[09:18:36] This is prokka 1.12 [09:18:36] Written by Torsten Seemann [09:18:36] Homepage is https://github.com/tseemann/prokka [09:18:36] Local time is Thu Oct 4 09:18:36 2018 [09:18:36] You are yquentin [09:18:36] Operating system is linux [09:18:36] You have BioPerl 1.006924 [09:18:36] System has 64 cores. [09:18:36] Will use maximum of 1 cores. [09:18:36] Annotating as >>> Bacteria <<< [09:18:36] Enabling options to ensure Genbank/ENA/DDJB submission compliance. [09:18:36] Creating new output folder: prokka/Aaam [09:18:36] Running: mkdir -p prokka\/Aaam [09:18:36] Using filename prefix: Aaam.XXX [09:18:36] Setting HMMER_NCPU=1 [09:18:36] Writing log to: prokka/Aaam/Aaam.log [09:18:36] Command: /usr/local/bioinfo/src/PROKKA/prokka-1.12/bin/prokka /home/formation/public_html/M2_Phylogenomique/data/Synechococcus/DNA/Aaam.fas --outdir prokka/Aaam --compliant --addgenes --prefix Aaam --locustag Aaam.g --genus Synechococcus --species Synechococcus sp. --strain CC9902 --kingdom Bacteria --cpus 1 [09:18:36] Appending to PATH: /usr/local/bioinfo/src/PROKKA/prokka-1.12/bin/../binaries/linux [09:18:36] Appending to PATH: /usr/local/bioinfo/src/PROKKA/prokka-1.12/bin/../binaries/linux/../common [09:18:36] Appending to PATH: /usr/local/bioinfo/src/PROKKA/prokka-1.12/bin [09:18:36] Looking for 'aragorn' - found /usr/local/bioinfo/src/PROKKA/prokka-1.12/binaries/linux/aragorn [09:18:36] Determined aragorn version is 1.2 [09:18:36] Looking for 'blastp' - found /usr/local/bioinfo/src/PROKKA/prokka-1.12/binaries/linux/blastp [09:18:37] Determined blastp version is 2.4 [09:18:37] Looking for 'cmpress' - found /usr/local/bioinfo/src/PROKKA/prokka-1.12/binaries/linux/cmpress [09:18:37] Determined cmpress version is 1.1 [09:18:37] Looking for 'cmscan' - found /usr/local/bioinfo/src/PROKKA/prokka-1.12/binaries/linux/cmscan [09:18:37] Determined cmscan version is 1.1 [09:18:37] Looking for 'egrep' - found /usr/bin/egrep [09:18:37] Looking for 'find' - found /usr/bin/find [09:18:37] Looking for 'grep' - found /usr/bin/grep [09:18:37] Looking for 'hmmpress' - found /usr/local/bioinfo/src/PROKKA/prokka-1.12/binaries/linux/hmmpress [09:18:37] Determined hmmpress version is 3.1 [09:18:37] Looking for 'hmmscan' - found /usr/local/bioinfo/src/PROKKA/prokka-1.12/binaries/linux/hmmscan [09:18:37] Determined hmmscan version is 3.1 [09:18:37] Looking for 'java' - found /usr/bin/java [09:18:37] Looking for 'less' - found /usr/bin/less [09:18:37] 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/Aaam.fas [09:18:39] Wrote 1 contigs totalling 2234828 bp. [09:18:39] Predicting tRNAs and tmRNAs [09:18:39] Running: aragorn -l -gc11 -w prokka\/Aaam\/Aaam\.fna [09:18:40] 1 tRNA-Gly c[37495,37566] 33 (ccc) [09:18:40] 2 tRNA-Gly c[82790,82861] 33 (gcc) [09:18:40] 3 tRNA-Arg [185994,186070] 36 (cct) [09:18:40] 4 tRNA-Met [273874,273946] 34 (cat) [09:18:40] 5 tRNA-Asn c[326596,326669] 34 (gtt) [09:18:40] 6 tRNA-Ile [374981,375056] 36 (gat) [09:18:40] 7 tRNA-Ala [375065,375138] 34 (tgc) [09:18:40] 8 tRNA-Leu [435379,435460] 35 (gag) [09:18:40] 9 tmRNA* [444505,444822] 177,227 ANNIVRFSRQAAPVAA* [09:18:40] 10 tRNA-Val c[536143,536214] 33 (gac) [09:18:40] 11 tRNA-Gly [582310,582380] 33 (tcc) [09:18:40] 12 tRNA-Thr c[595601,595673] 34 (cgt) [09:18:40] 13 tRNA-Glu c[767229,767302] 35 (ttc) [09:18:40] 14 tRNA-Met [842899,842975] 35 (cat) [09:18:40] 15 tRNA-Leu c[890757,890842] 35 (taa) [09:18:40] 16 tRNA-Ser [1047607,1047696] 36 (gga) [09:18:40] 17 tRNA-Met c[1115621,1115696] 36 (cat) [09:18:40] 18 tRNA-Ser [1164330,1164417] 35 (tga) [09:18:40] 19 tRNA-Pro [1270496,1270569] 35 (ggg) [09:18:40] 20 tRNA-Lys [1390974,1391045] 33 (ttt) [09:18:40] 21 tRNA-Pro [1392403,1392477] 35 (tgg) [09:18:40] 22 tRNA-Ala c[1432801,1432876] 35 (ggc) [09:18:40] 23 tRNA-Leu c[1482119,1482203] 35 (cag) [09:18:40] 24 tRNA-Leu [1483715,1483797] 35 (caa) [09:18:40] 25 tRNA-His [1489927,1490000] 34 (gtg) [09:18:40] 26 tRNA-Ser c[1508809,1508895] 37 (cga) [09:18:40] 27 tRNA-Trp [1655548,1655624] 35 (cca) [09:18:40] 28 tRNA-Asp [1656112,1656187] 36 (gtc) [09:18:40] 29 tRNA-Val [1670904,1670975] 33 (cac) [09:18:40] 30 tRNA-Arg [1726445,1726520] 36 (tct) [09:18:40] 31 tRNA-Tyr [1758329,1758412] 35 (gta) [09:18:40] 32 tRNA-Thr [1758421,1758492] 33 (ggt) [09:18:40] 33 tRNA-Ala c[1776931,1777004] 34 (tgc) [09:18:40] 34 tRNA-Ile c[1777013,1777088] 36 (gat) [09:18:40] 35 tRNA-Thr [1786870,1786941] 33 (tgt) [09:18:40] 36 tRNA-Phe [1801122,1801194] 34 (gaa) [09:18:40] 37 tRNA-Cys c[1835071,1835141] 33 (gca) [09:18:40] 38 tRNA-Arg c[1850951,1851026] 36 (ccg) [09:18:40] 39 tRNA-Gln c[1865880,1865951] 33 (ttg) [09:18:40] 40 tRNA-Ser [1887732,1887822] 36 (gct) [09:18:40] 41 tRNA-Pro c[1917906,1917980] 35 (cgg) [09:18:40] 42 tRNA-Ala [1956937,1957010] 34 (cgc) [09:18:40] 43 tRNA-Leu c[1965703,1965786] 36 (tag) [09:18:40] 44 tRNA-Arg c[1998797,1998871] 35 (acg) [09:18:40] 45 tRNA-Val c[2134910,2134981] 33 (tac) [09:18:40] Found 45 tRNAs [09:18:40] Predicting Ribosomal RNAs [09:18:40] You need either Barrnap or RNAmmer installed to predict rRNAs! [09:18:40] Skipping ncRNA search, enable with --rfam if desired. [09:18:40] Total of 44 tRNA + rRNA features [09:18:40] Searching for CRISPR repeats [09:18:41] Found 0 CRISPRs [09:18:41] Predicting coding sequences [09:18:41] Contigs total 2234828 bp, so using single mode [09:18:41] Running: prodigal -i prokka\/Aaam\/Aaam\.fna -c -m -g 11 -p single -f sco -q [09:18:53] Excluding CDS which overlaps existing RNA (tRNA) at gnl|Prokka|Aaam.g_1:435351..436742 on + strand [09:18:54] Excluding CDS which overlaps existing RNA (tRNA) at gnl|Prokka|Aaam.g_1:1047185..1047640 on - strand [09:18:54] Excluding CDS which overlaps existing RNA (tRNA) at gnl|Prokka|Aaam.g_1:1164294..1164557 on + strand [09:18:54] Excluding CDS which overlaps existing RNA (tRNA) at gnl|Prokka|Aaam.g_1:1432762..1432941 on + strand [09:18:54] Excluding CDS which overlaps existing RNA (tRNA) at gnl|Prokka|Aaam.g_1:1483721..1484989 on + strand [09:18:54] Excluding CDS which overlaps existing RNA (tRNA) at gnl|Prokka|Aaam.g_1:1508696..1508926 on + strand [09:18:54] Excluding CDS which overlaps existing RNA (tRNA) at gnl|Prokka|Aaam.g_1:1655592..1655846 on + strand [09:18:55] Excluding CDS which overlaps existing RNA (tRNA) at gnl|Prokka|Aaam.g_1:1834977..1836410 on + strand [09:18:55] Excluding CDS which overlaps existing RNA (tRNA) at gnl|Prokka|Aaam.g_1:1851020..1851217 on + strand [09:18:55] Excluding CDS which overlaps existing RNA (tRNA) at gnl|Prokka|Aaam.g_1:1865119..1865952 on - strand [09:18:55] Excluding CDS which overlaps existing RNA (tRNA) at gnl|Prokka|Aaam.g_1:1964618..1965742 on - strand [09:18:55] Found 2449 CDS [09:18:55] Connecting features back to sequences [09:18:55] Not using genus-specific database. Try --usegenus to enable it. [09:18:55] Annotating CDS, please be patient. [09:18:55] Will use 1 CPUs for similarity searching. [09:18:56] There are still 2449 unannotated CDS left (started with 2449) [09:18:56] Will use blast to search against /usr/local/bioinfo/src/PROKKA/prokka-1.12/bin/../db/kingdom/Bacteria/sprot with 1 CPUs [09:18:56] Running: cat prokka\/Aaam\/sprot\.faa | parallel --gnu --plain -j 1 --block 343563 --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\/Aaam\/sprot\.blast 2> /dev/null [09:21:48] Modify product: N utilization substance protein B homolog => N utilization substance protein B [09:21:48] Modify product: Probable peptidyl-prolyl cis-trans isomerase => putative peptidyl-prolyl cis-trans isomerase [09:21:48] Modify product: Uncharacterized membrane protein Rv0364 => putative membrane protein [09:21:48] Modify product: Probable ABC transporter-binding protein DR_1438 => putative ABC transporter-binding protein [09:21:48] Modify product: Uncharacterized hydrolase YxeP => putative hydrolase YxeP [09:21:48] Modify product: Cyclic nucleotide-gated potassium channel mll3241 => Cyclic nucleotide-gated potassium channel [09:21:48] Modify product: Uncharacterized FAD-linked oxidoreductase Rv2280 => putative FAD-linked oxidoreductase [09:21:48] Modify product: Uncharacterized glycosyltransferase sll0501 => putative glycosyltransferase [09:21:48] Modify product: Probable ribonucleotide transport ATP-binding protein mkl => putative ribonucleotide transport ATP-binding protein mkl [09:21:49] Modify product: Epimerase family protein Rv2216 => Epimerase family protein [09:21:49] Modify product: Vitamin K epoxide reductase homolog => Vitamin K epoxide reductase [09:21:49] Modify product: Uncharacterized ABC transporter ATP-binding protein YheS => putative ABC transporter ATP-binding protein YheS [09:21:49] Modify product: Uncharacterized transporter Rv2685 => putative transporter [09:21:49] Modify product: Probable ATP-dependent transporter SufC => putative ATP-dependent transporter SufC [09:21:49] Modify product: Probable cysteine desulfurase => putative cysteine desulfurase [09:21:49] Modify product: Probable peptidoglycan glycosyltransferase FtsW => putative peptidoglycan glycosyltransferase FtsW [09:21:49] Modify product: Probable 30S ribosomal protein PSRP-3 => putative 30S ribosomal protein PSRP-3 [09:21:49] Modify product: Probable transcriptional regulatory protein aq_1575 => putative transcriptional regulatory protein [09:21:49] Modify product: Putative outer membrane protein assembly factor TP_0326 => Putative outer membrane protein assembly factor [09:21:49] Modify product: Probable phospholipid ABC transporter permease protein MlaE => putative phospholipid ABC transporter permease protein MlaE [09:21:49] Modify product: Glycogen operon protein GlgX homolog => Glycogen operon protein GlgX [09:21:49] Modify product: Probable dual-specificity RNA methyltransferase RlmN => putative dual-specificity RNA methyltransferase RlmN [09:21:49] Modify product: Probable trans-aconitate 2-methyltransferase => putative trans-aconitate 2-methyltransferase [09:21:49] Modify product: Probable helicase HelY => putative helicase HelY [09:21:49] Modify product: Probable tRNA-dihydrouridine synthase => putative tRNA-dihydrouridine synthase [09:21:49] Modify product: Uncharacterized MFS-type transporter Rv0037c => putative MFS-type transporter [09:21:49] Modify product: Uncharacterized tRNA/rRNA methyltransferase HI_0380 => putative tRNA/rRNA methyltransferase [09:21:49] Modify product: Uncharacterized oxidoreductase MSMEG_1603/MSMEI_1564 => putative oxidoreductase/MSMEI_1564 [09:21:49] Modify product: 1,4-alpha-glucan branching enzyme TTHA1902 => 1,4-alpha-glucan branching enzyme [09:21:49] Modify product: Bifunctional protein FolD => Bifunctional protein FolD protein [09:21:49] Modify product: Probable murein peptide carboxypeptidase => putative murein peptide carboxypeptidase [09:21:49] Modify product: Probable glutamine ABC transporter permease protein GlnM => putative glutamine ABC transporter permease protein GlnM [09:21:49] Modify product: Uncharacterized ABC transporter ATP-binding protein TM_0288 => putative ABC transporter ATP-binding protein [09:21:49] Modify product: Uncharacterized glycosyltransferase Rv0539 => putative glycosyltransferase [09:21:49] Modify product: Uncharacterized ABC transporter ATP-binding protein YlmA => putative ABC transporter ATP-binding protein YlmA [09:21:49] Modify product: Probable ABC transporter-binding protein DR_1438 => putative ABC transporter-binding protein [09:21:49] Modify product: Phosphorylated carbohydrates phosphatase TM_1254 => Phosphorylated carbohydrates phosphatase [09:21:49] Modify product: Probable CtpA-like serine protease => putative CtpA-like serine protease [09:21:49] Modify product: Uncharacterized oxidoreductase Rv0484c => putative oxidoreductase [09:21:50] Modify product: GTP-binding protein TypA/BipA homolog => GTP-binding protein TypA/BipA [09:21:50] Modify product: Uncharacterized protease YdcP => putative protease YdcP [09:21:50] Modify product: Uncharacterized glycosyltransferase EpsJ => putative glycosyltransferase EpsJ [09:21:50] Modify product: Uncharacterized ABC transporter ATP-binding protein Rv0986 => putative ABC transporter ATP-binding protein [09:21:50] Modify product: Uncharacterized zinc protease Rv2782c => putative zinc protease [09:21:50] Modify product: Uncharacterized zinc protease Rv2782c => putative zinc protease [09:21:50] Modify product: Probable multidrug resistance ABC transporter ATP-binding/permease protein YheI => putative multidrug resistance ABC transporter ATP-binding/permease protein YheI [09:21:50] Modify product: Phosphorylated carbohydrates phosphatase TM_1254 => Phosphorylated carbohydrates phosphatase [09:21:50] Modify product: Probable 2-phosphosulfolactate phosphatase => putative 2-phosphosulfolactate phosphatase [09:21:50] Modify product: Probable L,D-transpeptidase YnhG => putative L,D-transpeptidase YnhG [09:21:50] Modify product: Uncharacterized oxidoreductase SA2266 => putative oxidoreductase [09:21:50] Modify product: Probable protein kinase UbiB => putative protein kinase UbiB [09:21:50] Modify product: Putative multidrug export ATP-binding/permease protein SA1683 => Putative multidrug export ATP-binding/permease protein [09:21:50] Modify product: Uncharacterized FAD-linked oxidoreductase Rv2280 => putative FAD-linked oxidoreductase [09:21:50] Modify product: Oxygen-independent coproporphyrinogen-III oxidase-like protein sll1917 => Oxygen-independent coproporphyrinogen-III oxidase-like protein [09:21:50] Modify product: Uncharacterized PIN and TRAM-domain containing protein YacL => putative PIN and TRAM-domain containing protein YacL [09:21:50] Modify product: Uncharacterized MscS family protein YkuT => putative MscS family protein YkuT [09:21:50] Modify product: Maf-like protein Rv3282 => Maf-like protein [09:21:50] Modify product: Laccase domain protein Rv2149c => Laccase domain protein [09:21:50] Modify product: Uncharacterized sugar kinase YdjH => putative sugar kinase YdjH [09:21:50] Modify product: Thylakoid-associated single-stranded DNA-binding protein slr1034 => Thylakoid-associated single-stranded DNA-binding protein [09:21:50] Modify product: Uncharacterized FAD-linked oxidoreductase Rv2280 => putative FAD-linked oxidoreductase [09:21:50] Modify product: Probable murein peptide carboxypeptidase => putative murein peptide carboxypeptidase [09:21:50] Modify product: Probable doxorubicin resistance ABC transporter permease protein DrrC => putative doxorubicin resistance ABC transporter permease protein DrrC [09:21:50] Modify product: Probable cytochrome c oxidase subunit 1 => putative cytochrome c oxidase subunit 1 [09:21:50] Modify product: Uncharacterized ABC transporter ATP-binding protein YknY => putative ABC transporter ATP-binding protein YknY [09:21:50] Modify product: Phage shock protein A homolog => Phage shock protein A [09:21:50] Modify product: Uncharacterized inner membrane transporter YedA => putative inner membrane transporter YedA [09:21:50] Modify product: Vitamin K epoxide reductase homolog => Vitamin K epoxide reductase [09:21:50] Modify product: Probable CtpA-like serine protease => putative CtpA-like serine protease [09:21:50] Modify product: Putative esterase aq_1494 => Putative esterase [09:21:50] Modify product: Probable phycoerythrobilin lyase CpeT => putative phycoerythrobilin lyase CpeT [09:21:50] Modify product: Uncharacterized phycocyanin operon protein Z => putative phycocyanin operon protein Z [09:21:50] Modify product: Uncharacterized phycocyanin operon protein Z => putative phycocyanin operon protein Z [09:21:50] Modify product: Uncharacterized phycocyanin operon protein Z => putative phycocyanin operon protein Z [09:21:50] Modify product: Uncharacterized oxidoreductase Rv2298 => putative oxidoreductase [09:21:50] Modify product: Probable adenylyltransferase/sulfurtransferase MoeZ => putative adenylyltransferase/sulfurtransferase MoeZ [09:21:50] Modify product: Probable cobalt-factor III C(17)-methyltransferase => putative cobalt-factor III C(17)-methyltransferase [09:21:50] Modify product: PKHD-type hydroxylase Sbal_3634 => PKHD-type hydroxylase [09:21:50] Modify product: Probable bifunctional SAT/APS kinase => putative bifunctional SAT/APS kinase [09:21:50] Modify product: NADH dehydrogenase-like protein SA0802 => NADH dehydrogenase-like protein [09:21:50] Modify product: Probable undecaprenyl-phosphate N-acetylglucosaminyl 1-phosphate transferase => putative undecaprenyl-phosphate N-acetylglucosaminyl 1-phosphate transferase [09:21:50] Modify product: Probable adenylyl-sulfate kinase => putative adenylyl-sulfate kinase [09:21:50] Modify product: Probable glutaredoxin ssr2061 => putative glutaredoxin [09:21:50] Modify product: Probable nicotinate-nucleotide pyrophosphorylase [carboxylating] => putative nicotinate-nucleotide pyrophosphorylase [carboxylating] [09:21:51] Modify product: Probable protein kinase UbiB => putative protein kinase UbiB [09:21:51] Modify product: Probable nitrate transporter NarT => putative nitrate transporter NarT [09:21:51] Modify product: Probable formate transporter 1 => putative formate transporter 1 [09:21:51] Modify product: Probable protein kinase UbiB => putative protein kinase UbiB [09:21:51] Cleaned 88 /product names [09:21:51] Deleting unwanted file: prokka/Aaam/sprot.faa [09:21:51] Deleting unwanted file: prokka/Aaam/sprot.blast [09:21:51] There are still 1213 unannotated CDS left (started with 2449) [09:21:51] Will use hmmer3 to search against /usr/local/bioinfo/src/PROKKA/prokka-1.12/bin/../db/hmm/HAMAP.hmm with 1 CPUs [09:21:51] Running: cat prokka\/Aaam\/HAMAP\.hmm\.faa | parallel --gnu --plain -j 1 --block 119869 --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\/Aaam\/HAMAP\.hmm\.hmmer3 2> /dev/null [09:23:39] Deleting unwanted file: prokka/Aaam/HAMAP.hmm.faa [09:23:39] Deleting unwanted file: prokka/Aaam/HAMAP.hmm.hmmer3 [09:23:39] Labelling remaining 1141 proteins as 'hypothetical protein' [09:23:39] Possible /pseudo 'Putative fluoride ion transporter CrcB' at gnl|Prokka|Aaam.g_1 position 145225 [09:23:39] Possible /pseudo 'S-layer protein SlpA' at gnl|Prokka|Aaam.g_1 position 337693 [09:23:39] Possible /pseudo 'DNA-directed RNA polymerase subunit beta'' at gnl|Prokka|Aaam.g_1 position 615979 [09:23:39] Possible /pseudo 'putative zinc protease' at gnl|Prokka|Aaam.g_1 position 1219112 [09:23:39] Possible /pseudo 'ATP-dependent Clp protease proteolytic subunit' at gnl|Prokka|Aaam.g_1 position 1499179 [09:23:39] Possible /pseudo 'putative phycocyanin operon protein Z' at gnl|Prokka|Aaam.g_1 position 1818038 [09:23:39] Found 1092 unique /gene codes. [09:23:39] Fixed 2 duplicate /gene - pipB2_1 pipB2_2 [09:23:39] Fixed 2 duplicate /gene - ftsH2_1 ftsH2_2 [09:23:39] Fixed 2 duplicate /gene - mnmC_1 mnmC_2 [09:23:39] Fixed 2 duplicate /gene - ykuD_1 ykuD_2 [09:23:39] Fixed 2 duplicate /gene - pds_1 pds_2 [09:23:39] Fixed 2 duplicate /gene - psbD1_1 psbD1_2 [09:23:39] Fixed 2 duplicate /gene - mshA_1 mshA_2 [09:23:39] Fixed 2 duplicate /gene - mgl_1 mgl_2 [09:23:39] Fixed 2 duplicate /gene - cobD_1 cobD_2 [09:23:39] Fixed 2 duplicate /gene - rluD_1 rluD_2 [09:23:39] Fixed 2 duplicate /gene - petJ_1 petJ_2 [09:23:39] Fixed 2 duplicate /gene - rpsA_1 rpsA_2 [09:23:39] Fixed 2 duplicate /gene - galE_1 galE_2 [09:23:39] Fixed 2 duplicate /gene - cpcS_1 cpcS_2 [09:23:39] Fixed 2 duplicate /gene - dnaK2_1 dnaK2_2 [09:23:39] Fixed 4 duplicate /gene - clpP_1 clpP_2 clpP_3 clpP_4 [09:23:39] Fixed 2 duplicate /gene - ynaI_1 ynaI_2 [09:23:39] Fixed 2 duplicate /gene - trmH_1 trmH_2 [09:23:39] Fixed 2 duplicate /gene - nuoL_1 nuoL_2 [09:23:39] Fixed 2 duplicate /gene - msbA_1 msbA_2 [09:23:39] Fixed 2 duplicate /gene - gyrA_1 gyrA_2 [09:23:39] Fixed 2 duplicate /gene - btuR_1 btuR_2 [09:23:39] Fixed 3 duplicate /gene - mprA_1 mprA_2 mprA_3 [09:23:39] Fixed 2 duplicate /gene - mnmE_1 mnmE_2 [09:23:39] Fixed 2 duplicate /gene - crtI_1 crtI_2 [09:23:39] Fixed 2 duplicate /gene - bicA_1 bicA_2 [09:23:39] Fixed 2 duplicate /gene - bchI_1 bchI_2 [09:23:39] Fixed 3 duplicate /gene - lytB_1 lytB_2 lytB_3 [09:23:39] Fixed 2 duplicate /gene - plsC_1 plsC_2 [09:23:39] Fixed 2 duplicate /gene - ubiE_1 ubiE_2 [09:23:39] Fixed 2 duplicate /gene - perR_1 perR_2 [09:23:39] Fixed 2 duplicate /gene - arlS_1 arlS_2 [09:23:39] Fixed 2 duplicate /gene - msrB_1 msrB_2 [09:23:39] Fixed 2 duplicate /gene - pyrB_1 pyrB_2 [09:23:39] Fixed 3 duplicate /gene - sigA2_1 sigA2_2 sigA2_3 [09:23:39] Fixed 2 duplicate /gene - pseB_1 pseB_2 [09:23:39] Fixed 2 duplicate /gene - cca_1 cca_2 [09:23:39] Fixed 3 duplicate /gene - trxA_1 trxA_2 trxA_3 [09:23:39] Fixed 2 duplicate /gene - ppa_1 ppa_2 [09:23:39] Fixed 2 duplicate /gene - pcyA_1 pcyA_2 [09:23:39] Fixed 2 duplicate /gene - lexA_1 lexA_2 [09:23:39] Fixed 3 duplicate /gene - cpcG_1 cpcG_2 cpcG_3 [09:23:39] Fixed 2 duplicate /gene - yciC_1 yciC_2 [09:23:39] Fixed 2 duplicate /gene - hhoA_1 hhoA_2 [09:23:39] Fixed 3 duplicate /gene - bcp_1 bcp_2 bcp_3 [09:23:39] Fixed 2 duplicate /gene - sigA_1 sigA_2 [09:23:39] Fixed 2 duplicate /gene - sdh_1 sdh_2 [09:23:39] Fixed 2 duplicate /gene - speA_1 speA_2 [09:23:39] Fixed 2 duplicate /gene - crcB_1 crcB_2 [09:23:39] Fixed 2 duplicate /gene - ppiB_1 ppiB_2 [09:23:39] Fixed 2 duplicate /gene - petF_1 petF_2 [09:23:39] Fixed 4 duplicate /gene - bshA_1 bshA_2 bshA_3 bshA_4 [09:23:39] Fixed 2 duplicate /gene - cobN_1 cobN_2 [09:23:39] Fixed 2 duplicate /gene - znuC_1 znuC_2 [09:23:39] Fixed 4 duplicate /gene - slpA_1 slpA_2 slpA_3 slpA_4 [09:23:39] Fixed 2 duplicate /gene - gph_1 gph_2 [09:23:39] Fixed 4 duplicate /gene - mpeC_1 mpeC_2 mpeC_3 mpeC_4 [09:23:39] Fixed 2 duplicate /gene - trxB_1 trxB_2 [09:23:39] Fixed 2 duplicate /gene - recD_1 recD_2 [09:23:39] Fixed 2 duplicate /gene - smc_1 smc_2 [09:23:39] Fixed 2 duplicate /gene - psaE_1 psaE_2 [09:23:39] Fixed 3 duplicate /gene - ubiB_1 ubiB_2 ubiB_3 [09:23:39] Fixed 2 duplicate /gene - rpoC_1 rpoC_2 [09:23:39] Fixed 2 duplicate /gene - mgtA_1 mgtA_2 [09:23:39] Fixed 2 duplicate /gene - lptD_1 lptD_2 [09:23:39] Fixed 2 duplicate /gene - clpS_1 clpS_2 [09:23:39] Fixed 2 duplicate /gene - ugpC_1 ugpC_2 [09:23:39] Fixed 2 duplicate /gene - prmC_1 prmC_2 [09:23:39] Fixed 2 duplicate /gene - iscS_1 iscS_2 [09:23:39] Fixed 2 duplicate /gene - corC_1 corC_2 [09:23:39] Fixed 2 duplicate /gene - kmo_1 kmo_2 [09:23:39] Fixed 2 duplicate /gene - legI_1 legI_2 [09:23:39] Fixed 2 duplicate /gene - sir_1 sir_2 [09:23:39] Fixed 2 duplicate /gene - mepM_1 mepM_2 [09:23:39] Fixed 3 duplicate /gene - psbA2_1 psbA2_2 psbA2_3 [09:23:39] Fixed 2 duplicate /gene - der_1 der_2 [09:23:39] Fixed 3 duplicate /gene - ndhD1_1 ndhD1_2 ndhD1_3 [09:23:39] Fixed 2 duplicate /gene - cbpA_1 cbpA_2 [09:23:39] Fixed 2 duplicate /gene - lip1_1 lip1_2 [09:23:39] Fixed 2 duplicate /gene - hpf_1 hpf_2 [09:23:39] Fixed 2 duplicate /gene - csgA_1 csgA_2 [09:23:39] Fixed 4 duplicate /gene - bepA_1 bepA_2 bepA_3 bepA_4 [09:23:39] Fixed 2 duplicate /gene - mntB_1 mntB_2 [09:23:39] Fixed 2 duplicate /gene - rnr_1 rnr_2 [09:23:39] Fixed 2 duplicate /gene - ubiG_1 ubiG_2 [09:23:39] Fixed 2 duplicate /gene - lapB_1 lapB_2 [09:23:39] Fixed 2 duplicate /gene - ccmK_1 ccmK_2 [09:23:39] Fixed 2 duplicate /gene - dnaX_1 dnaX_2 [09:23:39] Fixed 2 duplicate /gene - atpG_1 atpG_2 [09:23:39] Fixed 2 duplicate /gene - purE_1 purE_2 [09:23:39] Fixed 4 duplicate /gene - dnaJ_1 dnaJ_2 dnaJ_3 dnaJ_4 [09:23:39] Fixed 2 duplicate /gene - rlpA_1 rlpA_2 [09:23:39] Fixed 2 duplicate /gene - ykfA_1 ykfA_2 [09:23:39] Fixed 2 duplicate /gene - pyrC_1 pyrC_2 [09:23:39] Fixed 2 duplicate /gene - phoP_1 phoP_2 [09:23:39] Fixed 95 colliding /gene names. [09:23:39] Adding /locus_tag identifiers [09:23:40] Assigned 2494 locus_tags to CDS and RNA features. [09:23:40] Writing outputs to prokka/Aaam/ [09:23:43] Generating annotation statistics file [09:23:43] Generating Genbank and Sequin files [09:23:43] 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\/Aaam\/Aaam\.err -i prokka\/Aaam\/Aaam\.fsa 2> /dev/null [09:23:50] Deleting unwanted file: prokka/Aaam/errorsummary.val [09:23:50] Deleting unwanted file: prokka/Aaam/Aaam.dr [09:23:50] Deleting unwanted file: prokka/Aaam/Aaam.fixedproducts [09:23:50] Deleting unwanted file: prokka/Aaam/Aaam.ecn [09:23:50] Deleting unwanted file: prokka/Aaam/Aaam.val [09:23:50] Repairing broken .GBK output that tbl2asn produces... [09:23:50] Running: sed 's/COORDINATES: profile/COORDINATES:profile/' < prokka\/Aaam\/Aaam\.gbf > prokka\/Aaam\/Aaam\.gbk [09:23:50] Deleting unwanted file: prokka/Aaam/Aaam.gbf [09:23:50] Output files: [09:23:50] prokka/Aaam/Aaam.sqn [09:23:50] prokka/Aaam/Aaam.fna [09:23:50] prokka/Aaam/Aaam.tsv [09:23:50] prokka/Aaam/Aaam.gff [09:23:50] prokka/Aaam/Aaam.gbk [09:23:50] prokka/Aaam/Aaam.faa [09:23:50] prokka/Aaam/Aaam.txt [09:23:50] prokka/Aaam/Aaam.fsa [09:23:50] prokka/Aaam/Aaam.err [09:23:50] prokka/Aaam/Aaam.log [09:23:50] prokka/Aaam/Aaam.tbl [09:23:50] prokka/Aaam/Aaam.ffn [09:23:50] Annotation finished successfully. [09:23:50] Walltime used: 5.23 minutes [09:23:50] If you use this result please cite the Prokka paper: [09:23:50] Seemann T (2014) Prokka: rapid prokaryotic genome annotation. Bioinformatics. 30(14):2068-9. [09:23:50] Type 'prokka --citation' for more details. [09:23:50] Thank you, come again.