diff --git a/test/data/annotate/exp_files/exp_ALL-GENOMES-QC.lst b/test/data/annotate/exp_files/exp_ALL-GENOMES-QC.lst
index ec6c0fb477026bc66abe8fdfc7460f57191a5b31..ebe711bc93e6b5658d59e8a7b291ca392b0d9b8b 100644
--- a/test/data/annotate/exp_files/exp_ALL-GENOMES-QC.lst
+++ b/test/data/annotate/exp_files/exp_ALL-GENOMES-QC.lst
@@ -1,4 +1,5 @@
 orig_name	to_annotate	gsize	nb_conts	L90
 B2_A3_5.fasta-changeName.fna	B2_A3_5.fasta-changeName.fna	120529	5	4
 H299_H561.fasta-all.fna	H299_H561.fasta-all.fna	13259	7	3
-A_H738.fasta-all.fna	A_H738.fasta-all.fna	20031	5	1
+A_H738.fasta-all.fna	A_H738.fasta-all.fna	20066	5	1
+complete_genome.fna	complete_genome.fna	88	1	1
diff --git a/test/data/annotate/exp_files/exp_A_H738.fasta-all.fna_prokka-split3N.fna b/test/data/annotate/exp_files/exp_A_H738.fasta-all.fna_prokka-split3N.fna
new file mode 100644
index 0000000000000000000000000000000000000000..f284e70de0bce8992f89f5d8611b735ef13b0680
--- /dev/null
+++ b/test/data/annotate/exp_files/exp_A_H738.fasta-all.fna_prokka-split3N.fna
@@ -0,0 +1,14 @@
+>1_H738_S10 L001_R1_001_(paired)_contig_1
+GAAATATAGGGGCAAATCCATTGTGTATTCCTGACGGCAAAAATAAGGAATATAAAGAAATGATTGCTTTGGTTTCTTACAACACATCATTCCCTTTTCATTTAATAAAGCGGCATGATACAAAGTGAACATGATTTCGATTTACATTGCCACCATACCGCTTCAGACAACCGGTACATTACTTTGTTATAAGACGTGATATATAATTCAAAACAACGTGGTTTTGATTATTCATATCTCATAATAAAAGTCGCGTCAGCATTTGCTTGCCCTGCTGATGCACTTGTACCGGTGCCTTTATAACGTGCAGAAAAATGAAGAACGTTGGTCCCGGGGATCAAGTTCTGGTTGGTTGAGAAGCTATTCCCATCAGGTTTGAGAATTGCGGATGTATTATCAAGTATTTCAATACCGACACCCGTTGCTGTTGTTGTATTGGTACTGGATGCAATGGCCAATAAATTATCATTGATTGCATCAGCCTGACCAGAAAATGCAACGGCAGCATTAGCGGCAACAACAGGATCGCAGTCGTTCAACTGAATGGTGAATGGAATTAATGCAGAGGTATTACCAACAGCATTGAAAATATCGGTACGATATTGACCGAGTGTGACAACCTGGTCTGCCGAGTCAGTATTCACTGAACAGGCAGCATTCACCAGTTCGCCTTCAAAGTGAATTGTACCGCCATCTACAACGGCAGCATAACTACCCGTAGCGGCGAATAGTGCGGCAGCCAGCGCAGACGAAATAAATCTTAATTTCATATATATTCCTTCAATCTCATTTATCGACTCCACATCCGTATATAACCGATTACTTTATTTAAGACACTGATAGTAGTAAATTCCTTTTTATCCTCTAAGAATGTCTTAATTGAAAATATGCACTCTATTCTAAAAAATAGAGAGCCCCGTTAGATGAATACTTCCGCGCAAAATATATTCAACACAAATATAGACCTGAAGCGGTAAATTACCAGGCTGAAAATTCTTTTTATATTGTCAGGTATTTCTTAAATTATCTTAATCCTTAGACAAGGAAATAAATCAGTTCCAGATTTACAACGCCATCATGGACGAAAAATGAAGCTTTCAGTCTCAGCGACGGTGCGCCTCACCTTCGCAAGAGGTCGCTTCACGCGATAAATCTGAAACGAAACCTGACAGCGCGCCCCGCTTCTGACAAAATAGGCGCATCCCCTTCGATCTACGTAACAGATGGAATCCTCTCTCTGATGGCAGCAAAGATTATTGACGGTAAAACGATTGCGCAGCAGGTGCGCTCTGAAGTTGCTCAAAAAGTTCAGGCGCGTATTGCAGCCGGACTGCGGGCACCAGGACTGGCCGTTGTGCTGGTGGGTAGTAACCCTGCATCGCAAATTTATGTCGCAAGCAAACGCAAGGCTTGTGAAGAAGTCGGGTTCGTCTCCCGCTCTTATGACCTCCCGGAAACCACCAGCGAAGCGGAGCTGCTGGAGCTTATCGATACGCTGAATGCCGACAACACCATCGATGGCATTCTGGTTCAACTGCCGTTACCGGCGGGTATTGATAACGTCAAAGTGCTGGAACGTATTCATCCGGACAAAGACGTGGACGGTTTCCATCCTTACAACGTCGGTCGTCTGTGCCAGCGCGCGCCGCGTCTGCGTCCCTGCACCCCGCGCGGTATCGTCACGCTGCTTGAGCGTTACAACATTGATACCTTCGGCCTCAACGCCGTGGTGATTGGCGCATCGAATATCGTTGGCCGCCCGATGAGCATGGAACTGCTGCTGGCAGGTTGCACCACTACAGTGACTCACCGCTTCACTAAAAATCTGCGTCATCACGTAGAAAATGCCGATCTATTGATCGTTGCCGTTGGCAAGCCAGGCTTTATTCCCGGTGACTGGATCAAAGAAGGCGCAATTGTGATTGATGTCGGCATCAACCGTCTGGAAAATGGCAAAGTTGTGGGCGACGTCGTGTTTGAAGACGCGGCTAAACGCGCCTCATACATTACGCCTGTTCCCGGCGGCGTTGGCCCGATGACGGTTGCCACGCTGATTGAAAACACGCTACAGGCGTGCGTTGAATATCATGATCCACAGGATGAGTAACATGGCGACATTTTCTTTAGGTAAACATCCGCACGTTGAGCTGTGCGACTTGCTGAAACTGGAAGGCTGGAGCGAAAGCGGCGCGCAGGCGAAAATCGCGATTGCCGAAGGCCAGGTGAAAGTCGACGGTGCGGTTGAAACGCGCAAACGCTGCAAAATCGTCGCCGGTCAGACAGTGAGTTTTGCAGGTCACAGCGTACAGGTTGTTGCCTGATCCCTTTCCCGGCCTGTATCAACAGGCCGGTTCTCTTTTCAGACTTTTGCCCTCTACGCCCCGTTCATCCATGCTGATAGCATCGACATTTTGCCGAAGCGACCATCATGCCAACCGTTATTACGCACGCCGCCGTTCCCCTATGCATTGGTTTAGGGTTGGGTTCGAAAGTCATCCCTCCGCGTCTGTTATTTGCCGGAATCATCCTGGCGATGCTGCCCGACGCCGACGTATTGTCGTTTAAATTTGGCGTTGCTTACGGCAATGTTTTTGGTCATCGCGGGTTTACCCATTCGCTGGTGTTTGCGTTTGTTGTCCCGCTGTTATGTGTGTTTATTGGACGCCGATGGTTCAGGGCTGGGCTGATTCGCTGCTGGCTGTTTTTAACCGTCTCGTTGCTATCGCACAGCTTGCTGGATTCGGTAACCACTGGCGGTAAAGGCGTTGGCTGGCTGTGGCCGTGGTCAGATGAACGCTTTTTCGCTCCCTGGCAGGTGATAAAAGTCGCGCCGTTTGCATTGTCTCGTTACACCACGCCGTACGGGCATCAGGTGATTATTTCTGAATTGATGTGGGTGTGGTTGCCGGGGATGCTACTGATGGGAATGTTGTGGTGGCGCAGACGATAACCGGATGCGAAAACTCGCATCCGGCAATAGCGCAATTACTTACGACGCCAGGTGGTCCCTTGCGGGCCATCTTCCAGCACGATCCCCATCTCGTTAAGACGATCACGCGCCGCATCCGCCGCCGCCCAGTCTTTCGCTTTACGGGCATCCAGACGCTGTTGAATTAACGCTTCAATCTCAGCCACTTCGCT
+>2_H738_S10 L001_R1_001_(paired)_contig_1
+GTCGTCTGCCTGCGCGCCGCTTTGCAGGAACGCTTCCGGTTCTTGCTCCAGCAGGCCCAATACAGCGGAAAGTTTACGCAGGTGAGATGCCATTGCATTCGCCGCTGCCATATCTTCTGCTTTCAGACGGTTTACTTCACGCGCCATATCAAACAGTACGGAATAGGCTTCCGGGGTGTTGAAATCGTCGTCCATCGCTTCAATAAAGCGCGCTTCAAACGCTTCGCCACCGGCAGGCGCAACGGTTTTATCTGTGCCGCGCAGCGCAGTGTAGAGACGCTCCAGCGCCGCACGCGCCTGCTTCAGGTTCTCTTCGCTGTAGTTCAACTGGCTGCGATAGTGGCCCGACATCAGGAAGTAACGCACGGTTTCCGCGTCGTAGTATTTCAGCACATCGCGCACGGTAAAGAAGTTACCCAGCGATTTGGACATCTTCTCGCGGTCAACCATCACCATCCCCGAGTGCATCCAGTAGTTCACATACTGACCATCATGGGCACAGGTGGACTGCGCGATTTCGTTTTCGTGGTGCGGGAACATCAGGTCTGAACCGCCGCCGTGGATATCAAAGTGGTTACCCAGCTGCTTGCAGTTCATTGCCGAACATTCAATGTGCCAGCCAGGACGACCCGCGCCCCACGGAGACGGCCAGCTCGGTTCGCCCTCTTTCGACATCTTCCACAGAACGAAGTCCATTGGGTTGCGTTTGTCGTCGACCACGTCAACGCGCGCGCCTGCCTGCAGCTGGTCGAGATCCTGACGCGACAGCACGCCATAAGTTGGATCGGTCGGGACGTCGAACATCACGTCGCCGTTGTCCGCCACATAAGCGTGACCTTTGGCGATCAGTTGTTCAGTGAGTTCAATAATTTCTGCGATATGGTGCGTCGCGCGCGGCTCCATATCCGGGCGCAGAATGTTCAAAGCATCAAAATCTTTGTGCATTTCGGCGATCATGCGATCCACCATCGCCACAAAGCTTTCGCCATTTTCATTGGCGCGTTTGATGATTTTGTCGTCGATATCGGTAATGTTGCGCACATACTTCAGTTTATAGCCGAGGAAACGCAGATAGCGCGCAACCACGTCAAAAGCAACAAAGGTACGCCCGTGACCGATATGACAGAGATCGTAAACGGTGATTCCACACACGTACATGCCGACTTCCCCGGCGTGAATAGGCTTAAATTCCTCTTTTTGGCGTGTCAGAGTATTGAAGATTTTTAGCATCGAAGATTCCGTTTAGACATGTGTGGGTAATTGAGTTGCGTATAATACCCATATTTCCCGCGCGAATCAGCATACATTGCGTGATGATCCGATCGTGCGGTTATGCTATAACACCACCCTATATATGACCCGAACTGGGTTGAAGCACCAATCAAACGGAACAGGATGCAAAAATGGTTACTTTCCACACCAATCACGGCGATATTGTCATCAAAACTTTTGACGATAAAGCACCTGAAACAGTTAAAAACTTCCTGGACTACTGCCGCGAAGGTTTTTACAACAACACCATTTTCCACCGTGTTATCAACGGCTTTATGATTCAGGGCGGCGGTTTTGAACCGGGCATGAAACAAAAAGCCACCAAAGAACCGATCAAAAACGAAGCCAACAACGGCCTGAAAAATACCCGTGGTACGCTGGCAATGGCACGTACTCAGGCTCCGCACTCTGCAACTGCACAGTTCTTCATCAACGTGGTTGATAACGACTTCCTGAACTTCTCTGGCGAAAGCCTGCAAGGTTGGGGCTACTGCGTGTTTGCTGAAGTGGTTGACGGCATGGACGTGGTAGACAAAATCAAAGGTGTTGCAACCGGTCGTAGCGGTATGCACCAGGACGTGCCAAAAGAAGACGTTATCATTGAAAGCGTGACCGTTAGCGAGTAATCGTGGCGACACTCTTTATTGCAGATCTTCATCTCTGCGTGGAAGAACCGGCGATCACCGCCGGTTTTCTGCGTTTTTTAGCGGGGGAAGCCCGCAAGGCCGACGCGCTGTATATTCTTGGCGATCTGTTTGAAGCATGGATTGGCGACGACGATCCCAACCCACTCCATCGCAAGATGGCGGCGGCGATCAAAGCGGTGTCCGATTCCGGCGTTCCCTGTTATTTCATTCATGGCAACCGTGATTTTCTGCTCGGCAAACGCTTTGCCCGTGAAAGTGGCATGACGTTATTGCCGGAAGAAAAGGTGCTCGAACTTTATGGTCGCCGGGTGTTGATTATGCATGGCGACACGCTGTGCACCGATGACGCGGGTTATCAGGCTTTTCGCGCCAAGGTCCACAAACCCTGGCTGCAGACGCTATTCCTCGCCCTGCCGTTGTTTGTGCGCAAACGCATTGCCGCGCGAATGCGCGCGAACAGCAAAGAAGCCAACAGCAGTAAATCGCTGGCGATCATGGACGTTAACCAAAACGCGGTGGTCAGTGCGATGGAAAAACATCAGGTGCAATGGCTGATCCACGGGCATACCCATCGCCCGGCGGTGCATGAACTTATCGCTAATCAGCAACCTGCTTTTCGCGTGGTACTGGGTGCCTGGCATACGGAAGGTTCAATGGTGAAAGTCACGGCGGATGACGTTGAGCTGATTCATTTTCCGTTTTAAAAAACCCGCAACTTTGCTGATTTCACAGCCACGCAACCGTTTTCCTTGCTCTCTTTCCGTGCTATTCTCTGTGCCCTCTAAAGCCGAGAGTTGTGCACCACAGGAGTTTTAAGACGCATGTCTTCCCGCAATAATCCGGCGCGTGTCGCCATCGTGATGGGGTCCAAAAGCGACTGGGCTACCATGCAGTTCGCCGCCGAAATCTTCGAAATCCTGAATGTCCCGCACCACGTTGAAGTGGTTTCTGCTCACCGCACCCCCGATAAACTGTTCAGCTTCGCCGAAAGCGCCGAAGAGAACGGTTATCAGGTGATTATTGCGGGCGCAGGCGGCGCAGCGCATCTGCCAGGCATGATTGCCGCCAAAACGCTGGTGCCGGTGCTGGGCGTGCCAGTACAGAGCGCCGCACTGAGCGGTGTCGATAGCCTCTACTCCATCGTACAAATGCCGCGCGGCATTCCGGTGGGTACGCTGGCGATTGGTAAAGCTGGCGCGGCAAACGCGGCGTTACTGGCAGCACAAATTCTTGCGACTCATGATAAAGAACTGCACCAGCGTCTGAATGACTGGCGCAAAGCCCAGACCGACGAAGTGCTGGAAAACCCGGACCCGCGAGGTGCGGCATGAAACAGGTTTGCGTCCTCGGTAACGGGCAGTTAGGCCGTATGCTGCGTCAGGCAGGCGAACCGTTAGGCATTGCTGTCTGGCCAGTCGGGCTGGACGCTGAACCGGCGGCGGTGCCTTTTCAACAAAGCGTGATTACCGCTGAGATAGAACGCTGGCCGGAAACCGCATTAACCCGCGAGCTGGCGCGCCATCCGGCCTTTGTGAACCGCGATGTGTTCCCGATTATTGCTGACCGTCTGACTCAGAAGCAGCTTTTCGATAAGCTCCACCTGCCGACTGCACCGTGGCAGTTACTTGCCGAACGCAGCGAGTGGCCTGCGGTGTTTGATCGTTTAGGTGAGCTGGCGATTGTTAAGCGTCGCACTGGTGGTTATGACGGTCGCGGTCAATGGCGTTTACGCGCAAATGAAACCGAACAGTTACCGGCAGAGTGTTACGGCGAATGTATTGTCGAGCAGGGCATTAACTTCTCTGGTGAAGTGTCGCTGGTTGGCGCGCGCGGCTTTGATGGCAGCACCGTGTTTTATCCGCTGACGCATAACCTGCATCAGGACGGTATTTTGCGCACCAGCGTCGCTTTTCCGCAGGCCAACGCACAGCAGCAGGCGCAAGCCGAAGAGATGCTGTCGGCGATTATGCAGGAGCTGGGCTATGTGGGCGTGATGGCGATGGAGTGTTTTGTTACCCCGCAAGGTCTGTTGATCAACGAACTGGCACCGCGTGTGCATAACAGCGGTCACTGGACACAAAACGGTGCCAGCATCAGCCAGTTTGAGCTGCATCTGCGGGCGATTACCGATCTGCCGTTACCGCAACCAGTGGTGAATAATCCGTCGGTGATGATCAATCTGATTGGTAGCGATGTGAATTATGACTGGCTGAAACTGCCGCTGGTGCATCTGCACTGGTACGACAAAGAAGTCCGTCCGGGGCGTAAAGTGGGGCATCTGAATTTGACCGACAGCGACACATCGCGTCTGACTGCGACGCTGGAAGCCTTAATCC
+>3_H738_S10 L001_R1_001_(paired)_contig_1
+CGCTGCTGCCGCCGGAATATGCCAGCGGCGTGATTTGGGCGCAGAGTAAGTTCGGTTAACTGGTGCTCTATTCTTGCCGGATGCGGCGTAAACGCCTTATCCGGCCTACCGATCCGGTACCCATTGTAGGCCTGATAAGATGCGTCAAGCATCGCATCAGGCATTGTGCACCAATTGCCGGATGCGGCACCGGTTGTAGGCCTGATAAGACGCGTCAAGCGTCGCATCAGGCACAAATGTCTAATGCCTACGACTACAGCGAAATACAGGTCCCCGCTTCGCCCGCCAGCGTCTCTTCAATTCGCGATAACGCCCCAATCCACGCGGGTTTACCACGGCTTCTGACATAACCACTCACCGCCGTTACCTTCGGCCCCATCGAACCATCGGCTTTGGCAAATGGCGCTAACTCATCCGGTGTGGCATGGCGAATGGCACGTTGCTGCGGCGTTCCCCAGTTTTCATATACCGCATCAGCATCGGTGAGGATCACCAGTCCATCTGCATTAATCTGCTCGGCGAGCAACGCAGCGGCGAGATCTTTATCAATCACTGCTTCACTCCCTGCTCCGTCATCCGTCACAGGCACACCGCCGCCGCCACTGCAAATCACCACATGCCCCTCTTTTAGCAACAACTCGATGGCTTCGCTGTCGAGAATTTTACGCGGTTGCGGAGACGCCACCACCCGGCGCAAATATTTACCATCACGTTTCATCTGCCAGCCGTAAGCCGCTTCCAGTGCCTCTTGTTCTTCTGGCTGATAAACCGGACCAATAAATTTCTCTGGCTGCAAAAACGCCGGATCATCAGGCGAAACCTCAATGCGCGTCAGCACCGTCGTCACGGGCGGCATCTGCGGCTGTGCGCTCAAACTCTGCGCCAGCATATAGCCAATCATCCCCTGGCTTTCCGCAACCAGCACATCCAGCGGATACGGTTCTACCTCTTTCCACGCCAGATTCTGCAATGCCAGCAGCCCCACCTGCGGCCCGTTGCCGTGAACAATCGCCAACCGATAAGAACGGGCCAGGCGTGCCAGCGCGGGTACAGCACTGGCGATATTGCGATATTGATTTTCTGCCGTCAGCGCCTCACCGCGCTGGAGTAAGGCGTTGCCCCCAAGAGCCACAACCAGTGTTTTCATGGTTTTCCTTGTAATAATTGTTGGCCAAGCCAGAACCCCAGCAGCGTATCTGCCCCTGACGTATGCCCCAGCGCCAGCAGCGAATCAATCGCAACAGCGGTACGTTTCGGGCAACTCAGAGCATGAACAAAGTGCAGGAGTGGCGAGGCGAAATATCCTTGCGCGGCATAACGTAAATAACTGACGCTCACCGCTGTGGTAACGAGTTGCAGATTGTCGGAACAGGCAAAAAACGGACGACCGGAGCGCGCATCTAAAGCGCCATAATACCAGGCCGCCAGCAGCATTCCGCTCAGCGTGTCATCATGACTCGGCGTTAATCCGGGGCCTTTACCCAGCCAGTGCCGCCAGTCGGTCTTAACGCCATTGAGCGCGGCCTGAAAACAGTGACGAAACTGGCGTAACTCAGCAGGCAGCGGATCGCTTGCCGCCAACGCCAGTGGCCCGAAAAGCCCGGTTTCCTCCGCGCGTTGCATCCATGCAGCTGCAAGTGGTTGAGGATGCGCAGGCGGCGTAATACGCAGCAAACAATAACGCTGTGGCTGTTTAACCGTGAAACGCCCGAGGCGAATCCCTTGAGCCACAACCTGTGGTCGTTCATTGCCGCATAATCCACCGCATAACGCATCGAATTGCGCACGGCGAAGCACCCATCCTCCGGGGCCGAAACCACTACCCTGACGATGCAACGTTAACAGTTCGCCGCTTTCCGTCATCAGGTTAATCGCCCGCCGCCACACTCCCGCTAACCGCCAGGACTGGCGATAATTCGGTGCGCTACTACTGGCAAGCAGAGGATGGATGATCGTCATTGCGCGTTCCTCAACCAATACCCATGCTTTCAGCCAGTGCTTCCAGCGCCTGTTCAAAGCACGCCAGCGGTGCCCGCACGGTGCCTGCGCCAATCTGCCCGATCCCCGCCTCTTTATGGGCGATACCGGTATTGATGAGTGGCGTAATGCCGGTTTCTACCACGCGACGAATGTCCAGCCCCAGGCACGCGCCCTGAAAATCCCAGCTTGGGATCTGCAACTGCATATTGCGTTCAAGGTAAATTTCCGCCATCTCTTCAGATACCGCTCTTGCCGCTTCCATGCCACCCGCACCGACAAAGCGCGTTACGCCAGGCGCTGCGATCATTGCCGCACCTCCGATACCAAAGGTTTCGGTAATCGCGCTATCGCCCATATCCGGGTTCGCCTGCTCCTGCGAGAAGCCGGTGAAAAACAGACCTTGCGGAGTGTTTACAGGCGCAGTAAACCAGCGTTCGCCCAGCCCGCTTACCCGAATCCCGAACATATTGCCGTTGCGGGTCATTGCCGTGACGATGCTGCCTGCGCGGATCATCGCGCCAGCATCCATCGCCGCCTTGCAGTAAGCCATCGCGAGGTTGAGGAAGAACTGATCGGTCACGCTGAGGAAATCCATCACTTCGGCGATGTGCTGTTTATCATGATCGAGGCGAGCAATTTGTGGGGCCAGCGCACGCATTAACAGTGCAGAGGAAGCAATATTGCGTTGATGGAACTCATCGCCCATCGTAATGCCCTGCGCCATCATCGCCGTGAGATCGATACCGCGCTCCATGCGCCCCAGCGCCGCGCTTAATACTGGCATTAACACATCGCGCATCCAGCGATGGCGAGTCAGGACATCTTCGCCGTAAGCGCCAAAACGCATCACTTTGCCGATACCTTCGTTGAGGTTGCAGTACGCCCGGTTGCCGTCGGTCACGTTCTCAACCACCAGCATCGGCATACTGGCAGAAGTAATACCGCCCATTGGCCCGACGGCATTCACATGGTGACAAGGAATGAAGTTCACTTCCCCCTGCTCCAGTATTGCCAGCGCCTGCGCTTCATCTTTCGCCCAACCTTCGAACAGACATGCGCCCACGCACGCCCCTTTCATGGGTCCGGTCATCTCCTGCCAGCGCATTGGCGGCCCGGCGTGAAGCAGTGTTTTGCCCTCGTTTAGTTCGCTGATAAGTGAAGAAGCCGGTTGCACATCCAGCCAGTGTGGACGAGCGCGACGAATTTGTTCGATAACCGCAGCATTGGCTTGCGCCACTGATGTAAACATGGGAACCCCTTATTGCAAACGTTCTAATAAACGAGCCAGTTTTTTATTGCCACCGGCGACTGGCGACCATTGGTAATGCACAACCGGTTTGCTGGCGCTTTGTAGCTCCAGCGCAAAGCTGCGTAATCCGATGTTAATCACGGCGACGTTTTCCAGTAATGACGGTGTGTGTTGCTGTGCGGCAGGCGAGAGCGGATGAATTAACGCTGCCGCCAGCAAGGTGGCTTCCGGTAGCGAACTCACGACCGCAATCCCCGCATCTTCCAGCGTGGCGATTTGCTGCGAGCGGCATTGCGGGTCACGTTCAGTGCCTGTCACCGTGGCAATGGCATACAGTGGTTGATTATCTAAACGCGCGGCACAGGCTTTTTGCCAGGCGCTCACCAGCGAGGCGGCAGGATCGGCGGTCGCACCGAAGCCAATCACGACATCAAGCAGCAACACGCGCACTTGCGGTTTAGCGCCGAGATCGGCAATTAACTGGTTGCGTAAGGTTGGGTCGATCATCGGATGGGGACGCCCGACGGTGTAGAAATCATCGCCGAGGTCAATAATCTGGTGGCTATCGGCGTCCAGCATCATGCCATGTTGATGGGTATCGTCGGCTTCCACGCCAAGGTGTCCGGCAAGTAATCCCGCCGCTTCGGCAGCCAGCGTACCGCCGGTATACAAACCGCAAATAAATCCGCTGCTGACAGGCGCTATTGCGTTACGTCGCGCCGTGACGCGTGAAAGCAGGCAAGCCAGGCGTGCGGCCTCATCCAGCGAGGAGGCAAACCAGACATTCTCGTCGCGGGCCACCGCCGGGGTATAACCTAAAAACAGCGCCACCGTCGGTTTGCCGGTTGCTTTCATGGCATTAACAATTTTCAGACGCACAGCTTCGGCAGGTGGTTTTGAAACAAATGCCAGCACTTCGCTTTTCTCGTCTGCACTGAGCATTTCCAGCGCTGTTAGCGCACTGATGCCGCCCACTTCACGGCTGAGGTCGCGCCCGCCAAGGCCAATCGCGTGAGTAATTCCCTCCCCTGCCAGCGCAATCTGCGAACACAGCTCCTGAATCCCGGTACCGGAAGCGCCAATGACGCCAATATTGCCTTCCGGCATCACGTTAGCAAAAGCCAGCGGTGTGCCGGCAATCATCGACGTACCGCAGTCCGGCCCCATCACCAGCAAGCCTTTTTCCCGCGCGCGGGTTTTAAGTTGGATTTCATCTTCCAGCGTGACGTTATCGGAGAACATCATCACGTTGAGGTTGCGATCCAGCGCCTGGTTTGCCAGCTCCGCCGCATACTCGCCAGCCACTGAAATCAGCGCCAGATTGGCATCGGGTAATTTCTGACAGGCACTGTCCCAGCGACGCACCTGCATCAACGCCTGGCTGCTGCCTGACCCCTGCGCCAGTTGTTTTAGCGCCTCTTCAAGCTGCTGCATAATCGCCTGCGCGATCCCCGCATCCGCCGCTTCGCTACGAATTGCCACGCAAATATCGTTCGGCGTGGCGTTATTAAAATCGTCATGCCAGAAACCTGTGGTATCTAATAACGCTTTATTGGCGGGCGTACCCATCATTACGGAAACATCATCAACATTTTCTGATTCGCTGAGTTTTCGTGAAATAATCATTAAACTGACCGAATCCTGAAAACACCCTTTTTTAATAAAGGCGTGGATCATAACAACTCCTTAAAAATTGCACCCATGGCAATTGCACGAGCAGTGTTAATGTGGCGATTACGGTATCGATGACAACGAGTAAATAAGGTGATGAATATCACACAGGAATTATTAACAAAAGAATTCAAATAACCACCAGGCTATTACTCATTATTTTTTAATAAGCGTTGTTGTTTTAAAAATCAGGTTAAAAGTGAGCGGATTATCAAATAAATTCTAACTATATTTTTTTGCCTGTCTGGATCACATAATCCAGATATTTTCCCTGTATGTTAATTGCAGTCATGCTTCACACCGTCGTTAAAAAGGAAGACAGATGAAAATCAGTCGGGAAACACTCCACCAGCTAATTGAGAATAAACTCTGCCAGGCTGGGTTAAAACGTGAGCACGCTGCAACCGTGGCTGAAGTATTGGTTTACGCCGATGCCAGAGGGATCCACTCTCATGGCGCGGTGCGCGTGGAATACTACGCGGAACGCATTTCAAAAGGCGGCACCAACCGCGAACCGGAGTTTCGTCTTGAGGAAACCGGGCCGTGCTCGGCAATTTTACATGCCGACAATGCCGCCGGACAGGTCGCGGCGAAAATGGGTATGGAACATGCCATCAAAACCGCCCAGCAAAATGGCGTTGCGGTGGTCGGTATCAGCCGGATGGGTCACAGCGGCGCAATCTCTTATTTTGTGCAGCAGGCAGCCCGCGCCGGATTCATTGGCATTTCGATGTGCCAGTCCGATCCAATGGTGGTGCCGTTTGGCGGCGCGGAAATTTACTACGGTACTAACCCCCTGGCCTTTGCCGCGCCGGGAGAAGGCGACGAGATCCTTACCTTTGATATGGCGACTACCGTACAGGCATGGGGAAAAGTGCTCGACGCCCGCTCGCGTAATATGTCTATCCCGGATACCTGGGCGGTCGATAAAAACGGTGTACCAACAACCGATCCGTTCGCGGTACATGCTCTGCTCCCCGCCGCCGGGCCAAAAGGGTATGGCCTGATGATGATGATTGACGTCCTCTCAGGCGTCTTACTCGGCTTACCGTTCGGGCGACAGGTTAGTTCGATGTATGACGATTTACACGCAGGGCGTAATTTGGGGCAATTACATATAGTTATTAATCCGAACTTTTTCTCCTCCAGCGAATTATTCCGTCAACATCTTAGCCAGACCATGCGCGAATTAAATGCCATTACCCCCGCGCCCGGTTTTAATCAGGTTTATTATCCCGGACAGGATCAGGATATTAAACAACGCAAAGCCGCCGTCGAAGGCATCGAAATTGTTGATGATATTTACCAGTATTTAATTTCCGACGCGCTTTATAACACGTCATACGAAACGAAAAATCCCTTTGCGCAATAATTATTGAGACAGGACTTTCTTATGATTACACATTTCCGTCAAGCTATAGAAGAAACGCTGCCCTGGCTTTCCTCTTTTGGCGCTGACCCAGCGGGTGGGATGACCCGTTTACTTTATTCGCCGGAATGGCTGGAAACCCAGCAGCAATTTAAAAAAAGAATGGCAGCAAGCGGGCTGGAAACACGTTTCGATGAAGTGGGGAATTTATACGGTCGCCTGAATGGCACCGAATATCCACAGGAAGTGGTTCTGAGCGGTTCGCATATCGATACCGTGGTTAACGGCGGTAACCTTGACGGGCAATTCGGCGCGCTGGCGGCGTGGCTGGCAATTGACTGGCTGAAAACGCAATACGGCGCGCCGCTACGTACGGTCGAAGTGGTGGCGATGGCAGAAGAAGAAGGCAGCCGCTTCCCGTATGTCTTCTGGGGCAGTAAAAATATTTTTGGGCTGGCGAATCCTGACGACGTGCGGAATATCTGTGATGCCAAAGGAAATAGTTTTGTCGATGCGATGAAGGCTTGCGGATTTACTCTTCCGAACGCCCCACTAACTCCGCGTCAGGATATTAAAGCCTTTGTTGAACTGCATATTGAACAGGGCTGTGTGCTGGAAAGTAATGGGCAATCAATTGGCGTGGTGAATGCAATTGTCGGGCAGCGTCGTTATACGGTAACGCTGAACGGCGAATCAAACCATGCAGGCACCACGCCGATGGGTTATCGTCGTGATACAGTTTACGCTTTCAGTCGCATTTGCCATCAGTCGGTCGAAAAAGCGAAAAGGATGGGCGATCCGCTGGTTCTGACCTTTGGCAAAGTAGAGCCGCGCCCGAATACGGTAAATGTGGTGCCGGGTAAAACCACGTTCACCATTGATTGTCGTCATACCGACGCTGCCGTGCTGCGCGATTTCACCCAACAGTTAGAAAACGACATGCGGGCGATTTGCGATGAAATGGACATTGGTATTGATATCGATTTATGGATGGACGAAGAACCCGTGCCGATGAATAAGGAGCTGGTCGCCACCCTGACAGAATTGTGTGAAAGAGAAAAACTGAATTACCGGGTGATGCACAGTGGTGCCGGGCACGACGCGCAAATTTTCGCGCCTCGCGTACCAACCTGCATGATTTTTATCCCCAGCATCAACGGGATCAGCCATAACCCGGCGGAACGCACCAATATTACCGACCTTGCCGAAGGGGTCAAAACGTTGGCACTCATGCTTTATCAACTTGCCTGGCAGAAATAAGGAGTCATAAATGGGATATTTAAATAACGTCACCGGTTACCGCGAAGATTTACTGGCTAACCGTGCGATTGTTAAACACGGTAATTTCGCACTGTTAACCCCGGATGGTCTGGTAAAAAATATTATTCCGGGCTTTGAAAATTGTGACGCGACAATCCTCTCCACGCCAAAGCTGGGTGCCTCTTTTGTTGATTATCTGGTCACACTGCATCAAAACGGTGGCAACCAACAGGGCTTCGGTGGCGAAGGCATTGAAACGTTCCTGTATGTGATCTCTGGAAATATCACTGCCAAAGCCGAAGGCAAAACATTTGCCTTAAGCGAAGGTGGCTATCTTTATTGCCCGCCAGGCTCCTTAATGACGTTTGTTAACGCCCAGGCCGAAGACAGCCAAATCTTTTTATATAAGCGCCGCTATGTTCCGGTAGAAGGCTATGCACCGTGGCTGGTTTCTGGCAATGCCAGCGAACTGGAACGCATTCATTATGAAGGCATGGACGATGTTATTCTGCTGGATTTTCTGCCCAAAGAGTTAGGTTTTGATATGAACATGCATATCCTCTCTTTTGCACCAGGTGCCAGCCACGGTTATATCGAAACACACGTTCAGGAACACGGTGCCTATATTCTTTCCGGTCAGGGGGTTTATAACCTCGACAATAACTGGATCCCGGTGAAAAAAGGCGATTACATCTTTATGGGCGCTTATTCTTTACAGGCTGGTTATGGTGTAGGGCGTGGTGAAGCGTTCAGCTATATTTACTCGAAAGATTGTAACCGCGACGTAGAGATTTAAGTCATACCACTCGCCTGATTATTTTTAGCTATGTTGGATTTTGCCACGGTTTATACCGTGGCTTTTTTTGTAACATTGCCTGATGCGCTTCGCTTATCAGGCCTACATGATCTCTGCAATATATAGAATTTGCGCGATTTTCAGGAAGGATATGGTACTCATGCCGCATCCGGCATGAGTACTGCACTCTTATGCGATATAAATCGCATCCGCTTTAAAGGTAAGGGTTAGTTTTTAATTCCCTGACCTATTTTAATGGCGCAGGCAATATTTCGCGCGCTGTTGAAGAGATTGGTTTCACCGCTGGCGAGCACTTCGGCTAAAGGTGCCAGACGAGGCAAAATGCTGAATACCGCGTCAATGCCGTACTGGTGCACCACTTCCACGCCATCACCCAATACGCCAGCAATCCCAATCACCGGTACATTAAACTGCTTCGCCACCGACGCCACACCCAGCGGCGCTTTACCGCCTGCCGTTTGCGAGTCGATGCGCCCTTCCCCGGTAATCACCAGTGCTGCGCCCTGCACTGCCTGCGCAAGATTGACCGCATTCAACACAATTTCAATGCCCGGTTTAATATCCGCATTGAGAAATACCGCCGCCGCAATACCCATACCGCCCGCAGCGCCGCCGCCCGCCATCTGGCAGACATTAATTTCAGTTTGCTGTTGTAAAACACGGGCGTAATTTTGCAGCCCCTGTTCAAGTTCTTCGACCATCTCCGGCGTTGCCCCTTTTTGCGGGCCAAACACCGCCGCCGCGCCGCGTGCCCCTACCAGCGGGTTATCAACGTCACATGCTACTTCAATATGGCAATTCGCCAGACGCGGATCGCATTCATCCATCTCAATGCTTGCCACGCGCGCTAAATTACCACCGTTTGCCGCCAGCGCCTGACCGTCGGCATCAAGGAAACGCACACCGAGCGCCTGCGCCATGCCCATACCGCCGTCGACCGTCGCACTGCCGCCAATGCCGAGAATAATATGGCGAATGTCGTTATCCAGCGCATGACGAATTAACTCCCCCGTACCAAAACTGGAGGCCAGCAACGGATTACGCTTTTCAGGCGCGACCAGCATCAGGCCACTTGCTGCCGCCATCTCAATCACCGCCGTTTTCCCGTCGCCGGTAAGGCCATAAAAAGCATTCACTTTTTCGCCCATCGGCCCGCAGACTTCAAGCGTCACGATGTTGCCGCCCGTCGCGGCGACCATCGCATCCACCGTCCCTTCGCCGCCATCCGCTATCGGCAAACAGATATAGTTCGCATCGGGAAAGAGGGTCGAAAACCCGGCTTTAATTGCCTGACAACATTTTTCTGCACTTAAGCTCTCTTTAAAAGAGTCTGGCGCAATGACAATCTTCATTATCAATCCTTTTTCAACAAATTATTCGATGCGTTCCCACGGAATAAGGTTATCCATAAGAACAGCCAGTAAAATCCCGACCAATAAGCCGTTACTGAGCAGAGGACGAAGCGTTAATGGAAGGTCTTGCAGATACACAGGCGGTAATGCCATTAAAAATATGCCGACAAATAACGGCAATGCGAGTCGATAAATATTGCGAGCGGTAAACGTTATTTGCTGGCTAAACACCAGCGCGGAAAAGAGTAAAGGCAGATAAGAAACCAGCATGACCGCACTACTCACGGGTAAAGGGATACTGCAAAACAGTCGCGTGAGTGCAGGAACCAGCGCCACCAGCAGGCAAATAACGCTGCCATAAATAAACGAACGCCGCGTGTAATCGCCAGTCTGGGTTAATAAACCAATGGATGAAACAAACGGTGAAAATGGAATTACCGCCAGCGGTACGGTTATCAGCGTCATAAATCCGGTCGCCACAAAGCTACGACGATAACGCGTATTCCCTGCGCCCTGCTGCGGATAAAAAACATCCGTGCCCCGAATCGCACCGTAGGTATTGCTGATATTTACCAGACCTGTAATCACCGCCGTCAGAATAATTCCCGGCGACAAAGCACCGCCACTGCCGAGCGGGAACCACTGCCAGTGCAACTCACCGGAGAGCGAGTGCGAAGAAGGAAAGCAAAAGTACCACAACAACCAGCCGGTTATGGTGCCGACCAGCAGGCCATAACGGGCAAAACGTTGCGGCAGGAAGATAATCATCGCCAGTACCAGGCACATCACCGCCACCGAGAGCGCGAACGGCGGTAACTGAATTTTAAAATTCGGGTCGGCTATGCCAAACGGCAGCCCGAGCATACCTTTGAAAAAGATAGTGGTCAGCTGCGCGCCCAGCATCAACATAAACAAGACCATCACCGACGGCGTAAATAACCGTGCCAGGCGATGGCCTAATCCGCTAAAACCAATCAACATCGTCAGCACGCCGGAGAGTGCAATCCCCACTGCCAGGCTGGTGGCGATATCGTTGATCGGTGTCCCGCGCGATGCTTCACCAAGGGTGATAGTAAGGATGGTTCCCCACCACAGGCCACCTGGCCCTTCCATAATAGCGCGACGATGACCGCAAAACGCCTGAGCGAAGCAGGCCAGTGCGGTAGCAAGAAAAGCATATTGCGTGAGCGTAAGCAGGCTACTTTGCGGCAACTGAAAAGCAGAAAGTAGCGTAGGAGGAACCACAACCGTGTTGCAAAAAATAAAGAAAAACCACTGAAATCCTGATAACAGGCTTTCGCGGCTGACTGCAAAATTGAACATAAACACACCTTAACCGGAGAATGCCCGCCGCAAGGACGGGCATTGCAGGGGCCAGATTACTGCTGATGTTTAAGGATAAATTGACCTTTCGGCGCAACAGGGAAGCCCTGTTCAATGTCGTAAATCACATCACCACGTAAGATGGTTTTCGTGATACGCGCGCCAATGGTACGGCCAACATACGGGCTGACTTTGTGGCGATATTCCAGATCGTCATTGGTAAGAACATAGCTGCTATTCGGCTGAATGAAGACGAAGTCGGCATCTTTTCCTGGGGCGATACGGCCTTTTTGCTGCAGACCGAAAATATCTGCTGCGTTAGTCGCCATTAATTTGCCGAACATTGGCAGAGACATACCGCGTTTCTGTACCGCTTCATCGAACATCACGTCCATGCAGCTTTGCAGACCGGCGATACCGCCCCATGCTTTCATGATGTTACCGGCTTTCATTTCCGGCGGGCATGGAGAGTGGTCGGAAACCAGGCAGTCGATTTCACCGTTAAACAGTTTTTCCCACATGCCTTTCTGGTTTTCCAGATCGCGGATCGGCGGTGAACACTTCGCCAGAGTACCGATTTCTTCGAACTGATCGGTATCCAGTACAAAGTAATGCGGGCAGGATTCACAAGTAACGTCCTGACCTTCCTGACGTGCACGAGTCACTTCCTCAACACCTTCCGGGCTGCTGACGTGGCAAACGTGCAGACGGCAACCAGCAACTTTCGCCAGATACAGTACGCGGCGAATTGCTTCCACTTCGGTAAATACCGGACGCGAAGCCACATAGTCATGAGCGGTTACGCGACCTTCACGCTTCGCTTCTTCGCCCAGTTCGTCACAAATCAGCGCGTTTTCGCAGTGCACCAGCACCGGCTGACCCAGTTCGCCCAGCTTCTGCGCACCTTTGAAGAACTGCCAGTCGTTTACATCACGGAAGTCGTTGTCGATACCGCGATCGCCACAGGTCGCAACGAAGCATTTGAAGCCGACAACGCCCACTTCATCCAGCTCATGCAGACGGTCGATGTTGTAAGACACCAGGCCACCGAGTTGTGCCGCATCAATAGTCAGCTTGCCTTTAGCGGCATCGAACTTCAGTTCAATTGAAGCGCGGTCAACCGTTGCAGGCAGCTGGTTGAGCGGCATTTCGATCATGGTGGTGATACCACCTTTTGCCGCTGCGCGAGTACCGGTTTCATAACCTTCCCAGTGGCTACGACCCGGTTCAGAAATATGGGTGTGCGCATCAACCATGCCCGGCGAAACCACCAGACCAGACGCATCCATAACTTCTTTTGCATCGCCCAGATCCTGACCGATAGCAGCAATTTTTCCGCCTTTAACGGCGATATCTACAACGCGAGCTTCGTTTTCTAAAATAACGGTGCCGTTTTTAATGATTAAATCAAAAGACATAACAAACTCCTTGTAAAATACAGATTGGTTTTTAACTCAATGTTCAATATCGGGATTAATTAACCTATGGTTTTTTGCTCTCCTGTTTTTTCTGCTGTTGTACGTTTCTTTAATAAGGCGTAGGCCGCAAAGGCGACGATGACGC
+>4_contig1 dgfdgd
+ACGTTGCTGCGAATCGAGCTGTCTAGCGATCGAG
+>5_contig2
+CGA
+>6_contig3
+ATTCGGGCTTGA
+>7_contig4
+AT
diff --git a/test/data/annotate/exp_files/exp_complete_genome.fna_prokka-split3N.fna b/test/data/annotate/exp_files/exp_complete_genome.fna_prokka-split3N.fna
new file mode 100644
index 0000000000000000000000000000000000000000..59df2730ff1596ed1c1fe1f3b4e332d9d85d0f67
--- /dev/null
+++ b/test/data/annotate/exp_files/exp_complete_genome.fna_prokka-split3N.fna
@@ -0,0 +1,2 @@
+>1_complete
+CCGCTTAGGCTAGCGCCAGCTAGGAGCGCTCGAGAGACACAGCATTACNCCGATATTATAGAGGCCGCGCTTAGCACGCTAGGACGCG
diff --git a/test/data/annotate/genomes/A_H738.fasta b/test/data/annotate/genomes/A_H738.fasta
index 279640c2a0dce53162a643f852636f5fbd2779f7..d4e777a5beede0b80cbed518ace578d27777050e 100755
--- a/test/data/annotate/genomes/A_H738.fasta
+++ b/test/data/annotate/genomes/A_H738.fasta
@@ -51,7 +51,7 @@ TTCTGAATTGATGTGGGTGTGGTTGCCGGGGATGCTACTGATGGGAATGTTGTGGTGGCG
 CAGACGATAACCGGATGCGAAAACTCGCATCCGGCAATAGCGCAATTACTTACGACGCCA
 GGTGGTCCCTTGCGGGCCATCTTCCAGCACGATCCCCATCTCGTTAAGACGATCACGCGC
 CGCATCCGCCGCCGCCCAGTCTTTCGCTTTACGGGCATCCAGACGCTGTTGAATTAACGC
-TTCAATCTCAGCCACTTCGCTGTCGTCTGCCTGCGCGCCGCTTTGCAGGAACGCTTCCGG
+TTCAATCTCAGCCACTTCGCTNNNNNNNNNGTCGTCTGCCTGCGCGCCGCTTTGCAGGAACGCTTCCGG
 TTCTTGCTCCAGCAGGCCCAATACAGCGGAAAGTTTACGCAGGTGAGATGCCATTGCATT
 CGCCGCTGCCATATCTTCTGCTTTCAGACGGTTTACTTCACGCGCCATATCAAACAGTAC
 GGAATAGGCTTCCGGGGTGTTGAAATCGTCGTCCATCGCTTCAATAAAGCGCGCTTCAAA
@@ -122,7 +122,7 @@ AACGGTGCCAGCATCAGCCAGTTTGAGCTGCATCTGCGGGCGATTACCGATCTGCCGTTA
 CCGCAACCAGTGGTGAATAATCCGTCGGTGATGATCAATCTGATTGGTAGCGATGTGAAT
 TATGACTGGCTGAAACTGCCGCTGGTGCATCTGCACTGGTACGACAAAGAAGTCCGTCCG
 GGGCGTAAAGTGGGGCATCTGAATTTGACCGACAGCGACACATCGCGTCTGACTGCGACG
-CTGGAAGCCTTAATCCCGCTGCTGCCGCCGGAATATGCCAGCGGCGTGATTTGGGCGCAG
+CTGGAAGCCTTAATCCNNNNNNNNNNNNNNNNNNNNNNNNNNCGCTGCTGCCGCCGGAATATGCCAGCGGCGTGATTTGGGCGCAG
 AGTAAGTTCGGTTAACTGGTGCTCTATTCTTGCCGGATGCGGCGTAAACGCCTTATCCGG
 CCTACCGATCCGGTACCCATTGTAGGCCTGATAAGATGCGTCAAGCATCGCATCAGGCAT
 TGTGCACCAATTGCCGGATGCGGCACCGGTTGTAGGCCTGATAAGACGCGTCAAGCGTCG
diff --git a/test/data/annotate/genomes/complete_genome.fna b/test/data/annotate/genomes/complete_genome.fna
new file mode 100644
index 0000000000000000000000000000000000000000..583e7b872877fbcb80e4a89ece5a0ce0371588ee
--- /dev/null
+++ b/test/data/annotate/genomes/complete_genome.fna
@@ -0,0 +1,5 @@
+>complete
+CCGCTTAGGCTAGCGCC
+AGCTAGGAGCGCTCGAGAGACA
+CAGCATTACNCCGATATTATAGAGGCCGCGCTTAGC
+ACGCTAGGACGCG
\ No newline at end of file
diff --git a/test/data/annotate/test_files/list_genomes-func-test-default.txt b/test/data/annotate/test_files/list_genomes-func-test-default.txt
index 0b6751d4ffbbbb196367df00254a07af68e0495e..ddd2dfb23d4a8ead62a49fb552101e7a03e377eb 100755
--- a/test/data/annotate/test_files/list_genomes-func-test-default.txt
+++ b/test/data/annotate/test_files/list_genomes-func-test-default.txt
@@ -1,3 +1,4 @@
 B2_A3_5.fasta-changeName.fna::ESCO.1116
 H299_H561.fasta genome6.fasta   ::  ESCO.1015
 A_H738.fasta genome1.fasta toto.fst ::.1015
+complete_genome.fna
\ No newline at end of file
diff --git a/test/test_functional/test_annote.py b/test/test_functional/test_annote.py
index c3cdfebfe420881bb474adc130496a9cf112640d..62d3053f6ff617d905a0a5807fe0c692f7f3165b 100755
--- a/test/test_functional/test_annote.py
+++ b/test/test_functional/test_annote.py
@@ -123,11 +123,11 @@ def test_main_given_tmp_verbose3(capsys):
     list_file = os.path.join(TEST_DIR, "list_genomes-func-test-default.txt")
     tmpdir = os.path.join(GENEPATH, "tmp_funcGivenTmp")
     name = "ESCO"
-    l90 = 1
+    l90 = 10
     date = "0417"
     verbose = 3
     annot.main("cmd", list_file, GEN_PATH, GENEPATH, name, date, l90,
-               cutn=0, tmp_dir=tmpdir, verbose=verbose)
+               cutn=3, tmp_dir=tmpdir, verbose=verbose)
     out, err = capsys.readouterr()
     # Check that warnings are written to stderr
     assert "WARNING" in err
@@ -135,11 +135,22 @@ def test_main_given_tmp_verbose3(capsys):
             "concatenating ['A_H738.fasta', 'genome1.fasta', 'toto.fst']") in err
     # Check that tmp files exist in the right folder
     # -> 2 fna files created (concatenations)
+    # -> + 3 files created (split 5N)
     assert os.path.isfile(os.path.join(tmpdir, "A_H738.fasta-all.fna"))
     assert os.path.isfile(os.path.join(tmpdir, "H299_H561.fasta-all.fna"))
+    assert len(glob.glob(os.path.join(tmpdir, '*.fna'))) == 6
+    assert len(glob.glob(os.path.join(tmpdir, '*split3N.fna'))) == 4
+    # Check that split contigs were renamed with unique ID at the begining of the header
+    res_file = os.path.join(tmpdir, "A_H738.fasta-all.fna_prokka-split3N.fna")
+    exp_file = os.path.join(EXP_DIR, "exp_A_H738.fasta-all.fna_prokka-split3N.fna")
+    assert tutil.compare_order_content(exp_file, res_file)
+    # Check that even for complete genome, contig was renamed with ID
+    res_file = os.path.join(tmpdir, "complete_genome.fna_prokka-split3N.fna")
+    exp_file = os.path.join(EXP_DIR, "exp_complete_genome.fna_prokka-split3N.fna")
+    assert tutil.compare_order_content(exp_file, res_file)
     # Test that prokka folder is in the right directory
     # Only 1 genome annotated by  prokka (the 2 others do not have appropriate L90/nbcont)
-    assert os.path.isdir(os.path.join(tmpdir, "A_H738.fasta-all.fna-prokkaRes"))
+    assert os.path.isdir(os.path.join(tmpdir, "A_H738.fasta-all.fna_prokka-split3N.fna-prokkaRes"))
     assert not os.path.isdir(os.path.join(tmpdir, "H299_H561.fasta-all.fna-prokkaRes"))
 
 
@@ -150,7 +161,7 @@ def test_main_all_discard_nbcont(capsys):
     """
     list_file = os.path.join(TEST_DIR, "list_genomes-func-test-default.txt")
     name = "ESCO"
-    nbcont = 1
+    nbcont = 0
     cutn = 0
     date = "0417"
     annot.main("cmd", list_file, GEN_PATH, GENEPATH, name, date, nbcont=nbcont, cutn=cutn)
@@ -200,6 +211,7 @@ def test_main_existresdirforce(capsys):
     """
     Test that, when the pipeline is run on an existing result directory, but force option is on,
     it removes the result folders and runs again.
+    Result folders contain expected files, the ones put before are removed
     """
     list_file = os.path.join(TEST_DIR, "list_genomes-func-test-default.txt")
     # Create output directory with a prt file in Proteins folder
@@ -209,28 +221,47 @@ def test_main_existresdirforce(capsys):
     assert os.path.isfile(os.path.join(protdir, "toto.prt"))
     name = "ESCO"
     date = "0417"
-    l90 = 1
+    l90 = 5
+    cutn = 3
     annot.main("cmd", list_file, GEN_PATH, GENEPATH, name, date, force=True, l90=l90,
-               prodigal_only=True)
+               prodigal_only=True, cutn = cutn, small=True)
     out, err = capsys.readouterr()
 
+    # Check that tmp files exist in the right folder
+    # -> 2 fna files created (concatenations)
+    # -> + 3 files created (split 5N)
+    assert os.path.isfile(os.path.join(GENEPATH, "tmp_files", "A_H738.fasta-all.fna"))
+    assert os.path.isfile(os.path.join(GENEPATH, "tmp_files", "H299_H561.fasta-all.fna"))
+    assert len(glob.glob(os.path.join(GENEPATH, "tmp_files", '*.fna'))) == 6
+    assert len(glob.glob(os.path.join(GENEPATH, "tmp_files", '*split3N.fna'))) == 4
+    # Check that split contigs were renamed with unique ID at the begining of the header
+    res_file = os.path.join(GENEPATH, "tmp_files", "A_H738.fasta-all.fna_prodigal-split3N.fna")
+    exp_file = os.path.join(EXP_DIR, "exp_A_H738.fasta-all.fna_prokka-split3N.fna")
+    assert tutil.compare_order_content(exp_file, res_file)
+    # Check that even for complete genome, contig was renamed with ID
+    res_file = os.path.join(GENEPATH, "tmp_files", "complete_genome.fna_prodigal-split3N.fna")
+    exp_file = os.path.join(EXP_DIR, "exp_complete_genome.fna_prokka-split3N.fna")
+    assert tutil.compare_order_content(exp_file, res_file)
 
     # Check that tmp files exist in the right folder (result/tmp_files)
     assert os.path.isfile(os.path.join(GENEPATH, "tmp_files",
-                                       "B2_A3_5.fasta-changeName.fna_prodigal-split5N.fna"))
+                                       "B2_A3_5.fasta-changeName.fna_prodigal-split3N.fna"))
     assert os.path.isfile(os.path.join(GENEPATH, "tmp_files",
-                                       "H299_H561.fasta-all.fna_prodigal-split5N.fna"))
+                                       "H299_H561.fasta-all.fna_prodigal-split3N.fna"))
     assert os.path.isfile(os.path.join(GENEPATH, "tmp_files",
                                        "H299_H561.fasta-all.fna"))
     assert os.path.isfile(os.path.join(GENEPATH, "tmp_files",
-                                       "A_H738.fasta-all.fna_prodigal-split5N.fna"))
+                                       "A_H738.fasta-all.fna_prodigal-split3N.fna"))
     assert os.path.isfile(os.path.join(GENEPATH, "tmp_files",
                                        "A_H738.fasta-all.fna"))
     # Test all result folders are empty (in particular Proteins) as no genome is annotated
     assert os.path.isdir(protdir)
-    assert len(os.listdir(protdir)) == 1
+    assert len(os.listdir(protdir)) == 4
     assert not os.path.isfile(os.path.join(protdir, "toto.prt"))
-    assert os.path.isfile(os.path.join(protdir, "ESCO.1015.00001.prt"))
+    assert os.path.isfile(os.path.join(protdir, "ESCO.0417.00001.prt"))
+    assert os.path.isfile(os.path.join(protdir, "ESCO.1015.00002.prt"))
+    assert os.path.isfile(os.path.join(protdir, "ESCO.1015.00003.prt"))
+    assert os.path.isfile(os.path.join(protdir, "ESCO.1116.00004.prt"))
 
 
 def test_run_exist_resdir(caplog):