diff --git a/Examples/1-res-Annotate/Genes/EXAM.0219.00001.gen b/Examples/1-res-Annotate/Genes/EXAM.0219.00001.gen deleted file mode 100644 index b51d618b9eb022c635025692e6e73618f80224f5..0000000000000000000000000000000000000000 --- a/Examples/1-res-Annotate/Genes/EXAM.0219.00001.gen +++ /dev/null @@ -1,169 +0,0 @@ ->EXAM.0219.00001.b0001_00001 1668 glnS | Glutamine--tRNA ligase | 6.1.1.18 | similar to AA sequence:UniProtKB:P00962 -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.0219.00001.b0001_00002 831 amiD | N-acetylmuramoyl-L-alanine amidase AmiD | 3.5.1.28 | similar to AA sequence:UniProtKB:P75820 -ATGAAAGCGCTACTGTGGCTGGTGGGTCTCGCGTTGCTGTTAACAGGCTGCGCGAGCGAA -AAAGGAATTATCGATAAAGAGGGATATCAGCTTGATACCCGACATCGGGCGCAGGCGGCC -TATCCGCGCATTAAAGTCCTGGTGATTCACTATACGGCGGAAAACTTTGACGTTTCGCTG -GCGACGTTAACGGGTCGCAACGTCAGTTCGCATTACCTGATTCCCGCAACCCCGCCATTA -TATGGCGGTAAACCGCGCATCTGGCAACTGGTGCCGGAACAGGATCAGGCCTGGCATGCG -GGCGTCAGTTTCTGGCGAGGCGCCACGCGTCTCAATGATACGTCTATTGGCATTGAGCTG -GAAAATCGTGGTTGGCGAATGTCCGGCGGGGTGAAATCTTTCGCGCCGTTTGAATCCGCG -CAAATTCAGGCATTGATTCCGTTAGCGAAGGATATTATCGCGCGCTATAACATCAAACCG -CAGAATGTGGTGGCCCATGCGGATATCGCGCCGCAGCGTAAAGACGATCCCGGCCCGCGC -TTCCCGTGGCGCGAGCTGGCGGCGCAGGGGATTAGCGCCTGGCCTGACGCCCAGCGTGTG -GCGTTTTATCTGGCTGGACGCGCGCCGTATACGCCAGTCGATACCGCAACGGTGCTTGCG -TTACTCTCGCGCTATGGCTATGAAGTCAAAGCCGATATGACGGCACGCGAGCAGCAGCGG -GTGATTATGGCGTTCCAGATGCACTTCCGTCCGGCGCAATGGAACGGTATCGCAGATGCC -GAAACGCAGGCGATTGCCGAAGCATTACTGGAGAAGTACGGCCAGGATTAA ->EXAM.0219.00001.b0002_00003 381 hpcD | 5-carboxymethyl-2-hydroxymuconate Delta-isomerase | 5.3.3.10 | similar to AA sequence:UniProtKB:Q05354 -ATGCCGCACTTTATTGCTGAATGTACTGAAAATATTCGCGAGCAGGCTGATTTACCCGGC -CTGTTCAGCAAGGTAAACGAGGCGCTGGCCGCCAGCGGGATTTTCCCCATCGGCGGTATC -CGCAGTCGCGCCCACTGGCTGGATACCTGGCAGATGGCTGACGGTAAGCATGATTACGCG -TTTGTGCATATGACGCTGAAAATCGGCGCCGGGCGCAGCCTGGAGAGCCGTCAGGAAGTT -GGCGAAATGCTGTTTGGGCTGATTAAAGCCCACTTCGCCGACCTGATGGAGAACCGCTAT -CTGGCGCTGTCGTTTGAGATTGCCGAGCTACATCCGACGCTCAATTACAAACAAAACAAC -GTACACGCGTTATTTAAATAG ->EXAM.0219.00001.i0002_00004 1410 NA | hypothetical protein | 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.0219.00001.i0002_00005 774 hisP | Histidine transport ATP-binding protein HisP | NA | similar to AA sequence:UniProtKB:P02915 -ATGTCAGAAAATAAATTACACGTTATCGATTTGCACAAACGCTACGGCGGTCATGAAGTG -CTGAAAGGGGTATCGCTGCAGGCCCGCGCCGGAGATGTGATTAGCATCATCGGCTCGTCC -GGCTCCGGTAAAAGCACTTTTTTGCGCTGTATTAACTTCCTCGAAAAACCGAGCGAAGGC -GCGATTATCGTGAACGGTCAGAACATTAATCTGGTGCGCGACAAAGATGGGCAGCTCAAA -GTGGCGGATAAAAATCAGCTACGCTTGTTGCGTACCCGCCTGACGATGGTGTTTCAGCAC -TTCAACCTCTGGAGCCACATGACGGTGCTGGAAAATGTGATGGAAGCGCCGATTCAGGTA -CTGGGATTAAGCAAGCACGACGCGCGCGAGCGGGCGTTGAAATATCTGGCGAAGGTGGGG -ATTGATGAGCGCGCTCAGGGCAAATATCCCGTCCATCTCTCCGGCGGCCAACAGCAGCGC -GTTTCTATTGCGCGCGCGCTGGCGATGGAACCTGACGTTTTACTGTTCGATGAACCCACA -TCGGCGCTCGATCCTGAACTGGTCGGCGAAGTGTTGCGCATCATGCAACAACTGGCGGAA -GAAGGCAAAACGATGGTGGTGGTCACGCATGAAATGGGCTTCGCTCGCCATGTCTCTTCG -CACGTTATTTTTCTGCATCAGGGGAAAATTGAAGAAGAGGGTGATCCGGAGCAGGTGTTC -GGCAATCCGCAAAGCCCGCGTTTACAGCAATTCCTGAAAGGCTCGCTGAAATAA ->EXAM.0219.00001.i0002_00006 735 trmD_1 | tRNA (guanine-N(1)-)-methyltransferase | 2.1.1.228 | similar to AA sequence:UniProtKB:P0A873 -ATGTTCCGCGCAATTACCGATTACGGGGTAACTGGCCGGGCAGTAAAAAAAGGCCTGCTG -AACATCCAAAGCTGGAGTCCTCGCGACTTCGCGCATGACCGGCACCGTACCGTGGACGAC -CGTCCTTACGGCGGCGGACCGGGGATGTTAATGATGGTGCAACCCTTGCGGGACGCCATT -CACGCAGCAAAAGCCGCGGCAGGTGAAGGCGCTAAAGTGATTTATCTGTCGCCTCAGGGA -CGCAAGCTTGATCAAGCGGGCGTTAGCGAGCTGGCCACGAATCAGAAGCTTATTCTGGTG -TGTGGTCGCTACGAAGGCGTAGATGAGCGCGTAATTCAGACCGAAATTGACGAAGAATGG -TCAATTGGCGATTACGTTCTCAGCGGTGGCGAACTACCGGCAATGACGCTGATTGACTCC -GTCGCCCGGTTTATACCGGGGGTTCTGGGGCATGAGGCATCAGCAATCGAAGATTCGTTT -GCTGATGGGTTGCTGGATTGTCCGCACTATACGCGCCCTGAAGTGTTAGAGGGGATGGAA -GTACCGCCAGTATTGCTGTCGGGAAACCATGCTGAGATACGTCGCTGGCGTTTGAAACAG -TCGCTGGGCCGAACCTGGCTTAGAAGACCTGAACTTCTGGAAAACCTGGCTCTGACTGAA -GAGCAAGCAAGGTTGCTGGCGGAGTTCAAAACAGAACACGCACAACAGCAGCATAAACAT -GATGGGATGGCATAG ->EXAM.0219.00001.i0002_00007 828 trmD_2 | tRNA (guanine-N(1)-)-methyltransferase | 2.1.1.228 | similar to AA sequence:UniProtKB:P0A873 -ATGATGGGATGGCATAGCCGTCATATGGGCTCTCAGAGGAGACGCGCTAATGCGCAGTAC -GTGTTTATTGGCATAGTTAGCCTGTTTCCTGAAATGTTCCGCGCAATTACCGATTACGGG -GTAACTGGCCGGGCAGTAAAAAAAGGCCTGCTGAACATCCAAAGCTGGAGTCCTCGCGAC -TTCGCGCATGACCGGCACCGTACCGTGGACGACCGTCCTTACGGCGGCGGACCGGGGATG -TTAATGATGGTGCAACCCTTGCGGGACGCCATTCACGCAGCAAAAGCCGCGGCAGGTGAA -GGCGCTAAAGTGATTTATCTGTCGCCTCAGGGACGCAAGCTTGATCAAGCGGGCGTTAGC -GAGCTGGCCACGAATCAGAAGCTTATTCTGGTGTGTGGTCGCTACGAAGGCGTAGATGAG -CGCGTAATTCAGACCGAAATTGACGAAGAATGGTCAATTGGCGATTACGTTCTCAGCGGT -GGCGAACTACCGGCAATGACGCTGATTGACTCCGTCGCCCGGTTTATACCGGGGGTTCTG -GGGCATGAGGCATCAGCAATCGAAGATTCGTTTGCTGATGGGTTGCTGGATTGTCCGCAC -TATACGCGCCCTGAAGTGTTAGAGGGGATGGAAGTACCGCCAGTATTGCTGTCGGGAAAC -CATGCTGAGATACGTCGCTGGCGTTTGAAACAGTCGCTGGGCCGAACCTGGCTTAGAAGA -CCTGAACTTCTGGAAAACCTGGCTCTGACTGAAGAGCAAGCAAGGTTGCTGGCGGAGTTC -AAAACAGAACACGCACAACAGCAGCATAAACATGATGGGATGGCATAG ->EXAM.0219.00001.i0002_00008 465 NA | hypothetical protein | NA | NA -ATGAAGTTTGTTGCGCCCGAACAGGCACCGGAACAGGCGGAGGTCATCAAAAATACGCCG -TTCTGGCCTGATGTGGACCTGTCGGAATTTCGCAGTGTGATGCGCACTGACGGCACGGTG -ACGCAGCCGCGTTTAAAGCAGGTCGTGCTGACGGCGATCTCTGAGGTTAACGCTGAGCTG -TACGACTTCCGCAACCGTCAGCAGATGCTGGGCTGGCGGACACTTGCTGAGGTTCCCGCA -GAAATGCTGGACGGTAAAAGCGAGCGTATCCGGCACTACCACAACGCTGTTTTTTGCTGG -GCGCGCGCTGTGCTTAATGAGCGTTATCAGGACTATGACGCCACGGCGTCAGGCGTGAAG -CGAGGGGAGGAGCTGGCGGAGGCCAGCGGCGATCTGTGGCGTGATGCCCGCTGGGCCATC -AGCCGGGTGCAGGATGTACCGCACTGTACGGTGGAGCTTATCTGA ->EXAM.0219.00001.i0002_00009 261 NA | hypothetical protein | NA | NA -ATGGCCGGGTTGCACGCGCCATATGCATATAGCGCGCATCATGCGGTGAATTTCTGTTCT -GAGTATAAACGTGGCTTTGTATTGGGTTTTACACACCGTATGTTCGAAAAGACCGGCGAT -CGTCAACTTAGCGCGTGGGAGGCTGGAATTCTGACGCGTCGCTATGGTCTGGATAAAGAA -ATGGTGATGGATTTCTTTAAAGAGAATCATTCCGGGATGGCGGTTCGCTTCTTTATGGCC -GGTTATCGACTCGAAGGTTGA ->EXAM.0219.00001.i0002_00010 582 NA | hypothetical protein | NA | NA -ATGTCTACGCTTCTCTATTTGCACGGATTCAACAGTTCCCCTCGCTCGGCAAAAGCGTGC -CAGCTAAAAAACTGGCTGGCGGAGCGTCATCCGCATGTTGAGATGATCGTCCCTCAGCTG -CCGCCGTATCCTGCCGATGCGGCGGAGTTGCTGGAATCTCTCGTGCTTGAGCATGGCGGT -GCGCCATTAGGGCTGGTAGGATCGTCGCTGGGTGGTTATTACGCCACCTGGCTGTCGCAA -TGTTTTATGCTGCCGGCTGTGGTGGTGAATCCCGCCGTGCGGCCCTTTGAATTACTGACC -GACTATCTCGGTCAGAACGAGAACCCCTACACCGGGCAGCAATATGTGCTAGAGTCTCGC -CATATTTATGATCTTAAAGTCATGCAGATTGACCCGCTGGAAGCGCCGGACCTGATCTGG -CTACTGCAACAGACGGGCGATGAAGTGCTGTATTACCGCCAGGCGGTGGCATATTACGCC -TCCTGCCGTCAGACAGTGACCGAGGGTGGTAATCACGCATTCACGGGCTTCGAAGATTAT -TTCAACCAGATTGTCGATTTTCTTGGACTGCACAGTTGCTGA ->EXAM.0219.00001.b0002_00011 1308 dctM | C4-dicarboxylate TRAP transporter large permease protein DctM | NA | similar to AA sequence:UniProtKB:O07838 -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/1-res-Annotate/Genes/EXAM.1216.00002.gen b/Examples/1-res-Annotate/Genes/EXAM.1216.00002.gen deleted file mode 100644 index be5612c5b28d275f90fb47566718e6fcbb595233..0000000000000000000000000000000000000000 --- a/Examples/1-res-Annotate/Genes/EXAM.1216.00002.gen +++ /dev/null @@ -1,158 +0,0 @@ ->EXAM.1216.00002.b0001_00001 831 amiD_1 | N-acetylmuramoyl-L-alanine amidase AmiD | 3.5.1.28 | similar to AA sequence:UniProtKB:P75820 -ATGAGAGCGCTACTGTGGCTGGTGGGTCTTGCGTTGCTGTTAACAGGCTGCGCGAGCGAA -AAAGGAATTATCGATGAAGAGGGATATCAGCTTGATACCCGACATCGGGCGCAGGCGGCC -TATCCGCGCATTAAAGTCCTGGTGATTCACTATACGGCGGAAAACTTTGACGTTTCGCTG -GCGACGTTAACGGGCCGCAACGTCAGTTCGCATTACCTGATTCCCGCAACCCCGCCATTA -TATGGCGGTAAACCGCGCATCTGGCAACTGGTGCCGGAACAGGATCAGGCCTGGCATGCG -GGCGTCAGTTTCTGGCGAGGCGCCACGCGTCTCAATGATACGTCTATTGGCATTGAGCTG -GAAAATCGCGGCTGGCGAATGTCCGGCGGGGTGAAATCTTTCGCGCCGTTTGAATCCGCG -CAAATTCAGGCATTGATTCCGTTAGCGAAGGACATTATCGCGCGCTATGACATCAAACCG -CAGAATGTGGTGGCCCATGCGGATATCGCGCCGCAGCGTAAAGACGATCCCGGCCCGCGC -TTCCCGTGGCGCGAGCTGGCGGCACAGGGGATTGGCGCCTGGCCTGACGCCCAGCGTGTG -GCGTTTTATCTGGCTGGACGCGCGCCGTATACGCCAGTCGATACCGCAACGGTGCTTGCG -TTACTCTCGCGCTATGGCTATGAAGTCAAAGCCGATATGACGGCGCGCGAGCAACAGCGG -GTGATTATGGCGTTCCAGATGCACTTCCGTCCGGCGCAATGGAACGGTATCGCAGATGCC -GAAACGCAGGCGATTGCCGAAGCATTACTGGAGAAGTACGGCCAGGATTAA ->EXAM.1216.00002.i0001_00002 831 amiD_2 | N-acetylmuramoyl-L-alanine amidase AmiD | 3.5.1.28 | similar to AA sequence:UniProtKB:P75820 -ATGAGAGCGCTACTGTGGCTGGTGGGTCTTGCGTTGCTGTTAACAGGCTGCGCGAGCGAA -AAAGGAATTATCGATGAAGAGGGATATCAGCTTGATACCCGACATCGGGCGCAGGCGGCC -TATCCGCGCATTAAAGTCCTGGTGATTCACTATACGGCGGAAAACTTTGACGTTTCGCTG -GCGACGTTAACGGGCCGCAACGTCAGTTCGCATTACCTGATTCCCGCAACCCCGCCATTA -TATGGCGGTAAACCGCGCATCTGGCAACTGGTGCCGGAACAGGATCAGGCCTGGCATGCG -GGCGTCAGTTTCTGGCGAGGCGCCACGCGTCTCAATGATACGTCTATTGGCATTGAGCTG -GAAAATCGCGGCTGGCGAATGTCCGGCGGGGTGAAATCTTTCGCGCCGTTTGAATCCGCG -CAAATTCAGGCATTGATTCCGTTAGCGAAGGACATTATCGCGCGCTATGACATCAAACCG -CAGAATGTGGTGGCCCATGCGGATATCGCGCCGCAGCGTAAAGACGATCCCGGCCCGCGC -TTCCCGTGGCGCGAGCTGGCGGCACAGGGGATTGGCGCCTGGCCTGACGCCCAGCGTGTG -GCGTTTTATCTGGCTGGACGCGCGCCGTATACGCCAGTCGATACCGCAACGGTGCTTGCG -TTACTCTCGCGCTATGGCTATGAAGTCAAAGCCGATATGACGGCGCGCGAGCAACAGCGG -GTGATTATGGCGTTCCAGATGCACTTCCGTCCGGCGCAATGGAACGGTATCGCAGATGCC -GAAACGCAGGCGATTGCCGAAGCATTACTGGAGAAGTACGGCCAGGATTAA ->EXAM.1216.00002.i0001_00003 474 hpcD | 5-carboxymethyl-2-hydroxymuconate Delta-isomerase | 5.3.3.10 | similar to AA sequence:UniProtKB:Q05354 -ATGCCGAAACGCAGGCGATTGCCGAAGCATTACTGGAGAAGTACGGCCAGGATTAACAGG -GCGCGGTATCGCGAGGACTCTCTCTTCGAGGACATGCCGCACTTTATTGCTGAATGTACT -GAAAATATTCGCGAGCAGGCTGATTTACCCGGCCTGTTCAGCAAGGTAAACGAGGCGCTG -GCCGCCAGCGGGATTTTCCCCATCGGCGGTATCCGCAGTCGCGCCCACTGGCTGGATACC -TGGCAGATGGCTGACGGTAAGCATGATTACGCGTTTGTGCATATGACGCTGAAAATCGGC -GCCGGGCGCAGCCTGGAGAGCCGTCAGGAAGTCGGCGAAATGCTGTTCGGGCTGATTAAA -GCCCACTTCGCCGACCTGATGGAGAACCGCTATCTGGCGCTGTCGTTTGAGATTGCCGAG -TTACATCCAACGCTCAATTACAAACAAAACAACGTACACGCGTTATTTAAATAG ->EXAM.1216.00002.i0001_00004 225 pspB | Phage shock protein B | NA | similar to AA sequence:UniProtKB:P0AFM9 -ATGAGCGCGCTATTTCTGGCCATCCCGTTAACCATTTTTGTGTTGTTTGTGTTACCGATT -TGGCTGTGGCTGCATTACAGCAACCGCGCCGGTCGGGGAGAACTGTCGCAAAGCGAGCAG -CAACGCTTACTGCAACTCACAGACGACGCGCAACGTATGCGCGAGCGCATTCAGGCGCTG -GAAGACATTCTTGATGCAGAGCATCCGAACTGGAGAGAGCGCTAA ->EXAM.1216.00002.i0001_00005 1404 NA | hypothetical protein | 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.i0001_00006 774 hisP | Histidine transport ATP-binding protein HisP | NA | similar to AA sequence:UniProtKB:P02915 -ATGTCAGAAAATAAATTACACGTTATCGATTTGCACAAACGCTACGGCGGTCATGAAGTG -CTGAAAGGGGTATCGCTGCAGGCCCGCGCCGGAGATGTGATTAGCATCATCGGCTCGTCC -GGCTCCGGTAAAAGCACTTTTTTGCGCTGTATTAACTTCCTCGAAAAACCGAGCGAAGAC -GCGATTATCGTGAACGGTCAGAACATTAATCTGGTGCGCGACAAAGACGGGCAGCTCAAA -GTGGCGGATAAAAATCAGCTACGCTTGTTGCGTACCCGCCTGACGATGGTGTTTCAGCAC -TTTAACCTCTGGAGCCACATGACGGTGCTGGAAAATGTGATGGAAGCGCCGATTCAGGTA -CTGGGATTAAGCAAGCACGACGCGCGCGAGCGGGCGTTGAAATATCTGGCGAAGGTGGGG -ATTGATGAGCGCGCTCAGGGCAAATATCCCGTTCATCTCTCCGGTGGCCAACAGCAGCGC -GTTTCTATTGCGCGCGCGCTGGCGATGGAACCTGACGTTTTACTGTTCGATGAACCCACT -TCGGCGCTCGATCCTGAACTGGTCGGCGAAGTGTTGCGCATCATGCAACAACTGGCGGAA -GAAGGCAAAACGATGGTGGTGGTCACGCATGAAATGGGCTTCGTTCGCCATGTCTCTTCG -CACGTTATTTTTCTGCATCAGGGGAAAATTGAAGAAGAGGGCGATCCGGAGCAGGTGTTC -GGCAATCCGCAAAGCCCGCGTTTACAGCAATTCCTGAAAGGCTCGCTGAAATAA ->EXAM.1216.00002.i0001_00007 792 trmD | tRNA (guanine-N(1)-)-methyltransferase | 2.1.1.228 | similar to AA sequence:UniProtKB:P0A873 -ATGCGCGCGATATATCGGCGATGCGTGTTTATTGGCATCGTTAGCCTGTTTCCTGAAATG -TTCCGCGCAATTACCGATTACGGGGTAACTGGCCGGGCAGTAAAAAATGGCCTGCTGAAC -ATCCAAAGCTGGAGTCCTCGCGACTTCACGCATGACCGGCACCGTACCGTGGACGATCGT -CCTTACGGCGGCGGACCAGGGATGTTAATGATGGTGCAACCCTTGCGGGACGCCATTCAC -GCAGCAAAAGCCGCGGCAGGTGAAGGCGCTAAAGTGATTTATCTGTCGCCTCAGGGACGC -AAGCTTGATCAAGCGGGCGTTAGCGAGCTGGCCACGAATCAGAAGCTTATTCTGGTGTGT -GGTCGCTACGAAGGCGTAGATGAGCGCGTAATTCAGACCGAAATTGACGAAGAATGGTCA -ATTGGCGATTACGTTCTCAGCGGTGGCGAACTACCGGCAATGACGCTGATTGACTCCGTC -GCCCGGTTTATACCGGGAGTTCTGGGGCATGAAGCATCAGCAATCGAAGATTCGTTTGCT -GATGGGTTGCTGGATTGTCCGCACTATACGCGCCCTGAAGTGTTAGAGGGGATGGAAGTA -CCGCCAGTATTGCTGTCGGGAAACCATGCTGAGATACGTCGCTGGCGTTTGAAACAGTCG -CTGGGCCGAACCTGGCTTAGAAGACCTGAACTTCTGGAAAACCTGGCTCTGACTGAAGAG -CAAGCAAGGTTGCTGGCGGAGTTCAAAACAGAACACGCACAACAGCAGCATAAACATGAT -GGGATGGCATAG ->EXAM.1216.00002.b0001_00008 288 NA | hypothetical protein | NA | NA -ATGAATAATCATTTTGGGAAAGGGTTAATGGCCGGGTTGCACGCGCCATATGCATATAGC -GCGCATCATGCGGTGAATTTCTGTTCTGAGTATAAACGTGGCTTTGTATTGGGTTTTACA -CACCGTATGTTCGAAAAGACCGGCGATCGTCAACTTAGCGCGTGGGAGGCTGGAATTCTG -ACGCGTCGCTATGGTCTGGATAAAGAAATGGTGATGGATTTCTTTAAAGAGAATCATTCC -GGGATGGCGGTTCGCTTCTTTATGGCCGGTTATCGACTCGAAGGTTGA ->EXAM.1216.00002.b0002_00009 582 NA | hypothetical protein | NA | NA -ATGTCTACGCTTCTCTATTTGCACGGATTCAACAGTTCCCCTCGCTCGGCAAAAGCGTGC -CAGCTAAAAAACTGGCTGGCGGAGCGTCATCCGCATGTTGAGATGATCGTCCCTCAACTA -CCGCCGTATCCTGCCGATGCGGCGGAGTTGCTGGAGTCTCTCGTGCTTGAGCATGGCGGT -GCGCCATTAGGGCTGGTAGGATCGTCGCTGGGTGGTTATTACGCCACCTGGCTGTCGCAA -TGTTTTATGCTGCCGGCTGTGGTGGTGAATCCCGCCGTGCGGCCCTTTGAATTACTGACC -GACTATCTCGGTCAGAACGAGAACCCCTACACCGGGCAGCAATATGTGCTAGAGTCTCGC -CATATTTATGATCTTAAAGTCATGCAGATTGACCCGCTGGAAGCGCCGGACCTGATCTGG -CTACTGCAACAGACGGGCGATGAAGTGCTGGATTACCGCCAGGCGGTGGCATATTACGCC -TCCTGCCGTCAGACAGTGACCGAGGGTGGTAATCACGCATTCACGGGCTTCGAAGATTAT -TTCAACCAGATTGTCGATTTTCTTGGACTGCACAGTTGCTGA ->EXAM.1216.00002.b0002_00010 1308 dctM | C4-dicarboxylate TRAP transporter large permease protein DctM | NA | similar to AA sequence:UniProtKB:O07838 -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.b0003_00011 255 NA | hypothetical protein | NA | NA -ATGATAATTAATGGGAAATTAATTAAAGCAAAAGACTTAGCTAAGGCTGCAGGTGTATCT -CGTTCAACAGTGATTAAATATTACGGCATTAGCCGTGAGAATTACGAAAGGGTAGCAACT -GAAAGAAGGAAGCTTGCTTTTGAACTAAGAGCATCAGGTTTAAAATGGAAAGAAGTTGCT -GAAAAAATGAACACGACAAAATATAGCGCAATTGCATATTATAGACGATATTTAGCATTA -GAGAAAAACAAATAA ->EXAM.1216.00002.b0003_00012 780 NA | Insertion sequence IS5376 putative ATP-binding protein | NA | similar to AA sequence:UniProtKB:Q45619 -ATGGTCGAACTGCAACATCAACGGCTGATGGTGCTTGCCGAACAGCTCCAGCTGGACAGT -CTTATCGGCGCAGCGCCGGCGCTGTCGCAACAGGCGGTGGATCAGGAATGGAGCTACATG -GACTTCCTGGAGCACCTGTTACATGAGGAGAAACTGGCCCGGCATCAGCGTAAACAGGCG -ATGTACACGCGGATGGCAGCCTTCCCGGCGGTAAAGACGTTCGAGGAGTACGACTTCACC -TTCGCCACCGGCGCTCCTCAGAAGCAAATCCAGTCGCTGCGATCCCTGAGCTTCATAGAG -CGTAACGAAAACATCGTGTTGCTGGGGCCATCGGGCGTGGGAAAAACGCATCTGGCGATA -GCCATGGGCTACGAAGCAGTACGGGCGGGCATCAAGGTTCGCTTCACAACAGCAGCGGAC -CTGCTGCTACAGCTGTCCACTTCACAGCGTCAGGGCCGTTACAAAACGACTCTCAATCGT -GGTGTCATGGCCCCGAAGCTGCTTATCATCGATGAAATAGGTTATCTGCCGTTCAGTCAG -GAGGAAGCCAAGCTGTTCTTCCAGGTCATCGCCAAACGTTACGAGAAGAGCGCGATGATC -CTGACCTCCAACCTGCCGTTCGGGCAGTGGGATCAGACGTTCGCCGGTGATGCAGCGCTG -ACATCGGCGATGCTGGACCGGATCTTACATCACTCACACGTCGTGCAAATAAAAGGGGAA -AGCTATCGACTGAAGCAGAAACGAAAGGCCGGGGTTATAGCTGAAGCTAATCCTGAGTAA diff --git a/Examples/1-res-Annotate/Genes/GEN2.0219.00001.gen b/Examples/1-res-Annotate/Genes/GEN2.0219.00001.gen deleted file mode 100644 index 63fed11564a754973c279b1a561afd4d445a59a3..0000000000000000000000000000000000000000 --- a/Examples/1-res-Annotate/Genes/GEN2.0219.00001.gen +++ /dev/null @@ -1,185 +0,0 @@ ->GEN2.0219.00001.b0001_00001 774 hisP | Histidine transport ATP-binding protein HisP | NA | similar to AA sequence:UniProtKB:P02915 -ATGTCAGAAAATAAATTACACGTTATCGATTTGCACAAACGCTACGGCGGTCATGAAGTG -CTGAAAGGGGTATCGCTGCAGGCCCGCGCCGGAGATGTGATTAGCATTATCGGCTCGTCC -GGTTCCGGTAAAAGCACTTTTTTGCGCTGCATTAACTTCCTCGAAAAATCGAGCGAAGGC -GCGATTATCGTGAACGGTCAGAACATTAATCTGGTGCGCGACAAAGACGGGCAGCTCAAA -GTGGCGGATAAAAATCAGCTACGCTTGTTGCGTACCCGCCTGACGATGGTGTTTCAGCAC -TTTAACCTCTGGAACCACATGACGGTGCTGGAAAATGTGATGGAAGCGCCGATTCAGGTA -CTGGGATTAAGCAAGCACGACGCGCGCGAGCGGGCGTTGAAATATCTGGCGAAGGTGGGG -ATTGATGAGCGCGCTCAGGGCAAATATCCCGTCCATCTCTCCGGCGGCCAACAGCAGCGC -GTTTCTATTGCGCGCGCGCTGGCGATGGAACCTGACGTTTTACTGTTCGATGAACCCACA -TCGGCGCTCGATCCTGAACTGGTCGGCGAAGTGTTGCGCATCATGCAACAACTGGCGGAA -GAAGGCAAAACGATGGTGGTGGTCACGCATGAAATGGGCTTCGCCCGCCATGTCTCTTCG -CACGTGATTTTTCTGCATCAGGGGAAAATTGAAGAAGAGGGCAATCCGGAGCAGGTGTTC -GGCAATCCGCAAAGCCCGCGTTTACAGCAATTCCTGAAAGGCTCGCTGAAATAA ->GEN2.0219.00001.b0001_00002 1404 NA | hypothetical protein | 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 ->GEN2.0219.00001.b0002_00003 225 pspB | Phage shock protein B | NA | similar to AA sequence:UniProtKB:P0AFM9 -ATGAGCGCGCTATTTCTGGCCATCCCGTTAACCATTTTTGTGTTGTTTGTGTTACCGATT -TGGCTGTGGCTGCATTACAGCAACCGCGCCGGTCGGGGAGAACTGTCGCAAAGCGAGCAG -CAACGCTTACTGCAACTCACAGACGACGCGCAACGTATGCGCGAGCGCATTCAGGCGCTG -GAAGATATTCTTGATGCAGAGCATCCGAACTGGAGAGAGCGCTAA ->GEN2.0219.00001.i0002_00004 381 hpcD | 5-carboxymethyl-2-hydroxymuconate Delta-isomerase | 5.3.3.10 | similar to AA sequence:UniProtKB:Q05354 -ATGCCGCACTTTATTGCTGAATGTACTGAAAATATTCGCGAGCAGGCTGATTTACCAAGC -CTGTTCAGCAAGGTAAACGAGGCGCTGGCCGCCACCGGGATTTTCCCCATCGGCGGTATC -CGCAGTCGCGCCCACTGGCTGGATACCTGGCAGATGGCTGACGGTAAGCATGATTACGCG -TTTGTGCATATGACGCTGAAAATCGGCGCCGGGCGCAGCCTGGAGAGCCGTCAGGAAGTC -GGCGAAATGCTGTTTGGGCTGATTAAAGCCCACTTCGCCGACCTGATGGAGAACCGCTAT -CTGGCGCTGTCGTTTGAGATTGCCGAGTTACATCCAACGCTCAATTACAAACAAAACAAC -GTACACGCGTTATTTAAATAG ->GEN2.0219.00001.i0002_00005 834 amiD | N-acetylmuramoyl-L-alanine amidase AmiD | 3.5.1.28 | similar to AA sequence:UniProtKB:P75820 -ATGATGAAAGCGCTACTGTGGCTGGTTGGTCTCGCGTTGCTGTTAACAGGCTGCGCGAGC -GAAAAAGGAATTATCGATAAAGAGGGATATCAGCTTGATACCCGACATCGGGCGCAGGCG -GCCTATCCGCGCATTAAAGTCCTGGTGATTCACTATACGGCGGAAAACTTTGACGTTTCG -CTGGCGACGTTAACGGGTCGCAACGTCAGTTCGCATTACCTGATTCCCGCAACCCCGCCA -TTATATGGCGGTAAACCGCGCATCTGGCAACTGGTGCCGGAACAGGATCAGGCTTGGCAT -GCGGGCGTCAGTTTCTGGCGAGGCGCCACGCGTCTCAATGATACGTCTATTGGCATTGAG -CTGGAAAATCGCGGCTGGCGAATGTCCGGCGGGGTGAAATCTTTCGCGCCGTTTGAATCC -GCGCAAATTCAGGCATTGATCCCGTTAGCGAAGGACATTATCGCGCGCTATGACATCAAA -CCGCAGAATGTGGTGGCCCATGCGGATATCGCGCCGCAGCGTAAAGACGATCCCGGCCCG -CGCTTCCCGTGGCGCGAGCTGGCGGCACAGGGGATTGGCGCCTGGCCTGACGCCCAGCGT -GTGGCGTTTTATCTGGCTGGACGCGCGCCGTATACGCCAGTCGATACCGCAACGGTGCTT -GCGTTACTCTCGCGCTATGGCTATGAAGTCAAAGCCGATATGACGGCGCGCGAGCAACAG -CGGGTGATTATGGCGTTCCAGATGCACTTCCGTCCGGCGCAATGGAACGGTATCGCAGAT -GCCGAAACGCAGGCGATTGCCGAAGCATTACTGGAGAAGTACGGCCAGGATTAA ->GEN2.0219.00001.b0002_00006 1668 glnS | Glutamine--tRNA ligase | 6.1.1.18 | similar to AA sequence:UniProtKB:P00962 -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 ->GEN2.0219.00001.b0003_00007 768 trmD | tRNA (guanine-N(1)-)-methyltransferase | 2.1.1.228 | similar to AA sequence:UniProtKB:P0A873 -GTGTTTATTGGCATCGTTAGCCTGTTTCCTGAAATGTTCCGCGCAATTACCGATTACGGG -GTAACTGGCCGGGCAGTAAAAAAAGGCCTGCTGAACATCCAAAGCTGGAGTCCTCGCGAC -TTCGCGCATGACCGGCACCGTACCGTGGACGACCGTCCTTACGGCGGCGGACCGGGGATG -TTAATGATGGTGCAACCCTTGCGGGACGCCATTCATGCAGCAAAAGCCGCGGCAGGTGAA -GGCGCTAAAGTGATTTATCTGTCGCCTCAGGGACGCAAGCTTGATCAAGCGGGCGTTAGC -GAGCTGGCCACGAATCAGAAACTCATTCTGGTGTGTGGTCGCTACGAAGGCGTAGATGAG -CGCGTAATTCAGGCCGAAATTGACGAAGAATGGTCAATTGGCGATTACGTTCTCAGCGGT -GGCGAACTACCGGCAATGACGCTGATTGACTCCGTCGCCCGGTTTATACCGGGGGTTCTG -GGGCATGAGGCATCAGCAATCGAAGATTCGTTTGCTGATGGGTTGCTGGATTGTCCGCAC -TATACGCGCCCTGAAGTGTTAGAGGGGATGGAAGTACCGCCAGTATTGCTGTCGGGAAAC -CATGCTGAGATACGTCGCTGGCGTTTGAAACAGTCACTGGGCCGAACCTGGCTTAGAAGA -CCTGAACTTCTGGAAAACCTGGCTCTGACTGAAGAGCAAGCAAGGTTGCTGGCGGAGTTC -AAAACAGAACACGCACAACAGCAGCATAAACATGATGGGATGGCATAG ->GEN2.0219.00001.i0003_00008 261 NA | hypothetical protein | NA | NA -ATGGCCGGGTTGCACGCGCCATATGCATATAGCGCGCATCATGCGGTGAATTTCTGTTCT -GAGTATAAACGTGGCTTTGTATTGGGTTTTACACACCGTATGTTCGAAAAGACCGGCGAT -CGTCAACTTAGCGCGTGGGAGGCCGGAATTCTGACGCGTCGCTATGGTCTGGATAAAGAA -ATGGTGATGGATTTCTTTAAAGAGAATCATTCCGGGATGGCGGTTCGCTTCTTTATGGCT -GGTTATCGACTCGAAGGTTGA ->GEN2.0219.00001.i0003_00009 582 NA | hypothetical protein | NA | NA -ATGTCTACGCTTCTCTATTTGCACGGATTCAACAGTTCCCCTCGCTCGGCAAAAGCGTGC -CAGCTAAAAAACTGGCTGGCGGAGCGTCATCCGCATGTTGAGATGATCGTCCCTCAACTG -CCGCCGTATCCTGCCGATGCGGCGGAGTTGCTGGAATCTCTCGTACTTGAGCATGGCGGT -GCGCCATTAGGGCTGGTAGGATCGTCGCTGGGTGGTTATTACGCCACCTGGCTGTCGCAA -TGTTTTATGCTGCCGGCTGTGGTGGTGAATCCCGCCGTGCGGCCCTTTGAATTACTGACC -GACTATCTCGGTCAGAACGAGAACCCCTACACCGGGCAGCAATATGTGCTAGAGTCTCGC -CATATTTATGATCTTAAAGTCATGCAGATTGACCCGCTGGAAGCGCCGGACCTGATCTGG -CTACTGCAACAGACGGGCGATGAAGTGCTGGATTACCGCCAGGCGGTGGCATATTACGCC -TCCTGCCGTCAGACAGTGACCGAGGGGGGTAATCACGCATTCACGGGCTTCGAAGATTAT -TTCAACCAGATTGTCGATTTTCTTGGACTGCACAGTTGCTGA ->GEN2.0219.00001.b0003_00010 369 NA | hypothetical protein | NA | NA -ATGATGCGCACTGATGGCACGGTGACGCAGCCGCGTTTAAAGCAGGTTGCGCTGTCGGCA -ATTTCGGAGGTCAACGCAGAGCTGTATGAGTTTCGCAGACGCCAGCAGATGCTGGGGTAT -GCCTCGCTGGCAGAAGTCCCGGCGGAACAACTGGACGGCAAAAGCGAGCGCATTCAGCAC -TATTTCAACGCGGTTTACTGCTGGGCACGCGCCATGCTCAACGAACGTTACCAGGACTAT -GACGCCACGGCATCCGGTGTGAAGCGGGGCGAAGAACTGGCAGAAGCCAGCGGTGATTTG -TGGCGTGACGCCCGCTGGGCCATCAGCCGGGTGCAGGATGCGCCGCACTGCACAGTGGAG -CTTATCTGA ->GEN2.0219.00001.b0004_00011 1308 dctM | C4-dicarboxylate TRAP transporter large permease protein DctM | NA | similar to AA sequence:UniProtKB:O07838 -ATGATTGACCCTATTTTTGCGTCCTGTACGCTAATTGCCGTCTTTGTTGTTTTACTGGCC -ATGGGCGCGCCTATCGGGATCTGCATCGTTATCGCCTCTTTCAGCACCATGATGCTGGTA -CTGCCTTTCGATATTTCGATGTTCGCCACCGCGCAAAAAATGTTCTCCAGCCTGGACAGT -TTTGCCTTGCTGGCCGTGCCGTTCTTCGTTTTGTCCGGGGTGATCATGAATAGCGGGGGA -ATTGCCGCCCGACTGGTCAATTTTGCCAAACTGTTTACTGGCAAACTGCCCGGCTCGCTC -TCTTACACCAACATCGTCGGCAATATGATGTTCGGTGCAATTTCCGGATCGGCGATTGCC -GCCTCAACCTCTATCGGCGGCGTGATGGTGCCGATGAGCGCGCGCGAAGGTTACGATCGC -GGTTTTGCGGCCGCGGTGAATATCGCCTCCGCGCCGACGGGAATGTTAATTCCGCCCACC -ACGGCTTTTATCCTTTATGCGCTGGCAAGCGGGGGAACATCGATTGCCGCTCTGTTCGCC -GGCGGTCTGGTCGCGGGAGTGCTGTGGGGCGTTGGCTGTATGCTGGTCACGCTGGTGGTC -GCTAAGCGTCGAAATTATCGGGTTTTCTTCACCGTCCAAAAAGGCATGGCGCTAAAAGTT -GCCGTTGAGGCCATTCCCAGCCTGTTACTGATCGTGATTATTGTCGGCGGCATTGTGCAG -GGGATTTTCACCGCCATTGAAGCCTCCGCGATTGCCGTGGTGTATACGTTATTGCTGACG -ATAGTGTTTTACCGCACGCTGAAAATTAAGGATTTGCCTTCGATTTTGCTCCAGACAGTG -GTAATGACCGGGGTCATCATGTTCCTGCTGGCAACCTCTTCGGCGATGTCCTTCTCGATG -TCGATCACCAATATTCCTGCGGCGCTGAGCGATATGATCCTCGGTATTTCCGCCAATAAA -CTGGTTATCCTGTTAGTCATTACCGTCTTTTTGTTGATTATCGGCGCATTTATGGATATC -GGTCCGGCCATTCTGATTTTTACCCCGATTCTGCTGCCGATTATGACTAAACTGGGCGTC -GATCCGGTGCATTTCGGCATTATCATGATCTATAACCTGGCGATAGGCACCATTACGCCG -CCAGTTGGCAGTGGTTTATATGTCGGGGCGAGCGTCGGTAAGGTCAAAGTTGAGGACGTT -ATCAAACCGTTGATGCCTTTTTACGGCGCGATTATCGGCGTTCTGTTATTAATTACCTAC -ATTCCGGAAATCACACTGTTTTTACCCCGTCTACTGGGCATCATGTAA ->GEN2.0219.00001.i0004_00012 465 NA | hypothetical protein | NA | NA -ATGAAGTTTGTTGCGCCAGAACAGGCACCGGAACAGGCGGAGGTCATCAAAAATACGCCG -TTCTGGCCTGATGTGAACCTGTCGGAATTTCGCAGTGTGATGCGCACTGACGGCACGGTG -ACGCAGCCGCGTTTAAAGCAGGTCGTGCTGACGGCGATCTCTGAGGTTAACGCTGAGCTG -TACGACTTCCGCAACCGTCAGCAGATGCTGGGCTGGCGGACACTTGCTGAGGTTCCCGCA -GAAATGCTGGACGGTAAAAGCGAGCGTATCCGGCACTACCACAACGCTGTTTTTTGCTGG -GCGCGCGCTGTGCTTAATGAGCGTTATCAGGACTATGACGCCACGGCGTCAGGCGTGAAG -CGAGGGGAGGAGCTGGCGGAGGCCAGCGGCGATCTGTGGCGTGATGCCCGCTGGGCCATC -AGCCGGGTGCAGGATGCACCGCACTGTACGGTGGAGCTTATCTGA ->GEN2.0219.00001.b0004_00013 1014 xerC | Tyrosine recombinase XerC | NA | similar to AA sequence:UniProtKB:P39776 -ATGGAAACAAATATTACCTGGCAACAATTGATAGATGAATATTTCTTCGCAAAACCTCTG -CGCTCAGCATCTGAATGGAGTTACACCAAAGTCTTCAAATCATTTGTACATTATATGGGG -CCGTTAAGCTGCCCTAATGATGTGACATATCACAAAGTGCTTGCCTGGCGCCGTTTTCTT -TTAAAAGAGAAAAAGCTGTCCGGACGTACCTGGAATAACAAGGTGGCGCATATGCGGGCC -ATCTTTAACTACGGAATACAGCGAGGGTTACTGCACTATGACGAAAATCCGTTTAACAAT -TCGGTAGTTAAACCGGACAAGAAGAGAAAGAAAACGCTCACTCAGGCACAGATTGAGTAT -GCCTATCAGATCATGGAGCAGTATGAAAATCAGGAGAATACAGGGCTGGGACTGAAATAT -TCCCGCTGCGCCTTATTTCCTGCATGGTTCTGGCTCACTGTCCTGGATACGCTCTATTAC -ACAGGGATACGTCAGAACCAGTTATTACATATTCGGCTGAATGATGTTGATTTGAGAGAA -GGGCAGATTCGGCTGATTACGGAGGGGTGTAAAAATCACAAAGAACACTATGTGCCGGTG -ATCAGTTTTCTGCGTCCACGGCTGACCTGTTTAATGGAGAAAGCGCAGAGCGAAGGATTG -AAAGGTAATGACCGCCTGTTCAATATTGCACTTTTTACCGGCAAAGATCCCGCCATTGGC -GATGACATGGATTCTCCTCAGGTAAGAGCATTCTTCCGTCGTCTGTCCAAGGAGTGTCAG -TTTGCGATCAGTCCTCATCGTTTCAGACACACGCTGGCCACGGAGATGATGAAAATGCCG -GAACAGAATCTGCATATGGCGCAAAGTGTGCTGGGTCATTCAAACATGAAATCCACGCTG -GAGTATGTGGAGAATGATATTGCAGTGATGGGGAGGGCTCTGGAAGCGCAGTTTATGCAG -ATTAAGGCAGCACATGCCCGAAGCATTTACAGTGGGTTGACAAAGAATAGATAA diff --git a/Examples/1-res-Annotate/Genes/GEN4.1111.00001.gen b/Examples/1-res-Annotate/Genes/GEN4.1111.00001.gen deleted file mode 100644 index 91d8ef700197e5048f23c5da39581ad95e81c110..0000000000000000000000000000000000000000 --- a/Examples/1-res-Annotate/Genes/GEN4.1111.00001.gen +++ /dev/null @@ -1,128 +0,0 @@ ->GEN4.1111.00001.b0001_00001 831 amiD | N-acetylmuramoyl-L-alanine amidase AmiD | 3.5.1.28 | similar to AA sequence:UniProtKB:P75820 -ATGAAAGCGCTACTGTGGCTGGTGGGTCTCGCGTTGCTGTTAACAGGCTGCGCGAGCGAA -AAAGGAATTATCGATAAAGAGGGATATCAGCTTGATACCCGACATCGGGCGCAGGCGGCC -TATCCGCGCATTAAAGTCCTGGTGATTCACTATACGGCGGAAAACTTTGACGTTTCGCTG -GCGACGTTAACGGGCCGCAACGTCAGTTCGCATTACCTGATTCCCGCAACCCCGCCATTA -TATGGCGGTAAACCGCGCATCTGGCAACTGGTGCCGGAACAGGATCAGGCCTGGCATGCG -GGCGTCAGTTTCTGGCGAGGCGCCACGCGTCTCAATGATACGTCTATTGGCATTGAGCTG -GAAAATCGCGGCTGGCGAATGTCCGGCGGGGTGAAATCTTTCGCGCCGTTTGAATCCGCG -CAAATTCAGGCATTGATTCCGTTAGCGAAGGACATTATCGCGCGCTATGACATCAAACCG -CAGAATGTGGTGGCCCATGCGGATATCGCGCCGCAGCGTAAAGACGATCCCGGCCCGCGC -TTCCCGTGGCGCGAGCTGGCGGCGCAGGGGATTGGCGCCTGGCCTGACGCCCAGCGTGTG -GCGTTTTATCTGGCTGGACGCGCGCCGTATACGCCAGTCGATACCGCAACGGTGCTTGCG -TTACTCTCGCGCTATGGCTATGAAGTCAAAGCCGATATGACGGCGCGCGAGCAGCAGCGG -GTGATTATGGCGTTCCAGATGCACTTCCGTCCGGCGCAATGGAACGGTATCGCAGATGCC -GAAACGCAGGCGATTGCCGAAGCATTACTGGAGAAGTACGGCCAGGATTAA ->GEN4.1111.00001.i0001_00002 381 hpcD | 5-carboxymethyl-2-hydroxymuconate Delta-isomerase | 5.3.3.10 | similar to AA sequence:UniProtKB:Q05354 -ATGCCGCACTTTATTGCTGAATGTACTGAAAATATTCGCGAGCAGGCTGATTTACCCGGC -CTGTTCAGCAAGGTAAACGAGGCGCTGGCCGCCAGCGGGATTTTCCCCATCGGCGGTATC -CGCAGTCGCGCCCACTGGCTGGATACCTGGCAGATGGCTGACGGTAAGCATGATTATGCG -TTTGTGCATATGACGCTGAAAATCGGTACCGGGCGCAGCCTGGAGAGCCGTCAGGAAGTC -GGCGAAATGCTGTTTGGGCTGATTAAAGCCCACTTCGCCGACCTGATGGAGAACCGCTAT -CTGGCGCTGTCGTTTGAGATTGCCGAGCTACATCCGACGCTCAATTACAAACAAAACAAC -GTACACGCGTTATTTAAATAG ->GEN4.1111.00001.i0001_00003 804 hpcG | 2-oxo-hept-4-ene-1,7-dioate hydratase | 4.2.1.163 | similar to AA sequence:UniProtKB:P42270 -ATGCTCGATAAACAGACCCATACCCTGATCGCCCAGCGACTTAATCAGGCTGAAAAACAG -CGTGAACAAATTCGCGCAGTGTCGCTGGATTATCCCAACATCACTATTGAAGATGCCTAT -GCCGTACAGCGTGAATGGGTCAATATCAAGATCGCCGAAGGGCGCACGCTCAAAGGCCAC -AAAATCGGCCTGACCTCAAAAGCGATGCAGGCCAGCTCGCAAATCAGCGAACCGGATTAC -GGCGCGCTGCTTGACGATATGTTCTTCCATGACGGCGGCGATATCCCCACCGACCGTTTT -ATCGTCCCGCGTATTGAAGTGGAGCTGGCGTTCGTGCTGGCGAAACCGCTGCGCGGCCCT -CACTGCACGCTGTTCGACGTCTACAACGCCACGGATTATGTGATTCCGGCGCTGGAACTG -ATTGACGCCCGCAGCCACAACATCGACCCGGAAACCCAGCGCCCGCGCAAAGTGTTCGAC -ACCATTTCCGACAACGCCGCCAACGCCGGGGTGATCCTCGGTGGTCGCCCCATCAAACCA -GACGAGCTGGATCTGCGCTGGATCTCCGCGCTGCTCTATCGCAACGGCGTGATCGAAGAA -ACCGGCGTCGCCGCAGGCGTGCTGAATCATCCGGCCAACGGCGTGGCGTGGCTGGCGAAC -AAGCTTGCCCCCTACGATGTCCAGCTTGAAGCCGGGCAGATCATCCTCGGCGGCTCGTTC -ACCCGCCCGGTGCCGGCGAGCAAGGGCGACACCTTCCATGTCGATTACGGCAACATGGGC -GCGATCAGTTGCCGGTTTGTGTAA ->GEN4.1111.00001.i0001_00004 1404 NA | hypothetical protein | 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.i0001_00005 774 hisP | Histidine transport ATP-binding protein HisP | NA | similar to AA sequence:UniProtKB:P02915 -ATGTCAGAAAATAAATTACACGTTATCGATTTGCACAAACGCTACGGCGGTCATGAAGTG -CTGAAAGGGGTATCGTTGCAGGCCCGCGCCGGAGATGTGATTAGCATCATCGGCTCGTCC -GGCTCCGGTAAAAGCACTTTTTTGCGCTGTATTAACTTCCTCGAAAAACCGAGCGAAGGC -GCGATTATCGTGAACGGTCAGAACATTAATCTGGTGCGCGACAAAGACGGGCAGCTCAAA -GTGGCGGATAAAAATCAGCTACGCTTGTTGCGTACCCGCCTGACGATGGTGTTTCAGCAC -TTTAACCTCTGGAGCCACATGACGGTGCTGGAAAATGTGATGGAAGCGCCGATTCAGGTA -CTGGGATTAAGCAAGCACGACGCGCGCGAGCGGGCGTTGAAATATCTGGCGAAGGTGGGG -ATTGATGAGCGCGCTCAGGGCAAATATCCCGTCCATCTCTCCGGCGGCCAACAGCAGCGC -GTTTCTATTGCGCGCGCGCTGGCGATGGAACCTGACGTTTTACTGTTCGATGAACCCACA -TCGGCGCTCGATCCTGAACTGGTCGGCGAAGTGTTGCGCATCATGCAACAACTGGCGGAA -GAAGGCAAAACGATGGTGGTGGTCACGCATGAAATGGGCTTCGCCCGCCATGTCTCTTCG -CACGTTATTTTTCTGCATCAGGGGAAAATTGAAGAAGAGGGCGATCCGGAGCAGGTGTTC -GGCAATCCGCAAAGCCCGCGTTTACAGCAATTCCTGAAAGGCTCGCTGAAATAA ->GEN4.1111.00001.i0001_00006 768 trmD | tRNA (guanine-N(1)-)-methyltransferase | 2.1.1.228 | similar to AA sequence:UniProtKB:P0A873 -GTGTTTATTGGCATCGTTAGCCTGTTTCCTGAAATGTTCCGCGCAATTACCGATTACGGG -GTAACTGGCCGGGCAGTAAAAAAAGGCCTGCTGAACATCCAAAGCTGGAGTCCTCGCGAC -TTCGCGCATGACCGGCACCGTACCGTGGACGACCGTCCTTACGGCGGCGGACCGGGGATG -TTAATGATGGTGCAACCCTTGCGGGACGCCATTCACGCAGCAAAAGCCGCGGCAGGTGAA -GGCGCTAAAGTGATTTATCTGTCGCCTCAGGGACGCAAGCTTGATCAAGCGGGCGTTAGC -GAGCTGGCCACGAATCAGAAGCTTATTCTGGTGTGTGGTCGCTACGAAGGCGTAGATGAG -CGCGTAATTCAGACCGAAATTGACGAAGAATGGTCAATTGGCGATTACGTTCTCAGCGGT -GGCGAACTACCGGCAATGACGCTGATTGACTCCGTCGCCCGGTTTATACCGGGGGTTCTG -GGGCATGAGGCATCAGCAATCGAAGATTCGTTTGCTGATGGGTTGCTGGATTGTCCGCAC -TATACGCGCCCTGAAGTGTTAGAGGGGATGGAAGTACCGCCAGTATTGCTGTCGGGAAAC -CATGCCGAGATACGTCGCTGGCGCTTGAAACAGTCGCTGGGCCGAACCTGGCTTAGAAGA -CCTGAACTTCTGGAAAACCTGGCTCTGACTGAAGAGCAAGCAAGGTTGCTGGCGGAGTTC -AAAACAGAACACGCACAACAGCAGCATAAACATGATGGGATGGCATAG ->GEN4.1111.00001.i0001_00007 261 NA | hypothetical protein | NA | NA -ATGGCTGGGTTGCACGCGCCATATGCATATAGCGCGCATCATGCGGTGAATTTCTGTTCT -GAGTATAAACGTGGCTTTGTATTGGGTTTTACACACCGTATGTTCGAAAAGACCGGCGAT -CGTCAACTTAGCGCGTGGGAGGCCGGAATTCTGACGCGTCGCTATGGTCTGGATAAAGAA -ATGGTGATGGATTTCTTTAAAGAGAATCATTCCGGGATGGCGGTTCGCTTCTTTATGGTC -GGTTATCGACTCGAAGGTTGA ->GEN4.1111.00001.i0001_00008 582 NA | hypothetical protein | NA | NA -ATGTCTACGCTTCTCTATTTGCACGGATTCAACAGTTCCCCTCGCTCGGCAAAAGCGTGC -CAGCTAAAAAACTGGCTGGCGGAGCGTCATCCGCATGTCGAGATGATCGTCCCTCAACTA -CCGCCGTATCCTGCCGATGCGGCGGAGTTGCTGGAATCTCTCGTGCTTGAGCATGGCGGT -GCGCCATTAGGGCTGGTAGGATCGTCGCTGGGTGGTTATTACGCCACCTGGCTGTCGCAA -TGTTTTATGCTGCCGGCTGTGGTGGTGAATCCCGCCGTGCGGCCCTTTGAATTACTGACC -GACTATCTCGGTCAGAACGAGAACCCCTACACCGGGCAGCAATATGTGCTAGAGTCTCGC -CATATTTATGATCTTAAAGTCATGCAGATTGACCCGCTGGAAGCGCCGGACCTGATCTGG -CTACTGCAACAGACGGGCGATGAAGTGCTGGATTACCGCCAGGCGGTGGCATATTACGCC -TCCTGCCGTCAGACAGTGACCGAGGGTGGTAATCACGCATTCACGGGCTTCGAAGATTAT -TTCAACCAGATTGTCGATTTTCTTGGACTGCACAGTTGCTGA ->GEN4.1111.00001.b0001_00009 1083 dctM | C4-dicarboxylate TRAP transporter large permease protein DctM | NA | similar to AA sequence:UniProtKB:O07838 -ATGAATAGCGGGGGAATTGCCGCCCGGCTGGTCAATTTTGCCAAACTGTTTACTGGCAAA -CTGCCCGGCTCGCTCTCTTATACCAACATCGTCGGCAATATGATGTTCGGTGCAATTTCC -GGATCGGCAATTGCCGCCTCAACCTCCATCGGCGGCGTGATGGTGCCGATGAGCGCGCGC -GAAGGTTACGATCGCGGCTTTGCGGCCGCGGTGAATATCGCCTCCGCGCCGACGGGAATG -TTAATTCCGCCCACCACGGCTTTTATCCTTTATGCGCTGGCAAGCGGGGGAACATCGATT -GCCGCTCTGTTCGCCGGCGGTCTGGTCGCGGGAGTGCTGTGGGGCGTTGGCTGTATGCTG -GTCACGCTGGTGGTCGCTAAGCGTCGAAATTATCGGGTTTTCTTCACCGTCCAAAAAGGC -ATGGCGCTAAAAGTTGCCGTTGAGGCCATTCCCAGCCTGCTGCTGATCGTGATTATCGTC -GGCGGCATTGTGCAGGGGATTTTCACCGCCATTGAAGCCTCCGCGATTGCCGTGGTGTAT -ACATTATTGTTGACGATGGTGTTTTACCGCACGCTGAAAATTAAGGATTTGCCTTCGATT -TTGCTCCAGACAGTGGTAATGACCGGGGTCATCATGTTCCTGCTGGCAACCTCTTCGGCG -ATGTCCTTCTCGATGTCGATCACCAATATTCCTGCGGCGCTGAGCGATATGATCCTCGGT -ATTTCCGCCAATAAACTGGTTATCCTGTTAGTCATTACCGTCTTTTTGTTGATTATCGGC -GCATTTATGGATATCGGTCCGGCCATTCTGATTTTTACCCCGATTCTGCTGCCGATCATG -GCTAAACTGGGCGTCGATCCGGTGCATTTTGGCATTATCATGATCTATAACCTGGCGATT -GGCACCATTACGCCGCCAGTTGGCAGTGGTTTATATGTCGGGGCGAGCGTCGGTAAGGTC -AAAGTTGAGGAAGTGATTAAACCGTTGCTGCCTTTTTACGGCGCGATTATCGGCGTTCTG -TTATTAATTACCTACATTCCGGAAATCACACTGTTCTTACCCCGTCTACTGGGCATCATG -TAA diff --git a/Examples/1-res-Annotate/LSTINFO-list_genomes.lst b/Examples/1-res-Annotate/LSTINFO-list_genomes.lst deleted file mode 100644 index 7c51ff2c46ca7362b2d6fb2576eb4fd7a5eebf23..0000000000000000000000000000000000000000 --- a/Examples/1-res-Annotate/LSTINFO-list_genomes.lst +++ /dev/null @@ -1,5 +0,0 @@ -gembase_name orig_name gsize nb_conts L90 -EXAM.0219.00001 genome1.fst 9808 2 2 -EXAM.1216.00002 genome3-chromo.fst-all.fna 8817 3 3 -GEN2.0219.00001 genome2.fst 10711 4 4 -GEN4.1111.00001 genome4.fst 7134 1 1 diff --git a/Examples/1-res-Annotate/LSTINFO/EXAM.0219.00001.lst b/Examples/1-res-Annotate/LSTINFO/EXAM.0219.00001.lst deleted file mode 100644 index 2311964a8a8a2534bd269f71ba0f8c3400e480bd..0000000000000000000000000000000000000000 --- a/Examples/1-res-Annotate/LSTINFO/EXAM.0219.00001.lst +++ /dev/null @@ -1,11 +0,0 @@ -213 1880 D CDS EXAM.0219.00001.b0001_00001 glnS | Glutamine--tRNA ligase | 6.1.1.18 | similar to AA sequence:UniProtKB:P00962 -1916 2746 D CDS EXAM.0219.00001.b0001_00002 amiD | N-acetylmuramoyl-L-alanine amidase AmiD | 3.5.1.28 | similar to AA sequence:UniProtKB:P75820 -16 396 D CDS EXAM.0219.00001.b0002_00003 hpcD | 5-carboxymethyl-2-hydroxymuconate Delta-isomerase | 5.3.3.10 | similar to AA sequence:UniProtKB:Q05354 -428 1837 D CDS EXAM.0219.00001.i0002_00004 NA | hypothetical protein | NA | NA -1869 2642 D CDS EXAM.0219.00001.i0002_00005 hisP | Histidine transport ATP-binding protein HisP | NA | similar to AA sequence:UniProtKB:P02915 -2709 3443 D CDS EXAM.0219.00001.i0002_00006 trmD_1 | tRNA (guanine-N(1)-)-methyltransferase | 2.1.1.228 | similar to AA sequence:UniProtKB:P0A873 -3427 4254 D CDS EXAM.0219.00001.i0002_00007 trmD_2 | tRNA (guanine-N(1)-)-methyltransferase | 2.1.1.228 | similar to AA sequence:UniProtKB:P0A873 -4299 4763 D CDS EXAM.0219.00001.i0002_00008 NA | hypothetical protein | NA | NA -4818 5078 D CDS EXAM.0219.00001.i0002_00009 NA | hypothetical protein | NA | NA -5117 5698 D CDS EXAM.0219.00001.i0002_00010 NA | hypothetical protein | NA | NA -5717 7024 D CDS EXAM.0219.00001.b0002_00011 dctM | C4-dicarboxylate TRAP transporter large permease protein DctM | NA | similar to AA sequence:UniProtKB:O07838 diff --git a/Examples/1-res-Annotate/LSTINFO/EXAM.1216.00002.lst b/Examples/1-res-Annotate/LSTINFO/EXAM.1216.00002.lst deleted file mode 100644 index 8bf48ea4de46727cf88a6a26b61df13a601de0ed..0000000000000000000000000000000000000000 --- a/Examples/1-res-Annotate/LSTINFO/EXAM.1216.00002.lst +++ /dev/null @@ -1,12 +0,0 @@ -1 831 D CDS EXAM.1216.00002.b0001_00001 amiD_1 | N-acetylmuramoyl-L-alanine amidase AmiD | 3.5.1.28 | similar to AA sequence:UniProtKB:P75820 -880 1710 D CDS EXAM.1216.00002.i0001_00002 amiD_2 | N-acetylmuramoyl-L-alanine amidase AmiD | 3.5.1.28 | similar to AA sequence:UniProtKB:P75820 -1655 2128 D CDS EXAM.1216.00002.i0001_00003 hpcD | 5-carboxymethyl-2-hydroxymuconate Delta-isomerase | 5.3.3.10 | similar to AA sequence:UniProtKB:Q05354 -2172 2396 D CDS EXAM.1216.00002.i0001_00004 pspB | Phage shock protein B | NA | similar to AA sequence:UniProtKB:P0AFM9 -2425 3828 D CDS EXAM.1216.00002.i0001_00005 NA | hypothetical protein | NA | NA -3863 4636 D CDS EXAM.1216.00002.i0001_00006 hisP | Histidine transport ATP-binding protein HisP | NA | similar to AA sequence:UniProtKB:P02915 -4641 5432 D CDS EXAM.1216.00002.i0001_00007 trmD | tRNA (guanine-N(1)-)-methyltransferase | 2.1.1.228 | similar to AA sequence:UniProtKB:P0A873 -5460 5747 D CDS EXAM.1216.00002.b0001_00008 NA | hypothetical protein | NA | NA -1 582 D CDS EXAM.1216.00002.b0002_00009 NA | hypothetical protein | NA | NA -629 1936 D CDS EXAM.1216.00002.b0002_00010 dctM | C4-dicarboxylate TRAP transporter large permease protein DctM | NA | similar to AA sequence:UniProtKB:O07838 -26 280 D CDS EXAM.1216.00002.b0003_00011 NA | hypothetical protein | NA | NA -323 1102 D CDS EXAM.1216.00002.b0003_00012 NA | Insertion sequence IS5376 putative ATP-binding protein | NA | similar to AA sequence:UniProtKB:Q45619 diff --git a/Examples/1-res-Annotate/LSTINFO/GEN2.0219.00001.lst b/Examples/1-res-Annotate/LSTINFO/GEN2.0219.00001.lst deleted file mode 100644 index 5c3a772d94307bed42c76d1adf8ec2c760d4c62a..0000000000000000000000000000000000000000 --- a/Examples/1-res-Annotate/LSTINFO/GEN2.0219.00001.lst +++ /dev/null @@ -1,13 +0,0 @@ -1 774 D CDS GEN2.0219.00001.b0001_00001 hisP | Histidine transport ATP-binding protein HisP | NA | similar to AA sequence:UniProtKB:P02915 -857 2260 D CDS GEN2.0219.00001.b0001_00002 NA | hypothetical protein | NA | NA -28 252 D CDS GEN2.0219.00001.b0002_00003 pspB | Phage shock protein B | NA | similar to AA sequence:UniProtKB:P0AFM9 -301 681 D CDS GEN2.0219.00001.i0002_00004 hpcD | 5-carboxymethyl-2-hydroxymuconate Delta-isomerase | 5.3.3.10 | similar to AA sequence:UniProtKB:Q05354 -764 1597 D CDS GEN2.0219.00001.i0002_00005 amiD | N-acetylmuramoyl-L-alanine amidase AmiD | 3.5.1.28 | similar to AA sequence:UniProtKB:P75820 -1628 3295 D CDS GEN2.0219.00001.b0002_00006 glnS | Glutamine--tRNA ligase | 6.1.1.18 | similar to AA sequence:UniProtKB:P00962 -30 797 D CDS GEN2.0219.00001.b0003_00007 trmD | tRNA (guanine-N(1)-)-methyltransferase | 2.1.1.228 | similar to AA sequence:UniProtKB:P0A873 -862 1122 D CDS GEN2.0219.00001.i0003_00008 NA | hypothetical protein | NA | NA -1170 1751 D CDS GEN2.0219.00001.i0003_00009 NA | hypothetical protein | NA | NA -1895 2263 D CDS GEN2.0219.00001.b0003_00010 NA | hypothetical protein | NA | NA -1 1308 D CDS GEN2.0219.00001.b0004_00011 dctM | C4-dicarboxylate TRAP transporter large permease protein DctM | NA | similar to AA sequence:UniProtKB:O07838 -1340 1804 D CDS GEN2.0219.00001.i0004_00012 NA | hypothetical protein | NA | NA -1832 2845 D CDS GEN2.0219.00001.b0004_00013 xerC | Tyrosine recombinase XerC | NA | similar to AA sequence:UniProtKB:P39776 diff --git a/Examples/1-res-Annotate/LSTINFO/GEN4.1111.00001.lst b/Examples/1-res-Annotate/LSTINFO/GEN4.1111.00001.lst deleted file mode 100644 index 7a86a11ffd5632a867c73ee5a267edc8a956a903..0000000000000000000000000000000000000000 --- a/Examples/1-res-Annotate/LSTINFO/GEN4.1111.00001.lst +++ /dev/null @@ -1,9 +0,0 @@ -1 831 D CDS GEN4.1111.00001.b0001_00001 amiD | N-acetylmuramoyl-L-alanine amidase AmiD | 3.5.1.28 | similar to AA sequence:UniProtKB:P75820 -861 1241 D CDS GEN4.1111.00001.i0001_00002 hpcD | 5-carboxymethyl-2-hydroxymuconate Delta-isomerase | 5.3.3.10 | similar to AA sequence:UniProtKB:Q05354 -1271 2074 D CDS GEN4.1111.00001.i0001_00003 hpcG | 2-oxo-hept-4-ene-1,7-dioate hydratase | 4.2.1.163 | similar to AA sequence:UniProtKB:P42270 -2111 3514 D CDS GEN4.1111.00001.i0001_00004 NA | hypothetical protein | NA | NA -3535 4308 D CDS GEN4.1111.00001.i0001_00005 hisP | Histidine transport ATP-binding protein HisP | NA | similar to AA sequence:UniProtKB:P02915 -4327 5094 D CDS GEN4.1111.00001.i0001_00006 trmD | tRNA (guanine-N(1)-)-methyltransferase | 2.1.1.228 | similar to AA sequence:UniProtKB:P0A873 -5138 5398 D CDS GEN4.1111.00001.i0001_00007 NA | hypothetical protein | NA | NA -5413 5994 D CDS GEN4.1111.00001.i0001_00008 NA | hypothetical protein | NA | NA -6052 7134 D CDS GEN4.1111.00001.b0001_00009 dctM | C4-dicarboxylate TRAP transporter large permease protein DctM | NA | similar to AA sequence:UniProtKB:O07838 diff --git a/Examples/1-res-Annotate/Proteins/EXAM.0219.00001.prt b/Examples/1-res-Annotate/Proteins/EXAM.0219.00001.prt deleted file mode 100644 index e07e3d351df0e2622d0d41e7bc0876cf14a9fbbc..0000000000000000000000000000000000000000 --- a/Examples/1-res-Annotate/Proteins/EXAM.0219.00001.prt +++ /dev/null @@ -1,69 +0,0 @@ ->EXAM.0219.00001.b0001_00001 1668 glnS | Glutamine--tRNA ligase | 6.1.1.18 | similar to AA sequence:UniProtKB:P00962 -MSEAEARPTNFIRQIIDEDLASGKHTTVHTRFPPEPNGYLHIGHAKSICLNFGIAQDYQG -QCNLRFDDTNPVKEDIEYVDSIKNDVEWLGFHWSGDIRYSSDYFDQLHAYAVELINKGLA -YVDELTPEQIREYRGTLTAPGKNSPFRDRSVEENLALFEKMRTGGFEEGKACLRAKIDMA -SPFIVMRDPVLYRIKFAEHHQTGNKWCIYPMYDFTHCISDALEGITHSLCTLEFQDNRRL -YDWVLDNITIPVHPRQYEFSRLNLEYTVMSKRKLNLLVTDKHVEGWDDPRMPTISGLRRR -GYTAASIREFCKRIGVTKQDNTIEMASLESCIREDLNENAPRAMAVIDPVKLVIENYPQG -ESEMVTMPNHPNKPEMGSREVPFSGEIWIDRADFREEANKQYKRLVMGKEVRLRNAYVIK -AERVEKDAEGNITTIFCTYDADTLSKDPADGRKVKGVIHWVSAAHALPIEIRLYDRLFSV -PNPGAAEDFLSVINPESLVIKQGYGEPSLKAAVAGKAFQFEREGYFCLDSRYATADKLVF -NRTVGLRDTWAKAGE ->EXAM.0219.00001.b0001_00002 831 amiD | N-acetylmuramoyl-L-alanine amidase AmiD | 3.5.1.28 | similar to AA sequence:UniProtKB:P75820 -MKALLWLVGLALLLTGCASEKGIIDKEGYQLDTRHRAQAAYPRIKVLVIHYTAENFDVSL -ATLTGRNVSSHYLIPATPPLYGGKPRIWQLVPEQDQAWHAGVSFWRGATRLNDTSIGIEL -ENRGWRMSGGVKSFAPFESAQIQALIPLAKDIIARYNIKPQNVVAHADIAPQRKDDPGPR -FPWRELAAQGISAWPDAQRVAFYLAGRAPYTPVDTATVLALLSRYGYEVKADMTAREQQR -VIMAFQMHFRPAQWNGIADAETQAIAEALLEKYGQD ->EXAM.0219.00001.b0002_00003 381 hpcD | 5-carboxymethyl-2-hydroxymuconate Delta-isomerase | 5.3.3.10 | similar to AA sequence:UniProtKB:Q05354 -MPHFIAECTENIREQADLPGLFSKVNEALAASGIFPIGGIRSRAHWLDTWQMADGKHDYA -FVHMTLKIGAGRSLESRQEVGEMLFGLIKAHFADLMENRYLALSFEIAELHPTLNYKQNN -VHALFK ->EXAM.0219.00001.i0002_00004 1410 NA | hypothetical protein | NA | NA -MSMPATKFSRRTLLTAGSALAVLPFLRALPVQAREPRETVDIKDYPADDGIASFKQAFAD -GQTVVVPPGWVCENINAAITIPAGKTLRVQGAVRGNGRGRFILQDGCQVVGEQGGSLHNV -TLDVRGSDCVIKGVAMSGFGPVAQIFIGGKEPQVMRNLIIDDITVTHANYAILRQGFHNQ -MDGARITHSRFSDLQGDAIEWNVAIHDRDILISDHVIERINCTNGKINWGIGIGLAGSTY -DNSYPEDQAVKNFVVANITGSDCRQLVHVENGKHFVIRNVKAKNITPGFSKNAGIDNATI -AIYGCDNFVIDNIDMTNSAGMLIGYGVVKGKYLSIPQNFKLNAIRLDNRQVAYKLRGIQI -SSGNTPSFVAITNVRMTRATLELHNQPQHLFLRNINVMQTSAIGPALKMHFDLRKDVRGQ -FMARQDTLLSLANVHAINENGQSSVDIDRINHQTVNVEAVNFSLPKRGG ->EXAM.0219.00001.i0002_00005 774 hisP | Histidine transport ATP-binding protein HisP | NA | similar to AA sequence:UniProtKB:P02915 -MSENKLHVIDLHKRYGGHEVLKGVSLQARAGDVISIIGSSGSGKSTFLRCINFLEKPSEG -AIIVNGQNINLVRDKDGQLKVADKNQLRLLRTRLTMVFQHFNLWSHMTVLENVMEAPIQV -LGLSKHDARERALKYLAKVGIDERAQGKYPVHLSGGQQQRVSIARALAMEPDVLLFDEPT -SALDPELVGEVLRIMQQLAEEGKTMVVVTHEMGFARHVSSHVIFLHQGKIEEEGDPEQVF -GNPQSPRLQQFLKGSLK ->EXAM.0219.00001.i0002_00006 735 trmD_1 | tRNA (guanine-N(1)-)-methyltransferase | 2.1.1.228 | similar to AA sequence:UniProtKB:P0A873 -MFRAITDYGVTGRAVKKGLLNIQSWSPRDFAHDRHRTVDDRPYGGGPGMLMMVQPLRDAI -HAAKAAAGEGAKVIYLSPQGRKLDQAGVSELATNQKLILVCGRYEGVDERVIQTEIDEEW -SIGDYVLSGGELPAMTLIDSVARFIPGVLGHEASAIEDSFADGLLDCPHYTRPEVLEGME -VPPVLLSGNHAEIRRWRLKQSLGRTWLRRPELLENLALTEEQARLLAEFKTEHAQQQHKH -DGMA ->EXAM.0219.00001.i0002_00007 828 trmD_2 | tRNA (guanine-N(1)-)-methyltransferase | 2.1.1.228 | similar to AA sequence:UniProtKB:P0A873 -MMGWHSRHMGSQRRRANAQYVFIGIVSLFPEMFRAITDYGVTGRAVKKGLLNIQSWSPRD -FAHDRHRTVDDRPYGGGPGMLMMVQPLRDAIHAAKAAAGEGAKVIYLSPQGRKLDQAGVS -ELATNQKLILVCGRYEGVDERVIQTEIDEEWSIGDYVLSGGELPAMTLIDSVARFIPGVL -GHEASAIEDSFADGLLDCPHYTRPEVLEGMEVPPVLLSGNHAEIRRWRLKQSLGRTWLRR -PELLENLALTEEQARLLAEFKTEHAQQQHKHDGMA ->EXAM.0219.00001.i0002_00008 465 NA | hypothetical protein | NA | NA -MKFVAPEQAPEQAEVIKNTPFWPDVDLSEFRSVMRTDGTVTQPRLKQVVLTAISEVNAEL -YDFRNRQQMLGWRTLAEVPAEMLDGKSERIRHYHNAVFCWARAVLNERYQDYDATASGVK -RGEELAEASGDLWRDARWAISRVQDVPHCTVELI ->EXAM.0219.00001.i0002_00009 261 NA | hypothetical protein | NA | NA -MAGLHAPYAYSAHHAVNFCSEYKRGFVLGFTHRMFEKTGDRQLSAWEAGILTRRYGLDKE -MVMDFFKENHSGMAVRFFMAGYRLEG ->EXAM.0219.00001.i0002_00010 582 NA | hypothetical protein | NA | NA -MSTLLYLHGFNSSPRSAKACQLKNWLAERHPHVEMIVPQLPPYPADAAELLESLVLEHGG -APLGLVGSSLGGYYATWLSQCFMLPAVVVNPAVRPFELLTDYLGQNENPYTGQQYVLESR -HIYDLKVMQIDPLEAPDLIWLLQQTGDEVLYYRQAVAYYASCRQTVTEGGNHAFTGFEDY -FNQIVDFLGLHSC ->EXAM.0219.00001.b0002_00011 1308 dctM | C4-dicarboxylate TRAP transporter large permease protein DctM | NA | similar to AA sequence:UniProtKB:O07838 -MIDPIFASCTLIAVFVVLLAMGAPIGICIVIASFSTMMLVLPFDISMFATAQKMFSSLDS -FALLAVPFFVLSGVIMNSGGIAARLVNFAKLFTGKLPGSLSYTNIVGNMMFGAISGSAIA -ASTSIGGVMVPMSAREGYDRGFAAAVNIASAPTGMLIPPTTAFILYALASGGTSIAALFA -GGLVAGVLWGVGCMLVTLVVAKRRNYRVFFTVQKGMALKVAVEAIPSLLLIVIIVGGIVQ -GIFTAIEASAIAVVYTLLLTMVFYRTLKIKDLPSILLQTVVMTGVIMFLLATSSAMSFSM -SITNIPAALSDMILGISANKLVILLVITVFLLIIGAFMDIGPAILIFTPILLPIMAKLGV -DPVHFGIIMIYNLAIGTITPPVGSGLYVGASVGKVKVEEVIKPLLPFYGAIIGVLLLITY -IPEITLFLPRLLGIM diff --git a/Examples/1-res-Annotate/Proteins/EXAM.1216.00002.prt b/Examples/1-res-Annotate/Proteins/EXAM.1216.00002.prt deleted file mode 100644 index 82124bdfe988a7543ff47e3597fab93a41155985..0000000000000000000000000000000000000000 --- a/Examples/1-res-Annotate/Proteins/EXAM.1216.00002.prt +++ /dev/null @@ -1,66 +0,0 @@ ->EXAM.1216.00002.b0001_00001 831 amiD_1 | N-acetylmuramoyl-L-alanine amidase AmiD | 3.5.1.28 | similar to AA sequence:UniProtKB:P75820 -MRALLWLVGLALLLTGCASEKGIIDEEGYQLDTRHRAQAAYPRIKVLVIHYTAENFDVSL -ATLTGRNVSSHYLIPATPPLYGGKPRIWQLVPEQDQAWHAGVSFWRGATRLNDTSIGIEL -ENRGWRMSGGVKSFAPFESAQIQALIPLAKDIIARYDIKPQNVVAHADIAPQRKDDPGPR -FPWRELAAQGIGAWPDAQRVAFYLAGRAPYTPVDTATVLALLSRYGYEVKADMTAREQQR -VIMAFQMHFRPAQWNGIADAETQAIAEALLEKYGQD ->EXAM.1216.00002.i0001_00002 831 amiD_2 | N-acetylmuramoyl-L-alanine amidase AmiD | 3.5.1.28 | similar to AA sequence:UniProtKB:P75820 -MRALLWLVGLALLLTGCASEKGIIDEEGYQLDTRHRAQAAYPRIKVLVIHYTAENFDVSL -ATLTGRNVSSHYLIPATPPLYGGKPRIWQLVPEQDQAWHAGVSFWRGATRLNDTSIGIEL -ENRGWRMSGGVKSFAPFESAQIQALIPLAKDIIARYDIKPQNVVAHADIAPQRKDDPGPR -FPWRELAAQGIGAWPDAQRVAFYLAGRAPYTPVDTATVLALLSRYGYEVKADMTAREQQR -VIMAFQMHFRPAQWNGIADAETQAIAEALLEKYGQD ->EXAM.1216.00002.i0001_00003 474 hpcD | 5-carboxymethyl-2-hydroxymuconate Delta-isomerase | 5.3.3.10 | similar to AA sequence:UniProtKB:Q05354 -MPKRRRLPKHYWRSTARINRARYREDSLFEDMPHFIAECTENIREQADLPGLFSKVNEAL -AASGIFPIGGIRSRAHWLDTWQMADGKHDYAFVHMTLKIGAGRSLESRQEVGEMLFGLIK -AHFADLMENRYLALSFEIAELHPTLNYKQNNVHALFK ->EXAM.1216.00002.i0001_00004 225 pspB | Phage shock protein B | NA | similar to AA sequence:UniProtKB:P0AFM9 -MSALFLAIPLTIFVLFVLPIWLWLHYSNRAGRGELSQSEQQRLLQLTDDAQRMRERIQAL -EDILDAEHPNWRER ->EXAM.1216.00002.i0001_00005 1404 NA | hypothetical protein | NA | NA -MPATKFSRRTLLTAGSALAVLPFLRALPVQAREPRETVDIKDYPADDGIASFKQAFADGQ -TVVVPPGWVCENINAAITIPAGKTLRVQGAVRGNGRGRFILQDGCQVVGEQGGSLHNVTL -DVRGSDCVIKGVAMSGFGPVAQIFIGGKEPQVMRNLIIDDITVTHANYAILRQGFHNQMD -GARITHSRFSDLQGDAIEWNVAIHDRDILISDHVIERIDCTNGKINWGIGIGLAGSTYDN -SYPEDQAVKNFVVANITGSDCRQLVHVENGKHFVIRNVKAKNITPDFSKNAGIDNATIAI -YGCDNFVIDNIDMTNSAGMLIGYGVVKGKYLSIPQNFKLNAIRLDNRQVAYKLRGIQISS -GNTPSFVAITNVRMTRATLELHNQPQHLFLRNINVMQTSAIGPALKMHFDLRKDVRGQFM -ARQDTLLSLANVHAINENGQSSVDIDRINHQTVNVEAVNFSLPKRGG ->EXAM.1216.00002.i0001_00006 774 hisP | Histidine transport ATP-binding protein HisP | NA | similar to AA sequence:UniProtKB:P02915 -MSENKLHVIDLHKRYGGHEVLKGVSLQARAGDVISIIGSSGSGKSTFLRCINFLEKPSED -AIIVNGQNINLVRDKDGQLKVADKNQLRLLRTRLTMVFQHFNLWSHMTVLENVMEAPIQV -LGLSKHDARERALKYLAKVGIDERAQGKYPVHLSGGQQQRVSIARALAMEPDVLLFDEPT -SALDPELVGEVLRIMQQLAEEGKTMVVVTHEMGFVRHVSSHVIFLHQGKIEEEGDPEQVF -GNPQSPRLQQFLKGSLK ->EXAM.1216.00002.i0001_00007 792 trmD | tRNA (guanine-N(1)-)-methyltransferase | 2.1.1.228 | similar to AA sequence:UniProtKB:P0A873 -MRAIYRRCVFIGIVSLFPEMFRAITDYGVTGRAVKNGLLNIQSWSPRDFTHDRHRTVDDR -PYGGGPGMLMMVQPLRDAIHAAKAAAGEGAKVIYLSPQGRKLDQAGVSELATNQKLILVC -GRYEGVDERVIQTEIDEEWSIGDYVLSGGELPAMTLIDSVARFIPGVLGHEASAIEDSFA -DGLLDCPHYTRPEVLEGMEVPPVLLSGNHAEIRRWRLKQSLGRTWLRRPELLENLALTEE -QARLLAEFKTEHAQQQHKHDGMA ->EXAM.1216.00002.b0001_00008 288 NA | hypothetical protein | NA | NA -MNNHFGKGLMAGLHAPYAYSAHHAVNFCSEYKRGFVLGFTHRMFEKTGDRQLSAWEAGIL -TRRYGLDKEMVMDFFKENHSGMAVRFFMAGYRLEG ->EXAM.1216.00002.b0002_00009 582 NA | hypothetical protein | NA | NA -MSTLLYLHGFNSSPRSAKACQLKNWLAERHPHVEMIVPQLPPYPADAAELLESLVLEHGG -APLGLVGSSLGGYYATWLSQCFMLPAVVVNPAVRPFELLTDYLGQNENPYTGQQYVLESR -HIYDLKVMQIDPLEAPDLIWLLQQTGDEVLDYRQAVAYYASCRQTVTEGGNHAFTGFEDY -FNQIVDFLGLHSC ->EXAM.1216.00002.b0002_00010 1308 dctM | C4-dicarboxylate TRAP transporter large permease protein DctM | NA | similar to AA sequence:UniProtKB:O07838 -MIDPIFASCTLIAVFVVLLAMGAPIGICIVIASFSTMMLVLPFDISMFATAQKMFSSLDS -FALLAVPFFVLSGVIMNSGGIAARLINFAKLFTGKLPGSLSYTNIVGNMMFGAISGSAIA -ASTSIGGVMVPMSAREGYDRGFAAAVNIASAPTGMLIPPTTAFILYALASGGTSIAALFA -GGLVAGVLWGVGCMLVTLVVAKRRNYRVFFTVQKGMALKVAVEAIPSLLLIVIIVGGIVQ -GIFTAIEASAIAVVYTLLLTMVFYRTLKIKDLPSILLQTVVMTGVIMFLLATSSAMSFSM -SITNIPAALSDMILGISANKLVILLVITVFLLIIGAFMDIGPAILIFTPILLPIMAKLGV -DPVHLGIIMIYNLAIGTITPPVGSGLYVGASVGKVKVEEVIKPLLPFYGAIIGVLLLITY -IPEIILFLPRLLGIM ->EXAM.1216.00002.b0003_00011 255 NA | hypothetical protein | NA | NA -MIINGKLIKAKDLAKAAGVSRSTVIKYYGISRENYERVATERRKLAFELRASGLKWKEVA -EKMNTTKYSAIAYYRRYLALEKNK ->EXAM.1216.00002.b0003_00012 780 NA | Insertion sequence IS5376 putative ATP-binding protein | NA | similar to AA sequence:UniProtKB:Q45619 -MVELQHQRLMVLAEQLQLDSLIGAAPALSQQAVDQEWSYMDFLEHLLHEEKLARHQRKQA -MYTRMAAFPAVKTFEEYDFTFATGAPQKQIQSLRSLSFIERNENIVLLGPSGVGKTHLAI -AMGYEAVRAGIKVRFTTAADLLLQLSTSQRQGRYKTTLNRGVMAPKLLIIDEIGYLPFSQ -EEAKLFFQVIAKRYEKSAMILTSNLPFGQWDQTFAGDAALTSAMLDRILHHSHVVQIKGE -SYRLKQKRKAGVIAEANPE diff --git a/Examples/1-res-Annotate/Proteins/GEN2.0219.00001.prt b/Examples/1-res-Annotate/Proteins/GEN2.0219.00001.prt deleted file mode 100644 index dd6ca8c2299c22eadc436d18081bb8bd09737ed6..0000000000000000000000000000000000000000 --- a/Examples/1-res-Annotate/Proteins/GEN2.0219.00001.prt +++ /dev/null @@ -1,77 +0,0 @@ ->GEN2.0219.00001.b0001_00001 774 hisP | Histidine transport ATP-binding protein HisP | NA | similar to AA sequence:UniProtKB:P02915 -MSENKLHVIDLHKRYGGHEVLKGVSLQARAGDVISIIGSSGSGKSTFLRCINFLEKSSEG -AIIVNGQNINLVRDKDGQLKVADKNQLRLLRTRLTMVFQHFNLWNHMTVLENVMEAPIQV -LGLSKHDARERALKYLAKVGIDERAQGKYPVHLSGGQQQRVSIARALAMEPDVLLFDEPT -SALDPELVGEVLRIMQQLAEEGKTMVVVTHEMGFARHVSSHVIFLHQGKIEEEGNPEQVF -GNPQSPRLQQFLKGSLK ->GEN2.0219.00001.b0001_00002 1404 NA | hypothetical protein | NA | NA -MPATKFSRRTLLTAGSALAVLPFLRALPVQAREPRQTVDIKDYPADDGIASFKQAFADGQ -TVVVPSGWVCENINAAITIPAGKTLRIQGAVRGNGRGRFILLDGCQVVGEQGGSLHNVTL -DVRGSDCVIKGVTMSGFGPVAQIFIGGKEPQVMRNLIIDDITVTHANYAILRQGFHNQMD -GARITHSRFSDLQGDAIEWNVAIHDRDILISDHVIERIDCTNGKINWGIGIGLAGSAYDN -SYPEDQAVKNFVVANITGSDCRQLVHVENGKHFVIRNVKAKNITPDFSKNAGIDNATIAI -YGCDNFVIDNIDMTNSAGMLIGYGVVKGKYLSIPQNFKLNAIRLDNRQVAYKLRGIQISS -GNAPSFVAITNVRMTRATLELHNQPQHLFLRNINVMQTSAIGPALKMHFDLRKDVRGQFM -ARQDTLLSLANVHAINENGQSSVDIDRINHQTVNVEAVNFSLPKRGG ->GEN2.0219.00001.b0002_00003 225 pspB | Phage shock protein B | NA | similar to AA sequence:UniProtKB:P0AFM9 -MSALFLAIPLTIFVLFVLPIWLWLHYSNRAGRGELSQSEQQRLLQLTDDAQRMRERIQAL -EDILDAEHPNWRER ->GEN2.0219.00001.i0002_00004 381 hpcD | 5-carboxymethyl-2-hydroxymuconate Delta-isomerase | 5.3.3.10 | similar to AA sequence:UniProtKB:Q05354 -MPHFIAECTENIREQADLPSLFSKVNEALAATGIFPIGGIRSRAHWLDTWQMADGKHDYA -FVHMTLKIGAGRSLESRQEVGEMLFGLIKAHFADLMENRYLALSFEIAELHPTLNYKQNN -VHALFK ->GEN2.0219.00001.i0002_00005 834 amiD | N-acetylmuramoyl-L-alanine amidase AmiD | 3.5.1.28 | similar to AA sequence:UniProtKB:P75820 -MMKALLWLVGLALLLTGCASEKGIIDKEGYQLDTRHRAQAAYPRIKVLVIHYTAENFDVS -LATLTGRNVSSHYLIPATPPLYGGKPRIWQLVPEQDQAWHAGVSFWRGATRLNDTSIGIE -LENRGWRMSGGVKSFAPFESAQIQALIPLAKDIIARYDIKPQNVVAHADIAPQRKDDPGP -RFPWRELAAQGIGAWPDAQRVAFYLAGRAPYTPVDTATVLALLSRYGYEVKADMTAREQQ -RVIMAFQMHFRPAQWNGIADAETQAIAEALLEKYGQD ->GEN2.0219.00001.b0002_00006 1668 glnS | Glutamine--tRNA ligase | 6.1.1.18 | similar to AA sequence:UniProtKB:P00962 -MSEAEARPTNFIRQIIDEDLASGKHTTVHTRFPPEPNGYLHIGHAKSICLNFGIAQDYQG -QCNLRFDDTNPVKEDIEYVDSIKNDVEWLGFHWSGDIRYSSDYFDQLHAYAVELINKGLA -YVDELTPEQIREYRGTLTAPGKNSPFRDRSVEENLALFEKMRTGGFEEGKACLRAKIDMA -SPFIVMRDPVLYRIKFAEHHQTGTKWCIYPMYDFTHCISDALEGITHSLCTLEFQDNRRL -YDWVLDNITIPVHPRQYEFSRLNLEYTVMSKRKLNLLVTDKHVEGWDDPRMPTISGLRRR -GYTAASIREFCKRIGVTKQDNTIEMASLESCIREDLNENAPRAMAVIDPVKLVIENYPQG -ESEMVTMPNHPNKPEMGSREVPFSGEIWIDRADFREEANKQYKRLVMGKEVRLRNAYVIK -AERVEKDAEGNITTIFCTYDADTLSKDPADGRKVKGVIHWVSVAHALPIEIRLYDRLFSV -PNPGAAEDFLSVINPESLVIKQGYGEPSLKAAVAGKAFQFEREGYFCLDSRYATADKLVF -NRTVGLRDTWAKAGE ->GEN2.0219.00001.b0003_00007 768 trmD | tRNA (guanine-N(1)-)-methyltransferase | 2.1.1.228 | similar to AA sequence:UniProtKB:P0A873 -MFIGIVSLFPEMFRAITDYGVTGRAVKKGLLNIQSWSPRDFAHDRHRTVDDRPYGGGPGM -LMMVQPLRDAIHAAKAAAGEGAKVIYLSPQGRKLDQAGVSELATNQKLILVCGRYEGVDE -RVIQAEIDEEWSIGDYVLSGGELPAMTLIDSVARFIPGVLGHEASAIEDSFADGLLDCPH -YTRPEVLEGMEVPPVLLSGNHAEIRRWRLKQSLGRTWLRRPELLENLALTEEQARLLAEF -KTEHAQQQHKHDGMA ->GEN2.0219.00001.i0003_00008 261 NA | hypothetical protein | NA | NA -MAGLHAPYAYSAHHAVNFCSEYKRGFVLGFTHRMFEKTGDRQLSAWEAGILTRRYGLDKE -MVMDFFKENHSGMAVRFFMAGYRLEG ->GEN2.0219.00001.i0003_00009 582 NA | hypothetical protein | NA | NA -MSTLLYLHGFNSSPRSAKACQLKNWLAERHPHVEMIVPQLPPYPADAAELLESLVLEHGG -APLGLVGSSLGGYYATWLSQCFMLPAVVVNPAVRPFELLTDYLGQNENPYTGQQYVLESR -HIYDLKVMQIDPLEAPDLIWLLQQTGDEVLDYRQAVAYYASCRQTVTEGGNHAFTGFEDY -FNQIVDFLGLHSC ->GEN2.0219.00001.b0003_00010 369 NA | hypothetical protein | NA | NA -MMRTDGTVTQPRLKQVALSAISEVNAELYEFRRRQQMLGYASLAEVPAEQLDGKSERIQH -YFNAVYCWARAMLNERYQDYDATASGVKRGEELAEASGDLWRDARWAISRVQDAPHCTVE -LI ->GEN2.0219.00001.b0004_00011 1308 dctM | C4-dicarboxylate TRAP transporter large permease protein DctM | NA | similar to AA sequence:UniProtKB:O07838 -MIDPIFASCTLIAVFVVLLAMGAPIGICIVIASFSTMMLVLPFDISMFATAQKMFSSLDS -FALLAVPFFVLSGVIMNSGGIAARLVNFAKLFTGKLPGSLSYTNIVGNMMFGAISGSAIA -ASTSIGGVMVPMSAREGYDRGFAAAVNIASAPTGMLIPPTTAFILYALASGGTSIAALFA -GGLVAGVLWGVGCMLVTLVVAKRRNYRVFFTVQKGMALKVAVEAIPSLLLIVIIVGGIVQ -GIFTAIEASAIAVVYTLLLTIVFYRTLKIKDLPSILLQTVVMTGVIMFLLATSSAMSFSM -SITNIPAALSDMILGISANKLVILLVITVFLLIIGAFMDIGPAILIFTPILLPIMTKLGV -DPVHFGIIMIYNLAIGTITPPVGSGLYVGASVGKVKVEDVIKPLMPFYGAIIGVLLLITY -IPEITLFLPRLLGIM ->GEN2.0219.00001.i0004_00012 465 NA | hypothetical protein | NA | NA -MKFVAPEQAPEQAEVIKNTPFWPDVNLSEFRSVMRTDGTVTQPRLKQVVLTAISEVNAEL -YDFRNRQQMLGWRTLAEVPAEMLDGKSERIRHYHNAVFCWARAVLNERYQDYDATASGVK -RGEELAEASGDLWRDARWAISRVQDAPHCTVELI ->GEN2.0219.00001.b0004_00013 1014 xerC | Tyrosine recombinase XerC | NA | similar to AA sequence:UniProtKB:P39776 -METNITWQQLIDEYFFAKPLRSASEWSYTKVFKSFVHYMGPLSCPNDVTYHKVLAWRRFL -LKEKKLSGRTWNNKVAHMRAIFNYGIQRGLLHYDENPFNNSVVKPDKKRKKTLTQAQIEY -AYQIMEQYENQENTGLGLKYSRCALFPAWFWLTVLDTLYYTGIRQNQLLHIRLNDVDLRE -GQIRLITEGCKNHKEHYVPVISFLRPRLTCLMEKAQSEGLKGNDRLFNIALFTGKDPAIG -DDMDSPQVRAFFRRLSKECQFAISPHRFRHTLATEMMKMPEQNLHMAQSVLGHSNMKSTL -EYVENDIAVMGRALEAQFMQIKAAHARSIYSGLTKNR diff --git a/Examples/1-res-Annotate/Proteins/GEN4.1111.00001.prt b/Examples/1-res-Annotate/Proteins/GEN4.1111.00001.prt deleted file mode 100644 index dccb76f56958d6f413a43f2d33a3ccd3aa04f4df..0000000000000000000000000000000000000000 --- a/Examples/1-res-Annotate/Proteins/GEN4.1111.00001.prt +++ /dev/null @@ -1,52 +0,0 @@ ->GEN4.1111.00001.b0001_00001 831 amiD | N-acetylmuramoyl-L-alanine amidase AmiD | 3.5.1.28 | similar to AA sequence:UniProtKB:P75820 -MKALLWLVGLALLLTGCASEKGIIDKEGYQLDTRHRAQAAYPRIKVLVIHYTAENFDVSL -ATLTGRNVSSHYLIPATPPLYGGKPRIWQLVPEQDQAWHAGVSFWRGATRLNDTSIGIEL -ENRGWRMSGGVKSFAPFESAQIQALIPLAKDIIARYDIKPQNVVAHADIAPQRKDDPGPR -FPWRELAAQGIGAWPDAQRVAFYLAGRAPYTPVDTATVLALLSRYGYEVKADMTAREQQR -VIMAFQMHFRPAQWNGIADAETQAIAEALLEKYGQD ->GEN4.1111.00001.i0001_00002 381 hpcD | 5-carboxymethyl-2-hydroxymuconate Delta-isomerase | 5.3.3.10 | similar to AA sequence:UniProtKB:Q05354 -MPHFIAECTENIREQADLPGLFSKVNEALAASGIFPIGGIRSRAHWLDTWQMADGKHDYA -FVHMTLKIGTGRSLESRQEVGEMLFGLIKAHFADLMENRYLALSFEIAELHPTLNYKQNN -VHALFK ->GEN4.1111.00001.i0001_00003 804 hpcG | 2-oxo-hept-4-ene-1,7-dioate hydratase | 4.2.1.163 | similar to AA sequence:UniProtKB:P42270 -MLDKQTHTLIAQRLNQAEKQREQIRAVSLDYPNITIEDAYAVQREWVNIKIAEGRTLKGH -KIGLTSKAMQASSQISEPDYGALLDDMFFHDGGDIPTDRFIVPRIEVELAFVLAKPLRGP -HCTLFDVYNATDYVIPALELIDARSHNIDPETQRPRKVFDTISDNAANAGVILGGRPIKP -DELDLRWISALLYRNGVIEETGVAAGVLNHPANGVAWLANKLAPYDVQLEAGQIILGGSF -TRPVPASKGDTFHVDYGNMGAISCRFV ->GEN4.1111.00001.i0001_00004 1404 NA | hypothetical protein | NA | NA -MPVNKFSRRTLLTAGSALAVLPFLRALPVQAREPRETVDIKDYPADDGIASFKQAFADGQ -TVVLPPGWVCENINAAITIPAGKTLRVQGAVRGNGRGRFILQDGCQVVGEQGGSLHNVTL -DVRGSDCVIKGVTMSGFGPVAQIFIGGKEPQVMRNLIIDDITVTHANYAILRQGFHNQMD -GARITHSRFSDLQGDAIEWNVAIHDRDILISDHVIERIDCTNGKINWGIGIGLAGSTYDN -SYPEDQAVKNFVVANITGSDCRQLVHVENGKHFVIRNVKAKNITPDFSKNAGIDNATIAI -YGCDNFVIDNIDMTNSAGMLIGYGVVKGKYLSIPQNFKLNAIRLDNRQVAYKLRGIQISS -GNIPSFVAITNVRMTRATLELHNQPQHLFLRNINVMQTSAIGPALKMHFDLRKDVRGQFM -ARQDTLLSLANVHAINENGQSSVDIDRINHQTVNVEAVNFSLPKRGG ->GEN4.1111.00001.i0001_00005 774 hisP | Histidine transport ATP-binding protein HisP | NA | similar to AA sequence:UniProtKB:P02915 -MSENKLHVIDLHKRYGGHEVLKGVSLQARAGDVISIIGSSGSGKSTFLRCINFLEKPSEG -AIIVNGQNINLVRDKDGQLKVADKNQLRLLRTRLTMVFQHFNLWSHMTVLENVMEAPIQV -LGLSKHDARERALKYLAKVGIDERAQGKYPVHLSGGQQQRVSIARALAMEPDVLLFDEPT -SALDPELVGEVLRIMQQLAEEGKTMVVVTHEMGFARHVSSHVIFLHQGKIEEEGDPEQVF -GNPQSPRLQQFLKGSLK ->GEN4.1111.00001.i0001_00006 768 trmD | tRNA (guanine-N(1)-)-methyltransferase | 2.1.1.228 | similar to AA sequence:UniProtKB:P0A873 -MFIGIVSLFPEMFRAITDYGVTGRAVKKGLLNIQSWSPRDFAHDRHRTVDDRPYGGGPGM -LMMVQPLRDAIHAAKAAAGEGAKVIYLSPQGRKLDQAGVSELATNQKLILVCGRYEGVDE -RVIQTEIDEEWSIGDYVLSGGELPAMTLIDSVARFIPGVLGHEASAIEDSFADGLLDCPH -YTRPEVLEGMEVPPVLLSGNHAEIRRWRLKQSLGRTWLRRPELLENLALTEEQARLLAEF -KTEHAQQQHKHDGMA ->GEN4.1111.00001.i0001_00007 261 NA | hypothetical protein | NA | NA -MAGLHAPYAYSAHHAVNFCSEYKRGFVLGFTHRMFEKTGDRQLSAWEAGILTRRYGLDKE -MVMDFFKENHSGMAVRFFMVGYRLEG ->GEN4.1111.00001.i0001_00008 582 NA | hypothetical protein | NA | NA -MSTLLYLHGFNSSPRSAKACQLKNWLAERHPHVEMIVPQLPPYPADAAELLESLVLEHGG -APLGLVGSSLGGYYATWLSQCFMLPAVVVNPAVRPFELLTDYLGQNENPYTGQQYVLESR -HIYDLKVMQIDPLEAPDLIWLLQQTGDEVLDYRQAVAYYASCRQTVTEGGNHAFTGFEDY -FNQIVDFLGLHSC ->GEN4.1111.00001.b0001_00009 1083 dctM | C4-dicarboxylate TRAP transporter large permease protein DctM | NA | similar to AA sequence:UniProtKB:O07838 -MNSGGIAARLVNFAKLFTGKLPGSLSYTNIVGNMMFGAISGSAIAASTSIGGVMVPMSAR -EGYDRGFAAAVNIASAPTGMLIPPTTAFILYALASGGTSIAALFAGGLVAGVLWGVGCML -VTLVVAKRRNYRVFFTVQKGMALKVAVEAIPSLLLIVIIVGGIVQGIFTAIEASAIAVVY -TLLLTMVFYRTLKIKDLPSILLQTVVMTGVIMFLLATSSAMSFSMSITNIPAALSDMILG -ISANKLVILLVITVFLLIIGAFMDIGPAILIFTPILLPIMAKLGVDPVHFGIIMIYNLAI -GTITPPVGSGLYVGASVGKVKVEEVIKPLLPFYGAIIGVLLLITYIPEITLFLPRLLGIM diff --git a/Examples/1-res-Annotate/QC_L90-list_genomes.png b/Examples/1-res-Annotate/QC_L90-list_genomes.png deleted file mode 100644 index e501adc9b9429b8ce0ac215a40d81c39a5620bef..0000000000000000000000000000000000000000 Binary files a/Examples/1-res-Annotate/QC_L90-list_genomes.png and /dev/null differ diff --git a/Examples/1-res-Annotate/QC_nb-contigs-list_genomes.png b/Examples/1-res-Annotate/QC_nb-contigs-list_genomes.png deleted file mode 100644 index cee148de2bd0f0ba91c0cf7928a092fd4378ca93..0000000000000000000000000000000000000000 Binary files a/Examples/1-res-Annotate/QC_nb-contigs-list_genomes.png and /dev/null differ diff --git a/Examples/1-res-Annotate/Replicons/EXAM.0219.00001.fna b/Examples/1-res-Annotate/Replicons/EXAM.0219.00001.fna deleted file mode 100644 index 3ee2afdd2e0dfe944155dd39bed6ce8300128b12..0000000000000000000000000000000000000000 --- a/Examples/1-res-Annotate/Replicons/EXAM.0219.00001.fna +++ /dev/null @@ -1,4 +0,0 @@ ->EXAM.0219.00001.0001 -ATGTGTAAAAGCCGGAGGGGTTATCTTTTCCCGGCTTTTTATTATCAATTACTCATTAACTCCTGTTCCGTTCTTTTGCGTTTAATCACCGGAATATCTCCGGTATTGTTCAGCGCCCCGGAAATGTTTTTAACCACTGTTCTGCACTCCGTTTATTAAACGCGCTCAGCGCGCGCTCATATATCGCGCGCGCGCGCGCGCATATATATATAATGAGTGAGGCTGAAGCCCGCCCGACTAACTTTATTCGTCAGATTATTGATGAAGATCTGGCGAGTGGTAAACATACCACTGTCCATACCCGTTTTCCGCCGGAGCCGAATGGCTATCTGCATATCGGCCACGCGAAATCTATCTGCCTGAACTTTGGCATCGCGCAAGATTATCAGGGCCAGTGCAACCTGCGTTTCGATGACACCAACCCGGTAAAAGAAGATATCGAGTACGTTGATTCGATCAAAAACGACGTCGAGTGGTTAGGCTTTCACTGGTCTGGCGATATTCGCTACTCCTCCGATTACTTTGACCAACTGCACGCCTATGCGGTCGAGCTAATCAATAAAGGCCTGGCCTATGTTGATGAGCTGACGCCGGAGCAGATCCGTGAATACCGCGGTACGCTGACCGCGCCGGGTAAAAACAGCCCGTTCCGCGATCGCAGCGTCGAAGAGAACCTCGCGCTATTTGAAAAAATGCGTACCGGCGGTTTTGAAGAGGGTAAAGCCTGTCTGCGCGCTAAAATCGACATGGCGTCGCCGTTTATCGTGATGCGCGATCCGGTGCTGTATCGCATTAAATTCGCCGAGCATCATCAGACTGGCAACAAGTGGTGCATCTATCCGATGTACGACTTTACTCACTGCATCAGCGATGCGCTGGAAGGCATTACTCATTCTCTGTGTACGCTGGAGTTCCAGGATAACCGTCGTCTGTACGACTGGGTGCTGGACAACATCACCATTCCGGTTCACCCGCGCCAGTACGAATTCTCGCGCCTGAATCTGGAATACACCGTGATGTCCAAGCGTAAGCTGAACCTGCTGGTGACCGACAAACACGTCGAAGGTTGGGACGATCCGCGTATGCCGACTATTTCCGGTCTGCGCCGTCGCGGCTATACCGCGGCTTCTATTCGTGAGTTCTGCAAACGCATCGGCGTCACCAAGCAGGACAACACTATTGAGATGGCGTCGCTGGAATCCTGCATTCGCGAAGATCTGAACGAAAACGCGCCGCGCGCGATGGCGGTAATCGATCCGGTAAAACTGGTTATCGAAAATTACCCGCAGGGTGAGAGCGAAATGGTTACCATGCCTAACCATCCGAATAAACCGGAGATGGGCAGCCGTGAAGTGCCGTTTAGCGGTGAGATCTGGATCGATCGCGCAGATTTCCGCGAAGAAGCGAACAAACAGTACAAACGTCTGGTGATGGGCAAAGAAGTGCGTCTGCGTAATGCCTACGTCATTAAAGCGGAGCGCGTAGAGAAGGATGCCGAAGGGAATATCACCACCATCTTCTGTACCTATGATGCTGATACGCTGAGTAAAGATCCGGCTGACGGGCGTAAAGTGAAAGGCGTAATCCACTGGGTTAGCGCAGCACATGCGCTGCCGATTGAAATTCGTCTCTACGACCGTCTGTTCAGCGTGCCGAATCCGGGCGCCGCGGAGGACTTCCTGTCTGTTATCAACCCCGAATCATTAGTGATTAAGCAGGGGTATGGCGAGCCGTCGCTGAAAGCGGCGGTAGCAGGAAAAGCTTTCCAGTTTGAACGTGAAGGCTACTTCTGCCTCGACAGCCGCTATGCAACGGCCGATAAGCTGGTCTTTAACCGCACCGTGGGCCTGCGTGATACCTGGGCGAAAGCGGGCGAGTAACGCGCATAGGCGGCCTTCAAGGAGGCGCTAGGCGAATGAAAGCGCTACTGTGGCTGGTGGGTCTCGCGTTGCTGTTAACAGGCTGCGCGAGCGAAAAAGGAATTATCGATAAAGAGGGATATCAGCTTGATACCCGACATCGGGCGCAGGCGGCCTATCCGCGCATTAAAGTCCTGGTGATTCACTATACGGCGGAAAACTTTGACGTTTCGCTGGCGACGTTAACGGGTCGCAACGTCAGTTCGCATTACCTGATTCCCGCAACCCCGCCATTATATGGCGGTAAACCGCGCATCTGGCAACTGGTGCCGGAACAGGATCAGGCCTGGCATGCGGGCGTCAGTTTCTGGCGAGGCGCCACGCGTCTCAATGATACGTCTATTGGCATTGAGCTGGAAAATCGTGGTTGGCGAATGTCCGGCGGGGTGAAATCTTTCGCGCCGTTTGAATCCGCGCAAATTCAGGCATTGATTCCGTTAGCGAAGGATATTATCGCGCGCTATAACATCAAACCGCAGAATGTGGTGGCCCATGCGGATATCGCGCCGCAGCGTAAAGACGATCCCGGCCCGCGCTTCCCGTGGCGCGAGCTGGCGGCGCAGGGGATTAGCGCCTGGCCTGACGCCCAGCGTGTGGCGTTTTATCTGGCTGGACGCGCGCCGTATACGCCAGTCGATACCGCAACGGTGCTTGCGTTACTCTCGCGCTATGGCTATGAAGTCAAAGCCGATATGACGGCACGCGAGCAGCAGCGGGTGATTATGGCGTTCCAGATGCACTTCCGTCCGGCGCAATGGAACGGTATCGCAGATGCCGAAACGCAGGCGATTGCCGAAGCATTACTGGAGAAGTACGGCCAGGATTAACGCGATAGGCGCGCGAGATTACGCGCGCAGTATCGCGC ->EXAM.0219.00001.0002 -CGCGCATAGCGCGCAATGCCGCACTTTATTGCTGAATGTACTGAAAATATTCGCGAGCAGGCTGATTTACCCGGCCTGTTCAGCAAGGTAAACGAGGCGCTGGCCGCCAGCGGGATTTTCCCCATCGGCGGTATCCGCAGTCGCGCCCACTGGCTGGATACCTGGCAGATGGCTGACGGTAAGCATGATTACGCGTTTGTGCATATGACGCTGAAAATCGGCGCCGGGCGCAGCCTGGAGAGCCGTCAGGAAGTTGGCGAAATGCTGTTTGGGCTGATTAAAGCCCACTTCGCCGACCTGATGGAGAACCGCTATCTGGCGCTGTCGTTTGAGATTGCCGAGCTACATCCGACGCTCAATTACAAACAAAACAACGTACACGCGTTATTTAAATAGCCGATATGAGGCGCGGCGCTATAAGGCGCTCATGAGCATGCCCGCGACTAAATTCTCCCGACGTACCCTCCTGACGGCAGGTTCTGCGCTTGCTGTTCTTCCTTTTCTGCGCGCCTTGCCGGTACAGGCGCGTGAACCTCGCGAGACCGTCGATATTAAGGATTATCCGGCGGATGACGGTATCGCCTCGTTCAAACAGGCCTTCGCCGACGGACAGACCGTGGTCGTACCGCCAGGATGGGTGTGTGAAAATATCAATGCGGCGATAACGATTCCGGCGGGAAAAACGCTGCGGGTACAGGGCGCGGTGCGTGGGAATGGCCGGGGACGGTTTATTTTGCAGGACGGGTGTCAGGTGGTGGGGGAGCAGGGCGGCAGTCTGCACAATGTGACGCTGGATGTTCGCGGGTCGGACTGTGTGATTAAAGGCGTGGCGATGAGCGGCTTTGGCCCCGTCGCGCAAATTTTCATCGGTGGTAAGGAACCGCAGGTGATGCGTAATCTCATTATCGATGACATCACCGTTACCCACGCCAACTACGCCATTCTCCGCCAGGGATTTCATAACCAAATGGATGGCGCGCGGATTACGCATAGCCGCTTTAGCGATTTACAGGGGGACGCCATTGAGTGGAATGTCGCGATTCACGACCGCGACATCCTGATTTCCGATCATGTCATCGAACGCATTAATTGTACCAATGGCAAAATCAACTGGGGGATCGGCATCGGGCTGGCGGGTAGCACCTATGACAACAGTTATCCTGAAGACCAGGCAGTAAAAAACTTTGTGGTGGCCAATATTACCGGATCTGATTGCCGACAGCTTGTGCACGTAGAAAATGGCAAACATTTCGTCATTCGCAATGTCAAAGCCAAAAACATCACGCCCGGTTTCAGTAAAAATGCGGGTATTGATAACGCAACGATCGCAATTTATGGCTGTGATAATTTCGTCATTGATAATATTGATATGACGAATAGTGCCGGGATGCTCATCGGCTATGGCGTCGTTAAAGGAAAATACCTGTCAATTCCGCAAAACTTTAAATTAAACGCTATTCGGTTGGATAATCGCCAGGTTGCTTATAAATTACGCGGCATTCAAATTTCCTCCGGCAACACCCCCTCTTTTGTCGCCATCACCAATGTACGGATGACGCGTGCTACGCTGGAACTGCATAATCAACCGCAGCACCTCTTTCTGCGCAATATCAACGTGATGCAAACTTCAGCGATTGGCCCGGCGTTAAAAATGCATTTCGATTTGCGTAAAGATGTACGTGGTCAATTTATGGCCCGCCAGGACACGCTGCTTTCCCTCGCTAATGTTCATGCCATCAATGAAAACGGGCAGAGTTCCGTGGATATCGACAGGATTAATCACCAAACCGTGAATGTCGAAGCAGTGAATTTTTCGCTGCCGAAGCGGGGAGGGTAACGAATTCCGCGGCATATAGCGGCGCGATAGCATGTCAGAAAATAAATTACACGTTATCGATTTGCACAAACGCTACGGCGGTCATGAAGTGCTGAAAGGGGTATCGCTGCAGGCCCGCGCCGGAGATGTGATTAGCATCATCGGCTCGTCCGGCTCCGGTAAAAGCACTTTTTTGCGCTGTATTAACTTCCTCGAAAAACCGAGCGAAGGCGCGATTATCGTGAACGGTCAGAACATTAATCTGGTGCGCGACAAAGATGGGCAGCTCAAAGTGGCGGATAAAAATCAGCTACGCTTGTTGCGTACCCGCCTGACGATGGTGTTTCAGCACTTCAACCTCTGGAGCCACATGACGGTGCTGGAAAATGTGATGGAAGCGCCGATTCAGGTACTGGGATTAAGCAAGCACGACGCGCGCGAGCGGGCGTTGAAATATCTGGCGAAGGTGGGGATTGATGAGCGCGCTCAGGGCAAATATCCCGTCCATCTCTCCGGCGGCCAACAGCAGCGCGTTTCTATTGCGCGCGCGCTGGCGATGGAACCTGACGTTTTACTGTTCGATGAACCCACATCGGCGCTCGATCCTGAACTGGTCGGCGAAGTGTTGCGCATCATGCAACAACTGGCGGAAGAAGGCAAAACGATGGTGGTGGTCACGCATGAAATGGGCTTCGCTCGCCATGTCTCTTCGCACGTTATTTTTCTGCATCAGGGGAAAATTGAAGAAGAGGGTGATCCGGAGCAGGTGTTCGGCAATCCGCAAAGCCCGCGTTTACAGCAATTCCTGAAAGGCTCGCTGAAATAACGCTCAGAGGCGCGCGCGCGCTATATACGCGCAGTGTTTATTGGCATAGTTAGCCTGTTTCCTGAAATGTTCCGCGCAATTACCGATTACGGGGTAACTGGCCGGGCAGTAAAAAAAGGCCTGCTGAACATCCAAAGCTGGAGTCCTCGCGACTTCGCGCATGACCGGCACCGTACCGTGGACGACCGTCCTTACGGCGGCGGACCGGGGATGTTAATGATGGTGCAACCCTTGCGGGACGCCATTCACGCAGCAAAAGCCGCGGCAGGTGAAGGCGCTAAAGTGATTTATCTGTCGCCTCAGGGACGCAAGCTTGATCAAGCGGGCGTTAGCGAGCTGGCCACGAATCAGAAGCTTATTCTGGTGTGTGGTCGCTACGAAGGCGTAGATGAGCGCGTAATTCAGACCGAAATTGACGAAGAATGGTCAATTGGCGATTACGTTCTCAGCGGTGGCGAACTACCGGCAATGACGCTGATTGACTCCGTCGCCCGGTTTATACCGGGGGTTCTGGGGCATGAGGCATCAGCAATCGAAGATTCGTTTGCTGATGGGTTGCTGGATTGTCCGCACTATACGCGCCCTGAAGTGTTAGAGGGGATGGAAGTACCGCCAGTATTGCTGTCGGGAAACCATGCTGAGATACGTCGCTGGCGTTTGAAACAGTCGCTGGGCCGAACCTGGCTTAGAAGACCTGAACTTCTGGAAAACCTGGCTCTGACTGAAGAGCAAGCAAGGTTGCTGGCGGAGTTCAAAACAGAACACGCACAACAGCAGCATAAACATGATGGGATGGCATAGCCGTCATATGGGCTCTCAGAGGAGACGCGCTAATGCGCAGTACGTGTTTATTGGCATAGTTAGCCTGTTTCCTGAAATGTTCCGCGCAATTACCGATTACGGGGTAACTGGCCGGGCAGTAAAAAAAGGCCTGCTGAACATCCAAAGCTGGAGTCCTCGCGACTTCGCGCATGACCGGCACCGTACCGTGGACGACCGTCCTTACGGCGGCGGACCGGGGATGTTAATGATGGTGCAACCCTTGCGGGACGCCATTCACGCAGCAAAAGCCGCGGCAGGTGAAGGCGCTAAAGTGATTTATCTGTCGCCTCAGGGACGCAAGCTTGATCAAGCGGGCGTTAGCGAGCTGGCCACGAATCAGAAGCTTATTCTGGTGTGTGGTCGCTACGAAGGCGTAGATGAGCGCGTAATTCAGACCGAAATTGACGAAGAATGGTCAATTGGCGATTACGTTCTCAGCGGTGGCGAACTACCGGCAATGACGCTGATTGACTCCGTCGCCCGGTTTATACCGGGGGTTCTGGGGCATGAGGCATCAGCAATCGAAGATTCGTTTGCTGATGGGTTGCTGGATTGTCCGCACTATACGCGCCCTGAAGTGTTAGAGGGGATGGAAGTACCGCCAGTATTGCTGTCGGGAAACCATGCTGAGATACGTCGCTGGCGTTTGAAACAGTCGCTGGGCCGAACCTGGCTTAGAAGACCTGAACTTCTGGAAAACCTGGCTCTGACTGAAGAGCAAGCAAGGTTGCTGGCGGAGTTCAAAACAGAACACGCACAACAGCAGCATAAACATGATGGGATGGCATAGCGCATACGCGCGCGATATATATTCGCGCAGAGGCGCGCATAGCGATGAAGTTTGTTGCGCCCGAACAGGCACCGGAACAGGCGGAGGTCATCAAAAATACGCCGTTCTGGCCTGATGTGGACCTGTCGGAATTTCGCAGTGTGATGCGCACTGACGGCACGGTGACGCAGCCGCGTTTAAAGCAGGTCGTGCTGACGGCGATCTCTGAGGTTAACGCTGAGCTGTACGACTTCCGCAACCGTCAGCAGATGCTGGGCTGGCGGACACTTGCTGAGGTTCCCGCAGAAATGCTGGACGGTAAAAGCGAGCGTATCCGGCACTACCACAACGCTGTTTTTTGCTGGGCGCGCGCTGTGCTTAATGAGCGTTATCAGGACTATGACGCCACGGCGTCAGGCGTGAAGCGAGGGGAGGAGCTGGCGGAGGCCAGCGGCGATCTGTGGCGTGATGCCCGCTGGGCCATCAGCCGGGTGCAGGATGTACCGCACTGTACGGTGGAGCTTATCTGAACGGCTAGCGCGTAGCGGCAGTCTCGGATGAATAATCATTTTGGGAAAGGGTTAATGGCCGGGTTGCACGCGCCATATGCATATAGCGCGCATCATGCGGTGAATTTCTGTTCTGAGTATAAACGTGGCTTTGTATTGGGTTTTACACACCGTATGTTCGAAAAGACCGGCGATCGTCAACTTAGCGCGTGGGAGGCTGGAATTCTGACGCGTCGCTATGGTCTGGATAAAGAAATGGTGATGGATTTCTTTAAAGAGAATCATTCCGGGATGGCGGTTCGCTTCTTTATGGCCGGTTATCGACTCGAAGGTTGACGATCGCGCGCAGGAGGAGAGCTCTCTTCTTCTAGAGCATGTCTACGCTTCTCTATTTGCACGGATTCAACAGTTCCCCTCGCTCGGCAAAAGCGTGCCAGCTAAAAAACTGGCTGGCGGAGCGTCATCCGCATGTTGAGATGATCGTCCCTCAGCTGCCGCCGTATCCTGCCGATGCGGCGGAGTTGCTGGAATCTCTCGTGCTTGAGCATGGCGGTGCGCCATTAGGGCTGGTAGGATCGTCGCTGGGTGGTTATTACGCCACCTGGCTGTCGCAATGTTTTATGCTGCCGGCTGTGGTGGTGAATCCCGCCGTGCGGCCCTTTGAATTACTGACCGACTATCTCGGTCAGAACGAGAACCCCTACACCGGGCAGCAATATGTGCTAGAGTCTCGCCATATTTATGATCTTAAAGTCATGCAGATTGACCCGCTGGAAGCGCCGGACCTGATCTGGCTACTGCAACAGACGGGCGATGAAGTGCTGTATTACCGCCAGGCGGTGGCATATTACGCCTCCTGCCGTCAGACAGTGACCGAGGGTGGTAATCACGCATTCACGGGCTTCGAAGATTATTTCAACCAGATTGTCGATTTTCTTGGACTGCACAGTTGCTGACGGCTATGCGCGCGCTCGATGATTGACCCTATTTTTGCGTCCTGTACGCTAATTGCCGTCTTTGTTGTTTTACTGGCCATGGGCGCGCCTATCGGGATCTGCATCGTTATCGCCTCTTTCAGCACCATGATGCTGGTACTGCCTTTCGATATTTCGATGTTCGCCACCGCGCAAAAAATGTTCTCCAGCCTGGACAGTTTTGCCTTGCTGGCCGTGCCGTTCTTCGTTTTGTCCGGGGTGATCATGAATAGCGGGGGAATTGCCGCCCGGCTGGTCAATTTTGCCAAACTGTTTACTGGCAAACTGCCCGGCTCGCTCTCTTATACCAACATCGTCGGCAATATGATGTTCGGTGCAATTTCCGGATCGGCGATTGCCGCCTCAACCTCCATCGGCGGCGTGATGGTGCCGATGAGCGCGCGCGAAGGTTACGATCGCGGCTTTGCGGCCGCGGTGAATATCGCCTCCGCGCCGACGGGAATGTTAATTCCGCCCACCACGGCTTTTATCCTTTACGCGCTGGCAAGCGGGGGAACATCGATTGCCGCTCTGTTCGCCGGCGGTCTGGTCGCGGGAGTGCTGTGGGGCGTTGGCTGTATGCTGGTCACGCTGGTGGTCGCTAAGCGTCGAAATTATCGGGTTTTCTTCACCGTCCAAAAAGGTATGGCGCTAAAAGTTGCCGTTGAGGCCATTCCCAGCCTGCTGCTGATCGTGATTATTGTCGGCGGCATTGTGCAGGGGATTTTCACCGCCATTGAAGCCTCCGCGATTGCCGTGGTGTATACGTTATTGCTGACGATGGTGTTTTACCGCACGCTGAAAATTAAGGATTTGCCTTCGATTTTGCTCCAGACAGTGGTAATGACCGGGGTCATCATGTTCCTGCTGGCAACCTCTTCGGCGATGTCCTTCTCGATGTCGATCACCAATATTCCTGCGGCGCTGAGCGATATGATCCTCGGTATTTCCGCCAATAAACTGGTTATCCTGTTAGTCATTACCGTCTTTTTGTTGATTATCGGCGCATTTATGGATATTGGTCCGGCCATTCTGATTTTTACCCCGATTCTGCTGCCAATCATGGCTAAACTGGGCGTCGATCCGGTGCATTTCGGCATTATCATGATCTATAACCTGGCGATTGGCACCATTACGCCGCCAGTTGGCAGTGGTTTATATGTCGGGGCGAGCGTCGGTAAGGTCAAAGTTGAGGAAGTGATTAAACCGTTGCTGCCTTTTTACGGCGCGATTATCGGCGTTCTGTTATTAATTACCTACATTCCGGAAATCACACTGTTCTTACCCCGTCTACTGGGCATCATGTAA diff --git a/Examples/1-res-Annotate/Replicons/EXAM.1216.00002.fna b/Examples/1-res-Annotate/Replicons/EXAM.1216.00002.fna deleted file mode 100644 index a6c8c7d61a21ec35944197e0e76c7e01cfd13245..0000000000000000000000000000000000000000 --- a/Examples/1-res-Annotate/Replicons/EXAM.1216.00002.fna +++ /dev/null @@ -1,6 +0,0 @@ ->EXAM.1216.00002.0001 -ATGAGAGCGCTACTGTGGCTGGTGGGTCTTGCGTTGCTGTTAACAGGCTGCGCGAGCGAAAAAGGAATTATCGATGAAGAGGGATATCAGCTTGATACCCGACATCGGGCGCAGGCGGCCTATCCGCGCATTAAAGTCCTGGTGATTCACTATACGGCGGAAAACTTTGACGTTTCGCTGGCGACGTTAACGGGCCGCAACGTCAGTTCGCATTACCTGATTCCCGCAACCCCGCCATTATATGGCGGTAAACCGCGCATCTGGCAACTGGTGCCGGAACAGGATCAGGCCTGGCATGCGGGCGTCAGTTTCTGGCGAGGCGCCACGCGTCTCAATGATACGTCTATTGGCATTGAGCTGGAAAATCGCGGCTGGCGAATGTCCGGCGGGGTGAAATCTTTCGCGCCGTTTGAATCCGCGCAAATTCAGGCATTGATTCCGTTAGCGAAGGACATTATCGCGCGCTATGACATCAAACCGCAGAATGTGGTGGCCCATGCGGATATCGCGCCGCAGCGTAAAGACGATCCCGGCCCGCGCTTCCCGTGGCGCGAGCTGGCGGCACAGGGGATTGGCGCCTGGCCTGACGCCCAGCGTGTGGCGTTTTATCTGGCTGGACGCGCGCCGTATACGCCAGTCGATACCGCAACGGTGCTTGCGTTACTCTCGCGCTATGGCTATGAAGTCAAAGCCGATATGACGGCGCGCGAGCAACAGCGGGTGATTATGGCGTTCCAGATGCACTTCCGTCCGGCGCAATGGAACGGTATCGCAGATGCCGAAACGCAGGCGATTGCCGAAGCATTACTGGAGAAGTACGGCCAGGATTAACGAGTCCGGGAGCGGCGAGATTCCGGGCAGAGGAGGCGGCTATAGCGGATGAGAGCGCTACTGTGGCTGGTGGGTCTTGCGTTGCTGTTAACAGGCTGCGCGAGCGAAAAAGGAATTATCGATGAAGAGGGATATCAGCTTGATACCCGACATCGGGCGCAGGCGGCCTATCCGCGCATTAAAGTCCTGGTGATTCACTATACGGCGGAAAACTTTGACGTTTCGCTGGCGACGTTAACGGGCCGCAACGTCAGTTCGCATTACCTGATTCCCGCAACCCCGCCATTATATGGCGGTAAACCGCGCATCTGGCAACTGGTGCCGGAACAGGATCAGGCCTGGCATGCGGGCGTCAGTTTCTGGCGAGGCGCCACGCGTCTCAATGATACGTCTATTGGCATTGAGCTGGAAAATCGCGGCTGGCGAATGTCCGGCGGGGTGAAATCTTTCGCGCCGTTTGAATCCGCGCAAATTCAGGCATTGATTCCGTTAGCGAAGGACATTATCGCGCGCTATGACATCAAACCGCAGAATGTGGTGGCCCATGCGGATATCGCGCCGCAGCGTAAAGACGATCCCGGCCCGCGCTTCCCGTGGCGCGAGCTGGCGGCACAGGGGATTGGCGCCTGGCCTGACGCCCAGCGTGTGGCGTTTTATCTGGCTGGACGCGCGCCGTATACGCCAGTCGATACCGCAACGGTGCTTGCGTTACTCTCGCGCTATGGCTATGAAGTCAAAGCCGATATGACGGCGCGCGAGCAACAGCGGGTGATTATGGCGTTCCAGATGCACTTCCGTCCGGCGCAATGGAACGGTATCGCAGATGCCGAAACGCAGGCGATTGCCGAAGCATTACTGGAGAAGTACGGCCAGGATTAACAGGGCGCGGTATCGCGAGGACTCTCTCTTCGAGGACATGCCGCACTTTATTGCTGAATGTACTGAAAATATTCGCGAGCAGGCTGATTTACCCGGCCTGTTCAGCAAGGTAAACGAGGCGCTGGCCGCCAGCGGGATTTTCCCCATCGGCGGTATCCGCAGTCGCGCCCACTGGCTGGATACCTGGCAGATGGCTGACGGTAAGCATGATTACGCGTTTGTGCATATGACGCTGAAAATCGGCGCCGGGCGCAGCCTGGAGAGCCGTCAGGAAGTCGGCGAAATGCTGTTCGGGCTGATTAAAGCCCACTTCGCCGACCTGATGGAGAACCGCTATCTGGCGCTGTCGTTTGAGATTGCCGAGTTACATCCAACGCTCAATTACAAACAAAACAACGTACACGCGTTATTTAAATAGCCCGAGTATTAGCGCGCGGCGGCGCTATAGGCGCGCTATAGGCATGAGCGCGCTATTTCTGGCCATCCCGTTAACCATTTTTGTGTTGTTTGTGTTACCGATTTGGCTGTGGCTGCATTACAGCAACCGCGCCGGTCGGGGAGAACTGTCGCAAAGCGAGCAGCAACGCTTACTGCAACTCACAGACGACGCGCAACGTATGCGCGAGCGCATTCAGGCGCTGGAAGACATTCTTGATGCAGAGCATCCGAACTGGAGAGAGCGCTAACGAGAGTCTCGGAGGAGCGGCGCTCTGGATGCCCGCGACTAAATTCTCCCGACGTACCCTCCTGACGGCAGGTTCTGCGCTTGCTGTTCTTCCTTTCCTGCGCGCCTTGCCGGTACAGGCGCGTGAACCTCGCGAGACCGTCGATATTAAGGATTATCCGGCGGATGACGGTATCGCCTCGTTCAAACAGGCCTTCGCCGACGGACAGACCGTGGTCGTACCGCCAGGATGGGTGTGTGAAAATATCAATGCGGCGATAACGATTCCGGCGGGAAAAACGCTGCGGGTACAGGGCGCGGTGCGTGGGAATGGCCGGGGACGGTTTATTTTGCAGGACGGGTGTCAGGTGGTGGGGGAGCAGGGCGGCAGTCTGCACAATGTGACGCTGGATGTTCGCGGGTCGGACTGTGTGATTAAAGGCGTGGCGATGAGCGGCTTTGGCCCCGTCGCGCAAATTTTCATCGGTGGTAAGGAACCGCAGGTGATGCGTAATCTCATTATCGATGACATCACCGTTACCCACGCCAACTACGCCATTCTCCGCCAGGGATTTCATAACCAAATGGACGGCGCGAGGATTACGCATAGCCGCTTTAGCGATTTACAGGGGGACGCCATTGAGTGGAATGTCGCGATTCACGACCGCGATATCCTGATTTCCGATCATGTCATCGAACGCATTGATTGTACCAATGGCAAAATCAACTGGGGGATCGGCATCGGGCTGGCGGGTAGCACCTATGACAACAGTTATCCTGAAGACCAGGCAGTAAAAAACTTTGTGGTGGCCAATATTACCGGATCTGATTGCCGACAGCTTGTGCACGTAGAAAATGGCAAACATTTCGTCATTCGCAATGTCAAAGCCAAAAACATCACGCCCGATTTCAGTAAAAATGCGGGTATTGATAACGCAACGATCGCAATTTATGGCTGTGATAATTTCGTCATTGATAATATTGATATGACGAATAGTGCCGGGATGCTCATCGGCTATGGCGTCGTTAAAGGAAAATACCTGTCAATTCCGCAAAACTTTAAATTAAACGCTATTCGGTTGGATAATCGCCAGGTTGCTTATAAATTACGCGGCATTCAAATTTCCTCCGGCAACACCCCCTCTTTTGTCGCCATCACCAATGTACGGATGACGCGTGCTACGCTGGAACTGCATAATCAACCGCAGCACCTCTTCCTGCGTAATATCAACGTGATGCAAACTTCAGCGATTGGCCCGGCGTTAAAAATGCATTTCGATTTGCGTAAAGATGTCCGTGGTCAATTTATGGCCCGCCAGGACACGCTGCTTTCCCTCGCTAATGTTCATGCCATCAATGAAAACGGGCAGAGTTCCGTGGATATCGACAGGATTAATCACCAAACCGTGAATGTCGAAGCAGTGAATTTTTCGCTGCCGAAGCGGGGAGGGTAACGCGTCTGCGCGCGCGGAGAGAGGCTCTCAGGACATGTCAGAAAATAAATTACACGTTATCGATTTGCACAAACGCTACGGCGGTCATGAAGTGCTGAAAGGGGTATCGCTGCAGGCCCGCGCCGGAGATGTGATTAGCATCATCGGCTCGTCCGGCTCCGGTAAAAGCACTTTTTTGCGCTGTATTAACTTCCTCGAAAAACCGAGCGAAGACGCGATTATCGTGAACGGTCAGAACATTAATCTGGTGCGCGACAAAGACGGGCAGCTCAAAGTGGCGGATAAAAATCAGCTACGCTTGTTGCGTACCCGCCTGACGATGGTGTTTCAGCACTTTAACCTCTGGAGCCACATGACGGTGCTGGAAAATGTGATGGAAGCGCCGATTCAGGTACTGGGATTAAGCAAGCACGACGCGCGCGAGCGGGCGTTGAAATATCTGGCGAAGGTGGGGATTGATGAGCGCGCTCAGGGCAAATATCCCGTTCATCTCTCCGGTGGCCAACAGCAGCGCGTTTCTATTGCGCGCGCGCTGGCGATGGAACCTGACGTTTTACTGTTCGATGAACCCACTTCGGCGCTCGATCCTGAACTGGTCGGCGAAGTGTTGCGCATCATGCAACAACTGGCGGAAGAAGGCAAAACGATGGTGGTGGTCACGCATGAAATGGGCTTCGTTCGCCATGTCTCTTCGCACGTTATTTTTCTGCATCAGGGGAAAATTGAAGAAGAGGGCGATCCGGAGCAGGTGTTCGGCAATCCGCAAAGCCCGCGTTTACAGCAATTCCTGAAAGGCTCGCTGAAATAACCGGATGCGCGCGATATATCGGCGATGCGTGTTTATTGGCATCGTTAGCCTGTTTCCTGAAATGTTCCGCGCAATTACCGATTACGGGGTAACTGGCCGGGCAGTAAAAAATGGCCTGCTGAACATCCAAAGCTGGAGTCCTCGCGACTTCACGCATGACCGGCACCGTACCGTGGACGATCGTCCTTACGGCGGCGGACCAGGGATGTTAATGATGGTGCAACCCTTGCGGGACGCCATTCACGCAGCAAAAGCCGCGGCAGGTGAAGGCGCTAAAGTGATTTATCTGTCGCCTCAGGGACGCAAGCTTGATCAAGCGGGCGTTAGCGAGCTGGCCACGAATCAGAAGCTTATTCTGGTGTGTGGTCGCTACGAAGGCGTAGATGAGCGCGTAATTCAGACCGAAATTGACGAAGAATGGTCAATTGGCGATTACGTTCTCAGCGGTGGCGAACTACCGGCAATGACGCTGATTGACTCCGTCGCCCGGTTTATACCGGGAGTTCTGGGGCATGAAGCATCAGCAATCGAAGATTCGTTTGCTGATGGGTTGCTGGATTGTCCGCACTATACGCGCCCTGAAGTGTTAGAGGGGATGGAAGTACCGCCAGTATTGCTGTCGGGAAACCATGCTGAGATACGTCGCTGGCGTTTGAAACAGTCGCTGGGCCGAACCTGGCTTAGAAGACCTGAACTTCTGGAAAACCTGGCTCTGACTGAAGAGCAAGCAAGGTTGCTGGCGGAGTTCAAAACAGAACACGCACAACAGCAGCATAAACATGATGGGATGGCATAGCCGGCTCTGCGAGAGAGGAGCGCTCGCATGAATAATCATTTTGGGAAAGGGTTAATGGCCGGGTTGCACGCGCCATATGCATATAGCGCGCATCATGCGGTGAATTTCTGTTCTGAGTATAAACGTGGCTTTGTATTGGGTTTTACACACCGTATGTTCGAAAAGACCGGCGATCGTCAACTTAGCGCGTGGGAGGCTGGAATTCTGACGCGTCGCTATGGTCTGGATAAAGAAATGGTGATGGATTTCTTTAAAGAGAATCATTCCGGGATGGCGGTTCGCTTCTTTATGGCCGGTTATCGACTCGAAGGTTGA ->EXAM.1216.00002.0002 -ATGTCTACGCTTCTCTATTTGCACGGATTCAACAGTTCCCCTCGCTCGGCAAAAGCGTGCCAGCTAAAAAACTGGCTGGCGGAGCGTCATCCGCATGTTGAGATGATCGTCCCTCAACTACCGCCGTATCCTGCCGATGCGGCGGAGTTGCTGGAGTCTCTCGTGCTTGAGCATGGCGGTGCGCCATTAGGGCTGGTAGGATCGTCGCTGGGTGGTTATTACGCCACCTGGCTGTCGCAATGTTTTATGCTGCCGGCTGTGGTGGTGAATCCCGCCGTGCGGCCCTTTGAATTACTGACCGACTATCTCGGTCAGAACGAGAACCCCTACACCGGGCAGCAATATGTGCTAGAGTCTCGCCATATTTATGATCTTAAAGTCATGCAGATTGACCCGCTGGAAGCGCCGGACCTGATCTGGCTACTGCAACAGACGGGCGATGAAGTGCTGGATTACCGCCAGGCGGTGGCATATTACGCCTCCTGCCGTCAGACAGTGACCGAGGGTGGTAATCACGCATTCACGGGCTTCGAAGATTATTTCAACCAGATTGTCGATTTTCTTGGACTGCACAGTTGCTGACGCGTAGCGGCCGGAATCTTCTCGGAGAGGCGCTTCTCTCTCGGAGATGATTGACCCTATTTTTGCGTCCTGTACGCTAATTGCCGTCTTTGTTGTTTTACTGGCCATGGGCGCGCCTATCGGGATCTGCATCGTTATCGCCTCTTTCAGCACCATGATGCTGGTACTGCCTTTCGATATTTCGATGTTCGCCACCGCGCAAAAAATGTTCTCCAGCCTGGACAGTTTTGCCTTGCTGGCCGTGCCGTTCTTCGTTTTGTCCGGGGTGATCATGAATAGCGGGGGAATTGCCGCCCGGCTGATCAATTTTGCCAAACTGTTTACTGGCAAACTGCCCGGTTCGCTCTCTTATACCAACATCGTCGGCAATATGATGTTCGGTGCAATTTCCGGATCGGCAATTGCCGCCTCAACCTCCATCGGCGGCGTGATGGTGCCGATGAGCGCGCGCGAAGGTTACGATCGCGGCTTTGCGGCCGCGGTGAATATCGCCTCCGCGCCGACGGGAATGTTAATTCCGCCCACCACGGCTTTTATCCTTTATGCGCTGGCAAGCGGGGGAACATCGATTGCCGCTCTGTTCGCCGGCGGTCTGGTCGCGGGAGTGCTGTGGGGCGTTGGCTGTATGCTGGTCACGCTGGTAGTCGCTAAGCGTCGAAATTATCGGGTTTTCTTCACCGTCCAAAAAGGCATGGCGCTAAAAGTTGCCGTTGAGGCCATTCCCAGCCTGTTACTGATCGTGATTATCGTCGGCGGCATTGTGCAGGGGATTTTCACCGCCATTGAAGCCTCCGCGATTGCCGTGGTGTATACGTTATTGCTGACGATGGTGTTTTACCGCACGCTGAAAATTAAGGATTTGCCTTCGATTTTGCTCCAGACAGTGGTAATGACCGGGGTCATCATGTTCCTGCTGGCAACCTCTTCGGCGATGTCCTTCTCAATGTCGATCACCAATATTCCTGCGGCGCTGAGCGATATGATCCTCGGTATTTCCGCCAATAAACTGGTTATCCTGTTAGTCATTACCGTCTTTTTGTTGATTATCGGCGCATTTATGGATATCGGTCCGGCCATTCTGATTTTTACCCCGATTCTGCTGCCGATCATGGCTAAACTGGGCGTCGATCCGGTGCATTTGGGCATTATCATGATCTATAACCTGGCGATTGGCACCATTACGCCGCCAGTTGGCAGTGGTTTATATGTCGGGGCGAGCGTCGGTAAGGTCAAAGTTGAGGAAGTGATTAAACCGTTGCTGCCTTTTTACGGCGCGATTATCGGCGTTCTGTTATTAATTACCTACATTCCGGAAATCATACTGTTCTTACCCCGTCTACTGGGCATCATGTAAACCCGATGGCGCGCAGAGGCGCGAGTTCTGGA ->EXAM.1216.00002.0003 -CACAGGGCTTAGAGGCGCTATGGCAATGATAATTAATGGGAAATTAATTAAAGCAAAAGACTTAGCTAAGGCTGCAGGTGTATCTCGTTCAACAGTGATTAAATATTACGGCATTAGCCGTGAGAATTACGAAAGGGTAGCAACTGAAAGAAGGAAGCTTGCTTTTGAACTAAGAGCATCAGGTTTAAAATGGAAAGAAGTTGCTGAAAAAATGAACACGACAAAATATAGCGCAATTGCATATTATAGACGATATTTAGCATTAGAGAAAAACAAATAACAGGCGCTAAGGCGGCGATCCTAGCGCGCGATCGCGCATGCGATGGTCGAACTGCAACATCAACGGCTGATGGTGCTTGCCGAACAGCTCCAGCTGGACAGTCTTATCGGCGCAGCGCCGGCGCTGTCGCAACAGGCGGTGGATCAGGAATGGAGCTACATGGACTTCCTGGAGCACCTGTTACATGAGGAGAAACTGGCCCGGCATCAGCGTAAACAGGCGATGTACACGCGGATGGCAGCCTTCCCGGCGGTAAAGACGTTCGAGGAGTACGACTTCACCTTCGCCACCGGCGCTCCTCAGAAGCAAATCCAGTCGCTGCGATCCCTGAGCTTCATAGAGCGTAACGAAAACATCGTGTTGCTGGGGCCATCGGGCGTGGGAAAAACGCATCTGGCGATAGCCATGGGCTACGAAGCAGTACGGGCGGGCATCAAGGTTCGCTTCACAACAGCAGCGGACCTGCTGCTACAGCTGTCCACTTCACAGCGTCAGGGCCGTTACAAAACGACTCTCAATCGTGGTGTCATGGCCCCGAAGCTGCTTATCATCGATGAAATAGGTTATCTGCCGTTCAGTCAGGAGGAAGCCAAGCTGTTCTTCCAGGTCATCGCCAAACGTTACGAGAAGAGCGCGATGATCCTGACCTCCAACCTGCCGTTCGGGCAGTGGGATCAGACGTTCGCCGGTGATGCAGCGCTGACATCGGCGATGCTGGACCGGATCTTACATCACTCACACGTCGTGCAAATAAAAGGGGAAAGCTATCGACTGAAGCAGAAACGAAAGGCCGGGGTTATAGCTGAAGCTAATCCTGAGTAA diff --git a/Examples/1-res-Annotate/Replicons/GEN2.0219.00001.fna b/Examples/1-res-Annotate/Replicons/GEN2.0219.00001.fna deleted file mode 100644 index df3fc3c1d8dfd5565b489da5f2295ddf9eb19bce..0000000000000000000000000000000000000000 --- a/Examples/1-res-Annotate/Replicons/GEN2.0219.00001.fna +++ /dev/null @@ -1,8 +0,0 @@ ->GEN2.0219.00001.0001 -ATGTCAGAAAATAAATTACACGTTATCGATTTGCACAAACGCTACGGCGGTCATGAAGTGCTGAAAGGGGTATCGCTGCAGGCCCGCGCCGGAGATGTGATTAGCATTATCGGCTCGTCCGGTTCCGGTAAAAGCACTTTTTTGCGCTGCATTAACTTCCTCGAAAAATCGAGCGAAGGCGCGATTATCGTGAACGGTCAGAACATTAATCTGGTGCGCGACAAAGACGGGCAGCTCAAAGTGGCGGATAAAAATCAGCTACGCTTGTTGCGTACCCGCCTGACGATGGTGTTTCAGCACTTTAACCTCTGGAACCACATGACGGTGCTGGAAAATGTGATGGAAGCGCCGATTCAGGTACTGGGATTAAGCAAGCACGACGCGCGCGAGCGGGCGTTGAAATATCTGGCGAAGGTGGGGATTGATGAGCGCGCTCAGGGCAAATATCCCGTCCATCTCTCCGGCGGCCAACAGCAGCGCGTTTCTATTGCGCGCGCGCTGGCGATGGAACCTGACGTTTTACTGTTCGATGAACCCACATCGGCGCTCGATCCTGAACTGGTCGGCGAAGTGTTGCGCATCATGCAACAACTGGCGGAAGAAGGCAAAACGATGGTGGTGGTCACGCATGAAATGGGCTTCGCCCGCCATGTCTCTTCGCACGTGATTTTTCTGCATCAGGGGAAAATTGAAGAAGAGGGCAATCCGGAGCAGGTGTTCGGCAATCCGCAAAGCCCGCGTTTACAGCAATTCCTGAAAGGCTCGCTGAAATAAACGCTAGAGGACGCGCCTCTCAGAGAGCGCGCTCTCTCAGAGAGGCGCGCGCCTCTTTCGCAGAGACCNNCGCTCATGAGCGATGCCCGCGACTAAATTCTCCCGACGTACCCTCCTGACGGCAGGTTCCGCGCTTGCTGTTCTTCCTTTTCTGCGCGCCTTGCCGGTACAGGCGCGTGAACCTCGCCAGACCGTCGATATTAAGGATTATCCGGCGGATGACGGTATCGCCTCGTTCAAACAGGCCTTCGCCGACGGGCAGACTGTGGTCGTGCCGTCAGGATGGGTGTGTGAAAATATCAATGCGGCGATAACGATTCCGGCGGGAAAAACGCTGCGGATACAGGGCGCGGTGCGTGGGAATGGCCGGGGACGGTTTATTTTGCTGGACGGGTGTCAGGTGGTGGGGGAGCAGGGCGGCAGTCTGCACAATGTGACGCTGGATGTTCGCGGGTCGGACTGTGTGATTAAAGGCGTGACGATGAGCGGCTTTGGCCCCGTCGCGCAAATTTTCATCGGCGGTAAGGAACCGCAGGTGATGCGTAATCTCATTATCGATGACATCACCGTTACCCACGCCAACTACGCCATTCTCCGCCAGGGATTTCATAACCAAATGGACGGCGCGCGGATTACGCATAGTCGCTTTAGCGATTTGCAGGGGGACGCCATTGAGTGGAATGTCGCGATTCATGACCGCGACATCCTGATTTCCGATCATGTCATCGAACGCATTGATTGTACCAATGGCAAAATCAACTGGGGGATCGGCATCGGGCTGGCGGGTAGCGCCTATGACAATAGTTATCCTGAAGACCAGGCAGTAAAAAACTTTGTGGTGGCCAATATTACCGGATCTGATTGCCGACAACTGGTACACGTAGAAAATGGCAAACATTTCGTCATTCGCAATGTCAAAGCCAAAAACATCACGCCCGATTTCAGTAAAAATGCGGGTATTGATAACGCAACGATCGCCATTTATGGCTGTGATAATTTCGTCATTGATAATATTGATATGACGAATAGTGCCGGGATGCTCATCGGCTATGGCGTCGTTAAAGGAAAATACCTGTCAATTCCGCAAAACTTTAAATTAAACGCTATTCGGTTGGATAATCGCCAGGTTGCTTATAAATTACGCGGCATTCAAATTTCCTCCGGTAACGCCCCCTCATTTGTTGCCATCACCAATGTACGGATGACGCGTGCTACGCTGGAACTGCATAATCAACCGCAGCACCTCTTTTTGCGTAATATCAACGTGATGCAAACTTCAGCGATTGGCCCGGCGTTAAAAATGCATTTTGATTTGCGTAAAGATGTCCGTGGTCAATTTATGGCCCGCCAGGACACGCTGCTTTCCCTCGCTAATGTTCATGCCATCAATGAAAACGGGCAGAGTTCCGTGGATATCGACAGGATTAATCACCAAACCGTGAATGTCGAAGCAGTGAATTTTTCGCTGCCGAAGCGGGGAGGGTAACACTCGCGCATAGAGAGCTCTCAGAGGAGCGCGCGCGCTATAGCGCGC ->GEN2.0219.00001.0002 -CGCGATAATATAGCGCGCGCTCATAGCATGAGCGCGCTATTTCTGGCCATCCCGTTAACCATTTTTGTGTTGTTTGTGTTACCGATTTGGCTGTGGCTGCATTACAGCAACCGCGCCGGTCGGGGAGAACTGTCGCAAAGCGAGCAGCAACGCTTACTGCAACTCACAGACGACGCGCAACGTATGCGCGAGCGCATTCAGGCGCTGGAAGATATTCTTGATGCAGAGCATCCGAACTGGAGAGAGCGCTAACGCCATATTATAGCGCGCCTCATAAGAGCGGCCTATAGCGCGCTANNNATGCCGCACTTTATTGCTGAATGTACTGAAAATATTCGCGAGCAGGCTGATTTACCAAGCCTGTTCAGCAAGGTAAACGAGGCGCTGGCCGCCACCGGGATTTTCCCCATCGGCGGTATCCGCAGTCGCGCCCACTGGCTGGATACCTGGCAGATGGCTGACGGTAAGCATGATTACGCGTTTGTGCATATGACGCTGAAAATCGGCGCCGGGCGCAGCCTGGAGAGCCGTCAGGAAGTCGGCGAAATGCTGTTTGGGCTGATTAAAGCCCACTTCGCCGACCTGATGGAGAACCGCTATCTGGCGCTGTCGTTTGAGATTGCCGAGTTACATCCAACGCTCAATTACAAACAAAACAACGTACACGCGTTATTTAAATAGCCAGAGATTCGCGCGTTCAGAGAGGAGCTCTCTCATAGACGCGCGCATATGCGCTCTAGAGAGGCGCGCCTAATGGCGCGCTATGATGAAAGCGCTACTGTGGCTGGTTGGTCTCGCGTTGCTGTTAACAGGCTGCGCGAGCGAAAAAGGAATTATCGATAAAGAGGGATATCAGCTTGATACCCGACATCGGGCGCAGGCGGCCTATCCGCGCATTAAAGTCCTGGTGATTCACTATACGGCGGAAAACTTTGACGTTTCGCTGGCGACGTTAACGGGTCGCAACGTCAGTTCGCATTACCTGATTCCCGCAACCCCGCCATTATATGGCGGTAAACCGCGCATCTGGCAACTGGTGCCGGAACAGGATCAGGCTTGGCATGCGGGCGTCAGTTTCTGGCGAGGCGCCACGCGTCTCAATGATACGTCTATTGGCATTGAGCTGGAAAATCGCGGCTGGCGAATGTCCGGCGGGGTGAAATCTTTCGCGCCGTTTGAATCCGCGCAAATTCAGGCATTGATCCCGTTAGCGAAGGACATTATCGCGCGCTATGACATCAAACCGCAGAATGTGGTGGCCCATGCGGATATCGCGCCGCAGCGTAAAGACGATCCCGGCCCGCGCTTCCCGTGGCGCGAGCTGGCGGCACAGGGGATTGGCGCCTGGCCTGACGCCCAGCGTGTGGCGTTTTATCTGGCTGGACGCGCGCCGTATACGCCAGTCGATACCGCAACGGTGCTTGCGTTACTCTCGCGCTATGGCTATGAAGTCAAAGCCGATATGACGGCGCGCGAGCAACAGCGGGTGATTATGGCGTTCCAGATGCACTTCCGTCCGGCGCAATGGAACGGTATCGCAGATGCCGAAACGCAGGCGATTGCCGAAGCATTACTGGAGAAGTACGGCCAGGATTAACAAAGCGCTCTCAGAGAGAGCGCTCTGCAGATGAGTGAGGCTGAAGCCCGCCCGACTAACTTTATTCGTCAGATTATTGATGAAGATCTGGCGAGTGGTAAACATACCACTGTCCATACCCGTTTTCCGCCGGAGCCGAATGGCTATCTGCACATCGGCCACGCGAAATCTATCTGCCTGAACTTTGGCATCGCGCAAGATTATCAGGGCCAGTGCAACCTGCGTTTCGATGACACCAACCCGGTAAAAGAAGATATCGAGTACGTTGATTCGATCAAAAACGACGTCGAGTGGTTAGGCTTTCACTGGTCTGGCGATATTCGCTACTCCTCCGATTACTTTGACCAACTGCACGCCTATGCGGTCGAGCTCATCAATAAAGGCCTGGCCTACGTTGATGAGCTGACGCCGGAGCAGATCCGCGAATACCGTGGTACGCTGACCGCGCCGGGTAAAAACAGCCCGTTCCGCGATCGCAGCGTGGAAGAAAACCTCGCGCTATTTGAAAAAATGCGTACCGGCGGTTTTGAAGAGGGTAAAGCCTGTCTGCGCGCTAAAATCGACATGGCGTCGCCGTTTATCGTGATGCGCGATCCGGTGCTGTATCGCATTAAATTCGCCGAGCATCATCAGACCGGCACGAAGTGGTGCATCTATCCGATGTACGACTTTACTCACTGCATCAGCGATGCGCTGGAAGGCATTACTCATTCTCTGTGTACGCTGGAGTTCCAGGACAACCGTCGTCTGTACGACTGGGTGCTGGACAACATCACCATTCCGGTTCACCCGCGCCAGTACGAATTCTCGCGCCTGAATCTGGAATACACCGTGATGTCCAAGCGTAAGCTGAACCTGCTGGTGACCGACAAACACGTCGAAGGTTGGGATGATCCGCGTATGCCGACTATTTCCGGTCTGCGCCGTCGCGGCTATACCGCGGCTTCTATTCGTGAGTTCTGCAAACGCATCGGCGTCACCAAGCAGGACAACACTATTGAGATGGCGTCGCTGGAATCCTGCATTCGCGAAGATCTGAACGAAAACGCGCCGCGCGCGATGGCGGTAATCGATCCGGTAAAACTGGTTATCGAAAACTACCCGCAGGGCGAGAGCGAAATGGTTACCATGCCTAACCATCCGAATAAACCGGAGATGGGCAGCCGTGAAGTGCCGTTTAGCGGTGAGATCTGGATCGATCGCGCGGATTTCCGCGAAGAAGCGAACAAACAGTACAAACGTCTGGTGATGGGCAAAGAAGTGCGTCTGCGTAATGCCTACGTCATTAAAGCGGAGCGCGTAGAGAAGGATGCCGAAGGGAATATCACCACCATCTTCTGTACCTATGATGCTGATACGCTGAGTAAAGATCCGGCTGACGGGCGTAAAGTGAAAGGCGTAATCCACTGGGTTAGCGTAGCACATGCGCTGCCGATTGAAATTCGTCTCTACGACCGTCTGTTCAGCGTGCCGAACCCGGGCGCCGCGGAGGACTTCCTGTCTGTTATCAACCCCGAATCATTAGTGATTAAGCAGGGGTATGGCGAGCCGTCGCTGAAAGCGGCGGTAGCAGGGAAAGCTTTCCAGTTTGAACGTGAAGGTTACTTCTGCCTTGACAGCCGCTATGCAACGGCCGATAAGCTGGTCTTTAACCGCACCGTGGGCCTGCGTGATACCTGGGCGAAAGCGGGCGAATAA ->GEN2.0219.00001.0003 -ACGCGCTATAGGGCTCTCAGAGAGTCTCAGTGTTTATTGGCATCGTTAGCCTGTTTCCTGAAATGTTCCGCGCAATTACCGATTACGGGGTAACTGGCCGGGCAGTAAAAAAAGGCCTGCTGAACATCCAAAGCTGGAGTCCTCGCGACTTCGCGCATGACCGGCACCGTACCGTGGACGACCGTCCTTACGGCGGCGGACCGGGGATGTTAATGATGGTGCAACCCTTGCGGGACGCCATTCATGCAGCAAAAGCCGCGGCAGGTGAAGGCGCTAAAGTGATTTATCTGTCGCCTCAGGGACGCAAGCTTGATCAAGCGGGCGTTAGCGAGCTGGCCACGAATCAGAAACTCATTCTGGTGTGTGGTCGCTACGAAGGCGTAGATGAGCGCGTAATTCAGGCCGAAATTGACGAAGAATGGTCAATTGGCGATTACGTTCTCAGCGGTGGCGAACTACCGGCAATGACGCTGATTGACTCCGTCGCCCGGTTTATACCGGGGGTTCTGGGGCATGAGGCATCAGCAATCGAAGATTCGTTTGCTGATGGGTTGCTGGATTGTCCGCACTATACGCGCCCTGAAGTGTTAGAGGGGATGGAAGTACCGCCAGTATTGCTGTCGGGAAACCATGCTGAGATACGTCGCTGGCGTTTGAAACAGTCACTGGGCCGAACCTGGCTTAGAAGACCTGAACTTCTGGAAAACCTGGCTCTGACTGAAGAGCAAGCAAGGTTGCTGGCGGAGTTCAAAACAGAACACGCACAACAGCAGCATAAACATGATGGGATGGCATAGCGAGATCGCGCATAGCGCGCGGCGAGATCCGCGAGACATGAATAATCATTTTGGGAAAGGGTTAATGGCCGGGTTGCACGCGCCATATGCATATAGCGCGCATCATGCGGTGAATTTCTGTTCTGAGTATAAACGTGGCTTTGTATTGGGTTTTACACACCGTATGTTCGAAAAGACCGGCGATCGTCAACTTAGCGCGTGGGAGGCCGGAATTCTGACGCGTCGCTATGGTCTGGATAAAGAAATGGTGATGGATTTCTTTAAAGAGAATCATTCCGGGATGGCGGTTCGCTTCTTTATGGCTGGTTATCGACTCGAAGGTTGAACGCCTCTAGAGCGCTAGAGGCGCGCGCGATATACGCGGCGCGAGACATGTCTACGCTTCTCTATTTGCACGGATTCAACAGTTCCCCTCGCTCGGCAAAAGCGTGCCAGCTAAAAAACTGGCTGGCGGAGCGTCATCCGCATGTTGAGATGATCGTCCCTCAACTGCCGCCGTATCCTGCCGATGCGGCGGAGTTGCTGGAATCTCTCGTACTTGAGCATGGCGGTGCGCCATTAGGGCTGGTAGGATCGTCGCTGGGTGGTTATTACGCCACCTGGCTGTCGCAATGTTTTATGCTGCCGGCTGTGGTGGTGAATCCCGCCGTGCGGCCCTTTGAATTACTGACCGACTATCTCGGTCAGAACGAGAACCCCTACACCGGGCAGCAATATGTGCTAGAGTCTCGCCATATTTATGATCTTAAAGTCATGCAGATTGACCCGCTGGAAGCGCCGGACCTGATCTGGCTACTGCAACAGACGGGCGATGAAGTGCTGGATTACCGCCAGGCGGTGGCATATTACGCCTCCTGCCGTCAGACAGTGACCGAGGGGGGTAATCACGCATTCACGGGCTTCGAAGATTATTTCAACCAGATTGTCGATTTTCTTGGACTGCACAGTTGCTGACCGGATATACGCGCGCGCGCTATATAGCGCGCGCGGCGATATAGCGCATGAAGTTTGTTGCGCCAGAACAGGCACCGGAACAGGCGGAAATCATCAGAAATACGCCGTTCTGGCCTGATGTGGACCTGTCGGAGTTTCGCAGCATGATGCGCACTGATGGCACGGTGACGCAGCCGCGTTTAAAGCAGGTTGCGCTGTCGGCAATTTCGGAGGTCAACGCAGAGCTGTATGAGTTTCGCAGACGCCAGCAGATGCTGGGGTATGCCTCGCTGGCAGAAGTCCCGGCGGAACAACTGGACGGCAAAAGCGAGCGCATTCAGCACTATTTCAACGCGGTTTACTGCTGGGCACGCGCCATGCTCAACGAACGTTACCAGGACTATGACGCCACGGCATCCGGTGTGAAGCGGGGCGAAGAACTGGCAGAAGCCAGCGGTGATTTGTGGCGTGACGCCCGCTGGGCCATCAGCCGGGTGCAGGATGCGCCGCACTGCACAGTGGAGCTTATCTGA ->GEN2.0219.00001.0004 -ATGATTGACCCTATTTTTGCGTCCTGTACGCTAATTGCCGTCTTTGTTGTTTTACTGGCCATGGGCGCGCCTATCGGGATCTGCATCGTTATCGCCTCTTTCAGCACCATGATGCTGGTACTGCCTTTCGATATTTCGATGTTCGCCACCGCGCAAAAAATGTTCTCCAGCCTGGACAGTTTTGCCTTGCTGGCCGTGCCGTTCTTCGTTTTGTCCGGGGTGATCATGAATAGCGGGGGAATTGCCGCCCGACTGGTCAATTTTGCCAAACTGTTTACTGGCAAACTGCCCGGCTCGCTCTCTTACACCAACATCGTCGGCAATATGATGTTCGGTGCAATTTCCGGATCGGCGATTGCCGCCTCAACCTCTATCGGCGGCGTGATGGTGCCGATGAGCGCGCGCGAAGGTTACGATCGCGGTTTTGCGGCCGCGGTGAATATCGCCTCCGCGCCGACGGGAATGTTAATTCCGCCCACCACGGCTTTTATCCTTTATGCGCTGGCAAGCGGGGGAACATCGATTGCCGCTCTGTTCGCCGGCGGTCTGGTCGCGGGAGTGCTGTGGGGCGTTGGCTGTATGCTGGTCACGCTGGTGGTCGCTAAGCGTCGAAATTATCGGGTTTTCTTCACCGTCCAAAAAGGCATGGCGCTAAAAGTTGCCGTTGAGGCCATTCCCAGCCTGTTACTGATCGTGATTATTGTCGGCGGCATTGTGCAGGGGATTTTCACCGCCATTGAAGCCTCCGCGATTGCCGTGGTGTATACGTTATTGCTGACGATAGTGTTTTACCGCACGCTGAAAATTAAGGATTTGCCTTCGATTTTGCTCCAGACAGTGGTAATGACCGGGGTCATCATGTTCCTGCTGGCAACCTCTTCGGCGATGTCCTTCTCGATGTCGATCACCAATATTCCTGCGGCGCTGAGCGATATGATCCTCGGTATTTCCGCCAATAAACTGGTTATCCTGTTAGTCATTACCGTCTTTTTGTTGATTATCGGCGCATTTATGGATATCGGTCCGGCCATTCTGATTTTTACCCCGATTCTGCTGCCGATTATGACTAAACTGGGCGTCGATCCGGTGCATTTCGGCATTATCATGATCTATAACCTGGCGATAGGCACCATTACGCCGCCAGTTGGCAGTGGTTTATATGTCGGGGCGAGCGTCGGTAAGGTCAAAGTTGAGGACGTTATCAAACCGTTGATGCCTTTTTACGGCGCGATTATCGGCGTTCTGTTATTAATTACCTACATTCCGGAAATCACACTGTTTTTACCCCGTCTACTGGGCATCATGTAAACGCTCATAGGCGGCGCGCGCGCTCTCAGGAATGAAGTTTGTTGCGCCAGAACAGGCACCGGAACAGGCGGAGGTCATCAAAAATACGCCGTTCTGGCCTGATGTGAACCTGTCGGAATTTCGCAGTGTGATGCGCACTGACGGCACGGTGACGCAGCCGCGTTTAAAGCAGGTCGTGCTGACGGCGATCTCTGAGGTTAACGCTGAGCTGTACGACTTCCGCAACCGTCAGCAGATGCTGGGCTGGCGGACACTTGCTGAGGTTCCCGCAGAAATGCTGGACGGTAAAAGCGAGCGTATCCGGCACTACCACAACGCTGTTTTTTGCTGGGCGCGCGCTGTGCTTAATGAGCGTTATCAGGACTATGACGCCACGGCGTCAGGCGTGAAGCGAGGGGAGGAGCTGGCGGAGGCCAGCGGCGATCTGTGGCGTGATGCCCGCTGGGCCATCAGCCGGGTGCAGGATGCACCGCACTGTACGGTGGAGCTTATCTGACGCTCATAGGCGCGCGCTCATAGCGCGATGGAAACAAATATTACCTGGCAACAATTGATAGATGAATATTTCTTCGCAAAACCTCTGCGCTCAGCATCTGAATGGAGTTACACCAAAGTCTTCAAATCATTTGTACATTATATGGGGCCGTTAAGCTGCCCTAATGATGTGACATATCACAAAGTGCTTGCCTGGCGCCGTTTTCTTTTAAAAGAGAAAAAGCTGTCCGGACGTACCTGGAATAACAAGGTGGCGCATATGCGGGCCATCTTTAACTACGGAATACAGCGAGGGTTACTGCACTATGACGAAAATCCGTTTAACAATTCGGTAGTTAAACCGGACAAGAAGAGAAAGAAAACGCTCACTCAGGCACAGATTGAGTATGCCTATCAGATCATGGAGCAGTATGAAAATCAGGAGAATACAGGGCTGGGACTGAAATATTCCCGCTGCGCCTTATTTCCTGCATGGTTCTGGCTCACTGTCCTGGATACGCTCTATTACACAGGGATACGTCAGAACCAGTTATTACATATTCGGCTGAATGATGTTGATTTGAGAGAAGGGCAGATTCGGCTGATTACGGAGGGGTGTAAAAATCACAAAGAACACTATGTGCCGGTGATCAGTTTTCTGCGTCCACGGCTGACCTGTTTAATGGAGAAAGCGCAGAGCGAAGGATTGAAAGGTAATGACCGCCTGTTCAATATTGCACTTTTTACCGGCAAAGATCCCGCCATTGGCGATGACATGGATTCTCCTCAGGTAAGAGCATTCTTCCGTCGTCTGTCCAAGGAGTGTCAGTTTGCGATCAGTCCTCATCGTTTCAGACACACGCTGGCCACGGAGATGATGAAAATGCCGGAACAGAATCTGCATATGGCGCAAAGTGTGCTGGGTCATTCAAACATGAAATCCACGCTGGAGTATGTGGAGAATGATATTGCAGTGATGGGGAGGGCTCTGGAAGCGCAGTTTATGCAGATTAAGGCAGCACATGCCCGAAGCATTTACAGTGGGTTGACAAAGAATAGATAA diff --git a/Examples/1-res-Annotate/Replicons/GEN4.1111.00001.fna b/Examples/1-res-Annotate/Replicons/GEN4.1111.00001.fna deleted file mode 100644 index 821ceba742387f28a70b51f06bf5c81ea8e31957..0000000000000000000000000000000000000000 --- a/Examples/1-res-Annotate/Replicons/GEN4.1111.00001.fna +++ /dev/null @@ -1,2 +0,0 @@ ->GEN4.1111.00001.0001 -ATGAAAGCGCTACTGTGGCTGGTGGGTCTCGCGTTGCTGTTAACAGGCTGCGCGAGCGAAAAAGGAATTATCGATAAAGAGGGATATCAGCTTGATACCCGACATCGGGCGCAGGCGGCCTATCCGCGCATTAAAGTCCTGGTGATTCACTATACGGCGGAAAACTTTGACGTTTCGCTGGCGACGTTAACGGGCCGCAACGTCAGTTCGCATTACCTGATTCCCGCAACCCCGCCATTATATGGCGGTAAACCGCGCATCTGGCAACTGGTGCCGGAACAGGATCAGGCCTGGCATGCGGGCGTCAGTTTCTGGCGAGGCGCCACGCGTCTCAATGATACGTCTATTGGCATTGAGCTGGAAAATCGCGGCTGGCGAATGTCCGGCGGGGTGAAATCTTTCGCGCCGTTTGAATCCGCGCAAATTCAGGCATTGATTCCGTTAGCGAAGGACATTATCGCGCGCTATGACATCAAACCGCAGAATGTGGTGGCCCATGCGGATATCGCGCCGCAGCGTAAAGACGATCCCGGCCCGCGCTTCCCGTGGCGCGAGCTGGCGGCGCAGGGGATTGGCGCCTGGCCTGACGCCCAGCGTGTGGCGTTTTATCTGGCTGGACGCGCGCCGTATACGCCAGTCGATACCGCAACGGTGCTTGCGTTACTCTCGCGCTATGGCTATGAAGTCAAAGCCGATATGACGGCGCGCGAGCAGCAGCGGGTGATTATGGCGTTCCAGATGCACTTCCGTCCGGCGCAATGGAACGGTATCGCAGATGCCGAAACGCAGGCGATTGCCGAAGCATTACTGGAGAAGTACGGCCAGGATTAACGCGATCGCGCGCATATCGCGCGCGATAGATGCCGCACTTTATTGCTGAATGTACTGAAAATATTCGCGAGCAGGCTGATTTACCCGGCCTGTTCAGCAAGGTAAACGAGGCGCTGGCCGCCAGCGGGATTTTCCCCATCGGCGGTATCCGCAGTCGCGCCCACTGGCTGGATACCTGGCAGATGGCTGACGGTAAGCATGATTATGCGTTTGTGCATATGACGCTGAAAATCGGTACCGGGCGCAGCCTGGAGAGCCGTCAGGAAGTCGGCGAAATGCTGTTTGGGCTGATTAAAGCCCACTTCGCCGACCTGATGGAGAACCGCTATCTGGCGCTGTCGTTTGAGATTGCCGAGCTACATCCGACGCTCAATTACAAACAAAACAACGTACACGCGTTATTTAAATAGCCGCATATGCGGCGCTCAGGAGCGCTAGCATGCTCGATAAACAGACCCATACCCTGATCGCCCAGCGACTTAATCAGGCTGAAAAACAGCGTGAACAAATTCGCGCAGTGTCGCTGGATTATCCCAACATCACTATTGAAGATGCCTATGCCGTACAGCGTGAATGGGTCAATATCAAGATCGCCGAAGGGCGCACGCTCAAAGGCCACAAAATCGGCCTGACCTCAAAAGCGATGCAGGCCAGCTCGCAAATCAGCGAACCGGATTACGGCGCGCTGCTTGACGATATGTTCTTCCATGACGGCGGCGATATCCCCACCGACCGTTTTATCGTCCCGCGTATTGAAGTGGAGCTGGCGTTCGTGCTGGCGAAACCGCTGCGCGGCCCTCACTGCACGCTGTTCGACGTCTACAACGCCACGGATTATGTGATTCCGGCGCTGGAACTGATTGACGCCCGCAGCCACAACATCGACCCGGAAACCCAGCGCCCGCGCAAAGTGTTCGACACCATTTCCGACAACGCCGCCAACGCCGGGGTGATCCTCGGTGGTCGCCCCATCAAACCAGACGAGCTGGATCTGCGCTGGATCTCCGCGCTGCTCTATCGCAACGGCGTGATCGAAGAAACCGGCGTCGCCGCAGGCGTGCTGAATCATCCGGCCAACGGCGTGGCGTGGCTGGCGAACAAGCTTGCCCCCTACGATGTCCAGCTTGAAGCCGGGCAGATCATCCTCGGCGGCTCGTTCACCCGCCCGGTGCCGGCGAGCAAGGGCGACACCTTCCATGTCGATTACGGCAACATGGGCGCGATCAGTTGCCGGTTTGTGTAACCAGATCCGCGCGCGCATATATATCGCGCGCATACGATGCCCGTGAATAAGTTCTCCCGACGTACCCTCCTGACGGCAGGTTCCGCGCTTGCTGTTCTTCCTTTTCTGCGCGCCTTGCCGGTACAGGCGCGTGAACCTCGCGAGACCGTCGATATTAAGGATTATCCGGCGGATGACGGTATCGCCTCGTTCAAACAGGCCTTCGCCGACGGACAGACCGTGGTCTTACCGCCAGGATGGGTGTGTGAAAATATCAATGCGGCGATAACGATTCCGGCGGGAAAAACGCTGCGGGTACAGGGCGCGGTGCGTGGGAATGGCCGGGGACGGTTTATTTTGCAGGACGGGTGTCAGGTGGTGGGGGAGCAGGGCGGCAGTCTGCACAATGTGACGCTGGATGTTCGCGGGTCGGACTGTGTGATTAAAGGCGTGACGATGAGCGGCTTTGGCCCCGTCGCGCAAATTTTCATCGGCGGTAAGGAACCGCAGGTGATGCGTAATCTCATTATCGATGACATCACCGTTACCCACGCCAACTACGCCATTCTCCGCCAGGGATTTCATAACCAAATGGACGGCGCGCGGATTACGCATAGCCGCTTTAGCGATTTGCAGGGGGACGCCATTGAGTGGAATGTCGCGATTCACGACCGCGACATCCTGATTTCCGATCATGTCATCGAACGCATTGATTGTACCAATGGCAAAATCAACTGGGGGATCGGCATCGGGCTGGCGGGTAGCACCTATGACAACAGTTATCCTGAAGATCAGGCAGTAAAAAACTTTGTGGTGGCCAATATTACCGGATCTGATTGCCGACAGCTGGTGCACGTAGAAAATGGCAAACATTTCGTCATTCGCAATGTCAAAGCCAAAAACATCACGCCCGATTTCAGTAAAAATGCGGGTATTGATAACGCAACGATCGCCATTTATGGCTGTGATAATTTCGTCATTGATAATATTGATATGACGAATAGTGCTGGGATGCTCATCGGCTATGGCGTCGTTAAAGGAAAATACCTGTCAATTCCGCAAAACTTTAAATTAAACGCTATTCGGTTGGATAATCGCCAGGTTGCTTATAAATTACGCGGCATTCAAATTTCCTCCGGCAACATCCCCTCTTTTGTCGCCATCACCAATGTACGGATGACGCGTGCTACGCTGGAACTGCATAATCAACCGCAGCACCTCTTTCTGCGTAATATCAACGTGATGCAAACTTCAGCGATTGGCCCGGCGTTAAAAATGCATTTCGATTTGCGTAAAGATGTCCGTGGTCAATTTATGGCCCGCCAGGACACGCTGCTTTCCCTCGCTAATGTTCATGCCATCAATGAAAACGGGCAGAGTTCCGTGGATATCGACAGGATTAATCACCAAACCGTGAATGTCGAAGCAGTGAATTTTTCGCTGCCGAAGCGGGGAGGGTAACAGAGCTCGCGCGATCGCGAATGTCAGAAAATAAATTACACGTTATCGATTTGCACAAACGCTACGGCGGTCATGAAGTGCTGAAAGGGGTATCGTTGCAGGCCCGCGCCGGAGATGTGATTAGCATCATCGGCTCGTCCGGCTCCGGTAAAAGCACTTTTTTGCGCTGTATTAACTTCCTCGAAAAACCGAGCGAAGGCGCGATTATCGTGAACGGTCAGAACATTAATCTGGTGCGCGACAAAGACGGGCAGCTCAAAGTGGCGGATAAAAATCAGCTACGCTTGTTGCGTACCCGCCTGACGATGGTGTTTCAGCACTTTAACCTCTGGAGCCACATGACGGTGCTGGAAAATGTGATGGAAGCGCCGATTCAGGTACTGGGATTAAGCAAGCACGACGCGCGCGAGCGGGCGTTGAAATATCTGGCGAAGGTGGGGATTGATGAGCGCGCTCAGGGCAAATATCCCGTCCATCTCTCCGGCGGCCAACAGCAGCGCGTTTCTATTGCGCGCGCGCTGGCGATGGAACCTGACGTTTTACTGTTCGATGAACCCACATCGGCGCTCGATCCTGAACTGGTCGGCGAAGTGTTGCGCATCATGCAACAACTGGCGGAAGAAGGCAAAACGATGGTGGTGGTCACGCATGAAATGGGCTTCGCCCGCCATGTCTCTTCGCACGTTATTTTTCTGCATCAGGGGAAAATTGAAGAAGAGGGCGATCCGGAGCAGGTGTTCGGCAATCCGCAAAGCCCGCGTTTACAGCAATTCCTGAAAGGCTCGCTGAAATAACAGATACGCGCATGGCGAGTGTTTATTGGCATCGTTAGCCTGTTTCCTGAAATGTTCCGCGCAATTACCGATTACGGGGTAACTGGCCGGGCAGTAAAAAAAGGCCTGCTGAACATCCAAAGCTGGAGTCCTCGCGACTTCGCGCATGACCGGCACCGTACCGTGGACGACCGTCCTTACGGCGGCGGACCGGGGATGTTAATGATGGTGCAACCCTTGCGGGACGCCATTCACGCAGCAAAAGCCGCGGCAGGTGAAGGCGCTAAAGTGATTTATCTGTCGCCTCAGGGACGCAAGCTTGATCAAGCGGGCGTTAGCGAGCTGGCCACGAATCAGAAGCTTATTCTGGTGTGTGGTCGCTACGAAGGCGTAGATGAGCGCGTAATTCAGACCGAAATTGACGAAGAATGGTCAATTGGCGATTACGTTCTCAGCGGTGGCGAACTACCGGCAATGACGCTGATTGACTCCGTCGCCCGGTTTATACCGGGGGTTCTGGGGCATGAGGCATCAGCAATCGAAGATTCGTTTGCTGATGGGTTGCTGGATTGTCCGCACTATACGCGCCCTGAAGTGTTAGAGGGGATGGAAGTACCGCCAGTATTGCTGTCGGGAAACCATGCCGAGATACGTCGCTGGCGCTTGAAACAGTCGCTGGGCCGAACCTGGCTTAGAAGACCTGAACTTCTGGAAAACCTGGCTCTGACTGAAGAGCAAGCAAGGTTGCTGGCGGAGTTCAAAACAGAACACGCACAACAGCAGCATAAACATGATGGGATGGCATAGCGATAGCGCTAGAGCGATGAATAATCATTTTGGGAAAGGGTTAATGGCTGGGTTGCACGCGCCATATGCATATAGCGCGCATCATGCGGTGAATTTCTGTTCTGAGTATAAACGTGGCTTTGTATTGGGTTTTACACACCGTATGTTCGAAAAGACCGGCGATCGTCAACTTAGCGCGTGGGAGGCCGGAATTCTGACGCGTCGCTATGGTCTGGATAAAGAAATGGTGATGGATTTCTTTAAAGAGAATCATTCCGGGATGGCGGTTCGCTTCTTTATGGTCGGTTATCGACTCGAAGGTTGACAGATGCGCGATCGATGTCTACGCTTCTCTATTTGCACGGATTCAACAGTTCCCCTCGCTCGGCAAAAGCGTGCCAGCTAAAAAACTGGCTGGCGGAGCGTCATCCGCATGTCGAGATGATCGTCCCTCAACTACCGCCGTATCCTGCCGATGCGGCGGAGTTGCTGGAATCTCTCGTGCTTGAGCATGGCGGTGCGCCATTAGGGCTGGTAGGATCGTCGCTGGGTGGTTATTACGCCACCTGGCTGTCGCAATGTTTTATGCTGCCGGCTGTGGTGGTGAATCCCGCCGTGCGGCCCTTTGAATTACTGACCGACTATCTCGGTCAGAACGAGAACCCCTACACCGGGCAGCAATATGTGCTAGAGTCTCGCCATATTTATGATCTTAAAGTCATGCAGATTGACCCGCTGGAAGCGCCGGACCTGATCTGGCTACTGCAACAGACGGGCGATGAAGTGCTGGATTACCGCCAGGCGGTGGCATATTACGCCTCCTGCCGTCAGACAGTGACCGAGGGTGGTAATCACGCATTCACGGGCTTCGAAGATTATTTCAACCAGATTGTCGATTTTCTTGGACTGCACAGTTGCTGACACGGATGCGCCATCGGCTTGCTGGCCGTGCCGTTCTTCGTTTTGTCCGGGGTGATCATGAATAGCGGGGGAATTGCCGCCCGGCTGGTCAATTTTGCCAAACTGTTTACTGGCAAACTGCCCGGCTCGCTCTCTTATACCAACATCGTCGGCAATATGATGTTCGGTGCAATTTCCGGATCGGCAATTGCCGCCTCAACCTCCATCGGCGGCGTGATGGTGCCGATGAGCGCGCGCGAAGGTTACGATCGCGGCTTTGCGGCCGCGGTGAATATCGCCTCCGCGCCGACGGGAATGTTAATTCCGCCCACCACGGCTTTTATCCTTTATGCGCTGGCAAGCGGGGGAACATCGATTGCCGCTCTGTTCGCCGGCGGTCTGGTCGCGGGAGTGCTGTGGGGCGTTGGCTGTATGCTGGTCACGCTGGTGGTCGCTAAGCGTCGAAATTATCGGGTTTTCTTCACCGTCCAAAAAGGCATGGCGCTAAAAGTTGCCGTTGAGGCCATTCCCAGCCTGCTGCTGATCGTGATTATCGTCGGCGGCATTGTGCAGGGGATTTTCACCGCCATTGAAGCCTCCGCGATTGCCGTGGTGTATACATTATTGTTGACGATGGTGTTTTACCGCACGCTGAAAATTAAGGATTTGCCTTCGATTTTGCTCCAGACAGTGGTAATGACCGGGGTCATCATGTTCCTGCTGGCAACCTCTTCGGCGATGTCCTTCTCGATGTCGATCACCAATATTCCTGCGGCGCTGAGCGATATGATCCTCGGTATTTCCGCCAATAAACTGGTTATCCTGTTAGTCATTACCGTCTTTTTGTTGATTATCGGCGCATTTATGGATATCGGTCCGGCCATTCTGATTTTTACCCCGATTCTGCTGCCGATCATGGCTAAACTGGGCGTCGATCCGGTGCATTTTGGCATTATCATGATCTATAACCTGGCGATTGGCACCATTACGCCGCCAGTTGGCAGTGGTTTATATGTCGGGGCGAGCGTCGGTAAGGTCAAAGTTGAGGAAGTGATTAAACCGTTGCTGCCTTTTTACGGCGCGATTATCGGCGTTCTGTTATTAATTACCTACATTCCGGAAATCACACTGTTCTTACCCCGTCTACTGGGCATCATGTAA diff --git a/Examples/1-res-Annotate/discarded-list_genomes.lst b/Examples/1-res-Annotate/discarded-list_genomes.lst deleted file mode 100644 index 5f702471df1cbfa5cbd91ee5e525d919b478954a..0000000000000000000000000000000000000000 --- a/Examples/1-res-Annotate/discarded-list_genomes.lst +++ /dev/null @@ -1 +0,0 @@ -orig_name gsize nb_conts L90 diff --git a/Examples/1-res-Annotate/genomeAPCAT-annotate_list_genomes.log b/Examples/1-res-Annotate/genomeAPCAT-annotate_list_genomes.log deleted file mode 100644 index 3b96fe66665e961b9b0039cfa111e2a3ce8a9a9b..0000000000000000000000000000000000000000 --- a/Examples/1-res-Annotate/genomeAPCAT-annotate_list_genomes.log +++ /dev/null @@ -1,9 +0,0 @@ -[2019-02-12 13:18:41] root :: INFO :: Let's start! -[2019-02-12 13:18:41] utils :: INFO :: Reading genomes -[2019-02-12 13:18:41] qc_annote.gseq :: INFO :: Cutting genomes at each stretch of at least 5 'N', and then, calculating genome size, number of contigs and L90. -[2019-02-12 13:18:41] qc_annote.gseq :: INFO :: Generating distribution of L90 and #contigs graphs. -[2019-02-12 13:18:41] utils :: INFO :: 0 genome was discarded. -[2019-02-12 13:18:41] utils :: INFO :: Writing discarded genomes to Examples/1-res-Annotate/discarded-list_genomes.lst -[2019-02-12 13:18:41] qc_annote.gseq :: INFO :: Renaming kept genomes according to their quality. -[2019-02-12 13:18:41] qc_annote.prokka :: INFO :: Annotating all genomes with prokka -[2019-02-12 13:18:54] qc_annote.ffunc :: INFO :: Formatting all genomes diff --git a/Examples/1-res-Annotate/genomeAPCAT-annotate_list_genomes.log.details b/Examples/1-res-Annotate/genomeAPCAT-annotate_list_genomes.log.details deleted file mode 100644 index 5e298e25772faebc3b7bf006a9c466e7c62c2dc6..0000000000000000000000000000000000000000 --- a/Examples/1-res-Annotate/genomeAPCAT-annotate_list_genomes.log.details +++ /dev/null @@ -1,32 +0,0 @@ -[2019-02-12 13:18:41] root :: INFO :: Let's start! -[2019-02-12 13:18:41] utils :: INFO :: Reading genomes -[2019-02-12 13:18:41] qc_annote.gseq :: INFO :: Cutting genomes at each stretch of at least 5 'N', and then, calculating genome size, number of contigs and L90. -[2019-02-12 13:18:41] qc_annote.gseq :: INFO :: Generating distribution of L90 and #contigs graphs. -[2019-02-12 13:18:41] matplotlib :: DEBUG :: $HOME=/Users/aperrin -[2019-02-12 13:18:41] matplotlib :: DEBUG :: CONFIGDIR=/Users/aperrin/.matplotlib -[2019-02-12 13:18:41] matplotlib :: DEBUG :: matplotlib data path: /usr/local/lib/python3.7/site-packages/matplotlib/mpl-data -[2019-02-12 13:18:41] matplotlib :: DEBUG :: loaded rc file /usr/local/lib/python3.7/site-packages/matplotlib/mpl-data/matplotlibrc -[2019-02-12 13:18:41] matplotlib :: DEBUG :: matplotlib version 3.0.0 -[2019-02-12 13:18:41] matplotlib :: DEBUG :: interactive is False -[2019-02-12 13:18:41] matplotlib :: DEBUG :: platform is darwin -[2019-02-12 13:18:41] matplotlib :: DEBUG :: loaded modules: ['sys', 'builtins', '_frozen_importlib', '_imp', '_thread', '_warnings', '_weakref', 'zipimport', '_frozen_importlib_external', '_io', 'marshal', 'posix', 'encodings', 'codecs', '_codecs', 'encodings.aliases', 'encodings.utf_8', '_signal', '__main__', 'encodings.latin_1', 'io', 'abc', '_abc', 'site', 'os', 'stat', '_stat', 'posixpath', 'genericpath', 'os.path', '_collections_abc', '_sitebuiltins', '_bootlocale', '_locale', 'types', 'importlib', 'importlib._bootstrap', 'importlib._bootstrap_external', 'warnings', 'importlib.util', 'importlib.abc', 'importlib.machinery', 'contextlib', 'collections', 'operator', '_operator', 'keyword', 'heapq', '_heapq', 'itertools', 'reprlib', '_collections', 'functools', '_functools', 'mpl_toolkits', 'sphinxcontrib', 'sitecustomize', 're', 'enum', 'sre_compile', '_sre', 'sre_parse', 'sre_constants', 'copyreg', 'pkg_resources', '__future__', 'time', 'zipfile', 'shutil', 'fnmatch', 'errno', 'zlib', 'bz2', '_compression', 'threading', 'traceback', 'linecache', 'tokenize', 'token', '_weakrefset', '_bz2', 'lzma', '_lzma', 'pwd', 'grp', 'struct', '_struct', 'binascii', 'pkgutil', 'weakref', 'platform', 'subprocess', 'signal', '_posixsubprocess', 'select', 'selectors', 'collections.abc', 'math', 'plistlib', 'datetime', '_datetime', 'xml', 'xml.parsers', 'xml.parsers.expat', 'pyexpat.errors', 'pyexpat.model', 'pyexpat', 'xml.parsers.expat.model', 'xml.parsers.expat.errors', 'email', 'email.parser', 'email.feedparser', 'email.errors', 'email._policybase', 'email.header', 'email.quoprimime', 'string', '_string', 'email.base64mime', 'base64', 'email.charset', 'email.encoders', 'quopri', 'email.utils', 'random', 'hashlib', '_hashlib', '_blake2', '_sha3', 'bisect', '_bisect', '_random', 'socket', '_socket', 'urllib', 'urllib.parse', 'email._parseaddr', 'calendar', 'locale', 'tempfile', 'textwrap', 'inspect', 'dis', 'opcode', '_opcode', 'pkg_resources.extern', 'pkg_resources._vendor', 'pkg_resources.extern.six', 'pkg_resources._vendor.six', 'pkg_resources.extern.six.moves', 'pkg_resources._vendor.six.moves', 'pkg_resources.py31compat', 'pkg_resources.extern.appdirs', 'pkg_resources._vendor.packaging.__about__', 'pkg_resources.extern.packaging', 'pkg_resources.extern.packaging.version', 'pkg_resources.extern.packaging._structures', 'pkg_resources.extern.packaging.specifiers', 'pkg_resources.extern.packaging._compat', 'pkg_resources.extern.packaging.requirements', 'copy', 'pprint', 'pkg_resources.extern.pyparsing', 'pkg_resources.extern.six.moves.urllib', 'pkg_resources.extern.packaging.markers', 'sysconfig', '_osx_support', '_sysconfigdata_m_darwin_darwin', 'email.message', 'uu', 'email._encoded_words', 'email.iterators', 'genomeAPCAT', 'genomeAPCAT.subcommands', 'genomeAPCAT.subcommands.annote', 'genomeAPCAT.subcommands.pangenome', 'genomeAPCAT.subcommands.corepers', 'genomeAPCAT.subcommands.align', 'genomeAPCAT.subcommands.tree', 'argparse', 'gettext', 'genomeAPCAT.utils', 'glob', 'logging', 'atexit', 'logging.handlers', 'pickle', '_compat_pickle', '_pickle', 'queue', '_queue', 'shlex', 'progressbar', 'progressbar.utils', 'python_utils', 'python_utils.time', 'six', 'python_utils.converters', 'python_utils.terminal', 'progressbar.shortcuts', 'progressbar.bar', 'timeit', 'gc', 'progressbar.widgets', 'progressbar.base', 'progressbar.__about__', 'multiprocessing', 'multiprocessing.context', 'multiprocessing.process', 'multiprocessing.reduction', 'array', '__mp_main__', 'genomeAPCAT.annote_module', 'genomeAPCAT.annote_module.genome_seq_functions', 'numpy', 'numpy._globals', 'numpy.__config__', 'numpy.version', 'numpy._import_tools', 'numpy.add_newdocs', 'numpy.lib', 'numpy.lib.info', 'numpy.lib.type_check', 'numpy.core', 'numpy.core.info', 'numpy.core.multiarray', 'numpy.core.umath', 'numpy.core._internal', 'numpy.compat', 'numpy.compat._inspect', 'numpy.compat.py3k', 'pathlib', 'ntpath', 'ctypes', '_ctypes', 'ctypes._endian', 'numpy.core.numerictypes', 'numbers', 'numpy.core.numeric', 'numpy.core.fromnumeric', 'numpy.core._methods', 'numpy.core.arrayprint', 'numpy.core.defchararray', 'numpy.core.records', 'numpy.core.memmap', 'numpy.core.function_base', 'numpy.core.machar', 'numpy.core.getlimits', 'numpy.core.shape_base', 'numpy.core.einsumfunc', 'numpy.testing', 'unittest', 'unittest.result', 'unittest.util', 'unittest.case', 'difflib', 'unittest.suite', 'unittest.loader', 'unittest.main', 'unittest.runner', 'unittest.signals', 'numpy.testing._private', 'numpy.testing._private.utils', 'numpy.lib.utils', 'numpy.testing._private.decorators', 'numpy.testing._private.nosetester', 'numpy.testing._private.pytesttester', 'numpy.lib.ufunclike', 'numpy.lib.index_tricks', 'numpy.lib.function_base', 'numpy.lib.twodim_base', 'numpy.lib.histograms', 'numpy.matrixlib', 'numpy.matrixlib.defmatrix', 'ast', '_ast', 'numpy.linalg', 'numpy.linalg.info', 'numpy.linalg.linalg', 'numpy.linalg.lapack_lite', 'numpy.linalg._umath_linalg', 'numpy.lib.stride_tricks', 'numpy.lib.mixins', 'numpy.lib.nanfunctions', 'numpy.lib.shape_base', 'numpy.lib.scimath', 'numpy.lib.polynomial', 'numpy.lib.arraysetops', 'numpy.lib.npyio', 'numpy.lib.format', 'numpy.lib._datasource', 'numpy.lib._iotools', 'numpy.lib.financial', 'decimal', '_decimal', 'numpy.lib.arrayterator', 'numpy.lib.arraypad', 'numpy.lib._version', 'numpy.core._multiarray_tests', 'numpy._distributor_init', 'numpy.fft', 'numpy.fft.info', 'numpy.fft.fftpack', 'numpy.fft.fftpack_lite', 'numpy.fft.helper', 'numpy.polynomial', 'numpy.polynomial.polynomial', 'numpy.polynomial.polyutils', 'numpy.polynomial._polybase', 'numpy.polynomial.chebyshev', 'numpy.polynomial.legendre', 'numpy.polynomial.hermite', 'numpy.polynomial.hermite_e', 'numpy.polynomial.laguerre', 'numpy.random', 'numpy.random.info', 'cython_runtime', 'mtrand', 'numpy.random.mtrand', 'numpy.ctypeslib', 'numpy.ma', 'numpy.ma.core', 'numpy.ma.extras', 'genomeAPCAT.annote_module.prokka_functions', 'genomeAPCAT.annote_module.format_functions', 'matplotlib', 'distutils', 'distutils.version', 'urllib.request', 'http', 'http.client', 'ssl', '_ssl', 'urllib.error', 'urllib.response', '_scproxy', 'matplotlib.cbook', 'gzip', 'matplotlib.cbook.deprecation', 'matplotlib.rcsetup', 'matplotlib.fontconfig_pattern', 'pyparsing', 'matplotlib.colors', 'matplotlib._color_data', 'cycler', 'six.moves', 'matplotlib._version', 'json', 'json.decoder', 'json.scanner', '_json', 'json.encoder', 'dateutil', 'dateutil._version'] -[2019-02-12 13:18:41] matplotlib :: DEBUG :: CACHEDIR=/Users/aperrin/.matplotlib -[2019-02-12 13:18:41] matplotlib.font_manager :: DEBUG :: Using fontManager instance from /Users/aperrin/.matplotlib/fontlist-v300.json -[2019-02-12 13:18:41] matplotlib.pyplot :: DEBUG :: Loaded backend agg version unknown. -[2019-02-12 13:18:41] matplotlib.axes._base :: DEBUG :: update_title_pos -[2019-02-12 13:18:41] matplotlib.font_manager :: DEBUG :: findfont: Matching :family=sans-serif:style=normal:variant=normal:weight=normal:stretch=normal:size=10.0 to DejaVu Sans ('/usr/local/lib/python3.7/site-packages/matplotlib/mpl-data/fonts/ttf/DejaVuSans.ttf') with score of 0.050000. -[2019-02-12 13:18:41] matplotlib.font_manager :: DEBUG :: findfont: Matching :family=sans-serif:style=normal:variant=normal:weight=normal:stretch=normal:size=12.0 to DejaVu Sans ('/usr/local/lib/python3.7/site-packages/matplotlib/mpl-data/fonts/ttf/DejaVuSans.ttf') with score of 0.050000. -[2019-02-12 13:18:41] matplotlib.axes._base :: DEBUG :: update_title_pos -[2019-02-12 13:18:41] utils :: INFO :: 0 genome was discarded. -[2019-02-12 13:18:41] utils :: INFO :: Writing discarded genomes to Examples/1-res-Annotate/discarded-list_genomes.lst -[2019-02-12 13:18:41] qc_annote.gseq :: INFO :: Renaming kept genomes according to their quality. -[2019-02-12 13:18:41] qc_annote.prokka :: INFO :: Annotating all genomes with prokka -[2019-02-12 13:18:41] run_prokka :: DETAIL :: Start annotating EXAM.0219.00001 Examples/1-res-Annotate/tmp_files/genome1.fst-split5N.fna -[2019-02-12 13:18:45] run_prokka :: DETAIL :: End annotating EXAM.0219.00001 Examples/1-res-Annotate/tmp_files/genome1.fst-split5N.fna -[2019-02-12 13:18:45] run_prokka :: DETAIL :: Start annotating GEN2.0219.00001 Examples/1-res-Annotate/tmp_files/genome2.fst-split5N.fna -[2019-02-12 13:18:48] run_prokka :: DETAIL :: End annotating GEN2.0219.00001 Examples/1-res-Annotate/tmp_files/genome2.fst-split5N.fna -[2019-02-12 13:18:48] run_prokka :: DETAIL :: Start annotating EXAM.1216.00002 Examples/1-res-Annotate/tmp_files/genome3-chromo.fst-all.fna-split5N.fna -[2019-02-12 13:18:51] run_prokka :: DETAIL :: End annotating EXAM.1216.00002 Examples/1-res-Annotate/tmp_files/genome3-chromo.fst-all.fna-split5N.fna -[2019-02-12 13:18:51] run_prokka :: DETAIL :: Start annotating GEN4.1111.00001 Examples/1-res-Annotate/tmp_files/genome4.fst-split5N.fna -[2019-02-12 13:18:54] run_prokka :: DETAIL :: End annotating GEN4.1111.00001 Examples/1-res-Annotate/tmp_files/genome4.fst-split5N.fna -[2019-02-12 13:18:54] qc_annote.ffunc :: INFO :: Formatting all genomes diff --git a/Examples/1-res-Annotate/genomeAPCAT-annotate_list_genomes.log.err b/Examples/1-res-Annotate/genomeAPCAT-annotate_list_genomes.log.err deleted file mode 100644 index e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000 diff --git a/Examples/1-res-Annotate/gff3/EXAM.0219.00001.gff b/Examples/1-res-Annotate/gff3/EXAM.0219.00001.gff deleted file mode 100644 index 32eed51cd4a2192fefb1cd5e9cc7e9b7f23a9196..0000000000000000000000000000000000000000 --- a/Examples/1-res-Annotate/gff3/EXAM.0219.00001.gff +++ /dev/null @@ -1,12 +0,0 @@ -##gff-version 3 -EXAM.0219.00001.0001 Prodigal:2.6 CDS 213 1880 . + . ID=EXAM.0219.00001.b0001_00001;eC_number=6.1.1.18;Name=glnS;gene=glnS;inference=similar to AA sequence:UniProtKB:P00962;locus_tag=EXAM.0219.00001.b0001_00001;product=Glutamine--tRNA ligase -EXAM.0219.00001.0001 Prodigal:2.6 CDS 1916 2746 . + . ID=EXAM.0219.00001.b0001_00002;eC_number=3.5.1.28;Name=amiD;gene=amiD;inference=similar to AA sequence:UniProtKB:P75820;locus_tag=EXAM.0219.00001.b0001_00002;product=N-acetylmuramoyl-L-alanine amidase AmiD -EXAM.0219.00001.0002 Prodigal:2.6 CDS 16 396 . + . ID=EXAM.0219.00001.b0002_00003;eC_number=5.3.3.10;Name=hpcD;gene=hpcD;inference=similar to AA sequence:UniProtKB:Q05354;locus_tag=EXAM.0219.00001.b0002_00003;product=5-carboxymethyl-2-hydroxymuconate Delta-isomerase -EXAM.0219.00001.0002 Prodigal:2.6 CDS 428 1837 . + . ID=EXAM.0219.00001.i0002_00004;locus_tag=EXAM.0219.00001.i0002_00004;product=hypothetical protein -EXAM.0219.00001.0002 Prodigal:2.6 CDS 1869 2642 . + . ID=EXAM.0219.00001.i0002_00005;Name=hisP;gene=hisP;inference=similar to AA sequence:UniProtKB:P02915;locus_tag=EXAM.0219.00001.i0002_00005;product=Histidine transport ATP-binding protein HisP -EXAM.0219.00001.0002 Prodigal:2.6 CDS 2709 3443 . + . ID=EXAM.0219.00001.i0002_00006;eC_number=2.1.1.228;Name=trmD_1;gene=trmD_1;inference=similar to AA sequence:UniProtKB:P0A873;locus_tag=EXAM.0219.00001.i0002_00006;product=tRNA (guanine-N(1)-)-methyltransferase -EXAM.0219.00001.0002 Prodigal:2.6 CDS 3427 4254 . + . ID=EXAM.0219.00001.i0002_00007;eC_number=2.1.1.228;Name=trmD_2;gene=trmD_2;inference=similar to AA sequence:UniProtKB:P0A873;locus_tag=EXAM.0219.00001.i0002_00007;product=tRNA (guanine-N(1)-)-methyltransferase -EXAM.0219.00001.0002 Prodigal:2.6 CDS 4299 4763 . + . ID=EXAM.0219.00001.i0002_00008;locus_tag=EXAM.0219.00001.i0002_00008;product=hypothetical protein -EXAM.0219.00001.0002 Prodigal:2.6 CDS 4818 5078 . + . ID=EXAM.0219.00001.i0002_00009;locus_tag=EXAM.0219.00001.i0002_00009;product=hypothetical protein -EXAM.0219.00001.0002 Prodigal:2.6 CDS 5117 5698 . + . ID=EXAM.0219.00001.i0002_00010;locus_tag=EXAM.0219.00001.i0002_00010;product=hypothetical protein -EXAM.0219.00001.0002 Prodigal:2.6 CDS 5717 7024 . + . ID=EXAM.0219.00001.b0002_00011;Name=dctM;gene=dctM;inference=similar to AA sequence:UniProtKB:O07838;locus_tag=EXAM.0219.00001.b0002_00011;product=C4-dicarboxylate TRAP transporter large permease protein DctM diff --git a/Examples/1-res-Annotate/gff3/EXAM.1216.00002.gff b/Examples/1-res-Annotate/gff3/EXAM.1216.00002.gff deleted file mode 100644 index cc778abd422fb59a33703cdeaed7fecfa7a933eb..0000000000000000000000000000000000000000 --- a/Examples/1-res-Annotate/gff3/EXAM.1216.00002.gff +++ /dev/null @@ -1,13 +0,0 @@ -##gff-version 3 -EXAM.1216.00002.0001 Prodigal:2.6 CDS 1 831 . + . ID=EXAM.1216.00002.b0001_00001;eC_number=3.5.1.28;Name=amiD_1;gene=amiD_1;inference=similar to AA sequence:UniProtKB:P75820;locus_tag=EXAM.1216.00002.b0001_00001;product=N-acetylmuramoyl-L-alanine amidase AmiD -EXAM.1216.00002.0001 Prodigal:2.6 CDS 880 1710 . + . ID=EXAM.1216.00002.i0001_00002;eC_number=3.5.1.28;Name=amiD_2;gene=amiD_2;inference=similar to AA sequence:UniProtKB:P75820;locus_tag=EXAM.1216.00002.i0001_00002;product=N-acetylmuramoyl-L-alanine amidase AmiD -EXAM.1216.00002.0001 Prodigal:2.6 CDS 1655 2128 . + . ID=EXAM.1216.00002.i0001_00003;eC_number=5.3.3.10;Name=hpcD;gene=hpcD;inference=similar to AA sequence:UniProtKB:Q05354;locus_tag=EXAM.1216.00002.i0001_00003;product=5-carboxymethyl-2-hydroxymuconate Delta-isomerase -EXAM.1216.00002.0001 Prodigal:2.6 CDS 2172 2396 . + . ID=EXAM.1216.00002.i0001_00004;Name=pspB;gene=pspB;inference=similar to AA sequence:UniProtKB:P0AFM9;locus_tag=EXAM.1216.00002.i0001_00004;product=Phage shock protein B -EXAM.1216.00002.0001 Prodigal:2.6 CDS 2425 3828 . + . ID=EXAM.1216.00002.i0001_00005;locus_tag=EXAM.1216.00002.i0001_00005;product=hypothetical protein -EXAM.1216.00002.0001 Prodigal:2.6 CDS 3863 4636 . + . ID=EXAM.1216.00002.i0001_00006;Name=hisP;gene=hisP;inference=similar to AA sequence:UniProtKB:P02915;locus_tag=EXAM.1216.00002.i0001_00006;product=Histidine transport ATP-binding protein HisP -EXAM.1216.00002.0001 Prodigal:2.6 CDS 4641 5432 . + . ID=EXAM.1216.00002.i0001_00007;eC_number=2.1.1.228;Name=trmD;gene=trmD;inference=similar to AA sequence:UniProtKB:P0A873;locus_tag=EXAM.1216.00002.i0001_00007;product=tRNA (guanine-N(1)-)-methyltransferase -EXAM.1216.00002.0001 Prodigal:2.6 CDS 5460 5747 . + . ID=EXAM.1216.00002.b0001_00008;locus_tag=EXAM.1216.00002.b0001_00008;product=hypothetical protein -EXAM.1216.00002.0002 Prodigal:2.6 CDS 1 582 . + . ID=EXAM.1216.00002.b0002_00009;locus_tag=EXAM.1216.00002.b0002_00009;product=hypothetical protein -EXAM.1216.00002.0002 Prodigal:2.6 CDS 629 1936 . + . ID=EXAM.1216.00002.b0002_00010;Name=dctM;gene=dctM;inference=similar to AA sequence:UniProtKB:O07838;locus_tag=EXAM.1216.00002.b0002_00010;product=C4-dicarboxylate TRAP transporter large permease protein DctM -EXAM.1216.00002.0003 Prodigal:2.6 CDS 26 280 . + . ID=EXAM.1216.00002.b0003_00011;locus_tag=EXAM.1216.00002.b0003_00011;product=hypothetical protein -EXAM.1216.00002.0003 Prodigal:2.6 CDS 323 1102 . + . ID=EXAM.1216.00002.b0003_00012;inference=similar to AA sequence:UniProtKB:Q45619;locus_tag=EXAM.1216.00002.b0003_00012;product=Insertion sequence IS5376 putative ATP-binding protein diff --git a/Examples/1-res-Annotate/gff3/GEN2.0219.00001.gff b/Examples/1-res-Annotate/gff3/GEN2.0219.00001.gff deleted file mode 100644 index cfa099cef564bed7d6de95e87e550cb7ebfc234b..0000000000000000000000000000000000000000 --- a/Examples/1-res-Annotate/gff3/GEN2.0219.00001.gff +++ /dev/null @@ -1,14 +0,0 @@ -##gff-version 3 -GEN2.0219.00001.0001 Prodigal:2.6 CDS 1 774 . + . ID=GEN2.0219.00001.b0001_00001;Name=hisP;gene=hisP;inference=similar to AA sequence:UniProtKB:P02915;locus_tag=GEN2.0219.00001.b0001_00001;product=Histidine transport ATP-binding protein HisP -GEN2.0219.00001.0001 Prodigal:2.6 CDS 857 2260 . + . ID=GEN2.0219.00001.b0001_00002;locus_tag=GEN2.0219.00001.b0001_00002;product=hypothetical protein -GEN2.0219.00001.0002 Prodigal:2.6 CDS 28 252 . + . ID=GEN2.0219.00001.b0002_00003;Name=pspB;gene=pspB;inference=similar to AA sequence:UniProtKB:P0AFM9;locus_tag=GEN2.0219.00001.b0002_00003;product=Phage shock protein B -GEN2.0219.00001.0002 Prodigal:2.6 CDS 301 681 . + . ID=GEN2.0219.00001.i0002_00004;eC_number=5.3.3.10;Name=hpcD;gene=hpcD;inference=similar to AA sequence:UniProtKB:Q05354;locus_tag=GEN2.0219.00001.i0002_00004;product=5-carboxymethyl-2-hydroxymuconate Delta-isomerase -GEN2.0219.00001.0002 Prodigal:2.6 CDS 764 1597 . + . ID=GEN2.0219.00001.i0002_00005;eC_number=3.5.1.28;Name=amiD;gene=amiD;inference=similar to AA sequence:UniProtKB:P75820;locus_tag=GEN2.0219.00001.i0002_00005;product=N-acetylmuramoyl-L-alanine amidase AmiD -GEN2.0219.00001.0002 Prodigal:2.6 CDS 1628 3295 . + . ID=GEN2.0219.00001.b0002_00006;eC_number=6.1.1.18;Name=glnS;gene=glnS;inference=similar to AA sequence:UniProtKB:P00962;locus_tag=GEN2.0219.00001.b0002_00006;product=Glutamine--tRNA ligase -GEN2.0219.00001.0003 Prodigal:2.6 CDS 30 797 . + . ID=GEN2.0219.00001.b0003_00007;eC_number=2.1.1.228;Name=trmD;gene=trmD;inference=similar to AA sequence:UniProtKB:P0A873;locus_tag=GEN2.0219.00001.b0003_00007;product=tRNA (guanine-N(1)-)-methyltransferase -GEN2.0219.00001.0003 Prodigal:2.6 CDS 862 1122 . + . ID=GEN2.0219.00001.i0003_00008;locus_tag=GEN2.0219.00001.i0003_00008;product=hypothetical protein -GEN2.0219.00001.0003 Prodigal:2.6 CDS 1170 1751 . + . ID=GEN2.0219.00001.i0003_00009;locus_tag=GEN2.0219.00001.i0003_00009;product=hypothetical protein -GEN2.0219.00001.0003 Prodigal:2.6 CDS 1895 2263 . + . ID=GEN2.0219.00001.b0003_00010;locus_tag=GEN2.0219.00001.b0003_00010;product=hypothetical protein -GEN2.0219.00001.0004 Prodigal:2.6 CDS 1 1308 . + . ID=GEN2.0219.00001.b0004_00011;Name=dctM;gene=dctM;inference=similar to AA sequence:UniProtKB:O07838;locus_tag=GEN2.0219.00001.b0004_00011;product=C4-dicarboxylate TRAP transporter large permease protein DctM -GEN2.0219.00001.0004 Prodigal:2.6 CDS 1340 1804 . + . ID=GEN2.0219.00001.i0004_00012;locus_tag=GEN2.0219.00001.i0004_00012;product=hypothetical protein -GEN2.0219.00001.0004 Prodigal:2.6 CDS 1832 2845 . + . ID=GEN2.0219.00001.b0004_00013;Name=xerC;gene=xerC;inference=similar to AA sequence:UniProtKB:P39776;locus_tag=GEN2.0219.00001.b0004_00013;product=Tyrosine recombinase XerC diff --git a/Examples/1-res-Annotate/gff3/GEN4.1111.00001.gff b/Examples/1-res-Annotate/gff3/GEN4.1111.00001.gff deleted file mode 100644 index 501e70cfc46444a97bc73caef44346c66030adf3..0000000000000000000000000000000000000000 --- a/Examples/1-res-Annotate/gff3/GEN4.1111.00001.gff +++ /dev/null @@ -1,10 +0,0 @@ -##gff-version 3 -GEN4.1111.00001.0001 Prodigal:2.6 CDS 1 831 . + . ID=GEN4.1111.00001.b0001_00001;eC_number=3.5.1.28;Name=amiD;gene=amiD;inference=similar to AA sequence:UniProtKB:P75820;locus_tag=GEN4.1111.00001.b0001_00001;product=N-acetylmuramoyl-L-alanine amidase AmiD -GEN4.1111.00001.0001 Prodigal:2.6 CDS 861 1241 . + . ID=GEN4.1111.00001.i0001_00002;eC_number=5.3.3.10;Name=hpcD;gene=hpcD;inference=similar to AA sequence:UniProtKB:Q05354;locus_tag=GEN4.1111.00001.i0001_00002;product=5-carboxymethyl-2-hydroxymuconate Delta-isomerase -GEN4.1111.00001.0001 Prodigal:2.6 CDS 1271 2074 . + . ID=GEN4.1111.00001.i0001_00003;eC_number=4.2.1.163;Name=hpcG;gene=hpcG;inference=similar to AA sequence:UniProtKB:P42270;locus_tag=GEN4.1111.00001.i0001_00003;product=2-oxo-hept-4-ene-1,7-dioate hydratase -GEN4.1111.00001.0001 Prodigal:2.6 CDS 2111 3514 . + . ID=GEN4.1111.00001.i0001_00004;locus_tag=GEN4.1111.00001.i0001_00004;product=hypothetical protein -GEN4.1111.00001.0001 Prodigal:2.6 CDS 3535 4308 . + . ID=GEN4.1111.00001.i0001_00005;Name=hisP;gene=hisP;inference=similar to AA sequence:UniProtKB:P02915;locus_tag=GEN4.1111.00001.i0001_00005;product=Histidine transport ATP-binding protein HisP -GEN4.1111.00001.0001 Prodigal:2.6 CDS 4327 5094 . + . ID=GEN4.1111.00001.i0001_00006;eC_number=2.1.1.228;Name=trmD;gene=trmD;inference=similar to AA sequence:UniProtKB:P0A873;locus_tag=GEN4.1111.00001.i0001_00006;product=tRNA (guanine-N(1)-)-methyltransferase -GEN4.1111.00001.0001 Prodigal:2.6 CDS 5138 5398 . + . ID=GEN4.1111.00001.i0001_00007;locus_tag=GEN4.1111.00001.i0001_00007;product=hypothetical protein -GEN4.1111.00001.0001 Prodigal:2.6 CDS 5413 5994 . + . ID=GEN4.1111.00001.i0001_00008;locus_tag=GEN4.1111.00001.i0001_00008;product=hypothetical protein -GEN4.1111.00001.0001 Prodigal:2.6 CDS 6052 7134 . + . ID=GEN4.1111.00001.b0001_00009;Name=dctM;gene=dctM;inference=similar to AA sequence:UniProtKB:O07838;locus_tag=GEN4.1111.00001.b0001_00009;product=C4-dicarboxylate TRAP transporter large permease protein DctM diff --git a/Examples/1-res-Annotate/tmp_files/genome1.fst-split5N.fna b/Examples/1-res-Annotate/tmp_files/genome1.fst-split5N.fna deleted file mode 100644 index 11feaae3628ca13667c0d695bbcacd5a2139310d..0000000000000000000000000000000000000000 --- a/Examples/1-res-Annotate/tmp_files/genome1.fst-split5N.fna +++ /dev/null @@ -1,4 +0,0 @@ ->genome1_1 -ATGTGTAAAAGCCGGAGGGGTTATCTTTTCCCGGCTTTTTATTATCAATTACTCATTAACTCCTGTTCCGTTCTTTTGCGTTTAATCACCGGAATATCTCCGGTATTGTTCAGCGCCCCGGAAATGTTTTTAACCACTGTTCTGCACTCCGTTTATTAAACGCGCTCAGCGCGCGCTCATATATCGCGCGCGCGCGCGCGCATATATATATAATGAGTGAGGCTGAAGCCCGCCCGACTAACTTTATTCGTCAGATTATTGATGAAGATCTGGCGAGTGGTAAACATACCACTGTCCATACCCGTTTTCCGCCGGAGCCGAATGGCTATCTGCATATCGGCCACGCGAAATCTATCTGCCTGAACTTTGGCATCGCGCAAGATTATCAGGGCCAGTGCAACCTGCGTTTCGATGACACCAACCCGGTAAAAGAAGATATCGAGTACGTTGATTCGATCAAAAACGACGTCGAGTGGTTAGGCTTTCACTGGTCTGGCGATATTCGCTACTCCTCCGATTACTTTGACCAACTGCACGCCTATGCGGTCGAGCTAATCAATAAAGGCCTGGCCTATGTTGATGAGCTGACGCCGGAGCAGATCCGTGAATACCGCGGTACGCTGACCGCGCCGGGTAAAAACAGCCCGTTCCGCGATCGCAGCGTCGAAGAGAACCTCGCGCTATTTGAAAAAATGCGTACCGGCGGTTTTGAAGAGGGTAAAGCCTGTCTGCGCGCTAAAATCGACATGGCGTCGCCGTTTATCGTGATGCGCGATCCGGTGCTGTATCGCATTAAATTCGCCGAGCATCATCAGACTGGCAACAAGTGGTGCATCTATCCGATGTACGACTTTACTCACTGCATCAGCGATGCGCTGGAAGGCATTACTCATTCTCTGTGTACGCTGGAGTTCCAGGATAACCGTCGTCTGTACGACTGGGTGCTGGACAACATCACCATTCCGGTTCACCCGCGCCAGTACGAATTCTCGCGCCTGAATCTGGAATACACCGTGATGTCCAAGCGTAAGCTGAACCTGCTGGTGACCGACAAACACGTCGAAGGTTGGGACGATCCGCGTATGCCGACTATTTCCGGTCTGCGCCGTCGCGGCTATACCGCGGCTTCTATTCGTGAGTTCTGCAAACGCATCGGCGTCACCAAGCAGGACAACACTATTGAGATGGCGTCGCTGGAATCCTGCATTCGCGAAGATCTGAACGAAAACGCGCCGCGCGCGATGGCGGTAATCGATCCGGTAAAACTGGTTATCGAAAATTACCCGCAGGGTGAGAGCGAAATGGTTACCATGCCTAACCATCCGAATAAACCGGAGATGGGCAGCCGTGAAGTGCCGTTTAGCGGTGAGATCTGGATCGATCGCGCAGATTTCCGCGAAGAAGCGAACAAACAGTACAAACGTCTGGTGATGGGCAAAGAAGTGCGTCTGCGTAATGCCTACGTCATTAAAGCGGAGCGCGTAGAGAAGGATGCCGAAGGGAATATCACCACCATCTTCTGTACCTATGATGCTGATACGCTGAGTAAAGATCCGGCTGACGGGCGTAAAGTGAAAGGCGTAATCCACTGGGTTAGCGCAGCACATGCGCTGCCGATTGAAATTCGTCTCTACGACCGTCTGTTCAGCGTGCCGAATCCGGGCGCCGCGGAGGACTTCCTGTCTGTTATCAACCCCGAATCATTAGTGATTAAGCAGGGGTATGGCGAGCCGTCGCTGAAAGCGGCGGTAGCAGGAAAAGCTTTCCAGTTTGAACGTGAAGGCTACTTCTGCCTCGACAGCCGCTATGCAACGGCCGATAAGCTGGTCTTTAACCGCACCGTGGGCCTGCGTGATACCTGGGCGAAAGCGGGCGAGTAACGCGCATAGGCGGCCTTCAAGGAGGCGCTAGGCGAATGAAAGCGCTACTGTGGCTGGTGGGTCTCGCGTTGCTGTTAACAGGCTGCGCGAGCGAAAAAGGAATTATCGATAAAGAGGGATATCAGCTTGATACCCGACATCGGGCGCAGGCGGCCTATCCGCGCATTAAAGTCCTGGTGATTCACTATACGGCGGAAAACTTTGACGTTTCGCTGGCGACGTTAACGGGTCGCAACGTCAGTTCGCATTACCTGATTCCCGCAACCCCGCCATTATATGGCGGTAAACCGCGCATCTGGCAACTGGTGCCGGAACAGGATCAGGCCTGGCATGCGGGCGTCAGTTTCTGGCGAGGCGCCACGCGTCTCAATGATACGTCTATTGGCATTGAGCTGGAAAATCGTGGTTGGCGAATGTCCGGCGGGGTGAAATCTTTCGCGCCGTTTGAATCCGCGCAAATTCAGGCATTGATTCCGTTAGCGAAGGATATTATCGCGCGCTATAACATCAAACCGCAGAATGTGGTGGCCCATGCGGATATCGCGCCGCAGCGTAAAGACGATCCCGGCCCGCGCTTCCCGTGGCGCGAGCTGGCGGCGCAGGGGATTAGCGCCTGGCCTGACGCCCAGCGTGTGGCGTTTTATCTGGCTGGACGCGCGCCGTATACGCCAGTCGATACCGCAACGGTGCTTGCGTTACTCTCGCGCTATGGCTATGAAGTCAAAGCCGATATGACGGCACGCGAGCAGCAGCGGGTGATTATGGCGTTCCAGATGCACTTCCGTCCGGCGCAATGGAACGGTATCGCAGATGCCGAAACGCAGGCGATTGCCGAAGCATTACTGGAGAAGTACGGCCAGGATTAACGCGATAGGCGCGCGAGATTACGCGCGCAGTATCGCGC ->genome1_2 -CGCGCATAGCGCGCAATGCCGCACTTTATTGCTGAATGTACTGAAAATATTCGCGAGCAGGCTGATTTACCCGGCCTGTTCAGCAAGGTAAACGAGGCGCTGGCCGCCAGCGGGATTTTCCCCATCGGCGGTATCCGCAGTCGCGCCCACTGGCTGGATACCTGGCAGATGGCTGACGGTAAGCATGATTACGCGTTTGTGCATATGACGCTGAAAATCGGCGCCGGGCGCAGCCTGGAGAGCCGTCAGGAAGTTGGCGAAATGCTGTTTGGGCTGATTAAAGCCCACTTCGCCGACCTGATGGAGAACCGCTATCTGGCGCTGTCGTTTGAGATTGCCGAGCTACATCCGACGCTCAATTACAAACAAAACAACGTACACGCGTTATTTAAATAGCCGATATGAGGCGCGGCGCTATAAGGCGCTCATGAGCATGCCCGCGACTAAATTCTCCCGACGTACCCTCCTGACGGCAGGTTCTGCGCTTGCTGTTCTTCCTTTTCTGCGCGCCTTGCCGGTACAGGCGCGTGAACCTCGCGAGACCGTCGATATTAAGGATTATCCGGCGGATGACGGTATCGCCTCGTTCAAACAGGCCTTCGCCGACGGACAGACCGTGGTCGTACCGCCAGGATGGGTGTGTGAAAATATCAATGCGGCGATAACGATTCCGGCGGGAAAAACGCTGCGGGTACAGGGCGCGGTGCGTGGGAATGGCCGGGGACGGTTTATTTTGCAGGACGGGTGTCAGGTGGTGGGGGAGCAGGGCGGCAGTCTGCACAATGTGACGCTGGATGTTCGCGGGTCGGACTGTGTGATTAAAGGCGTGGCGATGAGCGGCTTTGGCCCCGTCGCGCAAATTTTCATCGGTGGTAAGGAACCGCAGGTGATGCGTAATCTCATTATCGATGACATCACCGTTACCCACGCCAACTACGCCATTCTCCGCCAGGGATTTCATAACCAAATGGATGGCGCGCGGATTACGCATAGCCGCTTTAGCGATTTACAGGGGGACGCCATTGAGTGGAATGTCGCGATTCACGACCGCGACATCCTGATTTCCGATCATGTCATCGAACGCATTAATTGTACCAATGGCAAAATCAACTGGGGGATCGGCATCGGGCTGGCGGGTAGCACCTATGACAACAGTTATCCTGAAGACCAGGCAGTAAAAAACTTTGTGGTGGCCAATATTACCGGATCTGATTGCCGACAGCTTGTGCACGTAGAAAATGGCAAACATTTCGTCATTCGCAATGTCAAAGCCAAAAACATCACGCCCGGTTTCAGTAAAAATGCGGGTATTGATAACGCAACGATCGCAATTTATGGCTGTGATAATTTCGTCATTGATAATATTGATATGACGAATAGTGCCGGGATGCTCATCGGCTATGGCGTCGTTAAAGGAAAATACCTGTCAATTCCGCAAAACTTTAAATTAAACGCTATTCGGTTGGATAATCGCCAGGTTGCTTATAAATTACGCGGCATTCAAATTTCCTCCGGCAACACCCCCTCTTTTGTCGCCATCACCAATGTACGGATGACGCGTGCTACGCTGGAACTGCATAATCAACCGCAGCACCTCTTTCTGCGCAATATCAACGTGATGCAAACTTCAGCGATTGGCCCGGCGTTAAAAATGCATTTCGATTTGCGTAAAGATGTACGTGGTCAATTTATGGCCCGCCAGGACACGCTGCTTTCCCTCGCTAATGTTCATGCCATCAATGAAAACGGGCAGAGTTCCGTGGATATCGACAGGATTAATCACCAAACCGTGAATGTCGAAGCAGTGAATTTTTCGCTGCCGAAGCGGGGAGGGTAACGAATTCCGCGGCATATAGCGGCGCGATAGCATGTCAGAAAATAAATTACACGTTATCGATTTGCACAAACGCTACGGCGGTCATGAAGTGCTGAAAGGGGTATCGCTGCAGGCCCGCGCCGGAGATGTGATTAGCATCATCGGCTCGTCCGGCTCCGGTAAAAGCACTTTTTTGCGCTGTATTAACTTCCTCGAAAAACCGAGCGAAGGCGCGATTATCGTGAACGGTCAGAACATTAATCTGGTGCGCGACAAAGATGGGCAGCTCAAAGTGGCGGATAAAAATCAGCTACGCTTGTTGCGTACCCGCCTGACGATGGTGTTTCAGCACTTCAACCTCTGGAGCCACATGACGGTGCTGGAAAATGTGATGGAAGCGCCGATTCAGGTACTGGGATTAAGCAAGCACGACGCGCGCGAGCGGGCGTTGAAATATCTGGCGAAGGTGGGGATTGATGAGCGCGCTCAGGGCAAATATCCCGTCCATCTCTCCGGCGGCCAACAGCAGCGCGTTTCTATTGCGCGCGCGCTGGCGATGGAACCTGACGTTTTACTGTTCGATGAACCCACATCGGCGCTCGATCCTGAACTGGTCGGCGAAGTGTTGCGCATCATGCAACAACTGGCGGAAGAAGGCAAAACGATGGTGGTGGTCACGCATGAAATGGGCTTCGCTCGCCATGTCTCTTCGCACGTTATTTTTCTGCATCAGGGGAAAATTGAAGAAGAGGGTGATCCGGAGCAGGTGTTCGGCAATCCGCAAAGCCCGCGTTTACAGCAATTCCTGAAAGGCTCGCTGAAATAACGCTCAGAGGCGCGCGCGCGCTATATACGCGCAGTGTTTATTGGCATAGTTAGCCTGTTTCCTGAAATGTTCCGCGCAATTACCGATTACGGGGTAACTGGCCGGGCAGTAAAAAAAGGCCTGCTGAACATCCAAAGCTGGAGTCCTCGCGACTTCGCGCATGACCGGCACCGTACCGTGGACGACCGTCCTTACGGCGGCGGACCGGGGATGTTAATGATGGTGCAACCCTTGCGGGACGCCATTCACGCAGCAAAAGCCGCGGCAGGTGAAGGCGCTAAAGTGATTTATCTGTCGCCTCAGGGACGCAAGCTTGATCAAGCGGGCGTTAGCGAGCTGGCCACGAATCAGAAGCTTATTCTGGTGTGTGGTCGCTACGAAGGCGTAGATGAGCGCGTAATTCAGACCGAAATTGACGAAGAATGGTCAATTGGCGATTACGTTCTCAGCGGTGGCGAACTACCGGCAATGACGCTGATTGACTCCGTCGCCCGGTTTATACCGGGGGTTCTGGGGCATGAGGCATCAGCAATCGAAGATTCGTTTGCTGATGGGTTGCTGGATTGTCCGCACTATACGCGCCCTGAAGTGTTAGAGGGGATGGAAGTACCGCCAGTATTGCTGTCGGGAAACCATGCTGAGATACGTCGCTGGCGTTTGAAACAGTCGCTGGGCCGAACCTGGCTTAGAAGACCTGAACTTCTGGAAAACCTGGCTCTGACTGAAGAGCAAGCAAGGTTGCTGGCGGAGTTCAAAACAGAACACGCACAACAGCAGCATAAACATGATGGGATGGCATAGCCGTCATATGGGCTCTCAGAGGAGACGCGCTAATGCGCAGTACGTGTTTATTGGCATAGTTAGCCTGTTTCCTGAAATGTTCCGCGCAATTACCGATTACGGGGTAACTGGCCGGGCAGTAAAAAAAGGCCTGCTGAACATCCAAAGCTGGAGTCCTCGCGACTTCGCGCATGACCGGCACCGTACCGTGGACGACCGTCCTTACGGCGGCGGACCGGGGATGTTAATGATGGTGCAACCCTTGCGGGACGCCATTCACGCAGCAAAAGCCGCGGCAGGTGAAGGCGCTAAAGTGATTTATCTGTCGCCTCAGGGACGCAAGCTTGATCAAGCGGGCGTTAGCGAGCTGGCCACGAATCAGAAGCTTATTCTGGTGTGTGGTCGCTACGAAGGCGTAGATGAGCGCGTAATTCAGACCGAAATTGACGAAGAATGGTCAATTGGCGATTACGTTCTCAGCGGTGGCGAACTACCGGCAATGACGCTGATTGACTCCGTCGCCCGGTTTATACCGGGGGTTCTGGGGCATGAGGCATCAGCAATCGAAGATTCGTTTGCTGATGGGTTGCTGGATTGTCCGCACTATACGCGCCCTGAAGTGTTAGAGGGGATGGAAGTACCGCCAGTATTGCTGTCGGGAAACCATGCTGAGATACGTCGCTGGCGTTTGAAACAGTCGCTGGGCCGAACCTGGCTTAGAAGACCTGAACTTCTGGAAAACCTGGCTCTGACTGAAGAGCAAGCAAGGTTGCTGGCGGAGTTCAAAACAGAACACGCACAACAGCAGCATAAACATGATGGGATGGCATAGCGCATACGCGCGCGATATATATTCGCGCAGAGGCGCGCATAGCGATGAAGTTTGTTGCGCCCGAACAGGCACCGGAACAGGCGGAGGTCATCAAAAATACGCCGTTCTGGCCTGATGTGGACCTGTCGGAATTTCGCAGTGTGATGCGCACTGACGGCACGGTGACGCAGCCGCGTTTAAAGCAGGTCGTGCTGACGGCGATCTCTGAGGTTAACGCTGAGCTGTACGACTTCCGCAACCGTCAGCAGATGCTGGGCTGGCGGACACTTGCTGAGGTTCCCGCAGAAATGCTGGACGGTAAAAGCGAGCGTATCCGGCACTACCACAACGCTGTTTTTTGCTGGGCGCGCGCTGTGCTTAATGAGCGTTATCAGGACTATGACGCCACGGCGTCAGGCGTGAAGCGAGGGGAGGAGCTGGCGGAGGCCAGCGGCGATCTGTGGCGTGATGCCCGCTGGGCCATCAGCCGGGTGCAGGATGTACCGCACTGTACGGTGGAGCTTATCTGAACGGCTAGCGCGTAGCGGCAGTCTCGGATGAATAATCATTTTGGGAAAGGGTTAATGGCCGGGTTGCACGCGCCATATGCATATAGCGCGCATCATGCGGTGAATTTCTGTTCTGAGTATAAACGTGGCTTTGTATTGGGTTTTACACACCGTATGTTCGAAAAGACCGGCGATCGTCAACTTAGCGCGTGGGAGGCTGGAATTCTGACGCGTCGCTATGGTCTGGATAAAGAAATGGTGATGGATTTCTTTAAAGAGAATCATTCCGGGATGGCGGTTCGCTTCTTTATGGCCGGTTATCGACTCGAAGGTTGACGATCGCGCGCAGGAGGAGAGCTCTCTTCTTCTAGAGCATGTCTACGCTTCTCTATTTGCACGGATTCAACAGTTCCCCTCGCTCGGCAAAAGCGTGCCAGCTAAAAAACTGGCTGGCGGAGCGTCATCCGCATGTTGAGATGATCGTCCCTCAGCTGCCGCCGTATCCTGCCGATGCGGCGGAGTTGCTGGAATCTCTCGTGCTTGAGCATGGCGGTGCGCCATTAGGGCTGGTAGGATCGTCGCTGGGTGGTTATTACGCCACCTGGCTGTCGCAATGTTTTATGCTGCCGGCTGTGGTGGTGAATCCCGCCGTGCGGCCCTTTGAATTACTGACCGACTATCTCGGTCAGAACGAGAACCCCTACACCGGGCAGCAATATGTGCTAGAGTCTCGCCATATTTATGATCTTAAAGTCATGCAGATTGACCCGCTGGAAGCGCCGGACCTGATCTGGCTACTGCAACAGACGGGCGATGAAGTGCTGTATTACCGCCAGGCGGTGGCATATTACGCCTCCTGCCGTCAGACAGTGACCGAGGGTGGTAATCACGCATTCACGGGCTTCGAAGATTATTTCAACCAGATTGTCGATTTTCTTGGACTGCACAGTTGCTGACGGCTATGCGCGCGCTCGATGATTGACCCTATTTTTGCGTCCTGTACGCTAATTGCCGTCTTTGTTGTTTTACTGGCCATGGGCGCGCCTATCGGGATCTGCATCGTTATCGCCTCTTTCAGCACCATGATGCTGGTACTGCCTTTCGATATTTCGATGTTCGCCACCGCGCAAAAAATGTTCTCCAGCCTGGACAGTTTTGCCTTGCTGGCCGTGCCGTTCTTCGTTTTGTCCGGGGTGATCATGAATAGCGGGGGAATTGCCGCCCGGCTGGTCAATTTTGCCAAACTGTTTACTGGCAAACTGCCCGGCTCGCTCTCTTATACCAACATCGTCGGCAATATGATGTTCGGTGCAATTTCCGGATCGGCGATTGCCGCCTCAACCTCCATCGGCGGCGTGATGGTGCCGATGAGCGCGCGCGAAGGTTACGATCGCGGCTTTGCGGCCGCGGTGAATATCGCCTCCGCGCCGACGGGAATGTTAATTCCGCCCACCACGGCTTTTATCCTTTACGCGCTGGCAAGCGGGGGAACATCGATTGCCGCTCTGTTCGCCGGCGGTCTGGTCGCGGGAGTGCTGTGGGGCGTTGGCTGTATGCTGGTCACGCTGGTGGTCGCTAAGCGTCGAAATTATCGGGTTTTCTTCACCGTCCAAAAAGGTATGGCGCTAAAAGTTGCCGTTGAGGCCATTCCCAGCCTGCTGCTGATCGTGATTATTGTCGGCGGCATTGTGCAGGGGATTTTCACCGCCATTGAAGCCTCCGCGATTGCCGTGGTGTATACGTTATTGCTGACGATGGTGTTTTACCGCACGCTGAAAATTAAGGATTTGCCTTCGATTTTGCTCCAGACAGTGGTAATGACCGGGGTCATCATGTTCCTGCTGGCAACCTCTTCGGCGATGTCCTTCTCGATGTCGATCACCAATATTCCTGCGGCGCTGAGCGATATGATCCTCGGTATTTCCGCCAATAAACTGGTTATCCTGTTAGTCATTACCGTCTTTTTGTTGATTATCGGCGCATTTATGGATATTGGTCCGGCCATTCTGATTTTTACCCCGATTCTGCTGCCAATCATGGCTAAACTGGGCGTCGATCCGGTGCATTTCGGCATTATCATGATCTATAACCTGGCGATTGGCACCATTACGCCGCCAGTTGGCAGTGGTTTATATGTCGGGGCGAGCGTCGGTAAGGTCAAAGTTGAGGAAGTGATTAAACCGTTGCTGCCTTTTTACGGCGCGATTATCGGCGTTCTGTTATTAATTACCTACATTCCGGAAATCACACTGTTCTTACCCCGTCTACTGGGCATCATGTAA diff --git a/Examples/1-res-Annotate/tmp_files/genome1.fst-split5N.fna-prokka.log b/Examples/1-res-Annotate/tmp_files/genome1.fst-split5N.fna-prokka.log deleted file mode 100644 index 6aa806da49c94da5a8444327c8a94d809e958faf..0000000000000000000000000000000000000000 --- a/Examples/1-res-Annotate/tmp_files/genome1.fst-split5N.fna-prokka.log +++ /dev/null @@ -1,121 +0,0 @@ -[13:18:42] This is prokka 1.14-dev -[13:18:42] Written by Torsten Seemann <torsten.seemann@gmail.com> -[13:18:42] Homepage is https://github.com/tseemann/prokka -[13:18:42] Local time is Tue Feb 12 13:18:42 2019 -[13:18:42] You are aperrin -[13:18:42] Operating system is darwin -[13:18:42] You have BioPerl 1.006924 -[13:18:42] System has 8 cores. -[13:18:42] Will use maximum of 1 cores. -[13:18:42] Annotating as >>> Bacteria <<< -[13:18:42] Generating locus_tag from 'Examples/1-res-Annotate/tmp_files/genome1.fst-split5N.fna' contents. -[13:18:42] Setting --locustag GKEGNCBE from MD5 04e07cbef9b8a6b8d550f0d6ed3a8746 -[13:18:42] Creating new output folder: Examples/1-res-Annotate/tmp_files/genome1.fst-split5N.fna-prokkaRes -[13:18:42] Running: mkdir -p Examples\/1\-res\-Annotate\/tmp_files\/genome1\.fst\-split5N\.fna\-prokkaRes -[13:18:42] Using filename prefix: EXAM.0219.00001.XXX -[13:18:42] Setting HMMER_NCPU=1 -[13:18:42] Writing log to: Examples/1-res-Annotate/tmp_files/genome1.fst-split5N.fna-prokkaRes/EXAM.0219.00001.log -[13:18:42] Command: /usr/local/bin/prokka --outdir Examples/1-res-Annotate/tmp_files/genome1.fst-split5N.fna-prokkaRes --cpus 1 --prefix EXAM.0219.00001 Examples/1-res-Annotate/tmp_files/genome1.fst-split5N.fna -[13:18:42] Appending to PATH: /Users/aperrin/Softwares/src/prokka/bin/../binaries/darwin -[13:18:42] Appending to PATH: /Users/aperrin/Softwares/src/prokka/bin/../binaries/darwin/../common -[13:18:42] Appending to PATH: /Users/aperrin/Softwares/src/prokka/bin -[13:18:42] Looking for 'aragorn' - found /Users/aperrin/Softwares/src/prokka/bin/../binaries/darwin/aragorn -[13:18:42] Determined aragorn version is 1.2 -[13:18:42] Looking for 'barrnap' - found /usr/local/bin/barrnap -[13:18:42] Determined barrnap version is 0.8 -[13:18:42] Looking for 'blastp' - found /Users/aperrin/Softwares/bin/blastp -[13:18:42] Determined blastp version is 2.3 -[13:18:42] Looking for 'cmpress' - found /usr/local/bin/cmpress -[13:18:42] Determined cmpress version is 1.1 -[13:18:42] Looking for 'cmscan' - found /usr/local/bin/cmscan -[13:18:42] Determined cmscan version is 1.1 -[13:18:42] Looking for 'egrep' - found /usr/bin/egrep -[13:18:42] Looking for 'find' - found /usr/bin/find -[13:18:42] Looking for 'grep' - found /usr/bin/grep -[13:18:42] Looking for 'hmmpress' - found /Users/aperrin/Softwares/src/prokka/bin/../binaries/darwin/hmmpress -[13:18:42] Determined hmmpress version is 3.1 -[13:18:42] Looking for 'hmmscan' - found /usr/local/bin/hmmscan -[13:18:42] Determined hmmscan version is 3.1 -[13:18:42] Looking for 'java' - found /usr/bin/java -[13:18:42] Looking for 'less' - found /usr/bin/less -[13:18:42] Looking for 'makeblastdb' - found /Users/aperrin/Softwares/bin/makeblastdb -[13:18:42] Determined makeblastdb version is 2.3 -[13:18:42] Looking for 'minced' - found /Users/aperrin/Softwares/src/prokka/bin/../binaries/darwin/../common/minced -[13:18:42] Determined minced version is 2.0 -[13:18:42] Looking for 'parallel' - found /usr/local/bin/parallel -[13:18:42] Determined parallel version is 20181022 -[13:18:42] Looking for 'prodigal' - found /usr/local/bin/prodigal -[13:18:42] Determined prodigal version is 2.6 -[13:18:42] Looking for 'prokka-genbank_to_fasta_db' - found /Users/aperrin/Softwares/src/prokka/bin/prokka-genbank_to_fasta_db -[13:18:42] Looking for 'sed' - found /usr/bin/sed -[13:18:42] Looking for 'tbl2asn' - found /Users/aperrin/Softwares/src/prokka/bin/../binaries/darwin/tbl2asn -[13:18:42] Determined tbl2asn version is 25.6 -[13:18:42] Using genetic code table 11. -[13:18:42] Loading and checking input file: Examples/1-res-Annotate/tmp_files/genome1.fst-split5N.fna -[13:18:42] Wrote 2 contigs totalling 9808 bp. -[13:18:42] Predicting tRNAs and tmRNAs -[13:18:42] Running: aragorn -l -gc11 -w Examples\/1\-res\-Annotate\/tmp_files\/genome1\.fst\-split5N\.fna\-prokkaRes\/EXAM\.0219\.00001\.fna -[13:18:42] Found 0 tRNAs -[13:18:42] Predicting Ribosomal RNAs -[13:18:42] Running Barrnap with 1 threads -[13:18:42] Found 0 rRNAs -[13:18:42] Skipping ncRNA search, enable with --rfam if desired. -[13:18:42] Total of 0 tRNA + rRNA features -[13:18:42] Searching for CRISPR repeats -[13:18:43] Found 0 CRISPRs -[13:18:43] Predicting coding sequences -[13:18:43] Contigs total 9808 bp, so using meta mode -[13:18:43] Running: prodigal -i Examples\/1\-res\-Annotate\/tmp_files\/genome1\.fst\-split5N\.fna\-prokkaRes\/EXAM\.0219\.00001\.fna -c -m -g 11 -p meta -f sco -q -[13:18:43] Found 11 CDS -[13:18:43] Connecting features back to sequences -[13:18:43] Not using genus-specific database. Try --usegenus to enable it. -[13:18:43] Annotating CDS, please be patient. -[13:18:43] Will use 1 CPUs for similarity searching. -[13:18:43] There are still 11 unannotated CDS left (started with 11) -[13:18:43] Will use blast to search against /Users/aperrin/Softwares/src/prokka/db/kingdom/Bacteria/sprot with 1 CPUs -[13:18:43] Running: cat Examples\/1\-res\-Annotate\/tmp_files\/genome1\.fst\-split5N\.fna\-prokkaRes\/sprot\.faa | parallel --gnu --plain -j 1 --block 1558 --recstart '>' --pipe blastp -query - -db /Users/aperrin/Softwares/src/prokka/db/kingdom/Bacteria/sprot -evalue 1e-06 -num_threads 1 -num_descriptions 1 -num_alignments 1 -seg no > Examples\/1\-res\-Annotate\/tmp_files\/genome1\.fst\-split5N\.fna\-prokkaRes\/sprot\.blast 2> /dev/null -[13:18:44] Deleting unwanted file: Examples/1-res-Annotate/tmp_files/genome1.fst-split5N.fna-prokkaRes/sprot.faa -[13:18:44] Deleting unwanted file: Examples/1-res-Annotate/tmp_files/genome1.fst-split5N.fna-prokkaRes/sprot.blast -[13:18:44] There are still 4 unannotated CDS left (started with 11) -[13:18:44] Will use hmmer3 to search against /Users/aperrin/Softwares/src/prokka/db/hmm/HAMAP.hmm with 1 CPUs -[13:18:44] Running: cat Examples\/1\-res\-Annotate\/tmp_files\/genome1\.fst\-split5N\.fna\-prokkaRes\/HAMAP\.hmm\.faa | parallel --gnu --plain -j 1 --block 459 --recstart '>' --pipe hmmscan --noali --notextw --acc -E 1e-06 --cpu 1 /Users/aperrin/Softwares/src/prokka/db/hmm/HAMAP.hmm /dev/stdin > Examples\/1\-res\-Annotate\/tmp_files\/genome1\.fst\-split5N\.fna\-prokkaRes\/HAMAP\.hmm\.hmmer3 2> /dev/null -[13:18:44] Deleting unwanted file: Examples/1-res-Annotate/tmp_files/genome1.fst-split5N.fna-prokkaRes/HAMAP.hmm.faa -[13:18:44] Deleting unwanted file: Examples/1-res-Annotate/tmp_files/genome1.fst-split5N.fna-prokkaRes/HAMAP.hmm.hmmer3 -[13:18:44] Labelling remaining 4 proteins as 'hypothetical protein' -[13:18:44] Possible /pseudo 'tRNA (guanine-N(1)-)-methyltransferase' at genome1_2 position 3427 -[13:18:44] Found 6 unique /gene codes. -[13:18:44] Fixed 2 duplicate /gene - trmD_1 trmD_2 -[13:18:44] Fixed 1 colliding /gene names. -[13:18:44] Adding /locus_tag identifiers -[13:18:44] Assigned 11 locus_tags to CDS and RNA features. -[13:18:44] Writing outputs to Examples/1-res-Annotate/tmp_files/genome1.fst-split5N.fna-prokkaRes/ -[13:18:44] Generating annotation statistics file -[13:18:44] Generating Genbank and Sequin files -[13:18:44] Running: tbl2asn -V b -a r10k -l paired-ends -M n -N 1 -y 'Annotated using prokka 1.14-dev from https://github.com/tseemann/prokka' -Z Examples\/1\-res\-Annotate\/tmp_files\/genome1\.fst\-split5N\.fna\-prokkaRes\/EXAM\.0219\.00001\.err -i Examples\/1\-res\-Annotate\/tmp_files\/genome1\.fst\-split5N\.fna\-prokkaRes\/EXAM\.0219\.00001\.fsa 2> /dev/null -[13:18:45] Deleting unwanted file: Examples/1-res-Annotate/tmp_files/genome1.fst-split5N.fna-prokkaRes/errorsummary.val -[13:18:45] Deleting unwanted file: Examples/1-res-Annotate/tmp_files/genome1.fst-split5N.fna-prokkaRes/EXAM.0219.00001.dr -[13:18:45] Deleting unwanted file: Examples/1-res-Annotate/tmp_files/genome1.fst-split5N.fna-prokkaRes/EXAM.0219.00001.fixedproducts -[13:18:45] Deleting unwanted file: Examples/1-res-Annotate/tmp_files/genome1.fst-split5N.fna-prokkaRes/EXAM.0219.00001.ecn -[13:18:45] Deleting unwanted file: Examples/1-res-Annotate/tmp_files/genome1.fst-split5N.fna-prokkaRes/EXAM.0219.00001.val -[13:18:45] Repairing broken .GBK output that tbl2asn produces... -[13:18:45] Running: sed 's/COORDINATES: profile/COORDINATES:profile/' < Examples\/1\-res\-Annotate\/tmp_files\/genome1\.fst\-split5N\.fna\-prokkaRes\/EXAM\.0219\.00001\.gbf > Examples\/1\-res\-Annotate\/tmp_files\/genome1\.fst\-split5N\.fna\-prokkaRes\/EXAM\.0219\.00001\.gbk -[13:18:45] Deleting unwanted file: Examples/1-res-Annotate/tmp_files/genome1.fst-split5N.fna-prokkaRes/EXAM.0219.00001.gbf -[13:18:45] Output files: -[13:18:45] Examples/1-res-Annotate/tmp_files/genome1.fst-split5N.fna-prokkaRes/EXAM.0219.00001.txt -[13:18:45] Examples/1-res-Annotate/tmp_files/genome1.fst-split5N.fna-prokkaRes/EXAM.0219.00001.tsv -[13:18:45] Examples/1-res-Annotate/tmp_files/genome1.fst-split5N.fna-prokkaRes/EXAM.0219.00001.fna -[13:18:45] Examples/1-res-Annotate/tmp_files/genome1.fst-split5N.fna-prokkaRes/EXAM.0219.00001.err -[13:18:45] Examples/1-res-Annotate/tmp_files/genome1.fst-split5N.fna-prokkaRes/EXAM.0219.00001.gff -[13:18:45] Examples/1-res-Annotate/tmp_files/genome1.fst-split5N.fna-prokkaRes/EXAM.0219.00001.sqn -[13:18:45] Examples/1-res-Annotate/tmp_files/genome1.fst-split5N.fna-prokkaRes/EXAM.0219.00001.tbl -[13:18:45] Examples/1-res-Annotate/tmp_files/genome1.fst-split5N.fna-prokkaRes/EXAM.0219.00001.gbk -[13:18:45] Examples/1-res-Annotate/tmp_files/genome1.fst-split5N.fna-prokkaRes/EXAM.0219.00001.log -[13:18:45] Examples/1-res-Annotate/tmp_files/genome1.fst-split5N.fna-prokkaRes/EXAM.0219.00001.ffn -[13:18:45] Examples/1-res-Annotate/tmp_files/genome1.fst-split5N.fna-prokkaRes/EXAM.0219.00001.faa -[13:18:45] Examples/1-res-Annotate/tmp_files/genome1.fst-split5N.fna-prokkaRes/EXAM.0219.00001.fsa -[13:18:45] Annotation finished successfully. -[13:18:45] Walltime used: 0.05 minutes -[13:18:45] If you use this result please cite the Prokka paper: -[13:18:45] Seemann T (2014) Prokka: rapid prokaryotic genome annotation. Bioinformatics. 30(14):2068-9. -[13:18:45] Type 'prokka --citation' for more details. -[13:18:45] Share and enjoy! diff --git a/Examples/1-res-Annotate/tmp_files/genome1.fst-split5N.fna-prokkaRes/EXAM.0219.00001.err b/Examples/1-res-Annotate/tmp_files/genome1.fst-split5N.fna-prokkaRes/EXAM.0219.00001.err deleted file mode 100644 index 9837b5a1951f8b0fabc962ef6fbdf29c7b38b6fb..0000000000000000000000000000000000000000 --- a/Examples/1-res-Annotate/tmp_files/genome1.fst-split5N.fna-prokkaRes/EXAM.0219.00001.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/1-res-Annotate/tmp_files/genome1.fst-split5N.fna-prokkaRes/EXAM.0219.00001:genome1_1_1 (length 555) -Examples/1-res-Annotate/tmp_files/genome1.fst-split5N.fna-prokkaRes/EXAM.0219.00001:genome1_1_2 (length 276) -Examples/1-res-Annotate/tmp_files/genome1.fst-split5N.fna-prokkaRes/EXAM.0219.00001:genome1_2_1 (length 126) -Examples/1-res-Annotate/tmp_files/genome1.fst-split5N.fna-prokkaRes/EXAM.0219.00001:genome1_2_2 (length 469) -Examples/1-res-Annotate/tmp_files/genome1.fst-split5N.fna-prokkaRes/EXAM.0219.00001:genome1_2_3 (length 257) -Examples/1-res-Annotate/tmp_files/genome1.fst-split5N.fna-prokkaRes/EXAM.0219.00001:genome1_2_4 (length 244) -Examples/1-res-Annotate/tmp_files/genome1.fst-split5N.fna-prokkaRes/EXAM.0219.00001:genome1_2_5 (length 275) -Examples/1-res-Annotate/tmp_files/genome1.fst-split5N.fna-prokkaRes/EXAM.0219.00001:genome1_2_6 (length 154) -Examples/1-res-Annotate/tmp_files/genome1.fst-split5N.fna-prokkaRes/EXAM.0219.00001:genome1_2_7 (length 86) -Examples/1-res-Annotate/tmp_files/genome1.fst-split5N.fna-prokkaRes/EXAM.0219.00001:genome1_2_8 (length 193) -Examples/1-res-Annotate/tmp_files/genome1.fst-split5N.fna-prokkaRes/EXAM.0219.00001: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/1-res-Annotate/tmp_files/genome1.fst-split5N.fna-prokkaRes/EXAM.0219.00001:genome1_1 (length 2784) -Examples/1-res-Annotate/tmp_files/genome1.fst-split5N.fna-prokkaRes/EXAM.0219.00001: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/1-res-Annotate/tmp_files/genome1.fst-split5N.fna-prokkaRes/EXAM.0219.00001:CDS Glutamine--tRNA ligase genome1_1:213-1880 GKEGNCBE_00001 - -DiscRep_SUB:FEATURE_LOCATION_CONFLICT::Coding region xref gene does not exist -Examples/1-res-Annotate/tmp_files/genome1.fst-split5N.fna-prokkaRes/EXAM.0219.00001: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/1-res-Annotate/tmp_files/genome1.fst-split5N.fna-prokkaRes/EXAM.0219.00001: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/1-res-Annotate/tmp_files/genome1.fst-split5N.fna-prokkaRes/EXAM.0219.00001:CDS hypothetical protein genome1_2:428-1837 GKEGNCBE_00004 - -DiscRep_SUB:FEATURE_LOCATION_CONFLICT::Coding region xref gene does not exist -Examples/1-res-Annotate/tmp_files/genome1.fst-split5N.fna-prokkaRes/EXAM.0219.00001: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/1-res-Annotate/tmp_files/genome1.fst-split5N.fna-prokkaRes/EXAM.0219.00001: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/1-res-Annotate/tmp_files/genome1.fst-split5N.fna-prokkaRes/EXAM.0219.00001: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/1-res-Annotate/tmp_files/genome1.fst-split5N.fna-prokkaRes/EXAM.0219.00001:CDS hypothetical protein genome1_2:4299-4763 GKEGNCBE_00008 - -DiscRep_SUB:FEATURE_LOCATION_CONFLICT::Coding region xref gene does not exist -Examples/1-res-Annotate/tmp_files/genome1.fst-split5N.fna-prokkaRes/EXAM.0219.00001:CDS hypothetical protein genome1_2:4818-5078 GKEGNCBE_00009 - -DiscRep_SUB:FEATURE_LOCATION_CONFLICT::Coding region xref gene does not exist -Examples/1-res-Annotate/tmp_files/genome1.fst-split5N.fna-prokkaRes/EXAM.0219.00001:CDS hypothetical protein genome1_2:5117-5698 GKEGNCBE_00010 - -DiscRep_SUB:FEATURE_LOCATION_CONFLICT::Coding region xref gene does not exist -Examples/1-res-Annotate/tmp_files/genome1.fst-split5N.fna-prokkaRes/EXAM.0219.00001: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/1-res-Annotate/tmp_files/genome1.fst-split5N.fna-prokkaRes/EXAM.0219.00001:CDS tRNA (guanine-N(1)-)-methyltransferase genome1_2:2709-3443 GKEGNCBE_00006 -Examples/1-res-Annotate/tmp_files/genome1.fst-split5N.fna-prokkaRes/EXAM.0219.00001: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/1-res-Annotate/tmp_files/genome1.fst-split5N.fna-prokkaRes/EXAM.0219.00001:genome1_1:Annotated using prokka 1.14-dev from https://github.com/tseemann/prokka -Examples/1-res-Annotate/tmp_files/genome1.fst-split5N.fna-prokkaRes/EXAM.0219.00001:genome1_2:Annotated using prokka 1.14-dev from https://github.com/tseemann/prokka - -DiscRep_ALL:MISSING_GENOMEASSEMBLY_COMMENTS::2 bioseqs are missing GenomeAssembly structured comments -Examples/1-res-Annotate/tmp_files/genome1.fst-split5N.fna-prokkaRes/EXAM.0219.00001:genome1_1 (length 2784) -Examples/1-res-Annotate/tmp_files/genome1.fst-split5N.fna-prokkaRes/EXAM.0219.00001:genome1_2 (length 7024) - -DiscRep_ALL:MOLTYPE_NOT_MRNA::2 molecule types are not set as mRNA. -Examples/1-res-Annotate/tmp_files/genome1.fst-split5N.fna-prokkaRes/EXAM.0219.00001:genome1_1 (length 2784) -Examples/1-res-Annotate/tmp_files/genome1.fst-split5N.fna-prokkaRes/EXAM.0219.00001:genome1_2 (length 7024) - -DiscRep_ALL:TECHNIQUE_NOT_TSA::2 technique are not set as TSA -Examples/1-res-Annotate/tmp_files/genome1.fst-split5N.fna-prokkaRes/EXAM.0219.00001:genome1_1 (length 2784) -Examples/1-res-Annotate/tmp_files/genome1.fst-split5N.fna-prokkaRes/EXAM.0219.00001:genome1_2 (length 7024) - -DiscRep_ALL:MISSING_STRUCTURED_COMMENT::2 sequences do not include structured comments. -Examples/1-res-Annotate/tmp_files/genome1.fst-split5N.fna-prokkaRes/EXAM.0219.00001:genome1_1 (length 2784) -Examples/1-res-Annotate/tmp_files/genome1.fst-split5N.fna-prokkaRes/EXAM.0219.00001:genome1_2 (length 7024) - -DiscRep_ALL:MISSING_PROJECT::13 sequences do not include project. -Examples/1-res-Annotate/tmp_files/genome1.fst-split5N.fna-prokkaRes/EXAM.0219.00001:genome1_1 (length 2784) -Examples/1-res-Annotate/tmp_files/genome1.fst-split5N.fna-prokkaRes/EXAM.0219.00001:genome1_1_1 (length 555) -Examples/1-res-Annotate/tmp_files/genome1.fst-split5N.fna-prokkaRes/EXAM.0219.00001:genome1_1_2 (length 276) -Examples/1-res-Annotate/tmp_files/genome1.fst-split5N.fna-prokkaRes/EXAM.0219.00001:genome1_2 (length 7024) -Examples/1-res-Annotate/tmp_files/genome1.fst-split5N.fna-prokkaRes/EXAM.0219.00001:genome1_2_1 (length 126) -Examples/1-res-Annotate/tmp_files/genome1.fst-split5N.fna-prokkaRes/EXAM.0219.00001:genome1_2_2 (length 469) -Examples/1-res-Annotate/tmp_files/genome1.fst-split5N.fna-prokkaRes/EXAM.0219.00001:genome1_2_3 (length 257) -Examples/1-res-Annotate/tmp_files/genome1.fst-split5N.fna-prokkaRes/EXAM.0219.00001:genome1_2_4 (length 244) -Examples/1-res-Annotate/tmp_files/genome1.fst-split5N.fna-prokkaRes/EXAM.0219.00001:genome1_2_5 (length 275) -Examples/1-res-Annotate/tmp_files/genome1.fst-split5N.fna-prokkaRes/EXAM.0219.00001:genome1_2_6 (length 154) -Examples/1-res-Annotate/tmp_files/genome1.fst-split5N.fna-prokkaRes/EXAM.0219.00001:genome1_2_7 (length 86) -Examples/1-res-Annotate/tmp_files/genome1.fst-split5N.fna-prokkaRes/EXAM.0219.00001:genome1_2_8 (length 193) -Examples/1-res-Annotate/tmp_files/genome1.fst-split5N.fna-prokkaRes/EXAM.0219.00001: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/1-res-Annotate/tmp_files/genome1.fst-split5N.fna-prokkaRes/EXAM.0219.00001:genome1_1 (length 2784) -Examples/1-res-Annotate/tmp_files/genome1.fst-split5N.fna-prokkaRes/EXAM.0219.00001:genome1_2 (length 7024) - diff --git a/Examples/1-res-Annotate/tmp_files/genome1.fst-split5N.fna-prokkaRes/EXAM.0219.00001.faa b/Examples/1-res-Annotate/tmp_files/genome1.fst-split5N.fna-prokkaRes/EXAM.0219.00001.faa deleted file mode 100644 index 2bb9f621de719842530393507763f132848a7e16..0000000000000000000000000000000000000000 --- a/Examples/1-res-Annotate/tmp_files/genome1.fst-split5N.fna-prokkaRes/EXAM.0219.00001.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/1-res-Annotate/tmp_files/genome1.fst-split5N.fna-prokkaRes/EXAM.0219.00001.ffn b/Examples/1-res-Annotate/tmp_files/genome1.fst-split5N.fna-prokkaRes/EXAM.0219.00001.ffn deleted file mode 100644 index 8bf92ebb8dfd9e743a03a529ee7eda731975d893..0000000000000000000000000000000000000000 --- a/Examples/1-res-Annotate/tmp_files/genome1.fst-split5N.fna-prokkaRes/EXAM.0219.00001.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/1-res-Annotate/tmp_files/genome1.fst-split5N.fna-prokkaRes/EXAM.0219.00001.fna b/Examples/1-res-Annotate/tmp_files/genome1.fst-split5N.fna-prokkaRes/EXAM.0219.00001.fna deleted file mode 100644 index 325b3340782ba0db58b1693fab267c634919957a..0000000000000000000000000000000000000000 --- a/Examples/1-res-Annotate/tmp_files/genome1.fst-split5N.fna-prokkaRes/EXAM.0219.00001.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/1-res-Annotate/tmp_files/genome1.fst-split5N.fna-prokkaRes/EXAM.0219.00001.fsa b/Examples/1-res-Annotate/tmp_files/genome1.fst-split5N.fna-prokkaRes/EXAM.0219.00001.fsa deleted file mode 100644 index ca5e180abfba3f98289887814c4d89b20e9e1bb6..0000000000000000000000000000000000000000 --- a/Examples/1-res-Annotate/tmp_files/genome1.fst-split5N.fna-prokkaRes/EXAM.0219.00001.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/1-res-Annotate/tmp_files/genome1.fst-split5N.fna-prokkaRes/EXAM.0219.00001.gbk b/Examples/1-res-Annotate/tmp_files/genome1.fst-split5N.fna-prokkaRes/EXAM.0219.00001.gbk deleted file mode 100644 index 027b74e27c977b2871b77d3534abbb8400722fd0..0000000000000000000000000000000000000000 --- a/Examples/1-res-Annotate/tmp_files/genome1.fst-split5N.fna-prokkaRes/EXAM.0219.00001.gbk +++ /dev/null @@ -1,346 +0,0 @@ -LOCUS genome1_1 2784 bp DNA linear 12-FEB-2019 -DEFINITION Genus species strain strain. -ACCESSION -VERSION -KEYWORDS . -SOURCE Genus species - ORGANISM Genus species - Unclassified. -COMMENT Annotated using prokka 1.14-dev 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:2.6" - /inference="similar to AA sequence:UniProtKB:P00962" - /codon_start=1 - /transl_table=11 - /product="Glutamine--tRNA ligase" - /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:2.6" - /inference="similar to AA sequence:UniProtKB:P75820" - /codon_start=1 - /transl_table=11 - /product="N-acetylmuramoyl-L-alanine amidase AmiD" - /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 12-FEB-2019 -DEFINITION Genus species strain strain. -ACCESSION -VERSION -KEYWORDS . -SOURCE Genus species - ORGANISM Genus species - Unclassified. -COMMENT Annotated using prokka 1.14-dev 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:2.6" - /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:2.6" - /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:2.6" - /inference="similar to AA sequence:UniProtKB:P02915" - /codon_start=1 - /transl_table=11 - /product="Histidine transport ATP-binding protein HisP" - /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:2.6" - /inference="similar to AA sequence:UniProtKB:P0A873" - /codon_start=1 - /transl_table=11 - /product="tRNA (guanine-N(1)-)-methyltransferase" - /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:2.6" - /inference="similar to AA sequence:UniProtKB:P0A873" - /codon_start=1 - /transl_table=11 - /product="tRNA (guanine-N(1)-)-methyltransferase" - /translation="MMGWHSRHMGSQRRRANAQYVFIGIVSLFPEMFRAITDYGVTGR - AVKKGLLNIQSWSPRDFAHDRHRTVDDRPYGGGPGMLMMVQPLRDAIHAAKAAAGEGA - KVIYLSPQGRKLDQAGVSELATNQKLILVCGRYEGVDERVIQTEIDEEWSIGDYVLSG - GELPAMTLIDSVARFIPGVLGHEASAIEDSFADGLLDCPHYTRPEVLEGMEVPPVLLS - GNHAEIRRWRLKQSLGRTWLRRPELLENLALTEEQARLLAEFKTEHAQQQHKHDGMA" - CDS 4299..4763 - /locus_tag="GKEGNCBE_00008" - /inference="ab initio prediction:Prodigal:2.6" - /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:2.6" - /codon_start=1 - /transl_table=11 - /product="hypothetical protein" - /translation="MAGLHAPYAYSAHHAVNFCSEYKRGFVLGFTHRMFEKTGDRQLS - AWEAGILTRRYGLDKEMVMDFFKENHSGMAVRFFMAGYRLEG" - CDS 5117..5698 - /locus_tag="GKEGNCBE_00010" - /inference="ab initio prediction:Prodigal:2.6" - /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:2.6" - /inference="similar to AA sequence:UniProtKB:O07838" - /codon_start=1 - /transl_table=11 - /product="C4-dicarboxylate TRAP transporter large permease - protein DctM" - /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/1-res-Annotate/tmp_files/genome1.fst-split5N.fna-prokkaRes/EXAM.0219.00001.gff b/Examples/1-res-Annotate/tmp_files/genome1.fst-split5N.fna-prokkaRes/EXAM.0219.00001.gff deleted file mode 100644 index 71be830b6d848e2d4a9641eb01096ab1ddf42428..0000000000000000000000000000000000000000 --- a/Examples/1-res-Annotate/tmp_files/genome1.fst-split5N.fna-prokkaRes/EXAM.0219.00001.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:2.6 CDS 213 1880 . + 0 ID=GKEGNCBE_00001;eC_number=6.1.1.18;Name=glnS;dbxref=COG:COG0008;gene=glnS;inference=ab initio prediction:Prodigal:2.6,similar to AA sequence:UniProtKB:P00962;locus_tag=GKEGNCBE_00001;product=Glutamine--tRNA ligase -genome1_1 Prodigal:2.6 CDS 1916 2746 . + 0 ID=GKEGNCBE_00002;eC_number=3.5.1.28;Name=amiD;dbxref=COG:COG3023;gene=amiD;inference=ab initio prediction:Prodigal:2.6,similar to AA sequence:UniProtKB:P75820;locus_tag=GKEGNCBE_00002;product=N-acetylmuramoyl-L-alanine amidase AmiD -genome1_2 Prodigal:2.6 CDS 16 396 . + 0 ID=GKEGNCBE_00003;eC_number=5.3.3.10;Name=hpcD;gene=hpcD;inference=ab initio prediction:Prodigal:2.6,similar to AA sequence:UniProtKB:Q05354;locus_tag=GKEGNCBE_00003;product=5-carboxymethyl-2-hydroxymuconate Delta-isomerase -genome1_2 Prodigal:2.6 CDS 428 1837 . + 0 ID=GKEGNCBE_00004;inference=ab initio prediction:Prodigal:2.6;locus_tag=GKEGNCBE_00004;product=hypothetical protein -genome1_2 Prodigal:2.6 CDS 1869 2642 . + 0 ID=GKEGNCBE_00005;Name=hisP;dbxref=COG:COG4598;gene=hisP;inference=ab initio prediction:Prodigal:2.6,similar to AA sequence:UniProtKB:P02915;locus_tag=GKEGNCBE_00005;product=Histidine transport ATP-binding protein HisP -genome1_2 Prodigal:2.6 CDS 2709 3443 . + 0 ID=GKEGNCBE_00006;eC_number=2.1.1.228;Name=trmD_1;dbxref=COG:COG0336;gene=trmD_1;inference=ab initio prediction:Prodigal:2.6,similar to AA sequence:UniProtKB:P0A873;locus_tag=GKEGNCBE_00006;product=tRNA (guanine-N(1)-)-methyltransferase -genome1_2 Prodigal:2.6 CDS 3427 4254 . + 0 ID=GKEGNCBE_00007;eC_number=2.1.1.228;Name=trmD_2;dbxref=COG:COG0336;gene=trmD_2;inference=ab initio prediction:Prodigal:2.6,similar to AA sequence:UniProtKB:P0A873;locus_tag=GKEGNCBE_00007;product=tRNA (guanine-N(1)-)-methyltransferase -genome1_2 Prodigal:2.6 CDS 4299 4763 . + 0 ID=GKEGNCBE_00008;inference=ab initio prediction:Prodigal:2.6;locus_tag=GKEGNCBE_00008;product=hypothetical protein -genome1_2 Prodigal:2.6 CDS 4818 5078 . + 0 ID=GKEGNCBE_00009;inference=ab initio prediction:Prodigal:2.6;locus_tag=GKEGNCBE_00009;product=hypothetical protein -genome1_2 Prodigal:2.6 CDS 5117 5698 . + 0 ID=GKEGNCBE_00010;inference=ab initio prediction:Prodigal:2.6;locus_tag=GKEGNCBE_00010;product=hypothetical protein -genome1_2 Prodigal:2.6 CDS 5717 7024 . + 0 ID=GKEGNCBE_00011;Name=dctM;dbxref=COG:COG1593;gene=dctM;inference=ab initio prediction:Prodigal:2.6,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/1-res-Annotate/tmp_files/genome1.fst-split5N.fna-prokkaRes/EXAM.0219.00001.log b/Examples/1-res-Annotate/tmp_files/genome1.fst-split5N.fna-prokkaRes/EXAM.0219.00001.log deleted file mode 100644 index 6aa806da49c94da5a8444327c8a94d809e958faf..0000000000000000000000000000000000000000 --- a/Examples/1-res-Annotate/tmp_files/genome1.fst-split5N.fna-prokkaRes/EXAM.0219.00001.log +++ /dev/null @@ -1,121 +0,0 @@ -[13:18:42] This is prokka 1.14-dev -[13:18:42] Written by Torsten Seemann <torsten.seemann@gmail.com> -[13:18:42] Homepage is https://github.com/tseemann/prokka -[13:18:42] Local time is Tue Feb 12 13:18:42 2019 -[13:18:42] You are aperrin -[13:18:42] Operating system is darwin -[13:18:42] You have BioPerl 1.006924 -[13:18:42] System has 8 cores. -[13:18:42] Will use maximum of 1 cores. -[13:18:42] Annotating as >>> Bacteria <<< -[13:18:42] Generating locus_tag from 'Examples/1-res-Annotate/tmp_files/genome1.fst-split5N.fna' contents. -[13:18:42] Setting --locustag GKEGNCBE from MD5 04e07cbef9b8a6b8d550f0d6ed3a8746 -[13:18:42] Creating new output folder: Examples/1-res-Annotate/tmp_files/genome1.fst-split5N.fna-prokkaRes -[13:18:42] Running: mkdir -p Examples\/1\-res\-Annotate\/tmp_files\/genome1\.fst\-split5N\.fna\-prokkaRes -[13:18:42] Using filename prefix: EXAM.0219.00001.XXX -[13:18:42] Setting HMMER_NCPU=1 -[13:18:42] Writing log to: Examples/1-res-Annotate/tmp_files/genome1.fst-split5N.fna-prokkaRes/EXAM.0219.00001.log -[13:18:42] Command: /usr/local/bin/prokka --outdir Examples/1-res-Annotate/tmp_files/genome1.fst-split5N.fna-prokkaRes --cpus 1 --prefix EXAM.0219.00001 Examples/1-res-Annotate/tmp_files/genome1.fst-split5N.fna -[13:18:42] Appending to PATH: /Users/aperrin/Softwares/src/prokka/bin/../binaries/darwin -[13:18:42] Appending to PATH: /Users/aperrin/Softwares/src/prokka/bin/../binaries/darwin/../common -[13:18:42] Appending to PATH: /Users/aperrin/Softwares/src/prokka/bin -[13:18:42] Looking for 'aragorn' - found /Users/aperrin/Softwares/src/prokka/bin/../binaries/darwin/aragorn -[13:18:42] Determined aragorn version is 1.2 -[13:18:42] Looking for 'barrnap' - found /usr/local/bin/barrnap -[13:18:42] Determined barrnap version is 0.8 -[13:18:42] Looking for 'blastp' - found /Users/aperrin/Softwares/bin/blastp -[13:18:42] Determined blastp version is 2.3 -[13:18:42] Looking for 'cmpress' - found /usr/local/bin/cmpress -[13:18:42] Determined cmpress version is 1.1 -[13:18:42] Looking for 'cmscan' - found /usr/local/bin/cmscan -[13:18:42] Determined cmscan version is 1.1 -[13:18:42] Looking for 'egrep' - found /usr/bin/egrep -[13:18:42] Looking for 'find' - found /usr/bin/find -[13:18:42] Looking for 'grep' - found /usr/bin/grep -[13:18:42] Looking for 'hmmpress' - found /Users/aperrin/Softwares/src/prokka/bin/../binaries/darwin/hmmpress -[13:18:42] Determined hmmpress version is 3.1 -[13:18:42] Looking for 'hmmscan' - found /usr/local/bin/hmmscan -[13:18:42] Determined hmmscan version is 3.1 -[13:18:42] Looking for 'java' - found /usr/bin/java -[13:18:42] Looking for 'less' - found /usr/bin/less -[13:18:42] Looking for 'makeblastdb' - found /Users/aperrin/Softwares/bin/makeblastdb -[13:18:42] Determined makeblastdb version is 2.3 -[13:18:42] Looking for 'minced' - found /Users/aperrin/Softwares/src/prokka/bin/../binaries/darwin/../common/minced -[13:18:42] Determined minced version is 2.0 -[13:18:42] Looking for 'parallel' - found /usr/local/bin/parallel -[13:18:42] Determined parallel version is 20181022 -[13:18:42] Looking for 'prodigal' - found /usr/local/bin/prodigal -[13:18:42] Determined prodigal version is 2.6 -[13:18:42] Looking for 'prokka-genbank_to_fasta_db' - found /Users/aperrin/Softwares/src/prokka/bin/prokka-genbank_to_fasta_db -[13:18:42] Looking for 'sed' - found /usr/bin/sed -[13:18:42] Looking for 'tbl2asn' - found /Users/aperrin/Softwares/src/prokka/bin/../binaries/darwin/tbl2asn -[13:18:42] Determined tbl2asn version is 25.6 -[13:18:42] Using genetic code table 11. -[13:18:42] Loading and checking input file: Examples/1-res-Annotate/tmp_files/genome1.fst-split5N.fna -[13:18:42] Wrote 2 contigs totalling 9808 bp. -[13:18:42] Predicting tRNAs and tmRNAs -[13:18:42] Running: aragorn -l -gc11 -w Examples\/1\-res\-Annotate\/tmp_files\/genome1\.fst\-split5N\.fna\-prokkaRes\/EXAM\.0219\.00001\.fna -[13:18:42] Found 0 tRNAs -[13:18:42] Predicting Ribosomal RNAs -[13:18:42] Running Barrnap with 1 threads -[13:18:42] Found 0 rRNAs -[13:18:42] Skipping ncRNA search, enable with --rfam if desired. -[13:18:42] Total of 0 tRNA + rRNA features -[13:18:42] Searching for CRISPR repeats -[13:18:43] Found 0 CRISPRs -[13:18:43] Predicting coding sequences -[13:18:43] Contigs total 9808 bp, so using meta mode -[13:18:43] Running: prodigal -i Examples\/1\-res\-Annotate\/tmp_files\/genome1\.fst\-split5N\.fna\-prokkaRes\/EXAM\.0219\.00001\.fna -c -m -g 11 -p meta -f sco -q -[13:18:43] Found 11 CDS -[13:18:43] Connecting features back to sequences -[13:18:43] Not using genus-specific database. Try --usegenus to enable it. -[13:18:43] Annotating CDS, please be patient. -[13:18:43] Will use 1 CPUs for similarity searching. -[13:18:43] There are still 11 unannotated CDS left (started with 11) -[13:18:43] Will use blast to search against /Users/aperrin/Softwares/src/prokka/db/kingdom/Bacteria/sprot with 1 CPUs -[13:18:43] Running: cat Examples\/1\-res\-Annotate\/tmp_files\/genome1\.fst\-split5N\.fna\-prokkaRes\/sprot\.faa | parallel --gnu --plain -j 1 --block 1558 --recstart '>' --pipe blastp -query - -db /Users/aperrin/Softwares/src/prokka/db/kingdom/Bacteria/sprot -evalue 1e-06 -num_threads 1 -num_descriptions 1 -num_alignments 1 -seg no > Examples\/1\-res\-Annotate\/tmp_files\/genome1\.fst\-split5N\.fna\-prokkaRes\/sprot\.blast 2> /dev/null -[13:18:44] Deleting unwanted file: Examples/1-res-Annotate/tmp_files/genome1.fst-split5N.fna-prokkaRes/sprot.faa -[13:18:44] Deleting unwanted file: Examples/1-res-Annotate/tmp_files/genome1.fst-split5N.fna-prokkaRes/sprot.blast -[13:18:44] There are still 4 unannotated CDS left (started with 11) -[13:18:44] Will use hmmer3 to search against /Users/aperrin/Softwares/src/prokka/db/hmm/HAMAP.hmm with 1 CPUs -[13:18:44] Running: cat Examples\/1\-res\-Annotate\/tmp_files\/genome1\.fst\-split5N\.fna\-prokkaRes\/HAMAP\.hmm\.faa | parallel --gnu --plain -j 1 --block 459 --recstart '>' --pipe hmmscan --noali --notextw --acc -E 1e-06 --cpu 1 /Users/aperrin/Softwares/src/prokka/db/hmm/HAMAP.hmm /dev/stdin > Examples\/1\-res\-Annotate\/tmp_files\/genome1\.fst\-split5N\.fna\-prokkaRes\/HAMAP\.hmm\.hmmer3 2> /dev/null -[13:18:44] Deleting unwanted file: Examples/1-res-Annotate/tmp_files/genome1.fst-split5N.fna-prokkaRes/HAMAP.hmm.faa -[13:18:44] Deleting unwanted file: Examples/1-res-Annotate/tmp_files/genome1.fst-split5N.fna-prokkaRes/HAMAP.hmm.hmmer3 -[13:18:44] Labelling remaining 4 proteins as 'hypothetical protein' -[13:18:44] Possible /pseudo 'tRNA (guanine-N(1)-)-methyltransferase' at genome1_2 position 3427 -[13:18:44] Found 6 unique /gene codes. -[13:18:44] Fixed 2 duplicate /gene - trmD_1 trmD_2 -[13:18:44] Fixed 1 colliding /gene names. -[13:18:44] Adding /locus_tag identifiers -[13:18:44] Assigned 11 locus_tags to CDS and RNA features. -[13:18:44] Writing outputs to Examples/1-res-Annotate/tmp_files/genome1.fst-split5N.fna-prokkaRes/ -[13:18:44] Generating annotation statistics file -[13:18:44] Generating Genbank and Sequin files -[13:18:44] Running: tbl2asn -V b -a r10k -l paired-ends -M n -N 1 -y 'Annotated using prokka 1.14-dev from https://github.com/tseemann/prokka' -Z Examples\/1\-res\-Annotate\/tmp_files\/genome1\.fst\-split5N\.fna\-prokkaRes\/EXAM\.0219\.00001\.err -i Examples\/1\-res\-Annotate\/tmp_files\/genome1\.fst\-split5N\.fna\-prokkaRes\/EXAM\.0219\.00001\.fsa 2> /dev/null -[13:18:45] Deleting unwanted file: Examples/1-res-Annotate/tmp_files/genome1.fst-split5N.fna-prokkaRes/errorsummary.val -[13:18:45] Deleting unwanted file: Examples/1-res-Annotate/tmp_files/genome1.fst-split5N.fna-prokkaRes/EXAM.0219.00001.dr -[13:18:45] Deleting unwanted file: Examples/1-res-Annotate/tmp_files/genome1.fst-split5N.fna-prokkaRes/EXAM.0219.00001.fixedproducts -[13:18:45] Deleting unwanted file: Examples/1-res-Annotate/tmp_files/genome1.fst-split5N.fna-prokkaRes/EXAM.0219.00001.ecn -[13:18:45] Deleting unwanted file: Examples/1-res-Annotate/tmp_files/genome1.fst-split5N.fna-prokkaRes/EXAM.0219.00001.val -[13:18:45] Repairing broken .GBK output that tbl2asn produces... -[13:18:45] Running: sed 's/COORDINATES: profile/COORDINATES:profile/' < Examples\/1\-res\-Annotate\/tmp_files\/genome1\.fst\-split5N\.fna\-prokkaRes\/EXAM\.0219\.00001\.gbf > Examples\/1\-res\-Annotate\/tmp_files\/genome1\.fst\-split5N\.fna\-prokkaRes\/EXAM\.0219\.00001\.gbk -[13:18:45] Deleting unwanted file: Examples/1-res-Annotate/tmp_files/genome1.fst-split5N.fna-prokkaRes/EXAM.0219.00001.gbf -[13:18:45] Output files: -[13:18:45] Examples/1-res-Annotate/tmp_files/genome1.fst-split5N.fna-prokkaRes/EXAM.0219.00001.txt -[13:18:45] Examples/1-res-Annotate/tmp_files/genome1.fst-split5N.fna-prokkaRes/EXAM.0219.00001.tsv -[13:18:45] Examples/1-res-Annotate/tmp_files/genome1.fst-split5N.fna-prokkaRes/EXAM.0219.00001.fna -[13:18:45] Examples/1-res-Annotate/tmp_files/genome1.fst-split5N.fna-prokkaRes/EXAM.0219.00001.err -[13:18:45] Examples/1-res-Annotate/tmp_files/genome1.fst-split5N.fna-prokkaRes/EXAM.0219.00001.gff -[13:18:45] Examples/1-res-Annotate/tmp_files/genome1.fst-split5N.fna-prokkaRes/EXAM.0219.00001.sqn -[13:18:45] Examples/1-res-Annotate/tmp_files/genome1.fst-split5N.fna-prokkaRes/EXAM.0219.00001.tbl -[13:18:45] Examples/1-res-Annotate/tmp_files/genome1.fst-split5N.fna-prokkaRes/EXAM.0219.00001.gbk -[13:18:45] Examples/1-res-Annotate/tmp_files/genome1.fst-split5N.fna-prokkaRes/EXAM.0219.00001.log -[13:18:45] Examples/1-res-Annotate/tmp_files/genome1.fst-split5N.fna-prokkaRes/EXAM.0219.00001.ffn -[13:18:45] Examples/1-res-Annotate/tmp_files/genome1.fst-split5N.fna-prokkaRes/EXAM.0219.00001.faa -[13:18:45] Examples/1-res-Annotate/tmp_files/genome1.fst-split5N.fna-prokkaRes/EXAM.0219.00001.fsa -[13:18:45] Annotation finished successfully. -[13:18:45] Walltime used: 0.05 minutes -[13:18:45] If you use this result please cite the Prokka paper: -[13:18:45] Seemann T (2014) Prokka: rapid prokaryotic genome annotation. Bioinformatics. 30(14):2068-9. -[13:18:45] Type 'prokka --citation' for more details. -[13:18:45] Share and enjoy! diff --git a/Examples/1-res-Annotate/tmp_files/genome1.fst-split5N.fna-prokkaRes/EXAM.0219.00001.sqn b/Examples/1-res-Annotate/tmp_files/genome1.fst-split5N.fna-prokkaRes/EXAM.0219.00001.sqn deleted file mode 100644 index 3090e4316b98bf27b0d8f2e8d65566383ec6e0da..0000000000000000000000000000000000000000 --- a/Examples/1-res-Annotate/tmp_files/genome1.fst-split5N.fna-prokkaRes/EXAM.0219.00001.sqn +++ /dev/null @@ -1,1042 +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-dev 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 2 } , - { - label - str "day" , - data - int 12 } , - { - label - str "year" , - data - int 2019 } } } , - create-date - std { - year 2019 , - month 2 , - day 12 } } , - 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:2.6" } , - { - qual "inference" , - val "similar to AA sequence:UniProtKB:P00962" } } , - xref { - { - data - gene { - locus "glnS" , - locus-tag "GKEGNCBE_00001" } } } } , - { - 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:2.6" } , - { - qual "inference" , - val "similar to AA sequence:UniProtKB:P75820" } } , - xref { - { - data - gene { - locus "amiD" , - locus-tag "GKEGNCBE_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-dev 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 2 } , - { - label - str "day" , - data - int 12 } , - { - label - str "year" , - data - int 2019 } } } , - create-date - std { - year 2019 , - month 2 , - day 12 } } , - 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:2.6" } , - { - 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:2.6" } } , - 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:2.6" } , - { - qual "inference" , - val "similar to AA sequence:UniProtKB:P02915" } } , - xref { - { - data - gene { - locus "hisP" , - locus-tag "GKEGNCBE_00005" } } } } , - { - 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:2.6" } , - { - qual "inference" , - val "similar to AA sequence:UniProtKB:P0A873" } } , - xref { - { - data - gene { - locus "trmD_1" , - locus-tag "GKEGNCBE_00006" } } } } , - { - 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:2.6" } , - { - qual "inference" , - val "similar to AA sequence:UniProtKB:P0A873" } } , - xref { - { - data - gene { - locus "trmD_2" , - locus-tag "GKEGNCBE_00007" } } } } , - { - 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:2.6" } } , - 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:2.6" } } , - 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:2.6" } } , - 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:2.6" } , - { - qual "inference" , - val "similar to AA sequence:UniProtKB:O07838" } } , - xref { - { - data - gene { - locus "dctM" , - locus-tag "GKEGNCBE_00011" } } } } } } } } } } diff --git a/Examples/1-res-Annotate/tmp_files/genome1.fst-split5N.fna-prokkaRes/EXAM.0219.00001.tbl b/Examples/1-res-Annotate/tmp_files/genome1.fst-split5N.fna-prokkaRes/EXAM.0219.00001.tbl deleted file mode 100644 index bdd6ca8975f47bbc5faaa1b68bca20be27923aef..0000000000000000000000000000000000000000 --- a/Examples/1-res-Annotate/tmp_files/genome1.fst-split5N.fna-prokkaRes/EXAM.0219.00001.tbl +++ /dev/null @@ -1,71 +0,0 @@ ->Feature genome1_1 -213 1880 CDS - EC_number 6.1.1.18 - dbxref COG:COG0008 - gene glnS - inference ab initio prediction:Prodigal:2.6 - inference similar to AA sequence:UniProtKB:P00962 - locus_tag GKEGNCBE_00001 - product Glutamine--tRNA ligase -1916 2746 CDS - EC_number 3.5.1.28 - dbxref COG:COG3023 - gene amiD - inference ab initio prediction:Prodigal:2.6 - 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:2.6 - 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:2.6 - locus_tag GKEGNCBE_00004 - product hypothetical protein -1869 2642 CDS - dbxref COG:COG4598 - gene hisP - inference ab initio prediction:Prodigal:2.6 - 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 - dbxref COG:COG0336 - gene trmD_1 - inference ab initio prediction:Prodigal:2.6 - 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 - dbxref COG:COG0336 - gene trmD_2 - inference ab initio prediction:Prodigal:2.6 - 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:2.6 - locus_tag GKEGNCBE_00008 - product hypothetical protein -4818 5078 CDS - inference ab initio prediction:Prodigal:2.6 - locus_tag GKEGNCBE_00009 - product hypothetical protein -5117 5698 CDS - inference ab initio prediction:Prodigal:2.6 - locus_tag GKEGNCBE_00010 - product hypothetical protein -5717 7024 CDS - dbxref COG:COG1593 - gene dctM - inference ab initio prediction:Prodigal:2.6 - inference similar to AA sequence:UniProtKB:O07838 - locus_tag GKEGNCBE_00011 - product C4-dicarboxylate TRAP transporter large permease protein DctM diff --git a/Examples/1-res-Annotate/tmp_files/genome1.fst-split5N.fna-prokkaRes/EXAM.0219.00001.tsv b/Examples/1-res-Annotate/tmp_files/genome1.fst-split5N.fna-prokkaRes/EXAM.0219.00001.tsv deleted file mode 100644 index f71d90c382bab07dddd2ad815ac182c57bae9b46..0000000000000000000000000000000000000000 --- a/Examples/1-res-Annotate/tmp_files/genome1.fst-split5N.fna-prokkaRes/EXAM.0219.00001.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/1-res-Annotate/tmp_files/genome1.fst-split5N.fna-prokkaRes/EXAM.0219.00001.txt b/Examples/1-res-Annotate/tmp_files/genome1.fst-split5N.fna-prokkaRes/EXAM.0219.00001.txt deleted file mode 100644 index 9cd2780b0722866f0837937f638f91238d44ab84..0000000000000000000000000000000000000000 --- a/Examples/1-res-Annotate/tmp_files/genome1.fst-split5N.fna-prokkaRes/EXAM.0219.00001.txt +++ /dev/null @@ -1,4 +0,0 @@ -organism: Genus species strain -contigs: 2 -bases: 9808 -CDS: 11 diff --git a/Examples/1-res-Annotate/tmp_files/genome2.fst-split5N.fna b/Examples/1-res-Annotate/tmp_files/genome2.fst-split5N.fna deleted file mode 100644 index b7998dca8c972be06796a2c1298a23b43c0e2006..0000000000000000000000000000000000000000 --- a/Examples/1-res-Annotate/tmp_files/genome2.fst-split5N.fna +++ /dev/null @@ -1,8 +0,0 @@ ->this_is_genome_1 -ATGTCAGAAAATAAATTACACGTTATCGATTTGCACAAACGCTACGGCGGTCATGAAGTGCTGAAAGGGGTATCGCTGCAGGCCCGCGCCGGAGATGTGATTAGCATTATCGGCTCGTCCGGTTCCGGTAAAAGCACTTTTTTGCGCTGCATTAACTTCCTCGAAAAATCGAGCGAAGGCGCGATTATCGTGAACGGTCAGAACATTAATCTGGTGCGCGACAAAGACGGGCAGCTCAAAGTGGCGGATAAAAATCAGCTACGCTTGTTGCGTACCCGCCTGACGATGGTGTTTCAGCACTTTAACCTCTGGAACCACATGACGGTGCTGGAAAATGTGATGGAAGCGCCGATTCAGGTACTGGGATTAAGCAAGCACGACGCGCGCGAGCGGGCGTTGAAATATCTGGCGAAGGTGGGGATTGATGAGCGCGCTCAGGGCAAATATCCCGTCCATCTCTCCGGCGGCCAACAGCAGCGCGTTTCTATTGCGCGCGCGCTGGCGATGGAACCTGACGTTTTACTGTTCGATGAACCCACATCGGCGCTCGATCCTGAACTGGTCGGCGAAGTGTTGCGCATCATGCAACAACTGGCGGAAGAAGGCAAAACGATGGTGGTGGTCACGCATGAAATGGGCTTCGCCCGCCATGTCTCTTCGCACGTGATTTTTCTGCATCAGGGGAAAATTGAAGAAGAGGGCAATCCGGAGCAGGTGTTCGGCAATCCGCAAAGCCCGCGTTTACAGCAATTCCTGAAAGGCTCGCTGAAATAAACGCTAGAGGACGCGCCTCTCAGAGAGCGCGCTCTCTCAGAGAGGCGCGCGCCTCTTTCGCAGAGACCNNCGCTCATGAGCGATGCCCGCGACTAAATTCTCCCGACGTACCCTCCTGACGGCAGGTTCCGCGCTTGCTGTTCTTCCTTTTCTGCGCGCCTTGCCGGTACAGGCGCGTGAACCTCGCCAGACCGTCGATATTAAGGATTATCCGGCGGATGACGGTATCGCCTCGTTCAAACAGGCCTTCGCCGACGGGCAGACTGTGGTCGTGCCGTCAGGATGGGTGTGTGAAAATATCAATGCGGCGATAACGATTCCGGCGGGAAAAACGCTGCGGATACAGGGCGCGGTGCGTGGGAATGGCCGGGGACGGTTTATTTTGCTGGACGGGTGTCAGGTGGTGGGGGAGCAGGGCGGCAGTCTGCACAATGTGACGCTGGATGTTCGCGGGTCGGACTGTGTGATTAAAGGCGTGACGATGAGCGGCTTTGGCCCCGTCGCGCAAATTTTCATCGGCGGTAAGGAACCGCAGGTGATGCGTAATCTCATTATCGATGACATCACCGTTACCCACGCCAACTACGCCATTCTCCGCCAGGGATTTCATAACCAAATGGACGGCGCGCGGATTACGCATAGTCGCTTTAGCGATTTGCAGGGGGACGCCATTGAGTGGAATGTCGCGATTCATGACCGCGACATCCTGATTTCCGATCATGTCATCGAACGCATTGATTGTACCAATGGCAAAATCAACTGGGGGATCGGCATCGGGCTGGCGGGTAGCGCCTATGACAATAGTTATCCTGAAGACCAGGCAGTAAAAAACTTTGTGGTGGCCAATATTACCGGATCTGATTGCCGACAACTGGTACACGTAGAAAATGGCAAACATTTCGTCATTCGCAATGTCAAAGCCAAAAACATCACGCCCGATTTCAGTAAAAATGCGGGTATTGATAACGCAACGATCGCCATTTATGGCTGTGATAATTTCGTCATTGATAATATTGATATGACGAATAGTGCCGGGATGCTCATCGGCTATGGCGTCGTTAAAGGAAAATACCTGTCAATTCCGCAAAACTTTAAATTAAACGCTATTCGGTTGGATAATCGCCAGGTTGCTTATAAATTACGCGGCATTCAAATTTCCTCCGGTAACGCCCCCTCATTTGTTGCCATCACCAATGTACGGATGACGCGTGCTACGCTGGAACTGCATAATCAACCGCAGCACCTCTTTTTGCGTAATATCAACGTGATGCAAACTTCAGCGATTGGCCCGGCGTTAAAAATGCATTTTGATTTGCGTAAAGATGTCCGTGGTCAATTTATGGCCCGCCAGGACACGCTGCTTTCCCTCGCTAATGTTCATGCCATCAATGAAAACGGGCAGAGTTCCGTGGATATCGACAGGATTAATCACCAAACCGTGAATGTCGAAGCAGTGAATTTTTCGCTGCCGAAGCGGGGAGGGTAACACTCGCGCATAGAGAGCTCTCAGAGGAGCGCGCGCGCTATAGCGCGC ->this_is_genome_2 -CGCGATAATATAGCGCGCGCTCATAGCATGAGCGCGCTATTTCTGGCCATCCCGTTAACCATTTTTGTGTTGTTTGTGTTACCGATTTGGCTGTGGCTGCATTACAGCAACCGCGCCGGTCGGGGAGAACTGTCGCAAAGCGAGCAGCAACGCTTACTGCAACTCACAGACGACGCGCAACGTATGCGCGAGCGCATTCAGGCGCTGGAAGATATTCTTGATGCAGAGCATCCGAACTGGAGAGAGCGCTAACGCCATATTATAGCGCGCCTCATAAGAGCGGCCTATAGCGCGCTANNNATGCCGCACTTTATTGCTGAATGTACTGAAAATATTCGCGAGCAGGCTGATTTACCAAGCCTGTTCAGCAAGGTAAACGAGGCGCTGGCCGCCACCGGGATTTTCCCCATCGGCGGTATCCGCAGTCGCGCCCACTGGCTGGATACCTGGCAGATGGCTGACGGTAAGCATGATTACGCGTTTGTGCATATGACGCTGAAAATCGGCGCCGGGCGCAGCCTGGAGAGCCGTCAGGAAGTCGGCGAAATGCTGTTTGGGCTGATTAAAGCCCACTTCGCCGACCTGATGGAGAACCGCTATCTGGCGCTGTCGTTTGAGATTGCCGAGTTACATCCAACGCTCAATTACAAACAAAACAACGTACACGCGTTATTTAAATAGCCAGAGATTCGCGCGTTCAGAGAGGAGCTCTCTCATAGACGCGCGCATATGCGCTCTAGAGAGGCGCGCCTAATGGCGCGCTATGATGAAAGCGCTACTGTGGCTGGTTGGTCTCGCGTTGCTGTTAACAGGCTGCGCGAGCGAAAAAGGAATTATCGATAAAGAGGGATATCAGCTTGATACCCGACATCGGGCGCAGGCGGCCTATCCGCGCATTAAAGTCCTGGTGATTCACTATACGGCGGAAAACTTTGACGTTTCGCTGGCGACGTTAACGGGTCGCAACGTCAGTTCGCATTACCTGATTCCCGCAACCCCGCCATTATATGGCGGTAAACCGCGCATCTGGCAACTGGTGCCGGAACAGGATCAGGCTTGGCATGCGGGCGTCAGTTTCTGGCGAGGCGCCACGCGTCTCAATGATACGTCTATTGGCATTGAGCTGGAAAATCGCGGCTGGCGAATGTCCGGCGGGGTGAAATCTTTCGCGCCGTTTGAATCCGCGCAAATTCAGGCATTGATCCCGTTAGCGAAGGACATTATCGCGCGCTATGACATCAAACCGCAGAATGTGGTGGCCCATGCGGATATCGCGCCGCAGCGTAAAGACGATCCCGGCCCGCGCTTCCCGTGGCGCGAGCTGGCGGCACAGGGGATTGGCGCCTGGCCTGACGCCCAGCGTGTGGCGTTTTATCTGGCTGGACGCGCGCCGTATACGCCAGTCGATACCGCAACGGTGCTTGCGTTACTCTCGCGCTATGGCTATGAAGTCAAAGCCGATATGACGGCGCGCGAGCAACAGCGGGTGATTATGGCGTTCCAGATGCACTTCCGTCCGGCGCAATGGAACGGTATCGCAGATGCCGAAACGCAGGCGATTGCCGAAGCATTACTGGAGAAGTACGGCCAGGATTAACAAAGCGCTCTCAGAGAGAGCGCTCTGCAGATGAGTGAGGCTGAAGCCCGCCCGACTAACTTTATTCGTCAGATTATTGATGAAGATCTGGCGAGTGGTAAACATACCACTGTCCATACCCGTTTTCCGCCGGAGCCGAATGGCTATCTGCACATCGGCCACGCGAAATCTATCTGCCTGAACTTTGGCATCGCGCAAGATTATCAGGGCCAGTGCAACCTGCGTTTCGATGACACCAACCCGGTAAAAGAAGATATCGAGTACGTTGATTCGATCAAAAACGACGTCGAGTGGTTAGGCTTTCACTGGTCTGGCGATATTCGCTACTCCTCCGATTACTTTGACCAACTGCACGCCTATGCGGTCGAGCTCATCAATAAAGGCCTGGCCTACGTTGATGAGCTGACGCCGGAGCAGATCCGCGAATACCGTGGTACGCTGACCGCGCCGGGTAAAAACAGCCCGTTCCGCGATCGCAGCGTGGAAGAAAACCTCGCGCTATTTGAAAAAATGCGTACCGGCGGTTTTGAAGAGGGTAAAGCCTGTCTGCGCGCTAAAATCGACATGGCGTCGCCGTTTATCGTGATGCGCGATCCGGTGCTGTATCGCATTAAATTCGCCGAGCATCATCAGACCGGCACGAAGTGGTGCATCTATCCGATGTACGACTTTACTCACTGCATCAGCGATGCGCTGGAAGGCATTACTCATTCTCTGTGTACGCTGGAGTTCCAGGACAACCGTCGTCTGTACGACTGGGTGCTGGACAACATCACCATTCCGGTTCACCCGCGCCAGTACGAATTCTCGCGCCTGAATCTGGAATACACCGTGATGTCCAAGCGTAAGCTGAACCTGCTGGTGACCGACAAACACGTCGAAGGTTGGGATGATCCGCGTATGCCGACTATTTCCGGTCTGCGCCGTCGCGGCTATACCGCGGCTTCTATTCGTGAGTTCTGCAAACGCATCGGCGTCACCAAGCAGGACAACACTATTGAGATGGCGTCGCTGGAATCCTGCATTCGCGAAGATCTGAACGAAAACGCGCCGCGCGCGATGGCGGTAATCGATCCGGTAAAACTGGTTATCGAAAACTACCCGCAGGGCGAGAGCGAAATGGTTACCATGCCTAACCATCCGAATAAACCGGAGATGGGCAGCCGTGAAGTGCCGTTTAGCGGTGAGATCTGGATCGATCGCGCGGATTTCCGCGAAGAAGCGAACAAACAGTACAAACGTCTGGTGATGGGCAAAGAAGTGCGTCTGCGTAATGCCTACGTCATTAAAGCGGAGCGCGTAGAGAAGGATGCCGAAGGGAATATCACCACCATCTTCTGTACCTATGATGCTGATACGCTGAGTAAAGATCCGGCTGACGGGCGTAAAGTGAAAGGCGTAATCCACTGGGTTAGCGTAGCACATGCGCTGCCGATTGAAATTCGTCTCTACGACCGTCTGTTCAGCGTGCCGAACCCGGGCGCCGCGGAGGACTTCCTGTCTGTTATCAACCCCGAATCATTAGTGATTAAGCAGGGGTATGGCGAGCCGTCGCTGAAAGCGGCGGTAGCAGGGAAAGCTTTCCAGTTTGAACGTGAAGGTTACTTCTGCCTTGACAGCCGCTATGCAACGGCCGATAAGCTGGTCTTTAACCGCACCGTGGGCCTGCGTGATACCTGGGCGAAAGCGGGCGAATAA ->this_is_genome_3 -ACGCGCTATAGGGCTCTCAGAGAGTCTCAGTGTTTATTGGCATCGTTAGCCTGTTTCCTGAAATGTTCCGCGCAATTACCGATTACGGGGTAACTGGCCGGGCAGTAAAAAAAGGCCTGCTGAACATCCAAAGCTGGAGTCCTCGCGACTTCGCGCATGACCGGCACCGTACCGTGGACGACCGTCCTTACGGCGGCGGACCGGGGATGTTAATGATGGTGCAACCCTTGCGGGACGCCATTCATGCAGCAAAAGCCGCGGCAGGTGAAGGCGCTAAAGTGATTTATCTGTCGCCTCAGGGACGCAAGCTTGATCAAGCGGGCGTTAGCGAGCTGGCCACGAATCAGAAACTCATTCTGGTGTGTGGTCGCTACGAAGGCGTAGATGAGCGCGTAATTCAGGCCGAAATTGACGAAGAATGGTCAATTGGCGATTACGTTCTCAGCGGTGGCGAACTACCGGCAATGACGCTGATTGACTCCGTCGCCCGGTTTATACCGGGGGTTCTGGGGCATGAGGCATCAGCAATCGAAGATTCGTTTGCTGATGGGTTGCTGGATTGTCCGCACTATACGCGCCCTGAAGTGTTAGAGGGGATGGAAGTACCGCCAGTATTGCTGTCGGGAAACCATGCTGAGATACGTCGCTGGCGTTTGAAACAGTCACTGGGCCGAACCTGGCTTAGAAGACCTGAACTTCTGGAAAACCTGGCTCTGACTGAAGAGCAAGCAAGGTTGCTGGCGGAGTTCAAAACAGAACACGCACAACAGCAGCATAAACATGATGGGATGGCATAGCGAGATCGCGCATAGCGCGCGGCGAGATCCGCGAGACATGAATAATCATTTTGGGAAAGGGTTAATGGCCGGGTTGCACGCGCCATATGCATATAGCGCGCATCATGCGGTGAATTTCTGTTCTGAGTATAAACGTGGCTTTGTATTGGGTTTTACACACCGTATGTTCGAAAAGACCGGCGATCGTCAACTTAGCGCGTGGGAGGCCGGAATTCTGACGCGTCGCTATGGTCTGGATAAAGAAATGGTGATGGATTTCTTTAAAGAGAATCATTCCGGGATGGCGGTTCGCTTCTTTATGGCTGGTTATCGACTCGAAGGTTGAACGCCTCTAGAGCGCTAGAGGCGCGCGCGATATACGCGGCGCGAGACATGTCTACGCTTCTCTATTTGCACGGATTCAACAGTTCCCCTCGCTCGGCAAAAGCGTGCCAGCTAAAAAACTGGCTGGCGGAGCGTCATCCGCATGTTGAGATGATCGTCCCTCAACTGCCGCCGTATCCTGCCGATGCGGCGGAGTTGCTGGAATCTCTCGTACTTGAGCATGGCGGTGCGCCATTAGGGCTGGTAGGATCGTCGCTGGGTGGTTATTACGCCACCTGGCTGTCGCAATGTTTTATGCTGCCGGCTGTGGTGGTGAATCCCGCCGTGCGGCCCTTTGAATTACTGACCGACTATCTCGGTCAGAACGAGAACCCCTACACCGGGCAGCAATATGTGCTAGAGTCTCGCCATATTTATGATCTTAAAGTCATGCAGATTGACCCGCTGGAAGCGCCGGACCTGATCTGGCTACTGCAACAGACGGGCGATGAAGTGCTGGATTACCGCCAGGCGGTGGCATATTACGCCTCCTGCCGTCAGACAGTGACCGAGGGGGGTAATCACGCATTCACGGGCTTCGAAGATTATTTCAACCAGATTGTCGATTTTCTTGGACTGCACAGTTGCTGACCGGATATACGCGCGCGCGCTATATAGCGCGCGCGGCGATATAGCGCATGAAGTTTGTTGCGCCAGAACAGGCACCGGAACAGGCGGAAATCATCAGAAATACGCCGTTCTGGCCTGATGTGGACCTGTCGGAGTTTCGCAGCATGATGCGCACTGATGGCACGGTGACGCAGCCGCGTTTAAAGCAGGTTGCGCTGTCGGCAATTTCGGAGGTCAACGCAGAGCTGTATGAGTTTCGCAGACGCCAGCAGATGCTGGGGTATGCCTCGCTGGCAGAAGTCCCGGCGGAACAACTGGACGGCAAAAGCGAGCGCATTCAGCACTATTTCAACGCGGTTTACTGCTGGGCACGCGCCATGCTCAACGAACGTTACCAGGACTATGACGCCACGGCATCCGGTGTGAAGCGGGGCGAAGAACTGGCAGAAGCCAGCGGTGATTTGTGGCGTGACGCCCGCTGGGCCATCAGCCGGGTGCAGGATGCGCCGCACTGCACAGTGGAGCTTATCTGA ->this_is_genome_4 -ATGATTGACCCTATTTTTGCGTCCTGTACGCTAATTGCCGTCTTTGTTGTTTTACTGGCCATGGGCGCGCCTATCGGGATCTGCATCGTTATCGCCTCTTTCAGCACCATGATGCTGGTACTGCCTTTCGATATTTCGATGTTCGCCACCGCGCAAAAAATGTTCTCCAGCCTGGACAGTTTTGCCTTGCTGGCCGTGCCGTTCTTCGTTTTGTCCGGGGTGATCATGAATAGCGGGGGAATTGCCGCCCGACTGGTCAATTTTGCCAAACTGTTTACTGGCAAACTGCCCGGCTCGCTCTCTTACACCAACATCGTCGGCAATATGATGTTCGGTGCAATTTCCGGATCGGCGATTGCCGCCTCAACCTCTATCGGCGGCGTGATGGTGCCGATGAGCGCGCGCGAAGGTTACGATCGCGGTTTTGCGGCCGCGGTGAATATCGCCTCCGCGCCGACGGGAATGTTAATTCCGCCCACCACGGCTTTTATCCTTTATGCGCTGGCAAGCGGGGGAACATCGATTGCCGCTCTGTTCGCCGGCGGTCTGGTCGCGGGAGTGCTGTGGGGCGTTGGCTGTATGCTGGTCACGCTGGTGGTCGCTAAGCGTCGAAATTATCGGGTTTTCTTCACCGTCCAAAAAGGCATGGCGCTAAAAGTTGCCGTTGAGGCCATTCCCAGCCTGTTACTGATCGTGATTATTGTCGGCGGCATTGTGCAGGGGATTTTCACCGCCATTGAAGCCTCCGCGATTGCCGTGGTGTATACGTTATTGCTGACGATAGTGTTTTACCGCACGCTGAAAATTAAGGATTTGCCTTCGATTTTGCTCCAGACAGTGGTAATGACCGGGGTCATCATGTTCCTGCTGGCAACCTCTTCGGCGATGTCCTTCTCGATGTCGATCACCAATATTCCTGCGGCGCTGAGCGATATGATCCTCGGTATTTCCGCCAATAAACTGGTTATCCTGTTAGTCATTACCGTCTTTTTGTTGATTATCGGCGCATTTATGGATATCGGTCCGGCCATTCTGATTTTTACCCCGATTCTGCTGCCGATTATGACTAAACTGGGCGTCGATCCGGTGCATTTCGGCATTATCATGATCTATAACCTGGCGATAGGCACCATTACGCCGCCAGTTGGCAGTGGTTTATATGTCGGGGCGAGCGTCGGTAAGGTCAAAGTTGAGGACGTTATCAAACCGTTGATGCCTTTTTACGGCGCGATTATCGGCGTTCTGTTATTAATTACCTACATTCCGGAAATCACACTGTTTTTACCCCGTCTACTGGGCATCATGTAAACGCTCATAGGCGGCGCGCGCGCTCTCAGGAATGAAGTTTGTTGCGCCAGAACAGGCACCGGAACAGGCGGAGGTCATCAAAAATACGCCGTTCTGGCCTGATGTGAACCTGTCGGAATTTCGCAGTGTGATGCGCACTGACGGCACGGTGACGCAGCCGCGTTTAAAGCAGGTCGTGCTGACGGCGATCTCTGAGGTTAACGCTGAGCTGTACGACTTCCGCAACCGTCAGCAGATGCTGGGCTGGCGGACACTTGCTGAGGTTCCCGCAGAAATGCTGGACGGTAAAAGCGAGCGTATCCGGCACTACCACAACGCTGTTTTTTGCTGGGCGCGCGCTGTGCTTAATGAGCGTTATCAGGACTATGACGCCACGGCGTCAGGCGTGAAGCGAGGGGAGGAGCTGGCGGAGGCCAGCGGCGATCTGTGGCGTGATGCCCGCTGGGCCATCAGCCGGGTGCAGGATGCACCGCACTGTACGGTGGAGCTTATCTGACGCTCATAGGCGCGCGCTCATAGCGCGATGGAAACAAATATTACCTGGCAACAATTGATAGATGAATATTTCTTCGCAAAACCTCTGCGCTCAGCATCTGAATGGAGTTACACCAAAGTCTTCAAATCATTTGTACATTATATGGGGCCGTTAAGCTGCCCTAATGATGTGACATATCACAAAGTGCTTGCCTGGCGCCGTTTTCTTTTAAAAGAGAAAAAGCTGTCCGGACGTACCTGGAATAACAAGGTGGCGCATATGCGGGCCATCTTTAACTACGGAATACAGCGAGGGTTACTGCACTATGACGAAAATCCGTTTAACAATTCGGTAGTTAAACCGGACAAGAAGAGAAAGAAAACGCTCACTCAGGCACAGATTGAGTATGCCTATCAGATCATGGAGCAGTATGAAAATCAGGAGAATACAGGGCTGGGACTGAAATATTCCCGCTGCGCCTTATTTCCTGCATGGTTCTGGCTCACTGTCCTGGATACGCTCTATTACACAGGGATACGTCAGAACCAGTTATTACATATTCGGCTGAATGATGTTGATTTGAGAGAAGGGCAGATTCGGCTGATTACGGAGGGGTGTAAAAATCACAAAGAACACTATGTGCCGGTGATCAGTTTTCTGCGTCCACGGCTGACCTGTTTAATGGAGAAAGCGCAGAGCGAAGGATTGAAAGGTAATGACCGCCTGTTCAATATTGCACTTTTTACCGGCAAAGATCCCGCCATTGGCGATGACATGGATTCTCCTCAGGTAAGAGCATTCTTCCGTCGTCTGTCCAAGGAGTGTCAGTTTGCGATCAGTCCTCATCGTTTCAGACACACGCTGGCCACGGAGATGATGAAAATGCCGGAACAGAATCTGCATATGGCGCAAAGTGTGCTGGGTCATTCAAACATGAAATCCACGCTGGAGTATGTGGAGAATGATATTGCAGTGATGGGGAGGGCTCTGGAAGCGCAGTTTATGCAGATTAAGGCAGCACATGCCCGAAGCATTTACAGTGGGTTGACAAAGAATAGATAA diff --git a/Examples/1-res-Annotate/tmp_files/genome2.fst-split5N.fna-prokka.log b/Examples/1-res-Annotate/tmp_files/genome2.fst-split5N.fna-prokka.log deleted file mode 100644 index 4e555a8670fed1a2ffe74b977bb3d5ef3b2fa5ba..0000000000000000000000000000000000000000 --- a/Examples/1-res-Annotate/tmp_files/genome2.fst-split5N.fna-prokka.log +++ /dev/null @@ -1,119 +0,0 @@ -[13:18:45] This is prokka 1.14-dev -[13:18:45] Written by Torsten Seemann <torsten.seemann@gmail.com> -[13:18:45] Homepage is https://github.com/tseemann/prokka -[13:18:45] Local time is Tue Feb 12 13:18:45 2019 -[13:18:45] You are aperrin -[13:18:45] Operating system is darwin -[13:18:45] You have BioPerl 1.006924 -[13:18:45] System has 8 cores. -[13:18:45] Will use maximum of 1 cores. -[13:18:45] Annotating as >>> Bacteria <<< -[13:18:45] Generating locus_tag from 'Examples/1-res-Annotate/tmp_files/genome2.fst-split5N.fna' contents. -[13:18:45] Setting --locustag OHLPOIIB from MD5 8159822bce92b47adcc120629558b9c6 -[13:18:45] Creating new output folder: Examples/1-res-Annotate/tmp_files/genome2.fst-split5N.fna-prokkaRes -[13:18:45] Running: mkdir -p Examples\/1\-res\-Annotate\/tmp_files\/genome2\.fst\-split5N\.fna\-prokkaRes -[13:18:45] Using filename prefix: GEN2.0219.00001.XXX -[13:18:45] Setting HMMER_NCPU=1 -[13:18:45] Writing log to: Examples/1-res-Annotate/tmp_files/genome2.fst-split5N.fna-prokkaRes/GEN2.0219.00001.log -[13:18:45] Command: /usr/local/bin/prokka --outdir Examples/1-res-Annotate/tmp_files/genome2.fst-split5N.fna-prokkaRes --cpus 1 --prefix GEN2.0219.00001 Examples/1-res-Annotate/tmp_files/genome2.fst-split5N.fna -[13:18:45] Appending to PATH: /Users/aperrin/Softwares/src/prokka/bin/../binaries/darwin -[13:18:45] Appending to PATH: /Users/aperrin/Softwares/src/prokka/bin/../binaries/darwin/../common -[13:18:45] Appending to PATH: /Users/aperrin/Softwares/src/prokka/bin -[13:18:45] Looking for 'aragorn' - found /Users/aperrin/Softwares/src/prokka/bin/../binaries/darwin/aragorn -[13:18:45] Determined aragorn version is 1.2 -[13:18:45] Looking for 'barrnap' - found /usr/local/bin/barrnap -[13:18:45] Determined barrnap version is 0.8 -[13:18:45] Looking for 'blastp' - found /Users/aperrin/Softwares/bin/blastp -[13:18:45] Determined blastp version is 2.3 -[13:18:45] Looking for 'cmpress' - found /usr/local/bin/cmpress -[13:18:45] Determined cmpress version is 1.1 -[13:18:45] Looking for 'cmscan' - found /usr/local/bin/cmscan -[13:18:45] Determined cmscan version is 1.1 -[13:18:45] Looking for 'egrep' - found /usr/bin/egrep -[13:18:45] Looking for 'find' - found /usr/bin/find -[13:18:45] Looking for 'grep' - found /usr/bin/grep -[13:18:45] Looking for 'hmmpress' - found /Users/aperrin/Softwares/src/prokka/bin/../binaries/darwin/hmmpress -[13:18:45] Determined hmmpress version is 3.1 -[13:18:45] Looking for 'hmmscan' - found /usr/local/bin/hmmscan -[13:18:45] Determined hmmscan version is 3.1 -[13:18:45] Looking for 'java' - found /usr/bin/java -[13:18:45] Looking for 'less' - found /usr/bin/less -[13:18:45] Looking for 'makeblastdb' - found /Users/aperrin/Softwares/bin/makeblastdb -[13:18:45] Determined makeblastdb version is 2.3 -[13:18:45] Looking for 'minced' - found /Users/aperrin/Softwares/src/prokka/bin/../binaries/darwin/../common/minced -[13:18:45] Determined minced version is 2.0 -[13:18:45] Looking for 'parallel' - found /usr/local/bin/parallel -[13:18:45] Determined parallel version is 20181022 -[13:18:45] Looking for 'prodigal' - found /usr/local/bin/prodigal -[13:18:45] Determined prodigal version is 2.6 -[13:18:45] Looking for 'prokka-genbank_to_fasta_db' - found /Users/aperrin/Softwares/src/prokka/bin/prokka-genbank_to_fasta_db -[13:18:45] Looking for 'sed' - found /usr/bin/sed -[13:18:45] Looking for 'tbl2asn' - found /Users/aperrin/Softwares/src/prokka/bin/../binaries/darwin/tbl2asn -[13:18:45] Determined tbl2asn version is 25.6 -[13:18:45] Using genetic code table 11. -[13:18:45] Loading and checking input file: Examples/1-res-Annotate/tmp_files/genome2.fst-split5N.fna -[13:18:45] Wrote 4 contigs totalling 10711 bp. -[13:18:45] Predicting tRNAs and tmRNAs -[13:18:45] Running: aragorn -l -gc11 -w Examples\/1\-res\-Annotate\/tmp_files\/genome2\.fst\-split5N\.fna\-prokkaRes\/GEN2\.0219\.00001\.fna -[13:18:45] Found 0 tRNAs -[13:18:45] Predicting Ribosomal RNAs -[13:18:45] Running Barrnap with 1 threads -[13:18:45] Found 0 rRNAs -[13:18:45] Skipping ncRNA search, enable with --rfam if desired. -[13:18:45] Total of 0 tRNA + rRNA features -[13:18:45] Searching for CRISPR repeats -[13:18:46] Found 0 CRISPRs -[13:18:46] Predicting coding sequences -[13:18:46] Contigs total 10711 bp, so using meta mode -[13:18:46] Running: prodigal -i Examples\/1\-res\-Annotate\/tmp_files\/genome2\.fst\-split5N\.fna\-prokkaRes\/GEN2\.0219\.00001\.fna -c -m -g 11 -p meta -f sco -q -[13:18:46] Found 13 CDS -[13:18:46] Connecting features back to sequences -[13:18:46] Not using genus-specific database. Try --usegenus to enable it. -[13:18:46] Annotating CDS, please be patient. -[13:18:46] Will use 1 CPUs for similarity searching. -[13:18:46] There are still 13 unannotated CDS left (started with 13) -[13:18:46] Will use blast to search against /Users/aperrin/Softwares/src/prokka/db/kingdom/Bacteria/sprot with 1 CPUs -[13:18:46] Running: cat Examples\/1\-res\-Annotate\/tmp_files\/genome2\.fst\-split5N\.fna\-prokkaRes\/sprot\.faa | parallel --gnu --plain -j 1 --block 1697 --recstart '>' --pipe blastp -query - -db /Users/aperrin/Softwares/src/prokka/db/kingdom/Bacteria/sprot -evalue 1e-06 -num_threads 1 -num_descriptions 1 -num_alignments 1 -seg no > Examples\/1\-res\-Annotate\/tmp_files\/genome2\.fst\-split5N\.fna\-prokkaRes\/sprot\.blast 2> /dev/null -[13:18:47] Deleting unwanted file: Examples/1-res-Annotate/tmp_files/genome2.fst-split5N.fna-prokkaRes/sprot.faa -[13:18:47] Deleting unwanted file: Examples/1-res-Annotate/tmp_files/genome2.fst-split5N.fna-prokkaRes/sprot.blast -[13:18:47] There are still 5 unannotated CDS left (started with 13) -[13:18:47] Will use hmmer3 to search against /Users/aperrin/Softwares/src/prokka/db/hmm/HAMAP.hmm with 1 CPUs -[13:18:47] Running: cat Examples\/1\-res\-Annotate\/tmp_files\/genome2\.fst\-split5N\.fna\-prokkaRes\/HAMAP\.hmm\.faa | parallel --gnu --plain -j 1 --block 521 --recstart '>' --pipe hmmscan --noali --notextw --acc -E 1e-06 --cpu 1 /Users/aperrin/Softwares/src/prokka/db/hmm/HAMAP.hmm /dev/stdin > Examples\/1\-res\-Annotate\/tmp_files\/genome2\.fst\-split5N\.fna\-prokkaRes\/HAMAP\.hmm\.hmmer3 2> /dev/null -[13:18:48] Deleting unwanted file: Examples/1-res-Annotate/tmp_files/genome2.fst-split5N.fna-prokkaRes/HAMAP.hmm.faa -[13:18:48] Deleting unwanted file: Examples/1-res-Annotate/tmp_files/genome2.fst-split5N.fna-prokkaRes/HAMAP.hmm.hmmer3 -[13:18:48] Labelling remaining 5 proteins as 'hypothetical protein' -[13:18:48] Found 8 unique /gene codes. -[13:18:48] Fixed 0 colliding /gene names. -[13:18:48] Adding /locus_tag identifiers -[13:18:48] Assigned 13 locus_tags to CDS and RNA features. -[13:18:48] Writing outputs to Examples/1-res-Annotate/tmp_files/genome2.fst-split5N.fna-prokkaRes/ -[13:18:48] Generating annotation statistics file -[13:18:48] Generating Genbank and Sequin files -[13:18:48] Running: tbl2asn -V b -a r10k -l paired-ends -M n -N 1 -y 'Annotated using prokka 1.14-dev from https://github.com/tseemann/prokka' -Z Examples\/1\-res\-Annotate\/tmp_files\/genome2\.fst\-split5N\.fna\-prokkaRes\/GEN2\.0219\.00001\.err -i Examples\/1\-res\-Annotate\/tmp_files\/genome2\.fst\-split5N\.fna\-prokkaRes\/GEN2\.0219\.00001\.fsa 2> /dev/null -[13:18:48] Deleting unwanted file: Examples/1-res-Annotate/tmp_files/genome2.fst-split5N.fna-prokkaRes/errorsummary.val -[13:18:48] Deleting unwanted file: Examples/1-res-Annotate/tmp_files/genome2.fst-split5N.fna-prokkaRes/GEN2.0219.00001.dr -[13:18:48] Deleting unwanted file: Examples/1-res-Annotate/tmp_files/genome2.fst-split5N.fna-prokkaRes/GEN2.0219.00001.fixedproducts -[13:18:48] Deleting unwanted file: Examples/1-res-Annotate/tmp_files/genome2.fst-split5N.fna-prokkaRes/GEN2.0219.00001.ecn -[13:18:48] Deleting unwanted file: Examples/1-res-Annotate/tmp_files/genome2.fst-split5N.fna-prokkaRes/GEN2.0219.00001.val -[13:18:48] Repairing broken .GBK output that tbl2asn produces... -[13:18:48] Running: sed 's/COORDINATES: profile/COORDINATES:profile/' < Examples\/1\-res\-Annotate\/tmp_files\/genome2\.fst\-split5N\.fna\-prokkaRes\/GEN2\.0219\.00001\.gbf > Examples\/1\-res\-Annotate\/tmp_files\/genome2\.fst\-split5N\.fna\-prokkaRes\/GEN2\.0219\.00001\.gbk -[13:18:48] Deleting unwanted file: Examples/1-res-Annotate/tmp_files/genome2.fst-split5N.fna-prokkaRes/GEN2.0219.00001.gbf -[13:18:48] Output files: -[13:18:48] Examples/1-res-Annotate/tmp_files/genome2.fst-split5N.fna-prokkaRes/GEN2.0219.00001.gff -[13:18:48] Examples/1-res-Annotate/tmp_files/genome2.fst-split5N.fna-prokkaRes/GEN2.0219.00001.tbl -[13:18:48] Examples/1-res-Annotate/tmp_files/genome2.fst-split5N.fna-prokkaRes/GEN2.0219.00001.sqn -[13:18:48] Examples/1-res-Annotate/tmp_files/genome2.fst-split5N.fna-prokkaRes/GEN2.0219.00001.fna -[13:18:48] Examples/1-res-Annotate/tmp_files/genome2.fst-split5N.fna-prokkaRes/GEN2.0219.00001.tsv -[13:18:48] Examples/1-res-Annotate/tmp_files/genome2.fst-split5N.fna-prokkaRes/GEN2.0219.00001.err -[13:18:48] Examples/1-res-Annotate/tmp_files/genome2.fst-split5N.fna-prokkaRes/GEN2.0219.00001.txt -[13:18:48] Examples/1-res-Annotate/tmp_files/genome2.fst-split5N.fna-prokkaRes/GEN2.0219.00001.fsa -[13:18:48] Examples/1-res-Annotate/tmp_files/genome2.fst-split5N.fna-prokkaRes/GEN2.0219.00001.faa -[13:18:48] Examples/1-res-Annotate/tmp_files/genome2.fst-split5N.fna-prokkaRes/GEN2.0219.00001.log -[13:18:48] Examples/1-res-Annotate/tmp_files/genome2.fst-split5N.fna-prokkaRes/GEN2.0219.00001.ffn -[13:18:48] Examples/1-res-Annotate/tmp_files/genome2.fst-split5N.fna-prokkaRes/GEN2.0219.00001.gbk -[13:18:48] Annotation finished successfully. -[13:18:48] Walltime used: 0.05 minutes -[13:18:48] If you use this result please cite the Prokka paper: -[13:18:48] Seemann T (2014) Prokka: rapid prokaryotic genome annotation. Bioinformatics. 30(14):2068-9. -[13:18:48] Type 'prokka --citation' for more details. -[13:18:48] Share and enjoy! diff --git a/Examples/1-res-Annotate/tmp_files/genome2.fst-split5N.fna-prokkaRes/GEN2.0219.00001.err b/Examples/1-res-Annotate/tmp_files/genome2.fst-split5N.fna-prokkaRes/GEN2.0219.00001.err deleted file mode 100644 index d2f6f3262c91bdc696d481b4c91e4962e933b261..0000000000000000000000000000000000000000 --- a/Examples/1-res-Annotate/tmp_files/genome2.fst-split5N.fna-prokkaRes/GEN2.0219.00001.err +++ /dev/null @@ -1,146 +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:4 nucleotide Bioseqs are present -FEATURE_LOCATION_CONFLICT:13 features have inconsistent gene locations. -DISC_QUALITY_SCORES:Quality scores are missing on all sequences. -ONCALLER_COMMENT_PRESENT:4 comment descriptors were found (all same) -MISSING_GENOMEASSEMBLY_COMMENTS:4 bioseqs are missing GenomeAssembly structured comments -MOLTYPE_NOT_MRNA:4 molecule types are not set as mRNA. -TECHNIQUE_NOT_TSA:4 technique are not set as TSA -MISSING_STRUCTURED_COMMENT:4 sequences do not include structured comments. -MISSING_PROJECT:17 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/1-res-Annotate/tmp_files/genome2.fst-split5N.fna-prokkaRes/GEN2.0219.00001:this_is_genome_1_1 (length 257) -Examples/1-res-Annotate/tmp_files/genome2.fst-split5N.fna-prokkaRes/GEN2.0219.00001:this_is_genome_1_2 (length 467) -Examples/1-res-Annotate/tmp_files/genome2.fst-split5N.fna-prokkaRes/GEN2.0219.00001:this_is_genome_2_1 (length 74) -Examples/1-res-Annotate/tmp_files/genome2.fst-split5N.fna-prokkaRes/GEN2.0219.00001:this_is_genome_2_2 (length 126) -Examples/1-res-Annotate/tmp_files/genome2.fst-split5N.fna-prokkaRes/GEN2.0219.00001:this_is_genome_2_3 (length 277) -Examples/1-res-Annotate/tmp_files/genome2.fst-split5N.fna-prokkaRes/GEN2.0219.00001:this_is_genome_2_4 (length 555) -Examples/1-res-Annotate/tmp_files/genome2.fst-split5N.fna-prokkaRes/GEN2.0219.00001:this_is_genome_3_1 (length 255) -Examples/1-res-Annotate/tmp_files/genome2.fst-split5N.fna-prokkaRes/GEN2.0219.00001:this_is_genome_3_2 (length 86) -Examples/1-res-Annotate/tmp_files/genome2.fst-split5N.fna-prokkaRes/GEN2.0219.00001:this_is_genome_3_3 (length 193) -Examples/1-res-Annotate/tmp_files/genome2.fst-split5N.fna-prokkaRes/GEN2.0219.00001:this_is_genome_3_4 (length 122) -Examples/1-res-Annotate/tmp_files/genome2.fst-split5N.fna-prokkaRes/GEN2.0219.00001:this_is_genome_4_1 (length 435) -Examples/1-res-Annotate/tmp_files/genome2.fst-split5N.fna-prokkaRes/GEN2.0219.00001:this_is_genome_4_2 (length 154) -Examples/1-res-Annotate/tmp_files/genome2.fst-split5N.fna-prokkaRes/GEN2.0219.00001:this_is_genome_4_3 (length 337) - -DiscRep_ALL:DISC_SOURCE_QUALS_ASNDISC::strain (all present, all same) -DiscRep_SUB:DISC_SOURCE_QUALS_ASNDISC::4 sources have 'strain' for strain -DiscRep_ALL:DISC_SOURCE_QUALS_ASNDISC::taxname (all present, all same) -DiscRep_SUB:DISC_SOURCE_QUALS_ASNDISC::4 sources have 'Genus species' for taxname -DiscRep_ALL:DISC_FEATURE_COUNT::CDS: 13 present -DiscRep_ALL:DISC_COUNT_NUCLEOTIDES::4 nucleotide Bioseqs are present -Examples/1-res-Annotate/tmp_files/genome2.fst-split5N.fna-prokkaRes/GEN2.0219.00001:this_is_genome_1 (length 2308, 2 other) -Examples/1-res-Annotate/tmp_files/genome2.fst-split5N.fna-prokkaRes/GEN2.0219.00001:this_is_genome_2 (length 3295, 3 other) -Examples/1-res-Annotate/tmp_files/genome2.fst-split5N.fna-prokkaRes/GEN2.0219.00001:this_is_genome_3 (length 2263) -Examples/1-res-Annotate/tmp_files/genome2.fst-split5N.fna-prokkaRes/GEN2.0219.00001:this_is_genome_4 (length 2845) - -DiscRep_ALL:FEATURE_LOCATION_CONFLICT::13 features have inconsistent gene locations. -DiscRep_SUB:FEATURE_LOCATION_CONFLICT::Coding region xref gene does not exist -Examples/1-res-Annotate/tmp_files/genome2.fst-split5N.fna-prokkaRes/GEN2.0219.00001:CDS Histidine transport ATP-binding protein HisP this_is_genome_1:1-774 OHLPOIIB_00001 - -DiscRep_SUB:FEATURE_LOCATION_CONFLICT::Coding region xref gene does not exist -Examples/1-res-Annotate/tmp_files/genome2.fst-split5N.fna-prokkaRes/GEN2.0219.00001:CDS hypothetical protein this_is_genome_1:857-2260 OHLPOIIB_00002 - -DiscRep_SUB:FEATURE_LOCATION_CONFLICT::Coding region xref gene does not exist -Examples/1-res-Annotate/tmp_files/genome2.fst-split5N.fna-prokkaRes/GEN2.0219.00001:CDS Phage shock protein B this_is_genome_2:28-252 OHLPOIIB_00003 - -DiscRep_SUB:FEATURE_LOCATION_CONFLICT::Coding region xref gene does not exist -Examples/1-res-Annotate/tmp_files/genome2.fst-split5N.fna-prokkaRes/GEN2.0219.00001:CDS 5-carboxymethyl-2-hydroxymuconate Delta-isomerase this_is_genome_2:301-681 OHLPOIIB_00004 - -DiscRep_SUB:FEATURE_LOCATION_CONFLICT::Coding region xref gene does not exist -Examples/1-res-Annotate/tmp_files/genome2.fst-split5N.fna-prokkaRes/GEN2.0219.00001:CDS N-acetylmuramoyl-L-alanine amidase AmiD this_is_genome_2:764-1597 OHLPOIIB_00005 - -DiscRep_SUB:FEATURE_LOCATION_CONFLICT::Coding region xref gene does not exist -Examples/1-res-Annotate/tmp_files/genome2.fst-split5N.fna-prokkaRes/GEN2.0219.00001:CDS Glutamine--tRNA ligase this_is_genome_2:1628-3295 OHLPOIIB_00006 - -DiscRep_SUB:FEATURE_LOCATION_CONFLICT::Coding region xref gene does not exist -Examples/1-res-Annotate/tmp_files/genome2.fst-split5N.fna-prokkaRes/GEN2.0219.00001:CDS tRNA (guanine-N(1)-)-methyltransferase this_is_genome_3:30-797 OHLPOIIB_00007 - -DiscRep_SUB:FEATURE_LOCATION_CONFLICT::Coding region xref gene does not exist -Examples/1-res-Annotate/tmp_files/genome2.fst-split5N.fna-prokkaRes/GEN2.0219.00001:CDS hypothetical protein this_is_genome_3:862-1122 OHLPOIIB_00008 - -DiscRep_SUB:FEATURE_LOCATION_CONFLICT::Coding region xref gene does not exist -Examples/1-res-Annotate/tmp_files/genome2.fst-split5N.fna-prokkaRes/GEN2.0219.00001:CDS hypothetical protein this_is_genome_3:1170-1751 OHLPOIIB_00009 - -DiscRep_SUB:FEATURE_LOCATION_CONFLICT::Coding region xref gene does not exist -Examples/1-res-Annotate/tmp_files/genome2.fst-split5N.fna-prokkaRes/GEN2.0219.00001:CDS hypothetical protein this_is_genome_3:1895-2263 OHLPOIIB_00010 - -DiscRep_SUB:FEATURE_LOCATION_CONFLICT::Coding region xref gene does not exist -Examples/1-res-Annotate/tmp_files/genome2.fst-split5N.fna-prokkaRes/GEN2.0219.00001:CDS C4-dicarboxylate TRAP transporter large permease protein DctM this_is_genome_4:1-1308 OHLPOIIB_00011 - -DiscRep_SUB:FEATURE_LOCATION_CONFLICT::Coding region xref gene does not exist -Examples/1-res-Annotate/tmp_files/genome2.fst-split5N.fna-prokkaRes/GEN2.0219.00001:CDS hypothetical protein this_is_genome_4:1340-1804 OHLPOIIB_00012 - -DiscRep_SUB:FEATURE_LOCATION_CONFLICT::Coding region xref gene does not exist -Examples/1-res-Annotate/tmp_files/genome2.fst-split5N.fna-prokkaRes/GEN2.0219.00001:CDS Tyrosine recombinase XerC this_is_genome_4:1832-2845 OHLPOIIB_00013 - -DiscRep_ALL:DISC_QUALITY_SCORES::Quality scores are missing on all sequences. - -DiscRep_ALL:ONCALLER_COMMENT_PRESENT::4 comment descriptors were found (all same) -Examples/1-res-Annotate/tmp_files/genome2.fst-split5N.fna-prokkaRes/GEN2.0219.00001:this_is_genome_1:Annotated using prokka 1.14-dev from https://github.com/tseemann/prokka -Examples/1-res-Annotate/tmp_files/genome2.fst-split5N.fna-prokkaRes/GEN2.0219.00001:this_is_genome_2:Annotated using prokka 1.14-dev from https://github.com/tseemann/prokka -Examples/1-res-Annotate/tmp_files/genome2.fst-split5N.fna-prokkaRes/GEN2.0219.00001:this_is_genome_3:Annotated using prokka 1.14-dev from https://github.com/tseemann/prokka -Examples/1-res-Annotate/tmp_files/genome2.fst-split5N.fna-prokkaRes/GEN2.0219.00001:this_is_genome_4:Annotated using prokka 1.14-dev from https://github.com/tseemann/prokka - -DiscRep_ALL:MISSING_GENOMEASSEMBLY_COMMENTS::4 bioseqs are missing GenomeAssembly structured comments -Examples/1-res-Annotate/tmp_files/genome2.fst-split5N.fna-prokkaRes/GEN2.0219.00001:this_is_genome_1 (length 2308, 2 other) -Examples/1-res-Annotate/tmp_files/genome2.fst-split5N.fna-prokkaRes/GEN2.0219.00001:this_is_genome_2 (length 3295, 3 other) -Examples/1-res-Annotate/tmp_files/genome2.fst-split5N.fna-prokkaRes/GEN2.0219.00001:this_is_genome_3 (length 2263) -Examples/1-res-Annotate/tmp_files/genome2.fst-split5N.fna-prokkaRes/GEN2.0219.00001:this_is_genome_4 (length 2845) - -DiscRep_ALL:MOLTYPE_NOT_MRNA::4 molecule types are not set as mRNA. -Examples/1-res-Annotate/tmp_files/genome2.fst-split5N.fna-prokkaRes/GEN2.0219.00001:this_is_genome_1 (length 2308, 2 other) -Examples/1-res-Annotate/tmp_files/genome2.fst-split5N.fna-prokkaRes/GEN2.0219.00001:this_is_genome_2 (length 3295, 3 other) -Examples/1-res-Annotate/tmp_files/genome2.fst-split5N.fna-prokkaRes/GEN2.0219.00001:this_is_genome_3 (length 2263) -Examples/1-res-Annotate/tmp_files/genome2.fst-split5N.fna-prokkaRes/GEN2.0219.00001:this_is_genome_4 (length 2845) - -DiscRep_ALL:TECHNIQUE_NOT_TSA::4 technique are not set as TSA -Examples/1-res-Annotate/tmp_files/genome2.fst-split5N.fna-prokkaRes/GEN2.0219.00001:this_is_genome_1 (length 2308, 2 other) -Examples/1-res-Annotate/tmp_files/genome2.fst-split5N.fna-prokkaRes/GEN2.0219.00001:this_is_genome_2 (length 3295, 3 other) -Examples/1-res-Annotate/tmp_files/genome2.fst-split5N.fna-prokkaRes/GEN2.0219.00001:this_is_genome_3 (length 2263) -Examples/1-res-Annotate/tmp_files/genome2.fst-split5N.fna-prokkaRes/GEN2.0219.00001:this_is_genome_4 (length 2845) - -DiscRep_ALL:MISSING_STRUCTURED_COMMENT::4 sequences do not include structured comments. -Examples/1-res-Annotate/tmp_files/genome2.fst-split5N.fna-prokkaRes/GEN2.0219.00001:this_is_genome_1 (length 2308, 2 other) -Examples/1-res-Annotate/tmp_files/genome2.fst-split5N.fna-prokkaRes/GEN2.0219.00001:this_is_genome_2 (length 3295, 3 other) -Examples/1-res-Annotate/tmp_files/genome2.fst-split5N.fna-prokkaRes/GEN2.0219.00001:this_is_genome_3 (length 2263) -Examples/1-res-Annotate/tmp_files/genome2.fst-split5N.fna-prokkaRes/GEN2.0219.00001:this_is_genome_4 (length 2845) - -DiscRep_ALL:MISSING_PROJECT::17 sequences do not include project. -Examples/1-res-Annotate/tmp_files/genome2.fst-split5N.fna-prokkaRes/GEN2.0219.00001:this_is_genome_1 (length 2308, 2 other) -Examples/1-res-Annotate/tmp_files/genome2.fst-split5N.fna-prokkaRes/GEN2.0219.00001:this_is_genome_1_1 (length 257) -Examples/1-res-Annotate/tmp_files/genome2.fst-split5N.fna-prokkaRes/GEN2.0219.00001:this_is_genome_1_2 (length 467) -Examples/1-res-Annotate/tmp_files/genome2.fst-split5N.fna-prokkaRes/GEN2.0219.00001:this_is_genome_2 (length 3295, 3 other) -Examples/1-res-Annotate/tmp_files/genome2.fst-split5N.fna-prokkaRes/GEN2.0219.00001:this_is_genome_2_1 (length 74) -Examples/1-res-Annotate/tmp_files/genome2.fst-split5N.fna-prokkaRes/GEN2.0219.00001:this_is_genome_2_2 (length 126) -Examples/1-res-Annotate/tmp_files/genome2.fst-split5N.fna-prokkaRes/GEN2.0219.00001:this_is_genome_2_3 (length 277) -Examples/1-res-Annotate/tmp_files/genome2.fst-split5N.fna-prokkaRes/GEN2.0219.00001:this_is_genome_2_4 (length 555) -Examples/1-res-Annotate/tmp_files/genome2.fst-split5N.fna-prokkaRes/GEN2.0219.00001:this_is_genome_3 (length 2263) -Examples/1-res-Annotate/tmp_files/genome2.fst-split5N.fna-prokkaRes/GEN2.0219.00001:this_is_genome_3_1 (length 255) -Examples/1-res-Annotate/tmp_files/genome2.fst-split5N.fna-prokkaRes/GEN2.0219.00001:this_is_genome_3_2 (length 86) -Examples/1-res-Annotate/tmp_files/genome2.fst-split5N.fna-prokkaRes/GEN2.0219.00001:this_is_genome_3_3 (length 193) -Examples/1-res-Annotate/tmp_files/genome2.fst-split5N.fna-prokkaRes/GEN2.0219.00001:this_is_genome_3_4 (length 122) -Examples/1-res-Annotate/tmp_files/genome2.fst-split5N.fna-prokkaRes/GEN2.0219.00001:this_is_genome_4 (length 2845) -Examples/1-res-Annotate/tmp_files/genome2.fst-split5N.fna-prokkaRes/GEN2.0219.00001:this_is_genome_4_1 (length 435) -Examples/1-res-Annotate/tmp_files/genome2.fst-split5N.fna-prokkaRes/GEN2.0219.00001:this_is_genome_4_2 (length 154) -Examples/1-res-Annotate/tmp_files/genome2.fst-split5N.fna-prokkaRes/GEN2.0219.00001:this_is_genome_4_3 (length 337) - -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::4 Molinfos are missing field technique -Examples/1-res-Annotate/tmp_files/genome2.fst-split5N.fna-prokkaRes/GEN2.0219.00001:this_is_genome_1 (length 2308, 2 other) -Examples/1-res-Annotate/tmp_files/genome2.fst-split5N.fna-prokkaRes/GEN2.0219.00001:this_is_genome_2 (length 3295, 3 other) -Examples/1-res-Annotate/tmp_files/genome2.fst-split5N.fna-prokkaRes/GEN2.0219.00001:this_is_genome_3 (length 2263) -Examples/1-res-Annotate/tmp_files/genome2.fst-split5N.fna-prokkaRes/GEN2.0219.00001:this_is_genome_4 (length 2845) - diff --git a/Examples/1-res-Annotate/tmp_files/genome2.fst-split5N.fna-prokkaRes/GEN2.0219.00001.faa b/Examples/1-res-Annotate/tmp_files/genome2.fst-split5N.fna-prokkaRes/GEN2.0219.00001.faa deleted file mode 100644 index e1d7e1891450800eb67bf2f829dd0f52874e135b..0000000000000000000000000000000000000000 --- a/Examples/1-res-Annotate/tmp_files/genome2.fst-split5N.fna-prokkaRes/GEN2.0219.00001.faa +++ /dev/null @@ -1,77 +0,0 @@ ->OHLPOIIB_00001 Histidine transport ATP-binding protein HisP -MSENKLHVIDLHKRYGGHEVLKGVSLQARAGDVISIIGSSGSGKSTFLRCINFLEKSSEG -AIIVNGQNINLVRDKDGQLKVADKNQLRLLRTRLTMVFQHFNLWNHMTVLENVMEAPIQV -LGLSKHDARERALKYLAKVGIDERAQGKYPVHLSGGQQQRVSIARALAMEPDVLLFDEPT -SALDPELVGEVLRIMQQLAEEGKTMVVVTHEMGFARHVSSHVIFLHQGKIEEEGNPEQVF -GNPQSPRLQQFLKGSLK ->OHLPOIIB_00002 hypothetical protein -MPATKFSRRTLLTAGSALAVLPFLRALPVQAREPRQTVDIKDYPADDGIASFKQAFADGQ -TVVVPSGWVCENINAAITIPAGKTLRIQGAVRGNGRGRFILLDGCQVVGEQGGSLHNVTL -DVRGSDCVIKGVTMSGFGPVAQIFIGGKEPQVMRNLIIDDITVTHANYAILRQGFHNQMD -GARITHSRFSDLQGDAIEWNVAIHDRDILISDHVIERIDCTNGKINWGIGIGLAGSAYDN -SYPEDQAVKNFVVANITGSDCRQLVHVENGKHFVIRNVKAKNITPDFSKNAGIDNATIAI -YGCDNFVIDNIDMTNSAGMLIGYGVVKGKYLSIPQNFKLNAIRLDNRQVAYKLRGIQISS -GNAPSFVAITNVRMTRATLELHNQPQHLFLRNINVMQTSAIGPALKMHFDLRKDVRGQFM -ARQDTLLSLANVHAINENGQSSVDIDRINHQTVNVEAVNFSLPKRGG ->OHLPOIIB_00003 Phage shock protein B -MSALFLAIPLTIFVLFVLPIWLWLHYSNRAGRGELSQSEQQRLLQLTDDAQRMRERIQAL -EDILDAEHPNWRER ->OHLPOIIB_00004 5-carboxymethyl-2-hydroxymuconate Delta-isomerase -MPHFIAECTENIREQADLPSLFSKVNEALAATGIFPIGGIRSRAHWLDTWQMADGKHDYA -FVHMTLKIGAGRSLESRQEVGEMLFGLIKAHFADLMENRYLALSFEIAELHPTLNYKQNN -VHALFK ->OHLPOIIB_00005 N-acetylmuramoyl-L-alanine amidase AmiD -MMKALLWLVGLALLLTGCASEKGIIDKEGYQLDTRHRAQAAYPRIKVLVIHYTAENFDVS -LATLTGRNVSSHYLIPATPPLYGGKPRIWQLVPEQDQAWHAGVSFWRGATRLNDTSIGIE -LENRGWRMSGGVKSFAPFESAQIQALIPLAKDIIARYDIKPQNVVAHADIAPQRKDDPGP -RFPWRELAAQGIGAWPDAQRVAFYLAGRAPYTPVDTATVLALLSRYGYEVKADMTAREQQ -RVIMAFQMHFRPAQWNGIADAETQAIAEALLEKYGQD ->OHLPOIIB_00006 Glutamine--tRNA ligase -MSEAEARPTNFIRQIIDEDLASGKHTTVHTRFPPEPNGYLHIGHAKSICLNFGIAQDYQG -QCNLRFDDTNPVKEDIEYVDSIKNDVEWLGFHWSGDIRYSSDYFDQLHAYAVELINKGLA -YVDELTPEQIREYRGTLTAPGKNSPFRDRSVEENLALFEKMRTGGFEEGKACLRAKIDMA -SPFIVMRDPVLYRIKFAEHHQTGTKWCIYPMYDFTHCISDALEGITHSLCTLEFQDNRRL -YDWVLDNITIPVHPRQYEFSRLNLEYTVMSKRKLNLLVTDKHVEGWDDPRMPTISGLRRR -GYTAASIREFCKRIGVTKQDNTIEMASLESCIREDLNENAPRAMAVIDPVKLVIENYPQG -ESEMVTMPNHPNKPEMGSREVPFSGEIWIDRADFREEANKQYKRLVMGKEVRLRNAYVIK -AERVEKDAEGNITTIFCTYDADTLSKDPADGRKVKGVIHWVSVAHALPIEIRLYDRLFSV -PNPGAAEDFLSVINPESLVIKQGYGEPSLKAAVAGKAFQFEREGYFCLDSRYATADKLVF -NRTVGLRDTWAKAGE ->OHLPOIIB_00007 tRNA (guanine-N(1)-)-methyltransferase -MFIGIVSLFPEMFRAITDYGVTGRAVKKGLLNIQSWSPRDFAHDRHRTVDDRPYGGGPGM -LMMVQPLRDAIHAAKAAAGEGAKVIYLSPQGRKLDQAGVSELATNQKLILVCGRYEGVDE -RVIQAEIDEEWSIGDYVLSGGELPAMTLIDSVARFIPGVLGHEASAIEDSFADGLLDCPH -YTRPEVLEGMEVPPVLLSGNHAEIRRWRLKQSLGRTWLRRPELLENLALTEEQARLLAEF -KTEHAQQQHKHDGMA ->OHLPOIIB_00008 hypothetical protein -MAGLHAPYAYSAHHAVNFCSEYKRGFVLGFTHRMFEKTGDRQLSAWEAGILTRRYGLDKE -MVMDFFKENHSGMAVRFFMAGYRLEG ->OHLPOIIB_00009 hypothetical protein -MSTLLYLHGFNSSPRSAKACQLKNWLAERHPHVEMIVPQLPPYPADAAELLESLVLEHGG -APLGLVGSSLGGYYATWLSQCFMLPAVVVNPAVRPFELLTDYLGQNENPYTGQQYVLESR -HIYDLKVMQIDPLEAPDLIWLLQQTGDEVLDYRQAVAYYASCRQTVTEGGNHAFTGFEDY -FNQIVDFLGLHSC ->OHLPOIIB_00010 hypothetical protein -MMRTDGTVTQPRLKQVALSAISEVNAELYEFRRRQQMLGYASLAEVPAEQLDGKSERIQH -YFNAVYCWARAMLNERYQDYDATASGVKRGEELAEASGDLWRDARWAISRVQDAPHCTVE -LI ->OHLPOIIB_00011 C4-dicarboxylate TRAP transporter large permease protein DctM -MIDPIFASCTLIAVFVVLLAMGAPIGICIVIASFSTMMLVLPFDISMFATAQKMFSSLDS -FALLAVPFFVLSGVIMNSGGIAARLVNFAKLFTGKLPGSLSYTNIVGNMMFGAISGSAIA -ASTSIGGVMVPMSAREGYDRGFAAAVNIASAPTGMLIPPTTAFILYALASGGTSIAALFA -GGLVAGVLWGVGCMLVTLVVAKRRNYRVFFTVQKGMALKVAVEAIPSLLLIVIIVGGIVQ -GIFTAIEASAIAVVYTLLLTIVFYRTLKIKDLPSILLQTVVMTGVIMFLLATSSAMSFSM -SITNIPAALSDMILGISANKLVILLVITVFLLIIGAFMDIGPAILIFTPILLPIMTKLGV -DPVHFGIIMIYNLAIGTITPPVGSGLYVGASVGKVKVEDVIKPLMPFYGAIIGVLLLITY -IPEITLFLPRLLGIM ->OHLPOIIB_00012 hypothetical protein -MKFVAPEQAPEQAEVIKNTPFWPDVNLSEFRSVMRTDGTVTQPRLKQVVLTAISEVNAEL -YDFRNRQQMLGWRTLAEVPAEMLDGKSERIRHYHNAVFCWARAVLNERYQDYDATASGVK -RGEELAEASGDLWRDARWAISRVQDAPHCTVELI ->OHLPOIIB_00013 Tyrosine recombinase XerC -METNITWQQLIDEYFFAKPLRSASEWSYTKVFKSFVHYMGPLSCPNDVTYHKVLAWRRFL -LKEKKLSGRTWNNKVAHMRAIFNYGIQRGLLHYDENPFNNSVVKPDKKRKKTLTQAQIEY -AYQIMEQYENQENTGLGLKYSRCALFPAWFWLTVLDTLYYTGIRQNQLLHIRLNDVDLRE -GQIRLITEGCKNHKEHYVPVISFLRPRLTCLMEKAQSEGLKGNDRLFNIALFTGKDPAIG -DDMDSPQVRAFFRRLSKECQFAISPHRFRHTLATEMMKMPEQNLHMAQSVLGHSNMKSTL -EYVENDIAVMGRALEAQFMQIKAAHARSIYSGLTKNR diff --git a/Examples/1-res-Annotate/tmp_files/genome2.fst-split5N.fna-prokkaRes/GEN2.0219.00001.ffn b/Examples/1-res-Annotate/tmp_files/genome2.fst-split5N.fna-prokkaRes/GEN2.0219.00001.ffn deleted file mode 100644 index dfb0f1dbe14cb5dee51af28c1445f24e73a962d1..0000000000000000000000000000000000000000 --- a/Examples/1-res-Annotate/tmp_files/genome2.fst-split5N.fna-prokkaRes/GEN2.0219.00001.ffn +++ /dev/null @@ -1,185 +0,0 @@ ->OHLPOIIB_00001 Histidine transport ATP-binding protein HisP -ATGTCAGAAAATAAATTACACGTTATCGATTTGCACAAACGCTACGGCGGTCATGAAGTG -CTGAAAGGGGTATCGCTGCAGGCCCGCGCCGGAGATGTGATTAGCATTATCGGCTCGTCC -GGTTCCGGTAAAAGCACTTTTTTGCGCTGCATTAACTTCCTCGAAAAATCGAGCGAAGGC -GCGATTATCGTGAACGGTCAGAACATTAATCTGGTGCGCGACAAAGACGGGCAGCTCAAA -GTGGCGGATAAAAATCAGCTACGCTTGTTGCGTACCCGCCTGACGATGGTGTTTCAGCAC -TTTAACCTCTGGAACCACATGACGGTGCTGGAAAATGTGATGGAAGCGCCGATTCAGGTA -CTGGGATTAAGCAAGCACGACGCGCGCGAGCGGGCGTTGAAATATCTGGCGAAGGTGGGG -ATTGATGAGCGCGCTCAGGGCAAATATCCCGTCCATCTCTCCGGCGGCCAACAGCAGCGC -GTTTCTATTGCGCGCGCGCTGGCGATGGAACCTGACGTTTTACTGTTCGATGAACCCACA -TCGGCGCTCGATCCTGAACTGGTCGGCGAAGTGTTGCGCATCATGCAACAACTGGCGGAA -GAAGGCAAAACGATGGTGGTGGTCACGCATGAAATGGGCTTCGCCCGCCATGTCTCTTCG -CACGTGATTTTTCTGCATCAGGGGAAAATTGAAGAAGAGGGCAATCCGGAGCAGGTGTTC -GGCAATCCGCAAAGCCCGCGTTTACAGCAATTCCTGAAAGGCTCGCTGAAATAA ->OHLPOIIB_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 ->OHLPOIIB_00003 Phage shock protein B -ATGAGCGCGCTATTTCTGGCCATCCCGTTAACCATTTTTGTGTTGTTTGTGTTACCGATT -TGGCTGTGGCTGCATTACAGCAACCGCGCCGGTCGGGGAGAACTGTCGCAAAGCGAGCAG -CAACGCTTACTGCAACTCACAGACGACGCGCAACGTATGCGCGAGCGCATTCAGGCGCTG -GAAGATATTCTTGATGCAGAGCATCCGAACTGGAGAGAGCGCTAA ->OHLPOIIB_00004 5-carboxymethyl-2-hydroxymuconate Delta-isomerase -ATGCCGCACTTTATTGCTGAATGTACTGAAAATATTCGCGAGCAGGCTGATTTACCAAGC -CTGTTCAGCAAGGTAAACGAGGCGCTGGCCGCCACCGGGATTTTCCCCATCGGCGGTATC -CGCAGTCGCGCCCACTGGCTGGATACCTGGCAGATGGCTGACGGTAAGCATGATTACGCG -TTTGTGCATATGACGCTGAAAATCGGCGCCGGGCGCAGCCTGGAGAGCCGTCAGGAAGTC -GGCGAAATGCTGTTTGGGCTGATTAAAGCCCACTTCGCCGACCTGATGGAGAACCGCTAT -CTGGCGCTGTCGTTTGAGATTGCCGAGTTACATCCAACGCTCAATTACAAACAAAACAAC -GTACACGCGTTATTTAAATAG ->OHLPOIIB_00005 N-acetylmuramoyl-L-alanine amidase AmiD -ATGATGAAAGCGCTACTGTGGCTGGTTGGTCTCGCGTTGCTGTTAACAGGCTGCGCGAGC -GAAAAAGGAATTATCGATAAAGAGGGATATCAGCTTGATACCCGACATCGGGCGCAGGCG -GCCTATCCGCGCATTAAAGTCCTGGTGATTCACTATACGGCGGAAAACTTTGACGTTTCG -CTGGCGACGTTAACGGGTCGCAACGTCAGTTCGCATTACCTGATTCCCGCAACCCCGCCA -TTATATGGCGGTAAACCGCGCATCTGGCAACTGGTGCCGGAACAGGATCAGGCTTGGCAT -GCGGGCGTCAGTTTCTGGCGAGGCGCCACGCGTCTCAATGATACGTCTATTGGCATTGAG -CTGGAAAATCGCGGCTGGCGAATGTCCGGCGGGGTGAAATCTTTCGCGCCGTTTGAATCC -GCGCAAATTCAGGCATTGATCCCGTTAGCGAAGGACATTATCGCGCGCTATGACATCAAA -CCGCAGAATGTGGTGGCCCATGCGGATATCGCGCCGCAGCGTAAAGACGATCCCGGCCCG -CGCTTCCCGTGGCGCGAGCTGGCGGCACAGGGGATTGGCGCCTGGCCTGACGCCCAGCGT -GTGGCGTTTTATCTGGCTGGACGCGCGCCGTATACGCCAGTCGATACCGCAACGGTGCTT -GCGTTACTCTCGCGCTATGGCTATGAAGTCAAAGCCGATATGACGGCGCGCGAGCAACAG -CGGGTGATTATGGCGTTCCAGATGCACTTCCGTCCGGCGCAATGGAACGGTATCGCAGAT -GCCGAAACGCAGGCGATTGCCGAAGCATTACTGGAGAAGTACGGCCAGGATTAA ->OHLPOIIB_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 ->OHLPOIIB_00007 tRNA (guanine-N(1)-)-methyltransferase -GTGTTTATTGGCATCGTTAGCCTGTTTCCTGAAATGTTCCGCGCAATTACCGATTACGGG -GTAACTGGCCGGGCAGTAAAAAAAGGCCTGCTGAACATCCAAAGCTGGAGTCCTCGCGAC -TTCGCGCATGACCGGCACCGTACCGTGGACGACCGTCCTTACGGCGGCGGACCGGGGATG -TTAATGATGGTGCAACCCTTGCGGGACGCCATTCATGCAGCAAAAGCCGCGGCAGGTGAA -GGCGCTAAAGTGATTTATCTGTCGCCTCAGGGACGCAAGCTTGATCAAGCGGGCGTTAGC -GAGCTGGCCACGAATCAGAAACTCATTCTGGTGTGTGGTCGCTACGAAGGCGTAGATGAG -CGCGTAATTCAGGCCGAAATTGACGAAGAATGGTCAATTGGCGATTACGTTCTCAGCGGT -GGCGAACTACCGGCAATGACGCTGATTGACTCCGTCGCCCGGTTTATACCGGGGGTTCTG -GGGCATGAGGCATCAGCAATCGAAGATTCGTTTGCTGATGGGTTGCTGGATTGTCCGCAC -TATACGCGCCCTGAAGTGTTAGAGGGGATGGAAGTACCGCCAGTATTGCTGTCGGGAAAC -CATGCTGAGATACGTCGCTGGCGTTTGAAACAGTCACTGGGCCGAACCTGGCTTAGAAGA -CCTGAACTTCTGGAAAACCTGGCTCTGACTGAAGAGCAAGCAAGGTTGCTGGCGGAGTTC -AAAACAGAACACGCACAACAGCAGCATAAACATGATGGGATGGCATAG ->OHLPOIIB_00008 hypothetical protein -ATGGCCGGGTTGCACGCGCCATATGCATATAGCGCGCATCATGCGGTGAATTTCTGTTCT -GAGTATAAACGTGGCTTTGTATTGGGTTTTACACACCGTATGTTCGAAAAGACCGGCGAT -CGTCAACTTAGCGCGTGGGAGGCCGGAATTCTGACGCGTCGCTATGGTCTGGATAAAGAA -ATGGTGATGGATTTCTTTAAAGAGAATCATTCCGGGATGGCGGTTCGCTTCTTTATGGCT -GGTTATCGACTCGAAGGTTGA ->OHLPOIIB_00009 hypothetical protein -ATGTCTACGCTTCTCTATTTGCACGGATTCAACAGTTCCCCTCGCTCGGCAAAAGCGTGC -CAGCTAAAAAACTGGCTGGCGGAGCGTCATCCGCATGTTGAGATGATCGTCCCTCAACTG -CCGCCGTATCCTGCCGATGCGGCGGAGTTGCTGGAATCTCTCGTACTTGAGCATGGCGGT -GCGCCATTAGGGCTGGTAGGATCGTCGCTGGGTGGTTATTACGCCACCTGGCTGTCGCAA -TGTTTTATGCTGCCGGCTGTGGTGGTGAATCCCGCCGTGCGGCCCTTTGAATTACTGACC -GACTATCTCGGTCAGAACGAGAACCCCTACACCGGGCAGCAATATGTGCTAGAGTCTCGC -CATATTTATGATCTTAAAGTCATGCAGATTGACCCGCTGGAAGCGCCGGACCTGATCTGG -CTACTGCAACAGACGGGCGATGAAGTGCTGGATTACCGCCAGGCGGTGGCATATTACGCC -TCCTGCCGTCAGACAGTGACCGAGGGGGGTAATCACGCATTCACGGGCTTCGAAGATTAT -TTCAACCAGATTGTCGATTTTCTTGGACTGCACAGTTGCTGA ->OHLPOIIB_00010 hypothetical protein -ATGATGCGCACTGATGGCACGGTGACGCAGCCGCGTTTAAAGCAGGTTGCGCTGTCGGCA -ATTTCGGAGGTCAACGCAGAGCTGTATGAGTTTCGCAGACGCCAGCAGATGCTGGGGTAT -GCCTCGCTGGCAGAAGTCCCGGCGGAACAACTGGACGGCAAAAGCGAGCGCATTCAGCAC -TATTTCAACGCGGTTTACTGCTGGGCACGCGCCATGCTCAACGAACGTTACCAGGACTAT -GACGCCACGGCATCCGGTGTGAAGCGGGGCGAAGAACTGGCAGAAGCCAGCGGTGATTTG -TGGCGTGACGCCCGCTGGGCCATCAGCCGGGTGCAGGATGCGCCGCACTGCACAGTGGAG -CTTATCTGA ->OHLPOIIB_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 ->OHLPOIIB_00012 hypothetical protein -ATGAAGTTTGTTGCGCCAGAACAGGCACCGGAACAGGCGGAGGTCATCAAAAATACGCCG -TTCTGGCCTGATGTGAACCTGTCGGAATTTCGCAGTGTGATGCGCACTGACGGCACGGTG -ACGCAGCCGCGTTTAAAGCAGGTCGTGCTGACGGCGATCTCTGAGGTTAACGCTGAGCTG -TACGACTTCCGCAACCGTCAGCAGATGCTGGGCTGGCGGACACTTGCTGAGGTTCCCGCA -GAAATGCTGGACGGTAAAAGCGAGCGTATCCGGCACTACCACAACGCTGTTTTTTGCTGG -GCGCGCGCTGTGCTTAATGAGCGTTATCAGGACTATGACGCCACGGCGTCAGGCGTGAAG -CGAGGGGAGGAGCTGGCGGAGGCCAGCGGCGATCTGTGGCGTGATGCCCGCTGGGCCATC -AGCCGGGTGCAGGATGCACCGCACTGTACGGTGGAGCTTATCTGA ->OHLPOIIB_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/1-res-Annotate/tmp_files/genome2.fst-split5N.fna-prokkaRes/GEN2.0219.00001.fna b/Examples/1-res-Annotate/tmp_files/genome2.fst-split5N.fna-prokkaRes/GEN2.0219.00001.fna deleted file mode 100644 index 500883173662b59ed235adfba0c1c25579abf859..0000000000000000000000000000000000000000 --- a/Examples/1-res-Annotate/tmp_files/genome2.fst-split5N.fna-prokkaRes/GEN2.0219.00001.fna +++ /dev/null @@ -1,184 +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 diff --git a/Examples/1-res-Annotate/tmp_files/genome2.fst-split5N.fna-prokkaRes/GEN2.0219.00001.fsa b/Examples/1-res-Annotate/tmp_files/genome2.fst-split5N.fna-prokkaRes/GEN2.0219.00001.fsa deleted file mode 100644 index cca31356970595150a952c269dce73d8f53e0e0d..0000000000000000000000000000000000000000 --- a/Examples/1-res-Annotate/tmp_files/genome2.fst-split5N.fna-prokkaRes/GEN2.0219.00001.fsa +++ /dev/null @@ -1,184 +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 diff --git a/Examples/1-res-Annotate/tmp_files/genome2.fst-split5N.fna-prokkaRes/GEN2.0219.00001.gbk b/Examples/1-res-Annotate/tmp_files/genome2.fst-split5N.fna-prokkaRes/GEN2.0219.00001.gbk deleted file mode 100644 index 6150ab31320117628112981efd3c7fdb6042456c..0000000000000000000000000000000000000000 --- a/Examples/1-res-Annotate/tmp_files/genome2.fst-split5N.fna-prokkaRes/GEN2.0219.00001.gbk +++ /dev/null @@ -1,415 +0,0 @@ -LOCUS this_is_genome_1 2308 bp DNA linear 12-FEB-2019 -DEFINITION Genus species strain strain. -ACCESSION -VERSION -KEYWORDS . -SOURCE Genus species - ORGANISM Genus species - Unclassified. -COMMENT Annotated using prokka 1.14-dev 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="OHLPOIIB_00001" - /inference="ab initio prediction:Prodigal:2.6" - /inference="similar to AA sequence:UniProtKB:P02915" - /codon_start=1 - /transl_table=11 - /product="Histidine transport ATP-binding protein HisP" - /translation="MSENKLHVIDLHKRYGGHEVLKGVSLQARAGDVISIIGSSGSGK - STFLRCINFLEKSSEGAIIVNGQNINLVRDKDGQLKVADKNQLRLLRTRLTMVFQHFN - LWNHMTVLENVMEAPIQVLGLSKHDARERALKYLAKVGIDERAQGKYPVHLSGGQQQR - VSIARALAMEPDVLLFDEPTSALDPELVGEVLRIMQQLAEEGKTMVVVTHEMGFARHV - SSHVIFLHQGKIEEEGNPEQVFGNPQSPRLQQFLKGSLK" - CDS 857..2260 - /locus_tag="OHLPOIIB_00002" - /inference="ab initio prediction:Prodigal:2.6" - /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 12-FEB-2019 -DEFINITION Genus species strain strain. -ACCESSION -VERSION -KEYWORDS . -SOURCE Genus species - ORGANISM Genus species - Unclassified. -COMMENT Annotated using prokka 1.14-dev 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="OHLPOIIB_00003" - /inference="ab initio prediction:Prodigal:2.6" - /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="OHLPOIIB_00004" - /EC_number="5.3.3.10" - /inference="ab initio prediction:Prodigal:2.6" - /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="OHLPOIIB_00005" - /EC_number="3.5.1.28" - /inference="ab initio prediction:Prodigal:2.6" - /inference="similar to AA sequence:UniProtKB:P75820" - /codon_start=1 - /transl_table=11 - /product="N-acetylmuramoyl-L-alanine amidase AmiD" - /translation="MMKALLWLVGLALLLTGCASEKGIIDKEGYQLDTRHRAQAAYPR - IKVLVIHYTAENFDVSLATLTGRNVSSHYLIPATPPLYGGKPRIWQLVPEQDQAWHAG - VSFWRGATRLNDTSIGIELENRGWRMSGGVKSFAPFESAQIQALIPLAKDIIARYDIK - PQNVVAHADIAPQRKDDPGPRFPWRELAAQGIGAWPDAQRVAFYLAGRAPYTPVDTAT - VLALLSRYGYEVKADMTAREQQRVIMAFQMHFRPAQWNGIADAETQAIAEALLEKYGQ - D" - CDS 1628..3295 - /gene="glnS" - /locus_tag="OHLPOIIB_00006" - /EC_number="6.1.1.18" - /inference="ab initio prediction:Prodigal:2.6" - /inference="similar to AA sequence:UniProtKB:P00962" - /codon_start=1 - /transl_table=11 - /product="Glutamine--tRNA ligase" - /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 12-FEB-2019 -DEFINITION Genus species strain strain. -ACCESSION -VERSION -KEYWORDS . -SOURCE Genus species - ORGANISM Genus species - Unclassified. -COMMENT Annotated using prokka 1.14-dev 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="OHLPOIIB_00007" - /EC_number="2.1.1.228" - /inference="ab initio prediction:Prodigal:2.6" - /inference="similar to AA sequence:UniProtKB:P0A873" - /codon_start=1 - /transl_table=11 - /product="tRNA (guanine-N(1)-)-methyltransferase" - /translation="MFIGIVSLFPEMFRAITDYGVTGRAVKKGLLNIQSWSPRDFAHD - RHRTVDDRPYGGGPGMLMMVQPLRDAIHAAKAAAGEGAKVIYLSPQGRKLDQAGVSEL - ATNQKLILVCGRYEGVDERVIQAEIDEEWSIGDYVLSGGELPAMTLIDSVARFIPGVL - GHEASAIEDSFADGLLDCPHYTRPEVLEGMEVPPVLLSGNHAEIRRWRLKQSLGRTWL - RRPELLENLALTEEQARLLAEFKTEHAQQQHKHDGMA" - CDS 862..1122 - /locus_tag="OHLPOIIB_00008" - /inference="ab initio prediction:Prodigal:2.6" - /codon_start=1 - /transl_table=11 - /product="hypothetical protein" - /translation="MAGLHAPYAYSAHHAVNFCSEYKRGFVLGFTHRMFEKTGDRQLS - AWEAGILTRRYGLDKEMVMDFFKENHSGMAVRFFMAGYRLEG" - CDS 1170..1751 - /locus_tag="OHLPOIIB_00009" - /inference="ab initio prediction:Prodigal:2.6" - /codon_start=1 - /transl_table=11 - /product="hypothetical protein" - /translation="MSTLLYLHGFNSSPRSAKACQLKNWLAERHPHVEMIVPQLPPYP - ADAAELLESLVLEHGGAPLGLVGSSLGGYYATWLSQCFMLPAVVVNPAVRPFELLTDY - LGQNENPYTGQQYVLESRHIYDLKVMQIDPLEAPDLIWLLQQTGDEVLDYRQAVAYYA - SCRQTVTEGGNHAFTGFEDYFNQIVDFLGLHSC" - CDS 1895..2263 - /locus_tag="OHLPOIIB_00010" - /inference="ab initio prediction:Prodigal:2.6" - /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 12-FEB-2019 -DEFINITION Genus species strain strain. -ACCESSION -VERSION -KEYWORDS . -SOURCE Genus species - ORGANISM Genus species - Unclassified. -COMMENT Annotated using prokka 1.14-dev 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="OHLPOIIB_00011" - /inference="ab initio prediction:Prodigal:2.6" - /inference="similar to AA sequence:UniProtKB:O07838" - /codon_start=1 - /transl_table=11 - /product="C4-dicarboxylate TRAP transporter large permease - protein DctM" - /translation="MIDPIFASCTLIAVFVVLLAMGAPIGICIVIASFSTMMLVLPFD - ISMFATAQKMFSSLDSFALLAVPFFVLSGVIMNSGGIAARLVNFAKLFTGKLPGSLSY - TNIVGNMMFGAISGSAIAASTSIGGVMVPMSAREGYDRGFAAAVNIASAPTGMLIPPT - TAFILYALASGGTSIAALFAGGLVAGVLWGVGCMLVTLVVAKRRNYRVFFTVQKGMAL - KVAVEAIPSLLLIVIIVGGIVQGIFTAIEASAIAVVYTLLLTIVFYRTLKIKDLPSIL - LQTVVMTGVIMFLLATSSAMSFSMSITNIPAALSDMILGISANKLVILLVITVFLLII - GAFMDIGPAILIFTPILLPIMTKLGVDPVHFGIIMIYNLAIGTITPPVGSGLYVGASV - GKVKVEDVIKPLMPFYGAIIGVLLLITYIPEITLFLPRLLGIM" - CDS 1340..1804 - /locus_tag="OHLPOIIB_00012" - /inference="ab initio prediction:Prodigal:2.6" - /codon_start=1 - /transl_table=11 - /product="hypothetical protein" - /translation="MKFVAPEQAPEQAEVIKNTPFWPDVNLSEFRSVMRTDGTVTQPR - LKQVVLTAISEVNAELYDFRNRQQMLGWRTLAEVPAEMLDGKSERIRHYHNAVFCWAR - AVLNERYQDYDATASGVKRGEELAEASGDLWRDARWAISRVQDAPHCTVELI" - CDS 1832..2845 - /gene="xerC" - /locus_tag="OHLPOIIB_00013" - /inference="ab initio prediction:Prodigal:2.6" - /inference="similar to AA sequence:UniProtKB:P39776" - /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 -// diff --git a/Examples/1-res-Annotate/tmp_files/genome2.fst-split5N.fna-prokkaRes/GEN2.0219.00001.gff b/Examples/1-res-Annotate/tmp_files/genome2.fst-split5N.fna-prokkaRes/GEN2.0219.00001.gff deleted file mode 100644 index 401a3a9388641ab76096af266eba40dd541e3030..0000000000000000000000000000000000000000 --- a/Examples/1-res-Annotate/tmp_files/genome2.fst-split5N.fna-prokkaRes/GEN2.0219.00001.gff +++ /dev/null @@ -1,203 +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 -this_is_genome_1 Prodigal:2.6 CDS 1 774 . + 0 ID=OHLPOIIB_00001;Name=hisP;dbxref=COG:COG4598;gene=hisP;inference=ab initio prediction:Prodigal:2.6,similar to AA sequence:UniProtKB:P02915;locus_tag=OHLPOIIB_00001;product=Histidine transport ATP-binding protein HisP -this_is_genome_1 Prodigal:2.6 CDS 857 2260 . + 0 ID=OHLPOIIB_00002;inference=ab initio prediction:Prodigal:2.6;locus_tag=OHLPOIIB_00002;product=hypothetical protein -this_is_genome_2 Prodigal:2.6 CDS 28 252 . + 0 ID=OHLPOIIB_00003;Name=pspB;gene=pspB;inference=ab initio prediction:Prodigal:2.6,similar to AA sequence:UniProtKB:P0AFM9;locus_tag=OHLPOIIB_00003;product=Phage shock protein B -this_is_genome_2 Prodigal:2.6 CDS 301 681 . + 0 ID=OHLPOIIB_00004;eC_number=5.3.3.10;Name=hpcD;gene=hpcD;inference=ab initio prediction:Prodigal:2.6,similar to AA sequence:UniProtKB:Q05354;locus_tag=OHLPOIIB_00004;product=5-carboxymethyl-2-hydroxymuconate Delta-isomerase -this_is_genome_2 Prodigal:2.6 CDS 764 1597 . + 0 ID=OHLPOIIB_00005;eC_number=3.5.1.28;Name=amiD;dbxref=COG:COG3023;gene=amiD;inference=ab initio prediction:Prodigal:2.6,similar to AA sequence:UniProtKB:P75820;locus_tag=OHLPOIIB_00005;product=N-acetylmuramoyl-L-alanine amidase AmiD -this_is_genome_2 Prodigal:2.6 CDS 1628 3295 . + 0 ID=OHLPOIIB_00006;eC_number=6.1.1.18;Name=glnS;dbxref=COG:COG0008;gene=glnS;inference=ab initio prediction:Prodigal:2.6,similar to AA sequence:UniProtKB:P00962;locus_tag=OHLPOIIB_00006;product=Glutamine--tRNA ligase -this_is_genome_3 Prodigal:2.6 CDS 30 797 . + 0 ID=OHLPOIIB_00007;eC_number=2.1.1.228;Name=trmD;dbxref=COG:COG0336;gene=trmD;inference=ab initio prediction:Prodigal:2.6,similar to AA sequence:UniProtKB:P0A873;locus_tag=OHLPOIIB_00007;product=tRNA (guanine-N(1)-)-methyltransferase -this_is_genome_3 Prodigal:2.6 CDS 862 1122 . + 0 ID=OHLPOIIB_00008;inference=ab initio prediction:Prodigal:2.6;locus_tag=OHLPOIIB_00008;product=hypothetical protein -this_is_genome_3 Prodigal:2.6 CDS 1170 1751 . + 0 ID=OHLPOIIB_00009;inference=ab initio prediction:Prodigal:2.6;locus_tag=OHLPOIIB_00009;product=hypothetical protein -this_is_genome_3 Prodigal:2.6 CDS 1895 2263 . + 0 ID=OHLPOIIB_00010;inference=ab initio prediction:Prodigal:2.6;locus_tag=OHLPOIIB_00010;product=hypothetical protein -this_is_genome_4 Prodigal:2.6 CDS 1 1308 . + 0 ID=OHLPOIIB_00011;Name=dctM;dbxref=COG:COG1593;gene=dctM;inference=ab initio prediction:Prodigal:2.6,similar to AA sequence:UniProtKB:O07838;locus_tag=OHLPOIIB_00011;product=C4-dicarboxylate TRAP transporter large permease protein DctM -this_is_genome_4 Prodigal:2.6 CDS 1340 1804 . + 0 ID=OHLPOIIB_00012;inference=ab initio prediction:Prodigal:2.6;locus_tag=OHLPOIIB_00012;product=hypothetical protein -this_is_genome_4 Prodigal:2.6 CDS 1832 2845 . + 0 ID=OHLPOIIB_00013;Name=xerC;dbxref=COG:COG4974;gene=xerC;inference=ab initio prediction:Prodigal:2.6,similar to AA sequence:UniProtKB:P39776;locus_tag=OHLPOIIB_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 diff --git a/Examples/1-res-Annotate/tmp_files/genome2.fst-split5N.fna-prokkaRes/GEN2.0219.00001.log b/Examples/1-res-Annotate/tmp_files/genome2.fst-split5N.fna-prokkaRes/GEN2.0219.00001.log deleted file mode 100644 index 4e555a8670fed1a2ffe74b977bb3d5ef3b2fa5ba..0000000000000000000000000000000000000000 --- a/Examples/1-res-Annotate/tmp_files/genome2.fst-split5N.fna-prokkaRes/GEN2.0219.00001.log +++ /dev/null @@ -1,119 +0,0 @@ -[13:18:45] This is prokka 1.14-dev -[13:18:45] Written by Torsten Seemann <torsten.seemann@gmail.com> -[13:18:45] Homepage is https://github.com/tseemann/prokka -[13:18:45] Local time is Tue Feb 12 13:18:45 2019 -[13:18:45] You are aperrin -[13:18:45] Operating system is darwin -[13:18:45] You have BioPerl 1.006924 -[13:18:45] System has 8 cores. -[13:18:45] Will use maximum of 1 cores. -[13:18:45] Annotating as >>> Bacteria <<< -[13:18:45] Generating locus_tag from 'Examples/1-res-Annotate/tmp_files/genome2.fst-split5N.fna' contents. -[13:18:45] Setting --locustag OHLPOIIB from MD5 8159822bce92b47adcc120629558b9c6 -[13:18:45] Creating new output folder: Examples/1-res-Annotate/tmp_files/genome2.fst-split5N.fna-prokkaRes -[13:18:45] Running: mkdir -p Examples\/1\-res\-Annotate\/tmp_files\/genome2\.fst\-split5N\.fna\-prokkaRes -[13:18:45] Using filename prefix: GEN2.0219.00001.XXX -[13:18:45] Setting HMMER_NCPU=1 -[13:18:45] Writing log to: Examples/1-res-Annotate/tmp_files/genome2.fst-split5N.fna-prokkaRes/GEN2.0219.00001.log -[13:18:45] Command: /usr/local/bin/prokka --outdir Examples/1-res-Annotate/tmp_files/genome2.fst-split5N.fna-prokkaRes --cpus 1 --prefix GEN2.0219.00001 Examples/1-res-Annotate/tmp_files/genome2.fst-split5N.fna -[13:18:45] Appending to PATH: /Users/aperrin/Softwares/src/prokka/bin/../binaries/darwin -[13:18:45] Appending to PATH: /Users/aperrin/Softwares/src/prokka/bin/../binaries/darwin/../common -[13:18:45] Appending to PATH: /Users/aperrin/Softwares/src/prokka/bin -[13:18:45] Looking for 'aragorn' - found /Users/aperrin/Softwares/src/prokka/bin/../binaries/darwin/aragorn -[13:18:45] Determined aragorn version is 1.2 -[13:18:45] Looking for 'barrnap' - found /usr/local/bin/barrnap -[13:18:45] Determined barrnap version is 0.8 -[13:18:45] Looking for 'blastp' - found /Users/aperrin/Softwares/bin/blastp -[13:18:45] Determined blastp version is 2.3 -[13:18:45] Looking for 'cmpress' - found /usr/local/bin/cmpress -[13:18:45] Determined cmpress version is 1.1 -[13:18:45] Looking for 'cmscan' - found /usr/local/bin/cmscan -[13:18:45] Determined cmscan version is 1.1 -[13:18:45] Looking for 'egrep' - found /usr/bin/egrep -[13:18:45] Looking for 'find' - found /usr/bin/find -[13:18:45] Looking for 'grep' - found /usr/bin/grep -[13:18:45] Looking for 'hmmpress' - found /Users/aperrin/Softwares/src/prokka/bin/../binaries/darwin/hmmpress -[13:18:45] Determined hmmpress version is 3.1 -[13:18:45] Looking for 'hmmscan' - found /usr/local/bin/hmmscan -[13:18:45] Determined hmmscan version is 3.1 -[13:18:45] Looking for 'java' - found /usr/bin/java -[13:18:45] Looking for 'less' - found /usr/bin/less -[13:18:45] Looking for 'makeblastdb' - found /Users/aperrin/Softwares/bin/makeblastdb -[13:18:45] Determined makeblastdb version is 2.3 -[13:18:45] Looking for 'minced' - found /Users/aperrin/Softwares/src/prokka/bin/../binaries/darwin/../common/minced -[13:18:45] Determined minced version is 2.0 -[13:18:45] Looking for 'parallel' - found /usr/local/bin/parallel -[13:18:45] Determined parallel version is 20181022 -[13:18:45] Looking for 'prodigal' - found /usr/local/bin/prodigal -[13:18:45] Determined prodigal version is 2.6 -[13:18:45] Looking for 'prokka-genbank_to_fasta_db' - found /Users/aperrin/Softwares/src/prokka/bin/prokka-genbank_to_fasta_db -[13:18:45] Looking for 'sed' - found /usr/bin/sed -[13:18:45] Looking for 'tbl2asn' - found /Users/aperrin/Softwares/src/prokka/bin/../binaries/darwin/tbl2asn -[13:18:45] Determined tbl2asn version is 25.6 -[13:18:45] Using genetic code table 11. -[13:18:45] Loading and checking input file: Examples/1-res-Annotate/tmp_files/genome2.fst-split5N.fna -[13:18:45] Wrote 4 contigs totalling 10711 bp. -[13:18:45] Predicting tRNAs and tmRNAs -[13:18:45] Running: aragorn -l -gc11 -w Examples\/1\-res\-Annotate\/tmp_files\/genome2\.fst\-split5N\.fna\-prokkaRes\/GEN2\.0219\.00001\.fna -[13:18:45] Found 0 tRNAs -[13:18:45] Predicting Ribosomal RNAs -[13:18:45] Running Barrnap with 1 threads -[13:18:45] Found 0 rRNAs -[13:18:45] Skipping ncRNA search, enable with --rfam if desired. -[13:18:45] Total of 0 tRNA + rRNA features -[13:18:45] Searching for CRISPR repeats -[13:18:46] Found 0 CRISPRs -[13:18:46] Predicting coding sequences -[13:18:46] Contigs total 10711 bp, so using meta mode -[13:18:46] Running: prodigal -i Examples\/1\-res\-Annotate\/tmp_files\/genome2\.fst\-split5N\.fna\-prokkaRes\/GEN2\.0219\.00001\.fna -c -m -g 11 -p meta -f sco -q -[13:18:46] Found 13 CDS -[13:18:46] Connecting features back to sequences -[13:18:46] Not using genus-specific database. Try --usegenus to enable it. -[13:18:46] Annotating CDS, please be patient. -[13:18:46] Will use 1 CPUs for similarity searching. -[13:18:46] There are still 13 unannotated CDS left (started with 13) -[13:18:46] Will use blast to search against /Users/aperrin/Softwares/src/prokka/db/kingdom/Bacteria/sprot with 1 CPUs -[13:18:46] Running: cat Examples\/1\-res\-Annotate\/tmp_files\/genome2\.fst\-split5N\.fna\-prokkaRes\/sprot\.faa | parallel --gnu --plain -j 1 --block 1697 --recstart '>' --pipe blastp -query - -db /Users/aperrin/Softwares/src/prokka/db/kingdom/Bacteria/sprot -evalue 1e-06 -num_threads 1 -num_descriptions 1 -num_alignments 1 -seg no > Examples\/1\-res\-Annotate\/tmp_files\/genome2\.fst\-split5N\.fna\-prokkaRes\/sprot\.blast 2> /dev/null -[13:18:47] Deleting unwanted file: Examples/1-res-Annotate/tmp_files/genome2.fst-split5N.fna-prokkaRes/sprot.faa -[13:18:47] Deleting unwanted file: Examples/1-res-Annotate/tmp_files/genome2.fst-split5N.fna-prokkaRes/sprot.blast -[13:18:47] There are still 5 unannotated CDS left (started with 13) -[13:18:47] Will use hmmer3 to search against /Users/aperrin/Softwares/src/prokka/db/hmm/HAMAP.hmm with 1 CPUs -[13:18:47] Running: cat Examples\/1\-res\-Annotate\/tmp_files\/genome2\.fst\-split5N\.fna\-prokkaRes\/HAMAP\.hmm\.faa | parallel --gnu --plain -j 1 --block 521 --recstart '>' --pipe hmmscan --noali --notextw --acc -E 1e-06 --cpu 1 /Users/aperrin/Softwares/src/prokka/db/hmm/HAMAP.hmm /dev/stdin > Examples\/1\-res\-Annotate\/tmp_files\/genome2\.fst\-split5N\.fna\-prokkaRes\/HAMAP\.hmm\.hmmer3 2> /dev/null -[13:18:48] Deleting unwanted file: Examples/1-res-Annotate/tmp_files/genome2.fst-split5N.fna-prokkaRes/HAMAP.hmm.faa -[13:18:48] Deleting unwanted file: Examples/1-res-Annotate/tmp_files/genome2.fst-split5N.fna-prokkaRes/HAMAP.hmm.hmmer3 -[13:18:48] Labelling remaining 5 proteins as 'hypothetical protein' -[13:18:48] Found 8 unique /gene codes. -[13:18:48] Fixed 0 colliding /gene names. -[13:18:48] Adding /locus_tag identifiers -[13:18:48] Assigned 13 locus_tags to CDS and RNA features. -[13:18:48] Writing outputs to Examples/1-res-Annotate/tmp_files/genome2.fst-split5N.fna-prokkaRes/ -[13:18:48] Generating annotation statistics file -[13:18:48] Generating Genbank and Sequin files -[13:18:48] Running: tbl2asn -V b -a r10k -l paired-ends -M n -N 1 -y 'Annotated using prokka 1.14-dev from https://github.com/tseemann/prokka' -Z Examples\/1\-res\-Annotate\/tmp_files\/genome2\.fst\-split5N\.fna\-prokkaRes\/GEN2\.0219\.00001\.err -i Examples\/1\-res\-Annotate\/tmp_files\/genome2\.fst\-split5N\.fna\-prokkaRes\/GEN2\.0219\.00001\.fsa 2> /dev/null -[13:18:48] Deleting unwanted file: Examples/1-res-Annotate/tmp_files/genome2.fst-split5N.fna-prokkaRes/errorsummary.val -[13:18:48] Deleting unwanted file: Examples/1-res-Annotate/tmp_files/genome2.fst-split5N.fna-prokkaRes/GEN2.0219.00001.dr -[13:18:48] Deleting unwanted file: Examples/1-res-Annotate/tmp_files/genome2.fst-split5N.fna-prokkaRes/GEN2.0219.00001.fixedproducts -[13:18:48] Deleting unwanted file: Examples/1-res-Annotate/tmp_files/genome2.fst-split5N.fna-prokkaRes/GEN2.0219.00001.ecn -[13:18:48] Deleting unwanted file: Examples/1-res-Annotate/tmp_files/genome2.fst-split5N.fna-prokkaRes/GEN2.0219.00001.val -[13:18:48] Repairing broken .GBK output that tbl2asn produces... -[13:18:48] Running: sed 's/COORDINATES: profile/COORDINATES:profile/' < Examples\/1\-res\-Annotate\/tmp_files\/genome2\.fst\-split5N\.fna\-prokkaRes\/GEN2\.0219\.00001\.gbf > Examples\/1\-res\-Annotate\/tmp_files\/genome2\.fst\-split5N\.fna\-prokkaRes\/GEN2\.0219\.00001\.gbk -[13:18:48] Deleting unwanted file: Examples/1-res-Annotate/tmp_files/genome2.fst-split5N.fna-prokkaRes/GEN2.0219.00001.gbf -[13:18:48] Output files: -[13:18:48] Examples/1-res-Annotate/tmp_files/genome2.fst-split5N.fna-prokkaRes/GEN2.0219.00001.gff -[13:18:48] Examples/1-res-Annotate/tmp_files/genome2.fst-split5N.fna-prokkaRes/GEN2.0219.00001.tbl -[13:18:48] Examples/1-res-Annotate/tmp_files/genome2.fst-split5N.fna-prokkaRes/GEN2.0219.00001.sqn -[13:18:48] Examples/1-res-Annotate/tmp_files/genome2.fst-split5N.fna-prokkaRes/GEN2.0219.00001.fna -[13:18:48] Examples/1-res-Annotate/tmp_files/genome2.fst-split5N.fna-prokkaRes/GEN2.0219.00001.tsv -[13:18:48] Examples/1-res-Annotate/tmp_files/genome2.fst-split5N.fna-prokkaRes/GEN2.0219.00001.err -[13:18:48] Examples/1-res-Annotate/tmp_files/genome2.fst-split5N.fna-prokkaRes/GEN2.0219.00001.txt -[13:18:48] Examples/1-res-Annotate/tmp_files/genome2.fst-split5N.fna-prokkaRes/GEN2.0219.00001.fsa -[13:18:48] Examples/1-res-Annotate/tmp_files/genome2.fst-split5N.fna-prokkaRes/GEN2.0219.00001.faa -[13:18:48] Examples/1-res-Annotate/tmp_files/genome2.fst-split5N.fna-prokkaRes/GEN2.0219.00001.log -[13:18:48] Examples/1-res-Annotate/tmp_files/genome2.fst-split5N.fna-prokkaRes/GEN2.0219.00001.ffn -[13:18:48] Examples/1-res-Annotate/tmp_files/genome2.fst-split5N.fna-prokkaRes/GEN2.0219.00001.gbk -[13:18:48] Annotation finished successfully. -[13:18:48] Walltime used: 0.05 minutes -[13:18:48] If you use this result please cite the Prokka paper: -[13:18:48] Seemann T (2014) Prokka: rapid prokaryotic genome annotation. Bioinformatics. 30(14):2068-9. -[13:18:48] Type 'prokka --citation' for more details. -[13:18:48] Share and enjoy! diff --git a/Examples/1-res-Annotate/tmp_files/genome2.fst-split5N.fna-prokkaRes/GEN2.0219.00001.sqn b/Examples/1-res-Annotate/tmp_files/genome2.fst-split5N.fna-prokkaRes/GEN2.0219.00001.sqn deleted file mode 100644 index bf085e79297a2ed59f80a72c9597a16cf084ff9b..0000000000000000000000000000000000000000 --- a/Examples/1-res-Annotate/tmp_files/genome2.fst-split5N.fna-prokkaRes/GEN2.0219.00001.sqn +++ /dev/null @@ -1,1318 +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-dev 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 2 } , - { - label - str "day" , - data - int 12 } , - { - label - str "year" , - data - int 2019 } } } , - create-date - std { - year 2019 , - month 2 , - day 12 } } , - 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 OHLPOIIB_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:2.6" } , - { - qual "inference" , - val "similar to AA sequence:UniProtKB:P02915" } } , - xref { - { - data - gene { - locus "hisP" , - locus-tag "OHLPOIIB_00001" } } } } , - { - 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:2.6" } } , - xref { - { - data - gene { - locus-tag "OHLPOIIB_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-dev 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 2 } , - { - label - str "day" , - data - int 12 } , - { - label - str "year" , - data - int 2019 } } } , - create-date - std { - year 2019 , - month 2 , - day 12 } } , - 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:2.6" } , - { - qual "inference" , - val "similar to AA sequence:UniProtKB:P0AFM9" } } , - xref { - { - data - gene { - locus "pspB" , - locus-tag "OHLPOIIB_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:2.6" } , - { - qual "inference" , - val "similar to AA sequence:UniProtKB:Q05354" } } , - xref { - { - data - gene { - locus "hpcD" , - locus-tag "OHLPOIIB_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:2.6" } , - { - qual "inference" , - val "similar to AA sequence:UniProtKB:P75820" } } , - xref { - { - data - gene { - locus "amiD" , - locus-tag "OHLPOIIB_00005" } } } } , - { - 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:2.6" } , - { - qual "inference" , - val "similar to AA sequence:UniProtKB:P00962" } } , - xref { - { - data - gene { - locus "glnS" , - locus-tag "OHLPOIIB_00006" } } } } } } } } , - set { - class nuc-prot , - descr { - source { - org { - taxname "Genus species" , - orgname { - mod { - { - subtype strain , - subname "strain" } } , - gcode 11 } } } , - comment "Annotated using prokka 1.14-dev 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 2 } , - { - label - str "day" , - data - int 12 } , - { - label - str "year" , - data - int 2019 } } } , - create-date - std { - year 2019 , - month 2 , - day 12 } } , - 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 OHLPOIIB_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 OHLPOIIB_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 OHLPOIIB_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:2.6" } , - { - qual "inference" , - val "similar to AA sequence:UniProtKB:P0A873" } } , - xref { - { - data - gene { - locus "trmD" , - locus-tag "OHLPOIIB_00007" } } } } , - { - 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:2.6" } } , - xref { - { - data - gene { - locus-tag "OHLPOIIB_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:2.6" } } , - xref { - { - data - gene { - locus-tag "OHLPOIIB_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:2.6" } } , - xref { - { - data - gene { - locus-tag "OHLPOIIB_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-dev 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 2 } , - { - label - str "day" , - data - int 12 } , - { - label - str "year" , - data - int 2019 } } } , - create-date - std { - year 2019 , - month 2 , - day 12 } } , - 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 OHLPOIIB_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:2.6" } , - { - qual "inference" , - val "similar to AA sequence:UniProtKB:O07838" } } , - xref { - { - data - gene { - locus "dctM" , - locus-tag "OHLPOIIB_00011" } } } } , - { - 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:2.6" } } , - xref { - { - data - gene { - locus-tag "OHLPOIIB_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:2.6" } , - { - qual "inference" , - val "similar to AA sequence:UniProtKB:P39776" } } , - xref { - { - data - gene { - locus "xerC" , - locus-tag "OHLPOIIB_00013" } } } } } } } } } } diff --git a/Examples/1-res-Annotate/tmp_files/genome2.fst-split5N.fna-prokkaRes/GEN2.0219.00001.tbl b/Examples/1-res-Annotate/tmp_files/genome2.fst-split5N.fna-prokkaRes/GEN2.0219.00001.tbl deleted file mode 100644 index a84c1e12fffdcf294a01f7461f87026eb390e347..0000000000000000000000000000000000000000 --- a/Examples/1-res-Annotate/tmp_files/genome2.fst-split5N.fna-prokkaRes/GEN2.0219.00001.tbl +++ /dev/null @@ -1,82 +0,0 @@ ->Feature this_is_genome_1 -1 774 CDS - dbxref COG:COG4598 - gene hisP - inference ab initio prediction:Prodigal:2.6 - inference similar to AA sequence:UniProtKB:P02915 - locus_tag OHLPOIIB_00001 - product Histidine transport ATP-binding protein HisP -857 2260 CDS - inference ab initio prediction:Prodigal:2.6 - locus_tag OHLPOIIB_00002 - product hypothetical protein ->Feature this_is_genome_2 -28 252 CDS - gene pspB - inference ab initio prediction:Prodigal:2.6 - inference similar to AA sequence:UniProtKB:P0AFM9 - locus_tag OHLPOIIB_00003 - product Phage shock protein B -301 681 CDS - EC_number 5.3.3.10 - gene hpcD - inference ab initio prediction:Prodigal:2.6 - inference similar to AA sequence:UniProtKB:Q05354 - locus_tag OHLPOIIB_00004 - product 5-carboxymethyl-2-hydroxymuconate Delta-isomerase -764 1597 CDS - EC_number 3.5.1.28 - dbxref COG:COG3023 - gene amiD - inference ab initio prediction:Prodigal:2.6 - inference similar to AA sequence:UniProtKB:P75820 - locus_tag OHLPOIIB_00005 - product N-acetylmuramoyl-L-alanine amidase AmiD -1628 3295 CDS - EC_number 6.1.1.18 - dbxref COG:COG0008 - gene glnS - inference ab initio prediction:Prodigal:2.6 - inference similar to AA sequence:UniProtKB:P00962 - locus_tag OHLPOIIB_00006 - product Glutamine--tRNA ligase ->Feature this_is_genome_3 -30 797 CDS - EC_number 2.1.1.228 - dbxref COG:COG0336 - gene trmD - inference ab initio prediction:Prodigal:2.6 - inference similar to AA sequence:UniProtKB:P0A873 - locus_tag OHLPOIIB_00007 - product tRNA (guanine-N(1)-)-methyltransferase -862 1122 CDS - inference ab initio prediction:Prodigal:2.6 - locus_tag OHLPOIIB_00008 - product hypothetical protein -1170 1751 CDS - inference ab initio prediction:Prodigal:2.6 - locus_tag OHLPOIIB_00009 - product hypothetical protein -1895 2263 CDS - inference ab initio prediction:Prodigal:2.6 - locus_tag OHLPOIIB_00010 - product hypothetical protein ->Feature this_is_genome_4 -1 1308 CDS - dbxref COG:COG1593 - gene dctM - inference ab initio prediction:Prodigal:2.6 - inference similar to AA sequence:UniProtKB:O07838 - locus_tag OHLPOIIB_00011 - product C4-dicarboxylate TRAP transporter large permease protein DctM -1340 1804 CDS - inference ab initio prediction:Prodigal:2.6 - locus_tag OHLPOIIB_00012 - product hypothetical protein -1832 2845 CDS - dbxref COG:COG4974 - gene xerC - inference ab initio prediction:Prodigal:2.6 - inference similar to AA sequence:UniProtKB:P39776 - locus_tag OHLPOIIB_00013 - product Tyrosine recombinase XerC diff --git a/Examples/1-res-Annotate/tmp_files/genome2.fst-split5N.fna-prokkaRes/GEN2.0219.00001.tsv b/Examples/1-res-Annotate/tmp_files/genome2.fst-split5N.fna-prokkaRes/GEN2.0219.00001.tsv deleted file mode 100644 index 73686a0ef5d0d079828e6630a7e50952851231d0..0000000000000000000000000000000000000000 --- a/Examples/1-res-Annotate/tmp_files/genome2.fst-split5N.fna-prokkaRes/GEN2.0219.00001.tsv +++ /dev/null @@ -1,14 +0,0 @@ -locus_tag ftype length_bp gene EC_number COG product -OHLPOIIB_00001 CDS 774 hisP COG4598 Histidine transport ATP-binding protein HisP -OHLPOIIB_00002 CDS 1404 hypothetical protein -OHLPOIIB_00003 CDS 225 pspB Phage shock protein B -OHLPOIIB_00004 CDS 381 hpcD 5.3.3.10 5-carboxymethyl-2-hydroxymuconate Delta-isomerase -OHLPOIIB_00005 CDS 834 amiD 3.5.1.28 COG3023 N-acetylmuramoyl-L-alanine amidase AmiD -OHLPOIIB_00006 CDS 1668 glnS 6.1.1.18 COG0008 Glutamine--tRNA ligase -OHLPOIIB_00007 CDS 768 trmD 2.1.1.228 COG0336 tRNA (guanine-N(1)-)-methyltransferase -OHLPOIIB_00008 CDS 261 hypothetical protein -OHLPOIIB_00009 CDS 582 hypothetical protein -OHLPOIIB_00010 CDS 369 hypothetical protein -OHLPOIIB_00011 CDS 1308 dctM COG1593 C4-dicarboxylate TRAP transporter large permease protein DctM -OHLPOIIB_00012 CDS 465 hypothetical protein -OHLPOIIB_00013 CDS 1014 xerC COG4974 Tyrosine recombinase XerC diff --git a/Examples/1-res-Annotate/tmp_files/genome2.fst-split5N.fna-prokkaRes/GEN2.0219.00001.txt b/Examples/1-res-Annotate/tmp_files/genome2.fst-split5N.fna-prokkaRes/GEN2.0219.00001.txt deleted file mode 100644 index 7c6686d050eb977ffdce18b3fd8062a41495ef9b..0000000000000000000000000000000000000000 --- a/Examples/1-res-Annotate/tmp_files/genome2.fst-split5N.fna-prokkaRes/GEN2.0219.00001.txt +++ /dev/null @@ -1,4 +0,0 @@ -organism: Genus species strain -contigs: 4 -bases: 10711 -CDS: 13 diff --git a/Examples/1-res-Annotate/tmp_files/genome3-chromo.fst-all.fna b/Examples/1-res-Annotate/tmp_files/genome3-chromo.fst-all.fna deleted file mode 100644 index 35d4e193748f3c3fa8abcaa61bc65ae4cae8054f..0000000000000000000000000000000000000000 --- a/Examples/1-res-Annotate/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/1-res-Annotate/tmp_files/genome3-chromo.fst-all.fna-split5N.fna b/Examples/1-res-Annotate/tmp_files/genome3-chromo.fst-all.fna-split5N.fna deleted file mode 100644 index 4ac241054ac16abe79be2b7ad970cc22310cad1c..0000000000000000000000000000000000000000 --- a/Examples/1-res-Annotate/tmp_files/genome3-chromo.fst-all.fna-split5N.fna +++ /dev/null @@ -1,6 +0,0 @@ ->header_genome3_1 -ATGAGAGCGCTACTGTGGCTGGTGGGTCTTGCGTTGCTGTTAACAGGCTGCGCGAGCGAAAAAGGAATTATCGATGAAGAGGGATATCAGCTTGATACCCGACATCGGGCGCAGGCGGCCTATCCGCGCATTAAAGTCCTGGTGATTCACTATACGGCGGAAAACTTTGACGTTTCGCTGGCGACGTTAACGGGCCGCAACGTCAGTTCGCATTACCTGATTCCCGCAACCCCGCCATTATATGGCGGTAAACCGCGCATCTGGCAACTGGTGCCGGAACAGGATCAGGCCTGGCATGCGGGCGTCAGTTTCTGGCGAGGCGCCACGCGTCTCAATGATACGTCTATTGGCATTGAGCTGGAAAATCGCGGCTGGCGAATGTCCGGCGGGGTGAAATCTTTCGCGCCGTTTGAATCCGCGCAAATTCAGGCATTGATTCCGTTAGCGAAGGACATTATCGCGCGCTATGACATCAAACCGCAGAATGTGGTGGCCCATGCGGATATCGCGCCGCAGCGTAAAGACGATCCCGGCCCGCGCTTCCCGTGGCGCGAGCTGGCGGCACAGGGGATTGGCGCCTGGCCTGACGCCCAGCGTGTGGCGTTTTATCTGGCTGGACGCGCGCCGTATACGCCAGTCGATACCGCAACGGTGCTTGCGTTACTCTCGCGCTATGGCTATGAAGTCAAAGCCGATATGACGGCGCGCGAGCAACAGCGGGTGATTATGGCGTTCCAGATGCACTTCCGTCCGGCGCAATGGAACGGTATCGCAGATGCCGAAACGCAGGCGATTGCCGAAGCATTACTGGAGAAGTACGGCCAGGATTAACGAGTCCGGGAGCGGCGAGATTCCGGGCAGAGGAGGCGGCTATAGCGGATGAGAGCGCTACTGTGGCTGGTGGGTCTTGCGTTGCTGTTAACAGGCTGCGCGAGCGAAAAAGGAATTATCGATGAAGAGGGATATCAGCTTGATACCCGACATCGGGCGCAGGCGGCCTATCCGCGCATTAAAGTCCTGGTGATTCACTATACGGCGGAAAACTTTGACGTTTCGCTGGCGACGTTAACGGGCCGCAACGTCAGTTCGCATTACCTGATTCCCGCAACCCCGCCATTATATGGCGGTAAACCGCGCATCTGGCAACTGGTGCCGGAACAGGATCAGGCCTGGCATGCGGGCGTCAGTTTCTGGCGAGGCGCCACGCGTCTCAATGATACGTCTATTGGCATTGAGCTGGAAAATCGCGGCTGGCGAATGTCCGGCGGGGTGAAATCTTTCGCGCCGTTTGAATCCGCGCAAATTCAGGCATTGATTCCGTTAGCGAAGGACATTATCGCGCGCTATGACATCAAACCGCAGAATGTGGTGGCCCATGCGGATATCGCGCCGCAGCGTAAAGACGATCCCGGCCCGCGCTTCCCGTGGCGCGAGCTGGCGGCACAGGGGATTGGCGCCTGGCCTGACGCCCAGCGTGTGGCGTTTTATCTGGCTGGACGCGCGCCGTATACGCCAGTCGATACCGCAACGGTGCTTGCGTTACTCTCGCGCTATGGCTATGAAGTCAAAGCCGATATGACGGCGCGCGAGCAACAGCGGGTGATTATGGCGTTCCAGATGCACTTCCGTCCGGCGCAATGGAACGGTATCGCAGATGCCGAAACGCAGGCGATTGCCGAAGCATTACTGGAGAAGTACGGCCAGGATTAACAGGGCGCGGTATCGCGAGGACTCTCTCTTCGAGGACATGCCGCACTTTATTGCTGAATGTACTGAAAATATTCGCGAGCAGGCTGATTTACCCGGCCTGTTCAGCAAGGTAAACGAGGCGCTGGCCGCCAGCGGGATTTTCCCCATCGGCGGTATCCGCAGTCGCGCCCACTGGCTGGATACCTGGCAGATGGCTGACGGTAAGCATGATTACGCGTTTGTGCATATGACGCTGAAAATCGGCGCCGGGCGCAGCCTGGAGAGCCGTCAGGAAGTCGGCGAAATGCTGTTCGGGCTGATTAAAGCCCACTTCGCCGACCTGATGGAGAACCGCTATCTGGCGCTGTCGTTTGAGATTGCCGAGTTACATCCAACGCTCAATTACAAACAAAACAACGTACACGCGTTATTTAAATAGCCCGAGTATTAGCGCGCGGCGGCGCTATAGGCGCGCTATAGGCATGAGCGCGCTATTTCTGGCCATCCCGTTAACCATTTTTGTGTTGTTTGTGTTACCGATTTGGCTGTGGCTGCATTACAGCAACCGCGCCGGTCGGGGAGAACTGTCGCAAAGCGAGCAGCAACGCTTACTGCAACTCACAGACGACGCGCAACGTATGCGCGAGCGCATTCAGGCGCTGGAAGACATTCTTGATGCAGAGCATCCGAACTGGAGAGAGCGCTAACGAGAGTCTCGGAGGAGCGGCGCTCTGGATGCCCGCGACTAAATTCTCCCGACGTACCCTCCTGACGGCAGGTTCTGCGCTTGCTGTTCTTCCTTTCCTGCGCGCCTTGCCGGTACAGGCGCGTGAACCTCGCGAGACCGTCGATATTAAGGATTATCCGGCGGATGACGGTATCGCCTCGTTCAAACAGGCCTTCGCCGACGGACAGACCGTGGTCGTACCGCCAGGATGGGTGTGTGAAAATATCAATGCGGCGATAACGATTCCGGCGGGAAAAACGCTGCGGGTACAGGGCGCGGTGCGTGGGAATGGCCGGGGACGGTTTATTTTGCAGGACGGGTGTCAGGTGGTGGGGGAGCAGGGCGGCAGTCTGCACAATGTGACGCTGGATGTTCGCGGGTCGGACTGTGTGATTAAAGGCGTGGCGATGAGCGGCTTTGGCCCCGTCGCGCAAATTTTCATCGGTGGTAAGGAACCGCAGGTGATGCGTAATCTCATTATCGATGACATCACCGTTACCCACGCCAACTACGCCATTCTCCGCCAGGGATTTCATAACCAAATGGACGGCGCGAGGATTACGCATAGCCGCTTTAGCGATTTACAGGGGGACGCCATTGAGTGGAATGTCGCGATTCACGACCGCGATATCCTGATTTCCGATCATGTCATCGAACGCATTGATTGTACCAATGGCAAAATCAACTGGGGGATCGGCATCGGGCTGGCGGGTAGCACCTATGACAACAGTTATCCTGAAGACCAGGCAGTAAAAAACTTTGTGGTGGCCAATATTACCGGATCTGATTGCCGACAGCTTGTGCACGTAGAAAATGGCAAACATTTCGTCATTCGCAATGTCAAAGCCAAAAACATCACGCCCGATTTCAGTAAAAATGCGGGTATTGATAACGCAACGATCGCAATTTATGGCTGTGATAATTTCGTCATTGATAATATTGATATGACGAATAGTGCCGGGATGCTCATCGGCTATGGCGTCGTTAAAGGAAAATACCTGTCAATTCCGCAAAACTTTAAATTAAACGCTATTCGGTTGGATAATCGCCAGGTTGCTTATAAATTACGCGGCATTCAAATTTCCTCCGGCAACACCCCCTCTTTTGTCGCCATCACCAATGTACGGATGACGCGTGCTACGCTGGAACTGCATAATCAACCGCAGCACCTCTTCCTGCGTAATATCAACGTGATGCAAACTTCAGCGATTGGCCCGGCGTTAAAAATGCATTTCGATTTGCGTAAAGATGTCCGTGGTCAATTTATGGCCCGCCAGGACACGCTGCTTTCCCTCGCTAATGTTCATGCCATCAATGAAAACGGGCAGAGTTCCGTGGATATCGACAGGATTAATCACCAAACCGTGAATGTCGAAGCAGTGAATTTTTCGCTGCCGAAGCGGGGAGGGTAACGCGTCTGCGCGCGCGGAGAGAGGCTCTCAGGACATGTCAGAAAATAAATTACACGTTATCGATTTGCACAAACGCTACGGCGGTCATGAAGTGCTGAAAGGGGTATCGCTGCAGGCCCGCGCCGGAGATGTGATTAGCATCATCGGCTCGTCCGGCTCCGGTAAAAGCACTTTTTTGCGCTGTATTAACTTCCTCGAAAAACCGAGCGAAGACGCGATTATCGTGAACGGTCAGAACATTAATCTGGTGCGCGACAAAGACGGGCAGCTCAAAGTGGCGGATAAAAATCAGCTACGCTTGTTGCGTACCCGCCTGACGATGGTGTTTCAGCACTTTAACCTCTGGAGCCACATGACGGTGCTGGAAAATGTGATGGAAGCGCCGATTCAGGTACTGGGATTAAGCAAGCACGACGCGCGCGAGCGGGCGTTGAAATATCTGGCGAAGGTGGGGATTGATGAGCGCGCTCAGGGCAAATATCCCGTTCATCTCTCCGGTGGCCAACAGCAGCGCGTTTCTATTGCGCGCGCGCTGGCGATGGAACCTGACGTTTTACTGTTCGATGAACCCACTTCGGCGCTCGATCCTGAACTGGTCGGCGAAGTGTTGCGCATCATGCAACAACTGGCGGAAGAAGGCAAAACGATGGTGGTGGTCACGCATGAAATGGGCTTCGTTCGCCATGTCTCTTCGCACGTTATTTTTCTGCATCAGGGGAAAATTGAAGAAGAGGGCGATCCGGAGCAGGTGTTCGGCAATCCGCAAAGCCCGCGTTTACAGCAATTCCTGAAAGGCTCGCTGAAATAACCGGATGCGCGCGATATATCGGCGATGCGTGTTTATTGGCATCGTTAGCCTGTTTCCTGAAATGTTCCGCGCAATTACCGATTACGGGGTAACTGGCCGGGCAGTAAAAAATGGCCTGCTGAACATCCAAAGCTGGAGTCCTCGCGACTTCACGCATGACCGGCACCGTACCGTGGACGATCGTCCTTACGGCGGCGGACCAGGGATGTTAATGATGGTGCAACCCTTGCGGGACGCCATTCACGCAGCAAAAGCCGCGGCAGGTGAAGGCGCTAAAGTGATTTATCTGTCGCCTCAGGGACGCAAGCTTGATCAAGCGGGCGTTAGCGAGCTGGCCACGAATCAGAAGCTTATTCTGGTGTGTGGTCGCTACGAAGGCGTAGATGAGCGCGTAATTCAGACCGAAATTGACGAAGAATGGTCAATTGGCGATTACGTTCTCAGCGGTGGCGAACTACCGGCAATGACGCTGATTGACTCCGTCGCCCGGTTTATACCGGGAGTTCTGGGGCATGAAGCATCAGCAATCGAAGATTCGTTTGCTGATGGGTTGCTGGATTGTCCGCACTATACGCGCCCTGAAGTGTTAGAGGGGATGGAAGTACCGCCAGTATTGCTGTCGGGAAACCATGCTGAGATACGTCGCTGGCGTTTGAAACAGTCGCTGGGCCGAACCTGGCTTAGAAGACCTGAACTTCTGGAAAACCTGGCTCTGACTGAAGAGCAAGCAAGGTTGCTGGCGGAGTTCAAAACAGAACACGCACAACAGCAGCATAAACATGATGGGATGGCATAGCCGGCTCTGCGAGAGAGGAGCGCTCGCATGAATAATCATTTTGGGAAAGGGTTAATGGCCGGGTTGCACGCGCCATATGCATATAGCGCGCATCATGCGGTGAATTTCTGTTCTGAGTATAAACGTGGCTTTGTATTGGGTTTTACACACCGTATGTTCGAAAAGACCGGCGATCGTCAACTTAGCGCGTGGGAGGCTGGAATTCTGACGCGTCGCTATGGTCTGGATAAAGAAATGGTGATGGATTTCTTTAAAGAGAATCATTCCGGGATGGCGGTTCGCTTCTTTATGGCCGGTTATCGACTCGAAGGTTGA ->genome3_plasmi_2 -ATGTCTACGCTTCTCTATTTGCACGGATTCAACAGTTCCCCTCGCTCGGCAAAAGCGTGCCAGCTAAAAAACTGGCTGGCGGAGCGTCATCCGCATGTTGAGATGATCGTCCCTCAACTACCGCCGTATCCTGCCGATGCGGCGGAGTTGCTGGAGTCTCTCGTGCTTGAGCATGGCGGTGCGCCATTAGGGCTGGTAGGATCGTCGCTGGGTGGTTATTACGCCACCTGGCTGTCGCAATGTTTTATGCTGCCGGCTGTGGTGGTGAATCCCGCCGTGCGGCCCTTTGAATTACTGACCGACTATCTCGGTCAGAACGAGAACCCCTACACCGGGCAGCAATATGTGCTAGAGTCTCGCCATATTTATGATCTTAAAGTCATGCAGATTGACCCGCTGGAAGCGCCGGACCTGATCTGGCTACTGCAACAGACGGGCGATGAAGTGCTGGATTACCGCCAGGCGGTGGCATATTACGCCTCCTGCCGTCAGACAGTGACCGAGGGTGGTAATCACGCATTCACGGGCTTCGAAGATTATTTCAACCAGATTGTCGATTTTCTTGGACTGCACAGTTGCTGACGCGTAGCGGCCGGAATCTTCTCGGAGAGGCGCTTCTCTCTCGGAGATGATTGACCCTATTTTTGCGTCCTGTACGCTAATTGCCGTCTTTGTTGTTTTACTGGCCATGGGCGCGCCTATCGGGATCTGCATCGTTATCGCCTCTTTCAGCACCATGATGCTGGTACTGCCTTTCGATATTTCGATGTTCGCCACCGCGCAAAAAATGTTCTCCAGCCTGGACAGTTTTGCCTTGCTGGCCGTGCCGTTCTTCGTTTTGTCCGGGGTGATCATGAATAGCGGGGGAATTGCCGCCCGGCTGATCAATTTTGCCAAACTGTTTACTGGCAAACTGCCCGGTTCGCTCTCTTATACCAACATCGTCGGCAATATGATGTTCGGTGCAATTTCCGGATCGGCAATTGCCGCCTCAACCTCCATCGGCGGCGTGATGGTGCCGATGAGCGCGCGCGAAGGTTACGATCGCGGCTTTGCGGCCGCGGTGAATATCGCCTCCGCGCCGACGGGAATGTTAATTCCGCCCACCACGGCTTTTATCCTTTATGCGCTGGCAAGCGGGGGAACATCGATTGCCGCTCTGTTCGCCGGCGGTCTGGTCGCGGGAGTGCTGTGGGGCGTTGGCTGTATGCTGGTCACGCTGGTAGTCGCTAAGCGTCGAAATTATCGGGTTTTCTTCACCGTCCAAAAAGGCATGGCGCTAAAAGTTGCCGTTGAGGCCATTCCCAGCCTGTTACTGATCGTGATTATCGTCGGCGGCATTGTGCAGGGGATTTTCACCGCCATTGAAGCCTCCGCGATTGCCGTGGTGTATACGTTATTGCTGACGATGGTGTTTTACCGCACGCTGAAAATTAAGGATTTGCCTTCGATTTTGCTCCAGACAGTGGTAATGACCGGGGTCATCATGTTCCTGCTGGCAACCTCTTCGGCGATGTCCTTCTCAATGTCGATCACCAATATTCCTGCGGCGCTGAGCGATATGATCCTCGGTATTTCCGCCAATAAACTGGTTATCCTGTTAGTCATTACCGTCTTTTTGTTGATTATCGGCGCATTTATGGATATCGGTCCGGCCATTCTGATTTTTACCCCGATTCTGCTGCCGATCATGGCTAAACTGGGCGTCGATCCGGTGCATTTGGGCATTATCATGATCTATAACCTGGCGATTGGCACCATTACGCCGCCAGTTGGCAGTGGTTTATATGTCGGGGCGAGCGTCGGTAAGGTCAAAGTTGAGGAAGTGATTAAACCGTTGCTGCCTTTTTACGGCGCGATTATCGGCGTTCTGTTATTAATTACCTACATTCCGGAAATCATACTGTTCTTACCCCGTCTACTGGGCATCATGTAAACCCGATGGCGCGCAGAGGCGCGAGTTCTGGA ->genome3_plasmi_3 -CACAGGGCTTAGAGGCGCTATGGCAATGATAATTAATGGGAAATTAATTAAAGCAAAAGACTTAGCTAAGGCTGCAGGTGTATCTCGTTCAACAGTGATTAAATATTACGGCATTAGCCGTGAGAATTACGAAAGGGTAGCAACTGAAAGAAGGAAGCTTGCTTTTGAACTAAGAGCATCAGGTTTAAAATGGAAAGAAGTTGCTGAAAAAATGAACACGACAAAATATAGCGCAATTGCATATTATAGACGATATTTAGCATTAGAGAAAAACAAATAACAGGCGCTAAGGCGGCGATCCTAGCGCGCGATCGCGCATGCGATGGTCGAACTGCAACATCAACGGCTGATGGTGCTTGCCGAACAGCTCCAGCTGGACAGTCTTATCGGCGCAGCGCCGGCGCTGTCGCAACAGGCGGTGGATCAGGAATGGAGCTACATGGACTTCCTGGAGCACCTGTTACATGAGGAGAAACTGGCCCGGCATCAGCGTAAACAGGCGATGTACACGCGGATGGCAGCCTTCCCGGCGGTAAAGACGTTCGAGGAGTACGACTTCACCTTCGCCACCGGCGCTCCTCAGAAGCAAATCCAGTCGCTGCGATCCCTGAGCTTCATAGAGCGTAACGAAAACATCGTGTTGCTGGGGCCATCGGGCGTGGGAAAAACGCATCTGGCGATAGCCATGGGCTACGAAGCAGTACGGGCGGGCATCAAGGTTCGCTTCACAACAGCAGCGGACCTGCTGCTACAGCTGTCCACTTCACAGCGTCAGGGCCGTTACAAAACGACTCTCAATCGTGGTGTCATGGCCCCGAAGCTGCTTATCATCGATGAAATAGGTTATCTGCCGTTCAGTCAGGAGGAAGCCAAGCTGTTCTTCCAGGTCATCGCCAAACGTTACGAGAAGAGCGCGATGATCCTGACCTCCAACCTGCCGTTCGGGCAGTGGGATCAGACGTTCGCCGGTGATGCAGCGCTGACATCGGCGATGCTGGACCGGATCTTACATCACTCACACGTCGTGCAAATAAAAGGGGAAAGCTATCGACTGAAGCAGAAACGAAAGGCCGGGGTTATAGCTGAAGCTAATCCTGAGTAA diff --git a/Examples/1-res-Annotate/tmp_files/genome3-chromo.fst-all.fna-split5N.fna-prokka.log b/Examples/1-res-Annotate/tmp_files/genome3-chromo.fst-all.fna-split5N.fna-prokka.log deleted file mode 100644 index 5b897f7f9cddeebf15360eadd439465292a33ed6..0000000000000000000000000000000000000000 --- a/Examples/1-res-Annotate/tmp_files/genome3-chromo.fst-all.fna-split5N.fna-prokka.log +++ /dev/null @@ -1,121 +0,0 @@ -[13:18:48] This is prokka 1.14-dev -[13:18:48] Written by Torsten Seemann <torsten.seemann@gmail.com> -[13:18:48] Homepage is https://github.com/tseemann/prokka -[13:18:48] Local time is Tue Feb 12 13:18:48 2019 -[13:18:48] You are aperrin -[13:18:48] Operating system is darwin -[13:18:48] You have BioPerl 1.006924 -[13:18:48] System has 8 cores. -[13:18:48] Will use maximum of 1 cores. -[13:18:48] Annotating as >>> Bacteria <<< -[13:18:48] Generating locus_tag from 'Examples/1-res-Annotate/tmp_files/genome3-chromo.fst-all.fna-split5N.fna' contents. -[13:18:48] Setting --locustag PFKCIMHH from MD5 9f4c2611ce3f44c6b2e6fb97579c5725 -[13:18:48] Creating new output folder: Examples/1-res-Annotate/tmp_files/genome3-chromo.fst-all.fna-split5N.fna-prokkaRes -[13:18:48] Running: mkdir -p Examples\/1\-res\-Annotate\/tmp_files\/genome3\-chromo\.fst\-all\.fna\-split5N\.fna\-prokkaRes -[13:18:48] Using filename prefix: EXAM.1216.00002.XXX -[13:18:48] Setting HMMER_NCPU=1 -[13:18:48] Writing log to: Examples/1-res-Annotate/tmp_files/genome3-chromo.fst-all.fna-split5N.fna-prokkaRes/EXAM.1216.00002.log -[13:18:48] Command: /usr/local/bin/prokka --outdir Examples/1-res-Annotate/tmp_files/genome3-chromo.fst-all.fna-split5N.fna-prokkaRes --cpus 1 --prefix EXAM.1216.00002 Examples/1-res-Annotate/tmp_files/genome3-chromo.fst-all.fna-split5N.fna -[13:18:48] Appending to PATH: /Users/aperrin/Softwares/src/prokka/bin/../binaries/darwin -[13:18:48] Appending to PATH: /Users/aperrin/Softwares/src/prokka/bin/../binaries/darwin/../common -[13:18:48] Appending to PATH: /Users/aperrin/Softwares/src/prokka/bin -[13:18:48] Looking for 'aragorn' - found /Users/aperrin/Softwares/src/prokka/bin/../binaries/darwin/aragorn -[13:18:48] Determined aragorn version is 1.2 -[13:18:48] Looking for 'barrnap' - found /usr/local/bin/barrnap -[13:18:48] Determined barrnap version is 0.8 -[13:18:48] Looking for 'blastp' - found /Users/aperrin/Softwares/bin/blastp -[13:18:48] Determined blastp version is 2.3 -[13:18:48] Looking for 'cmpress' - found /usr/local/bin/cmpress -[13:18:48] Determined cmpress version is 1.1 -[13:18:48] Looking for 'cmscan' - found /usr/local/bin/cmscan -[13:18:48] Determined cmscan version is 1.1 -[13:18:48] Looking for 'egrep' - found /usr/bin/egrep -[13:18:48] Looking for 'find' - found /usr/bin/find -[13:18:48] Looking for 'grep' - found /usr/bin/grep -[13:18:48] Looking for 'hmmpress' - found /Users/aperrin/Softwares/src/prokka/bin/../binaries/darwin/hmmpress -[13:18:48] Determined hmmpress version is 3.1 -[13:18:48] Looking for 'hmmscan' - found /usr/local/bin/hmmscan -[13:18:48] Determined hmmscan version is 3.1 -[13:18:48] Looking for 'java' - found /usr/bin/java -[13:18:48] Looking for 'less' - found /usr/bin/less -[13:18:48] Looking for 'makeblastdb' - found /Users/aperrin/Softwares/bin/makeblastdb -[13:18:48] Determined makeblastdb version is 2.3 -[13:18:48] Looking for 'minced' - found /Users/aperrin/Softwares/src/prokka/bin/../binaries/darwin/../common/minced -[13:18:48] Determined minced version is 2.0 -[13:18:48] Looking for 'parallel' - found /usr/local/bin/parallel -[13:18:49] Determined parallel version is 20181022 -[13:18:49] Looking for 'prodigal' - found /usr/local/bin/prodigal -[13:18:49] Determined prodigal version is 2.6 -[13:18:49] Looking for 'prokka-genbank_to_fasta_db' - found /Users/aperrin/Softwares/src/prokka/bin/prokka-genbank_to_fasta_db -[13:18:49] Looking for 'sed' - found /usr/bin/sed -[13:18:49] Looking for 'tbl2asn' - found /Users/aperrin/Softwares/src/prokka/bin/../binaries/darwin/tbl2asn -[13:18:49] Determined tbl2asn version is 25.6 -[13:18:49] Using genetic code table 11. -[13:18:49] Loading and checking input file: Examples/1-res-Annotate/tmp_files/genome3-chromo.fst-all.fna-split5N.fna -[13:18:49] Wrote 3 contigs totalling 8817 bp. -[13:18:49] Predicting tRNAs and tmRNAs -[13:18:49] Running: aragorn -l -gc11 -w Examples\/1\-res\-Annotate\/tmp_files\/genome3\-chromo\.fst\-all\.fna\-split5N\.fna\-prokkaRes\/EXAM\.1216\.00002\.fna -[13:18:49] Found 0 tRNAs -[13:18:49] Predicting Ribosomal RNAs -[13:18:49] Running Barrnap with 1 threads -[13:18:49] Found 0 rRNAs -[13:18:49] Skipping ncRNA search, enable with --rfam if desired. -[13:18:49] Total of 0 tRNA + rRNA features -[13:18:49] Searching for CRISPR repeats -[13:18:49] Found 0 CRISPRs -[13:18:49] Predicting coding sequences -[13:18:49] Contigs total 8817 bp, so using meta mode -[13:18:49] Running: prodigal -i Examples\/1\-res\-Annotate\/tmp_files\/genome3\-chromo\.fst\-all\.fna\-split5N\.fna\-prokkaRes\/EXAM\.1216\.00002\.fna -c -m -g 11 -p meta -f sco -q -[13:18:49] Found 12 CDS -[13:18:49] Connecting features back to sequences -[13:18:49] Not using genus-specific database. Try --usegenus to enable it. -[13:18:49] Annotating CDS, please be patient. -[13:18:49] Will use 1 CPUs for similarity searching. -[13:18:49] There are still 12 unannotated CDS left (started with 12) -[13:18:49] Will use blast to search against /Users/aperrin/Softwares/src/prokka/db/kingdom/Bacteria/sprot with 1 CPUs -[13:18:49] Running: cat Examples\/1\-res\-Annotate\/tmp_files\/genome3\-chromo\.fst\-all\.fna\-split5N\.fna\-prokkaRes\/sprot\.faa | parallel --gnu --plain -j 1 --block 1443 --recstart '>' --pipe blastp -query - -db /Users/aperrin/Softwares/src/prokka/db/kingdom/Bacteria/sprot -evalue 1e-06 -num_threads 1 -num_descriptions 1 -num_alignments 1 -seg no > Examples\/1\-res\-Annotate\/tmp_files\/genome3\-chromo\.fst\-all\.fna\-split5N\.fna\-prokkaRes\/sprot\.blast 2> /dev/null -[13:18:50] Deleting unwanted file: Examples/1-res-Annotate/tmp_files/genome3-chromo.fst-all.fna-split5N.fna-prokkaRes/sprot.faa -[13:18:50] Deleting unwanted file: Examples/1-res-Annotate/tmp_files/genome3-chromo.fst-all.fna-split5N.fna-prokkaRes/sprot.blast -[13:18:50] There are still 4 unannotated CDS left (started with 12) -[13:18:50] Will use hmmer3 to search against /Users/aperrin/Softwares/src/prokka/db/hmm/HAMAP.hmm with 1 CPUs -[13:18:50] Running: cat Examples\/1\-res\-Annotate\/tmp_files\/genome3\-chromo\.fst\-all\.fna\-split5N\.fna\-prokkaRes\/HAMAP\.hmm\.faa | parallel --gnu --plain -j 1 --block 427 --recstart '>' --pipe hmmscan --noali --notextw --acc -E 1e-06 --cpu 1 /Users/aperrin/Softwares/src/prokka/db/hmm/HAMAP.hmm /dev/stdin > Examples\/1\-res\-Annotate\/tmp_files\/genome3\-chromo\.fst\-all\.fna\-split5N\.fna\-prokkaRes\/HAMAP\.hmm\.hmmer3 2> /dev/null -[13:18:51] Deleting unwanted file: Examples/1-res-Annotate/tmp_files/genome3-chromo.fst-all.fna-split5N.fna-prokkaRes/HAMAP.hmm.faa -[13:18:51] Deleting unwanted file: Examples/1-res-Annotate/tmp_files/genome3-chromo.fst-all.fna-split5N.fna-prokkaRes/HAMAP.hmm.hmmer3 -[13:18:51] Labelling remaining 4 proteins as 'hypothetical protein' -[13:18:51] Possible /pseudo 'N-acetylmuramoyl-L-alanine amidase AmiD' at header_genome3_1 position 880 -[13:18:51] Found 6 unique /gene codes. -[13:18:51] Fixed 2 duplicate /gene - amiD_1 amiD_2 -[13:18:51] Fixed 1 colliding /gene names. -[13:18:51] Adding /locus_tag identifiers -[13:18:51] Assigned 12 locus_tags to CDS and RNA features. -[13:18:51] Writing outputs to Examples/1-res-Annotate/tmp_files/genome3-chromo.fst-all.fna-split5N.fna-prokkaRes/ -[13:18:51] Generating annotation statistics file -[13:18:51] Generating Genbank and Sequin files -[13:18:51] Running: tbl2asn -V b -a r10k -l paired-ends -M n -N 1 -y 'Annotated using prokka 1.14-dev from https://github.com/tseemann/prokka' -Z Examples\/1\-res\-Annotate\/tmp_files\/genome3\-chromo\.fst\-all\.fna\-split5N\.fna\-prokkaRes\/EXAM\.1216\.00002\.err -i Examples\/1\-res\-Annotate\/tmp_files\/genome3\-chromo\.fst\-all\.fna\-split5N\.fna\-prokkaRes\/EXAM\.1216\.00002\.fsa 2> /dev/null -[13:18:51] Deleting unwanted file: Examples/1-res-Annotate/tmp_files/genome3-chromo.fst-all.fna-split5N.fna-prokkaRes/errorsummary.val -[13:18:51] Deleting unwanted file: Examples/1-res-Annotate/tmp_files/genome3-chromo.fst-all.fna-split5N.fna-prokkaRes/EXAM.1216.00002.dr -[13:18:51] Deleting unwanted file: Examples/1-res-Annotate/tmp_files/genome3-chromo.fst-all.fna-split5N.fna-prokkaRes/EXAM.1216.00002.fixedproducts -[13:18:51] Deleting unwanted file: Examples/1-res-Annotate/tmp_files/genome3-chromo.fst-all.fna-split5N.fna-prokkaRes/EXAM.1216.00002.ecn -[13:18:51] Deleting unwanted file: Examples/1-res-Annotate/tmp_files/genome3-chromo.fst-all.fna-split5N.fna-prokkaRes/EXAM.1216.00002.val -[13:18:51] Repairing broken .GBK output that tbl2asn produces... -[13:18:51] Running: sed 's/COORDINATES: profile/COORDINATES:profile/' < Examples\/1\-res\-Annotate\/tmp_files\/genome3\-chromo\.fst\-all\.fna\-split5N\.fna\-prokkaRes\/EXAM\.1216\.00002\.gbf > Examples\/1\-res\-Annotate\/tmp_files\/genome3\-chromo\.fst\-all\.fna\-split5N\.fna\-prokkaRes\/EXAM\.1216\.00002\.gbk -[13:18:51] Deleting unwanted file: Examples/1-res-Annotate/tmp_files/genome3-chromo.fst-all.fna-split5N.fna-prokkaRes/EXAM.1216.00002.gbf -[13:18:51] Output files: -[13:18:51] Examples/1-res-Annotate/tmp_files/genome3-chromo.fst-all.fna-split5N.fna-prokkaRes/EXAM.1216.00002.log -[13:18:51] Examples/1-res-Annotate/tmp_files/genome3-chromo.fst-all.fna-split5N.fna-prokkaRes/EXAM.1216.00002.ffn -[13:18:51] Examples/1-res-Annotate/tmp_files/genome3-chromo.fst-all.fna-split5N.fna-prokkaRes/EXAM.1216.00002.gbk -[13:18:51] Examples/1-res-Annotate/tmp_files/genome3-chromo.fst-all.fna-split5N.fna-prokkaRes/EXAM.1216.00002.fsa -[13:18:51] Examples/1-res-Annotate/tmp_files/genome3-chromo.fst-all.fna-split5N.fna-prokkaRes/EXAM.1216.00002.faa -[13:18:51] Examples/1-res-Annotate/tmp_files/genome3-chromo.fst-all.fna-split5N.fna-prokkaRes/EXAM.1216.00002.txt -[13:18:51] Examples/1-res-Annotate/tmp_files/genome3-chromo.fst-all.fna-split5N.fna-prokkaRes/EXAM.1216.00002.gff -[13:18:51] Examples/1-res-Annotate/tmp_files/genome3-chromo.fst-all.fna-split5N.fna-prokkaRes/EXAM.1216.00002.tbl -[13:18:51] Examples/1-res-Annotate/tmp_files/genome3-chromo.fst-all.fna-split5N.fna-prokkaRes/EXAM.1216.00002.sqn -[13:18:51] Examples/1-res-Annotate/tmp_files/genome3-chromo.fst-all.fna-split5N.fna-prokkaRes/EXAM.1216.00002.tsv -[13:18:51] Examples/1-res-Annotate/tmp_files/genome3-chromo.fst-all.fna-split5N.fna-prokkaRes/EXAM.1216.00002.fna -[13:18:51] Examples/1-res-Annotate/tmp_files/genome3-chromo.fst-all.fna-split5N.fna-prokkaRes/EXAM.1216.00002.err -[13:18:51] Annotation finished successfully. -[13:18:51] Walltime used: 0.05 minutes -[13:18:51] If you use this result please cite the Prokka paper: -[13:18:51] Seemann T (2014) Prokka: rapid prokaryotic genome annotation. Bioinformatics. 30(14):2068-9. -[13:18:51] Type 'prokka --citation' for more details. -[13:18:51] Share and enjoy! diff --git a/Examples/1-res-Annotate/tmp_files/genome3-chromo.fst-all.fna-split5N.fna-prokkaRes/EXAM.1216.00002.err b/Examples/1-res-Annotate/tmp_files/genome3-chromo.fst-all.fna-split5N.fna-prokkaRes/EXAM.1216.00002.err deleted file mode 100644 index 2a0b1de27bde2245f0d664366b748b61b299cd72..0000000000000000000000000000000000000000 --- a/Examples/1-res-Annotate/tmp_files/genome3-chromo.fst-all.fna-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/1-res-Annotate/tmp_files/genome3-chromo.fst-all.fna-split5N.fna-prokkaRes/EXAM.1216.00002:header_genome3_1_1 (length 276) -Examples/1-res-Annotate/tmp_files/genome3-chromo.fst-all.fna-split5N.fna-prokkaRes/EXAM.1216.00002:header_genome3_1_2 (length 276) -Examples/1-res-Annotate/tmp_files/genome3-chromo.fst-all.fna-split5N.fna-prokkaRes/EXAM.1216.00002:header_genome3_1_3 (length 157) -Examples/1-res-Annotate/tmp_files/genome3-chromo.fst-all.fna-split5N.fna-prokkaRes/EXAM.1216.00002:header_genome3_1_4 (length 74) -Examples/1-res-Annotate/tmp_files/genome3-chromo.fst-all.fna-split5N.fna-prokkaRes/EXAM.1216.00002:header_genome3_1_5 (length 467) -Examples/1-res-Annotate/tmp_files/genome3-chromo.fst-all.fna-split5N.fna-prokkaRes/EXAM.1216.00002:header_genome3_1_6 (length 257) -Examples/1-res-Annotate/tmp_files/genome3-chromo.fst-all.fna-split5N.fna-prokkaRes/EXAM.1216.00002:header_genome3_1_7 (length 263) -Examples/1-res-Annotate/tmp_files/genome3-chromo.fst-all.fna-split5N.fna-prokkaRes/EXAM.1216.00002:header_genome3_1_8 (length 95) -Examples/1-res-Annotate/tmp_files/genome3-chromo.fst-all.fna-split5N.fna-prokkaRes/EXAM.1216.00002:genome3_plasmi_2_1 (length 193) -Examples/1-res-Annotate/tmp_files/genome3-chromo.fst-all.fna-split5N.fna-prokkaRes/EXAM.1216.00002:genome3_plasmi_2_2 (length 435) -Examples/1-res-Annotate/tmp_files/genome3-chromo.fst-all.fna-split5N.fna-prokkaRes/EXAM.1216.00002:genome3_plasmi_3_1 (length 84) -Examples/1-res-Annotate/tmp_files/genome3-chromo.fst-all.fna-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/1-res-Annotate/tmp_files/genome3-chromo.fst-all.fna-split5N.fna-prokkaRes/EXAM.1216.00002:header_genome3_1 (length 5747) -Examples/1-res-Annotate/tmp_files/genome3-chromo.fst-all.fna-split5N.fna-prokkaRes/EXAM.1216.00002:genome3_plasmi_2 (length 1968) -Examples/1-res-Annotate/tmp_files/genome3-chromo.fst-all.fna-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/1-res-Annotate/tmp_files/genome3-chromo.fst-all.fna-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/1-res-Annotate/tmp_files/genome3-chromo.fst-all.fna-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/1-res-Annotate/tmp_files/genome3-chromo.fst-all.fna-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/1-res-Annotate/tmp_files/genome3-chromo.fst-all.fna-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/1-res-Annotate/tmp_files/genome3-chromo.fst-all.fna-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/1-res-Annotate/tmp_files/genome3-chromo.fst-all.fna-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/1-res-Annotate/tmp_files/genome3-chromo.fst-all.fna-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/1-res-Annotate/tmp_files/genome3-chromo.fst-all.fna-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/1-res-Annotate/tmp_files/genome3-chromo.fst-all.fna-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/1-res-Annotate/tmp_files/genome3-chromo.fst-all.fna-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/1-res-Annotate/tmp_files/genome3-chromo.fst-all.fna-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/1-res-Annotate/tmp_files/genome3-chromo.fst-all.fna-split5N.fna-prokkaRes/EXAM.1216.00002:CDS Insertion sequence IS5376 putative ATP-binding protein 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/1-res-Annotate/tmp_files/genome3-chromo.fst-all.fna-split5N.fna-prokkaRes/EXAM.1216.00002:header_genome3_1:Annotated using prokka 1.14-dev from https://github.com/tseemann/prokka -Examples/1-res-Annotate/tmp_files/genome3-chromo.fst-all.fna-split5N.fna-prokkaRes/EXAM.1216.00002:genome3_plasmi_2:Annotated using prokka 1.14-dev from https://github.com/tseemann/prokka -Examples/1-res-Annotate/tmp_files/genome3-chromo.fst-all.fna-split5N.fna-prokkaRes/EXAM.1216.00002:genome3_plasmi_3:Annotated using prokka 1.14-dev from https://github.com/tseemann/prokka - -DiscRep_ALL:MISSING_GENOMEASSEMBLY_COMMENTS::3 bioseqs are missing GenomeAssembly structured comments -Examples/1-res-Annotate/tmp_files/genome3-chromo.fst-all.fna-split5N.fna-prokkaRes/EXAM.1216.00002:header_genome3_1 (length 5747) -Examples/1-res-Annotate/tmp_files/genome3-chromo.fst-all.fna-split5N.fna-prokkaRes/EXAM.1216.00002:genome3_plasmi_2 (length 1968) -Examples/1-res-Annotate/tmp_files/genome3-chromo.fst-all.fna-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/1-res-Annotate/tmp_files/genome3-chromo.fst-all.fna-split5N.fna-prokkaRes/EXAM.1216.00002:header_genome3_1 (length 5747) -Examples/1-res-Annotate/tmp_files/genome3-chromo.fst-all.fna-split5N.fna-prokkaRes/EXAM.1216.00002:genome3_plasmi_2 (length 1968) -Examples/1-res-Annotate/tmp_files/genome3-chromo.fst-all.fna-split5N.fna-prokkaRes/EXAM.1216.00002:genome3_plasmi_3 (length 1102) - -DiscRep_ALL:TECHNIQUE_NOT_TSA::3 technique are not set as TSA -Examples/1-res-Annotate/tmp_files/genome3-chromo.fst-all.fna-split5N.fna-prokkaRes/EXAM.1216.00002:header_genome3_1 (length 5747) -Examples/1-res-Annotate/tmp_files/genome3-chromo.fst-all.fna-split5N.fna-prokkaRes/EXAM.1216.00002:genome3_plasmi_2 (length 1968) -Examples/1-res-Annotate/tmp_files/genome3-chromo.fst-all.fna-split5N.fna-prokkaRes/EXAM.1216.00002:genome3_plasmi_3 (length 1102) - -DiscRep_ALL:MISSING_STRUCTURED_COMMENT::3 sequences do not include structured comments. -Examples/1-res-Annotate/tmp_files/genome3-chromo.fst-all.fna-split5N.fna-prokkaRes/EXAM.1216.00002:header_genome3_1 (length 5747) -Examples/1-res-Annotate/tmp_files/genome3-chromo.fst-all.fna-split5N.fna-prokkaRes/EXAM.1216.00002:genome3_plasmi_2 (length 1968) -Examples/1-res-Annotate/tmp_files/genome3-chromo.fst-all.fna-split5N.fna-prokkaRes/EXAM.1216.00002:genome3_plasmi_3 (length 1102) - -DiscRep_ALL:MISSING_PROJECT::15 sequences do not include project. -Examples/1-res-Annotate/tmp_files/genome3-chromo.fst-all.fna-split5N.fna-prokkaRes/EXAM.1216.00002:header_genome3_1 (length 5747) -Examples/1-res-Annotate/tmp_files/genome3-chromo.fst-all.fna-split5N.fna-prokkaRes/EXAM.1216.00002:header_genome3_1_1 (length 276) -Examples/1-res-Annotate/tmp_files/genome3-chromo.fst-all.fna-split5N.fna-prokkaRes/EXAM.1216.00002:header_genome3_1_2 (length 276) -Examples/1-res-Annotate/tmp_files/genome3-chromo.fst-all.fna-split5N.fna-prokkaRes/EXAM.1216.00002:header_genome3_1_3 (length 157) -Examples/1-res-Annotate/tmp_files/genome3-chromo.fst-all.fna-split5N.fna-prokkaRes/EXAM.1216.00002:header_genome3_1_4 (length 74) -Examples/1-res-Annotate/tmp_files/genome3-chromo.fst-all.fna-split5N.fna-prokkaRes/EXAM.1216.00002:header_genome3_1_5 (length 467) -Examples/1-res-Annotate/tmp_files/genome3-chromo.fst-all.fna-split5N.fna-prokkaRes/EXAM.1216.00002:header_genome3_1_6 (length 257) -Examples/1-res-Annotate/tmp_files/genome3-chromo.fst-all.fna-split5N.fna-prokkaRes/EXAM.1216.00002:header_genome3_1_7 (length 263) -Examples/1-res-Annotate/tmp_files/genome3-chromo.fst-all.fna-split5N.fna-prokkaRes/EXAM.1216.00002:header_genome3_1_8 (length 95) -Examples/1-res-Annotate/tmp_files/genome3-chromo.fst-all.fna-split5N.fna-prokkaRes/EXAM.1216.00002:genome3_plasmi_2 (length 1968) -Examples/1-res-Annotate/tmp_files/genome3-chromo.fst-all.fna-split5N.fna-prokkaRes/EXAM.1216.00002:genome3_plasmi_2_1 (length 193) -Examples/1-res-Annotate/tmp_files/genome3-chromo.fst-all.fna-split5N.fna-prokkaRes/EXAM.1216.00002:genome3_plasmi_2_2 (length 435) -Examples/1-res-Annotate/tmp_files/genome3-chromo.fst-all.fna-split5N.fna-prokkaRes/EXAM.1216.00002:genome3_plasmi_3 (length 1102) -Examples/1-res-Annotate/tmp_files/genome3-chromo.fst-all.fna-split5N.fna-prokkaRes/EXAM.1216.00002:genome3_plasmi_3_1 (length 84) -Examples/1-res-Annotate/tmp_files/genome3-chromo.fst-all.fna-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/1-res-Annotate/tmp_files/genome3-chromo.fst-all.fna-split5N.fna-prokkaRes/EXAM.1216.00002:genome3_plasmi_2 (length 1968) -Examples/1-res-Annotate/tmp_files/genome3-chromo.fst-all.fna-split5N.fna-prokkaRes/EXAM.1216.00002:genome3_plasmi_3 (length 1102) -Examples/1-res-Annotate/tmp_files/genome3-chromo.fst-all.fna-split5N.fna-prokkaRes/EXAM.1216.00002:header_genome3_1 (length 5747) - diff --git a/Examples/1-res-Annotate/tmp_files/genome3-chromo.fst-all.fna-split5N.fna-prokkaRes/EXAM.1216.00002.faa b/Examples/1-res-Annotate/tmp_files/genome3-chromo.fst-all.fna-split5N.fna-prokkaRes/EXAM.1216.00002.faa deleted file mode 100644 index b4ae62e66c2e02c8b6a49d5f9521fd5bdcaba8b4..0000000000000000000000000000000000000000 --- a/Examples/1-res-Annotate/tmp_files/genome3-chromo.fst-all.fna-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 Insertion sequence IS5376 putative ATP-binding protein -MVELQHQRLMVLAEQLQLDSLIGAAPALSQQAVDQEWSYMDFLEHLLHEEKLARHQRKQA -MYTRMAAFPAVKTFEEYDFTFATGAPQKQIQSLRSLSFIERNENIVLLGPSGVGKTHLAI -AMGYEAVRAGIKVRFTTAADLLLQLSTSQRQGRYKTTLNRGVMAPKLLIIDEIGYLPFSQ -EEAKLFFQVIAKRYEKSAMILTSNLPFGQWDQTFAGDAALTSAMLDRILHHSHVVQIKGE -SYRLKQKRKAGVIAEANPE diff --git a/Examples/1-res-Annotate/tmp_files/genome3-chromo.fst-all.fna-split5N.fna-prokkaRes/EXAM.1216.00002.ffn b/Examples/1-res-Annotate/tmp_files/genome3-chromo.fst-all.fna-split5N.fna-prokkaRes/EXAM.1216.00002.ffn deleted file mode 100644 index ed27b471be4586da2fb4866febe34252e5f0a708..0000000000000000000000000000000000000000 --- a/Examples/1-res-Annotate/tmp_files/genome3-chromo.fst-all.fna-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 Insertion sequence IS5376 putative ATP-binding protein -ATGGTCGAACTGCAACATCAACGGCTGATGGTGCTTGCCGAACAGCTCCAGCTGGACAGT -CTTATCGGCGCAGCGCCGGCGCTGTCGCAACAGGCGGTGGATCAGGAATGGAGCTACATG -GACTTCCTGGAGCACCTGTTACATGAGGAGAAACTGGCCCGGCATCAGCGTAAACAGGCG -ATGTACACGCGGATGGCAGCCTTCCCGGCGGTAAAGACGTTCGAGGAGTACGACTTCACC -TTCGCCACCGGCGCTCCTCAGAAGCAAATCCAGTCGCTGCGATCCCTGAGCTTCATAGAG -CGTAACGAAAACATCGTGTTGCTGGGGCCATCGGGCGTGGGAAAAACGCATCTGGCGATA -GCCATGGGCTACGAAGCAGTACGGGCGGGCATCAAGGTTCGCTTCACAACAGCAGCGGAC -CTGCTGCTACAGCTGTCCACTTCACAGCGTCAGGGCCGTTACAAAACGACTCTCAATCGT -GGTGTCATGGCCCCGAAGCTGCTTATCATCGATGAAATAGGTTATCTGCCGTTCAGTCAG -GAGGAAGCCAAGCTGTTCTTCCAGGTCATCGCCAAACGTTACGAGAAGAGCGCGATGATC -CTGACCTCCAACCTGCCGTTCGGGCAGTGGGATCAGACGTTCGCCGGTGATGCAGCGCTG -ACATCGGCGATGCTGGACCGGATCTTACATCACTCACACGTCGTGCAAATAAAAGGGGAA -AGCTATCGACTGAAGCAGAAACGAAAGGCCGGGGTTATAGCTGAAGCTAATCCTGAGTAA diff --git a/Examples/1-res-Annotate/tmp_files/genome3-chromo.fst-all.fna-split5N.fna-prokkaRes/EXAM.1216.00002.fna b/Examples/1-res-Annotate/tmp_files/genome3-chromo.fst-all.fna-split5N.fna-prokkaRes/EXAM.1216.00002.fna deleted file mode 100644 index 07bd5c4b160a7dc19f4e7c640e3813aeff601694..0000000000000000000000000000000000000000 --- a/Examples/1-res-Annotate/tmp_files/genome3-chromo.fst-all.fna-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/1-res-Annotate/tmp_files/genome3-chromo.fst-all.fna-split5N.fna-prokkaRes/EXAM.1216.00002.fsa b/Examples/1-res-Annotate/tmp_files/genome3-chromo.fst-all.fna-split5N.fna-prokkaRes/EXAM.1216.00002.fsa deleted file mode 100644 index b25cc5564aa6b94e47594a34e65b0524a5bcda96..0000000000000000000000000000000000000000 --- a/Examples/1-res-Annotate/tmp_files/genome3-chromo.fst-all.fna-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/1-res-Annotate/tmp_files/genome3-chromo.fst-all.fna-split5N.fna-prokkaRes/EXAM.1216.00002.gbk b/Examples/1-res-Annotate/tmp_files/genome3-chromo.fst-all.fna-split5N.fna-prokkaRes/EXAM.1216.00002.gbk deleted file mode 100644 index 924905915875881e6008f7a3d4f3bb0db7b9eb77..0000000000000000000000000000000000000000 --- a/Examples/1-res-Annotate/tmp_files/genome3-chromo.fst-all.fna-split5N.fna-prokkaRes/EXAM.1216.00002.gbk +++ /dev/null @@ -1,350 +0,0 @@ -LOCUS header_genome3_1 5747 bp DNA linear 12-FEB-2019 -DEFINITION Genus species strain strain. -ACCESSION -VERSION -KEYWORDS . -SOURCE Genus species - ORGANISM Genus species - Unclassified. -COMMENT Annotated using prokka 1.14-dev 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:2.6" - /inference="similar to AA sequence:UniProtKB:P75820" - /codon_start=1 - /transl_table=11 - /product="N-acetylmuramoyl-L-alanine amidase AmiD" - /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:2.6" - /inference="similar to AA sequence:UniProtKB:P75820" - /codon_start=1 - /transl_table=11 - /product="N-acetylmuramoyl-L-alanine amidase AmiD" - /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:2.6" - /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:2.6" - /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:2.6" - /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:2.6" - /inference="similar to AA sequence:UniProtKB:P02915" - /codon_start=1 - /transl_table=11 - /product="Histidine transport ATP-binding protein HisP" - /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:2.6" - /inference="similar to AA sequence:UniProtKB:P0A873" - /codon_start=1 - /transl_table=11 - /product="tRNA (guanine-N(1)-)-methyltransferase" - /translation="MRAIYRRCVFIGIVSLFPEMFRAITDYGVTGRAVKNGLLNIQSW - SPRDFTHDRHRTVDDRPYGGGPGMLMMVQPLRDAIHAAKAAAGEGAKVIYLSPQGRKL - DQAGVSELATNQKLILVCGRYEGVDERVIQTEIDEEWSIGDYVLSGGELPAMTLIDSV - ARFIPGVLGHEASAIEDSFADGLLDCPHYTRPEVLEGMEVPPVLLSGNHAEIRRWRLK - QSLGRTWLRRPELLENLALTEEQARLLAEFKTEHAQQQHKHDGMA" - CDS 5460..5747 - /locus_tag="PFKCIMHH_00008" - /inference="ab initio prediction:Prodigal:2.6" - /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 12-FEB-2019 -DEFINITION Genus species strain strain. -ACCESSION -VERSION -KEYWORDS . -SOURCE Genus species - ORGANISM Genus species - Unclassified. -COMMENT Annotated using prokka 1.14-dev 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:2.6" - /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:2.6" - /inference="similar to AA sequence:UniProtKB:O07838" - /codon_start=1 - /transl_table=11 - /product="C4-dicarboxylate TRAP transporter large permease - protein DctM" - /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 12-FEB-2019 -DEFINITION Genus species strain strain. -ACCESSION -VERSION -KEYWORDS . -SOURCE Genus species - ORGANISM Genus species - Unclassified. -COMMENT Annotated using prokka 1.14-dev 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:2.6" - /codon_start=1 - /transl_table=11 - /product="hypothetical protein" - /translation="MIINGKLIKAKDLAKAAGVSRSTVIKYYGISRENYERVATERRK - LAFELRASGLKWKEVAEKMNTTKYSAIAYYRRYLALEKNK" - CDS 323..1102 - /locus_tag="PFKCIMHH_00012" - /inference="ab initio prediction:Prodigal:2.6" - /inference="similar to AA sequence:UniProtKB:Q45619" - /codon_start=1 - /transl_table=11 - /product="Insertion sequence IS5376 putative ATP-binding - protein" - /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/1-res-Annotate/tmp_files/genome3-chromo.fst-all.fna-split5N.fna-prokkaRes/EXAM.1216.00002.gff b/Examples/1-res-Annotate/tmp_files/genome3-chromo.fst-all.fna-split5N.fna-prokkaRes/EXAM.1216.00002.gff deleted file mode 100644 index 46df1d1908945bc82b032bd6da755ffe027eed00..0000000000000000000000000000000000000000 --- a/Examples/1-res-Annotate/tmp_files/genome3-chromo.fst-all.fna-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:2.6 CDS 1 831 . + 0 ID=PFKCIMHH_00001;eC_number=3.5.1.28;Name=amiD_1;dbxref=COG:COG3023;gene=amiD_1;inference=ab initio prediction:Prodigal:2.6,similar to AA sequence:UniProtKB:P75820;locus_tag=PFKCIMHH_00001;product=N-acetylmuramoyl-L-alanine amidase AmiD -header_genome3_1 Prodigal:2.6 CDS 880 1710 . + 0 ID=PFKCIMHH_00002;eC_number=3.5.1.28;Name=amiD_2;dbxref=COG:COG3023;gene=amiD_2;inference=ab initio prediction:Prodigal:2.6,similar to AA sequence:UniProtKB:P75820;locus_tag=PFKCIMHH_00002;product=N-acetylmuramoyl-L-alanine amidase AmiD -header_genome3_1 Prodigal:2.6 CDS 1655 2128 . + 0 ID=PFKCIMHH_00003;eC_number=5.3.3.10;Name=hpcD;gene=hpcD;inference=ab initio prediction:Prodigal:2.6,similar to AA sequence:UniProtKB:Q05354;locus_tag=PFKCIMHH_00003;product=5-carboxymethyl-2-hydroxymuconate Delta-isomerase -header_genome3_1 Prodigal:2.6 CDS 2172 2396 . + 0 ID=PFKCIMHH_00004;Name=pspB;gene=pspB;inference=ab initio prediction:Prodigal:2.6,similar to AA sequence:UniProtKB:P0AFM9;locus_tag=PFKCIMHH_00004;product=Phage shock protein B -header_genome3_1 Prodigal:2.6 CDS 2425 3828 . + 0 ID=PFKCIMHH_00005;inference=ab initio prediction:Prodigal:2.6;locus_tag=PFKCIMHH_00005;product=hypothetical protein -header_genome3_1 Prodigal:2.6 CDS 3863 4636 . + 0 ID=PFKCIMHH_00006;Name=hisP;dbxref=COG:COG4598;gene=hisP;inference=ab initio prediction:Prodigal:2.6,similar to AA sequence:UniProtKB:P02915;locus_tag=PFKCIMHH_00006;product=Histidine transport ATP-binding protein HisP -header_genome3_1 Prodigal:2.6 CDS 4641 5432 . + 0 ID=PFKCIMHH_00007;eC_number=2.1.1.228;Name=trmD;dbxref=COG:COG0336;gene=trmD;inference=ab initio prediction:Prodigal:2.6,similar to AA sequence:UniProtKB:P0A873;locus_tag=PFKCIMHH_00007;product=tRNA (guanine-N(1)-)-methyltransferase -header_genome3_1 Prodigal:2.6 CDS 5460 5747 . + 0 ID=PFKCIMHH_00008;inference=ab initio prediction:Prodigal:2.6;locus_tag=PFKCIMHH_00008;product=hypothetical protein -genome3_plasmi_2 Prodigal:2.6 CDS 1 582 . + 0 ID=PFKCIMHH_00009;inference=ab initio prediction:Prodigal:2.6;locus_tag=PFKCIMHH_00009;product=hypothetical protein -genome3_plasmi_2 Prodigal:2.6 CDS 629 1936 . + 0 ID=PFKCIMHH_00010;Name=dctM;dbxref=COG:COG1593;gene=dctM;inference=ab initio prediction:Prodigal:2.6,similar to AA sequence:UniProtKB:O07838;locus_tag=PFKCIMHH_00010;product=C4-dicarboxylate TRAP transporter large permease protein DctM -genome3_plasmi_3 Prodigal:2.6 CDS 26 280 . + 0 ID=PFKCIMHH_00011;inference=ab initio prediction:Prodigal:2.6;locus_tag=PFKCIMHH_00011;product=hypothetical protein -genome3_plasmi_3 Prodigal:2.6 CDS 323 1102 . + 0 ID=PFKCIMHH_00012;inference=ab initio prediction:Prodigal:2.6,similar to AA sequence:UniProtKB:Q45619;locus_tag=PFKCIMHH_00012;product=Insertion sequence IS5376 putative ATP-binding protein -##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/1-res-Annotate/tmp_files/genome3-chromo.fst-all.fna-split5N.fna-prokkaRes/EXAM.1216.00002.log b/Examples/1-res-Annotate/tmp_files/genome3-chromo.fst-all.fna-split5N.fna-prokkaRes/EXAM.1216.00002.log deleted file mode 100644 index 5b897f7f9cddeebf15360eadd439465292a33ed6..0000000000000000000000000000000000000000 --- a/Examples/1-res-Annotate/tmp_files/genome3-chromo.fst-all.fna-split5N.fna-prokkaRes/EXAM.1216.00002.log +++ /dev/null @@ -1,121 +0,0 @@ -[13:18:48] This is prokka 1.14-dev -[13:18:48] Written by Torsten Seemann <torsten.seemann@gmail.com> -[13:18:48] Homepage is https://github.com/tseemann/prokka -[13:18:48] Local time is Tue Feb 12 13:18:48 2019 -[13:18:48] You are aperrin -[13:18:48] Operating system is darwin -[13:18:48] You have BioPerl 1.006924 -[13:18:48] System has 8 cores. -[13:18:48] Will use maximum of 1 cores. -[13:18:48] Annotating as >>> Bacteria <<< -[13:18:48] Generating locus_tag from 'Examples/1-res-Annotate/tmp_files/genome3-chromo.fst-all.fna-split5N.fna' contents. -[13:18:48] Setting --locustag PFKCIMHH from MD5 9f4c2611ce3f44c6b2e6fb97579c5725 -[13:18:48] Creating new output folder: Examples/1-res-Annotate/tmp_files/genome3-chromo.fst-all.fna-split5N.fna-prokkaRes -[13:18:48] Running: mkdir -p Examples\/1\-res\-Annotate\/tmp_files\/genome3\-chromo\.fst\-all\.fna\-split5N\.fna\-prokkaRes -[13:18:48] Using filename prefix: EXAM.1216.00002.XXX -[13:18:48] Setting HMMER_NCPU=1 -[13:18:48] Writing log to: Examples/1-res-Annotate/tmp_files/genome3-chromo.fst-all.fna-split5N.fna-prokkaRes/EXAM.1216.00002.log -[13:18:48] Command: /usr/local/bin/prokka --outdir Examples/1-res-Annotate/tmp_files/genome3-chromo.fst-all.fna-split5N.fna-prokkaRes --cpus 1 --prefix EXAM.1216.00002 Examples/1-res-Annotate/tmp_files/genome3-chromo.fst-all.fna-split5N.fna -[13:18:48] Appending to PATH: /Users/aperrin/Softwares/src/prokka/bin/../binaries/darwin -[13:18:48] Appending to PATH: /Users/aperrin/Softwares/src/prokka/bin/../binaries/darwin/../common -[13:18:48] Appending to PATH: /Users/aperrin/Softwares/src/prokka/bin -[13:18:48] Looking for 'aragorn' - found /Users/aperrin/Softwares/src/prokka/bin/../binaries/darwin/aragorn -[13:18:48] Determined aragorn version is 1.2 -[13:18:48] Looking for 'barrnap' - found /usr/local/bin/barrnap -[13:18:48] Determined barrnap version is 0.8 -[13:18:48] Looking for 'blastp' - found /Users/aperrin/Softwares/bin/blastp -[13:18:48] Determined blastp version is 2.3 -[13:18:48] Looking for 'cmpress' - found /usr/local/bin/cmpress -[13:18:48] Determined cmpress version is 1.1 -[13:18:48] Looking for 'cmscan' - found /usr/local/bin/cmscan -[13:18:48] Determined cmscan version is 1.1 -[13:18:48] Looking for 'egrep' - found /usr/bin/egrep -[13:18:48] Looking for 'find' - found /usr/bin/find -[13:18:48] Looking for 'grep' - found /usr/bin/grep -[13:18:48] Looking for 'hmmpress' - found /Users/aperrin/Softwares/src/prokka/bin/../binaries/darwin/hmmpress -[13:18:48] Determined hmmpress version is 3.1 -[13:18:48] Looking for 'hmmscan' - found /usr/local/bin/hmmscan -[13:18:48] Determined hmmscan version is 3.1 -[13:18:48] Looking for 'java' - found /usr/bin/java -[13:18:48] Looking for 'less' - found /usr/bin/less -[13:18:48] Looking for 'makeblastdb' - found /Users/aperrin/Softwares/bin/makeblastdb -[13:18:48] Determined makeblastdb version is 2.3 -[13:18:48] Looking for 'minced' - found /Users/aperrin/Softwares/src/prokka/bin/../binaries/darwin/../common/minced -[13:18:48] Determined minced version is 2.0 -[13:18:48] Looking for 'parallel' - found /usr/local/bin/parallel -[13:18:49] Determined parallel version is 20181022 -[13:18:49] Looking for 'prodigal' - found /usr/local/bin/prodigal -[13:18:49] Determined prodigal version is 2.6 -[13:18:49] Looking for 'prokka-genbank_to_fasta_db' - found /Users/aperrin/Softwares/src/prokka/bin/prokka-genbank_to_fasta_db -[13:18:49] Looking for 'sed' - found /usr/bin/sed -[13:18:49] Looking for 'tbl2asn' - found /Users/aperrin/Softwares/src/prokka/bin/../binaries/darwin/tbl2asn -[13:18:49] Determined tbl2asn version is 25.6 -[13:18:49] Using genetic code table 11. -[13:18:49] Loading and checking input file: Examples/1-res-Annotate/tmp_files/genome3-chromo.fst-all.fna-split5N.fna -[13:18:49] Wrote 3 contigs totalling 8817 bp. -[13:18:49] Predicting tRNAs and tmRNAs -[13:18:49] Running: aragorn -l -gc11 -w Examples\/1\-res\-Annotate\/tmp_files\/genome3\-chromo\.fst\-all\.fna\-split5N\.fna\-prokkaRes\/EXAM\.1216\.00002\.fna -[13:18:49] Found 0 tRNAs -[13:18:49] Predicting Ribosomal RNAs -[13:18:49] Running Barrnap with 1 threads -[13:18:49] Found 0 rRNAs -[13:18:49] Skipping ncRNA search, enable with --rfam if desired. -[13:18:49] Total of 0 tRNA + rRNA features -[13:18:49] Searching for CRISPR repeats -[13:18:49] Found 0 CRISPRs -[13:18:49] Predicting coding sequences -[13:18:49] Contigs total 8817 bp, so using meta mode -[13:18:49] Running: prodigal -i Examples\/1\-res\-Annotate\/tmp_files\/genome3\-chromo\.fst\-all\.fna\-split5N\.fna\-prokkaRes\/EXAM\.1216\.00002\.fna -c -m -g 11 -p meta -f sco -q -[13:18:49] Found 12 CDS -[13:18:49] Connecting features back to sequences -[13:18:49] Not using genus-specific database. Try --usegenus to enable it. -[13:18:49] Annotating CDS, please be patient. -[13:18:49] Will use 1 CPUs for similarity searching. -[13:18:49] There are still 12 unannotated CDS left (started with 12) -[13:18:49] Will use blast to search against /Users/aperrin/Softwares/src/prokka/db/kingdom/Bacteria/sprot with 1 CPUs -[13:18:49] Running: cat Examples\/1\-res\-Annotate\/tmp_files\/genome3\-chromo\.fst\-all\.fna\-split5N\.fna\-prokkaRes\/sprot\.faa | parallel --gnu --plain -j 1 --block 1443 --recstart '>' --pipe blastp -query - -db /Users/aperrin/Softwares/src/prokka/db/kingdom/Bacteria/sprot -evalue 1e-06 -num_threads 1 -num_descriptions 1 -num_alignments 1 -seg no > Examples\/1\-res\-Annotate\/tmp_files\/genome3\-chromo\.fst\-all\.fna\-split5N\.fna\-prokkaRes\/sprot\.blast 2> /dev/null -[13:18:50] Deleting unwanted file: Examples/1-res-Annotate/tmp_files/genome3-chromo.fst-all.fna-split5N.fna-prokkaRes/sprot.faa -[13:18:50] Deleting unwanted file: Examples/1-res-Annotate/tmp_files/genome3-chromo.fst-all.fna-split5N.fna-prokkaRes/sprot.blast -[13:18:50] There are still 4 unannotated CDS left (started with 12) -[13:18:50] Will use hmmer3 to search against /Users/aperrin/Softwares/src/prokka/db/hmm/HAMAP.hmm with 1 CPUs -[13:18:50] Running: cat Examples\/1\-res\-Annotate\/tmp_files\/genome3\-chromo\.fst\-all\.fna\-split5N\.fna\-prokkaRes\/HAMAP\.hmm\.faa | parallel --gnu --plain -j 1 --block 427 --recstart '>' --pipe hmmscan --noali --notextw --acc -E 1e-06 --cpu 1 /Users/aperrin/Softwares/src/prokka/db/hmm/HAMAP.hmm /dev/stdin > Examples\/1\-res\-Annotate\/tmp_files\/genome3\-chromo\.fst\-all\.fna\-split5N\.fna\-prokkaRes\/HAMAP\.hmm\.hmmer3 2> /dev/null -[13:18:51] Deleting unwanted file: Examples/1-res-Annotate/tmp_files/genome3-chromo.fst-all.fna-split5N.fna-prokkaRes/HAMAP.hmm.faa -[13:18:51] Deleting unwanted file: Examples/1-res-Annotate/tmp_files/genome3-chromo.fst-all.fna-split5N.fna-prokkaRes/HAMAP.hmm.hmmer3 -[13:18:51] Labelling remaining 4 proteins as 'hypothetical protein' -[13:18:51] Possible /pseudo 'N-acetylmuramoyl-L-alanine amidase AmiD' at header_genome3_1 position 880 -[13:18:51] Found 6 unique /gene codes. -[13:18:51] Fixed 2 duplicate /gene - amiD_1 amiD_2 -[13:18:51] Fixed 1 colliding /gene names. -[13:18:51] Adding /locus_tag identifiers -[13:18:51] Assigned 12 locus_tags to CDS and RNA features. -[13:18:51] Writing outputs to Examples/1-res-Annotate/tmp_files/genome3-chromo.fst-all.fna-split5N.fna-prokkaRes/ -[13:18:51] Generating annotation statistics file -[13:18:51] Generating Genbank and Sequin files -[13:18:51] Running: tbl2asn -V b -a r10k -l paired-ends -M n -N 1 -y 'Annotated using prokka 1.14-dev from https://github.com/tseemann/prokka' -Z Examples\/1\-res\-Annotate\/tmp_files\/genome3\-chromo\.fst\-all\.fna\-split5N\.fna\-prokkaRes\/EXAM\.1216\.00002\.err -i Examples\/1\-res\-Annotate\/tmp_files\/genome3\-chromo\.fst\-all\.fna\-split5N\.fna\-prokkaRes\/EXAM\.1216\.00002\.fsa 2> /dev/null -[13:18:51] Deleting unwanted file: Examples/1-res-Annotate/tmp_files/genome3-chromo.fst-all.fna-split5N.fna-prokkaRes/errorsummary.val -[13:18:51] Deleting unwanted file: Examples/1-res-Annotate/tmp_files/genome3-chromo.fst-all.fna-split5N.fna-prokkaRes/EXAM.1216.00002.dr -[13:18:51] Deleting unwanted file: Examples/1-res-Annotate/tmp_files/genome3-chromo.fst-all.fna-split5N.fna-prokkaRes/EXAM.1216.00002.fixedproducts -[13:18:51] Deleting unwanted file: Examples/1-res-Annotate/tmp_files/genome3-chromo.fst-all.fna-split5N.fna-prokkaRes/EXAM.1216.00002.ecn -[13:18:51] Deleting unwanted file: Examples/1-res-Annotate/tmp_files/genome3-chromo.fst-all.fna-split5N.fna-prokkaRes/EXAM.1216.00002.val -[13:18:51] Repairing broken .GBK output that tbl2asn produces... -[13:18:51] Running: sed 's/COORDINATES: profile/COORDINATES:profile/' < Examples\/1\-res\-Annotate\/tmp_files\/genome3\-chromo\.fst\-all\.fna\-split5N\.fna\-prokkaRes\/EXAM\.1216\.00002\.gbf > Examples\/1\-res\-Annotate\/tmp_files\/genome3\-chromo\.fst\-all\.fna\-split5N\.fna\-prokkaRes\/EXAM\.1216\.00002\.gbk -[13:18:51] Deleting unwanted file: Examples/1-res-Annotate/tmp_files/genome3-chromo.fst-all.fna-split5N.fna-prokkaRes/EXAM.1216.00002.gbf -[13:18:51] Output files: -[13:18:51] Examples/1-res-Annotate/tmp_files/genome3-chromo.fst-all.fna-split5N.fna-prokkaRes/EXAM.1216.00002.log -[13:18:51] Examples/1-res-Annotate/tmp_files/genome3-chromo.fst-all.fna-split5N.fna-prokkaRes/EXAM.1216.00002.ffn -[13:18:51] Examples/1-res-Annotate/tmp_files/genome3-chromo.fst-all.fna-split5N.fna-prokkaRes/EXAM.1216.00002.gbk -[13:18:51] Examples/1-res-Annotate/tmp_files/genome3-chromo.fst-all.fna-split5N.fna-prokkaRes/EXAM.1216.00002.fsa -[13:18:51] Examples/1-res-Annotate/tmp_files/genome3-chromo.fst-all.fna-split5N.fna-prokkaRes/EXAM.1216.00002.faa -[13:18:51] Examples/1-res-Annotate/tmp_files/genome3-chromo.fst-all.fna-split5N.fna-prokkaRes/EXAM.1216.00002.txt -[13:18:51] Examples/1-res-Annotate/tmp_files/genome3-chromo.fst-all.fna-split5N.fna-prokkaRes/EXAM.1216.00002.gff -[13:18:51] Examples/1-res-Annotate/tmp_files/genome3-chromo.fst-all.fna-split5N.fna-prokkaRes/EXAM.1216.00002.tbl -[13:18:51] Examples/1-res-Annotate/tmp_files/genome3-chromo.fst-all.fna-split5N.fna-prokkaRes/EXAM.1216.00002.sqn -[13:18:51] Examples/1-res-Annotate/tmp_files/genome3-chromo.fst-all.fna-split5N.fna-prokkaRes/EXAM.1216.00002.tsv -[13:18:51] Examples/1-res-Annotate/tmp_files/genome3-chromo.fst-all.fna-split5N.fna-prokkaRes/EXAM.1216.00002.fna -[13:18:51] Examples/1-res-Annotate/tmp_files/genome3-chromo.fst-all.fna-split5N.fna-prokkaRes/EXAM.1216.00002.err -[13:18:51] Annotation finished successfully. -[13:18:51] Walltime used: 0.05 minutes -[13:18:51] If you use this result please cite the Prokka paper: -[13:18:51] Seemann T (2014) Prokka: rapid prokaryotic genome annotation. Bioinformatics. 30(14):2068-9. -[13:18:51] Type 'prokka --citation' for more details. -[13:18:51] Share and enjoy! diff --git a/Examples/1-res-Annotate/tmp_files/genome3-chromo.fst-all.fna-split5N.fna-prokkaRes/EXAM.1216.00002.sqn b/Examples/1-res-Annotate/tmp_files/genome3-chromo.fst-all.fna-split5N.fna-prokkaRes/EXAM.1216.00002.sqn deleted file mode 100644 index 28bbce5bfc43d860c6f5597b8364755b32da770a..0000000000000000000000000000000000000000 --- a/Examples/1-res-Annotate/tmp_files/genome3-chromo.fst-all.fna-split5N.fna-prokkaRes/EXAM.1216.00002.sqn +++ /dev/null @@ -1,1159 +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-dev 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 2 } , - { - label - str "day" , - data - int 12 } , - { - label - str "year" , - data - int 2019 } } } , - create-date - std { - year 2019 , - month 2 , - day 12 } } , - 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:2.6" } , - { - qual "inference" , - val "similar to AA sequence:UniProtKB:P75820" } } , - xref { - { - data - gene { - locus "amiD_1" , - locus-tag "PFKCIMHH_00001" } } } } , - { - 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:2.6" } , - { - qual "inference" , - val "similar to AA sequence:UniProtKB:P75820" } } , - xref { - { - data - gene { - locus "amiD_2" , - locus-tag "PFKCIMHH_00002" } } } } , - { - 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:2.6" } , - { - 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:2.6" } , - { - 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:2.6" } } , - 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:2.6" } , - { - qual "inference" , - val "similar to AA sequence:UniProtKB:P02915" } } , - xref { - { - data - gene { - locus "hisP" , - locus-tag "PFKCIMHH_00006" } } } } , - { - 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:2.6" } , - { - qual "inference" , - val "similar to AA sequence:UniProtKB:P0A873" } } , - xref { - { - data - gene { - locus "trmD" , - locus-tag "PFKCIMHH_00007" } } } } , - { - 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:2.6" } } , - 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-dev 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 2 } , - { - label - str "day" , - data - int 12 } , - { - label - str "year" , - data - int 2019 } } } , - create-date - std { - year 2019 , - month 2 , - day 12 } } , - 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:2.6" } } , - 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:2.6" } , - { - qual "inference" , - val "similar to AA sequence:UniProtKB:O07838" } } , - xref { - { - data - gene { - locus "dctM" , - locus-tag "PFKCIMHH_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-dev 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 2 } , - { - label - str "day" , - data - int 12 } , - { - label - str "year" , - data - int 2019 } } } , - create-date - std { - year 2019 , - month 2 , - day 12 } } , - 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 "Insertion sequence IS5376 putative ATP-binding protein - [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 { - "Insertion sequence IS5376 putative ATP-binding - protein" } } , - 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:2.6" } } , - 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:2.6" } , - { - qual "inference" , - val "similar to AA sequence:UniProtKB:Q45619" } } , - xref { - { - data - gene { - locus-tag "PFKCIMHH_00012" } } } } } } } } } } diff --git a/Examples/1-res-Annotate/tmp_files/genome3-chromo.fst-all.fna-split5N.fna-prokkaRes/EXAM.1216.00002.tbl b/Examples/1-res-Annotate/tmp_files/genome3-chromo.fst-all.fna-split5N.fna-prokkaRes/EXAM.1216.00002.tbl deleted file mode 100644 index 834efec1575e3d9d3f0940ee9959c9e666791d43..0000000000000000000000000000000000000000 --- a/Examples/1-res-Annotate/tmp_files/genome3-chromo.fst-all.fna-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 - dbxref COG:COG3023 - gene amiD_1 - inference ab initio prediction:Prodigal:2.6 - 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 - dbxref COG:COG3023 - gene amiD_2 - inference ab initio prediction:Prodigal:2.6 - 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:2.6 - 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:2.6 - inference similar to AA sequence:UniProtKB:P0AFM9 - locus_tag PFKCIMHH_00004 - product Phage shock protein B -2425 3828 CDS - inference ab initio prediction:Prodigal:2.6 - locus_tag PFKCIMHH_00005 - product hypothetical protein -3863 4636 CDS - dbxref COG:COG4598 - gene hisP - inference ab initio prediction:Prodigal:2.6 - 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 - dbxref COG:COG0336 - gene trmD - inference ab initio prediction:Prodigal:2.6 - 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:2.6 - locus_tag PFKCIMHH_00008 - product hypothetical protein ->Feature genome3_plasmi_2 -1 582 CDS - inference ab initio prediction:Prodigal:2.6 - locus_tag PFKCIMHH_00009 - product hypothetical protein -629 1936 CDS - dbxref COG:COG1593 - gene dctM - inference ab initio prediction:Prodigal:2.6 - 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:2.6 - locus_tag PFKCIMHH_00011 - product hypothetical protein -323 1102 CDS - inference ab initio prediction:Prodigal:2.6 - inference similar to AA sequence:UniProtKB:Q45619 - locus_tag PFKCIMHH_00012 - product Insertion sequence IS5376 putative ATP-binding protein diff --git a/Examples/1-res-Annotate/tmp_files/genome3-chromo.fst-all.fna-split5N.fna-prokkaRes/EXAM.1216.00002.tsv b/Examples/1-res-Annotate/tmp_files/genome3-chromo.fst-all.fna-split5N.fna-prokkaRes/EXAM.1216.00002.tsv deleted file mode 100644 index 0afd4f8ff32399cb6040568faebd0a2145f3676b..0000000000000000000000000000000000000000 --- a/Examples/1-res-Annotate/tmp_files/genome3-chromo.fst-all.fna-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 Insertion sequence IS5376 putative ATP-binding protein diff --git a/Examples/1-res-Annotate/tmp_files/genome3-chromo.fst-all.fna-split5N.fna-prokkaRes/EXAM.1216.00002.txt b/Examples/1-res-Annotate/tmp_files/genome3-chromo.fst-all.fna-split5N.fna-prokkaRes/EXAM.1216.00002.txt deleted file mode 100644 index 89b53831ab4386399ff71a68e8a46275f9d39114..0000000000000000000000000000000000000000 --- a/Examples/1-res-Annotate/tmp_files/genome3-chromo.fst-all.fna-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/1-res-Annotate/tmp_files/genome4.fst-split5N.fna b/Examples/1-res-Annotate/tmp_files/genome4.fst-split5N.fna deleted file mode 100644 index 85013c024cf3d318b654b2e8b07613ef6052c0ae..0000000000000000000000000000000000000000 --- a/Examples/1-res-Annotate/tmp_files/genome4.fst-split5N.fna +++ /dev/null @@ -1,2 +0,0 @@ ->g4_1 -ATGAAAGCGCTACTGTGGCTGGTGGGTCTCGCGTTGCTGTTAACAGGCTGCGCGAGCGAAAAAGGAATTATCGATAAAGAGGGATATCAGCTTGATACCCGACATCGGGCGCAGGCGGCCTATCCGCGCATTAAAGTCCTGGTGATTCACTATACGGCGGAAAACTTTGACGTTTCGCTGGCGACGTTAACGGGCCGCAACGTCAGTTCGCATTACCTGATTCCCGCAACCCCGCCATTATATGGCGGTAAACCGCGCATCTGGCAACTGGTGCCGGAACAGGATCAGGCCTGGCATGCGGGCGTCAGTTTCTGGCGAGGCGCCACGCGTCTCAATGATACGTCTATTGGCATTGAGCTGGAAAATCGCGGCTGGCGAATGTCCGGCGGGGTGAAATCTTTCGCGCCGTTTGAATCCGCGCAAATTCAGGCATTGATTCCGTTAGCGAAGGACATTATCGCGCGCTATGACATCAAACCGCAGAATGTGGTGGCCCATGCGGATATCGCGCCGCAGCGTAAAGACGATCCCGGCCCGCGCTTCCCGTGGCGCGAGCTGGCGGCGCAGGGGATTGGCGCCTGGCCTGACGCCCAGCGTGTGGCGTTTTATCTGGCTGGACGCGCGCCGTATACGCCAGTCGATACCGCAACGGTGCTTGCGTTACTCTCGCGCTATGGCTATGAAGTCAAAGCCGATATGACGGCGCGCGAGCAGCAGCGGGTGATTATGGCGTTCCAGATGCACTTCCGTCCGGCGCAATGGAACGGTATCGCAGATGCCGAAACGCAGGCGATTGCCGAAGCATTACTGGAGAAGTACGGCCAGGATTAACGCGATCGCGCGCATATCGCGCGCGATAGATGCCGCACTTTATTGCTGAATGTACTGAAAATATTCGCGAGCAGGCTGATTTACCCGGCCTGTTCAGCAAGGTAAACGAGGCGCTGGCCGCCAGCGGGATTTTCCCCATCGGCGGTATCCGCAGTCGCGCCCACTGGCTGGATACCTGGCAGATGGCTGACGGTAAGCATGATTATGCGTTTGTGCATATGACGCTGAAAATCGGTACCGGGCGCAGCCTGGAGAGCCGTCAGGAAGTCGGCGAAATGCTGTTTGGGCTGATTAAAGCCCACTTCGCCGACCTGATGGAGAACCGCTATCTGGCGCTGTCGTTTGAGATTGCCGAGCTACATCCGACGCTCAATTACAAACAAAACAACGTACACGCGTTATTTAAATAGCCGCATATGCGGCGCTCAGGAGCGCTAGCATGCTCGATAAACAGACCCATACCCTGATCGCCCAGCGACTTAATCAGGCTGAAAAACAGCGTGAACAAATTCGCGCAGTGTCGCTGGATTATCCCAACATCACTATTGAAGATGCCTATGCCGTACAGCGTGAATGGGTCAATATCAAGATCGCCGAAGGGCGCACGCTCAAAGGCCACAAAATCGGCCTGACCTCAAAAGCGATGCAGGCCAGCTCGCAAATCAGCGAACCGGATTACGGCGCGCTGCTTGACGATATGTTCTTCCATGACGGCGGCGATATCCCCACCGACCGTTTTATCGTCCCGCGTATTGAAGTGGAGCTGGCGTTCGTGCTGGCGAAACCGCTGCGCGGCCCTCACTGCACGCTGTTCGACGTCTACAACGCCACGGATTATGTGATTCCGGCGCTGGAACTGATTGACGCCCGCAGCCACAACATCGACCCGGAAACCCAGCGCCCGCGCAAAGTGTTCGACACCATTTCCGACAACGCCGCCAACGCCGGGGTGATCCTCGGTGGTCGCCCCATCAAACCAGACGAGCTGGATCTGCGCTGGATCTCCGCGCTGCTCTATCGCAACGGCGTGATCGAAGAAACCGGCGTCGCCGCAGGCGTGCTGAATCATCCGGCCAACGGCGTGGCGTGGCTGGCGAACAAGCTTGCCCCCTACGATGTCCAGCTTGAAGCCGGGCAGATCATCCTCGGCGGCTCGTTCACCCGCCCGGTGCCGGCGAGCAAGGGCGACACCTTCCATGTCGATTACGGCAACATGGGCGCGATCAGTTGCCGGTTTGTGTAACCAGATCCGCGCGCGCATATATATCGCGCGCATACGATGCCCGTGAATAAGTTCTCCCGACGTACCCTCCTGACGGCAGGTTCCGCGCTTGCTGTTCTTCCTTTTCTGCGCGCCTTGCCGGTACAGGCGCGTGAACCTCGCGAGACCGTCGATATTAAGGATTATCCGGCGGATGACGGTATCGCCTCGTTCAAACAGGCCTTCGCCGACGGACAGACCGTGGTCTTACCGCCAGGATGGGTGTGTGAAAATATCAATGCGGCGATAACGATTCCGGCGGGAAAAACGCTGCGGGTACAGGGCGCGGTGCGTGGGAATGGCCGGGGACGGTTTATTTTGCAGGACGGGTGTCAGGTGGTGGGGGAGCAGGGCGGCAGTCTGCACAATGTGACGCTGGATGTTCGCGGGTCGGACTGTGTGATTAAAGGCGTGACGATGAGCGGCTTTGGCCCCGTCGCGCAAATTTTCATCGGCGGTAAGGAACCGCAGGTGATGCGTAATCTCATTATCGATGACATCACCGTTACCCACGCCAACTACGCCATTCTCCGCCAGGGATTTCATAACCAAATGGACGGCGCGCGGATTACGCATAGCCGCTTTAGCGATTTGCAGGGGGACGCCATTGAGTGGAATGTCGCGATTCACGACCGCGACATCCTGATTTCCGATCATGTCATCGAACGCATTGATTGTACCAATGGCAAAATCAACTGGGGGATCGGCATCGGGCTGGCGGGTAGCACCTATGACAACAGTTATCCTGAAGATCAGGCAGTAAAAAACTTTGTGGTGGCCAATATTACCGGATCTGATTGCCGACAGCTGGTGCACGTAGAAAATGGCAAACATTTCGTCATTCGCAATGTCAAAGCCAAAAACATCACGCCCGATTTCAGTAAAAATGCGGGTATTGATAACGCAACGATCGCCATTTATGGCTGTGATAATTTCGTCATTGATAATATTGATATGACGAATAGTGCTGGGATGCTCATCGGCTATGGCGTCGTTAAAGGAAAATACCTGTCAATTCCGCAAAACTTTAAATTAAACGCTATTCGGTTGGATAATCGCCAGGTTGCTTATAAATTACGCGGCATTCAAATTTCCTCCGGCAACATCCCCTCTTTTGTCGCCATCACCAATGTACGGATGACGCGTGCTACGCTGGAACTGCATAATCAACCGCAGCACCTCTTTCTGCGTAATATCAACGTGATGCAAACTTCAGCGATTGGCCCGGCGTTAAAAATGCATTTCGATTTGCGTAAAGATGTCCGTGGTCAATTTATGGCCCGCCAGGACACGCTGCTTTCCCTCGCTAATGTTCATGCCATCAATGAAAACGGGCAGAGTTCCGTGGATATCGACAGGATTAATCACCAAACCGTGAATGTCGAAGCAGTGAATTTTTCGCTGCCGAAGCGGGGAGGGTAACAGAGCTCGCGCGATCGCGAATGTCAGAAAATAAATTACACGTTATCGATTTGCACAAACGCTACGGCGGTCATGAAGTGCTGAAAGGGGTATCGTTGCAGGCCCGCGCCGGAGATGTGATTAGCATCATCGGCTCGTCCGGCTCCGGTAAAAGCACTTTTTTGCGCTGTATTAACTTCCTCGAAAAACCGAGCGAAGGCGCGATTATCGTGAACGGTCAGAACATTAATCTGGTGCGCGACAAAGACGGGCAGCTCAAAGTGGCGGATAAAAATCAGCTACGCTTGTTGCGTACCCGCCTGACGATGGTGTTTCAGCACTTTAACCTCTGGAGCCACATGACGGTGCTGGAAAATGTGATGGAAGCGCCGATTCAGGTACTGGGATTAAGCAAGCACGACGCGCGCGAGCGGGCGTTGAAATATCTGGCGAAGGTGGGGATTGATGAGCGCGCTCAGGGCAAATATCCCGTCCATCTCTCCGGCGGCCAACAGCAGCGCGTTTCTATTGCGCGCGCGCTGGCGATGGAACCTGACGTTTTACTGTTCGATGAACCCACATCGGCGCTCGATCCTGAACTGGTCGGCGAAGTGTTGCGCATCATGCAACAACTGGCGGAAGAAGGCAAAACGATGGTGGTGGTCACGCATGAAATGGGCTTCGCCCGCCATGTCTCTTCGCACGTTATTTTTCTGCATCAGGGGAAAATTGAAGAAGAGGGCGATCCGGAGCAGGTGTTCGGCAATCCGCAAAGCCCGCGTTTACAGCAATTCCTGAAAGGCTCGCTGAAATAACAGATACGCGCATGGCGAGTGTTTATTGGCATCGTTAGCCTGTTTCCTGAAATGTTCCGCGCAATTACCGATTACGGGGTAACTGGCCGGGCAGTAAAAAAAGGCCTGCTGAACATCCAAAGCTGGAGTCCTCGCGACTTCGCGCATGACCGGCACCGTACCGTGGACGACCGTCCTTACGGCGGCGGACCGGGGATGTTAATGATGGTGCAACCCTTGCGGGACGCCATTCACGCAGCAAAAGCCGCGGCAGGTGAAGGCGCTAAAGTGATTTATCTGTCGCCTCAGGGACGCAAGCTTGATCAAGCGGGCGTTAGCGAGCTGGCCACGAATCAGAAGCTTATTCTGGTGTGTGGTCGCTACGAAGGCGTAGATGAGCGCGTAATTCAGACCGAAATTGACGAAGAATGGTCAATTGGCGATTACGTTCTCAGCGGTGGCGAACTACCGGCAATGACGCTGATTGACTCCGTCGCCCGGTTTATACCGGGGGTTCTGGGGCATGAGGCATCAGCAATCGAAGATTCGTTTGCTGATGGGTTGCTGGATTGTCCGCACTATACGCGCCCTGAAGTGTTAGAGGGGATGGAAGTACCGCCAGTATTGCTGTCGGGAAACCATGCCGAGATACGTCGCTGGCGCTTGAAACAGTCGCTGGGCCGAACCTGGCTTAGAAGACCTGAACTTCTGGAAAACCTGGCTCTGACTGAAGAGCAAGCAAGGTTGCTGGCGGAGTTCAAAACAGAACACGCACAACAGCAGCATAAACATGATGGGATGGCATAGCGATAGCGCTAGAGCGATGAATAATCATTTTGGGAAAGGGTTAATGGCTGGGTTGCACGCGCCATATGCATATAGCGCGCATCATGCGGTGAATTTCTGTTCTGAGTATAAACGTGGCTTTGTATTGGGTTTTACACACCGTATGTTCGAAAAGACCGGCGATCGTCAACTTAGCGCGTGGGAGGCCGGAATTCTGACGCGTCGCTATGGTCTGGATAAAGAAATGGTGATGGATTTCTTTAAAGAGAATCATTCCGGGATGGCGGTTCGCTTCTTTATGGTCGGTTATCGACTCGAAGGTTGACAGATGCGCGATCGATGTCTACGCTTCTCTATTTGCACGGATTCAACAGTTCCCCTCGCTCGGCAAAAGCGTGCCAGCTAAAAAACTGGCTGGCGGAGCGTCATCCGCATGTCGAGATGATCGTCCCTCAACTACCGCCGTATCCTGCCGATGCGGCGGAGTTGCTGGAATCTCTCGTGCTTGAGCATGGCGGTGCGCCATTAGGGCTGGTAGGATCGTCGCTGGGTGGTTATTACGCCACCTGGCTGTCGCAATGTTTTATGCTGCCGGCTGTGGTGGTGAATCCCGCCGTGCGGCCCTTTGAATTACTGACCGACTATCTCGGTCAGAACGAGAACCCCTACACCGGGCAGCAATATGTGCTAGAGTCTCGCCATATTTATGATCTTAAAGTCATGCAGATTGACCCGCTGGAAGCGCCGGACCTGATCTGGCTACTGCAACAGACGGGCGATGAAGTGCTGGATTACCGCCAGGCGGTGGCATATTACGCCTCCTGCCGTCAGACAGTGACCGAGGGTGGTAATCACGCATTCACGGGCTTCGAAGATTATTTCAACCAGATTGTCGATTTTCTTGGACTGCACAGTTGCTGACACGGATGCGCCATCGGCTTGCTGGCCGTGCCGTTCTTCGTTTTGTCCGGGGTGATCATGAATAGCGGGGGAATTGCCGCCCGGCTGGTCAATTTTGCCAAACTGTTTACTGGCAAACTGCCCGGCTCGCTCTCTTATACCAACATCGTCGGCAATATGATGTTCGGTGCAATTTCCGGATCGGCAATTGCCGCCTCAACCTCCATCGGCGGCGTGATGGTGCCGATGAGCGCGCGCGAAGGTTACGATCGCGGCTTTGCGGCCGCGGTGAATATCGCCTCCGCGCCGACGGGAATGTTAATTCCGCCCACCACGGCTTTTATCCTTTATGCGCTGGCAAGCGGGGGAACATCGATTGCCGCTCTGTTCGCCGGCGGTCTGGTCGCGGGAGTGCTGTGGGGCGTTGGCTGTATGCTGGTCACGCTGGTGGTCGCTAAGCGTCGAAATTATCGGGTTTTCTTCACCGTCCAAAAAGGCATGGCGCTAAAAGTTGCCGTTGAGGCCATTCCCAGCCTGCTGCTGATCGTGATTATCGTCGGCGGCATTGTGCAGGGGATTTTCACCGCCATTGAAGCCTCCGCGATTGCCGTGGTGTATACATTATTGTTGACGATGGTGTTTTACCGCACGCTGAAAATTAAGGATTTGCCTTCGATTTTGCTCCAGACAGTGGTAATGACCGGGGTCATCATGTTCCTGCTGGCAACCTCTTCGGCGATGTCCTTCTCGATGTCGATCACCAATATTCCTGCGGCGCTGAGCGATATGATCCTCGGTATTTCCGCCAATAAACTGGTTATCCTGTTAGTCATTACCGTCTTTTTGTTGATTATCGGCGCATTTATGGATATCGGTCCGGCCATTCTGATTTTTACCCCGATTCTGCTGCCGATCATGGCTAAACTGGGCGTCGATCCGGTGCATTTTGGCATTATCATGATCTATAACCTGGCGATTGGCACCATTACGCCGCCAGTTGGCAGTGGTTTATATGTCGGGGCGAGCGTCGGTAAGGTCAAAGTTGAGGAAGTGATTAAACCGTTGCTGCCTTTTTACGGCGCGATTATCGGCGTTCTGTTATTAATTACCTACATTCCGGAAATCACACTGTTCTTACCCCGTCTACTGGGCATCATGTAA diff --git a/Examples/1-res-Annotate/tmp_files/genome4.fst-split5N.fna-prokka.log b/Examples/1-res-Annotate/tmp_files/genome4.fst-split5N.fna-prokka.log deleted file mode 100644 index 2d2168766f191824a1996d5ce2a42ff6654d9700..0000000000000000000000000000000000000000 --- a/Examples/1-res-Annotate/tmp_files/genome4.fst-split5N.fna-prokka.log +++ /dev/null @@ -1,119 +0,0 @@ -[13:18:51] This is prokka 1.14-dev -[13:18:51] Written by Torsten Seemann <torsten.seemann@gmail.com> -[13:18:51] Homepage is https://github.com/tseemann/prokka -[13:18:51] Local time is Tue Feb 12 13:18:51 2019 -[13:18:51] You are aperrin -[13:18:51] Operating system is darwin -[13:18:51] You have BioPerl 1.006924 -[13:18:51] System has 8 cores. -[13:18:51] Will use maximum of 1 cores. -[13:18:51] Annotating as >>> Bacteria <<< -[13:18:51] Generating locus_tag from 'Examples/1-res-Annotate/tmp_files/genome4.fst-split5N.fna' contents. -[13:18:51] Setting --locustag LIKMDGFN from MD5 5246d0f7b5f59e1da550241263d19049 -[13:18:51] Creating new output folder: Examples/1-res-Annotate/tmp_files/genome4.fst-split5N.fna-prokkaRes -[13:18:51] Running: mkdir -p Examples\/1\-res\-Annotate\/tmp_files\/genome4\.fst\-split5N\.fna\-prokkaRes -[13:18:51] Using filename prefix: GEN4.1111.00001.XXX -[13:18:51] Setting HMMER_NCPU=1 -[13:18:51] Writing log to: Examples/1-res-Annotate/tmp_files/genome4.fst-split5N.fna-prokkaRes/GEN4.1111.00001.log -[13:18:51] Command: /usr/local/bin/prokka --outdir Examples/1-res-Annotate/tmp_files/genome4.fst-split5N.fna-prokkaRes --cpus 1 --prefix GEN4.1111.00001 Examples/1-res-Annotate/tmp_files/genome4.fst-split5N.fna -[13:18:51] Appending to PATH: /Users/aperrin/Softwares/src/prokka/bin/../binaries/darwin -[13:18:51] Appending to PATH: /Users/aperrin/Softwares/src/prokka/bin/../binaries/darwin/../common -[13:18:51] Appending to PATH: /Users/aperrin/Softwares/src/prokka/bin -[13:18:51] Looking for 'aragorn' - found /Users/aperrin/Softwares/src/prokka/bin/../binaries/darwin/aragorn -[13:18:51] Determined aragorn version is 1.2 -[13:18:51] Looking for 'barrnap' - found /usr/local/bin/barrnap -[13:18:51] Determined barrnap version is 0.8 -[13:18:51] Looking for 'blastp' - found /Users/aperrin/Softwares/bin/blastp -[13:18:51] Determined blastp version is 2.3 -[13:18:51] Looking for 'cmpress' - found /usr/local/bin/cmpress -[13:18:51] Determined cmpress version is 1.1 -[13:18:51] Looking for 'cmscan' - found /usr/local/bin/cmscan -[13:18:51] Determined cmscan version is 1.1 -[13:18:51] Looking for 'egrep' - found /usr/bin/egrep -[13:18:51] Looking for 'find' - found /usr/bin/find -[13:18:51] Looking for 'grep' - found /usr/bin/grep -[13:18:51] Looking for 'hmmpress' - found /Users/aperrin/Softwares/src/prokka/bin/../binaries/darwin/hmmpress -[13:18:51] Determined hmmpress version is 3.1 -[13:18:51] Looking for 'hmmscan' - found /usr/local/bin/hmmscan -[13:18:51] Determined hmmscan version is 3.1 -[13:18:51] Looking for 'java' - found /usr/bin/java -[13:18:51] Looking for 'less' - found /usr/bin/less -[13:18:51] Looking for 'makeblastdb' - found /Users/aperrin/Softwares/bin/makeblastdb -[13:18:51] Determined makeblastdb version is 2.3 -[13:18:51] Looking for 'minced' - found /Users/aperrin/Softwares/src/prokka/bin/../binaries/darwin/../common/minced -[13:18:51] Determined minced version is 2.0 -[13:18:51] Looking for 'parallel' - found /usr/local/bin/parallel -[13:18:52] Determined parallel version is 20181022 -[13:18:52] Looking for 'prodigal' - found /usr/local/bin/prodigal -[13:18:52] Determined prodigal version is 2.6 -[13:18:52] Looking for 'prokka-genbank_to_fasta_db' - found /Users/aperrin/Softwares/src/prokka/bin/prokka-genbank_to_fasta_db -[13:18:52] Looking for 'sed' - found /usr/bin/sed -[13:18:52] Looking for 'tbl2asn' - found /Users/aperrin/Softwares/src/prokka/bin/../binaries/darwin/tbl2asn -[13:18:52] Determined tbl2asn version is 25.6 -[13:18:52] Using genetic code table 11. -[13:18:52] Loading and checking input file: Examples/1-res-Annotate/tmp_files/genome4.fst-split5N.fna -[13:18:52] Wrote 1 contigs totalling 7134 bp. -[13:18:52] Predicting tRNAs and tmRNAs -[13:18:52] Running: aragorn -l -gc11 -w Examples\/1\-res\-Annotate\/tmp_files\/genome4\.fst\-split5N\.fna\-prokkaRes\/GEN4\.1111\.00001\.fna -[13:18:52] Found 0 tRNAs -[13:18:52] Predicting Ribosomal RNAs -[13:18:52] Running Barrnap with 1 threads -[13:18:52] Found 0 rRNAs -[13:18:52] Skipping ncRNA search, enable with --rfam if desired. -[13:18:52] Total of 0 tRNA + rRNA features -[13:18:52] Searching for CRISPR repeats -[13:18:52] Found 0 CRISPRs -[13:18:52] Predicting coding sequences -[13:18:52] Contigs total 7134 bp, so using meta mode -[13:18:52] Running: prodigal -i Examples\/1\-res\-Annotate\/tmp_files\/genome4\.fst\-split5N\.fna\-prokkaRes\/GEN4\.1111\.00001\.fna -c -m -g 11 -p meta -f sco -q -[13:18:52] Found 9 CDS -[13:18:52] Connecting features back to sequences -[13:18:52] Not using genus-specific database. Try --usegenus to enable it. -[13:18:52] Annotating CDS, please be patient. -[13:18:52] Will use 1 CPUs for similarity searching. -[13:18:52] There are still 9 unannotated CDS left (started with 9) -[13:18:52] Will use blast to search against /Users/aperrin/Softwares/src/prokka/db/kingdom/Bacteria/sprot with 1 CPUs -[13:18:52] Running: cat Examples\/1\-res\-Annotate\/tmp_files\/genome4\.fst\-split5N\.fna\-prokkaRes\/sprot\.faa | parallel --gnu --plain -j 1 --block 1161 --recstart '>' --pipe blastp -query - -db /Users/aperrin/Softwares/src/prokka/db/kingdom/Bacteria/sprot -evalue 1e-06 -num_threads 1 -num_descriptions 1 -num_alignments 1 -seg no > Examples\/1\-res\-Annotate\/tmp_files\/genome4\.fst\-split5N\.fna\-prokkaRes\/sprot\.blast 2> /dev/null -[13:18:53] Deleting unwanted file: Examples/1-res-Annotate/tmp_files/genome4.fst-split5N.fna-prokkaRes/sprot.faa -[13:18:53] Deleting unwanted file: Examples/1-res-Annotate/tmp_files/genome4.fst-split5N.fna-prokkaRes/sprot.blast -[13:18:53] There are still 3 unannotated CDS left (started with 9) -[13:18:53] Will use hmmer3 to search against /Users/aperrin/Softwares/src/prokka/db/hmm/HAMAP.hmm with 1 CPUs -[13:18:53] Running: cat Examples\/1\-res\-Annotate\/tmp_files\/genome4\.fst\-split5N\.fna\-prokkaRes\/HAMAP\.hmm\.faa | parallel --gnu --plain -j 1 --block 379 --recstart '>' --pipe hmmscan --noali --notextw --acc -E 1e-06 --cpu 1 /Users/aperrin/Softwares/src/prokka/db/hmm/HAMAP.hmm /dev/stdin > Examples\/1\-res\-Annotate\/tmp_files\/genome4\.fst\-split5N\.fna\-prokkaRes\/HAMAP\.hmm\.hmmer3 2> /dev/null -[13:18:53] Deleting unwanted file: Examples/1-res-Annotate/tmp_files/genome4.fst-split5N.fna-prokkaRes/HAMAP.hmm.faa -[13:18:53] Deleting unwanted file: Examples/1-res-Annotate/tmp_files/genome4.fst-split5N.fna-prokkaRes/HAMAP.hmm.hmmer3 -[13:18:53] Labelling remaining 3 proteins as 'hypothetical protein' -[13:18:53] Found 6 unique /gene codes. -[13:18:53] Fixed 0 colliding /gene names. -[13:18:53] Adding /locus_tag identifiers -[13:18:53] Assigned 9 locus_tags to CDS and RNA features. -[13:18:53] Writing outputs to Examples/1-res-Annotate/tmp_files/genome4.fst-split5N.fna-prokkaRes/ -[13:18:53] Generating annotation statistics file -[13:18:53] Generating Genbank and Sequin files -[13:18:53] Running: tbl2asn -V b -a r10k -l paired-ends -M n -N 1 -y 'Annotated using prokka 1.14-dev from https://github.com/tseemann/prokka' -Z Examples\/1\-res\-Annotate\/tmp_files\/genome4\.fst\-split5N\.fna\-prokkaRes\/GEN4\.1111\.00001\.err -i Examples\/1\-res\-Annotate\/tmp_files\/genome4\.fst\-split5N\.fna\-prokkaRes\/GEN4\.1111\.00001\.fsa 2> /dev/null -[13:18:54] Deleting unwanted file: Examples/1-res-Annotate/tmp_files/genome4.fst-split5N.fna-prokkaRes/errorsummary.val -[13:18:54] Deleting unwanted file: Examples/1-res-Annotate/tmp_files/genome4.fst-split5N.fna-prokkaRes/GEN4.1111.00001.dr -[13:18:54] Deleting unwanted file: Examples/1-res-Annotate/tmp_files/genome4.fst-split5N.fna-prokkaRes/GEN4.1111.00001.fixedproducts -[13:18:54] Deleting unwanted file: Examples/1-res-Annotate/tmp_files/genome4.fst-split5N.fna-prokkaRes/GEN4.1111.00001.ecn -[13:18:54] Deleting unwanted file: Examples/1-res-Annotate/tmp_files/genome4.fst-split5N.fna-prokkaRes/GEN4.1111.00001.val -[13:18:54] Repairing broken .GBK output that tbl2asn produces... -[13:18:54] Running: sed 's/COORDINATES: profile/COORDINATES:profile/' < Examples\/1\-res\-Annotate\/tmp_files\/genome4\.fst\-split5N\.fna\-prokkaRes\/GEN4\.1111\.00001\.gbf > Examples\/1\-res\-Annotate\/tmp_files\/genome4\.fst\-split5N\.fna\-prokkaRes\/GEN4\.1111\.00001\.gbk -[13:18:54] Deleting unwanted file: Examples/1-res-Annotate/tmp_files/genome4.fst-split5N.fna-prokkaRes/GEN4.1111.00001.gbf -[13:18:54] Output files: -[13:18:54] Examples/1-res-Annotate/tmp_files/genome4.fst-split5N.fna-prokkaRes/GEN4.1111.00001.fsa -[13:18:54] Examples/1-res-Annotate/tmp_files/genome4.fst-split5N.fna-prokkaRes/GEN4.1111.00001.faa -[13:18:54] Examples/1-res-Annotate/tmp_files/genome4.fst-split5N.fna-prokkaRes/GEN4.1111.00001.log -[13:18:54] Examples/1-res-Annotate/tmp_files/genome4.fst-split5N.fna-prokkaRes/GEN4.1111.00001.ffn -[13:18:54] Examples/1-res-Annotate/tmp_files/genome4.fst-split5N.fna-prokkaRes/GEN4.1111.00001.gbk -[13:18:54] Examples/1-res-Annotate/tmp_files/genome4.fst-split5N.fna-prokkaRes/GEN4.1111.00001.gff -[13:18:54] Examples/1-res-Annotate/tmp_files/genome4.fst-split5N.fna-prokkaRes/GEN4.1111.00001.tbl -[13:18:54] Examples/1-res-Annotate/tmp_files/genome4.fst-split5N.fna-prokkaRes/GEN4.1111.00001.sqn -[13:18:54] Examples/1-res-Annotate/tmp_files/genome4.fst-split5N.fna-prokkaRes/GEN4.1111.00001.tsv -[13:18:54] Examples/1-res-Annotate/tmp_files/genome4.fst-split5N.fna-prokkaRes/GEN4.1111.00001.fna -[13:18:54] Examples/1-res-Annotate/tmp_files/genome4.fst-split5N.fna-prokkaRes/GEN4.1111.00001.err -[13:18:54] Examples/1-res-Annotate/tmp_files/genome4.fst-split5N.fna-prokkaRes/GEN4.1111.00001.txt -[13:18:54] Annotation finished successfully. -[13:18:54] Walltime used: 0.05 minutes -[13:18:54] If you use this result please cite the Prokka paper: -[13:18:54] Seemann T (2014) Prokka: rapid prokaryotic genome annotation. Bioinformatics. 30(14):2068-9. -[13:18:54] Type 'prokka --citation' for more details. -[13:18:54] Share and enjoy! diff --git a/Examples/1-res-Annotate/tmp_files/genome4.fst-split5N.fna-prokkaRes/GEN4.1111.00001.err b/Examples/1-res-Annotate/tmp_files/genome4.fst-split5N.fna-prokkaRes/GEN4.1111.00001.err deleted file mode 100644 index f57bb0e61a4773385690b5e8c9f095124859cdf6..0000000000000000000000000000000000000000 --- a/Examples/1-res-Annotate/tmp_files/genome4.fst-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/1-res-Annotate/tmp_files/genome4.fst-split5N.fna-prokkaRes/GEN4.1111.00001:g4_1_1 (length 276) -Examples/1-res-Annotate/tmp_files/genome4.fst-split5N.fna-prokkaRes/GEN4.1111.00001:g4_1_2 (length 126) -Examples/1-res-Annotate/tmp_files/genome4.fst-split5N.fna-prokkaRes/GEN4.1111.00001:g4_1_3 (length 267) -Examples/1-res-Annotate/tmp_files/genome4.fst-split5N.fna-prokkaRes/GEN4.1111.00001:g4_1_4 (length 467) -Examples/1-res-Annotate/tmp_files/genome4.fst-split5N.fna-prokkaRes/GEN4.1111.00001:g4_1_5 (length 257) -Examples/1-res-Annotate/tmp_files/genome4.fst-split5N.fna-prokkaRes/GEN4.1111.00001:g4_1_6 (length 255) -Examples/1-res-Annotate/tmp_files/genome4.fst-split5N.fna-prokkaRes/GEN4.1111.00001:g4_1_7 (length 86) -Examples/1-res-Annotate/tmp_files/genome4.fst-split5N.fna-prokkaRes/GEN4.1111.00001:g4_1_8 (length 193) -Examples/1-res-Annotate/tmp_files/genome4.fst-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/1-res-Annotate/tmp_files/genome4.fst-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/1-res-Annotate/tmp_files/genome4.fst-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/1-res-Annotate/tmp_files/genome4.fst-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/1-res-Annotate/tmp_files/genome4.fst-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/1-res-Annotate/tmp_files/genome4.fst-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/1-res-Annotate/tmp_files/genome4.fst-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/1-res-Annotate/tmp_files/genome4.fst-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/1-res-Annotate/tmp_files/genome4.fst-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/1-res-Annotate/tmp_files/genome4.fst-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/1-res-Annotate/tmp_files/genome4.fst-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/1-res-Annotate/tmp_files/genome4.fst-split5N.fna-prokkaRes/GEN4.1111.00001:g4_1:Annotated using prokka 1.14-dev from https://github.com/tseemann/prokka - -DiscRep_ALL:MISSING_GENOMEASSEMBLY_COMMENTS::1 bioseqs are missing GenomeAssembly structured comments -Examples/1-res-Annotate/tmp_files/genome4.fst-split5N.fna-prokkaRes/GEN4.1111.00001:g4_1 (length 7134) - -DiscRep_ALL:MOLTYPE_NOT_MRNA::1 molecule types are not set as mRNA. -Examples/1-res-Annotate/tmp_files/genome4.fst-split5N.fna-prokkaRes/GEN4.1111.00001:g4_1 (length 7134) - -DiscRep_ALL:TECHNIQUE_NOT_TSA::1 technique are not set as TSA -Examples/1-res-Annotate/tmp_files/genome4.fst-split5N.fna-prokkaRes/GEN4.1111.00001:g4_1 (length 7134) - -DiscRep_ALL:MISSING_STRUCTURED_COMMENT::1 sequences do not include structured comments. -Examples/1-res-Annotate/tmp_files/genome4.fst-split5N.fna-prokkaRes/GEN4.1111.00001:g4_1 (length 7134) - -DiscRep_ALL:MISSING_PROJECT::10 sequences do not include project. -Examples/1-res-Annotate/tmp_files/genome4.fst-split5N.fna-prokkaRes/GEN4.1111.00001:g4_1 (length 7134) -Examples/1-res-Annotate/tmp_files/genome4.fst-split5N.fna-prokkaRes/GEN4.1111.00001:g4_1_1 (length 276) -Examples/1-res-Annotate/tmp_files/genome4.fst-split5N.fna-prokkaRes/GEN4.1111.00001:g4_1_2 (length 126) -Examples/1-res-Annotate/tmp_files/genome4.fst-split5N.fna-prokkaRes/GEN4.1111.00001:g4_1_3 (length 267) -Examples/1-res-Annotate/tmp_files/genome4.fst-split5N.fna-prokkaRes/GEN4.1111.00001:g4_1_4 (length 467) -Examples/1-res-Annotate/tmp_files/genome4.fst-split5N.fna-prokkaRes/GEN4.1111.00001:g4_1_5 (length 257) -Examples/1-res-Annotate/tmp_files/genome4.fst-split5N.fna-prokkaRes/GEN4.1111.00001:g4_1_6 (length 255) -Examples/1-res-Annotate/tmp_files/genome4.fst-split5N.fna-prokkaRes/GEN4.1111.00001:g4_1_7 (length 86) -Examples/1-res-Annotate/tmp_files/genome4.fst-split5N.fna-prokkaRes/GEN4.1111.00001:g4_1_8 (length 193) -Examples/1-res-Annotate/tmp_files/genome4.fst-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/1-res-Annotate/tmp_files/genome4.fst-split5N.fna-prokkaRes/GEN4.1111.00001:g4_1 (length 7134) - diff --git a/Examples/1-res-Annotate/tmp_files/genome4.fst-split5N.fna-prokkaRes/GEN4.1111.00001.faa b/Examples/1-res-Annotate/tmp_files/genome4.fst-split5N.fna-prokkaRes/GEN4.1111.00001.faa deleted file mode 100644 index a9dac9220a5843883e83e742358b8227b5d843ff..0000000000000000000000000000000000000000 --- a/Examples/1-res-Annotate/tmp_files/genome4.fst-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/1-res-Annotate/tmp_files/genome4.fst-split5N.fna-prokkaRes/GEN4.1111.00001.ffn b/Examples/1-res-Annotate/tmp_files/genome4.fst-split5N.fna-prokkaRes/GEN4.1111.00001.ffn deleted file mode 100644 index 40721d61f9f565ea758dd19633045b3da0e82ace..0000000000000000000000000000000000000000 --- a/Examples/1-res-Annotate/tmp_files/genome4.fst-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/1-res-Annotate/tmp_files/genome4.fst-split5N.fna-prokkaRes/GEN4.1111.00001.fna b/Examples/1-res-Annotate/tmp_files/genome4.fst-split5N.fna-prokkaRes/GEN4.1111.00001.fna deleted file mode 100644 index c9dacd184cf1469f26718f4e1d00a44270105582..0000000000000000000000000000000000000000 --- a/Examples/1-res-Annotate/tmp_files/genome4.fst-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/1-res-Annotate/tmp_files/genome4.fst-split5N.fna-prokkaRes/GEN4.1111.00001.fsa b/Examples/1-res-Annotate/tmp_files/genome4.fst-split5N.fna-prokkaRes/GEN4.1111.00001.fsa deleted file mode 100644 index 79f8dbb42edbbe6742fcab99338d387343c11dc1..0000000000000000000000000000000000000000 --- a/Examples/1-res-Annotate/tmp_files/genome4.fst-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/1-res-Annotate/tmp_files/genome4.fst-split5N.fna-prokkaRes/GEN4.1111.00001.gbk b/Examples/1-res-Annotate/tmp_files/genome4.fst-split5N.fna-prokkaRes/GEN4.1111.00001.gbk deleted file mode 100644 index 126bfa9b50b3eda02bd01d9e39a7009eac9f839c..0000000000000000000000000000000000000000 --- a/Examples/1-res-Annotate/tmp_files/genome4.fst-split5N.fna-prokkaRes/GEN4.1111.00001.gbk +++ /dev/null @@ -1,254 +0,0 @@ -LOCUS g4_1 7134 bp DNA linear 12-FEB-2019 -DEFINITION Genus species strain strain. -ACCESSION -VERSION -KEYWORDS . -SOURCE Genus species - ORGANISM Genus species - Unclassified. -COMMENT Annotated using prokka 1.14-dev 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:2.6" - /inference="similar to AA sequence:UniProtKB:P75820" - /codon_start=1 - /transl_table=11 - /product="N-acetylmuramoyl-L-alanine amidase AmiD" - /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:2.6" - /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:2.6" - /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:2.6" - /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:2.6" - /inference="similar to AA sequence:UniProtKB:P02915" - /codon_start=1 - /transl_table=11 - /product="Histidine transport ATP-binding protein HisP" - /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:2.6" - /inference="similar to AA sequence:UniProtKB:P0A873" - /codon_start=1 - /transl_table=11 - /product="tRNA (guanine-N(1)-)-methyltransferase" - /translation="MFIGIVSLFPEMFRAITDYGVTGRAVKKGLLNIQSWSPRDFAHD - RHRTVDDRPYGGGPGMLMMVQPLRDAIHAAKAAAGEGAKVIYLSPQGRKLDQAGVSEL - ATNQKLILVCGRYEGVDERVIQTEIDEEWSIGDYVLSGGELPAMTLIDSVARFIPGVL - GHEASAIEDSFADGLLDCPHYTRPEVLEGMEVPPVLLSGNHAEIRRWRLKQSLGRTWL - RRPELLENLALTEEQARLLAEFKTEHAQQQHKHDGMA" - CDS 5138..5398 - /locus_tag="LIKMDGFN_00007" - /inference="ab initio prediction:Prodigal:2.6" - /codon_start=1 - /transl_table=11 - /product="hypothetical protein" - /translation="MAGLHAPYAYSAHHAVNFCSEYKRGFVLGFTHRMFEKTGDRQLS - AWEAGILTRRYGLDKEMVMDFFKENHSGMAVRFFMVGYRLEG" - CDS 5413..5994 - /locus_tag="LIKMDGFN_00008" - /inference="ab initio prediction:Prodigal:2.6" - /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:2.6" - /inference="similar to AA sequence:UniProtKB:O07838" - /codon_start=1 - /transl_table=11 - /product="C4-dicarboxylate TRAP transporter large permease - protein DctM" - /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/1-res-Annotate/tmp_files/genome4.fst-split5N.fna-prokkaRes/GEN4.1111.00001.gff b/Examples/1-res-Annotate/tmp_files/genome4.fst-split5N.fna-prokkaRes/GEN4.1111.00001.gff deleted file mode 100644 index 1ee608aac1393847560afc7f300043966f1d885c..0000000000000000000000000000000000000000 --- a/Examples/1-res-Annotate/tmp_files/genome4.fst-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:2.6 CDS 1 831 . + 0 ID=LIKMDGFN_00001;eC_number=3.5.1.28;Name=amiD;dbxref=COG:COG3023;gene=amiD;inference=ab initio prediction:Prodigal:2.6,similar to AA sequence:UniProtKB:P75820;locus_tag=LIKMDGFN_00001;product=N-acetylmuramoyl-L-alanine amidase AmiD -g4_1 Prodigal:2.6 CDS 861 1241 . + 0 ID=LIKMDGFN_00002;eC_number=5.3.3.10;Name=hpcD;gene=hpcD;inference=ab initio prediction:Prodigal:2.6,similar to AA sequence:UniProtKB:Q05354;locus_tag=LIKMDGFN_00002;product=5-carboxymethyl-2-hydroxymuconate Delta-isomerase -g4_1 Prodigal:2.6 CDS 1271 2074 . + 0 ID=LIKMDGFN_00003;eC_number=4.2.1.163;Name=hpcG;gene=hpcG;inference=ab initio prediction:Prodigal:2.6,similar to AA sequence:UniProtKB:P42270;locus_tag=LIKMDGFN_00003;product=2-oxo-hept-4-ene-1%2C7-dioate hydratase -g4_1 Prodigal:2.6 CDS 2111 3514 . + 0 ID=LIKMDGFN_00004;inference=ab initio prediction:Prodigal:2.6;locus_tag=LIKMDGFN_00004;product=hypothetical protein -g4_1 Prodigal:2.6 CDS 3535 4308 . + 0 ID=LIKMDGFN_00005;Name=hisP;dbxref=COG:COG4598;gene=hisP;inference=ab initio prediction:Prodigal:2.6,similar to AA sequence:UniProtKB:P02915;locus_tag=LIKMDGFN_00005;product=Histidine transport ATP-binding protein HisP -g4_1 Prodigal:2.6 CDS 4327 5094 . + 0 ID=LIKMDGFN_00006;eC_number=2.1.1.228;Name=trmD;dbxref=COG:COG0336;gene=trmD;inference=ab initio prediction:Prodigal:2.6,similar to AA sequence:UniProtKB:P0A873;locus_tag=LIKMDGFN_00006;product=tRNA (guanine-N(1)-)-methyltransferase -g4_1 Prodigal:2.6 CDS 5138 5398 . + 0 ID=LIKMDGFN_00007;inference=ab initio prediction:Prodigal:2.6;locus_tag=LIKMDGFN_00007;product=hypothetical protein -g4_1 Prodigal:2.6 CDS 5413 5994 . + 0 ID=LIKMDGFN_00008;inference=ab initio prediction:Prodigal:2.6;locus_tag=LIKMDGFN_00008;product=hypothetical protein -g4_1 Prodigal:2.6 CDS 6052 7134 . + 0 ID=LIKMDGFN_00009;Name=dctM;dbxref=COG:COG1593;gene=dctM;inference=ab initio prediction:Prodigal:2.6,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/1-res-Annotate/tmp_files/genome4.fst-split5N.fna-prokkaRes/GEN4.1111.00001.log b/Examples/1-res-Annotate/tmp_files/genome4.fst-split5N.fna-prokkaRes/GEN4.1111.00001.log deleted file mode 100644 index 2d2168766f191824a1996d5ce2a42ff6654d9700..0000000000000000000000000000000000000000 --- a/Examples/1-res-Annotate/tmp_files/genome4.fst-split5N.fna-prokkaRes/GEN4.1111.00001.log +++ /dev/null @@ -1,119 +0,0 @@ -[13:18:51] This is prokka 1.14-dev -[13:18:51] Written by Torsten Seemann <torsten.seemann@gmail.com> -[13:18:51] Homepage is https://github.com/tseemann/prokka -[13:18:51] Local time is Tue Feb 12 13:18:51 2019 -[13:18:51] You are aperrin -[13:18:51] Operating system is darwin -[13:18:51] You have BioPerl 1.006924 -[13:18:51] System has 8 cores. -[13:18:51] Will use maximum of 1 cores. -[13:18:51] Annotating as >>> Bacteria <<< -[13:18:51] Generating locus_tag from 'Examples/1-res-Annotate/tmp_files/genome4.fst-split5N.fna' contents. -[13:18:51] Setting --locustag LIKMDGFN from MD5 5246d0f7b5f59e1da550241263d19049 -[13:18:51] Creating new output folder: Examples/1-res-Annotate/tmp_files/genome4.fst-split5N.fna-prokkaRes -[13:18:51] Running: mkdir -p Examples\/1\-res\-Annotate\/tmp_files\/genome4\.fst\-split5N\.fna\-prokkaRes -[13:18:51] Using filename prefix: GEN4.1111.00001.XXX -[13:18:51] Setting HMMER_NCPU=1 -[13:18:51] Writing log to: Examples/1-res-Annotate/tmp_files/genome4.fst-split5N.fna-prokkaRes/GEN4.1111.00001.log -[13:18:51] Command: /usr/local/bin/prokka --outdir Examples/1-res-Annotate/tmp_files/genome4.fst-split5N.fna-prokkaRes --cpus 1 --prefix GEN4.1111.00001 Examples/1-res-Annotate/tmp_files/genome4.fst-split5N.fna -[13:18:51] Appending to PATH: /Users/aperrin/Softwares/src/prokka/bin/../binaries/darwin -[13:18:51] Appending to PATH: /Users/aperrin/Softwares/src/prokka/bin/../binaries/darwin/../common -[13:18:51] Appending to PATH: /Users/aperrin/Softwares/src/prokka/bin -[13:18:51] Looking for 'aragorn' - found /Users/aperrin/Softwares/src/prokka/bin/../binaries/darwin/aragorn -[13:18:51] Determined aragorn version is 1.2 -[13:18:51] Looking for 'barrnap' - found /usr/local/bin/barrnap -[13:18:51] Determined barrnap version is 0.8 -[13:18:51] Looking for 'blastp' - found /Users/aperrin/Softwares/bin/blastp -[13:18:51] Determined blastp version is 2.3 -[13:18:51] Looking for 'cmpress' - found /usr/local/bin/cmpress -[13:18:51] Determined cmpress version is 1.1 -[13:18:51] Looking for 'cmscan' - found /usr/local/bin/cmscan -[13:18:51] Determined cmscan version is 1.1 -[13:18:51] Looking for 'egrep' - found /usr/bin/egrep -[13:18:51] Looking for 'find' - found /usr/bin/find -[13:18:51] Looking for 'grep' - found /usr/bin/grep -[13:18:51] Looking for 'hmmpress' - found /Users/aperrin/Softwares/src/prokka/bin/../binaries/darwin/hmmpress -[13:18:51] Determined hmmpress version is 3.1 -[13:18:51] Looking for 'hmmscan' - found /usr/local/bin/hmmscan -[13:18:51] Determined hmmscan version is 3.1 -[13:18:51] Looking for 'java' - found /usr/bin/java -[13:18:51] Looking for 'less' - found /usr/bin/less -[13:18:51] Looking for 'makeblastdb' - found /Users/aperrin/Softwares/bin/makeblastdb -[13:18:51] Determined makeblastdb version is 2.3 -[13:18:51] Looking for 'minced' - found /Users/aperrin/Softwares/src/prokka/bin/../binaries/darwin/../common/minced -[13:18:51] Determined minced version is 2.0 -[13:18:51] Looking for 'parallel' - found /usr/local/bin/parallel -[13:18:52] Determined parallel version is 20181022 -[13:18:52] Looking for 'prodigal' - found /usr/local/bin/prodigal -[13:18:52] Determined prodigal version is 2.6 -[13:18:52] Looking for 'prokka-genbank_to_fasta_db' - found /Users/aperrin/Softwares/src/prokka/bin/prokka-genbank_to_fasta_db -[13:18:52] Looking for 'sed' - found /usr/bin/sed -[13:18:52] Looking for 'tbl2asn' - found /Users/aperrin/Softwares/src/prokka/bin/../binaries/darwin/tbl2asn -[13:18:52] Determined tbl2asn version is 25.6 -[13:18:52] Using genetic code table 11. -[13:18:52] Loading and checking input file: Examples/1-res-Annotate/tmp_files/genome4.fst-split5N.fna -[13:18:52] Wrote 1 contigs totalling 7134 bp. -[13:18:52] Predicting tRNAs and tmRNAs -[13:18:52] Running: aragorn -l -gc11 -w Examples\/1\-res\-Annotate\/tmp_files\/genome4\.fst\-split5N\.fna\-prokkaRes\/GEN4\.1111\.00001\.fna -[13:18:52] Found 0 tRNAs -[13:18:52] Predicting Ribosomal RNAs -[13:18:52] Running Barrnap with 1 threads -[13:18:52] Found 0 rRNAs -[13:18:52] Skipping ncRNA search, enable with --rfam if desired. -[13:18:52] Total of 0 tRNA + rRNA features -[13:18:52] Searching for CRISPR repeats -[13:18:52] Found 0 CRISPRs -[13:18:52] Predicting coding sequences -[13:18:52] Contigs total 7134 bp, so using meta mode -[13:18:52] Running: prodigal -i Examples\/1\-res\-Annotate\/tmp_files\/genome4\.fst\-split5N\.fna\-prokkaRes\/GEN4\.1111\.00001\.fna -c -m -g 11 -p meta -f sco -q -[13:18:52] Found 9 CDS -[13:18:52] Connecting features back to sequences -[13:18:52] Not using genus-specific database. Try --usegenus to enable it. -[13:18:52] Annotating CDS, please be patient. -[13:18:52] Will use 1 CPUs for similarity searching. -[13:18:52] There are still 9 unannotated CDS left (started with 9) -[13:18:52] Will use blast to search against /Users/aperrin/Softwares/src/prokka/db/kingdom/Bacteria/sprot with 1 CPUs -[13:18:52] Running: cat Examples\/1\-res\-Annotate\/tmp_files\/genome4\.fst\-split5N\.fna\-prokkaRes\/sprot\.faa | parallel --gnu --plain -j 1 --block 1161 --recstart '>' --pipe blastp -query - -db /Users/aperrin/Softwares/src/prokka/db/kingdom/Bacteria/sprot -evalue 1e-06 -num_threads 1 -num_descriptions 1 -num_alignments 1 -seg no > Examples\/1\-res\-Annotate\/tmp_files\/genome4\.fst\-split5N\.fna\-prokkaRes\/sprot\.blast 2> /dev/null -[13:18:53] Deleting unwanted file: Examples/1-res-Annotate/tmp_files/genome4.fst-split5N.fna-prokkaRes/sprot.faa -[13:18:53] Deleting unwanted file: Examples/1-res-Annotate/tmp_files/genome4.fst-split5N.fna-prokkaRes/sprot.blast -[13:18:53] There are still 3 unannotated CDS left (started with 9) -[13:18:53] Will use hmmer3 to search against /Users/aperrin/Softwares/src/prokka/db/hmm/HAMAP.hmm with 1 CPUs -[13:18:53] Running: cat Examples\/1\-res\-Annotate\/tmp_files\/genome4\.fst\-split5N\.fna\-prokkaRes\/HAMAP\.hmm\.faa | parallel --gnu --plain -j 1 --block 379 --recstart '>' --pipe hmmscan --noali --notextw --acc -E 1e-06 --cpu 1 /Users/aperrin/Softwares/src/prokka/db/hmm/HAMAP.hmm /dev/stdin > Examples\/1\-res\-Annotate\/tmp_files\/genome4\.fst\-split5N\.fna\-prokkaRes\/HAMAP\.hmm\.hmmer3 2> /dev/null -[13:18:53] Deleting unwanted file: Examples/1-res-Annotate/tmp_files/genome4.fst-split5N.fna-prokkaRes/HAMAP.hmm.faa -[13:18:53] Deleting unwanted file: Examples/1-res-Annotate/tmp_files/genome4.fst-split5N.fna-prokkaRes/HAMAP.hmm.hmmer3 -[13:18:53] Labelling remaining 3 proteins as 'hypothetical protein' -[13:18:53] Found 6 unique /gene codes. -[13:18:53] Fixed 0 colliding /gene names. -[13:18:53] Adding /locus_tag identifiers -[13:18:53] Assigned 9 locus_tags to CDS and RNA features. -[13:18:53] Writing outputs to Examples/1-res-Annotate/tmp_files/genome4.fst-split5N.fna-prokkaRes/ -[13:18:53] Generating annotation statistics file -[13:18:53] Generating Genbank and Sequin files -[13:18:53] Running: tbl2asn -V b -a r10k -l paired-ends -M n -N 1 -y 'Annotated using prokka 1.14-dev from https://github.com/tseemann/prokka' -Z Examples\/1\-res\-Annotate\/tmp_files\/genome4\.fst\-split5N\.fna\-prokkaRes\/GEN4\.1111\.00001\.err -i Examples\/1\-res\-Annotate\/tmp_files\/genome4\.fst\-split5N\.fna\-prokkaRes\/GEN4\.1111\.00001\.fsa 2> /dev/null -[13:18:54] Deleting unwanted file: Examples/1-res-Annotate/tmp_files/genome4.fst-split5N.fna-prokkaRes/errorsummary.val -[13:18:54] Deleting unwanted file: Examples/1-res-Annotate/tmp_files/genome4.fst-split5N.fna-prokkaRes/GEN4.1111.00001.dr -[13:18:54] Deleting unwanted file: Examples/1-res-Annotate/tmp_files/genome4.fst-split5N.fna-prokkaRes/GEN4.1111.00001.fixedproducts -[13:18:54] Deleting unwanted file: Examples/1-res-Annotate/tmp_files/genome4.fst-split5N.fna-prokkaRes/GEN4.1111.00001.ecn -[13:18:54] Deleting unwanted file: Examples/1-res-Annotate/tmp_files/genome4.fst-split5N.fna-prokkaRes/GEN4.1111.00001.val -[13:18:54] Repairing broken .GBK output that tbl2asn produces... -[13:18:54] Running: sed 's/COORDINATES: profile/COORDINATES:profile/' < Examples\/1\-res\-Annotate\/tmp_files\/genome4\.fst\-split5N\.fna\-prokkaRes\/GEN4\.1111\.00001\.gbf > Examples\/1\-res\-Annotate\/tmp_files\/genome4\.fst\-split5N\.fna\-prokkaRes\/GEN4\.1111\.00001\.gbk -[13:18:54] Deleting unwanted file: Examples/1-res-Annotate/tmp_files/genome4.fst-split5N.fna-prokkaRes/GEN4.1111.00001.gbf -[13:18:54] Output files: -[13:18:54] Examples/1-res-Annotate/tmp_files/genome4.fst-split5N.fna-prokkaRes/GEN4.1111.00001.fsa -[13:18:54] Examples/1-res-Annotate/tmp_files/genome4.fst-split5N.fna-prokkaRes/GEN4.1111.00001.faa -[13:18:54] Examples/1-res-Annotate/tmp_files/genome4.fst-split5N.fna-prokkaRes/GEN4.1111.00001.log -[13:18:54] Examples/1-res-Annotate/tmp_files/genome4.fst-split5N.fna-prokkaRes/GEN4.1111.00001.ffn -[13:18:54] Examples/1-res-Annotate/tmp_files/genome4.fst-split5N.fna-prokkaRes/GEN4.1111.00001.gbk -[13:18:54] Examples/1-res-Annotate/tmp_files/genome4.fst-split5N.fna-prokkaRes/GEN4.1111.00001.gff -[13:18:54] Examples/1-res-Annotate/tmp_files/genome4.fst-split5N.fna-prokkaRes/GEN4.1111.00001.tbl -[13:18:54] Examples/1-res-Annotate/tmp_files/genome4.fst-split5N.fna-prokkaRes/GEN4.1111.00001.sqn -[13:18:54] Examples/1-res-Annotate/tmp_files/genome4.fst-split5N.fna-prokkaRes/GEN4.1111.00001.tsv -[13:18:54] Examples/1-res-Annotate/tmp_files/genome4.fst-split5N.fna-prokkaRes/GEN4.1111.00001.fna -[13:18:54] Examples/1-res-Annotate/tmp_files/genome4.fst-split5N.fna-prokkaRes/GEN4.1111.00001.err -[13:18:54] Examples/1-res-Annotate/tmp_files/genome4.fst-split5N.fna-prokkaRes/GEN4.1111.00001.txt -[13:18:54] Annotation finished successfully. -[13:18:54] Walltime used: 0.05 minutes -[13:18:54] If you use this result please cite the Prokka paper: -[13:18:54] Seemann T (2014) Prokka: rapid prokaryotic genome annotation. Bioinformatics. 30(14):2068-9. -[13:18:54] Type 'prokka --citation' for more details. -[13:18:54] Share and enjoy! diff --git a/Examples/1-res-Annotate/tmp_files/genome4.fst-split5N.fna-prokkaRes/GEN4.1111.00001.sqn b/Examples/1-res-Annotate/tmp_files/genome4.fst-split5N.fna-prokkaRes/GEN4.1111.00001.sqn deleted file mode 100644 index cde29bf57f4b0c7718991f9a1678c2acbf175f68..0000000000000000000000000000000000000000 --- a/Examples/1-res-Annotate/tmp_files/genome4.fst-split5N.fna-prokkaRes/GEN4.1111.00001.sqn +++ /dev/null @@ -1,798 +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-dev 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 2 } , - { - label - str "day" , - data - int 12 } , - { - label - str "year" , - data - int 2019 } } } , - create-date - std { - year 2019 , - month 2 , - day 12 } } , - 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:2.6" } , - { - qual "inference" , - val "similar to AA sequence:UniProtKB:P75820" } } , - xref { - { - data - gene { - locus "amiD" , - locus-tag "LIKMDGFN_00001" } } } } , - { - 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:2.6" } , - { - 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:2.6" } , - { - 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:2.6" } } , - 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:2.6" } , - { - qual "inference" , - val "similar to AA sequence:UniProtKB:P02915" } } , - xref { - { - data - gene { - locus "hisP" , - locus-tag "LIKMDGFN_00005" } } } } , - { - 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:2.6" } , - { - qual "inference" , - val "similar to AA sequence:UniProtKB:P0A873" } } , - xref { - { - data - gene { - locus "trmD" , - locus-tag "LIKMDGFN_00006" } } } } , - { - 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:2.6" } } , - 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:2.6" } } , - 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:2.6" } , - { - qual "inference" , - val "similar to AA sequence:UniProtKB:O07838" } } , - xref { - { - data - gene { - locus "dctM" , - locus-tag "LIKMDGFN_00009" } } } } } } } } } } diff --git a/Examples/1-res-Annotate/tmp_files/genome4.fst-split5N.fna-prokkaRes/GEN4.1111.00001.tbl b/Examples/1-res-Annotate/tmp_files/genome4.fst-split5N.fna-prokkaRes/GEN4.1111.00001.tbl deleted file mode 100644 index 13f7f5d45429a32dbaea30869471d9f45f3c87bb..0000000000000000000000000000000000000000 --- a/Examples/1-res-Annotate/tmp_files/genome4.fst-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 - dbxref COG:COG3023 - gene amiD - inference ab initio prediction:Prodigal:2.6 - 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:2.6 - 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:2.6 - 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:2.6 - locus_tag LIKMDGFN_00004 - product hypothetical protein -3535 4308 CDS - dbxref COG:COG4598 - gene hisP - inference ab initio prediction:Prodigal:2.6 - 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 - dbxref COG:COG0336 - gene trmD - inference ab initio prediction:Prodigal:2.6 - 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:2.6 - locus_tag LIKMDGFN_00007 - product hypothetical protein -5413 5994 CDS - inference ab initio prediction:Prodigal:2.6 - locus_tag LIKMDGFN_00008 - product hypothetical protein -6052 7134 CDS - dbxref COG:COG1593 - gene dctM - inference ab initio prediction:Prodigal:2.6 - inference similar to AA sequence:UniProtKB:O07838 - locus_tag LIKMDGFN_00009 - product C4-dicarboxylate TRAP transporter large permease protein DctM diff --git a/Examples/1-res-Annotate/tmp_files/genome4.fst-split5N.fna-prokkaRes/GEN4.1111.00001.tsv b/Examples/1-res-Annotate/tmp_files/genome4.fst-split5N.fna-prokkaRes/GEN4.1111.00001.tsv deleted file mode 100644 index 6fb4e7be29674a310922cdb82a5fbe08125db815..0000000000000000000000000000000000000000 --- a/Examples/1-res-Annotate/tmp_files/genome4.fst-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/1-res-Annotate/tmp_files/genome4.fst-split5N.fna-prokkaRes/GEN4.1111.00001.txt b/Examples/1-res-Annotate/tmp_files/genome4.fst-split5N.fna-prokkaRes/GEN4.1111.00001.txt deleted file mode 100644 index 61a7be1fcd34429f898e3d10baea743e4d6e049c..0000000000000000000000000000000000000000 --- a/Examples/1-res-Annotate/tmp_files/genome4.fst-split5N.fna-prokkaRes/GEN4.1111.00001.txt +++ /dev/null @@ -1,4 +0,0 @@ -organism: Genus species strain -contigs: 1 -bases: 7134 -CDS: 9