGCGAGCAAGGGCGACACCTTCCATGTCGATTACGGCAACATGGGC
-GCGATCAGTTGCCGGTTTGTGTAA
->LIKMDGFN_00004 hypothetical protein
-ATGCCCGTGAATAAGTTCTCCCGACGTACCCTCCTGACGGCAGGTTCCGCGCTTGCTGTT
-CTTCCTTTTCTGCGCGCCTTGCCGGTACAGGCGCGTGAACCTCGCGAGACCGTCGATATT
-AAGGATTATCCGGCGGATGACGGTATCGCCTCGTTCAAACAGGCCTTCGCCGACGGACAG
-ACCGTGGTCTTACCGCCAGGATGGGTGTGTGAAAATATCAATGCGGCGATAACGATTCCG
-GCGGGAAAAACGCTGCGGGTACAGGGCGCGGTGCGTGGGAATGGCCGGGGACGGTTTATT
-TTGCAGGACGGGTGTCAGGTGGTGGGGGAGCAGGGCGGCAGTCTGCACAATGTGACGCTG
-GATGTTCGCGGGTCGGACTGTGTGATTAAAGGCGTGACGATGAGCGGCTTTGGCCCCGTC
-GCGCAAATTTTCATCGGCGGTAAGGAACCGCAGGTGATGCGTAATCTCATTATCGATGAC
-ATCACCGTTACCCACGCCAACTACGCCATTCTCCGCCAGGGATTTCATAACCAAATGGAC
-GGCGCGCGGATTACGCATAGCCGCTTTAGCGATTTGCAGGGGGACGCCATTGAGTGGAAT
-GTCGCGATTCACGACCGCGACATCCTGATTTCCGATCATGTCATCGAACGCATTGATTGT
-ACCAATGGCAAAATCAACTGGGGGATCGGCATCGGGCTGGCGGGTAGCACCTATGACAAC
-AGTTATCCTGAAGATCAGGCAGTAAAAAACTTTGTGGTGGCCAATATTACCGGATCTGAT
-TGCCGACAGCTGGTGCACGTAGAAAATGGCAAACATTTCGTCATTCGCAATGTCAAAGCC
-AAAAACATCACGCCCGATTTCAGTAAAAATGCGGGTATTGATAACGCAACGATCGCCATT
-TATGGCTGTGATAATTTCGTCATTGATAATATTGATATGACGAATAGTGCTGGGATGCTC
-ATCGGCTATGGCGTCGTTAAAGGAAAATACCTGTCAATTCCGCAAAACTTTAAATTAAAC
-GCTATTCGGTTGGATAATCGCCAGGTTGCTTATAAATTACGCGGCATTCAAATTTCCTCC
-GGCAACATCCCCTCTTTTGTCGCCATCACCAATGTACGGATGACGCGTGCTACGCTGGAA
-CTGCATAATCAACCGCAGCACCTCTTTCTGCGTAATATCAACGTGATGCAAACTTCAGCG
-ATTGGCCCGGCGTTAAAAATGCATTTCGATTTGCGTAAAGATGTCCGTGGTCAATTTATG
-GCCCGCCAGGACACGCTGCTTTCCCTCGCTAATGTTCATGCCATCAATGAAAACGGGCAG
-AGTTCCGTGGATATCGACAGGATTAATCACCAAACCGTGAATGTCGAAGCAGTGAATTTT
-TCGCTGCCGAAGCGGGGAGGGTAA
->LIKMDGFN_00005 Histidine transport ATP-binding protein HisP
-ATGTCAGAAAATAAATTACACGTTATCGATTTGCACAAACGCTACGGCGGTCATGAAGTG
-CTGAAAGGGGTATCGTTGCAGGCCCGCGCCGGAGATGTGATTAGCATCATCGGCTCGTCC
-GGCTCCGGTAAAAGCACTTTTTTGCGCTGTATTAACTTCCTCGAAAAACCGAGCGAAGGC
-GCGATTATCGTGAACGGTCAGAACATTAATCTGGTGCGCGACAAAGACGGGCAGCTCAAA
-GTGGCGGATAAAAATCAGCTACGCTTGTTGCGTACCCGCCTGACGATGGTGTTTCAGCAC
-TTTAACCTCTGGAGCCACATGACGGTGCTGGAAAATGTGATGGAAGCGCCGATTCAGGTA
-CTGGGATTAAGCAAGCACGACGCGCGCGAGCGGGCGTTGAAATATCTGGCGAAGGTGGGG
-ATTGATGAGCGCGCTCAGGGCAAATATCCCGTCCATCTCTCCGGCGGCCAACAGCAGCGC
-GTTTCTATTGCGCGCGCGCTGGCGATGGAACCTGACGTTTTACTGTTCGATGAACCCACA
-TCGGCGCTCGATCCTGAACTGGTCGGCGAAGTGTTGCGCATCATGCAACAACTGGCGGAA
-GAAGGCAAAACGATGGTGGTGGTCACGCATGAAATGGGCTTCGCCCGCCATGTCTCTTCG
-CACGTTATTTTTCTGCATCAGGGGAAAATTGAAGAAGAGGGCGATCCGGAGCAGGTGTTC
-GGCAATCCGCAAAGCCCGCGTTTACAGCAATTCCTGAAAGGCTCGCTGAAATAA
->LIKMDGFN_00006 tRNA (guanine-N(1)-)-methyltransferase
-GTGTTTATTGGCATCGTTAGCCTGTTTCCTGAAATGTTCCGCGCAATTACCGATTACGGG
-GTAACTGGCCGGGCAGTAAAAAAAGGCCTGCTGAACATCCAAAGCTGGAGTCCTCGCGAC
-TTCGCGCATGACCGGCACCGTACCGTGGACGACCGTCCTTACGGCGGCGGACCGGGGATG
-TTAATGATGGTGCAACCCTTGCGGGACGCCATTCACGCAGCAAAAGCCGCGGCAGGTGAA
-GGCGCTAAAGTGATTTATCTGTCGCCTCAGGGACGCAAGCTTGATCAAGCGGGCGTTAGC
-GAGCTGGCCACGAATCAGAAGCTTATTCTGGTGTGTGGTCGCTACGAAGGCGTAGATGAG
-CGCGTAATTCAGACCGAAATTGACGAAGAATGGTCAATTGGCGATTACGTTCTCAGCGGT
-GGCGAACTACCGGCAATGACGCTGATTGACTCCGTCGCCCGGTTTATACCGGGGGTTCTG
-GGGCATGAGGCATCAGCAATCGAAGATTCGTTTGCTGATGGGTTGCTGGATTGTCCGCAC
-TATACGCGCCCTGAAGTGTTAGAGGGGATGGAAGTACCGCCAGTATTGCTGTCGGGAAAC
-CATGCCGAGATACGTCGCTGGCGCTTGAAACAGTCGCTGGGCCGAACCTGGCTTAGAAGA
-CCTGAACTTCTGGAAAACCTGGCTCTGACTGAAGAGCAAGCAAGGTTGCTGGCGGAGTTC
-AAAACAGAACACGCACAACAGCAGCATAAACATGATGGGATGGCATAG
->LIKMDGFN_00007 hypothetical protein
-ATGGCTGGGTTGCACGCGCCATATGCATATAGCGCGCATCATGCGGTGAATTTCTGTTCT
-GAGTATAAACGTGGCTTTGTATTGGGTTTTACACACCGTATGTTCGAAAAGACCGGCGAT
-CGTCAACTTAGCGCGTGGGAGGCCGGAATTCTGACGCGTCGCTATGGTCTGGATAAAGAA
-ATGGTGATGGATTTCTTTAAAGAGAATCATTCCGGGATGGCGGTTCGCTTCTTTATGGTC
-GGTTATCGACTCGAAGGTTGA
->LIKMDGFN_00008 hypothetical protein
-ATGTCTACGCTTCTCTATTTGCACGGATTCAACAGTTCCCCTCGCTCGGCAAAAGCGTGC
-CAGCTAAAAAACTGGCTGGCGGAGCGTCATCCGCATGTCGAGATGATCGTCCCTCAACTA
-CCGCCGTATCCTGCCGATGCGGCGGAGTTGCTGGAATCTCTCGTGCTTGAGCATGGCGGT
-GCGCCATTAGGGCTGGTAGGATCGTCGCTGGGTGGTTATTACGCCACCTGGCTGTCGCAA
-TGTTTTATGCTGCCGGCTGTGGTGGTGAATCCCGCCGTGCGGCCCTTTGAATTACTGACC
-GACTATCTCGGTCAGAACGAGAACCCCTACACCGGGCAGCAATATGTGCTAGAGTCTCGC
-CATATTTATGATCTTAAAGTCATGCAGATTGACCCGCTGGAAGCGCCGGACCTGATCTGG
-CTACTGCAACAGACGGGCGATGAAGTGCTGGATTACCGCCAGGCGGTGGCATATTACGCC
-TCCTGCCGTCAGACAGTGACCGAGGGTGGTAATCACGCATTCACGGGCTTCGAAGATTAT
-TTCAACCAGATTGTCGATTTTCTTGGACTGCACAGTTGCTGA
->LIKMDGFN_00009 C4-dicarboxylate TRAP transporter large permease protein DctM
-ATGAATAGCGGGGGAATTGCCGCCCGGCTGGTCAATTTTGCCAAACTGTTTACTGGCAAA
-CTGCCCGGCTCGCTCTCTTATACCAACATCGTCGGCAATATGATGTTCGGTGCAATTTCC
-GGATCGGCAATTGCCGCCTCAACCTCCATCGGCGGCGTGATGGTGCCGATGAGCGCGCGC
-GAAGGTTACGATCGCGGCTTTGCGGCCGCGGTGAATATCGCCTCCGCGCCGACGGGAATG
-TTAATTCCGCCCACCACGGCTTTTATCCTTTATGCGCTGGCAAGCGGGGGAACATCGATT
-GCCGCTCTGTTCGCCGGCGGTCTGGTCGCGGGAGTGCTGTGGGGCGTTGGCTGTATGCTG
-GTCACGCTGGTGGTCGCTAAGCGTCGAAATTATCGGGTTTTCTTCACCGTCCAAAAAGGC
-ATGGCGCTAAAAGTTGCCGTTGAGGCCATTCCCAGCCTGCTGCTGATCGTGATTATCGTC
-GGCGGCATTGTGCAGGGGATTTTCACCGCCATTGAAGCCTCCGCGATTGCCGTGGTGTAT
-ACATTATTGTTGACGATGGTGTTTTACCGCACGCTGAAAATTAAGGATTTGCCTTCGATT
-TTGCTCCAGACAGTGGTAATGACCGGGGTCATCATGTTCCTGCTGGCAACCTCTTCGGCG
-ATGTCCTTCTCGATGTCGATCACCAATATTCCTGCGGCGCTGAGCGATATGATCCTCGGT
-ATTTCCGCCAATAAACTGGTTATCCTGTTAGTCATTACCGTCTTTTTGTTGATTATCGGC
-GCATTTATGGATATCGGTCCGGCCATTCTGATTTTTACCCCGATTCTGCTGCCGATCATG
-GCTAAACTGGGCGTCGATCCGGTGCATTTTGGCATTATCATGATCTATAACCTGGCGATT
-GGCACCATTACGCCGCCAGTTGGCAGTGGTTTATATGTCGGGGCGAGCGTCGGTAAGGTC
-AAAGTTGAGGAAGTGATTAAACCGTTGCTGCCTTTTTACGGCGCGATTATCGGCGTTCTG
-TTATTAATTACCTACATTCCGGAAATCACACTGTTCTTACCCCGTCTACTGGGCATCATG
-TAA
diff --git a/Examples/2-res-Annotate-prokka/tmp_files/genome4.fst_prokka-split5N.fna-prokkaRes/GEN4.1111.00001.fna b/Examples/2-res-Annotate-prokka/tmp_files/genome4.fst_prokka-split5N.fna-prokkaRes/GEN4.1111.00001.fna
deleted file mode 100644
index c9dacd184cf1469f26718f4e1d00a44270105582..0000000000000000000000000000000000000000
--- a/Examples/2-res-Annotate-prokka/tmp_files/genome4.fst_prokka-split5N.fna-prokkaRes/GEN4.1111.00001.fna
+++ /dev/null
@@ -1,120 +0,0 @@
->g4_1
-ATGAAAGCGCTACTGTGGCTGGTGGGTCTCGCGTTGCTGTTAACAGGCTGCGCGAGCGAA
-AAAGGAATTATCGATAAAGAGGGATATCAGCTTGATACCCGACATCGGGCGCAGGCGGCC
-TATCCGCGCATTAAAGTCCTGGTGATTCACTATACGGCGGAAAACTTTGACGTTTCGCTG
-GCGACGTTAACGGGCCGCAACGTCAGTTCGCATTACCTGATTCCCGCAACCCCGCCATTA
-TATGGCGGTAAACCGCGCATCTGGCAACTGGTGCCGGAACAGGATCAGGCCTGGCATGCG
-GGCGTCAGTTTCTGGCGAGGCGCCACGCGTCTCAATGATACGTCTATTGGCATTGAGCTG
-GAAAATCGCGGCTGGCGAATGTCCGGCGGGGTGAAATCTTTCGCGCCGTTTGAATCCGCG
-CAAATTCAGGCATTGATTCCGTTAGCGAAGGACATTATCGCGCGCTATGACATCAAACCG
-CAGAATGTGGTGGCCCATGCGGATATCGCGCCGCAGCGTAAAGACGATCCCGGCCCGCGC
-TTCCCGTGGCGCGAGCTGGCGGCGCAGGGGATTGGCGCCTGGCCTGACGCCCAGCGTGTG
-GCGTTTTATCTGGCTGGACGCGCGCCGTATACGCCAGTCGATACCGCAACGGTGCTTGCG
-TTACTCTCGCGCTATGGCTATGAAGTCAAAGCCGATATGACGGCGCGCGAGCAGCAGCGG
-GTGATTATGGCGTTCCAGATGCACTTCCGTCCGGCGCAATGGAACGGTATCGCAGATGCC
-GAAACGCAGGCGATTGCCGAAGCATTACTGGAGAAGTACGGCCAGGATTAACGCGATCGC
-GCGCATATCGCGCGCGATAGATGCCGCACTTTATTGCTGAATGTACTGAAAATATTCGCG
-AGCAGGCTGATTTACCCGGCCTGTTCAGCAAGGTAAACGAGGCGCTGGCCGCCAGCGGGA
-TTTTCCCCATCGGCGGTATCCGCAGTCGCGCCCACTGGCTGGATACCTGGCAGATGGCTG
-ACGGTAAGCATGATTATGCGTTTGTGCATATGACGCTGAAAATCGGTACCGGGCGCAGCC
-TGGAGAGCCGTCAGGAAGTCGGCGAAATGCTGTTTGGGCTGATTAAAGCCCACTTCGCCG
-ACCTGATGGAGAACCGCTATCTGGCGCTGTCGTTTGAGATTGCCGAGCTACATCCGACGC
-TCAATTACAAACAAAACAACGTACACGCGTTATTTAAATAGCCGCATATGCGGCGCTCAG
-GAGCGCTAGCATGCTCGATAAACAGACCCATACCCTGATCGCCCAGCGACTTAATCAGGC
-TGAAAAACAGCGTGAACAAATTCGCGCAGTGTCGCTGGATTATCCCAACATCACTATTGA
-AGATGCCTATGCCGTACAGCGTGAATGGGTCAATATCAAGATCGCCGAAGGGCGCACGCT
-CAAAGGCCACAAAATCGGCCTGACCTCAAAAGCGATGCAGGCCAGCTCGCAAATCAGCGA
-ACCGGATTACGGCGCGCTGCTTGACGATATGTTCTTCCATGACGGCGGCGATATCCCCAC
-CGACCGTTTTATCGTCCCGCGTATTGAAGTGGAGCTGGCGTTCGTGCTGGCGAAACCGCT
-GCGCGGCCCTCACTGCACGCTGTTCGACGTCTACAACGCCACGGATTATGTGATTCCGGC
-GCTGGAACTGATTGACGCCCGCAGCCACAACATCGACCCGGAAACCCAGCGCCCGCGCAA
-AGTGTTCGACACCATTTCCGACAACGCCGCCAACGCCGGGGTGATCCTCGGTGGTCGCCC
-CATCAAACCAGACGAGCTGGATCTGCGCTGGATCTCCGCGCTGCTCTATCGCAACGGCGT
-GATCGAAGAAACCGGCGTCGCCGCAGGCGTGCTGAATCATCCGGCCAACGGCGTGGCGTG
-GCTGGCGAACAAGCTTGCCCCCTACGATGTCCAGCTTGAAGCCGGGCAGATCATCCTCGG
-CGGCTCGTTCACCCGCCCGGTGCCGGCGAGCAAGGGCGACACCTTCCATGTCGATTACGG
-CAACATGGGCGCGATCAGTTGCCGGTTTGTGTAACCAGATCCGCGCGCGCATATATATCG
-CGCGCATACGATGCCCGTGAATAAGTTCTCCCGACGTACCCTCCTGACGGCAGGTTCCGC
-GCTTGCTGTTCTTCCTTTTCTGCGCGCCTTGCCGGTACAGGCGCGTGAACCTCGCGAGAC
-CGTCGATATTAAGGATTATCCGGCGGATGACGGTATCGCCTCGTTCAAACAGGCCTTCGC
-CGACGGACAGACCGTGGTCTTACCGCCAGGATGGGTGTGTGAAAATATCAATGCGGCGAT
-AACGATTCCGGCGGGAAAAACGCTGCGGGTACAGGGCGCGGTGCGTGGGAATGGCCGGGG
-ACGGTTTATTTTGCAGGACGGGTGTCAGGTGGTGGGGGAGCAGGGCGGCAGTCTGCACAA
-TGTGACGCTGGATGTTCGCGGGTCGGACTGTGTGATTAAAGGCGTGACGATGAGCGGCTT
-TGGCCCCGTCGCGCAAATTTTCATCGGCGGTAAGGAACCGCAGGTGATGCGTAATCTCAT
-TATCGATGACATCACCGTTACCCACGCCAACTACGCCATTCTCCGCCAGGGATTTCATAA
-CCAAATGGACGGCGCGCGGATTACGCATAGCCGCTTTAGCGATTTGCAGGGGGACGCCAT
-TGAGTGGAATGTCGCGATTCACGACCGCGACATCCTGATTTCCGATCATGTCATCGAACG
-CATTGATTGTACCAATGGCAAAATCAACTGGGGGATCGGCATCGGGCTGGCGGGTAGCAC
-CTATGACAACAGTTATCCTGAAGATCAGGCAGTAAAAAACTTTGTGGTGGCCAATATTAC
-CGGATCTGATTGCCGACAGCTGGTGCACGTAGAAAATGGCAAACATTTCGTCATTCGCAA
-TGTCAAAGCCAAAAACATCACGCCCGATTTCAGTAAAAATGCGGGTATTGATAACGCAAC
-GATCGCCATTTATGGCTGTGATAATTTCGTCATTGATAATATTGATATGACGAATAGTGC
-TGGGATGCTCATCGGCTATGGCGTCGTTAAAGGAAAATACCTGTCAATTCCGCAAAACTT
-TAAATTAAACGCTATTCGGTTGGATAATCGCCAGGTTGCTTATAAATTACGCGGCATTCA
-AATTTCCTCCGGCAACATCCCCTCTTTTGTCGCCATCACCAATGTACGGATGACGCGTGC
-TACGCTGGAACTGCATAATCAACCGCAGCACCTCTTTCTGCGTAATATCAACGTGATGCA
-AACTTCAGCGATTGGCCCGGCGTTAAAAATGCATTTCGATTTGCGTAAAGATGTCCGTGG
-TCAATTTATGGCCCGCCAGGACACGCTGCTTTCCCTCGCTAATGTTCATGCCATCAATGA
-AAACGGGCAGAGTTCCGTGGATATCGACAGGATTAATCACCAAACCGTGAATGTCGAAGC
-AGTGAATTTTTCGCTGCCGAAGCGGGGAGGGTAACAGAGCTCGCGCGATCGCGAATGTCA
-GAAAATAAATTACACGTTATCGATTTGCACAAACGCTACGGCGGTCATGAAGTGCTGAAA
-GGGGTATCGTTGCAGGCCCGCGCCGGAGATGTGATTAGCATCATCGGCTCGTCCGGCTCC
-GGTAAAAGCACTTTTTTGCGCTGTATTAACTTCCTCGAAAAACCGAGCGAAGGCGCGATT
-ATCGTGAACGGTCAGAACATTAATCTGGTGCGCGACAAAGACGGGCAGCTCAAAGTGGCG
-GATAAAAATCAGCTACGCTTGTTGCGTACCCGCCTGACGATGGTGTTTCAGCACTTTAAC
-CTCTGGAGCCACATGACGGTGCTGGAAAATGTGATGGAAGCGCCGATTCAGGTACTGGGA
-TTAAGCAAGCACGACGCGCGCGAGCGGGCGTTGAAATATCTGGCGAAGGTGGGGATTGAT
-GAGCGCGCTCAGGGCAAATATCCCGTCCATCTCTCCGGCGGCCAACAGCAGCGCGTTTCT
-ATTGCGCGCGCGCTGGCGATGGAACCTGACGTTTTACTGTTCGATGAACCCACATCGGCG
-CTCGATCCTGAACTGGTCGGCGAAGTGTTGCGCATCATGCAACAACTGGCGGAAGAAGGC
-AAAACGATGGTGGTGGTCACGCATGAAATGGGCTTCGCCCGCCATGTCTCTTCGCACGTT
-ATTTTTCTGCATCAGGGGAAAATTGAAGAAGAGGGCGATCCGGAGCAGGTGTTCGGCAAT
-CCGCAAAGCCCGCGTTTACAGCAATTCCTGAAAGGCTCGCTGAAATAACAGATACGCGCA
-TGGCGAGTGTTTATTGGCATCGTTAGCCTGTTTCCTGAAATGTTCCGCGCAATTACCGAT
-TACGGGGTAACTGGCCGGGCAGTAAAAAAAGGCCTGCTGAACATCCAAAGCTGGAGTCCT
-CGCGACTTCGCGCATGACCGGCACCGTACCGTGGACGACCGTCCTTACGGCGGCGGACCG
-GGGATGTTAATGATGGTGCAACCCTTGCGGGACGCCATTCACGCAGCAAAAGCCGCGGCA
-GGTGAAGGCGCTAAAGTGATTTATCTGTCGCCTCAGGGACGCAAGCTTGATCAAGCGGGC
-GTTAGCGAGCTGGCCACGAATCAGAAGCTTATTCTGGTGTGTGGTCGCTACGAAGGCGTA
-GATGAGCGCGTAATTCAGACCGAAATTGACGAAGAATGGTCAATTGGCGATTACGTTCTC
-AGCGGTGGCGAACTACCGGCAATGACGCTGATTGACTCCGTCGCCCGGTTTATACCGGGG
-GTTCTGGGGCATGAGGCATCAGCAATCGAAGATTCGTTTGCTGATGGGTTGCTGGATTGT
-CCGCACTATACGCGCCCTGAAGTGTTAGAGGGGATGGAAGTACCGCCAGTATTGCTGTCG
-GGAAACCATGCCGAGATACGTCGCTGGCGCTTGAAACAGTCGCTGGGCCGAACCTGGCTT
-AGAAGACCTGAACTTCTGGAAAACCTGGCTCTGACTGAAGAGCAAGCAAGGTTGCTGGCG
-GAGTTCAAAACAGAACACGCACAACAGCAGCATAAACATGATGGGATGGCATAGCGATAG
-CGCTAGAGCGATGAATAATCATTTTGGGAAAGGGTTAATGGCTGGGTTGCACGCGCCATA
-TGCATATAGCGCGCATCATGCGGTGAATTTCTGTTCTGAGTATAAACGTGGCTTTGTATT
-GGGTTTTACACACCGTATGTTCGAAAAGACCGGCGATCGTCAACTTAGCGCGTGGGAGGC
-CGGAATTCTGACGCGTCGCTATGGTCTGGATAAAGAAATGGTGATGGATTTCTTTAAAGA
-GAATCATTCCGGGATGGCGGTTCGCTTCTTTATGGTCGGTTATCGACTCGAAGGTTGACA
-GATGCGCGATCGATGTCTACGCTTCTCTATTTGCACGGATTCAACAGTTCCCCTCGCTCG
-GCAAAAGCGTGCCAGCTAAAAAACTGGCTGGCGGAGCGTCATCCGCATGTCGAGATGATC
-GTCCCTCAACTACCGCCGTATCCTGCCGATGCGGCGGAGTTGCTGGAATCTCTCGTGCTT
-GAGCATGGCGGTGCGCCATTAGGGCTGGTAGGATCGTCGCTGGGTGGTTATTACGCCACC
-TGGCTGTCGCAATGTTTTATGCTGCCGGCTGTGGTGGTGAATCCCGCCGTGCGGCCCTTT
-GAATTACTGACCGACTATCTCGGTCAGAACGAGAACCCCTACACCGGGCAGCAATATGTG
-CTAGAGTCTCGCCATATTTATGATCTTAAAGTCATGCAGATTGACCCGCTGGAAGCGCCG
-GACCTGATCTGGCTACTGCAACAGACGGGCGATGAAGTGCTGGATTACCGCCAGGCGGTG
-GCATATTACGCCTCCTGCCGTCAGACAGTGACCGAGGGTGGTAATCACGCATTCACGGGC
-TTCGAAGATTATTTCAACCAGATTGTCGATTTTCTTGGACTGCACAGTTGCTGACACGGA
-TGCGCCATCGGCTTGCTGGCCGTGCCGTTCTTCGTTTTGTCCGGGGTGATCATGAATAGC
-GGGGGAATTGCCGCCCGGCTGGTCAATTTTGCCAAACTGTTTACTGGCAAACTGCCCGGC
-TCGCTCTCTTATACCAACATCGTCGGCAATATGATGTTCGGTGCAATTTCCGGATCGGCA
-ATTGCCGCCTCAACCTCCATCGGCGGCGTGATGGTGCCGATGAGCGCGCGCGAAGGTTAC
-GATCGCGGCTTTGCGGCCGCGGTGAATATCGCCTCCGCGCCGACGGGAATGTTAATTCCG
-CCCACCACGGCTTTTATCCTTTATGCGCTGGCAAGCGGGGGAACATCGATTGCCGCTCTG
-TTCGCCGGCGGTCTGGTCGCGGGAGTGCTGTGGGGCGTTGGCTGTATGCTGGTCACGCTG
-GTGGTCGCTAAGCGTCGAAATTATCGGGTTTTCTTCACCGTCCAAAAAGGCATGGCGCTA
-AAAGTTGCCGTTGAGGCCATTCCCAGCCTGCTGCTGATCGTGATTATCGTCGGCGGCATT
-GTGCAGGGGATTTTCACCGCCATTGAAGCCTCCGCGATTGCCGTGGTGTATACATTATTG
-TTGACGATGGTGTTTTACCGCACGCTGAAAATTAAGGATTTGCCTTCGATTTTGCTCCAG
-ACAGTGGTAATGACCGGGGTCATCATGTTCCTGCTGGCAACCTCTTCGGCGATGTCCTTC
-TCGATGTCGATCACCAATATTCCTGCGGCGCTGAGCGATATGATCCTCGGTATTTCCGCC
-AATAAACTGGTTATCCTGTTAGTCATTACCGTCTTTTTGTTGATTATCGGCGCATTTATG
-GATATCGGTCCGGCCATTCTGATTTTTACCCCGATTCTGCTGCCGATCATGGCTAAACTG
-GGCGTCGATCCGGTGCATTTTGGCATTATCATGATCTATAACCTGGCGATTGGCACCATT
-ACGCCGCCAGTTGGCAGTGGTTTATATGTCGGGGCGAGCGTCGGTAAGGTCAAAGTTGAG
-GAAGTGATTAAACCGTTGCTGCCTTTTTACGGCGCGATTATCGGCGTTCTGTTATTAATT
-ACCTACATTCCGGAAATCACACTGTTCTTACCCCGTCTACTGGGCATCATGTAA
diff --git a/Examples/2-res-Annotate-prokka/tmp_files/genome4.fst_prokka-split5N.fna-prokkaRes/GEN4.1111.00001.fsa b/Examples/2-res-Annotate-prokka/tmp_files/genome4.fst_prokka-split5N.fna-prokkaRes/GEN4.1111.00001.fsa
deleted file mode 100644
index 79f8dbb42edbbe6742fcab99338d387343c11dc1..0000000000000000000000000000000000000000
--- a/Examples/2-res-Annotate-prokka/tmp_files/genome4.fst_prokka-split5N.fna-prokkaRes/GEN4.1111.00001.fsa
+++ /dev/null
@@ -1,120 +0,0 @@
->g4_1 [gcode=11] [organism=Genus species] [strain=strain]
-ATGAAAGCGCTACTGTGGCTGGTGGGTCTCGCGTTGCTGTTAACAGGCTGCGCGAGCGAA
-AAAGGAATTATCGATAAAGAGGGATATCAGCTTGATACCCGACATCGGGCGCAGGCGGCC
-TATCCGCGCATTAAAGTCCTGGTGATTCACTATACGGCGGAAAACTTTGACGTTTCGCTG
-GCGACGTTAACGGGCCGCAACGTCAGTTCGCATTACCTGATTCCCGCAACCCCGCCATTA
-TATGGCGGTAAACCGCGCATCTGGCAACTGGTGCCGGAACAGGATCAGGCCTGGCATGCG
-GGCGTCAGTTTCTGGCGAGGCGCCACGCGTCTCAATGATACGTCTATTGGCATTGAGCTG
-GAAAATCGCGGCTGGCGAATGTCCGGCGGGGTGAAATCTTTCGCGCCGTTTGAATCCGCG
-CAAATTCAGGCATTGATTCCGTTAGCGAAGGACATTATCGCGCGCTATGACATCAAACCG
-CAGAATGTGGTGGCCCATGCGGATATCGCGCCGCAGCGTAAAGACGATCCCGGCCCGCGC
-TTCCCGTGGCGCGAGCTGGCGGCGCAGGGGATTGGCGCCTGGCCTGACGCCCAGCGTGTG
-GCGTTTTATCTGGCTGGACGCGCGCCGTATACGCCAGTCGATACCGCAACGGTGCTTGCG
-TTACTCTCGCGCTATGGCTATGAAGTCAAAGCCGATATGACGGCGCGCGAGCAGCAGCGG
-GTGATTATGGCGTTCCAGATGCACTTCCGTCCGGCGCAATGGAACGGTATCGCAGATGCC
-GAAACGCAGGCGATTGCCGAAGCATTACTGGAGAAGTACGGCCAGGATTAACGCGATCGC
-GCGCATATCGCGCGCGATAGATGCCGCACTTTATTGCTGAATGTACTGAAAATATTCGCG
-AGCAGGCTGATTTACCCGGCCTGTTCAGCAAGGTAAACGAGGCGCTGGCCGCCAGCGGGA
-TTTTCCCCATCGGCGGTATCCGCAGTCGCGCCCACTGGCTGGATACCTGGCAGATGGCTG
-ACGGTAAGCATGATTATGCGTTTGTGCATATGACGCTGAAAATCGGTACCGGGCGCAGCC
-TGGAGAGCCGTCAGGAAGTCGGCGAAATGCTGTTTGGGCTGATTAAAGCCCACTTCGCCG
-ACCTGATGGAGAACCGCTATCTGGCGCTGTCGTTTGAGATTGCCGAGCTACATCCGACGC
-TCAATTACAAACAAAACAACGTACACGCGTTATTTAAATAGCCGCATATGCGGCGCTCAG
-GAGCGCTAGCATGCTCGATAAACAGACCCATACCCTGATCGCCCAGCGACTTAATCAGGC
-TGAAAAACAGCGTGAACAAATTCGCGCAGTGTCGCTGGATTATCCCAACATCACTATTGA
-AGATGCCTATGCCGTACAGCGTGAATGGGTCAATATCAAGATCGCCGAAGGGCGCACGCT
-CAAAGGCCACAAAATCGGCCTGACCTCAAAAGCGATGCAGGCCAGCTCGCAAATCAGCGA
-ACCGGATTACGGCGCGCTGCTTGACGATATGTTCTTCCATGACGGCGGCGATATCCCCAC
-CGACCGTTTTATCGTCCCGCGTATTGAAGTGGAGCTGGCGTTCGTGCTGGCGAAACCGCT
-GCGCGGCCCTCACTGCACGCTGTTCGACGTCTACAACGCCACGGATTATGTGATTCCGGC
-GCTGGAACTGATTGACGCCCGCAGCCACAACATCGACCCGGAAACCCAGCGCCCGCGCAA
-AGTGTTCGACACCATTTCCGACAACGCCGCCAACGCCGGGGTGATCCTCGGTGGTCGCCC
-CATCAAACCAGACGAGCTGGATCTGCGCTGGATCTCCGCGCTGCTCTATCGCAACGGCGT
-GATCGAAGAAACCGGCGTCGCCGCAGGCGTGCTGAATCATCCGGCCAACGGCGTGGCGTG
-GCTGGCGAACAAGCTTGCCCCCTACGATGTCCAGCTTGAAGCCGGGCAGATCATCCTCGG
-CGGCTCGTTCACCCGCCCGGTGCCGGCGAGCAAGGGCGACACCTTCCATGTCGATTACGG
-CAACATGGGCGCGATCAGTTGCCGGTTTGTGTAACCAGATCCGCGCGCGCATATATATCG
-CGCGCATACGATGCCCGTGAATAAGTTCTCCCGACGTACCCTCCTGACGGCAGGTTCCGC
-GCTTGCTGTTCTTCCTTTTCTGCGCGCCTTGCCGGTACAGGCGCGTGAACCTCGCGAGAC
-CGTCGATATTAAGGATTATCCGGCGGATGACGGTATCGCCTCGTTCAAACAGGCCTTCGC
-CGACGGACAGACCGTGGTCTTACCGCCAGGATGGGTGTGTGAAAATATCAATGCGGCGAT
-AACGATTCCGGCGGGAAAAACGCTGCGGGTACAGGGCGCGGTGCGTGGGAATGGCCGGGG
-ACGGTTTATTTTGCAGGACGGGTGTCAGGTGGTGGGGGAGCAGGGCGGCAGTCTGCACAA
-TGTGACGCTGGATGTTCGCGGGTCGGACTGTGTGATTAAAGGCGTGACGATGAGCGGCTT
-TGGCCCCGTCGCGCAAATTTTCATCGGCGGTAAGGAACCGCAGGTGATGCGTAATCTCAT
-TATCGATGACATCACCGTTACCCACGCCAACTACGCCATTCTCCGCCAGGGATTTCATAA
-CCAAATGGACGGCGCGCGGATTACGCATAGCCGCTTTAGCGATTTGCAGGGGGACGCCAT
-TGAGTGGAATGTCGCGATTCACGACCGCGACATCCTGATTTCCGATCATGTCATCGAACG
-CATTGATTGTACCAATGGCAAAATCAACTGGGGGATCGGCATCGGGCTGGCGGGTAGCAC
-CTATGACAACAGTTATCCTGAAGATCAGGCAGTAAAAAACTTTGTGGTGGCCAATATTAC
-CGGATCTGATTGCCGACAGCTGGTGCACGTAGAAAATGGCAAACATTTCGTCATTCGCAA
-TGTCAAAGCCAAAAACATCACGCCCGATTTCAGTAAAAATGCGGGTATTGATAACGCAAC
-GATCGCCATTTATGGCTGTGATAATTTCGTCATTGATAATATTGATATGACGAATAGTGC
-TGGGATGCTCATCGGCTATGGCGTCGTTAAAGGAAAATACCTGTCAATTCCGCAAAACTT
-TAAATTAAACGCTATTCGGTTGGATAATCGCCAGGTTGCTTATAAATTACGCGGCATTCA
-AATTTCCTCCGGCAACATCCCCTCTTTTGTCGCCATCACCAATGTACGGATGACGCGTGC
-TACGCTGGAACTGCATAATCAACCGCAGCACCTCTTTCTGCGTAATATCAACGTGATGCA
-AACTTCAGCGATTGGCCCGGCGTTAAAAATGCATTTCGATTTGCGTAAAGATGTCCGTGG
-TCAATTTATGGCCCGCCAGGACACGCTGCTTTCCCTCGCTAATGTTCATGCCATCAATGA
-AAACGGGCAGAGTTCCGTGGATATCGACAGGATTAATCACCAAACCGTGAATGTCGAAGC
-AGTGAATTTTTCGCTGCCGAAGCGGGGAGGGTAACAGAGCTCGCGCGATCGCGAATGTCA
-GAAAATAAATTACACGTTATCGATTTGCACAAACGCTACGGCGGTCATGAAGTGCTGAAA
-GGGGTATCGTTGCAGGCCCGCGCCGGAGATGTGATTAGCATCATCGGCTCGTCCGGCTCC
-GGTAAAAGCACTTTTTTGCGCTGTATTAACTTCCTCGAAAAACCGAGCGAAGGCGCGATT
-ATCGTGAACGGTCAGAACATTAATCTGGTGCGCGACAAAGACGGGCAGCTCAAAGTGGCG
-GATAAAAATCAGCTACGCTTGTTGCGTACCCGCCTGACGATGGTGTTTCAGCACTTTAAC
-CTCTGGAGCCACATGACGGTGCTGGAAAATGTGATGGAAGCGCCGATTCAGGTACTGGGA
-TTAAGCAAGCACGACGCGCGCGAGCGGGCGTTGAAATATCTGGCGAAGGTGGGGATTGAT
-GAGCGCGCTCAGGGCAAATATCCCGTCCATCTCTCCGGCGGCCAACAGCAGCGCGTTTCT
-ATTGCGCGCGCGCTGGCGATGGAACCTGACGTTTTACTGTTCGATGAACCCACATCGGCG
-CTCGATCCTGAACTGGTCGGCGAAGTGTTGCGCATCATGCAACAACTGGCGGAAGAAGGC
-AAAACGATGGTGGTGGTCACGCATGAAATGGGCTTCGCCCGCCATGTCTCTTCGCACGTT
-ATTTTTCTGCATCAGGGGAAAATTGAAGAAGAGGGCGATCCGGAGCAGGTGTTCGGCAAT
-CCGCAAAGCCCGCGTTTACAGCAATTCCTGAAAGGCTCGCTGAAATAACAGATACGCGCA
-TGGCGAGTGTTTATTGGCATCGTTAGCCTGTTTCCTGAAATGTTCCGCGCAATTACCGAT
-TACGGGGTAACTGGCCGGGCAGTAAAAAAAGGCCTGCTGAACATCCAAAGCTGGAGTCCT
-CGCGACTTCGCGCATGACCGGCACCGTACCGTGGACGACCGTCCTTACGGCGGCGGACCG
-GGGATGTTAATGATGGTGCAACCCTTGCGGGACGCCATTCACGCAGCAAAAGCCGCGGCA
-GGTGAAGGCGCTAAAGTGATTTATCTGTCGCCTCAGGGACGCAAGCTTGATCAAGCGGGC
-GTTAGCGAGCTGGCCACGAATCAGAAGCTTATTCTGGTGTGTGGTCGCTACGAAGGCGTA
-GATGAGCGCGTAATTCAGACCGAAATTGACGAAGAATGGTCAATTGGCGATTACGTTCTC
-AGCGGTGGCGAACTACCGGCAATGACGCTGATTGACTCCGTCGCCCGGTTTATACCGGGG
-GTTCTGGGGCATGAGGCATCAGCAATCGAAGATTCGTTTGCTGATGGGTTGCTGGATTGT
-CCGCACTATACGCGCCCTGAAGTGTTAGAGGGGATGGAAGTACCGCCAGTATTGCTGTCG
-GGAAACCATGCCGAGATACGTCGCTGGCGCTTGAAACAGTCGCTGGGCCGAACCTGGCTT
-AGAAGACCTGAACTTCTGGAAAACCTGGCTCTGACTGAAGAGCAAGCAAGGTTGCTGGCG
-GAGTTCAAAACAGAACACGCACAACAGCAGCATAAACATGATGGGATGGCATAGCGATAG
-CGCTAGAGCGATGAATAATCATTTTGGGAAAGGGTTAATGGCTGGGTTGCACGCGCCATA
-TGCATATAGCGCGCATCATGCGGTGAATTTCTGTTCTGAGTATAAACGTGGCTTTGTATT
-GGGTTTTACACACCGTATGTTCGAAAAGACCGGCGATCGTCAACTTAGCGCGTGGGAGGC
-CGGAATTCTGACGCGTCGCTATGGTCTGGATAAAGAAATGGTGATGGATTTCTTTAAAGA
-GAATCATTCCGGGATGGCGGTTCGCTTCTTTATGGTCGGTTATCGACTCGAAGGTTGACA
-GATGCGCGATCGATGTCTACGCTTCTCTATTTGCACGGATTCAACAGTTCCCCTCGCTCG
-GCAAAAGCGTGCCAGCTAAAAAACTGGCTGGCGGAGCGTCATCCGCATGTCGAGATGATC
-GTCCCTCAACTACCGCCGTATCCTGCCGATGCGGCGGAGTTGCTGGAATCTCTCGTGCTT
-GAGCATGGCGGTGCGCCATTAGGGCTGGTAGGATCGTCGCTGGGTGGTTATTACGCCACC
-TGGCTGTCGCAATGTTTTATGCTGCCGGCTGTGGTGGTGAATCCCGCCGTGCGGCCCTTT
-GAATTACTGACCGACTATCTCGGTCAGAACGAGAACCCCTACACCGGGCAGCAATATGTG
-CTAGAGTCTCGCCATATTTATGATCTTAAAGTCATGCAGATTGACCCGCTGGAAGCGCCG
-GACCTGATCTGGCTACTGCAACAGACGGGCGATGAAGTGCTGGATTACCGCCAGGCGGTG
-GCATATTACGCCTCCTGCCGTCAGACAGTGACCGAGGGTGGTAATCACGCATTCACGGGC
-TTCGAAGATTATTTCAACCAGATTGTCGATTTTCTTGGACTGCACAGTTGCTGACACGGA
-TGCGCCATCGGCTTGCTGGCCGTGCCGTTCTTCGTTTTGTCCGGGGTGATCATGAATAGC
-GGGGGAATTGCCGCCCGGCTGGTCAATTTTGCCAAACTGTTTACTGGCAAACTGCCCGGC
-TCGCTCTCTTATACCAACATCGTCGGCAATATGATGTTCGGTGCAATTTCCGGATCGGCA
-ATTGCCGCCTCAACCTCCATCGGCGGCGTGATGGTGCCGATGAGCGCGCGCGAAGGTTAC
-GATCGCGGCTTTGCGGCCGCGGTGAATATCGCCTCCGCGCCGACGGGAATGTTAATTCCG
-CCCACCACGGCTTTTATCCTTTATGCGCTGGCAAGCGGGGGAACATCGATTGCCGCTCTG
-TTCGCCGGCGGTCTGGTCGCGGGAGTGCTGTGGGGCGTTGGCTGTATGCTGGTCACGCTG
-GTGGTCGCTAAGCGTCGAAATTATCGGGTTTTCTTCACCGTCCAAAAAGGCATGGCGCTA
-AAAGTTGCCGTTGAGGCCATTCCCAGCCTGCTGCTGATCGTGATTATCGTCGGCGGCATT
-GTGCAGGGGATTTTCACCGCCATTGAAGCCTCCGCGATTGCCGTGGTGTATACATTATTG
-TTGACGATGGTGTTTTACCGCACGCTGAAAATTAAGGATTTGCCTTCGATTTTGCTCCAG
-ACAGTGGTAATGACCGGGGTCATCATGTTCCTGCTGGCAACCTCTTCGGCGATGTCCTTC
-TCGATGTCGATCACCAATATTCCTGCGGCGCTGAGCGATATGATCCTCGGTATTTCCGCC
-AATAAACTGGTTATCCTGTTAGTCATTACCGTCTTTTTGTTGATTATCGGCGCATTTATG
-GATATCGGTCCGGCCATTCTGATTTTTACCCCGATTCTGCTGCCGATCATGGCTAAACTG
-GGCGTCGATCCGGTGCATTTTGGCATTATCATGATCTATAACCTGGCGATTGGCACCATT
-ACGCCGCCAGTTGGCAGTGGTTTATATGTCGGGGCGAGCGTCGGTAAGGTCAAAGTTGAG
-GAAGTGATTAAACCGTTGCTGCCTTTTTACGGCGCGATTATCGGCGTTCTGTTATTAATT
-ACCTACATTCCGGAAATCACACTGTTCTTACCCCGTCTACTGGGCATCATGTAA
diff --git a/Examples/2-res-Annotate-prokka/tmp_files/genome4.fst_prokka-split5N.fna-prokkaRes/GEN4.1111.00001.gbk b/Examples/2-res-Annotate-prokka/tmp_files/genome4.fst_prokka-split5N.fna-prokkaRes/GEN4.1111.00001.gbk
deleted file mode 100644
index d7485db38ca5c2e6b57d755f2c8478c37a7aeb0e..0000000000000000000000000000000000000000
--- a/Examples/2-res-Annotate-prokka/tmp_files/genome4.fst_prokka-split5N.fna-prokkaRes/GEN4.1111.00001.gbk
+++ /dev/null
@@ -1,258 +0,0 @@
-LOCUS       g4_1                    7134 bp    DNA     linear       09-DEC-2019
-DEFINITION  Genus species strain strain.
-ACCESSION   
-VERSION
-KEYWORDS    .
-SOURCE      Genus species
-  ORGANISM  Genus species
-            Unclassified.
-COMMENT     Annotated using prokka 1.14.5 from
-            https://github.com/tseemann/prokka.
-FEATURES             Location/Qualifiers
-     source          1..7134
-                     /organism="Genus species"
-                     /mol_type="genomic DNA"
-                     /strain="strain"
-     CDS             1..831
-                     /gene="amiD"
-                     /locus_tag="LIKMDGFN_00001"
-                     /EC_number="3.5.1.28"
-                     /inference="ab initio prediction:Prodigal:002006"
-                     /inference="similar to AA sequence:UniProtKB:P75820"
-                     /codon_start=1
-                     /transl_table=11
-                     /product="N-acetylmuramoyl-L-alanine amidase AmiD"
-                     /db_xref="COG:COG3023"
-                     /translation="MKALLWLVGLALLLTGCASEKGIIDKEGYQLDTRHRAQAAYPRI
-                     KVLVIHYTAENFDVSLATLTGRNVSSHYLIPATPPLYGGKPRIWQLVPEQDQAWHAGV
-                     SFWRGATRLNDTSIGIELENRGWRMSGGVKSFAPFESAQIQALIPLAKDIIARYDIKP
-                     QNVVAHADIAPQRKDDPGPRFPWRELAAQGIGAWPDAQRVAFYLAGRAPYTPVDTATV
-                     LALLSRYGYEVKADMTAREQQRVIMAFQMHFRPAQWNGIADAETQAIAEALLEKYGQD
-                     "
-     CDS             861..1241
-                     /gene="hpcD"
-                     /locus_tag="LIKMDGFN_00002"
-                     /EC_number="5.3.3.10"
-                     /inference="ab initio prediction:Prodigal:002006"
-                     /inference="similar to AA sequence:UniProtKB:Q05354"
-                     /codon_start=1
-                     /transl_table=11
-                     /product="5-carboxymethyl-2-hydroxymuconate
-                     Delta-isomerase"
-                     /translation="MPHFIAECTENIREQADLPGLFSKVNEALAASGIFPIGGIRSRA
-                     HWLDTWQMADGKHDYAFVHMTLKIGTGRSLESRQEVGEMLFGLIKAHFADLMENRYLA
-                     LSFEIAELHPTLNYKQNNVHALFK"
-     CDS             1271..2074
-                     /gene="hpcG"
-                     /locus_tag="LIKMDGFN_00003"
-                     /EC_number="4.2.1.163"
-                     /inference="ab initio prediction:Prodigal:002006"
-                     /inference="similar to AA sequence:UniProtKB:P42270"
-                     /codon_start=1
-                     /transl_table=11
-                     /product="2-oxo-hept-4-ene-1,7-dioate hydratase"
-                     /translation="MLDKQTHTLIAQRLNQAEKQREQIRAVSLDYPNITIEDAYAVQR
-                     EWVNIKIAEGRTLKGHKIGLTSKAMQASSQISEPDYGALLDDMFFHDGGDIPTDRFIV
-                     PRIEVELAFVLAKPLRGPHCTLFDVYNATDYVIPALELIDARSHNIDPETQRPRKVFD
-                     TISDNAANAGVILGGRPIKPDELDLRWISALLYRNGVIEETGVAAGVLNHPANGVAWL
-                     ANKLAPYDVQLEAGQIILGGSFTRPVPASKGDTFHVDYGNMGAISCRFV"
-     CDS             2111..3514
-                     /locus_tag="LIKMDGFN_00004"
-                     /inference="ab initio prediction:Prodigal:002006"
-                     /codon_start=1
-                     /transl_table=11
-                     /product="hypothetical protein"
-                     /translation="MPVNKFSRRTLLTAGSALAVLPFLRALPVQAREPRETVDIKDYP
-                     ADDGIASFKQAFADGQTVVLPPGWVCENINAAITIPAGKTLRVQGAVRGNGRGRFILQ
-                     DGCQVVGEQGGSLHNVTLDVRGSDCVIKGVTMSGFGPVAQIFIGGKEPQVMRNLIIDD
-                     ITVTHANYAILRQGFHNQMDGARITHSRFSDLQGDAIEWNVAIHDRDILISDHVIERI
-                     DCTNGKINWGIGIGLAGSTYDNSYPEDQAVKNFVVANITGSDCRQLVHVENGKHFVIR
-                     NVKAKNITPDFSKNAGIDNATIAIYGCDNFVIDNIDMTNSAGMLIGYGVVKGKYLSIP
-                     QNFKLNAIRLDNRQVAYKLRGIQISSGNIPSFVAITNVRMTRATLELHNQPQHLFLRN
-                     INVMQTSAIGPALKMHFDLRKDVRGQFMARQDTLLSLANVHAINENGQSSVDIDRINH
-                     QTVNVEAVNFSLPKRGG"
-     CDS             3535..4308
-                     /gene="hisP"
-                     /locus_tag="LIKMDGFN_00005"
-                     /inference="ab initio prediction:Prodigal:002006"
-                     /inference="similar to AA sequence:UniProtKB:P02915"
-                     /codon_start=1
-                     /transl_table=11
-                     /product="Histidine transport ATP-binding protein HisP"
-                     /db_xref="COG:COG4598"
-                     /translation="MSENKLHVIDLHKRYGGHEVLKGVSLQARAGDVISIIGSSGSGK
-                     STFLRCINFLEKPSEGAIIVNGQNINLVRDKDGQLKVADKNQLRLLRTRLTMVFQHFN
-                     LWSHMTVLENVMEAPIQVLGLSKHDARERALKYLAKVGIDERAQGKYPVHLSGGQQQR
-                     VSIARALAMEPDVLLFDEPTSALDPELVGEVLRIMQQLAEEGKTMVVVTHEMGFARHV
-                     SSHVIFLHQGKIEEEGDPEQVFGNPQSPRLQQFLKGSLK"
-     CDS             4327..5094
-                     /gene="trmD"
-                     /locus_tag="LIKMDGFN_00006"
-                     /EC_number="2.1.1.228"
-                     /inference="ab initio prediction:Prodigal:002006"
-                     /inference="similar to AA sequence:UniProtKB:P0A873"
-                     /codon_start=1
-                     /transl_table=11
-                     /product="tRNA (guanine-N(1)-)-methyltransferase"
-                     /db_xref="COG:COG0336"
-                     /translation="MFIGIVSLFPEMFRAITDYGVTGRAVKKGLLNIQSWSPRDFAHD
-                     RHRTVDDRPYGGGPGMLMMVQPLRDAIHAAKAAAGEGAKVIYLSPQGRKLDQAGVSEL
-                     ATNQKLILVCGRYEGVDERVIQTEIDEEWSIGDYVLSGGELPAMTLIDSVARFIPGVL
-                     GHEASAIEDSFADGLLDCPHYTRPEVLEGMEVPPVLLSGNHAEIRRWRLKQSLGRTWL
-                     RRPELLENLALTEEQARLLAEFKTEHAQQQHKHDGMA"
-     CDS             5138..5398
-                     /locus_tag="LIKMDGFN_00007"
-                     /inference="ab initio prediction:Prodigal:002006"
-                     /codon_start=1
-                     /transl_table=11
-                     /product="hypothetical protein"
-                     /translation="MAGLHAPYAYSAHHAVNFCSEYKRGFVLGFTHRMFEKTGDRQLS
-                     AWEAGILTRRYGLDKEMVMDFFKENHSGMAVRFFMVGYRLEG"
-     CDS             5413..5994
-                     /locus_tag="LIKMDGFN_00008"
-                     /inference="ab initio prediction:Prodigal:002006"
-                     /codon_start=1
-                     /transl_table=11
-                     /product="hypothetical protein"
-                     /translation="MSTLLYLHGFNSSPRSAKACQLKNWLAERHPHVEMIVPQLPPYP
-                     ADAAELLESLVLEHGGAPLGLVGSSLGGYYATWLSQCFMLPAVVVNPAVRPFELLTDY
-                     LGQNENPYTGQQYVLESRHIYDLKVMQIDPLEAPDLIWLLQQTGDEVLDYRQAVAYYA
-                     SCRQTVTEGGNHAFTGFEDYFNQIVDFLGLHSC"
-     CDS             6052..7134
-                     /gene="dctM"
-                     /locus_tag="LIKMDGFN_00009"
-                     /inference="ab initio prediction:Prodigal:002006"
-                     /inference="similar to AA sequence:UniProtKB:O07838"
-                     /codon_start=1
-                     /transl_table=11
-                     /product="C4-dicarboxylate TRAP transporter large permease
-                     protein DctM"
-                     /db_xref="COG:COG1593"
-                     /translation="MNSGGIAARLVNFAKLFTGKLPGSLSYTNIVGNMMFGAISGSAI
-                     AASTSIGGVMVPMSAREGYDRGFAAAVNIASAPTGMLIPPTTAFILYALASGGTSIAA
-                     LFAGGLVAGVLWGVGCMLVTLVVAKRRNYRVFFTVQKGMALKVAVEAIPSLLLIVIIV
-                     GGIVQGIFTAIEASAIAVVYTLLLTMVFYRTLKIKDLPSILLQTVVMTGVIMFLLATS
-                     SAMSFSMSITNIPAALSDMILGISANKLVILLVITVFLLIIGAFMDIGPAILIFTPIL
-                     LPIMAKLGVDPVHFGIIMIYNLAIGTITPPVGSGLYVGASVGKVKVEEVIKPLLPFYG
-                     AIIGVLLLITYIPEITLFLPRLLGIM"
-ORIGIN      
-        1 atgaaagcgc tactgtggct ggtgggtctc gcgttgctgt taacaggctg cgcgagcgaa
-       61 aaaggaatta tcgataaaga gggatatcag cttgataccc gacatcgggc gcaggcggcc
-      121 tatccgcgca ttaaagtcct ggtgattcac tatacggcgg aaaactttga cgtttcgctg
-      181 gcgacgttaa cgggccgcaa cgtcagttcg cattacctga ttcccgcaac cccgccatta
-      241 tatggcggta aaccgcgcat ctggcaactg gtgccggaac aggatcaggc ctggcatgcg
-      301 ggcgtcagtt tctggcgagg cgccacgcgt ctcaatgata cgtctattgg cattgagctg
-      361 gaaaatcgcg gctggcgaat gtccggcggg gtgaaatctt tcgcgccgtt tgaatccgcg
-      421 caaattcagg cattgattcc gttagcgaag gacattatcg cgcgctatga catcaaaccg
-      481 cagaatgtgg tggcccatgc ggatatcgcg ccgcagcgta aagacgatcc cggcccgcgc
-      541 ttcccgtggc gcgagctggc ggcgcagggg attggcgcct ggcctgacgc ccagcgtgtg
-      601 gcgttttatc tggctggacg cgcgccgtat acgccagtcg ataccgcaac ggtgcttgcg
-      661 ttactctcgc gctatggcta tgaagtcaaa gccgatatga cggcgcgcga gcagcagcgg
-      721 gtgattatgg cgttccagat gcacttccgt ccggcgcaat ggaacggtat cgcagatgcc
-      781 gaaacgcagg cgattgccga agcattactg gagaagtacg gccaggatta acgcgatcgc
-      841 gcgcatatcg cgcgcgatag atgccgcact ttattgctga atgtactgaa aatattcgcg
-      901 agcaggctga tttacccggc ctgttcagca aggtaaacga ggcgctggcc gccagcggga
-      961 ttttccccat cggcggtatc cgcagtcgcg cccactggct ggatacctgg cagatggctg
-     1021 acggtaagca tgattatgcg tttgtgcata tgacgctgaa aatcggtacc gggcgcagcc
-     1081 tggagagccg tcaggaagtc ggcgaaatgc tgtttgggct gattaaagcc cacttcgccg
-     1141 acctgatgga gaaccgctat ctggcgctgt cgtttgagat tgccgagcta catccgacgc
-     1201 tcaattacaa acaaaacaac gtacacgcgt tatttaaata gccgcatatg cggcgctcag
-     1261 gagcgctagc atgctcgata aacagaccca taccctgatc gcccagcgac ttaatcaggc
-     1321 tgaaaaacag cgtgaacaaa ttcgcgcagt gtcgctggat tatcccaaca tcactattga
-     1381 agatgcctat gccgtacagc gtgaatgggt caatatcaag atcgccgaag ggcgcacgct
-     1441 caaaggccac aaaatcggcc tgacctcaaa agcgatgcag gccagctcgc aaatcagcga
-     1501 accggattac ggcgcgctgc ttgacgatat gttcttccat gacggcggcg atatccccac
-     1561 cgaccgtttt atcgtcccgc gtattgaagt ggagctggcg ttcgtgctgg cgaaaccgct
-     1621 gcgcggccct cactgcacgc tgttcgacgt ctacaacgcc acggattatg tgattccggc
-     1681 gctggaactg attgacgccc gcagccacaa catcgacccg gaaacccagc gcccgcgcaa
-     1741 agtgttcgac accatttccg acaacgccgc caacgccggg gtgatcctcg gtggtcgccc
-     1801 catcaaacca gacgagctgg atctgcgctg gatctccgcg ctgctctatc gcaacggcgt
-     1861 gatcgaagaa accggcgtcg ccgcaggcgt gctgaatcat ccggccaacg gcgtggcgtg
-     1921 gctggcgaac aagcttgccc cctacgatgt ccagcttgaa gccgggcaga tcatcctcgg
-     1981 cggctcgttc acccgcccgg tgccggcgag caagggcgac accttccatg tcgattacgg
-     2041 caacatgggc gcgatcagtt gccggtttgt gtaaccagat ccgcgcgcgc atatatatcg
-     2101 cgcgcatacg atgcccgtga ataagttctc ccgacgtacc ctcctgacgg caggttccgc
-     2161 gcttgctgtt cttccttttc tgcgcgcctt gccggtacag gcgcgtgaac ctcgcgagac
-     2221 cgtcgatatt aaggattatc cggcggatga cggtatcgcc tcgttcaaac aggccttcgc
-     2281 cgacggacag accgtggtct taccgccagg atgggtgtgt gaaaatatca atgcggcgat
-     2341 aacgattccg gcgggaaaaa cgctgcgggt acagggcgcg gtgcgtggga atggccgggg
-     2401 acggtttatt ttgcaggacg ggtgtcaggt ggtgggggag cagggcggca gtctgcacaa
-     2461 tgtgacgctg gatgttcgcg ggtcggactg tgtgattaaa ggcgtgacga tgagcggctt
-     2521 tggccccgtc gcgcaaattt tcatcggcgg taaggaaccg caggtgatgc gtaatctcat
-     2581 tatcgatgac atcaccgtta cccacgccaa ctacgccatt ctccgccagg gatttcataa
-     2641 ccaaatggac ggcgcgcgga ttacgcatag ccgctttagc gatttgcagg gggacgccat
-     2701 tgagtggaat gtcgcgattc acgaccgcga catcctgatt tccgatcatg tcatcgaacg
-     2761 cattgattgt accaatggca aaatcaactg ggggatcggc atcgggctgg cgggtagcac
-     2821 ctatgacaac agttatcctg aagatcaggc agtaaaaaac tttgtggtgg ccaatattac
-     2881 cggatctgat tgccgacagc tggtgcacgt agaaaatggc aaacatttcg tcattcgcaa
-     2941 tgtcaaagcc aaaaacatca cgcccgattt cagtaaaaat gcgggtattg ataacgcaac
-     3001 gatcgccatt tatggctgtg ataatttcgt cattgataat attgatatga cgaatagtgc
-     3061 tgggatgctc atcggctatg gcgtcgttaa aggaaaatac ctgtcaattc cgcaaaactt
-     3121 taaattaaac gctattcggt tggataatcg ccaggttgct tataaattac gcggcattca
-     3181 aatttcctcc ggcaacatcc cctcttttgt cgccatcacc aatgtacgga tgacgcgtgc
-     3241 tacgctggaa ctgcataatc aaccgcagca cctctttctg cgtaatatca acgtgatgca
-     3301 aacttcagcg attggcccgg cgttaaaaat gcatttcgat ttgcgtaaag atgtccgtgg
-     3361 tcaatttatg gcccgccagg acacgctgct ttccctcgct aatgttcatg ccatcaatga
-     3421 aaacgggcag agttccgtgg atatcgacag gattaatcac caaaccgtga atgtcgaagc
-     3481 agtgaatttt tcgctgccga agcggggagg gtaacagagc tcgcgcgatc gcgaatgtca
-     3541 gaaaataaat tacacgttat cgatttgcac aaacgctacg gcggtcatga agtgctgaaa
-     3601 ggggtatcgt tgcaggcccg cgccggagat gtgattagca tcatcggctc gtccggctcc
-     3661 ggtaaaagca cttttttgcg ctgtattaac ttcctcgaaa aaccgagcga aggcgcgatt
-     3721 atcgtgaacg gtcagaacat taatctggtg cgcgacaaag acgggcagct caaagtggcg
-     3781 gataaaaatc agctacgctt gttgcgtacc cgcctgacga tggtgtttca gcactttaac
-     3841 ctctggagcc acatgacggt gctggaaaat gtgatggaag cgccgattca ggtactggga
-     3901 ttaagcaagc acgacgcgcg cgagcgggcg ttgaaatatc tggcgaaggt ggggattgat
-     3961 gagcgcgctc agggcaaata tcccgtccat ctctccggcg gccaacagca gcgcgtttct
-     4021 attgcgcgcg cgctggcgat ggaacctgac gttttactgt tcgatgaacc cacatcggcg
-     4081 ctcgatcctg aactggtcgg cgaagtgttg cgcatcatgc aacaactggc ggaagaaggc
-     4141 aaaacgatgg tggtggtcac gcatgaaatg ggcttcgccc gccatgtctc ttcgcacgtt
-     4201 atttttctgc atcaggggaa aattgaagaa gagggcgatc cggagcaggt gttcggcaat
-     4261 ccgcaaagcc cgcgtttaca gcaattcctg aaaggctcgc tgaaataaca gatacgcgca
-     4321 tggcgagtgt ttattggcat cgttagcctg tttcctgaaa tgttccgcgc aattaccgat
-     4381 tacggggtaa ctggccgggc agtaaaaaaa ggcctgctga acatccaaag ctggagtcct
-     4441 cgcgacttcg cgcatgaccg gcaccgtacc gtggacgacc gtccttacgg cggcggaccg
-     4501 gggatgttaa tgatggtgca acccttgcgg gacgccattc acgcagcaaa agccgcggca
-     4561 ggtgaaggcg ctaaagtgat ttatctgtcg cctcagggac gcaagcttga tcaagcgggc
-     4621 gttagcgagc tggccacgaa tcagaagctt attctggtgt gtggtcgcta cgaaggcgta
-     4681 gatgagcgcg taattcagac cgaaattgac gaagaatggt caattggcga ttacgttctc
-     4741 agcggtggcg aactaccggc aatgacgctg attgactccg tcgcccggtt tataccgggg
-     4801 gttctggggc atgaggcatc agcaatcgaa gattcgtttg ctgatgggtt gctggattgt
-     4861 ccgcactata cgcgccctga agtgttagag gggatggaag taccgccagt attgctgtcg
-     4921 ggaaaccatg ccgagatacg tcgctggcgc ttgaaacagt cgctgggccg aacctggctt
-     4981 agaagacctg aacttctgga aaacctggct ctgactgaag agcaagcaag gttgctggcg
-     5041 gagttcaaaa cagaacacgc acaacagcag cataaacatg atgggatggc atagcgatag
-     5101 cgctagagcg atgaataatc attttgggaa agggttaatg gctgggttgc acgcgccata
-     5161 tgcatatagc gcgcatcatg cggtgaattt ctgttctgag tataaacgtg gctttgtatt
-     5221 gggttttaca caccgtatgt tcgaaaagac cggcgatcgt caacttagcg cgtgggaggc
-     5281 cggaattctg acgcgtcgct atggtctgga taaagaaatg gtgatggatt tctttaaaga
-     5341 gaatcattcc gggatggcgg ttcgcttctt tatggtcggt tatcgactcg aaggttgaca
-     5401 gatgcgcgat cgatgtctac gcttctctat ttgcacggat tcaacagttc ccctcgctcg
-     5461 gcaaaagcgt gccagctaaa aaactggctg gcggagcgtc atccgcatgt cgagatgatc
-     5521 gtccctcaac taccgccgta tcctgccgat gcggcggagt tgctggaatc tctcgtgctt
-     5581 gagcatggcg gtgcgccatt agggctggta ggatcgtcgc tgggtggtta ttacgccacc
-     5641 tggctgtcgc aatgttttat gctgccggct gtggtggtga atcccgccgt gcggcccttt
-     5701 gaattactga ccgactatct cggtcagaac gagaacccct acaccgggca gcaatatgtg
-     5761 ctagagtctc gccatattta tgatcttaaa gtcatgcaga ttgacccgct ggaagcgccg
-     5821 gacctgatct ggctactgca acagacgggc gatgaagtgc tggattaccg ccaggcggtg
-     5881 gcatattacg cctcctgccg tcagacagtg accgagggtg gtaatcacgc attcacgggc
-     5941 ttcgaagatt atttcaacca gattgtcgat tttcttggac tgcacagttg ctgacacgga
-     6001 tgcgccatcg gcttgctggc cgtgccgttc ttcgttttgt ccggggtgat catgaatagc
-     6061 gggggaattg ccgcccggct ggtcaatttt gccaaactgt ttactggcaa actgcccggc
-     6121 tcgctctctt ataccaacat cgtcggcaat atgatgttcg gtgcaatttc cggatcggca
-     6181 attgccgcct caacctccat cggcggcgtg atggtgccga tgagcgcgcg cgaaggttac
-     6241 gatcgcggct ttgcggccgc ggtgaatatc gcctccgcgc cgacgggaat gttaattccg
-     6301 cccaccacgg cttttatcct ttatgcgctg gcaagcgggg gaacatcgat tgccgctctg
-     6361 ttcgccggcg gtctggtcgc gggagtgctg tggggcgttg gctgtatgct ggtcacgctg
-     6421 gtggtcgcta agcgtcgaaa ttatcgggtt ttcttcaccg tccaaaaagg catggcgcta
-     6481 aaagttgccg ttgaggccat tcccagcctg ctgctgatcg tgattatcgt cggcggcatt
-     6541 gtgcagggga ttttcaccgc cattgaagcc tccgcgattg ccgtggtgta tacattattg
-     6601 ttgacgatgg tgttttaccg cacgctgaaa attaaggatt tgccttcgat tttgctccag
-     6661 acagtggtaa tgaccggggt catcatgttc ctgctggcaa cctcttcggc gatgtccttc
-     6721 tcgatgtcga tcaccaatat tcctgcggcg ctgagcgata tgatcctcgg tatttccgcc
-     6781 aataaactgg ttatcctgtt agtcattacc gtctttttgt tgattatcgg cgcatttatg
-     6841 gatatcggtc cggccattct gatttttacc ccgattctgc tgccgatcat ggctaaactg
-     6901 ggcgtcgatc cggtgcattt tggcattatc atgatctata acctggcgat tggcaccatt
-     6961 acgccgccag ttggcagtgg tttatatgtc ggggcgagcg tcggtaaggt caaagttgag
-     7021 gaagtgatta aaccgttgct gcctttttac ggcgcgatta tcggcgttct gttattaatt
-     7081 acctacattc cggaaatcac actgttctta ccccgtctac tgggcatcat gtaa
-//
diff --git a/Examples/2-res-Annotate-prokka/tmp_files/genome4.fst_prokka-split5N.fna-prokkaRes/GEN4.1111.00001.gff b/Examples/2-res-Annotate-prokka/tmp_files/genome4.fst_prokka-split5N.fna-prokkaRes/GEN4.1111.00001.gff
deleted file mode 100644
index 6f71f6c023ba16fb891308dbbfef887e88223811..0000000000000000000000000000000000000000
--- a/Examples/2-res-Annotate-prokka/tmp_files/genome4.fst_prokka-split5N.fna-prokkaRes/GEN4.1111.00001.gff
+++ /dev/null
@@ -1,132 +0,0 @@
-##gff-version 3
-##sequence-region g4_1 1 7134
-g4_1	Prodigal:002006	CDS	1	831	.	+	0	ID=LIKMDGFN_00001;eC_number=3.5.1.28;Name=amiD;db_xref=COG:COG3023;gene=amiD;inference=ab initio prediction:Prodigal:002006,similar to AA sequence:UniProtKB:P75820;locus_tag=LIKMDGFN_00001;product=N-acetylmuramoyl-L-alanine amidase AmiD
-g4_1	Prodigal:002006	CDS	861	1241	.	+	0	ID=LIKMDGFN_00002;eC_number=5.3.3.10;Name=hpcD;gene=hpcD;inference=ab initio prediction:Prodigal:002006,similar to AA sequence:UniProtKB:Q05354;locus_tag=LIKMDGFN_00002;product=5-carboxymethyl-2-hydroxymuconate Delta-isomerase
-g4_1	Prodigal:002006	CDS	1271	2074	.	+	0	ID=LIKMDGFN_00003;eC_number=4.2.1.163;Name=hpcG;gene=hpcG;inference=ab initio prediction:Prodigal:002006,similar to AA sequence:UniProtKB:P42270;locus_tag=LIKMDGFN_00003;product=2-oxo-hept-4-ene-1%2C7-dioate hydratase
-g4_1	Prodigal:002006	CDS	2111	3514	.	+	0	ID=LIKMDGFN_00004;inference=ab initio prediction:Prodigal:002006;locus_tag=LIKMDGFN_00004;product=hypothetical protein
-g4_1	Prodigal:002006	CDS	3535	4308	.	+	0	ID=LIKMDGFN_00005;Name=hisP;db_xref=COG:COG4598;gene=hisP;inference=ab initio prediction:Prodigal:002006,similar to AA sequence:UniProtKB:P02915;locus_tag=LIKMDGFN_00005;product=Histidine transport ATP-binding protein HisP
-g4_1	Prodigal:002006	CDS	4327	5094	.	+	0	ID=LIKMDGFN_00006;eC_number=2.1.1.228;Name=trmD;db_xref=COG:COG0336;gene=trmD;inference=ab initio prediction:Prodigal:002006,similar to AA sequence:UniProtKB:P0A873;locus_tag=LIKMDGFN_00006;product=tRNA (guanine-N(1)-)-methyltransferase
-g4_1	Prodigal:002006	CDS	5138	5398	.	+	0	ID=LIKMDGFN_00007;inference=ab initio prediction:Prodigal:002006;locus_tag=LIKMDGFN_00007;product=hypothetical protein
-g4_1	Prodigal:002006	CDS	5413	5994	.	+	0	ID=LIKMDGFN_00008;inference=ab initio prediction:Prodigal:002006;locus_tag=LIKMDGFN_00008;product=hypothetical protein
-g4_1	Prodigal:002006	CDS	6052	7134	.	+	0	ID=LIKMDGFN_00009;Name=dctM;db_xref=COG:COG1593;gene=dctM;inference=ab initio prediction:Prodigal:002006,similar to AA sequence:UniProtKB:O07838;locus_tag=LIKMDGFN_00009;product=C4-dicarboxylate TRAP transporter large permease protein DctM
-##FASTA
->g4_1
-ATGAAAGCGCTACTGTGGCTGGTGGGTCTCGCGTTGCTGTTAACAGGCTGCGCGAGCGAA
-AAAGGAATTATCGATAAAGAGGGATATCAGCTTGATACCCGACATCGGGCGCAGGCGGCC
-TATCCGCGCATTAAAGTCCTGGTGATTCACTATACGGCGGAAAACTTTGACGTTTCGCTG
-GCGACGTTAACGGGCCGCAACGTCAGTTCGCATTACCTGATTCCCGCAACCCCGCCATTA
-TATGGCGGTAAACCGCGCATCTGGCAACTGGTGCCGGAACAGGATCAGGCCTGGCATGCG
-GGCGTCAGTTTCTGGCGAGGCGCCACGCGTCTCAATGATACGTCTATTGGCATTGAGCTG
-GAAAATCGCGGCTGGCGAATGTCCGGCGGGGTGAAATCTTTCGCGCCGTTTGAATCCGCG
-CAAATTCAGGCATTGATTCCGTTAGCGAAGGACATTATCGCGCGCTATGACATCAAACCG
-CAGAATGTGGTGGCCCATGCGGATATCGCGCCGCAGCGTAAAGACGATCCCGGCCCGCGC
-TTCCCGTGGCGCGAGCTGGCGGCGCAGGGGATTGGCGCCTGGCCTGACGCCCAGCGTGTG
-GCGTTTTATCTGGCTGGACGCGCGCCGTATACGCCAGTCGATACCGCAACGGTGCTTGCG
-TTACTCTCGCGCTATGGCTATGAAGTCAAAGCCGATATGACGGCGCGCGAGCAGCAGCGG
-GTGATTATGGCGTTCCAGATGCACTTCCGTCCGGCGCAATGGAACGGTATCGCAGATGCC
-GAAACGCAGGCGATTGCCGAAGCATTACTGGAGAAGTACGGCCAGGATTAACGCGATCGC
-GCGCATATCGCGCGCGATAGATGCCGCACTTTATTGCTGAATGTACTGAAAATATTCGCG
-AGCAGGCTGATTTACCCGGCCTGTTCAGCAAGGTAAACGAGGCGCTGGCCGCCAGCGGGA
-TTTTCCCCATCGGCGGTATCCGCAGTCGCGCCCACTGGCTGGATACCTGGCAGATGGCTG
-ACGGTAAGCATGATTATGCGTTTGTGCATATGACGCTGAAAATCGGTACCGGGCGCAGCC
-TGGAGAGCCGTCAGGAAGTCGGCGAAATGCTGTTTGGGCTGATTAAAGCCCACTTCGCCG
-ACCTGATGGAGAACCGCTATCTGGCGCTGTCGTTTGAGATTGCCGAGCTACATCCGACGC
-TCAATTACAAACAAAACAACGTACACGCGTTATTTAAATAGCCGCATATGCGGCGCTCAG
-GAGCGCTAGCATGCTCGATAAACAGACCCATACCCTGATCGCCCAGCGACTTAATCAGGC
-TGAAAAACAGCGTGAACAAATTCGCGCAGTGTCGCTGGATTATCCCAACATCACTATTGA
-AGATGCCTATGCCGTACAGCGTGAATGGGTCAATATCAAGATCGCCGAAGGGCGCACGCT
-CAAAGGCCACAAAATCGGCCTGACCTCAAAAGCGATGCAGGCCAGCTCGCAAATCAGCGA
-ACCGGATTACGGCGCGCTGCTTGACGATATGTTCTTCCATGACGGCGGCGATATCCCCAC
-CGACCGTTTTATCGTCCCGCGTATTGAAGTGGAGCTGGCGTTCGTGCTGGCGAAACCGCT
-GCGCGGCCCTCACTGCACGCTGTTCGACGTCTACAACGCCACGGATTATGTGATTCCGGC
-GCTGGAACTGATTGACGCCCGCAGCCACAACATCGACCCGGAAACCCAGCGCCCGCGCAA
-AGTGTTCGACACCATTTCCGACAACGCCGCCAACGCCGGGGTGATCCTCGGTGGTCGCCC
-CATCAAACCAGACGAGCTGGATCTGCGCTGGATCTCCGCGCTGCTCTATCGCAACGGCGT
-GATCGAAGAAACCGGCGTCGCCGCAGGCGTGCTGAATCATCCGGCCAACGGCGTGGCGTG
-GCTGGCGAACAAGCTTGCCCCCTACGATGTCCAGCTTGAAGCCGGGCAGATCATCCTCGG
-CGGCTCGTTCACCCGCCCGGTGCCGGCGAGCAAGGGCGACACCTTCCATGTCGATTACGG
-CAACATGGGCGCGATCAGTTGCCGGTTTGTGTAACCAGATCCGCGCGCGCATATATATCG
-CGCGCATACGATGCCCGTGAATAAGTTCTCCCGACGTACCCTCCTGACGGCAGGTTCCGC
-GCTTGCTGTTCTTCCTTTTCTGCGCGCCTTGCCGGTACAGGCGCGTGAACCTCGCGAGAC
-CGTCGATATTAAGGATTATCCGGCGGATGACGGTATCGCCTCGTTCAAACAGGCCTTCGC
-CGACGGACAGACCGTGGTCTTACCGCCAGGATGGGTGTGTGAAAATATCAATGCGGCGAT
-AACGATTCCGGCGGGAAAAACGCTGCGGGTACAGGGCGCGGTGCGTGGGAATGGCCGGGG
-ACGGTTTATTTTGCAGGACGGGTGTCAGGTGGTGGGGGAGCAGGGCGGCAGTCTGCACAA
-TGTGACGCTGGATGTTCGCGGGTCGGACTGTGTGATTAAAGGCGTGACGATGAGCGGCTT
-TGGCCCCGTCGCGCAAATTTTCATCGGCGGTAAGGAACCGCAGGTGATGCGTAATCTCAT
-TATCGATGACATCACCGTTACCCACGCCAACTACGCCATTCTCCGCCAGGGATTTCATAA
-CCAAATGGACGGCGCGCGGATTACGCATAGCCGCTTTAGCGATTTGCAGGGGGACGCCAT
-TGAGTGGAATGTCGCGATTCACGACCGCGACATCCTGATTTCCGATCATGTCATCGAACG
-CATTGATTGTACCAATGGCAAAATCAACTGGGGGATCGGCATCGGGCTGGCGGGTAGCAC
-CTATGACAACAGTTATCCTGAAGATCAGGCAGTAAAAAACTTTGTGGTGGCCAATATTAC
-CGGATCTGATTGCCGACAGCTGGTGCACGTAGAAAATGGCAAACATTTCGTCATTCGCAA
-TGTCAAAGCCAAAAACATCACGCCCGATTTCAGTAAAAATGCGGGTATTGATAACGCAAC
-GATCGCCATTTATGGCTGTGATAATTTCGTCATTGATAATATTGATATGACGAATAGTGC
-TGGGATGCTCATCGGCTATGGCGTCGTTAAAGGAAAATACCTGTCAATTCCGCAAAACTT
-TAAATTAAACGCTATTCGGTTGGATAATCGCCAGGTTGCTTATAAATTACGCGGCATTCA
-AATTTCCTCCGGCAACATCCCCTCTTTTGTCGCCATCACCAATGTACGGATGACGCGTGC
-TACGCTGGAACTGCATAATCAACCGCAGCACCTCTTTCTGCGTAATATCAACGTGATGCA
-AACTTCAGCGATTGGCCCGGCGTTAAAAATGCATTTCGATTTGCGTAAAGATGTCCGTGG
-TCAATTTATGGCCCGCCAGGACACGCTGCTTTCCCTCGCTAATGTTCATGCCATCAATGA
-AAACGGGCAGAGTTCCGTGGATATCGACAGGATTAATCACCAAACCGTGAATGTCGAAGC
-AGTGAATTTTTCGCTGCCGAAGCGGGGAGGGTAACAGAGCTCGCGCGATCGCGAATGTCA
-GAAAATAAATTACACGTTATCGATTTGCACAAACGCTACGGCGGTCATGAAGTGCTGAAA
-GGGGTATCGTTGCAGGCCCGCGCCGGAGATGTGATTAGCATCATCGGCTCGTCCGGCTCC
-GGTAAAAGCACTTTTTTGCGCTGTATTAACTTCCTCGAAAAACCGAGCGAAGGCGCGATT
-ATCGTGAACGGTCAGAACATTAATCTGGTGCGCGACAAAGACGGGCAGCTCAAAGTGGCG
-GATAAAAATCAGCTACGCTTGTTGCGTACCCGCCTGACGATGGTGTTTCAGCACTTTAAC
-CTCTGGAGCCACATGACGGTGCTGGAAAATGTGATGGAAGCGCCGATTCAGGTACTGGGA
-TTAAGCAAGCACGACGCGCGCGAGCGGGCGTTGAAATATCTGGCGAAGGTGGGGATTGAT
-GAGCGCGCTCAGGGCAAATATCCCGTCCATCTCTCCGGCGGCCAACAGCAGCGCGTTTCT
-ATTGCGCGCGCGCTGGCGATGGAACCTGACGTTTTACTGTTCGATGAACCCACATCGGCG
-CTCGATCCTGAACTGGTCGGCGAAGTGTTGCGCATCATGCAACAACTGGCGGAAGAAGGC
-AAAACGATGGTGGTGGTCACGCATGAAATGGGCTTCGCCCGCCATGTCTCTTCGCACGTT
-ATTTTTCTGCATCAGGGGAAAATTGAAGAAGAGGGCGATCCGGAGCAGGTGTTCGGCAAT
-CCGCAAAGCCCGCGTTTACAGCAATTCCTGAAAGGCTCGCTGAAATAACAGATACGCGCA
-TGGCGAGTGTTTATTGGCATCGTTAGCCTGTTTCCTGAAATGTTCCGCGCAATTACCGAT
-TACGGGGTAACTGGCCGGGCAGTAAAAAAAGGCCTGCTGAACATCCAAAGCTGGAGTCCT
-CGCGACTTCGCGCATGACCGGCACCGTACCGTGGACGACCGTCCTTACGGCGGCGGACCG
-GGGATGTTAATGATGGTGCAACCCTTGCGGGACGCCATTCACGCAGCAAAAGCCGCGGCA
-GGTGAAGGCGCTAAAGTGATTTATCTGTCGCCTCAGGGACGCAAGCTTGATCAAGCGGGC
-GTTAGCGAGCTGGCCACGAATCAGAAGCTTATTCTGGTGTGTGGTCGCTACGAAGGCGTA
-GATGAGCGCGTAATTCAGACCGAAATTGACGAAGAATGGTCAATTGGCGATTACGTTCTC
-AGCGGTGGCGAACTACCGGCAATGACGCTGATTGACTCCGTCGCCCGGTTTATACCGGGG
-GTTCTGGGGCATGAGGCATCAGCAATCGAAGATTCGTTTGCTGATGGGTTGCTGGATTGT
-CCGCACTATACGCGCCCTGAAGTGTTAGAGGGGATGGAAGTACCGCCAGTATTGCTGTCG
-GGAAACCATGCCGAGATACGTCGCTGGCGCTTGAAACAGTCGCTGGGCCGAACCTGGCTT
-AGAAGACCTGAACTTCTGGAAAACCTGGCTCTGACTGAAGAGCAAGCAAGGTTGCTGGCG
-GAGTTCAAAACAGAACACGCACAACAGCAGCATAAACATGATGGGATGGCATAGCGATAG
-CGCTAGAGCGATGAATAATCATTTTGGGAAAGGGTTAATGGCTGGGTTGCACGCGCCATA
-TGCATATAGCGCGCATCATGCGGTGAATTTCTGTTCTGAGTATAAACGTGGCTTTGTATT
-GGGTTTTACACACCGTATGTTCGAAAAGACCGGCGATCGTCAACTTAGCGCGTGGGAGGC
-CGGAATTCTGACGCGTCGCTATGGTCTGGATAAAGAAATGGTGATGGATTTCTTTAAAGA
-GAATCATTCCGGGATGGCGGTTCGCTTCTTTATGGTCGGTTATCGACTCGAAGGTTGACA
-GATGCGCGATCGATGTCTACGCTTCTCTATTTGCACGGATTCAACAGTTCCCCTCGCTCG
-GCAAAAGCGTGCCAGCTAAAAAACTGGCTGGCGGAGCGTCATCCGCATGTCGAGATGATC
-GTCCCTCAACTACCGCCGTATCCTGCCGATGCGGCGGAGTTGCTGGAATCTCTCGTGCTT
-GAGCATGGCGGTGCGCCATTAGGGCTGGTAGGATCGTCGCTGGGTGGTTATTACGCCACC
-TGGCTGTCGCAATGTTTTATGCTGCCGGCTGTGGTGGTGAATCCCGCCGTGCGGCCCTTT
-GAATTACTGACCGACTATCTCGGTCAGAACGAGAACCCCTACACCGGGCAGCAATATGTG
-CTAGAGTCTCGCCATATTTATGATCTTAAAGTCATGCAGATTGACCCGCTGGAAGCGCCG
-GACCTGATCTGGCTACTGCAACAGACGGGCGATGAAGTGCTGGATTACCGCCAGGCGGTG
-GCATATTACGCCTCCTGCCGTCAGACAGTGACCGAGGGTGGTAATCACGCATTCACGGGC
-TTCGAAGATTATTTCAACCAGATTGTCGATTTTCTTGGACTGCACAGTTGCTGACACGGA
-TGCGCCATCGGCTTGCTGGCCGTGCCGTTCTTCGTTTTGTCCGGGGTGATCATGAATAGC
-GGGGGAATTGCCGCCCGGCTGGTCAATTTTGCCAAACTGTTTACTGGCAAACTGCCCGGC
-TCGCTCTCTTATACCAACATCGTCGGCAATATGATGTTCGGTGCAATTTCCGGATCGGCA
-ATTGCCGCCTCAACCTCCATCGGCGGCGTGATGGTGCCGATGAGCGCGCGCGAAGGTTAC
-GATCGCGGCTTTGCGGCCGCGGTGAATATCGCCTCCGCGCCGACGGGAATGTTAATTCCG
-CCCACCACGGCTTTTATCCTTTATGCGCTGGCAAGCGGGGGAACATCGATTGCCGCTCTG
-TTCGCCGGCGGTCTGGTCGCGGGAGTGCTGTGGGGCGTTGGCTGTATGCTGGTCACGCTG
-GTGGTCGCTAAGCGTCGAAATTATCGGGTTTTCTTCACCGTCCAAAAAGGCATGGCGCTA
-AAAGTTGCCGTTGAGGCCATTCCCAGCCTGCTGCTGATCGTGATTATCGTCGGCGGCATT
-GTGCAGGGGATTTTCACCGCCATTGAAGCCTCCGCGATTGCCGTGGTGTATACATTATTG
-TTGACGATGGTGTTTTACCGCACGCTGAAAATTAAGGATTTGCCTTCGATTTTGCTCCAG
-ACAGTGGTAATGACCGGGGTCATCATGTTCCTGCTGGCAACCTCTTCGGCGATGTCCTTC
-TCGATGTCGATCACCAATATTCCTGCGGCGCTGAGCGATATGATCCTCGGTATTTCCGCC
-AATAAACTGGTTATCCTGTTAGTCATTACCGTCTTTTTGTTGATTATCGGCGCATTTATG
-GATATCGGTCCGGCCATTCTGATTTTTACCCCGATTCTGCTGCCGATCATGGCTAAACTG
-GGCGTCGATCCGGTGCATTTTGGCATTATCATGATCTATAACCTGGCGATTGGCACCATT
-ACGCCGCCAGTTGGCAGTGGTTTATATGTCGGGGCGAGCGTCGGTAAGGTCAAAGTTGAG
-GAAGTGATTAAACCGTTGCTGCCTTTTTACGGCGCGATTATCGGCGTTCTGTTATTAATT
-ACCTACATTCCGGAAATCACACTGTTCTTACCCCGTCTACTGGGCATCATGTAA
diff --git a/Examples/2-res-Annotate-prokka/tmp_files/genome4.fst_prokka-split5N.fna-prokkaRes/GEN4.1111.00001.log b/Examples/2-res-Annotate-prokka/tmp_files/genome4.fst_prokka-split5N.fna-prokkaRes/GEN4.1111.00001.log
deleted file mode 100644
index db5cc442dc4f7834bc5164f48c66b3c1b87d3faf..0000000000000000000000000000000000000000
--- a/Examples/2-res-Annotate-prokka/tmp_files/genome4.fst_prokka-split5N.fna-prokkaRes/GEN4.1111.00001.log
+++ /dev/null
@@ -1,128 +0,0 @@
-[13:15:34] This is prokka 1.14.5
-[13:15:34] Written by Torsten Seemann <torsten.seemann@gmail.com>
-[13:15:34] Homepage is https://github.com/tseemann/prokka
-[13:15:34] Local time is Mon Dec  9 13:15:34 2019
-[13:15:34] You are aperrin
-[13:15:34] Operating system is darwin
-[13:15:34] You have BioPerl 1.007002
-[13:15:35] System has 8 cores.
-[13:15:35] Will use maximum of 1 cores.
-[13:15:35] Annotating as >>> Bacteria <<<
-[13:15:35] Generating locus_tag from 'Examples/2-res-Annotate-prokka/tmp_files/genome4.fst_prokka-split5N.fna' contents.
-[13:15:35] Setting --locustag LIKMDGFN from MD5 5246d0f7b5f59e1da550241263d19049
-[13:15:35] Creating new output folder: Examples/2-res-Annotate-prokka/tmp_files/genome4.fst_prokka-split5N.fna-prokkaRes
-[13:15:35] Running: mkdir -p Examples\/2\-res\-Annotate\-prokka\/tmp_files\/genome4\.fst_prokka\-split5N\.fna\-prokkaRes
-[13:15:35] Using filename prefix: GEN4.1111.00001.XXX
-[13:15:35] Setting HMMER_NCPU=1
-[13:15:35] Writing log to: Examples/2-res-Annotate-prokka/tmp_files/genome4.fst_prokka-split5N.fna-prokkaRes/GEN4.1111.00001.log
-[13:15:35] Command: /usr/local/bin/prokka --outdir Examples/2-res-Annotate-prokka/tmp_files/genome4.fst_prokka-split5N.fna-prokkaRes --cpus 1 --prefix GEN4.1111.00001 Examples/2-res-Annotate-prokka/tmp_files/genome4.fst_prokka-split5N.fna
-[13:15:35] Appending to PATH: /Users/aperrin/Softwares/src/prokka-dec.19/bin/../binaries/darwin
-[13:15:35] Appending to PATH: /Users/aperrin/Softwares/src/prokka-dec.19/bin/../binaries/darwin/../common
-[13:15:35] Appending to PATH: /Users/aperrin/Softwares/src/prokka-dec.19/bin
-[13:15:35] Looking for 'aragorn' - found /usr/local/bin/aragorn
-[13:15:35] Determined aragorn version is 001002 from 'ARAGORN v1.2.38 Dean Laslett'
-[13:15:35] Looking for 'barrnap' - found /usr/local/bin/barrnap
-[13:15:35] Determined barrnap version is 000008 from 'barrnap 0.8'
-[13:15:35] Looking for 'blastp' - found /Users/aperrin/Softwares/bin/blastp
-[13:15:35] Determined blastp version is 002009 from 'blastp: 2.9.0+'
-[13:15:35] Looking for 'cmpress' - found /usr/local/bin/cmpress
-[13:15:35] Determined cmpress version is 001001 from '# INFERNAL 1.1.2 (July 2016)'
-[13:15:35] Looking for 'cmscan' - found /usr/local/bin/cmscan
-[13:15:35] Determined cmscan version is 001001 from '# INFERNAL 1.1.2 (July 2016)'
-[13:15:35] Looking for 'egrep' - found /usr/bin/egrep
-[13:15:35] Looking for 'find' - found /usr/bin/find
-[13:15:35] Looking for 'grep' - found /usr/bin/grep
-[13:15:35] Looking for 'hmmpress' - found /Users/aperrin/Softwares/src/prokka-dec.19/bin/../binaries/darwin/hmmpress
-[13:15:35] Determined hmmpress version is 003001 from '# HMMER 3.1b1 (May 2013); http://hmmer.org/'
-[13:15:35] Looking for 'hmmscan' - found /usr/local/bin/hmmscan
-[13:15:35] Determined hmmscan version is 003001 from '# HMMER 3.1b2 (February 2015); http://hmmer.org/'
-[13:15:35] Looking for 'java' - found /usr/bin/java
-[13:15:35] Looking for 'makeblastdb' - found /Users/aperrin/Softwares/bin/makeblastdb
-[13:15:35] Determined makeblastdb version is 002009 from 'makeblastdb: 2.9.0+'
-[13:15:35] Looking for 'minced' - found /Users/aperrin/Softwares/src/prokka-dec.19/bin/../binaries/darwin/../common/minced
-[13:15:35] Determined minced version is 002000 from 'minced 0.2.0'
-[13:15:35] Looking for 'parallel' - found /usr/local/bin/parallel
-[13:15:35] Determined parallel version is 20181022 from 'GNU parallel 20181022'
-[13:15:35] Looking for 'prodigal' - found /usr/local/bin/prodigal
-[13:15:35] Determined prodigal version is 002006 from 'Prodigal V2.6.3: February, 2016'
-[13:15:35] Looking for 'prokka-genbank_to_fasta_db' - found /Users/aperrin/Softwares/src/prokka-dec.19/bin/prokka-genbank_to_fasta_db
-[13:15:35] Looking for 'sed' - found /usr/bin/sed
-[13:15:35] Looking for 'tbl2asn' - found /Users/aperrin/Softwares/src/prokka-dec.19/bin/../binaries/darwin/tbl2asn
-[13:15:35] Determined tbl2asn version is 025007 from 'tbl2asn 25.7   arguments:'
-[13:15:35] Using genetic code table 11.
-[13:15:35] Loading and checking input file: Examples/2-res-Annotate-prokka/tmp_files/genome4.fst_prokka-split5N.fna
-[13:15:35] Wrote 1 contigs totalling 7134 bp.
-[13:15:35] Predicting tRNAs and tmRNAs
-[13:15:35] Running: aragorn -l -gc11  -w Examples\/2\-res\-Annotate\-prokka\/tmp_files\/genome4\.fst_prokka\-split5N\.fna\-prokkaRes\/GEN4\.1111\.00001\.fna
-[13:15:35] Found 0 tRNAs
-[13:15:35] Predicting Ribosomal RNAs
-[13:15:35] Running Barrnap with 1 threads
-[13:15:35] Found 0 rRNAs
-[13:15:35] Skipping ncRNA search, enable with --rfam if desired.
-[13:15:35] Total of 0 tRNA + rRNA features
-[13:15:35] Searching for CRISPR repeats
-[13:15:35] Found 0 CRISPRs
-[13:15:35] Predicting coding sequences
-[13:15:35] Contigs total 7134 bp, so using meta mode
-[13:15:35] Running: prodigal -i Examples\/2\-res\-Annotate\-prokka\/tmp_files\/genome4\.fst_prokka\-split5N\.fna\-prokkaRes\/GEN4\.1111\.00001\.fna -c -m -g 11 -p meta -f sco -q
-[13:15:35] Found 9 CDS
-[13:15:35] Connecting features back to sequences
-[13:15:35] Not using genus-specific database. Try --usegenus to enable it.
-[13:15:35] Annotating CDS, please be patient.
-[13:15:35] Will use 1 CPUs for similarity searching.
-[13:15:35] There are still 9 unannotated CDS left (started with 9)
-[13:15:35] Will use blast to search against /Users/aperrin/Softwares/src/prokka-dec.19/db/kingdom/Bacteria/IS with 1 CPUs
-[13:15:35] Running: cat Examples\/2\-res\-Annotate\-prokka\/tmp_files\/genome4\.fst_prokka\-split5N\.fna\-prokkaRes\/GEN4\.1111\.00001\.IS\.tmp\.95380\.faa | parallel --gnu --plain -j 1 --block 1161 --recstart '>' --pipe blastp -query - -db /Users/aperrin/Softwares/src/prokka-dec.19/db/kingdom/Bacteria/IS -evalue 1e-30 -qcov_hsp_perc 90 -num_threads 1 -num_descriptions 1 -num_alignments 1 -seg no > Examples\/2\-res\-Annotate\-prokka\/tmp_files\/genome4\.fst_prokka\-split5N\.fna\-prokkaRes\/GEN4\.1111\.00001\.IS\.tmp\.95380\.blast 2> /dev/null
-[13:15:36] Deleting unwanted file: Examples/2-res-Annotate-prokka/tmp_files/genome4.fst_prokka-split5N.fna-prokkaRes/GEN4.1111.00001.IS.tmp.95380.faa
-[13:15:36] Deleting unwanted file: Examples/2-res-Annotate-prokka/tmp_files/genome4.fst_prokka-split5N.fna-prokkaRes/GEN4.1111.00001.IS.tmp.95380.blast
-[13:15:36] There are still 9 unannotated CDS left (started with 9)
-[13:15:36] Will use blast to search against /Users/aperrin/Softwares/src/prokka-dec.19/db/kingdom/Bacteria/AMR with 1 CPUs
-[13:15:36] Running: cat Examples\/2\-res\-Annotate\-prokka\/tmp_files\/genome4\.fst_prokka\-split5N\.fna\-prokkaRes\/GEN4\.1111\.00001\.AMR\.tmp\.95380\.faa | parallel --gnu --plain -j 1 --block 1161 --recstart '>' --pipe blastp -query - -db /Users/aperrin/Softwares/src/prokka-dec.19/db/kingdom/Bacteria/AMR -evalue 1e-300 -qcov_hsp_perc 90 -num_threads 1 -num_descriptions 1 -num_alignments 1 -seg no > Examples\/2\-res\-Annotate\-prokka\/tmp_files\/genome4\.fst_prokka\-split5N\.fna\-prokkaRes\/GEN4\.1111\.00001\.AMR\.tmp\.95380\.blast 2> /dev/null
-[13:15:36] Deleting unwanted file: Examples/2-res-Annotate-prokka/tmp_files/genome4.fst_prokka-split5N.fna-prokkaRes/GEN4.1111.00001.AMR.tmp.95380.faa
-[13:15:36] Deleting unwanted file: Examples/2-res-Annotate-prokka/tmp_files/genome4.fst_prokka-split5N.fna-prokkaRes/GEN4.1111.00001.AMR.tmp.95380.blast
-[13:15:36] There are still 9 unannotated CDS left (started with 9)
-[13:15:36] Will use blast to search against /Users/aperrin/Softwares/src/prokka-dec.19/db/kingdom/Bacteria/sprot with 1 CPUs
-[13:15:36] Running: cat Examples\/2\-res\-Annotate\-prokka\/tmp_files\/genome4\.fst_prokka\-split5N\.fna\-prokkaRes\/GEN4\.1111\.00001\.sprot\.tmp\.95380\.faa | parallel --gnu --plain -j 1 --block 1161 --recstart '>' --pipe blastp -query - -db /Users/aperrin/Softwares/src/prokka-dec.19/db/kingdom/Bacteria/sprot -evalue 1e-09 -qcov_hsp_perc 80 -num_threads 1 -num_descriptions 1 -num_alignments 1 -seg no > Examples\/2\-res\-Annotate\-prokka\/tmp_files\/genome4\.fst_prokka\-split5N\.fna\-prokkaRes\/GEN4\.1111\.00001\.sprot\.tmp\.95380\.blast 2> /dev/null
-[13:15:37] Deleting unwanted file: Examples/2-res-Annotate-prokka/tmp_files/genome4.fst_prokka-split5N.fna-prokkaRes/GEN4.1111.00001.sprot.tmp.95380.faa
-[13:15:37] Deleting unwanted file: Examples/2-res-Annotate-prokka/tmp_files/genome4.fst_prokka-split5N.fna-prokkaRes/GEN4.1111.00001.sprot.tmp.95380.blast
-[13:15:37] There are still 3 unannotated CDS left (started with 9)
-[13:15:37] Will use hmmer3 to search against /Users/aperrin/Softwares/src/prokka-dec.19/db/hmm/HAMAP.hmm with 1 CPUs
-[13:15:37] Running: cat Examples\/2\-res\-Annotate\-prokka\/tmp_files\/genome4\.fst_prokka\-split5N\.fna\-prokkaRes\/GEN4\.1111\.00001\.HAMAP\.hmm\.tmp\.95380\.faa | parallel --gnu --plain -j 1 --block 379 --recstart '>' --pipe hmmscan --noali --notextw --acc -E 1e-09 --cpu 1 /Users/aperrin/Softwares/src/prokka-dec.19/db/hmm/HAMAP.hmm /dev/stdin > Examples\/2\-res\-Annotate\-prokka\/tmp_files\/genome4\.fst_prokka\-split5N\.fna\-prokkaRes\/GEN4\.1111\.00001\.HAMAP\.hmm\.tmp\.95380\.hmmer3 2> /dev/null
-[13:15:38] Deleting unwanted file: Examples/2-res-Annotate-prokka/tmp_files/genome4.fst_prokka-split5N.fna-prokkaRes/GEN4.1111.00001.HAMAP.hmm.tmp.95380.faa
-[13:15:38] Deleting unwanted file: Examples/2-res-Annotate-prokka/tmp_files/genome4.fst_prokka-split5N.fna-prokkaRes/GEN4.1111.00001.HAMAP.hmm.tmp.95380.hmmer3
-[13:15:38] Labelling remaining 3 proteins as 'hypothetical protein'
-[13:15:38] Found 6 unique /gene codes.
-[13:15:38] Fixed 0 colliding /gene names.
-[13:15:38] Adding /locus_tag identifiers
-[13:15:38] Assigned 9 locus_tags to CDS and RNA features.
-[13:15:38] Writing outputs to Examples/2-res-Annotate-prokka/tmp_files/genome4.fst_prokka-split5N.fna-prokkaRes/
-[13:15:38] Generating annotation statistics file
-[13:15:38] Generating Genbank and Sequin files
-[13:15:38] Running: tbl2asn -V b -a r10k -l paired-ends -M n -N 1 -y 'Annotated using prokka 1.14.5 from https://github.com/tseemann/prokka' -Z Examples\/2\-res\-Annotate\-prokka\/tmp_files\/genome4\.fst_prokka\-split5N\.fna\-prokkaRes\/GEN4\.1111\.00001\.err -i Examples\/2\-res\-Annotate\-prokka\/tmp_files\/genome4\.fst_prokka\-split5N\.fna\-prokkaRes\/GEN4\.1111\.00001\.fsa 2> /dev/null
-[13:15:38] Deleting unwanted file: Examples/2-res-Annotate-prokka/tmp_files/genome4.fst_prokka-split5N.fna-prokkaRes/errorsummary.val
-[13:15:38] Deleting unwanted file: Examples/2-res-Annotate-prokka/tmp_files/genome4.fst_prokka-split5N.fna-prokkaRes/GEN4.1111.00001.dr
-[13:15:38] Deleting unwanted file: Examples/2-res-Annotate-prokka/tmp_files/genome4.fst_prokka-split5N.fna-prokkaRes/GEN4.1111.00001.fixedproducts
-[13:15:38] Deleting unwanted file: Examples/2-res-Annotate-prokka/tmp_files/genome4.fst_prokka-split5N.fna-prokkaRes/GEN4.1111.00001.ecn
-[13:15:38] Deleting unwanted file: Examples/2-res-Annotate-prokka/tmp_files/genome4.fst_prokka-split5N.fna-prokkaRes/GEN4.1111.00001.val
-[13:15:38] Repairing broken .GBK output that tbl2asn produces...
-[13:15:38] Running: sed 's/COORDINATES: profile/COORDINATES:profile/' < Examples\/2\-res\-Annotate\-prokka\/tmp_files\/genome4\.fst_prokka\-split5N\.fna\-prokkaRes\/GEN4\.1111\.00001\.gbf > Examples\/2\-res\-Annotate\-prokka\/tmp_files\/genome4\.fst_prokka\-split5N\.fna\-prokkaRes\/GEN4\.1111\.00001\.gbk
-[13:15:38] Deleting unwanted file: Examples/2-res-Annotate-prokka/tmp_files/genome4.fst_prokka-split5N.fna-prokkaRes/GEN4.1111.00001.gbf
-[13:15:38] Output files:
-[13:15:38] Examples/2-res-Annotate-prokka/tmp_files/genome4.fst_prokka-split5N.fna-prokkaRes/GEN4.1111.00001.fsa
-[13:15:38] Examples/2-res-Annotate-prokka/tmp_files/genome4.fst_prokka-split5N.fna-prokkaRes/GEN4.1111.00001.faa
-[13:15:38] Examples/2-res-Annotate-prokka/tmp_files/genome4.fst_prokka-split5N.fna-prokkaRes/GEN4.1111.00001.log
-[13:15:38] Examples/2-res-Annotate-prokka/tmp_files/genome4.fst_prokka-split5N.fna-prokkaRes/GEN4.1111.00001.ffn
-[13:15:38] Examples/2-res-Annotate-prokka/tmp_files/genome4.fst_prokka-split5N.fna-prokkaRes/GEN4.1111.00001.gbk
-[13:15:38] Examples/2-res-Annotate-prokka/tmp_files/genome4.fst_prokka-split5N.fna-prokkaRes/GEN4.1111.00001.gff
-[13:15:38] Examples/2-res-Annotate-prokka/tmp_files/genome4.fst_prokka-split5N.fna-prokkaRes/GEN4.1111.00001.tbl
-[13:15:38] Examples/2-res-Annotate-prokka/tmp_files/genome4.fst_prokka-split5N.fna-prokkaRes/GEN4.1111.00001.sqn
-[13:15:38] Examples/2-res-Annotate-prokka/tmp_files/genome4.fst_prokka-split5N.fna-prokkaRes/GEN4.1111.00001.tsv
-[13:15:38] Examples/2-res-Annotate-prokka/tmp_files/genome4.fst_prokka-split5N.fna-prokkaRes/GEN4.1111.00001.fna
-[13:15:38] Examples/2-res-Annotate-prokka/tmp_files/genome4.fst_prokka-split5N.fna-prokkaRes/GEN4.1111.00001.err
-[13:15:38] Examples/2-res-Annotate-prokka/tmp_files/genome4.fst_prokka-split5N.fna-prokkaRes/GEN4.1111.00001.txt
-[13:15:38] Annotation finished successfully.
-[13:15:38] Walltime used: 0.07 minutes
-[13:15:38] If you use this result please cite the Prokka paper:
-[13:15:38] Seemann T (2014) Prokka: rapid prokaryotic genome annotation. Bioinformatics. 30(14):2068-9.
-[13:15:38] Type 'prokka --citation' for more details.
-[13:15:38] Thank you, come again.
diff --git a/Examples/2-res-Annotate-prokka/tmp_files/genome4.fst_prokka-split5N.fna-prokkaRes/GEN4.1111.00001.sqn b/Examples/2-res-Annotate-prokka/tmp_files/genome4.fst_prokka-split5N.fna-prokkaRes/GEN4.1111.00001.sqn
deleted file mode 100644
index e2af4c87877c5ecd7a8500bc6786ec13cd315118..0000000000000000000000000000000000000000
--- a/Examples/2-res-Annotate-prokka/tmp_files/genome4.fst_prokka-split5N.fna-prokkaRes/GEN4.1111.00001.sqn
+++ /dev/null
@@ -1,818 +0,0 @@
-Seq-entry ::= set {
-  class genbank ,
-  seq-set {
-    set {
-      class nuc-prot ,
-      descr {
-        source {
-          org {
-            taxname "Genus species" ,
-            orgname {
-              mod {
-                {
-                  subtype strain ,
-                  subname "strain" } } ,
-              gcode 11 } } } ,
-        comment "Annotated using prokka 1.14.5 from
- https://github.com/tseemann/prokka" ,
-        user {
-          type
-            str "NcbiCleanup" ,
-          data {
-            {
-              label
-                str "method" ,
-              data
-                str "SeriousSeqEntryCleanup" } ,
-            {
-              label
-                str "version" ,
-              data
-                int 8 } ,
-            {
-              label
-                str "month" ,
-              data
-                int 12 } ,
-            {
-              label
-                str "day" ,
-              data
-                int 9 } ,
-            {
-              label
-                str "year" ,
-              data
-                int 2019 } } } ,
-        create-date
-          std {
-            year 2019 ,
-            month 12 ,
-            day 9 } } ,
-      seq-set {
-        seq {
-          id {
-            local
-              str "g4_1" } ,
-          descr {
-            molinfo {
-              biomol genomic } } ,
-          inst {
-            repr raw ,
-            mol dna ,
-            length 7134 ,
-            seq-data
-              iupacna "ATGAAAGCGCTACTGTGGCTGGTGGGTCTCGCGTTGCTGTTAACAGGCTGCGCGA
-GCGAAAAAGGAATTATCGATAAAGAGGGATATCAGCTTGATACCCGACATCGGGCGCAGGCGGCCTATCCGCGCATTA
-AAGTCCTGGTGATTCACTATACGGCGGAAAACTTTGACGTTTCGCTGGCGACGTTAACGGGCCGCAACGTCAGTTCGC
-ATTACCTGATTCCCGCAACCCCGCCATTATATGGCGGTAAACCGCGCATCTGGCAACTGGTGCCGGAACAGGATCAGG
-CCTGGCATGCGGGCGTCAGTTTCTGGCGAGGCGCCACGCGTCTCAATGATACGTCTATTGGCATTGAGCTGGAAAATC
-GCGGCTGGCGAATGTCCGGCGGGGTGAAATCTTTCGCGCCGTTTGAATCCGCGCAAATTCAGGCATTGATTCCGTTAG
-CGAAGGACATTATCGCGCGCTATGACATCAAACCGCAGAATGTGGTGGCCCATGCGGATATCGCGCCGCAGCGTAAAG
-ACGATCCCGGCCCGCGCTTCCCGTGGCGCGAGCTGGCGGCGCAGGGGATTGGCGCCTGGCCTGACGCCCAGCGTGTGG
-CGTTTTATCTGGCTGGACGCGCGCCGTATACGCCAGTCGATACCGCAACGGTGCTTGCGTTACTCTCGCGCTATGGCT
-ATGAAGTCAAAGCCGATATGACGGCGCGCGAGCAGCAGCGGGTGATTATGGCGTTCCAGATGCACTTCCGTCCGGCGC
-AATGGAACGGTATCGCAGATGCCGAAACGCAGGCGATTGCCGAAGCATTACTGGAGAAGTACGGCCAGGATTAACGCG
-ATCGCGCGCATATCGCGCGCGATAGATGCCGCACTTTATTGCTGAATGTACTGAAAATATTCGCGAGCAGGCTGATTT
-ACCCGGCCTGTTCAGCAAGGTAAACGAGGCGCTGGCCGCCAGCGGGATTTTCCCCATCGGCGGTATCCGCAGTCGCGC
-CCACTGGCTGGATACCTGGCAGATGGCTGACGGTAAGCATGATTATGCGTTTGTGCATATGACGCTGAAAATCGGTAC
-CGGGCGCAGCCTGGAGAGCCGTCAGGAAGTCGGCGAAATGCTGTTTGGGCTGATTAAAGCCCACTTCGCCGACCTGAT
-GGAGAACCGCTATCTGGCGCTGTCGTTTGAGATTGCCGAGCTACATCCGACGCTCAATTACAAACAAAACAACGTACA
-CGCGTTATTTAAATAGCCGCATATGCGGCGCTCAGGAGCGCTAGCATGCTCGATAAACAGACCCATACCCTGATCGCC
-CAGCGACTTAATCAGGCTGAAAAACAGCGTGAACAAATTCGCGCAGTGTCGCTGGATTATCCCAACATCACTATTGAA
-GATGCCTATGCCGTACAGCGTGAATGGGTCAATATCAAGATCGCCGAAGGGCGCACGCTCAAAGGCCACAAAATCGGC
-CTGACCTCAAAAGCGATGCAGGCCAGCTCGCAAATCAGCGAACCGGATTACGGCGCGCTGCTTGACGATATGTTCTTC
-CATGACGGCGGCGATATCCCCACCGACCGTTTTATCGTCCCGCGTATTGAAGTGGAGCTGGCGTTCGTGCTGGCGAAA
-CCGCTGCGCGGCCCTCACTGCACGCTGTTCGACGTCTACAACGCCACGGATTATGTGATTCCGGCGCTGGAACTGATT
-GACGCCCGCAGCCACAACATCGACCCGGAAACCCAGCGCCCGCGCAAAGTGTTCGACACCATTTCCGACAACGCCGCC
-AACGCCGGGGTGATCCTCGGTGGTCGCCCCATCAAACCAGACGAGCTGGATCTGCGCTGGATCTCCGCGCTGCTCTAT
-CGCAACGGCGTGATCGAAGAAACCGGCGTCGCCGCAGGCGTGCTGAATCATCCGGCCAACGGCGTGGCGTGGCTGGCG
-AACAAGCTTGCCCCCTACGATGTCCAGCTTGAAGCCGGGCAGATCATCCTCGGCGGCTCGTTCACCCGCCCGGTGCCG
-GCGAGCAAGGGCGACACCTTCCATGTCGATTACGGCAACATGGGCGCGATCAGTTGCCGGTTTGTGTAACCAGATCCG
-CGCGCGCATATATATCGCGCGCATACGATGCCCGTGAATAAGTTCTCCCGACGTACCCTCCTGACGGCAGGTTCCGCG
-CTTGCTGTTCTTCCTTTTCTGCGCGCCTTGCCGGTACAGGCGCGTGAACCTCGCGAGACCGTCGATATTAAGGATTAT
-CCGGCGGATGACGGTATCGCCTCGTTCAAACAGGCCTTCGCCGACGGACAGACCGTGGTCTTACCGCCAGGATGGGTG
-TGTGAAAATATCAATGCGGCGATAACGATTCCGGCGGGAAAAACGCTGCGGGTACAGGGCGCGGTGCGTGGGAATGGC
-CGGGGACGGTTTATTTTGCAGGACGGGTGTCAGGTGGTGGGGGAGCAGGGCGGCAGTCTGCACAATGTGACGCTGGAT
-GTTCGCGGGTCGGACTGTGTGATTAAAGGCGTGACGATGAGCGGCTTTGGCCCCGTCGCGCAAATTTTCATCGGCGGT
-AAGGAACCGCAGGTGATGCGTAATCTCATTATCGATGACATCACCGTTACCCACGCCAACTACGCCATTCTCCGCCAG
-GGATTTCATAACCAAATGGACGGCGCGCGGATTACGCATAGCCGCTTTAGCGATTTGCAGGGGGACGCCATTGAGTGG
-AATGTCGCGATTCACGACCGCGACATCCTGATTTCCGATCATGTCATCGAACGCATTGATTGTACCAATGGCAAAATC
-AACTGGGGGATCGGCATCGGGCTGGCGGGTAGCACCTATGACAACAGTTATCCTGAAGATCAGGCAGTAAAAAACTTT
-GTGGTGGCCAATATTACCGGATCTGATTGCCGACAGCTGGTGCACGTAGAAAATGGCAAACATTTCGTCATTCGCAAT
-GTCAAAGCCAAAAACATCACGCCCGATTTCAGTAAAAATGCGGGTATTGATAACGCAACGATCGCCATTTATGGCTGT
-GATAATTTCGTCATTGATAATATTGATATGACGAATAGTGCTGGGATGCTCATCGGCTATGGCGTCGTTAAAGGAAAA
-TACCTGTCAATTCCGCAAAACTTTAAATTAAACGCTATTCGGTTGGATAATCGCCAGGTTGCTTATAAATTACGCGGC
-ATTCAAATTTCCTCCGGCAACATCCCCTCTTTTGTCGCCATCACCAATGTACGGATGACGCGTGCTACGCTGGAACTG
-CATAATCAACCGCAGCACCTCTTTCTGCGTAATATCAACGTGATGCAAACTTCAGCGATTGGCCCGGCGTTAAAAATG
-CATTTCGATTTGCGTAAAGATGTCCGTGGTCAATTTATGGCCCGCCAGGACACGCTGCTTTCCCTCGCTAATGTTCAT
-GCCATCAATGAAAACGGGCAGAGTTCCGTGGATATCGACAGGATTAATCACCAAACCGTGAATGTCGAAGCAGTGAAT
-TTTTCGCTGCCGAAGCGGGGAGGGTAACAGAGCTCGCGCGATCGCGAATGTCAGAAAATAAATTACACGTTATCGATT
-TGCACAAACGCTACGGCGGTCATGAAGTGCTGAAAGGGGTATCGTTGCAGGCCCGCGCCGGAGATGTGATTAGCATCA
-TCGGCTCGTCCGGCTCCGGTAAAAGCACTTTTTTGCGCTGTATTAACTTCCTCGAAAAACCGAGCGAAGGCGCGATTA
-TCGTGAACGGTCAGAACATTAATCTGGTGCGCGACAAAGACGGGCAGCTCAAAGTGGCGGATAAAAATCAGCTACGCT
-TGTTGCGTACCCGCCTGACGATGGTGTTTCAGCACTTTAACCTCTGGAGCCACATGACGGTGCTGGAAAATGTGATGG
-AAGCGCCGATTCAGGTACTGGGATTAAGCAAGCACGACGCGCGCGAGCGGGCGTTGAAATATCTGGCGAAGGTGGGGA
-TTGATGAGCGCGCTCAGGGCAAATATCCCGTCCATCTCTCCGGCGGCCAACAGCAGCGCGTTTCTATTGCGCGCGCGC
-TGGCGATGGAACCTGACGTTTTACTGTTCGATGAACCCACATCGGCGCTCGATCCTGAACTGGTCGGCGAAGTGTTGC
-GCATCATGCAACAACTGGCGGAAGAAGGCAAAACGATGGTGGTGGTCACGCATGAAATGGGCTTCGCCCGCCATGTCT
-CTTCGCACGTTATTTTTCTGCATCAGGGGAAAATTGAAGAAGAGGGCGATCCGGAGCAGGTGTTCGGCAATCCGCAAA
-GCCCGCGTTTACAGCAATTCCTGAAAGGCTCGCTGAAATAACAGATACGCGCATGGCGAGTGTTTATTGGCATCGTTA
-GCCTGTTTCCTGAAATGTTCCGCGCAATTACCGATTACGGGGTAACTGGCCGGGCAGTAAAAAAAGGCCTGCTGAACA
-TCCAAAGCTGGAGTCCTCGCGACTTCGCGCATGACCGGCACCGTACCGTGGACGACCGTCCTTACGGCGGCGGACCGG
-GGATGTTAATGATGGTGCAACCCTTGCGGGACGCCATTCACGCAGCAAAAGCCGCGGCAGGTGAAGGCGCTAAAGTGA
-TTTATCTGTCGCCTCAGGGACGCAAGCTTGATCAAGCGGGCGTTAGCGAGCTGGCCACGAATCAGAAGCTTATTCTGG
-TGTGTGGTCGCTACGAAGGCGTAGATGAGCGCGTAATTCAGACCGAAATTGACGAAGAATGGTCAATTGGCGATTACG
-TTCTCAGCGGTGGCGAACTACCGGCAATGACGCTGATTGACTCCGTCGCCCGGTTTATACCGGGGGTTCTGGGGCATG
-AGGCATCAGCAATCGAAGATTCGTTTGCTGATGGGTTGCTGGATTGTCCGCACTATACGCGCCCTGAAGTGTTAGAGG
-GGATGGAAGTACCGCCAGTATTGCTGTCGGGAAACCATGCCGAGATACGTCGCTGGCGCTTGAAACAGTCGCTGGGCC
-GAACCTGGCTTAGAAGACCTGAACTTCTGGAAAACCTGGCTCTGACTGAAGAGCAAGCAAGGTTGCTGGCGGAGTTCA
-AAACAGAACACGCACAACAGCAGCATAAACATGATGGGATGGCATAGCGATAGCGCTAGAGCGATGAATAATCATTTT
-GGGAAAGGGTTAATGGCTGGGTTGCACGCGCCATATGCATATAGCGCGCATCATGCGGTGAATTTCTGTTCTGAGTAT
-AAACGTGGCTTTGTATTGGGTTTTACACACCGTATGTTCGAAAAGACCGGCGATCGTCAACTTAGCGCGTGGGAGGCC
-GGAATTCTGACGCGTCGCTATGGTCTGGATAAAGAAATGGTGATGGATTTCTTTAAAGAGAATCATTCCGGGATGGCG
-GTTCGCTTCTTTATGGTCGGTTATCGACTCGAAGGTTGACAGATGCGCGATCGATGTCTACGCTTCTCTATTTGCACG
-GATTCAACAGTTCCCCTCGCTCGGCAAAAGCGTGCCAGCTAAAAAACTGGCTGGCGGAGCGTCATCCGCATGTCGAGA
-TGATCGTCCCTCAACTACCGCCGTATCCTGCCGATGCGGCGGAGTTGCTGGAATCTCTCGTGCTTGAGCATGGCGGTG
-CGCCATTAGGGCTGGTAGGATCGTCGCTGGGTGGTTATTACGCCACCTGGCTGTCGCAATGTTTTATGCTGCCGGCTG
-TGGTGGTGAATCCCGCCGTGCGGCCCTTTGAATTACTGACCGACTATCTCGGTCAGAACGAGAACCCCTACACCGGGC
-AGCAATATGTGCTAGAGTCTCGCCATATTTATGATCTTAAAGTCATGCAGATTGACCCGCTGGAAGCGCCGGACCTGA
-TCTGGCTACTGCAACAGACGGGCGATGAAGTGCTGGATTACCGCCAGGCGGTGGCATATTACGCCTCCTGCCGTCAGA
-CAGTGACCGAGGGTGGTAATCACGCATTCACGGGCTTCGAAGATTATTTCAACCAGATTGTCGATTTTCTTGGACTGC
-ACAGTTGCTGACACGGATGCGCCATCGGCTTGCTGGCCGTGCCGTTCTTCGTTTTGTCCGGGGTGATCATGAATAGCG
-GGGGAATTGCCGCCCGGCTGGTCAATTTTGCCAAACTGTTTACTGGCAAACTGCCCGGCTCGCTCTCTTATACCAACA
-TCGTCGGCAATATGATGTTCGGTGCAATTTCCGGATCGGCAATTGCCGCCTCAACCTCCATCGGCGGCGTGATGGTGC
-CGATGAGCGCGCGCGAAGGTTACGATCGCGGCTTTGCGGCCGCGGTGAATATCGCCTCCGCGCCGACGGGAATGTTAA
-TTCCGCCCACCACGGCTTTTATCCTTTATGCGCTGGCAAGCGGGGGAACATCGATTGCCGCTCTGTTCGCCGGCGGTC
-TGGTCGCGGGAGTGCTGTGGGGCGTTGGCTGTATGCTGGTCACGCTGGTGGTCGCTAAGCGTCGAAATTATCGGGTTT
-TCTTCACCGTCCAAAAAGGCATGGCGCTAAAAGTTGCCGTTGAGGCCATTCCCAGCCTGCTGCTGATCGTGATTATCG
-TCGGCGGCATTGTGCAGGGGATTTTCACCGCCATTGAAGCCTCCGCGATTGCCGTGGTGTATACATTATTGTTGACGA
-TGGTGTTTTACCGCACGCTGAAAATTAAGGATTTGCCTTCGATTTTGCTCCAGACAGTGGTAATGACCGGGGTCATCA
-TGTTCCTGCTGGCAACCTCTTCGGCGATGTCCTTCTCGATGTCGATCACCAATATTCCTGCGGCGCTGAGCGATATGA
-TCCTCGGTATTTCCGCCAATAAACTGGTTATCCTGTTAGTCATTACCGTCTTTTTGTTGATTATCGGCGCATTTATGG
-ATATCGGTCCGGCCATTCTGATTTTTACCCCGATTCTGCTGCCGATCATGGCTAAACTGGGCGTCGATCCGGTGCATT
-TTGGCATTATCATGATCTATAACCTGGCGATTGGCACCATTACGCCGCCAGTTGGCAGTGGTTTATATGTCGGGGCGA
-GCGTCGGTAAGGTCAAAGTTGAGGAAGTGATTAAACCGTTGCTGCCTTTTTACGGCGCGATTATCGGCGTTCTGTTAT
-TAATTACCTACATTCCGGAAATCACACTGTTCTTACCCCGTCTACTGGGCATCATGTAA" } } ,
-        seq {
-          id {
-            local
-              str "g4_1_1" } ,
-          descr {
-            title "N-acetylmuramoyl-L-alanine amidase AmiD [Genus species]" ,
-            molinfo {
-              biomol peptide ,
-              tech concept-trans } } ,
-          inst {
-            repr raw ,
-            mol aa ,
-            length 276 ,
-            seq-data
-              ncbieaa "MKALLWLVGLALLLTGCASEKGIIDKEGYQLDTRHRAQAAYPRIKVLVIHYTAEN
-FDVSLATLTGRNVSSHYLIPATPPLYGGKPRIWQLVPEQDQAWHAGVSFWRGATRLNDTSIGIELENRGWRMSGGVKS
-FAPFESAQIQALIPLAKDIIARYDIKPQNVVAHADIAPQRKDDPGPRFPWRELAAQGIGAWPDAQRVAFYLAGRAPYT
-PVDTATVLALLSRYGYEVKADMTAREQQRVIMAFQMHFRPAQWNGIADAETQAIAEALLEKYGQD" } ,
-          annot {
-            {
-              data
-                ftable {
-                  {
-                    id
-                      local
-                        id 10 ,
-                    data
-                      prot {
-                        name {
-                          "N-acetylmuramoyl-L-alanine amidase AmiD" } ,
-                        ec {
-                          "3.5.1.28" } } ,
-                    location
-                      int {
-                        from 0 ,
-                        to 275 ,
-                        id
-                          local
-                            str "g4_1_1" } } } } } } ,
-        seq {
-          id {
-            local
-              str "g4_1_2" } ,
-          descr {
-            title "5-carboxymethyl-2-hydroxymuconate Delta-isomerase [Genus
- species]" ,
-            molinfo {
-              biomol peptide ,
-              tech concept-trans } } ,
-          inst {
-            repr raw ,
-            mol aa ,
-            length 126 ,
-            seq-data
-              ncbieaa "MPHFIAECTENIREQADLPGLFSKVNEALAASGIFPIGGIRSRAHWLDTWQMADG
-KHDYAFVHMTLKIGTGRSLESRQEVGEMLFGLIKAHFADLMENRYLALSFEIAELHPTLNYKQNNVHALFK" } ,
-          annot {
-            {
-              data
-                ftable {
-                  {
-                    id
-                      local
-                        id 11 ,
-                    data
-                      prot {
-                        name {
-                          "5-carboxymethyl-2-hydroxymuconate Delta-isomerase" } ,
-                        ec {
-                          "5.3.3.10" } } ,
-                    location
-                      int {
-                        from 0 ,
-                        to 125 ,
-                        id
-                          local
-                            str "g4_1_2" } } } } } } ,
-        seq {
-          id {
-            local
-              str "g4_1_3" } ,
-          descr {
-            title "2-oxo-hept-4-ene-1,7-dioate hydratase [Genus species]" ,
-            molinfo {
-              biomol peptide ,
-              tech concept-trans } } ,
-          inst {
-            repr raw ,
-            mol aa ,
-            length 267 ,
-            seq-data
-              ncbieaa "MLDKQTHTLIAQRLNQAEKQREQIRAVSLDYPNITIEDAYAVQREWVNIKIAEGR
-TLKGHKIGLTSKAMQASSQISEPDYGALLDDMFFHDGGDIPTDRFIVPRIEVELAFVLAKPLRGPHCTLFDVYNATDY
-VIPALELIDARSHNIDPETQRPRKVFDTISDNAANAGVILGGRPIKPDELDLRWISALLYRNGVIEETGVAAGVLNHP
-ANGVAWLANKLAPYDVQLEAGQIILGGSFTRPVPASKGDTFHVDYGNMGAISCRFV" } ,
-          annot {
-            {
-              data
-                ftable {
-                  {
-                    id
-                      local
-                        id 12 ,
-                    data
-                      prot {
-                        name {
-                          "2-oxo-hept-4-ene-1,7-dioate hydratase" } ,
-                        ec {
-                          "4.2.1.163" } } ,
-                    location
-                      int {
-                        from 0 ,
-                        to 266 ,
-                        id
-                          local
-                            str "g4_1_3" } } } } } } ,
-        seq {
-          id {
-            local
-              str "g4_1_4" } ,
-          descr {
-            title "hypothetical protein LIKMDGFN_00004 [Genus species]" ,
-            molinfo {
-              biomol peptide ,
-              tech concept-trans } } ,
-          inst {
-            repr raw ,
-            mol aa ,
-            length 467 ,
-            seq-data
-              ncbieaa "MPVNKFSRRTLLTAGSALAVLPFLRALPVQAREPRETVDIKDYPADDGIASFKQA
-FADGQTVVLPPGWVCENINAAITIPAGKTLRVQGAVRGNGRGRFILQDGCQVVGEQGGSLHNVTLDVRGSDCVIKGVT
-MSGFGPVAQIFIGGKEPQVMRNLIIDDITVTHANYAILRQGFHNQMDGARITHSRFSDLQGDAIEWNVAIHDRDILIS
-DHVIERIDCTNGKINWGIGIGLAGSTYDNSYPEDQAVKNFVVANITGSDCRQLVHVENGKHFVIRNVKAKNITPDFSK
-NAGIDNATIAIYGCDNFVIDNIDMTNSAGMLIGYGVVKGKYLSIPQNFKLNAIRLDNRQVAYKLRGIQISSGNIPSFV
-AITNVRMTRATLELHNQPQHLFLRNINVMQTSAIGPALKMHFDLRKDVRGQFMARQDTLLSLANVHAINENGQSSVDI
-DRINHQTVNVEAVNFSLPKRGG" } ,
-          annot {
-            {
-              data
-                ftable {
-                  {
-                    id
-                      local
-                        id 13 ,
-                    data
-                      prot {
-                        name {
-                          "hypothetical protein" } } ,
-                    location
-                      int {
-                        from 0 ,
-                        to 466 ,
-                        id
-                          local
-                            str "g4_1_4" } } } } } } ,
-        seq {
-          id {
-            local
-              str "g4_1_5" } ,
-          descr {
-            title "Histidine transport ATP-binding protein HisP [Genus
- species]" ,
-            molinfo {
-              biomol peptide ,
-              tech concept-trans } } ,
-          inst {
-            repr raw ,
-            mol aa ,
-            length 257 ,
-            seq-data
-              ncbieaa "MSENKLHVIDLHKRYGGHEVLKGVSLQARAGDVISIIGSSGSGKSTFLRCINFLE
-KPSEGAIIVNGQNINLVRDKDGQLKVADKNQLRLLRTRLTMVFQHFNLWSHMTVLENVMEAPIQVLGLSKHDARERAL
-KYLAKVGIDERAQGKYPVHLSGGQQQRVSIARALAMEPDVLLFDEPTSALDPELVGEVLRIMQQLAEEGKTMVVVTHE
-MGFARHVSSHVIFLHQGKIEEEGDPEQVFGNPQSPRLQQFLKGSLK" } ,
-          annot {
-            {
-              data
-                ftable {
-                  {
-                    id
-                      local
-                        id 14 ,
-                    data
-                      prot {
-                        name {
-                          "Histidine transport ATP-binding protein HisP" } } ,
-                    location
-                      int {
-                        from 0 ,
-                        to 256 ,
-                        id
-                          local
-                            str "g4_1_5" } } } } } } ,
-        seq {
-          id {
-            local
-              str "g4_1_6" } ,
-          descr {
-            title "tRNA (guanine-N(1)-)-methyltransferase [Genus species]" ,
-            molinfo {
-              biomol peptide ,
-              tech concept-trans } } ,
-          inst {
-            repr raw ,
-            mol aa ,
-            length 255 ,
-            seq-data
-              ncbieaa "MFIGIVSLFPEMFRAITDYGVTGRAVKKGLLNIQSWSPRDFAHDRHRTVDDRPYG
-GGPGMLMMVQPLRDAIHAAKAAAGEGAKVIYLSPQGRKLDQAGVSELATNQKLILVCGRYEGVDERVIQTEIDEEWSI
-GDYVLSGGELPAMTLIDSVARFIPGVLGHEASAIEDSFADGLLDCPHYTRPEVLEGMEVPPVLLSGNHAEIRRWRLKQ
-SLGRTWLRRPELLENLALTEEQARLLAEFKTEHAQQQHKHDGMA" } ,
-          annot {
-            {
-              data
-                ftable {
-                  {
-                    id
-                      local
-                        id 15 ,
-                    data
-                      prot {
-                        name {
-                          "tRNA (guanine-N(1)-)-methyltransferase" } ,
-                        ec {
-                          "2.1.1.228" } } ,
-                    location
-                      int {
-                        from 0 ,
-                        to 254 ,
-                        id
-                          local
-                            str "g4_1_6" } } } } } } ,
-        seq {
-          id {
-            local
-              str "g4_1_7" } ,
-          descr {
-            title "hypothetical protein LIKMDGFN_00007 [Genus species]" ,
-            molinfo {
-              biomol peptide ,
-              tech concept-trans } } ,
-          inst {
-            repr raw ,
-            mol aa ,
-            length 86 ,
-            seq-data
-              ncbieaa "MAGLHAPYAYSAHHAVNFCSEYKRGFVLGFTHRMFEKTGDRQLSAWEAGILTRRY
-GLDKEMVMDFFKENHSGMAVRFFMVGYRLEG" } ,
-          annot {
-            {
-              data
-                ftable {
-                  {
-                    id
-                      local
-                        id 16 ,
-                    data
-                      prot {
-                        name {
-                          "hypothetical protein" } } ,
-                    location
-                      int {
-                        from 0 ,
-                        to 85 ,
-                        id
-                          local
-                            str "g4_1_7" } } } } } } ,
-        seq {
-          id {
-            local
-              str "g4_1_8" } ,
-          descr {
-            title "hypothetical protein LIKMDGFN_00008 [Genus species]" ,
-            molinfo {
-              biomol peptide ,
-              tech concept-trans } } ,
-          inst {
-            repr raw ,
-            mol aa ,
-            length 193 ,
-            seq-data
-              ncbieaa "MSTLLYLHGFNSSPRSAKACQLKNWLAERHPHVEMIVPQLPPYPADAAELLESLV
-LEHGGAPLGLVGSSLGGYYATWLSQCFMLPAVVVNPAVRPFELLTDYLGQNENPYTGQQYVLESRHIYDLKVMQIDPL
-EAPDLIWLLQQTGDEVLDYRQAVAYYASCRQTVTEGGNHAFTGFEDYFNQIVDFLGLHSC" } ,
-          annot {
-            {
-              data
-                ftable {
-                  {
-                    id
-                      local
-                        id 17 ,
-                    data
-                      prot {
-                        name {
-                          "hypothetical protein" } } ,
-                    location
-                      int {
-                        from 0 ,
-                        to 192 ,
-                        id
-                          local
-                            str "g4_1_8" } } } } } } ,
-        seq {
-          id {
-            local
-              str "g4_1_9" } ,
-          descr {
-            title "C4-dicarboxylate TRAP transporter large permease protein
- DctM [Genus species]" ,
-            molinfo {
-              biomol peptide ,
-              tech concept-trans } } ,
-          inst {
-            repr raw ,
-            mol aa ,
-            length 360 ,
-            seq-data
-              ncbieaa "MNSGGIAARLVNFAKLFTGKLPGSLSYTNIVGNMMFGAISGSAIAASTSIGGVMV
-PMSAREGYDRGFAAAVNIASAPTGMLIPPTTAFILYALASGGTSIAALFAGGLVAGVLWGVGCMLVTLVVAKRRNYRV
-FFTVQKGMALKVAVEAIPSLLLIVIIVGGIVQGIFTAIEASAIAVVYTLLLTMVFYRTLKIKDLPSILLQTVVMTGVI
-MFLLATSSAMSFSMSITNIPAALSDMILGISANKLVILLVITVFLLIIGAFMDIGPAILIFTPILLPIMAKLGVDPVH
-FGIIMIYNLAIGTITPPVGSGLYVGASVGKVKVEEVIKPLLPFYGAIIGVLLLITYIPEITLFLPRLLGIM" } ,
-          annot {
-            {
-              data
-                ftable {
-                  {
-                    id
-                      local
-                        id 18 ,
-                    data
-                      prot {
-                        name {
-                          "C4-dicarboxylate TRAP transporter large permease
- protein DctM" } } ,
-                    location
-                      int {
-                        from 0 ,
-                        to 359 ,
-                        id
-                          local
-                            str "g4_1_9" } } } } } } } ,
-      annot {
-        {
-          data
-            ftable {
-              {
-                id
-                  local
-                    id 1 ,
-                data
-                  cdregion {
-                    frame one ,
-                    code {
-                      id 11 } } ,
-                product
-                  whole
-                    local
-                      str "g4_1_1" ,
-                location
-                  int {
-                    from 0 ,
-                    to 830 ,
-                    strand plus ,
-                    id
-                      local
-                        str "g4_1" } ,
-                qual {
-                  {
-                    qual "inference" ,
-                    val "ab initio prediction:Prodigal:002006" } ,
-                  {
-                    qual "inference" ,
-                    val "similar to AA sequence:UniProtKB:P75820" } } ,
-                xref {
-                  {
-                    data
-                      gene {
-                        locus "amiD" ,
-                        locus-tag "LIKMDGFN_00001" } } } ,
-                dbxref {
-                  {
-                    db "COG" ,
-                    tag
-                      str "COG3023" } } } ,
-              {
-                id
-                  local
-                    id 2 ,
-                data
-                  cdregion {
-                    frame one ,
-                    code {
-                      id 11 } } ,
-                product
-                  whole
-                    local
-                      str "g4_1_2" ,
-                location
-                  int {
-                    from 860 ,
-                    to 1240 ,
-                    strand plus ,
-                    id
-                      local
-                        str "g4_1" } ,
-                qual {
-                  {
-                    qual "inference" ,
-                    val "ab initio prediction:Prodigal:002006" } ,
-                  {
-                    qual "inference" ,
-                    val "similar to AA sequence:UniProtKB:Q05354" } } ,
-                xref {
-                  {
-                    data
-                      gene {
-                        locus "hpcD" ,
-                        locus-tag "LIKMDGFN_00002" } } } } ,
-              {
-                id
-                  local
-                    id 3 ,
-                data
-                  cdregion {
-                    frame one ,
-                    code {
-                      id 11 } } ,
-                product
-                  whole
-                    local
-                      str "g4_1_3" ,
-                location
-                  int {
-                    from 1270 ,
-                    to 2073 ,
-                    strand plus ,
-                    id
-                      local
-                        str "g4_1" } ,
-                qual {
-                  {
-                    qual "inference" ,
-                    val "ab initio prediction:Prodigal:002006" } ,
-                  {
-                    qual "inference" ,
-                    val "similar to AA sequence:UniProtKB:P42270" } } ,
-                xref {
-                  {
-                    data
-                      gene {
-                        locus "hpcG" ,
-                        locus-tag "LIKMDGFN_00003" } } } } ,
-              {
-                id
-                  local
-                    id 4 ,
-                data
-                  cdregion {
-                    frame one ,
-                    code {
-                      id 11 } } ,
-                product
-                  whole
-                    local
-                      str "g4_1_4" ,
-                location
-                  int {
-                    from 2110 ,
-                    to 3513 ,
-                    strand plus ,
-                    id
-                      local
-                        str "g4_1" } ,
-                qual {
-                  {
-                    qual "inference" ,
-                    val "ab initio prediction:Prodigal:002006" } } ,
-                xref {
-                  {
-                    data
-                      gene {
-                        locus-tag "LIKMDGFN_00004" } } } } ,
-              {
-                id
-                  local
-                    id 5 ,
-                data
-                  cdregion {
-                    frame one ,
-                    code {
-                      id 11 } } ,
-                product
-                  whole
-                    local
-                      str "g4_1_5" ,
-                location
-                  int {
-                    from 3534 ,
-                    to 4307 ,
-                    strand plus ,
-                    id
-                      local
-                        str "g4_1" } ,
-                qual {
-                  {
-                    qual "inference" ,
-                    val "ab initio prediction:Prodigal:002006" } ,
-                  {
-                    qual "inference" ,
-                    val "similar to AA sequence:UniProtKB:P02915" } } ,
-                xref {
-                  {
-                    data
-                      gene {
-                        locus "hisP" ,
-                        locus-tag "LIKMDGFN_00005" } } } ,
-                dbxref {
-                  {
-                    db "COG" ,
-                    tag
-                      str "COG4598" } } } ,
-              {
-                id
-                  local
-                    id 6 ,
-                data
-                  cdregion {
-                    frame one ,
-                    code {
-                      id 11 } } ,
-                product
-                  whole
-                    local
-                      str "g4_1_6" ,
-                location
-                  int {
-                    from 4326 ,
-                    to 5093 ,
-                    strand plus ,
-                    id
-                      local
-                        str "g4_1" } ,
-                qual {
-                  {
-                    qual "inference" ,
-                    val "ab initio prediction:Prodigal:002006" } ,
-                  {
-                    qual "inference" ,
-                    val "similar to AA sequence:UniProtKB:P0A873" } } ,
-                xref {
-                  {
-                    data
-                      gene {
-                        locus "trmD" ,
-                        locus-tag "LIKMDGFN_00006" } } } ,
-                dbxref {
-                  {
-                    db "COG" ,
-                    tag
-                      str "COG0336" } } } ,
-              {
-                id
-                  local
-                    id 7 ,
-                data
-                  cdregion {
-                    frame one ,
-                    code {
-                      id 11 } } ,
-                product
-                  whole
-                    local
-                      str "g4_1_7" ,
-                location
-                  int {
-                    from 5137 ,
-                    to 5397 ,
-                    strand plus ,
-                    id
-                      local
-                        str "g4_1" } ,
-                qual {
-                  {
-                    qual "inference" ,
-                    val "ab initio prediction:Prodigal:002006" } } ,
-                xref {
-                  {
-                    data
-                      gene {
-                        locus-tag "LIKMDGFN_00007" } } } } ,
-              {
-                id
-                  local
-                    id 8 ,
-                data
-                  cdregion {
-                    frame one ,
-                    code {
-                      id 11 } } ,
-                product
-                  whole
-                    local
-                      str "g4_1_8" ,
-                location
-                  int {
-                    from 5412 ,
-                    to 5993 ,
-                    strand plus ,
-                    id
-                      local
-                        str "g4_1" } ,
-                qual {
-                  {
-                    qual "inference" ,
-                    val "ab initio prediction:Prodigal:002006" } } ,
-                xref {
-                  {
-                    data
-                      gene {
-                        locus-tag "LIKMDGFN_00008" } } } } ,
-              {
-                id
-                  local
-                    id 9 ,
-                data
-                  cdregion {
-                    frame one ,
-                    code {
-                      id 11 } } ,
-                product
-                  whole
-                    local
-                      str "g4_1_9" ,
-                location
-                  int {
-                    from 6051 ,
-                    to 7133 ,
-                    strand plus ,
-                    id
-                      local
-                        str "g4_1" } ,
-                qual {
-                  {
-                    qual "inference" ,
-                    val "ab initio prediction:Prodigal:002006" } ,
-                  {
-                    qual "inference" ,
-                    val "similar to AA sequence:UniProtKB:O07838" } } ,
-                xref {
-                  {
-                    data
-                      gene {
-                        locus "dctM" ,
-                        locus-tag "LIKMDGFN_00009" } } } ,
-                dbxref {
-                  {
-                    db "COG" ,
-                    tag
-                      str "COG1593" } } } } } } } } }
diff --git a/Examples/2-res-Annotate-prokka/tmp_files/genome4.fst_prokka-split5N.fna-prokkaRes/GEN4.1111.00001.tbl b/Examples/2-res-Annotate-prokka/tmp_files/genome4.fst_prokka-split5N.fna-prokkaRes/GEN4.1111.00001.tbl
deleted file mode 100644
index c671a4f027cc37e2afd33d531e5f848d938475c8..0000000000000000000000000000000000000000
--- a/Examples/2-res-Annotate-prokka/tmp_files/genome4.fst_prokka-split5N.fna-prokkaRes/GEN4.1111.00001.tbl
+++ /dev/null
@@ -1,57 +0,0 @@
->Feature g4_1
-1	831	CDS
-			EC_number	3.5.1.28
-			db_xref	COG:COG3023
-			gene	amiD
-			inference	ab initio prediction:Prodigal:002006
-			inference	similar to AA sequence:UniProtKB:P75820
-			locus_tag	LIKMDGFN_00001
-			product	N-acetylmuramoyl-L-alanine amidase AmiD
-861	1241	CDS
-			EC_number	5.3.3.10
-			gene	hpcD
-			inference	ab initio prediction:Prodigal:002006
-			inference	similar to AA sequence:UniProtKB:Q05354
-			locus_tag	LIKMDGFN_00002
-			product	5-carboxymethyl-2-hydroxymuconate Delta-isomerase
-1271	2074	CDS
-			EC_number	4.2.1.163
-			gene	hpcG
-			inference	ab initio prediction:Prodigal:002006
-			inference	similar to AA sequence:UniProtKB:P42270
-			locus_tag	LIKMDGFN_00003
-			product	2-oxo-hept-4-ene-1,7-dioate hydratase
-2111	3514	CDS
-			inference	ab initio prediction:Prodigal:002006
-			locus_tag	LIKMDGFN_00004
-			product	hypothetical protein
-3535	4308	CDS
-			db_xref	COG:COG4598
-			gene	hisP
-			inference	ab initio prediction:Prodigal:002006
-			inference	similar to AA sequence:UniProtKB:P02915
-			locus_tag	LIKMDGFN_00005
-			product	Histidine transport ATP-binding protein HisP
-4327	5094	CDS
-			EC_number	2.1.1.228
-			db_xref	COG:COG0336
-			gene	trmD
-			inference	ab initio prediction:Prodigal:002006
-			inference	similar to AA sequence:UniProtKB:P0A873
-			locus_tag	LIKMDGFN_00006
-			product	tRNA (guanine-N(1)-)-methyltransferase
-5138	5398	CDS
-			inference	ab initio prediction:Prodigal:002006
-			locus_tag	LIKMDGFN_00007
-			product	hypothetical protein
-5413	5994	CDS
-			inference	ab initio prediction:Prodigal:002006
-			locus_tag	LIKMDGFN_00008
-			product	hypothetical protein
-6052	7134	CDS
-			db_xref	COG:COG1593
-			gene	dctM
-			inference	ab initio prediction:Prodigal:002006
-			inference	similar to AA sequence:UniProtKB:O07838
-			locus_tag	LIKMDGFN_00009
-			product	C4-dicarboxylate TRAP transporter large permease protein DctM
diff --git a/Examples/2-res-Annotate-prokka/tmp_files/genome4.fst_prokka-split5N.fna-prokkaRes/GEN4.1111.00001.tsv b/Examples/2-res-Annotate-prokka/tmp_files/genome4.fst_prokka-split5N.fna-prokkaRes/GEN4.1111.00001.tsv
deleted file mode 100644
index 6fb4e7be29674a310922cdb82a5fbe08125db815..0000000000000000000000000000000000000000
--- a/Examples/2-res-Annotate-prokka/tmp_files/genome4.fst_prokka-split5N.fna-prokkaRes/GEN4.1111.00001.tsv
+++ /dev/null
@@ -1,10 +0,0 @@
-locus_tag	ftype	length_bp	gene	EC_number	COG	product
-LIKMDGFN_00001	CDS	831	amiD	3.5.1.28	COG3023	N-acetylmuramoyl-L-alanine amidase AmiD
-LIKMDGFN_00002	CDS	381	hpcD	5.3.3.10		5-carboxymethyl-2-hydroxymuconate Delta-isomerase
-LIKMDGFN_00003	CDS	804	hpcG	4.2.1.163		2-oxo-hept-4-ene-1,7-dioate hydratase
-LIKMDGFN_00004	CDS	1404				hypothetical protein
-LIKMDGFN_00005	CDS	774	hisP		COG4598	Histidine transport ATP-binding protein HisP
-LIKMDGFN_00006	CDS	768	trmD	2.1.1.228	COG0336	tRNA (guanine-N(1)-)-methyltransferase
-LIKMDGFN_00007	CDS	261				hypothetical protein
-LIKMDGFN_00008	CDS	582				hypothetical protein
-LIKMDGFN_00009	CDS	1083	dctM		COG1593	C4-dicarboxylate TRAP transporter large permease protein DctM
diff --git a/Examples/2-res-Annotate-prokka/tmp_files/genome4.fst_prokka-split5N.fna-prokkaRes/GEN4.1111.00001.txt b/Examples/2-res-Annotate-prokka/tmp_files/genome4.fst_prokka-split5N.fna-prokkaRes/GEN4.1111.00001.txt
deleted file mode 100644
index 61a7be1fcd34429f898e3d10baea743e4d6e049c..0000000000000000000000000000000000000000
--- a/Examples/2-res-Annotate-prokka/tmp_files/genome4.fst_prokka-split5N.fna-prokkaRes/GEN4.1111.00001.txt
+++ /dev/null
@@ -1,4 +0,0 @@
-organism: Genus species strain 
-contigs: 1
-bases: 7134
-CDS: 9