[09:18:37] This is prokka 1.12 [09:18:37] Written by Torsten Seemann [09:18:37] Homepage is https://github.com/tseemann/prokka [09:18:37] Local time is Thu Oct 4 09:18:37 2018 [09:18:37] You are yquentin [09:18:37] Operating system is linux [09:18:37] You have BioPerl 1.006924 [09:18:37] System has 64 cores. [09:18:37] Will use maximum of 1 cores. [09:18:37] Annotating as >>> Bacteria <<< [09:18:37] Enabling options to ensure Genbank/ENA/DDJB submission compliance. [09:18:37] Creating new output folder: prokka/Aaan [09:18:37] Running: mkdir -p prokka\/Aaan [09:18:37] Using filename prefix: Aaan.XXX [09:18:37] Setting HMMER_NCPU=1 [09:18:37] Writing log to: prokka/Aaan/Aaan.log [09:18:37] Command: /usr/local/bioinfo/src/PROKKA/prokka-1.12/bin/prokka /home/formation/public_html/M2_Phylogenomique/data/Synechococcus/DNA/Aaan.fas --outdir prokka/Aaan --compliant --addgenes --prefix Aaan --locustag Aaan.g --genus Synechococcus --species Synechococcus sp. --strain CC9605 --kingdom Bacteria --cpus 1 [09:18:37] Appending to PATH: /usr/local/bioinfo/src/PROKKA/prokka-1.12/bin/../binaries/linux [09:18:37] Appending to PATH: /usr/local/bioinfo/src/PROKKA/prokka-1.12/bin/../binaries/linux/../common [09:18:37] Appending to PATH: /usr/local/bioinfo/src/PROKKA/prokka-1.12/bin [09:18:37] Looking for 'aragorn' - found /usr/local/bioinfo/src/PROKKA/prokka-1.12/binaries/linux/aragorn [09:18:37] Determined aragorn version is 1.2 [09:18:37] Looking for 'blastp' - found /usr/local/bioinfo/src/PROKKA/prokka-1.12/binaries/linux/blastp [09:18:38] Determined blastp version is 2.4 [09:18:38] Looking for 'cmpress' - found /usr/local/bioinfo/src/PROKKA/prokka-1.12/binaries/linux/cmpress [09:18:38] Determined cmpress version is 1.1 [09:18:38] Looking for 'cmscan' - found /usr/local/bioinfo/src/PROKKA/prokka-1.12/binaries/linux/cmscan [09:18:38] Determined cmscan version is 1.1 [09:18:38] Looking for 'egrep' - found /usr/bin/egrep [09:18:38] Looking for 'find' - found /usr/bin/find [09:18:38] Looking for 'grep' - found /usr/bin/grep [09:18:38] Looking for 'hmmpress' - found /usr/local/bioinfo/src/PROKKA/prokka-1.12/binaries/linux/hmmpress [09:18:38] Determined hmmpress version is 3.1 [09:18:38] Looking for 'hmmscan' - found /usr/local/bioinfo/src/PROKKA/prokka-1.12/binaries/linux/hmmscan [09:18:38] Determined hmmscan version is 3.1 [09:18:38] Looking for 'java' - found /usr/bin/java [09:18:38] Looking for 'less' - found /usr/bin/less [09:18:38] Looking for 'makeblastdb' - found /usr/local/bioinfo/src/PROKKA/prokka-1.12/binaries/linux/makeblastdb [09:18:38] Determined makeblastdb version is 2.4 [09:18:38] Looking for 'minced' - found /usr/local/bioinfo/src/PROKKA/prokka-1.12/binaries/common/minced [09:18:38] Determined minced version is 2.0 [09:18:38] Looking for 'parallel' - found /usr/local/bioinfo/src/PROKKA/prokka-1.12/binaries/common/parallel [09:18:39] Determined parallel version is 20150122 [09:18:39] Looking for 'prodigal' - found /usr/local/bioinfo/src/PROKKA/prokka-1.12/binaries/linux/prodigal [09:18:39] Determined prodigal version is 2.6 [09:18:39] Looking for 'prokka-genbank_to_fasta_db' - found /usr/local/bioinfo/src/PROKKA/prokka-1.12/bin/prokka-genbank_to_fasta_db [09:18:39] Looking for 'sed' - found /usr/bin/sed [09:18:39] Looking for 'tbl2asn' - found /usr/local/bioinfo/src/PROKKA/prokka-1.12/binaries/linux/tbl2asn [09:18:39] Determined tbl2asn version is 25.3 [09:18:39] Using genetic code table 11. [09:18:39] Loading and checking input file: /home/formation/public_html/M2_Phylogenomique/data/Synechococcus/DNA/Aaan.fas [09:18:39] Wrote 1 contigs totalling 2510659 bp. [09:18:39] Predicting tRNAs and tmRNAs [09:18:39] Running: aragorn -l -gc11 -w prokka\/Aaan\/Aaan\.fna [09:18:41] 1 tRNA-Gly c[40886,40957] 33 (ccc) [09:18:41] 2 tRNA-Gly [81036,81107] 33 (gcc) [09:18:41] 3 tRNA-Arg [152197,152272] 36 (cct) [09:18:41] 4 tRNA-Met [240013,240085] 34 (cat) [09:18:41] 5 tRNA-Arg [259938,260011] 35 (acg) [09:18:41] 6 tRNA-Leu [292702,292785] 36 (tag) [09:18:41] 7 tRNA-Ala c[300105,300178] 34 (cgc) [09:18:41] 8 tRNA-Pro [336548,336621] 35 (cgg) [09:18:41] 9 tRNA-Ser c[354909,354999] 36 (gct) [09:18:41] 10 tRNA-Gln [381452,381523] 33 (ttg) [09:18:41] 11 tRNA-Arg [394816,394891] 36 (ccg) [09:18:41] 12 tRNA-Cys [410669,410739] 33 (gca) [09:18:41] 13 tRNA-Phe c[443120,443192] 34 (gaa) [09:18:41] 14 tRNA-Thr c[465663,465734] 33 (tgt) [09:18:41] 15 tRNA-Ile [475472,475547] 36 (gat) [09:18:41] 16 tRNA-Ala [475556,475629] 34 (tgc) [09:18:41] 17 tRNA-Thr c[494153,494224] 33 (ggt) [09:18:41] 18 tRNA-Tyr c[494235,494316] 35 (gta) [09:18:41] 19 tRNA-Arg c[551437,551512] 36 (tct) [09:18:41] 20 tRNA-Val c[604748,604819] 33 (cac) [09:18:41] 21 tRNA-Asp c[619574,619649] 36 (gtc) [09:18:41] 22 tRNA-Trp c[620086,620162] 35 (cca) [09:18:41] 23 tRNA-Ser [778387,778475] 38 (cga) [09:18:41] 24 tRNA-His c[822295,822368] 34 (gtg) [09:18:41] 25 tRNA-Leu c[835602,835684] 35 (caa) [09:18:41] 26 tRNA-Leu [838685,838769] 35 (cag) [09:18:41] 27 tRNA-Ala [895864,895938] 35 (ggc) [09:18:41] 28 tRNA-Leu c[943285,943373] 35 (taa) [09:18:41] 29 tRNA-Pro c[1078026,1078099] 35 (ggg) [09:18:41] 30 tRNA-Ser c[1192408,1192496] 36 (tga) [09:18:41] 31 tRNA-Met [1240721,1240794] 35 (cat) [09:18:41] 32 tRNA-Ser c[1315833,1315920] 35 (gga) [09:18:41] 33 tRNA-Lys [1546958,1547029] 33 (ttt) [09:18:41] 34 tRNA-Pro [1548406,1548480] 35 (tgg) [09:18:41] 35 tRNA-Met c[1654070,1654146] 35 (cat) [09:18:41] 36 tRNA-Arg [1661149,1661236] 31 (tcg) [09:18:41] 37 tRNA-Glu [1737787,1737859] 35 (ttc) [09:18:41] 38 tRNA-Thr [1907303,1907375] 34 (cgt) [09:18:41] 39 tRNA-Gly c[1919691,1919762] 33 (tcc) [09:18:41] 40 tRNA-Val [1971387,1971459] 33 (gac) [09:18:41] 41 tmRNA* c[2063315,2063629] 174,224 ANNIVRFSRQAAPVAA* [09:18:41] 42 tRNA-Leu c[2073505,2073586] 35 (gag) [09:18:41] 43 tRNA-Ala c[2139231,2139304] 34 (tgc) [09:18:41] 44 tRNA-Ile c[2139313,2139388] 36 (gat) [09:18:41] 45 tRNA-Asn [2191229,2191302] 34 (gtt) [09:18:41] 46 tRNA-Val c[2400151,2400222] 33 (tac) [09:18:41] Found 46 tRNAs [09:18:41] Predicting Ribosomal RNAs [09:18:41] You need either Barrnap or RNAmmer installed to predict rRNAs! [09:18:41] Skipping ncRNA search, enable with --rfam if desired. [09:18:41] Total of 45 tRNA + rRNA features [09:18:41] Searching for CRISPR repeats [09:18:42] Found 0 CRISPRs [09:18:42] Predicting coding sequences [09:18:42] Contigs total 2510659 bp, so using single mode [09:18:42] Running: prodigal -i prokka\/Aaan\/Aaan\.fna -c -m -g 11 -p single -f sco -q [09:18:54] Excluding CDS which overlaps existing RNA (tRNA) at gnl|Prokka|Aaan.g_1:81047..81154 on - strand [09:18:55] Excluding CDS which overlaps existing RNA (tRNA) at gnl|Prokka|Aaan.g_1:465725..465931 on - strand [09:18:55] Excluding CDS which overlaps existing RNA (tRNA) at gnl|Prokka|Aaan.g_1:835385..835621 on + strand [09:18:55] Excluding CDS which overlaps existing RNA (tRNA) at gnl|Prokka|Aaan.g_1:943366..943665 on + strand [09:18:56] Excluding CDS which overlaps existing RNA (tRNA) at gnl|Prokka|Aaan.g_1:1660809..1662206 on + strand [09:18:57] Found 2887 CDS [09:18:57] Connecting features back to sequences [09:18:57] Not using genus-specific database. Try --usegenus to enable it. [09:18:57] Annotating CDS, please be patient. [09:18:57] Will use 1 CPUs for similarity searching. [09:18:59] There are still 2887 unannotated CDS left (started with 2887) [09:18:59] Will use blast to search against /usr/local/bioinfo/src/PROKKA/prokka-1.12/bin/../db/kingdom/Bacteria/sprot with 1 CPUs [09:18:59] Running: cat prokka\/Aaan\/sprot\.faa | parallel --gnu --plain -j 1 --block 376804 --recstart '>' --pipe blastp -query - -db /usr/local/bioinfo/src/PROKKA/prokka-1.12/bin/../db/kingdom/Bacteria/sprot -evalue 1e-06 -num_threads 1 -num_descriptions 1 -num_alignments 1 -seg no > prokka\/Aaan\/sprot\.blast 2> /dev/null [09:22:13] Modify product: N utilization substance protein B homolog => N utilization substance protein B [09:22:13] Modify product: Probable type II secretion system protein HxcR => putative type II secretion system protein HxcR [09:22:13] Modify product: Probable ABC transporter-binding protein DR_1438 => putative ABC transporter-binding protein [09:22:13] Modify product: Probable serine/threonine-protein kinase YbdM => putative serine/threonine-protein kinase YbdM [09:22:13] Modify product: Uncharacterized hydrolase YxeP => putative hydrolase YxeP [09:22:13] Modify product: Cyclic nucleotide-gated potassium channel mll3241 => Cyclic nucleotide-gated potassium channel [09:22:13] Modify product: Uncharacterized FAD-linked oxidoreductase Rv2280 => putative FAD-linked oxidoreductase [09:22:13] Modify product: Uncharacterized glycosyltransferase sll0501 => putative glycosyltransferase [09:22:13] Modify product: Probable phospholipid import ATP-binding protein MlaF => putative phospholipid import ATP-binding protein MlaF [09:22:13] Modify product: Probable undecaprenyl-phosphate N-acetylglucosaminyl 1-phosphate transferase => putative undecaprenyl-phosphate N-acetylglucosaminyl 1-phosphate transferase [09:22:13] Modify product: NADH dehydrogenase-like protein SA0802 => NADH dehydrogenase-like protein [09:22:13] Modify product: Probable bifunctional SAT/APS kinase => putative bifunctional SAT/APS kinase [09:22:13] Modify product: Probable cobalt-factor III C(17)-methyltransferase => putative cobalt-factor III C(17)-methyltransferase [09:22:13] Modify product: Probable endopeptidase p60 => putative endopeptidase p60 [09:22:13] Modify product: Probable adenylyltransferase/sulfurtransferase MoeZ => putative adenylyltransferase/sulfurtransferase MoeZ [09:22:13] Modify product: Uncharacterized oxidoreductase Rv2298 => putative oxidoreductase [09:22:13] Modify product: Uncharacterized phycocyanin operon protein Z => putative phycocyanin operon protein Z [09:22:13] Modify product: Uncharacterized phycocyanin operon protein Z => putative phycocyanin operon protein Z [09:22:13] Modify product: Probable phycoerythrobilin lyase CpeT => putative phycoerythrobilin lyase CpeT [09:22:14] Modify product: Putative esterase aq_1494 => Putative esterase [09:22:14] Modify product: Uncharacterized inner membrane transporter YedA => putative inner membrane transporter YedA [09:22:14] Modify product: Phage shock protein A homolog => Phage shock protein A [09:22:14] Modify product: Uncharacterized ABC transporter ATP-binding protein YknY => putative ABC transporter ATP-binding protein YknY [09:22:14] Modify product: Probable cytochrome c oxidase subunit 1 => putative cytochrome c oxidase subunit 1 [09:22:14] Modify product: Probable doxorubicin resistance ABC transporter permease protein DrrC => putative doxorubicin resistance ABC transporter permease protein DrrC [09:22:14] Modify product: Probable murein peptide carboxypeptidase => putative murein peptide carboxypeptidase [09:22:14] Modify product: Uncharacterized FAD-linked oxidoreductase Rv2280 => putative FAD-linked oxidoreductase [09:22:14] Modify product: Thylakoid-associated single-stranded DNA-binding protein slr1034 => Thylakoid-associated single-stranded DNA-binding protein [09:22:14] Modify product: Uncharacterized sugar kinase YdjH => putative sugar kinase YdjH [09:22:14] Modify product: Laccase domain protein Rv2149c => Laccase domain protein [09:22:14] Modify product: Maf-like protein Rv3282 => Maf-like protein [09:22:14] Modify product: Multidrug transporter PA4990 => Multidrug transporter [09:22:14] Modify product: Glycogen operon protein GlgX homolog => Glycogen operon protein GlgX [09:22:14] Modify product: Uncharacterized PIN and TRAM-domain containing protein YacL => putative PIN and TRAM-domain containing protein YacL [09:22:14] Modify product: Oxygen-independent coproporphyrinogen-III oxidase-like protein sll1917 => Oxygen-independent coproporphyrinogen-III oxidase-like protein [09:22:14] Modify product: Uncharacterized FAD-linked oxidoreductase Rv2280 => putative FAD-linked oxidoreductase [09:22:14] Modify product: Uncharacterized ABC transporter ATP-binding protein TM_0288 => putative ABC transporter ATP-binding protein [09:22:14] Modify product: Probable cytochrome c oxidase subunit 1 => putative cytochrome c oxidase subunit 1 [09:22:14] Modify product: Probable chromate transport protein => putative chromate transport protein [09:22:14] Modify product: Uncharacterized oxidoreductase CzcO => putative oxidoreductase CzcO [09:22:14] Modify product: Probable L,D-transpeptidase YnhG => putative L,D-transpeptidase YnhG [09:22:14] Modify product: Probable 2-phosphosulfolactate phosphatase => putative 2-phosphosulfolactate phosphatase [09:22:14] Modify product: Probable multidrug resistance ABC transporter ATP-binding/permease protein YheI => putative multidrug resistance ABC transporter ATP-binding/permease protein YheI [09:22:14] Modify product: Putative anti-sigma factor antagonist TM_1442 => Putative anti-sigma factor antagonist [09:22:14] Modify product: Cyclic nucleotide-gated potassium channel mll3241 => Cyclic nucleotide-gated potassium channel [09:22:14] Modify product: Uncharacterized zinc protease Rv2782c => putative zinc protease [09:22:14] Modify product: Uncharacterized zinc protease Rv2782c => putative zinc protease [09:22:14] Modify product: Uncharacterized ABC transporter permease Rv0072 => putative ABC transporter permease [09:22:14] Modify product: Uncharacterized ABC transporter ATP-binding protein Rv0986 => putative ABC transporter ATP-binding protein [09:22:14] Modify product: Uncharacterized glycosyltransferase EpsJ => putative glycosyltransferase EpsJ [09:22:14] Modify product: Uncharacterized protease YdcP => putative protease YdcP [09:22:14] Modify product: GTP-binding protein TypA/BipA homolog => GTP-binding protein TypA/BipA [09:22:14] Modify product: Uncharacterized ABC transporter ATP-binding protein Rv0986 => putative ABC transporter ATP-binding protein [09:22:14] Modify product: Phosphorylated carbohydrates phosphatase TM_1254 => Phosphorylated carbohydrates phosphatase [09:22:14] Modify product: Probable peroxiredoxin => putative peroxiredoxin [09:22:15] Modify product: Probable ferredoxin/ferredoxin--NADP reductase => putative ferredoxin/ferredoxin--NADP reductase [09:22:15] Modify product: Probable ABC transporter-binding protein DR_1438 => putative ABC transporter-binding protein [09:22:15] Modify product: Vitamin K epoxide reductase homolog => Vitamin K epoxide reductase [09:22:15] Modify product: Uncharacterized ABC transporter ATP-binding protein YlmA => putative ABC transporter ATP-binding protein YlmA [09:22:15] Modify product: Uncharacterized ABC transporter ATP-binding protein HI_1470 => putative ABC transporter ATP-binding protein [09:22:15] Modify product: PKHD-type hydroxylase Sbal_3634 => PKHD-type hydroxylase [09:22:15] Modify product: Probable protein kinase UbiB => putative protein kinase UbiB [09:22:15] Modify product: Probable glutamine ABC transporter permease protein GlnM => putative glutamine ABC transporter permease protein GlnM [09:22:15] Modify product: Putative multidrug export ATP-binding/permease protein SA1683 => Putative multidrug export ATP-binding/permease protein [09:22:15] Modify product: Probable murein peptide carboxypeptidase => putative murein peptide carboxypeptidase [09:22:15] Modify product: Uncharacterized oxidoreductase YhhX => putative oxidoreductase YhhX [09:22:15] Modify product: Bifunctional protein FolD => Bifunctional protein FolD protein [09:22:15] Modify product: 1,4-alpha-glucan branching enzyme TTHA1902 => 1,4-alpha-glucan branching enzyme [09:22:15] Modify product: Uncharacterized oxidoreductase MSMEG_1603/MSMEI_1564 => putative oxidoreductase/MSMEI_1564 [09:22:15] Modify product: Uncharacterized tRNA/rRNA methyltransferase HI_0380 => putative tRNA/rRNA methyltransferase [09:22:15] Modify product: Probable tRNA-dihydrouridine synthase => putative tRNA-dihydrouridine synthase [09:22:15] Modify product: Probable helicase HelY => putative helicase HelY [09:22:15] Modify product: Probable trans-aconitate 2-methyltransferase => putative trans-aconitate 2-methyltransferase [09:22:15] Modify product: Probable dual-specificity RNA methyltransferase RlmN => putative dual-specificity RNA methyltransferase RlmN [09:22:15] Modify product: Glycogen operon protein GlgX homolog => Glycogen operon protein GlgX [09:22:15] Modify product: Probable phospholipid ABC transporter permease protein MlaE => putative phospholipid ABC transporter permease protein MlaE [09:22:15] Modify product: Probable transcriptional regulatory protein aq_1575 => putative transcriptional regulatory protein [09:22:15] Modify product: Probable 30S ribosomal protein PSRP-3 => putative 30S ribosomal protein PSRP-3 [09:22:15] Modify product: Probable peptidoglycan glycosyltransferase FtsW => putative peptidoglycan glycosyltransferase FtsW [09:22:15] Modify product: Uncharacterized sugar epimerase YhfK => putative sugar epimerase YhfK [09:22:15] Modify product: Probable cysteine desulfurase => putative cysteine desulfurase [09:22:15] Modify product: Probable ATP-dependent transporter SufC => putative ATP-dependent transporter SufC [09:22:16] Modify product: Uncharacterized transporter Rv2685 => putative transporter [09:22:16] Modify product: Probable helicase HelY => putative helicase HelY [09:22:16] Modify product: Vitamin K epoxide reductase homolog => Vitamin K epoxide reductase [09:22:16] Modify product: Epimerase family protein SA0724 => Epimerase family protein [09:22:16] Modify product: Putative HTH-type transcriptional regulator Rv0890c => Putative HTH-type transcriptional regulator [09:22:16] Modify product: Probable adenylyl-sulfate kinase => putative adenylyl-sulfate kinase [09:22:16] Modify product: Probable glutaredoxin ssr2061 => putative glutaredoxin [09:22:16] Modify product: Probable nicotinate-nucleotide pyrophosphorylase [carboxylating] => putative nicotinate-nucleotide pyrophosphorylase [carboxylating] [09:22:16] Modify product: Probable protein kinase UbiB => putative protein kinase UbiB [09:22:16] Modify product: Probable nitrate transporter NarT => putative nitrate transporter NarT [09:22:16] Modify product: Probable formate transporter 1 => putative formate transporter 1 [09:22:16] Modify product: Probable L,D-transpeptidase YnhG => putative L,D-transpeptidase YnhG [09:22:16] Modify product: Probable protein kinase UbiB => putative protein kinase UbiB [09:22:16] Cleaned 95 /product names [09:22:16] Deleting unwanted file: prokka/Aaan/sprot.faa [09:22:16] Deleting unwanted file: prokka/Aaan/sprot.blast [09:22:17] There are still 1596 unannotated CDS left (started with 2887) [09:22:17] Will use hmmer3 to search against /usr/local/bioinfo/src/PROKKA/prokka-1.12/bin/../db/hmm/HAMAP.hmm with 1 CPUs [09:22:17] Running: cat prokka\/Aaan\/HAMAP\.hmm\.faa | parallel --gnu --plain -j 1 --block 145194 --recstart '>' --pipe hmmscan --noali --notextw --acc -E 1e-06 --cpu 1 /usr/local/bioinfo/src/PROKKA/prokka-1.12/bin/../db/hmm/HAMAP.hmm /dev/stdin > prokka\/Aaan\/HAMAP\.hmm\.hmmer3 2> /dev/null [09:24:30] Deleting unwanted file: prokka/Aaan/HAMAP.hmm.faa [09:24:30] Deleting unwanted file: prokka/Aaan/HAMAP.hmm.hmmer3 [09:24:30] Labelling remaining 1512 proteins as 'hypothetical protein' [09:24:30] Possible /pseudo 'Putative fluoride ion transporter CrcB' at gnl|Prokka|Aaan.g_1 position 91348 [09:24:30] Possible /pseudo 'GalNAc-alpha-(1->4)-GalNAc-alpha-(1->3)-diNAcBac-PP-undecaprenol alpha-1,4-N-acetyl-D-galactosaminyltransferase' at gnl|Prokka|Aaan.g_1 position 176384 [09:24:30] Possible /pseudo 'Ethanolamine utilization protein EutN' at gnl|Prokka|Aaan.g_1 position 723171 [09:24:30] Possible /pseudo 'ATP-dependent Clp protease proteolytic subunit' at gnl|Prokka|Aaan.g_1 position 810206 [09:24:30] Possible /pseudo 'Pseudooxynicotine oxidase' at gnl|Prokka|Aaan.g_1 position 878799 [09:24:30] Possible /pseudo 'Phosphate-binding protein PstS' at gnl|Prokka|Aaan.g_1 position 1076152 [09:24:30] Possible /pseudo 'putative zinc protease' at gnl|Prokka|Aaan.g_1 position 1134550 [09:24:30] Possible /pseudo 'Cystathionine gamma-synthase' at gnl|Prokka|Aaan.g_1 position 1813471 [09:24:30] Possible /pseudo 'DNA-directed RNA polymerase subunit beta'' at gnl|Prokka|Aaan.g_1 position 1886614 [09:24:30] Possible /pseudo 'S-layer protein SlpA' at gnl|Prokka|Aaan.g_1 position 2178101 [09:24:30] Possible /pseudo 'Formamidase' at gnl|Prokka|Aaan.g_1 position 2426508 [09:24:30] Possible /pseudo 'Formamidase' at gnl|Prokka|Aaan.g_1 position 2427291 [09:24:30] Possible /pseudo 'Formamidase' at gnl|Prokka|Aaan.g_1 position 2427549 [09:24:30] Found 1127 unique /gene codes. [09:24:30] Fixed 2 duplicate /gene - proA_1 proA_2 [09:24:30] Fixed 3 duplicate /gene - fmdA_1 fmdA_2 fmdA_3 [09:24:30] Fixed 3 duplicate /gene - ftsH2_1 ftsH2_2 ftsH2_3 [09:24:30] Fixed 2 duplicate /gene - phnD_1 phnD_2 [09:24:30] Fixed 2 duplicate /gene - mnmC_1 mnmC_2 [09:24:30] Fixed 3 duplicate /gene - pds_1 pds_2 pds_3 [09:24:30] Fixed 2 duplicate /gene - psbD1_1 psbD1_2 [09:24:30] Fixed 2 duplicate /gene - algA_1 algA_2 [09:24:30] Fixed 2 duplicate /gene - livQ_1 livQ_2 [09:24:30] Fixed 2 duplicate /gene - pglH_1 pglH_2 [09:24:30] Fixed 2 duplicate /gene - cobD_1 cobD_2 [09:24:30] Fixed 2 duplicate /gene - rluD_1 rluD_2 [09:24:30] Fixed 2 duplicate /gene - petJ_1 petJ_2 [09:24:30] Fixed 2 duplicate /gene - rpsA_1 rpsA_2 [09:24:30] Fixed 2 duplicate /gene - galE_1 galE_2 [09:24:30] Fixed 2 duplicate /gene - pecE_1 pecE_2 [09:24:30] Fixed 2 duplicate /gene - cpcS_1 cpcS_2 [09:24:30] Fixed 2 duplicate /gene - dnaK2_1 dnaK2_2 [09:24:30] Fixed 4 duplicate /gene - clpP_1 clpP_2 clpP_3 clpP_4 [09:24:30] Fixed 2 duplicate /gene - lpxB_1 lpxB_2 [09:24:30] Fixed 2 duplicate /gene - nuoL_1 nuoL_2 [09:24:30] Fixed 2 duplicate /gene - msbA_1 msbA_2 [09:24:30] Fixed 2 duplicate /gene - metB_1 metB_2 [09:24:30] Fixed 2 duplicate /gene - thiL_1 thiL_2 [09:24:30] Fixed 2 duplicate /gene - gyrA_1 gyrA_2 [09:24:30] Fixed 2 duplicate /gene - cysA_1 cysA_2 [09:24:30] Fixed 2 duplicate /gene - msrA_1 msrA_2 [09:24:30] Fixed 2 duplicate /gene - btuR_1 btuR_2 [09:24:30] Fixed 2 duplicate /gene - puo_1 puo_2 [09:24:30] Fixed 2 duplicate /gene - phrB_1 phrB_2 [09:24:30] Fixed 2 duplicate /gene - ctaE_1 ctaE_2 [09:24:30] Fixed 3 duplicate /gene - mprA_1 mprA_2 mprA_3 [09:24:30] Fixed 2 duplicate /gene - mnmE_1 mnmE_2 [09:24:30] Fixed 2 duplicate /gene - crtI_1 crtI_2 [09:24:30] Fixed 2 duplicate /gene - lysA_1 lysA_2 [09:24:30] Fixed 2 duplicate /gene - kpsU_1 kpsU_2 [09:24:30] Fixed 2 duplicate /gene - ribD_1 ribD_2 [09:24:30] Fixed 3 duplicate /gene - bicA_1 bicA_2 bicA_3 [09:24:30] Fixed 2 duplicate /gene - bchI_1 bchI_2 [09:24:30] Fixed 2 duplicate /gene - thrB_1 thrB_2 [09:24:30] Fixed 3 duplicate /gene - lytB_1 lytB_2 lytB_3 [09:24:30] Fixed 2 duplicate /gene - menG_1 menG_2 [09:24:30] Fixed 3 duplicate /gene - ntcA_1 ntcA_2 ntcA_3 [09:24:30] Fixed 2 duplicate /gene - plsC_1 plsC_2 [09:24:30] Fixed 2 duplicate /gene - perR_1 perR_2 [09:24:30] Fixed 2 duplicate /gene - msrB_1 msrB_2 [09:24:30] Fixed 2 duplicate /gene - pyrB_1 pyrB_2 [09:24:30] Fixed 2 duplicate /gene - vraR_1 vraR_2 [09:24:30] Fixed 3 duplicate /gene - sigA2_1 sigA2_2 sigA2_3 [09:24:30] Fixed 2 duplicate /gene - cca_1 cca_2 [09:24:30] Fixed 3 duplicate /gene - trxA_1 trxA_2 trxA_3 [09:24:30] Fixed 2 duplicate /gene - ppa_1 ppa_2 [09:24:30] Fixed 2 duplicate /gene - pcyA_1 pcyA_2 [09:24:30] Fixed 2 duplicate /gene - lexA_1 lexA_2 [09:24:30] Fixed 2 duplicate /gene - gloB_1 gloB_2 [09:24:30] Fixed 2 duplicate /gene - glgX_1 glgX_2 [09:24:30] Fixed 2 duplicate /gene - estB_1 estB_2 [09:24:30] Fixed 2 duplicate /gene - aofH_1 aofH_2 [09:24:30] Fixed 2 duplicate /gene - cpcG_1 cpcG_2 [09:24:30] Fixed 3 duplicate /gene - yciC_1 yciC_2 yciC_3 [09:24:30] Fixed 2 duplicate /gene - hhoA_1 hhoA_2 [09:24:30] Fixed 3 duplicate /gene - bcp_1 bcp_2 bcp_3 [09:24:30] Fixed 2 duplicate /gene - sigA_1 sigA_2 [09:24:30] Fixed 2 duplicate /gene - pao_1 pao_2 [09:24:30] Fixed 2 duplicate /gene - sdh_1 sdh_2 [09:24:30] Fixed 2 duplicate /gene - pilT_1 pilT_2 [09:24:30] Fixed 2 duplicate /gene - speA_1 speA_2 [09:24:30] Fixed 2 duplicate /gene - crcB_1 crcB_2 [09:24:30] Fixed 2 duplicate /gene - psaB_1 psaB_2 [09:24:30] Fixed 2 duplicate /gene - ettA_1 ettA_2 [09:24:30] Fixed 3 duplicate /gene - petF_1 petF_2 petF_3 [09:24:30] Fixed 2 duplicate /gene - cobN_1 cobN_2 [09:24:30] Fixed 2 duplicate /gene - rebM_1 rebM_2 [09:24:30] Fixed 6 duplicate /gene - slpA_1 slpA_2 slpA_3 slpA_4 slpA_5 slpA_6 [09:24:30] Fixed 2 duplicate /gene - gph_1 gph_2 [09:24:30] Fixed 2 duplicate /gene - eutN_1 eutN_2 [09:24:30] Fixed 3 duplicate /gene - mpeC_1 mpeC_2 mpeC_3 [09:24:30] Fixed 2 duplicate /gene - copA_1 copA_2 [09:24:30] Fixed 2 duplicate /gene - trxB_1 trxB_2 [09:24:30] Fixed 2 duplicate /gene - ctaD_1 ctaD_2 [09:24:30] Fixed 2 duplicate /gene - smc_1 smc_2 [09:24:30] Fixed 3 duplicate /gene - ubiB_1 ubiB_2 ubiB_3 [09:24:30] Fixed 2 duplicate /gene - rpoC_1 rpoC_2 [09:24:30] Fixed 2 duplicate /gene - pstS_1 pstS_2 [09:24:30] Fixed 3 duplicate /gene - mgtA_1 mgtA_2 mgtA_3 [09:24:30] Fixed 2 duplicate /gene - nifF_1 nifF_2 [09:24:30] Fixed 2 duplicate /gene - lptD_1 lptD_2 [09:24:30] Fixed 2 duplicate /gene - clpS_1 clpS_2 [09:24:30] Fixed 6 duplicate /gene - xerC_1 xerC_2 xerC_3 xerC_4 xerC_5 xerC_6 [09:24:30] Fixed 2 duplicate /gene - ilvE_1 ilvE_2 [09:24:30] Fixed 2 duplicate /gene - iscS_1 iscS_2 [09:24:30] Fixed 2 duplicate /gene - corC_1 corC_2 [09:24:30] Fixed 2 duplicate /gene - helY_1 helY_2 [09:24:30] Fixed 2 duplicate /gene - sir_1 sir_2 [09:24:30] Fixed 2 duplicate /gene - dcd_1 dcd_2 [09:24:30] Fixed 2 duplicate /gene - mepM_1 mepM_2 [09:24:30] Fixed 2 duplicate /gene - psbA2_1 psbA2_2 [09:24:30] Fixed 2 duplicate /gene - ynhG_1 ynhG_2 [09:24:30] Fixed 2 duplicate /gene - der_1 der_2 [09:24:30] Fixed 4 duplicate /gene - ndhD1_1 ndhD1_2 ndhD1_3 ndhD1_4 [09:24:30] Fixed 2 duplicate /gene - kdsA_1 kdsA_2 [09:24:30] Fixed 2 duplicate /gene - lip1_1 lip1_2 [09:24:30] Fixed 2 duplicate /gene - hpf_1 hpf_2 [09:24:30] Fixed 2 duplicate /gene - csgA_1 csgA_2 [09:24:30] Fixed 2 duplicate /gene - carA_1 carA_2 [09:24:30] Fixed 2 duplicate /gene - coxM_1 coxM_2 [09:24:30] Fixed 2 duplicate /gene - suhB_1 suhB_2 [09:24:30] Fixed 2 duplicate /gene - mtcA2_1 mtcA2_2 [09:24:30] Fixed 2 duplicate /gene - bepA_1 bepA_2 [09:24:30] Fixed 2 duplicate /gene - mntB_1 mntB_2 [09:24:30] Fixed 2 duplicate /gene - rnr_1 rnr_2 [09:24:30] Fixed 2 duplicate /gene - cpdA_1 cpdA_2 [09:24:30] Fixed 2 duplicate /gene - ubiG_1 ubiG_2 [09:24:30] Fixed 2 duplicate /gene - malK_1 malK_2 [09:24:30] Fixed 2 duplicate /gene - ccmK_1 ccmK_2 [09:24:30] Fixed 2 duplicate /gene - fabF_1 fabF_2 [09:24:30] Fixed 2 duplicate /gene - dnaX_1 dnaX_2 [09:24:30] Fixed 2 duplicate /gene - atpG_1 atpG_2 [09:24:30] Fixed 2 duplicate /gene - purE_1 purE_2 [09:24:30] Fixed 5 duplicate /gene - dnaJ_1 dnaJ_2 dnaJ_3 dnaJ_4 dnaJ_5 [09:24:30] Fixed 2 duplicate /gene - rlpA_1 rlpA_2 [09:24:30] Fixed 2 duplicate /gene - mdtA_1 mdtA_2 [09:24:30] Fixed 2 duplicate /gene - ykfA_1 ykfA_2 [09:24:30] Fixed 2 duplicate /gene - pyrC_1 pyrC_2 [09:24:30] Fixed 2 duplicate /gene - phoP_1 phoP_2 [09:24:30] Fixed 125 colliding /gene names. [09:24:30] Adding /locus_tag identifiers [09:24:30] Assigned 2933 locus_tags to CDS and RNA features. [09:24:30] Writing outputs to prokka/Aaan/ [09:24:34] Generating annotation statistics file [09:24:34] Generating Genbank and Sequin files [09:24:34] Running: tbl2asn -V b -a r10k -l paired-ends -M n -N 1 -y 'Annotated using prokka 1.12 from https://github.com/tseemann/prokka' -Z prokka\/Aaan\/Aaan\.err -i prokka\/Aaan\/Aaan\.fsa 2> /dev/null [09:24:44] Deleting unwanted file: prokka/Aaan/errorsummary.val [09:24:44] Deleting unwanted file: prokka/Aaan/Aaan.dr [09:24:44] Deleting unwanted file: prokka/Aaan/Aaan.fixedproducts [09:24:44] Deleting unwanted file: prokka/Aaan/Aaan.ecn [09:24:44] Deleting unwanted file: prokka/Aaan/Aaan.val [09:24:44] Repairing broken .GBK output that tbl2asn produces... [09:24:44] Running: sed 's/COORDINATES: profile/COORDINATES:profile/' < prokka\/Aaan\/Aaan\.gbf > prokka\/Aaan\/Aaan\.gbk [09:24:44] Deleting unwanted file: prokka/Aaan/Aaan.gbf [09:24:44] Output files: [09:24:44] prokka/Aaan/Aaan.gff [09:24:44] prokka/Aaan/Aaan.fsa [09:24:44] prokka/Aaan/Aaan.ffn [09:24:44] prokka/Aaan/Aaan.gbk [09:24:44] prokka/Aaan/Aaan.log [09:24:44] prokka/Aaan/Aaan.sqn [09:24:44] prokka/Aaan/Aaan.fna [09:24:44] prokka/Aaan/Aaan.faa [09:24:44] prokka/Aaan/Aaan.tsv [09:24:44] prokka/Aaan/Aaan.tbl [09:24:44] prokka/Aaan/Aaan.txt [09:24:44] prokka/Aaan/Aaan.err [09:24:44] Annotation finished successfully. [09:24:44] Walltime used: 6.12 minutes [09:24:44] If you use this result please cite the Prokka paper: [09:24:44] Seemann T (2014) Prokka: rapid prokaryotic genome annotation. Bioinformatics. 30(14):2068-9. [09:24:44] Type 'prokka --citation' for more details. [09:24:44] Share and enjoy!