[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/Aaap [09:18:37] Running: mkdir -p prokka\/Aaap [09:18:37] Using filename prefix: Aaap.XXX [09:18:37] Setting HMMER_NCPU=1 [09:18:37] Writing log to: prokka/Aaap/Aaap.log [09:18:37] Command: /usr/local/bioinfo/src/PROKKA/prokka-1.12/bin/prokka /home/formation/public_html/M2_Phylogenomique/data/Synechococcus/DNA/Aaap.fas --outdir prokka/Aaap --compliant --addgenes --prefix Aaap --locustag Aaap.g --genus Synechococcus --species Synechococcus sp. --strain WH 8102 --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 [09:18:38] Determined parallel version is 20150122 [09:18:38] 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/Aaap.fas [09:18:39] Wrote 1 contigs totalling 2434428 bp. [09:18:39] Predicting tRNAs and tmRNAs [09:18:39] Running: aragorn -l -gc11 -w prokka\/Aaap\/Aaap\.fna [09:18:41] 1 tRNA-Gly c[41242,41313] 33 (ccc) [09:18:41] 2 tRNA-Gly [85193,85264] 33 (gcc) [09:18:41] 3 tRNA-Val c[126433,126512] 37 (gac) [09:18:41] 4 tRNA-Arg [147823,147896] 35 (cct) [09:18:41] 5 tRNA-Met [238635,238708] 34 (cat) [09:18:41] 6 tRNA-Arg [258586,258660] 35 (acg) [09:18:41] 7 tRNA-Leu [291189,291270] 35 (tag) [09:18:41] 8 tRNA-Ala c[298547,298619] 34 (cgc) [09:18:41] 9 tRNA-Leu [331759,331841] 35 (gag) [09:18:41] 10 tmRNA* [342021,342339] 178,228 ANNIVRFSRHAAPVAA* [09:18:41] 11 tRNA-Val c[524800,524871] 33 (gac) [09:18:41] 12 tRNA-Gly [566619,566689] 33 (tcc) [09:18:41] 13 tRNA-Thr c[577305,577377] 34 (cgt) [09:18:41] 14 tRNA-Glu c[734693,734765] 35 (ttc) [09:18:41] 15 tRNA-Met [806346,806422] 35 (cat) [09:18:41] 16 tRNA-Pro c[858431,858505] 35 (tgg) [09:18:41] 17 tRNA-Lys c[860253,860324] 33 (ttt) [09:18:41] 18 tRNA-Pro c[1017787,1017860] 35 (ggg) [09:18:41] 19 tRNA-Ser c[1141505,1141593] 36 (tga) [09:18:41] 20 tRNA-Met [1205148,1205221] 35 (cat) [09:18:41] 21 tRNA-Ser c[1273818,1273907] 36 (gga) [09:18:41] 22 tRNA-Leu [1465129,1465214] 35 (taa) [09:18:41] 23 tRNA-Ala c[1524847,1524921] 35 (ggc) [09:18:41] 24 tRNA-Leu c[1569964,1570048] 35 (cag) [09:18:41] 25 tRNA-Leu [1571543,1571625] 35 (caa) [09:18:41] 26 tRNA-His [1577683,1577756] 34 (gtg) [09:18:41] 27 tRNA-Ser c[1606982,1607070] 38 (cga) [09:18:41] 28 tRNA-Trp [1745801,1745877] 35 (cca) [09:18:41] 29 tRNA-Asp [1746303,1746378] 36 (gtc) [09:18:41] 30 tRNA-Val [1761044,1761115] 33 (cac) [09:18:41] 31 tRNA-Arg [1813567,1813640] 35 (tct) [09:18:41] 32 tRNA-Tyr [1843149,1843230] 35 (gta) [09:18:41] 33 tRNA-Thr [1843241,1843313] 33 (ggt) [09:18:41] 34 tRNA-Ala c[1874313,1874386] 34 (tgc) [09:18:41] 35 tRNA-Ile c[1874395,1874470] 36 (gat) [09:18:41] 36 tRNA-Thr [1884157,1884228] 33 (tgt) [09:18:41] 37 tRNA-Phe [1898272,1898347] 35 (gaa) [09:18:41] 38 tRNA-Cys c[1930854,1930924] 33 (gca) [09:18:41] 39 tRNA-Arg c[1946700,1946775] 36 (ccg) [09:18:41] 40 tRNA-Gln c[1960075,1960148] 34 (ttg) [09:18:41] 41 tRNA-Ser [1982018,1982108] 36 (gct) [09:18:41] 42 tRNA-Pro c[2017608,2017681] 35 (cgg) [09:18:41] 43 tRNA-Ala c[2081253,2081326] 34 (tgc) [09:18:41] 44 tRNA-Ile c[2081335,2081410] 36 (gat) [09:18:41] 45 tRNA-Asn [2133291,2133363] 33 (gtt) [09:18:41] 46 tRNA-Val c[2322682,2322754] 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 2434428 bp, so using single mode [09:18:42] Running: prodigal -i prokka\/Aaap\/Aaap\.fna -c -m -g 11 -p single -f sco -q [09:18:54] Excluding CDS which overlaps existing RNA (tRNA) at gnl|Prokka|Aaap.g_1:126243..126506 on + strand [09:18:54] Excluding CDS which overlaps existing RNA (tRNA) at gnl|Prokka|Aaap.g_1:126508..126984 on - strand [09:18:55] Excluding CDS which overlaps existing RNA (tRNA) at gnl|Prokka|Aaap.g_1:566526..568772 on - strand [09:18:55] Excluding CDS which overlaps existing RNA (tRNA) at gnl|Prokka|Aaap.g_1:860252..860926 on + strand [09:18:56] Excluding CDS which overlaps existing RNA (tRNA) at gnl|Prokka|Aaap.g_1:1524888..1524995 on + strand [09:18:56] Excluding CDS which overlaps existing RNA (tRNA) at gnl|Prokka|Aaap.g_1:1883957..1884166 on + strand [09:18:56] Excluding CDS which overlaps existing RNA (tRNA) at gnl|Prokka|Aaap.g_1:1898316..1898606 on + strand [09:18:56] Excluding CDS which overlaps existing RNA (tRNA) at gnl|Prokka|Aaap.g_1:1930808..1932199 on + strand [09:18:57] Found 2712 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. [09:18:58] There are still 2712 unannotated CDS left (started with 2712) [09:18:58] Will use blast to search against /usr/local/bioinfo/src/PROKKA/prokka-1.12/bin/../db/kingdom/Bacteria/sprot with 1 CPUs [09:18:58] Running: cat prokka\/Aaap\/sprot\.faa | parallel --gnu --plain -j 1 --block 374631 --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\/Aaap\/sprot\.blast 2> /dev/null [09:22:07] Modify product: N utilization substance protein B homolog => N utilization substance protein B [09:22:07] Modify product: Probable ABC transporter-binding protein DR_1438 => putative ABC transporter-binding protein [09:22:07] Modify product: Uncharacterized hydrolase YxeP => putative hydrolase YxeP [09:22:07] Modify product: Cyclic nucleotide-gated potassium channel mll3241 => Cyclic nucleotide-gated potassium channel [09:22:07] Modify product: Uncharacterized FAD-linked oxidoreductase Rv2280 => putative FAD-linked oxidoreductase [09:22:07] Modify product: Uncharacterized glycosyltransferase sll0501 => putative glycosyltransferase [09:22:07] Modify product: Probable ribonucleotide transport ATP-binding protein mkl => putative ribonucleotide transport ATP-binding protein mkl [09:22:07] Modify product: Probable lipid II flippase MurJ => putative lipid II flippase MurJ [09:22:07] Modify product: Probable undecaprenyl-phosphate N-acetylglucosaminyl 1-phosphate transferase => putative undecaprenyl-phosphate N-acetylglucosaminyl 1-phosphate transferase [09:22:07] Modify product: NADH dehydrogenase-like protein SA0802 => NADH dehydrogenase-like protein [09:22:07] Modify product: Probable bifunctional SAT/APS kinase => putative bifunctional SAT/APS kinase [09:22:07] Modify product: Probable ATP-dependent transporter SufC => putative ATP-dependent transporter SufC [09:22:07] Modify product: Probable cysteine desulfurase => putative cysteine desulfurase [09:22:08] Modify product: Probable undecaprenyl-phosphate N-acetylglucosaminyl 1-phosphate transferase => putative undecaprenyl-phosphate N-acetylglucosaminyl 1-phosphate transferase [09:22:08] Modify product: Probable peptidoglycan glycosyltransferase FtsW => putative peptidoglycan glycosyltransferase FtsW [09:22:08] Modify product: Probable nicotinate-nucleotide adenylyltransferase => putative nicotinate-nucleotide adenylyltransferase [09:22:08] Modify product: Probable 30S ribosomal protein PSRP-3 => putative 30S ribosomal protein PSRP-3 [09:22:08] Modify product: Probable transcriptional regulatory protein aq_1575 => putative transcriptional regulatory protein [09:22:08] Modify product: Probable phospholipid ABC transporter permease protein MlaE => putative phospholipid ABC transporter permease protein MlaE [09:22:08] Modify product: Probable dual-specificity RNA methyltransferase RlmN => putative dual-specificity RNA methyltransferase RlmN [09:22:08] Modify product: Probable trans-aconitate 2-methyltransferase => putative trans-aconitate 2-methyltransferase [09:22:08] Modify product: Probable helicase HelY => putative helicase HelY [09:22:08] Modify product: Probable tRNA-dihydrouridine synthase => putative tRNA-dihydrouridine synthase [09:22:08] Modify product: Uncharacterized MFS-type transporter Rv0037c => putative MFS-type transporter [09:22:08] Modify product: Uncharacterized oxidoreductase MSMEG_1603/MSMEI_1564 => putative oxidoreductase/MSMEI_1564 [09:22:08] Modify product: 1,4-alpha-glucan branching enzyme TTHA1902 => 1,4-alpha-glucan branching enzyme [09:22:08] Modify product: Bifunctional protein FolD => Bifunctional protein FolD protein [09:22:08] Modify product: Probable glutaredoxin ssr2061 => putative glutaredoxin [09:22:08] Modify product: Probable murein peptide carboxypeptidase => putative murein peptide carboxypeptidase [09:22:08] Modify product: Uncharacterized ABC transporter ATP-binding protein TM_0288 => putative ABC transporter ATP-binding protein [09:22:08] Modify product: Probable glutamine ABC transporter permease protein GlnM => putative glutamine ABC transporter permease protein GlnM [09:22:08] Modify product: Probable protein kinase UbiB => putative protein kinase UbiB [09:22:08] Modify product: Probable 2-phosphosulfolactate phosphatase => putative 2-phosphosulfolactate phosphatase [09:22:08] Modify product: Phosphorylated carbohydrates phosphatase TM_1254 => Phosphorylated carbohydrates phosphatase [09:22:08] Modify product: Probable multidrug resistance ABC transporter ATP-binding/permease protein YheI => putative multidrug resistance ABC transporter ATP-binding/permease protein YheI [09:22:08] Modify product: Uncharacterized zinc protease Rv2782c => putative zinc protease [09:22:08] Modify product: Uncharacterized zinc protease Rv2782c => putative zinc protease [09:22:08] Modify product: Uncharacterized ABC transporter ATP-binding protein Rv0986 => putative ABC transporter ATP-binding protein [09:22:08] Modify product: Uncharacterized glycosyltransferase EpsJ => putative glycosyltransferase EpsJ [09:22:08] Modify product: Uncharacterized protease YdcP => putative protease YdcP [09:22:08] Modify product: GTP-binding protein TypA/BipA homolog => GTP-binding protein TypA/BipA [09:22:08] Modify product: Probable peroxiredoxin => putative peroxiredoxin [09:22:08] Modify product: Probable ABC transporter-binding protein DR_1438 => putative ABC transporter-binding protein [09:22:09] Modify product: Probable chromate transport protein => putative chromate transport protein [09:22:09] Modify product: Uncharacterized ABC transporter ATP-binding protein YlmA => putative ABC transporter ATP-binding protein YlmA [09:22:09] Modify product: Uncharacterized sugar epimerase YhfK => putative sugar epimerase YhfK [09:22:09] Modify product: Uncharacterized oxidoreductase CzcO => putative oxidoreductase CzcO [09:22:09] Modify product: Probable cytochrome c oxidase subunit 1 => putative cytochrome c oxidase subunit 1 [09:22:09] Modify product: Uncharacterized ABC transporter ATP-binding protein TM_0288 => putative ABC transporter ATP-binding protein [09:22:09] Modify product: Uncharacterized FAD-linked oxidoreductase Rv2280 => putative FAD-linked oxidoreductase [09:22:09] Modify product: Oxygen-independent coproporphyrinogen-III oxidase-like protein sll1917 => Oxygen-independent coproporphyrinogen-III oxidase-like protein [09:22:09] Modify product: Uncharacterized PIN and TRAM-domain containing protein YacL => putative PIN and TRAM-domain containing protein YacL [09:22:09] Modify product: Multidrug transporter PA4990 => Multidrug transporter [09:22:09] Modify product: Uncharacterized MscS family protein YkuT => putative MscS family protein YkuT [09:22:09] Modify product: Uncharacterized sugar kinase YdjH => putative sugar kinase YdjH [09:22:09] Modify product: Thylakoid-associated single-stranded DNA-binding protein slr1034 => Thylakoid-associated single-stranded DNA-binding protein [09:22:09] Modify product: Uncharacterized FAD-linked oxidoreductase Rv2280 => putative FAD-linked oxidoreductase [09:22:09] Modify product: Probable cytochrome c oxidase subunit 1 => putative cytochrome c oxidase subunit 1 [09:22:09] Modify product: Uncharacterized ABC transporter ATP-binding protein YknY => putative ABC transporter ATP-binding protein YknY [09:22:09] Modify product: Phage shock protein A homolog => Phage shock protein A [09:22:09] Modify product: Uncharacterized inner membrane transporter YedA => putative inner membrane transporter YedA [09:22:09] Modify product: Vitamin K epoxide reductase homolog => Vitamin K epoxide reductase [09:22:09] Modify product: Probable CtpA-like serine protease => putative CtpA-like serine protease [09:22:09] Modify product: Putative esterase aq_1494 => Putative esterase [09:22:09] Modify product: Probable phycoerythrobilin lyase CpeT => putative phycoerythrobilin lyase CpeT [09:22:09] Modify product: Uncharacterized phycocyanin operon protein Z => putative phycocyanin operon protein Z [09:22:09] Modify product: Uncharacterized oxidoreductase Rv2298 => putative oxidoreductase [09:22:09] Modify product: Probable adenylyltransferase/sulfurtransferase MoeZ => putative adenylyltransferase/sulfurtransferase MoeZ [09:22:09] Modify product: Probable cobalt-factor III C(17)-methyltransferase => putative cobalt-factor III C(17)-methyltransferase [09:22:09] Modify product: Uncharacterized transporter Rv2685 => putative transporter [09:22:09] Modify product: Vitamin K epoxide reductase homolog => Vitamin K epoxide reductase [09:22:09] Modify product: Epimerase family protein Rv2216 => Epimerase family protein [09:22:09] Modify product: Putative HTH-type transcriptional regulator Rv0890c => Putative HTH-type transcriptional regulator [09:22:10] Modify product: Probable adenylyl-sulfate kinase => putative adenylyl-sulfate kinase [09:22:10] Modify product: Probable glutaredoxin ssr2061 => putative glutaredoxin [09:22:10] Modify product: Probable nicotinate-nucleotide pyrophosphorylase [carboxylating] => putative nicotinate-nucleotide pyrophosphorylase [carboxylating] [09:22:10] Modify product: Probable protein kinase UbiB => putative protein kinase UbiB [09:22:10] Modify product: Uncharacterized HTH-type transcriptional regulator YybR => putative HTH-type transcriptional regulator YybR [09:22:10] Modify product: Probable molybdenum cofactor guanylyltransferase => putative molybdenum cofactor guanylyltransferase [09:22:10] Modify product: Probable nitrate transporter NarT => putative nitrate transporter NarT [09:22:10] Modify product: Probable protein kinase UbiB => putative protein kinase UbiB [09:22:10] Cleaned 81 /product names [09:22:10] Deleting unwanted file: prokka/Aaap/sprot.faa [09:22:10] Deleting unwanted file: prokka/Aaap/sprot.blast [09:22:11] There are still 1405 unannotated CDS left (started with 2712) [09:22:11] Will use hmmer3 to search against /usr/local/bioinfo/src/PROKKA/prokka-1.12/bin/../db/hmm/HAMAP.hmm with 1 CPUs [09:22:11] Running: cat prokka\/Aaap\/HAMAP\.hmm\.faa | parallel --gnu --plain -j 1 --block 139860 --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\/Aaap\/HAMAP\.hmm\.hmmer3 2> /dev/null [09:23:54] Deleting unwanted file: prokka/Aaap/HAMAP.hmm.faa [09:23:54] Deleting unwanted file: prokka/Aaap/HAMAP.hmm.hmmer3 [09:23:54] Labelling remaining 1324 proteins as 'hypothetical protein' [09:23:54] Possible /pseudo 'Twitching mobility protein' at gnl|Prokka|Aaap.g_1 position 21932 [09:23:54] Possible /pseudo 'Twitching mobility protein' at gnl|Prokka|Aaap.g_1 position 22138 [09:23:54] Possible /pseudo 'Putative fluoride ion transporter CrcB' at gnl|Prokka|Aaap.g_1 position 98819 [09:23:54] Possible /pseudo 'Translation initiation factor IF-2' at gnl|Prokka|Aaap.g_1 position 580446 [09:23:54] Possible /pseudo 'DNA-directed RNA polymerase subunit beta'' at gnl|Prokka|Aaap.g_1 position 597718 [09:23:54] Possible /pseudo 'putative zinc protease' at gnl|Prokka|Aaap.g_1 position 1070350 [09:23:54] Possible /pseudo 'ATP-dependent Clp protease proteolytic subunit' at gnl|Prokka|Aaap.g_1 position 1586757 [09:23:54] Possible /pseudo 'Ethanolamine utilization protein EutN' at gnl|Prokka|Aaap.g_1 position 1646812 [09:23:54] Possible /pseudo 'Twitching mobility protein' at gnl|Prokka|Aaap.g_1 position 1751737 [09:23:54] Possible /pseudo 'S-layer protein SlpA' at gnl|Prokka|Aaap.g_1 position 2119133 [09:23:54] Possible /pseudo 'S-layer protein SlpA' at gnl|Prokka|Aaap.g_1 position 2123030 [09:23:54] Possible /pseudo 'Ribosomal RNA small subunit methyltransferase H' at gnl|Prokka|Aaap.g_1 position 2194058 [09:23:54] Found 1139 unique /gene codes. [09:23:54] Fixed 2 duplicate /gene - ftsH2_1 ftsH2_2 [09:23:54] Fixed 3 duplicate /gene - gltS_1 gltS_2 gltS_3 [09:23:54] Fixed 2 duplicate /gene - tagO_1 tagO_2 [09:23:54] Fixed 2 duplicate /gene - mnmC_1 mnmC_2 [09:23:54] Fixed 2 duplicate /gene - fabG_1 fabG_2 [09:23:54] Fixed 3 duplicate /gene - pds_1 pds_2 pds_3 [09:23:54] Fixed 2 duplicate /gene - psbD1_1 psbD1_2 [09:23:54] Fixed 2 duplicate /gene - mshA_1 mshA_2 [09:23:54] Fixed 2 duplicate /gene - ltxA_1 ltxA_2 [09:23:54] Fixed 2 duplicate /gene - cobD_1 cobD_2 [09:23:54] Fixed 3 duplicate /gene - rluD_1 rluD_2 rluD_3 [09:23:54] Fixed 2 duplicate /gene - petJ_1 petJ_2 [09:23:54] Fixed 2 duplicate /gene - rpsA_1 rpsA_2 [09:23:54] Fixed 2 duplicate /gene - xerD_1 xerD_2 [09:23:54] Fixed 2 duplicate /gene - galE_1 galE_2 [09:23:54] Fixed 3 duplicate /gene - cpcS_1 cpcS_2 cpcS_3 [09:23:54] Fixed 2 duplicate /gene - dnaK2_1 dnaK2_2 [09:23:54] Fixed 4 duplicate /gene - clpP_1 clpP_2 clpP_3 clpP_4 [09:23:54] Fixed 2 duplicate /gene - lpxB_1 lpxB_2 [09:23:54] Fixed 2 duplicate /gene - trmH_1 trmH_2 [09:23:54] Fixed 2 duplicate /gene - nuoL_1 nuoL_2 [09:23:54] Fixed 2 duplicate /gene - secA_1 secA_2 [09:23:54] Fixed 2 duplicate /gene - era_1 era_2 [09:23:54] Fixed 2 duplicate /gene - msbA_1 msbA_2 [09:23:54] Fixed 2 duplicate /gene - thiL_1 thiL_2 [09:23:54] Fixed 2 duplicate /gene - gyrA_1 gyrA_2 [09:23:54] Fixed 2 duplicate /gene - msrA_1 msrA_2 [09:23:54] Fixed 2 duplicate /gene - btuR_1 btuR_2 [09:23:54] Fixed 2 duplicate /gene - hisF_1 hisF_2 [09:23:54] Fixed 2 duplicate /gene - ctaE_1 ctaE_2 [09:23:54] Fixed 2 duplicate /gene - mprA_1 mprA_2 [09:23:54] Fixed 2 duplicate /gene - mnmE_1 mnmE_2 [09:23:54] Fixed 2 duplicate /gene - crtI_1 crtI_2 [09:23:54] Fixed 2 duplicate /gene - kpsU_1 kpsU_2 [09:23:54] Fixed 3 duplicate /gene - bicA_1 bicA_2 bicA_3 [09:23:54] Fixed 2 duplicate /gene - bchI_1 bchI_2 [09:23:54] Fixed 2 duplicate /gene - lytB_1 lytB_2 [09:23:54] Fixed 2 duplicate /gene - ntcA_1 ntcA_2 [09:23:54] Fixed 3 duplicate /gene - ubiE_1 ubiE_2 ubiE_3 [09:23:54] Fixed 2 duplicate /gene - plsC_1 plsC_2 [09:23:54] Fixed 2 duplicate /gene - msrB_1 msrB_2 [09:23:54] Fixed 2 duplicate /gene - pyrB_1 pyrB_2 [09:23:54] Fixed 4 duplicate /gene - sigA2_1 sigA2_2 sigA2_3 sigA2_4 [09:23:54] Fixed 2 duplicate /gene - cca_1 cca_2 [09:23:54] Fixed 3 duplicate /gene - trxA_1 trxA_2 trxA_3 [09:23:54] Fixed 2 duplicate /gene - ppa_1 ppa_2 [09:23:54] Fixed 2 duplicate /gene - gltX_1 gltX_2 [09:23:54] Fixed 4 duplicate /gene - pimB_1 pimB_2 pimB_3 pimB_4 [09:23:54] Fixed 2 duplicate /gene - pcyA_1 pcyA_2 [09:23:54] Fixed 2 duplicate /gene - lexA_1 lexA_2 [09:23:54] Fixed 2 duplicate /gene - intA_1 intA_2 [09:23:54] Fixed 2 duplicate /gene - infB_1 infB_2 [09:23:54] Fixed 2 duplicate /gene - cpcG_1 cpcG_2 [09:23:54] Fixed 2 duplicate /gene - ltxB_1 ltxB_2 [09:23:54] Fixed 3 duplicate /gene - yciC_1 yciC_2 yciC_3 [09:23:54] Fixed 2 duplicate /gene - hhoA_1 hhoA_2 [09:23:54] Fixed 3 duplicate /gene - bcp_1 bcp_2 bcp_3 [09:23:54] Fixed 2 duplicate /gene - sdh_1 sdh_2 [09:23:54] Fixed 5 duplicate /gene - pilT_1 pilT_2 pilT_3 pilT_4 pilT_5 [09:23:54] Fixed 2 duplicate /gene - clcD_1 clcD_2 [09:23:54] Fixed 2 duplicate /gene - speA_1 speA_2 [09:23:54] Fixed 2 duplicate /gene - crcB_1 crcB_2 [09:23:54] Fixed 2 duplicate /gene - ettA_1 ettA_2 [09:23:54] Fixed 2 duplicate /gene - hisH_1 hisH_2 [09:23:54] Fixed 2 duplicate /gene - petF_1 petF_2 [09:23:54] Fixed 2 duplicate /gene - cobN_1 cobN_2 [09:23:54] Fixed 2 duplicate /gene - znuC_1 znuC_2 [09:23:54] Fixed 5 duplicate /gene - slpA_1 slpA_2 slpA_3 slpA_4 slpA_5 [09:23:54] Fixed 2 duplicate /gene - eutN_1 eutN_2 [09:23:54] Fixed 2 duplicate /gene - gph_1 gph_2 [09:23:54] Fixed 2 duplicate /gene - dapL_1 dapL_2 [09:23:54] Fixed 3 duplicate /gene - mpeC_1 mpeC_2 mpeC_3 [09:23:54] Fixed 2 duplicate /gene - recD_1 recD_2 [09:23:54] Fixed 2 duplicate /gene - amiC_1 amiC_2 [09:23:54] Fixed 2 duplicate /gene - ctaD_1 ctaD_2 [09:23:54] Fixed 2 duplicate /gene - smc_1 smc_2 [09:23:54] Fixed 3 duplicate /gene - ubiB_1 ubiB_2 ubiB_3 [09:23:54] Fixed 2 duplicate /gene - cugP_1 cugP_2 [09:23:54] Fixed 2 duplicate /gene - rpoC_1 rpoC_2 [09:23:54] Fixed 4 duplicate /gene - pstS_1 pstS_2 pstS_3 pstS_4 [09:23:54] Fixed 2 duplicate /gene - kpsD_1 kpsD_2 [09:23:54] Fixed 2 duplicate /gene - lptD_1 lptD_2 [09:23:54] Fixed 2 duplicate /gene - clpS_1 clpS_2 [09:23:54] Fixed 2 duplicate /gene - clpB1_1 clpB1_2 [09:23:54] Fixed 2 duplicate /gene - rsmH_1 rsmH_2 [09:23:54] Fixed 2 duplicate /gene - ugpC_1 ugpC_2 [09:23:54] Fixed 2 duplicate /gene - prmC_1 prmC_2 [09:23:54] Fixed 2 duplicate /gene - corC_1 corC_2 [09:23:54] Fixed 2 duplicate /gene - kmo_1 kmo_2 [09:23:54] Fixed 2 duplicate /gene - legI_1 legI_2 [09:23:54] Fixed 2 duplicate /gene - sir_1 sir_2 [09:23:54] Fixed 2 duplicate /gene - iolX_1 iolX_2 [09:23:54] Fixed 3 duplicate /gene - psbA2_1 psbA2_2 psbA2_3 [09:23:54] Fixed 2 duplicate /gene - acr1_1 acr1_2 [09:23:54] Fixed 3 duplicate /gene - ndhD1_1 ndhD1_2 ndhD1_3 [09:23:54] Fixed 2 duplicate /gene - cbpA_1 cbpA_2 [09:23:54] Fixed 2 duplicate /gene - sphR_1 sphR_2 [09:23:54] Fixed 2 duplicate /gene - lip1_1 lip1_2 [09:23:54] Fixed 2 duplicate /gene - hpf_1 hpf_2 [09:23:54] Fixed 2 duplicate /gene - csgA_1 csgA_2 [09:23:54] Fixed 2 duplicate /gene - radA_1 radA_2 [09:23:54] Fixed 4 duplicate /gene - bepA_1 bepA_2 bepA_3 bepA_4 [09:23:54] Fixed 2 duplicate /gene - mntB_1 mntB_2 [09:23:54] Fixed 2 duplicate /gene - rnr_1 rnr_2 [09:23:54] Fixed 3 duplicate /gene - rsgI2_1 rsgI2_2 rsgI2_3 [09:23:54] Fixed 2 duplicate /gene - ubiG_1 ubiG_2 [09:23:54] Fixed 2 duplicate /gene - sepF_1 sepF_2 [09:23:54] Fixed 2 duplicate /gene - ppiA_1 ppiA_2 [09:23:54] Fixed 3 duplicate /gene - hlyD_1 hlyD_2 hlyD_3 [09:23:54] Fixed 2 duplicate /gene - fur_1 fur_2 [09:23:54] Fixed 2 duplicate /gene - ccmK_1 ccmK_2 [09:23:54] Fixed 2 duplicate /gene - fabF_1 fabF_2 [09:23:54] Fixed 2 duplicate /gene - atpG_1 atpG_2 [09:23:54] Fixed 2 duplicate /gene - hlyB_1 hlyB_2 [09:23:54] Fixed 2 duplicate /gene - purE_1 purE_2 [09:23:54] Fixed 2 duplicate /gene - degU_1 degU_2 [09:23:54] Fixed 4 duplicate /gene - dnaJ_1 dnaJ_2 dnaJ_3 dnaJ_4 [09:23:54] Fixed 2 duplicate /gene - rlpA_1 rlpA_2 [09:23:54] Fixed 2 duplicate /gene - pyrC_1 pyrC_2 [09:23:54] Fixed 2 duplicate /gene - phoP_1 phoP_2 [09:23:54] Fixed 120 colliding /gene names. [09:23:54] Adding /locus_tag identifiers [09:23:54] Assigned 2758 locus_tags to CDS and RNA features. [09:23:54] Writing outputs to prokka/Aaap/ [09:23:58] Generating annotation statistics file [09:23:58] Generating Genbank and Sequin files [09:23:58] 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\/Aaap\/Aaap\.err -i prokka\/Aaap\/Aaap\.fsa 2> /dev/null [09:24:06] Deleting unwanted file: prokka/Aaap/errorsummary.val [09:24:06] Deleting unwanted file: prokka/Aaap/Aaap.dr [09:24:06] Deleting unwanted file: prokka/Aaap/Aaap.fixedproducts [09:24:06] Deleting unwanted file: prokka/Aaap/Aaap.ecn [09:24:06] Deleting unwanted file: prokka/Aaap/Aaap.val [09:24:06] Repairing broken .GBK output that tbl2asn produces... [09:24:06] Running: sed 's/COORDINATES: profile/COORDINATES:profile/' < prokka\/Aaap\/Aaap\.gbf > prokka\/Aaap\/Aaap\.gbk [09:24:06] Deleting unwanted file: prokka/Aaap/Aaap.gbf [09:24:06] Output files: [09:24:06] prokka/Aaap/Aaap.faa [09:24:06] prokka/Aaap/Aaap.gff [09:24:06] prokka/Aaap/Aaap.log [09:24:06] prokka/Aaap/Aaap.ffn [09:24:06] prokka/Aaap/Aaap.gbk [09:24:06] prokka/Aaap/Aaap.err [09:24:06] prokka/Aaap/Aaap.tbl [09:24:06] prokka/Aaap/Aaap.tsv [09:24:06] prokka/Aaap/Aaap.fna [09:24:06] prokka/Aaap/Aaap.sqn [09:24:06] prokka/Aaap/Aaap.fsa [09:24:06] prokka/Aaap/Aaap.txt [09:24:06] Annotation finished successfully. [09:24:06] Walltime used: 5.48 minutes [09:24:06] If you use this result please cite the Prokka paper: [09:24:06] Seemann T (2014) Prokka: rapid prokaryotic genome annotation. Bioinformatics. 30(14):2068-9. [09:24:06] Type 'prokka --citation' for more details. [09:24:06] Share and enjoy!