[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/Aaao [09:18:37] Running: mkdir -p prokka\/Aaao [09:18:37] Using filename prefix: Aaao.XXX [09:18:37] Setting HMMER_NCPU=1 [09:18:37] Writing log to: prokka/Aaao/Aaao.log [09:18:37] Command: /usr/local/bioinfo/src/PROKKA/prokka-1.12/bin/prokka /home/formation/public_html/M2_Phylogenomique/data/Synechococcus/DNA/Aaao.fas --outdir prokka/Aaao --compliant --addgenes --prefix Aaao --locustag Aaao.g --genus Synechococcus --species Synechococcus sp. --strain CC9311 --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/Aaao.fas [09:18:39] Wrote 1 contigs totalling 2606748 bp. [09:18:39] Predicting tRNAs and tmRNAs [09:18:39] Running: aragorn -l -gc11 -w prokka\/Aaao\/Aaao\.fna [09:18:40] 1 tRNA-Gly c[45490,45561] 33 (ccc) [09:18:40] 2 tRNA-Gly [87169,87240] 33 (gcc) [09:18:40] 3 tRNA-Arg [208369,208442] 35 (cct) [09:18:40] 4 tRNA-Met [288447,288519] 34 (cat) [09:18:40] 5 tRNA-Arg [308668,308741] 35 (acg) [09:18:40] 6 tRNA-Leu [344292,344375] 36 (tag) [09:18:40] 7 tRNA-Ala c[354855,354927] 34 (cgc) [09:18:40] 8 tRNA-Pro [398746,398820] 35 (cgg) [09:18:40] 9 tRNA-Ser c[417314,417404] 36 (gct) [09:18:40] 10 tRNA-Gln [439501,439572] 33 (ttg) [09:18:40] 11 tRNA-Arg [454675,454748] 35 (ccg) [09:18:40] 12 tRNA-Cys [470642,470712] 33 (gca) [09:18:40] 13 tRNA-Phe c[508475,508549] 35 (gaa) [09:18:40] 14 tRNA-Thr c[521704,521775] 33 (tgt) [09:18:40] 15 tRNA-Ile [531623,531698] 36 (gat) [09:18:40] 16 tRNA-Ala [531707,531780] 34 (tgc) [09:18:40] 17 tRNA-Thr c[554171,554242] 33 (ggt) [09:18:40] 18 tRNA-Tyr c[554253,554334] 35 (gta) [09:18:40] 19 tRNA-Ser [673777,673865] 38 (cga) [09:18:40] 20 tRNA-His c[691678,691751] 34 (gtg) [09:18:40] 21 tRNA-Leu c[698137,698218] 35 (caa) [09:18:40] 22 tRNA-Leu [699751,699832] 35 (cag) [09:18:40] 23 tRNA-Ala [768453,768527] 35 (ggc) [09:18:40] 24 tRNA-Glu c[907493,907566] 35 (ttc) [09:18:40] 25 tRNA-Pro c[1026731,1026804] 35 (tgg) [09:18:40] 26 tRNA-Lys c[1028873,1028944] 33 (ttt) [09:18:40] 27 tRNA-Met c[1078857,1078933] 35 (cat) [09:18:40] 28 tRNA-Ser c[1143399,1143485] 35 (tga) [09:18:40] 29 tRNA-Met c[1203942,1204016] 35 (cat) [09:18:40] 30 tRNA-Ser c[1274382,1274470] 36 (gga) [09:18:40] 31 tRNA-Pro [1506397,1506470] 35 (ggg) [09:18:40] 32 tRNA-Leu [1702995,1703080] 35 (taa) [09:18:40] 33 tRNA-Arg c[1846184,1846259] 36 (tct) [09:18:40] 34 tRNA-Val c[1900882,1900953] 33 (cac) [09:18:40] 35 tRNA-Asp c[1915632,1915707] 36 (gtc) [09:18:40] 36 tRNA-Trp c[1916233,1916309] 35 (cca) [09:18:40] 37 tRNA-Gly c[1930338,1930408] 33 (tcc) [09:18:40] 38 tRNA-Val [1984730,1984802] 33 (gac) [09:18:40] 39 tRNA-Thr [2087350,2087422] 34 (cgt) [09:18:40] 40 tmRNA* c[2143539,2143853] 174,224 ANNIVRFSRQAAPVAA* [09:18:40] 41 tRNA-Leu c[2154046,2154127] 35 (aag) [09:18:40] 42 tRNA-Ala c[2223177,2223250] 34 (tgc) [09:18:40] 43 tRNA-Ile c[2223259,2223334] 36 (gat) [09:18:40] 44 tRNA-Asn [2269768,2269839] 33 (gtt) [09:18:40] 45 tRNA-Val c[2498375,2498446] 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 2606748 bp, so using single mode [09:18:41] Running: prodigal -i prokka\/Aaao\/Aaao\.fna -c -m -g 11 -p single -f sco -q [09:18:54] Excluding CDS which overlaps existing RNA (tRNA) at gnl|Prokka|Aaao.g_1:469358..470764 on - strand [09:18:54] Excluding CDS which overlaps existing RNA (tRNA) at gnl|Prokka|Aaao.g_1:521600..521713 on + strand [09:18:54] Excluding CDS which overlaps existing RNA (tRNA) at gnl|Prokka|Aaao.g_1:521766..522035 on - strand [09:18:54] Excluding CDS which overlaps existing RNA (tRNA) at gnl|Prokka|Aaao.g_1:691706..692221 on + strand [09:18:54] Excluding CDS which overlaps existing RNA (tRNA) at gnl|Prokka|Aaao.g_1:699715..699870 on + strand [09:18:54] Excluding CDS which overlaps existing RNA (tRNA) at gnl|Prokka|Aaao.g_1:768259..768546 on - strand [09:18:55] Excluding CDS which overlaps existing RNA (tRNA) at gnl|Prokka|Aaao.g_1:1143373..1143660 on + strand [09:18:56] Excluding CDS which overlaps existing RNA (tRNA) at gnl|Prokka|Aaao.g_1:1916008..1916265 on - strand [09:18:56] Excluding CDS which overlaps existing RNA (tRNA) at gnl|Prokka|Aaao.g_1:2087422..2087535 on - strand [09:18:56] Excluding CDS which overlaps existing RNA (tRNA) at gnl|Prokka|Aaao.g_1:2269801..2270037 on - strand [09:18:56] Found 2869 CDS [09:18:56] Connecting features back to sequences [09:18:56] Not using genus-specific database. Try --usegenus to enable it. [09:18:56] Annotating CDS, please be patient. [09:18:56] Will use 1 CPUs for similarity searching. [09:18:58] There are still 2869 unannotated CDS left (started with 2869) [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\/Aaao\/sprot\.faa | parallel --gnu --plain -j 1 --block 388362 --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\/Aaao\/sprot\.blast 2> /dev/null [09:22:11] Modify product: N utilization substance protein B homolog => N utilization substance protein B [09:22:11] Modify product: Probable type II secretion system protein HxcR => putative type II secretion system protein HxcR [09:22:11] Modify product: Uncharacterized sugar kinase YdjH => putative sugar kinase YdjH [09:22:11] Modify product: Uncharacterized membrane protein Rv0364 => putative membrane protein [09:22:11] Modify product: Probable ABC transporter-binding protein DR_1438 => putative ABC transporter-binding protein [09:22:11] Modify product: Uncharacterized hydrolase YxeP => putative hydrolase YxeP [09:22:11] Modify product: Probable lipid II flippase MurJ => putative lipid II flippase MurJ [09:22:11] Modify product: Cyclic nucleotide-gated potassium channel mll3241 => Cyclic nucleotide-gated potassium channel [09:22:11] Modify product: Uncharacterized FAD-linked oxidoreductase Rv2280 => putative FAD-linked oxidoreductase [09:22:11] Modify product: Probable phospholipid import ATP-binding protein MlaF => putative phospholipid import ATP-binding protein MlaF [09:22:11] Modify product: Probable phospholipid ABC transporter-binding protein MlaD => putative phospholipid ABC transporter-binding protein MlaD [09:22:11] Modify product: Probable lipid II flippase MurJ => putative lipid II flippase MurJ [09:22:11] Modify product: Probable undecaprenyl-phosphate N-acetylglucosaminyl 1-phosphate transferase => putative undecaprenyl-phosphate N-acetylglucosaminyl 1-phosphate transferase [09:22:11] Modify product: Probable bifunctional SAT/APS kinase => putative bifunctional SAT/APS kinase [09:22:11] Modify product: Probable cobalt-factor III C(17)-methyltransferase => putative cobalt-factor III C(17)-methyltransferase [09:22:11] Modify product: Probable endopeptidase p60 => putative endopeptidase p60 [09:22:11] Modify product: Probable adenylyltransferase/sulfurtransferase MoeZ => putative adenylyltransferase/sulfurtransferase MoeZ [09:22:11] Modify product: Cyclic nucleotide-gated potassium channel mll3241 => Cyclic nucleotide-gated potassium channel [09:22:11] Modify product: Uncharacterized oxidoreductase Rv2298 => putative oxidoreductase [09:22:11] Modify product: Uncharacterized phycocyanin operon protein Z => putative phycocyanin operon protein Z [09:22:11] Modify product: Uncharacterized phycocyanin operon protein Z => putative phycocyanin operon protein Z [09:22:11] Modify product: Uncharacterized phycocyanin operon protein Z => putative phycocyanin operon protein Z [09:22:11] Modify product: Probable phycoerythrobilin lyase CpeT => putative phycoerythrobilin lyase CpeT [09:22:11] Modify product: Putative esterase aq_1494 => Putative esterase [09:22:11] Modify product: Probable CtpA-like serine protease => putative CtpA-like serine protease [09:22:12] Modify product: Probable tRNA-dihydrouridine synthase => putative tRNA-dihydrouridine synthase [09:22:12] Modify product: Uncharacterized MFS-type transporter Rv0037c => putative MFS-type transporter [09:22:12] Modify product: Leu/Ile/Val-binding protein homolog 3 => Leu/Ile/Val-binding protein [09:22:12] Modify product: Putative peroxiredoxin sll1621 => Putative peroxiredoxin [09:22:12] Modify product: Uncharacterized PIN and TRAM-domain containing protein YacL => putative PIN and TRAM-domain containing protein YacL [09:22:12] Modify product: Oxygen-independent coproporphyrinogen-III oxidase-like protein sll1917 => Oxygen-independent coproporphyrinogen-III oxidase-like protein [09:22:12] Modify product: Uncharacterized FAD-linked oxidoreductase Rv2280 => putative FAD-linked oxidoreductase [09:22:12] Modify product: Probable protein kinase UbiB => putative protein kinase UbiB [09:22:12] Modify product: Aldo/keto reductase slr0942 => Aldo/keto reductase [09:22:12] Modify product: Maf-like protein Rv3282 => Maf-like protein [09:22:12] Modify product: Uncharacterized oxidoreductase MSMEG_1603/MSMEI_1564 => putative oxidoreductase/MSMEI_1564 [09:22:12] Modify product: 1,4-alpha-glucan branching enzyme TTHA1902 => 1,4-alpha-glucan branching enzyme [09:22:12] Modify product: Bifunctional protein FolD => Bifunctional protein FolD protein [09:22:12] Modify product: Probable protein kinase UbiB => putative protein kinase UbiB [09:22:12] Modify product: Putative multidrug export ATP-binding/permease protein SA1683 => Putative multidrug export ATP-binding/permease protein [09:22:12] Modify product: Probable sensor histidine kinase TcrY => putative sensor histidine kinase TcrY [09:22:12] Modify product: Probable glutamine ABC transporter permease protein GlnM => putative glutamine ABC transporter permease protein GlnM [09:22:12] Modify product: Putative multidrug export ATP-binding/permease protein SA1683 => Putative multidrug export ATP-binding/permease protein [09:22:12] Modify product: Uncharacterized oxidoreductase SA2266 => putative oxidoreductase [09:22:12] Modify product: Uncharacterized ABC transporter ATP-binding protein Rv0986 => putative ABC transporter ATP-binding protein [09:22:12] Modify product: Uncharacterized protease YdcP => putative protease YdcP [09:22:12] Modify product: GTP-binding protein TypA/BipA homolog => GTP-binding protein TypA/BipA [09:22:12] Modify product: Phosphorylated carbohydrates phosphatase TM_1254 => Phosphorylated carbohydrates phosphatase [09:22:12] Modify product: Probable peroxiredoxin => putative peroxiredoxin [09:22:12] Modify product: Probable ferredoxin/ferredoxin--NADP reductase => putative ferredoxin/ferredoxin--NADP reductase [09:22:12] Modify product: Probable ABC transporter-binding protein DR_1438 => putative ABC transporter-binding protein [09:22:12] Modify product: Uncharacterized ABC transporter ATP-binding protein YlmA => putative ABC transporter ATP-binding protein YlmA [09:22:12] Modify product: Uncharacterized oxidoreductase Rv2900c => putative oxidoreductase [09:22:12] Modify product: Probable bacterial non-heme ferritin => putative bacterial non-heme ferritin [09:22:12] Modify product: PKHD-type hydroxylase Sbal_3634 => PKHD-type hydroxylase [09:22:12] Modify product: Probable 2-phosphosulfolactate phosphatase => putative 2-phosphosulfolactate phosphatase [09:22:12] Modify product: Phosphorylated carbohydrates phosphatase TM_1254 => Phosphorylated carbohydrates phosphatase [09:22:12] Modify product: Urea transporter DVU1160 => Urea transporter [09:22:12] Modify product: Probable multidrug resistance ABC transporter ATP-binding/permease protein YheI => putative multidrug resistance ABC transporter ATP-binding/permease protein YheI [09:22:12] Modify product: Uncharacterized zinc protease Rv2782c => putative zinc protease [09:22:12] Modify product: Uncharacterized zinc protease Rv2782c => putative zinc protease [09:22:12] Modify product: Uncharacterized ABC transporter ATP-binding protein Rv0986 => putative ABC transporter ATP-binding protein [09:22:12] Modify product: Uncharacterized ABC transporter ATP-binding protein Rv0986 => putative ABC transporter ATP-binding protein [09:22:13] Modify product: Probable murein peptide carboxypeptidase => putative murein peptide carboxypeptidase [09:22:13] Modify product: Probable L,D-transpeptidase YnhG => putative L,D-transpeptidase YnhG [09:22:13] Modify product: Uncharacterized ABC transporter ATP-binding protein HI_1470 => putative ABC transporter ATP-binding protein [09:22:13] Modify product: Uncharacterized sugar epimerase YhfK => putative sugar epimerase YhfK [09:22:13] Modify product: Probable cytochrome c oxidase subunit 1 => putative cytochrome c oxidase subunit 1 [09:22:13] Modify product: Uncharacterized ABC transporter ATP-binding protein TM_0288 => putative ABC transporter ATP-binding protein [09:22:13] Modify product: Probable oxidoreductase EphD => putative oxidoreductase EphD [09:22:13] Modify product: Laccase domain protein Rv2149c => Laccase domain protein [09:22:13] Modify product: Probable peptidoglycan D,D-transpeptidase PenA => putative peptidoglycan D,D-transpeptidase PenA [09:22:13] Modify product: Thylakoid-associated single-stranded DNA-binding protein slr1034 => Thylakoid-associated single-stranded DNA-binding protein [09:22:13] Modify product: Uncharacterized FAD-linked oxidoreductase Rv2280 => putative FAD-linked oxidoreductase [09:22:13] Modify product: Probable amino-acid metabolite efflux pump => putative amino-acid metabolite efflux pump [09:22:13] Modify product: Phage shock protein A homolog => Phage shock protein A [09:22:13] Modify product: Uncharacterized ABC transporter ATP-binding protein YknY => putative ABC transporter ATP-binding protein YknY [09:22:13] Modify product: Probable cytochrome c oxidase subunit 1 => putative cytochrome c oxidase subunit 1 [09:22:13] Modify product: Probable murein peptide carboxypeptidase => putative murein peptide carboxypeptidase [09:22:13] Modify product: Uncharacterized N-acetyltransferase YafP => putative N-acetyltransferase YafP [09:22:13] Modify product: Glycogen operon protein GlgX homolog => Glycogen operon protein GlgX [09:22:13] Modify product: Probable phospholipid ABC transporter permease protein MlaE => putative phospholipid ABC transporter permease protein MlaE [09:22:13] Modify product: Probable transcriptional regulatory protein aq_1575 => putative transcriptional regulatory protein [09:22:13] Modify product: Probable 30S ribosomal protein PSRP-3 => putative 30S ribosomal protein PSRP-3 [09:22:13] Modify product: Probable nicotinate-nucleotide adenylyltransferase => putative nicotinate-nucleotide adenylyltransferase [09:22:13] Modify product: Probable peptidoglycan glycosyltransferase FtsW => putative peptidoglycan glycosyltransferase FtsW [09:22:13] Modify product: Probable helicase HelY => putative helicase HelY [09:22:13] Modify product: Probable trans-aconitate 2-methyltransferase => putative trans-aconitate 2-methyltransferase [09:22:13] Modify product: Probable dual-specificity RNA methyltransferase RlmN => putative dual-specificity RNA methyltransferase RlmN [09:22:13] Modify product: Vitamin K epoxide reductase homolog => Vitamin K epoxide reductase [09:22:13] Modify product: Probable L,D-transpeptidase YnhG => putative L,D-transpeptidase YnhG [09:22:13] Modify product: Probable cysteine desulfurase => putative cysteine desulfurase [09:22:13] Modify product: Vitamin K epoxide reductase homolog => Vitamin K epoxide reductase [09:22:13] Modify product: Epimerase family protein Rv2216 => Epimerase family protein [09:22:13] Modify product: Probable copper-transporting ATPase PacS => putative copper-transporting ATPase PacS [09:22:13] Modify product: Putative HTH-type transcriptional regulator Rv0890c => Putative HTH-type transcriptional regulator [09:22:13] Modify product: Probable adenylyltransferase/sulfurtransferase MoeZ => putative adenylyltransferase/sulfurtransferase MoeZ [09:22:13] Modify product: Probable adenylyl-sulfate kinase => putative adenylyl-sulfate kinase [09:22:13] Modify product: Probable glutaredoxin ssr2061 => putative glutaredoxin [09:22:13] Modify product: Probable nicotinate-nucleotide pyrophosphorylase [carboxylating] => putative nicotinate-nucleotide pyrophosphorylase [carboxylating] [09:22:13] Modify product: Probable protein kinase UbiB => putative protein kinase UbiB [09:22:13] Modify product: Monocarboxylate 2-oxoacid-binding periplasmic protein all3028 => Monocarboxylate 2-oxoacid-binding periplasmic protein [09:22:14] Modify product: Uncharacterized signaling protein CC_0091 => putative signaling protein [09:22:14] Modify product: Probable nitrate transporter NarT => putative nitrate transporter NarT [09:22:14] Modify product: Probable formate transporter 1 => putative formate transporter 1 [09:22:14] Modify product: Probable protein kinase UbiB => putative protein kinase UbiB [09:22:14] Cleaned 106 /product names [09:22:14] Deleting unwanted file: prokka/Aaao/sprot.faa [09:22:14] Deleting unwanted file: prokka/Aaao/sprot.blast [09:22:14] There are still 1508 unannotated CDS left (started with 2869) [09:22:14] Will use hmmer3 to search against /usr/local/bioinfo/src/PROKKA/prokka-1.12/bin/../db/hmm/HAMAP.hmm with 1 CPUs [09:22:14] Running: cat prokka\/Aaao\/HAMAP\.hmm\.faa | parallel --gnu --plain -j 1 --block 138549 --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\/Aaao\/HAMAP\.hmm\.hmmer3 2> /dev/null [09:24:21] Deleting unwanted file: prokka/Aaao/HAMAP.hmm.faa [09:24:21] Deleting unwanted file: prokka/Aaao/HAMAP.hmm.hmmer3 [09:24:21] Labelling remaining 1427 proteins as 'hypothetical protein' [09:24:21] Possible /pseudo 'Putative fluoride ion transporter CrcB' at gnl|Prokka|Aaao.g_1 position 100098 [09:24:21] Possible /pseudo 'GalNAc-alpha-(1->4)-GalNAc-alpha-(1->3)-diNAcBac-PP-undecaprenol alpha-1,4-N-acetyl-D-galactosaminyltransferase' at gnl|Prokka|Aaao.g_1 position 229983 [09:24:21] Possible /pseudo 'putative phycocyanin operon protein Z' at gnl|Prokka|Aaao.g_1 position 489649 [09:24:21] Possible /pseudo 'ATP-dependent Clp protease proteolytic subunit' at gnl|Prokka|Aaao.g_1 position 680192 [09:24:21] Possible /pseudo 'Alpha-hemolysin translocation ATP-binding protein HlyB' at gnl|Prokka|Aaao.g_1 position 1094384 [09:24:21] Possible /pseudo 'S-layer protein SlpA' at gnl|Prokka|Aaao.g_1 position 1382769 [09:24:21] Possible /pseudo 'Multidrug resistance protein MdtB' at gnl|Prokka|Aaao.g_1 position 1466073 [09:24:21] Possible /pseudo 'putative zinc protease' at gnl|Prokka|Aaao.g_1 position 1510391 [09:24:21] Possible /pseudo 'Ribulose-phosphate 3-epimerase' at gnl|Prokka|Aaao.g_1 position 1538606 [09:24:21] Possible /pseudo 'DNA-directed RNA polymerase subunit beta'' at gnl|Prokka|Aaao.g_1 position 2067010 [09:24:21] Found 1152 unique /gene codes. [09:24:21] Fixed 2 duplicate /gene - yqgF_1 yqgF_2 [09:24:21] Fixed 2 duplicate /gene - pipB2_1 pipB2_2 [09:24:21] Fixed 3 duplicate /gene - pyrE_1 pyrE_2 pyrE_3 [09:24:21] Fixed 2 duplicate /gene - gnl_1 gnl_2 [09:24:21] Fixed 3 duplicate /gene - ftsH2_1 ftsH2_2 ftsH2_3 [09:24:21] Fixed 2 duplicate /gene - mnmC_1 mnmC_2 [09:24:21] Fixed 3 duplicate /gene - fabG_1 fabG_2 fabG_3 [09:24:21] Fixed 2 duplicate /gene - gatA_1 gatA_2 [09:24:21] Fixed 2 duplicate /gene - fcl_1 fcl_2 [09:24:21] Fixed 2 duplicate /gene - ykuD_1 ykuD_2 [09:24:21] Fixed 2 duplicate /gene - ald_1 ald_2 [09:24:21] Fixed 2 duplicate /gene - pds_1 pds_2 [09:24:21] Fixed 2 duplicate /gene - psbD1_1 psbD1_2 [09:24:21] Fixed 2 duplicate /gene - rpe_1 rpe_2 [09:24:21] Fixed 2 duplicate /gene - mgl_1 mgl_2 [09:24:21] Fixed 2 duplicate /gene - algA_1 algA_2 [09:24:21] Fixed 2 duplicate /gene - tal_1 tal_2 [09:24:21] Fixed 2 duplicate /gene - ltxA_1 ltxA_2 [09:24:21] Fixed 2 duplicate /gene - livQ_1 livQ_2 [09:24:21] Fixed 2 duplicate /gene - pglH_1 pglH_2 [09:24:21] Fixed 2 duplicate /gene - cobD_1 cobD_2 [09:24:21] Fixed 2 duplicate /gene - rluD_1 rluD_2 [09:24:21] Fixed 4 duplicate /gene - petJ_1 petJ_2 petJ_3 petJ_4 [09:24:21] Fixed 2 duplicate /gene - rpsA_1 rpsA_2 [09:24:21] Fixed 2 duplicate /gene - cpcS_1 cpcS_2 [09:24:21] Fixed 3 duplicate /gene - dnaK2_1 dnaK2_2 dnaK2_3 [09:24:21] Fixed 4 duplicate /gene - clpP_1 clpP_2 clpP_3 clpP_4 [09:24:21] Fixed 2 duplicate /gene - lpxB_1 lpxB_2 [09:24:21] Fixed 2 duplicate /gene - nuoL_1 nuoL_2 [09:24:21] Fixed 2 duplicate /gene - mntA_1 mntA_2 [09:24:21] Fixed 2 duplicate /gene - murJ_1 murJ_2 [09:24:21] Fixed 2 duplicate /gene - gyrA_1 gyrA_2 [09:24:21] Fixed 2 duplicate /gene - neuB_1 neuB_2 [09:24:21] Fixed 2 duplicate /gene - kdgK_1 kdgK_2 [09:24:21] Fixed 2 duplicate /gene - tetA_1 tetA_2 [09:24:21] Fixed 2 duplicate /gene - btuR_1 btuR_2 [09:24:21] Fixed 2 duplicate /gene - hisF_1 hisF_2 [09:24:21] Fixed 2 duplicate /gene - natA_1 natA_2 [09:24:21] Fixed 2 duplicate /gene - phrB_1 phrB_2 [09:24:21] Fixed 5 duplicate /gene - mprA_1 mprA_2 mprA_3 mprA_4 mprA_5 [09:24:21] Fixed 2 duplicate /gene - mnmE_1 mnmE_2 [09:24:21] Fixed 2 duplicate /gene - crtI_1 crtI_2 [09:24:21] Fixed 4 duplicate /gene - bicA_1 bicA_2 bicA_3 bicA_4 [09:24:21] Fixed 2 duplicate /gene - bchI_1 bchI_2 [09:24:21] Fixed 5 duplicate /gene - resE_1 resE_2 resE_3 resE_4 resE_5 [09:24:21] Fixed 2 duplicate /gene - clcA_1 clcA_2 [09:24:21] Fixed 3 duplicate /gene - lytB_1 lytB_2 lytB_3 [09:24:21] Fixed 3 duplicate /gene - menG_1 menG_2 menG_3 [09:24:21] Fixed 2 duplicate /gene - ntcA_1 ntcA_2 [09:24:21] Fixed 2 duplicate /gene - ubiE_1 ubiE_2 [09:24:21] Fixed 2 duplicate /gene - plsC_1 plsC_2 [09:24:21] Fixed 2 duplicate /gene - nadK_1 nadK_2 [09:24:21] Fixed 2 duplicate /gene - perR_1 perR_2 [09:24:21] Fixed 2 duplicate /gene - msrB_1 msrB_2 [09:24:21] Fixed 3 duplicate /gene - vraR_1 vraR_2 vraR_3 [09:24:21] Fixed 8 duplicate /gene - sigA2_1 sigA2_2 sigA2_3 sigA2_4 sigA2_5 sigA2_6 sigA2_7 sigA2_8 [09:24:21] Fixed 2 duplicate /gene - mlhB_1 mlhB_2 [09:24:21] Fixed 2 duplicate /gene - ppa_1 ppa_2 [09:24:21] Fixed 2 duplicate /gene - glgM_1 glgM_2 [09:24:21] Fixed 2 duplicate /gene - pcyA_1 pcyA_2 [09:24:21] Fixed 2 duplicate /gene - mdtB_1 mdtB_2 [09:24:21] Fixed 2 duplicate /gene - lexA_1 lexA_2 [09:24:21] Fixed 2 duplicate /gene - mscL_1 mscL_2 [09:24:21] Fixed 3 duplicate /gene - cpcG_1 cpcG_2 cpcG_3 [09:24:21] Fixed 2 duplicate /gene - psaK_1 psaK_2 [09:24:21] Fixed 3 duplicate /gene - yciC_1 yciC_2 yciC_3 [09:24:21] Fixed 2 duplicate /gene - hhoA_1 hhoA_2 [09:24:21] Fixed 5 duplicate /gene - ftnA_1 ftnA_2 ftnA_3 ftnA_4 ftnA_5 [09:24:21] Fixed 3 duplicate /gene - bcp_1 bcp_2 bcp_3 [09:24:21] Fixed 2 duplicate /gene - pilT_1 pilT_2 [09:24:21] Fixed 2 duplicate /gene - speA_1 speA_2 [09:24:21] Fixed 2 duplicate /gene - crcB_1 crcB_2 [09:24:21] Fixed 3 duplicate /gene - mexB_1 mexB_2 mexB_3 [09:24:21] Fixed 2 duplicate /gene - ettA_1 ettA_2 [09:24:21] Fixed 2 duplicate /gene - hisH_1 hisH_2 [09:24:21] Fixed 3 duplicate /gene - petF_1 petF_2 petF_3 [09:24:21] Fixed 2 duplicate /gene - cobN_1 cobN_2 [09:24:21] Fixed 2 duplicate /gene - dfa3_1 dfa3_2 [09:24:21] Fixed 6 duplicate /gene - slpA_1 slpA_2 slpA_3 slpA_4 slpA_5 slpA_6 [09:24:21] Fixed 2 duplicate /gene - gph_1 gph_2 [09:24:21] Fixed 2 duplicate /gene - dapL_1 dapL_2 [09:24:21] Fixed 4 duplicate /gene - mpeC_1 mpeC_2 mpeC_3 mpeC_4 [09:24:21] Fixed 3 duplicate /gene - trxB_1 trxB_2 trxB_3 [09:24:21] Fixed 2 duplicate /gene - cph2_1 cph2_2 [09:24:21] Fixed 2 duplicate /gene - ctaD_1 ctaD_2 [09:24:21] Fixed 2 duplicate /gene - mscS_1 mscS_2 [09:24:21] Fixed 2 duplicate /gene - smc_1 smc_2 [09:24:21] Fixed 4 duplicate /gene - ubiB_1 ubiB_2 ubiB_3 ubiB_4 [09:24:21] Fixed 2 duplicate /gene - rpoC_1 rpoC_2 [09:24:21] Fixed 3 duplicate /gene - glnA_1 glnA_2 glnA_3 [09:24:21] Fixed 2 duplicate /gene - bcsA_1 bcsA_2 [09:24:21] Fixed 2 duplicate /gene - ugpC_1 ugpC_2 [09:24:21] Fixed 2 duplicate /gene - prmC_1 prmC_2 [09:24:21] Fixed 2 duplicate /gene - corC_1 corC_2 [09:24:21] Fixed 2 duplicate /gene - kmo_1 kmo_2 [09:24:21] Fixed 2 duplicate /gene - sir_1 sir_2 [09:24:21] Fixed 2 duplicate /gene - mepM_1 mepM_2 [09:24:21] Fixed 3 duplicate /gene - psbA2_1 psbA2_2 psbA2_3 [09:24:21] Fixed 2 duplicate /gene - ynhG_1 ynhG_2 [09:24:21] Fixed 2 duplicate /gene - der_1 der_2 [09:24:21] Fixed 2 duplicate /gene - acr1_1 acr1_2 [09:24:21] Fixed 2 duplicate /gene - menH_1 menH_2 [09:24:21] Fixed 3 duplicate /gene - tam_1 tam_2 tam_3 [09:24:21] Fixed 3 duplicate /gene - ndhD1_1 ndhD1_2 ndhD1_3 [09:24:21] Fixed 2 duplicate /gene - hpf_1 hpf_2 [09:24:21] Fixed 2 duplicate /gene - csgA_1 csgA_2 [09:24:21] Fixed 2 duplicate /gene - hhoB_1 hhoB_2 [09:24:21] Fixed 2 duplicate /gene - coxM_1 coxM_2 [09:24:21] Fixed 2 duplicate /gene - suhB_1 suhB_2 [09:24:21] Fixed 2 duplicate /gene - yfcG_1 yfcG_2 [09:24:21] Fixed 2 duplicate /gene - mntB_1 mntB_2 [09:24:21] Fixed 2 duplicate /gene - rnr_1 rnr_2 [09:24:21] Fixed 2 duplicate /gene - mscK_1 mscK_2 [09:24:21] Fixed 2 duplicate /gene - ompR_1 ompR_2 [09:24:21] Fixed 2 duplicate /gene - cpdA_1 cpdA_2 [09:24:21] Fixed 2 duplicate /gene - ubiG_1 ubiG_2 [09:24:21] Fixed 2 duplicate /gene - sepF_1 sepF_2 [09:24:21] Fixed 2 duplicate /gene - petF1_1 petF1_2 [09:24:21] Fixed 2 duplicate /gene - cocE_1 cocE_2 [09:24:21] Fixed 2 duplicate /gene - ycf3_1 ycf3_2 [09:24:21] Fixed 2 duplicate /gene - ccmK_1 ccmK_2 [09:24:21] Fixed 2 duplicate /gene - dnaX_1 dnaX_2 [09:24:21] Fixed 2 duplicate /gene - atpG_1 atpG_2 [09:24:21] Fixed 2 duplicate /gene - hlyB_1 hlyB_2 [09:24:21] Fixed 2 duplicate /gene - purE_1 purE_2 [09:24:21] Fixed 2 duplicate /gene - eco_1 eco_2 [09:24:21] Fixed 2 duplicate /gene - ydjZ_1 ydjZ_2 [09:24:21] Fixed 5 duplicate /gene - dnaJ_1 dnaJ_2 dnaJ_3 dnaJ_4 dnaJ_5 [09:24:21] Fixed 2 duplicate /gene - moeZ_1 moeZ_2 [09:24:21] Fixed 2 duplicate /gene - ykfA_1 ykfA_2 [09:24:21] Fixed 2 duplicate /gene - pyrC_1 pyrC_2 [09:24:21] Fixed 2 duplicate /gene - phoP_1 phoP_2 [09:24:21] Fixed 132 colliding /gene names. [09:24:21] Adding /locus_tag identifiers [09:24:21] Assigned 2914 locus_tags to CDS and RNA features. [09:24:21] Writing outputs to prokka/Aaao/ [09:24:25] Generating annotation statistics file [09:24:25] Generating Genbank and Sequin files [09:24:25] 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\/Aaao\/Aaao\.err -i prokka\/Aaao\/Aaao\.fsa 2> /dev/null [09:24:34] Deleting unwanted file: prokka/Aaao/errorsummary.val [09:24:34] Deleting unwanted file: prokka/Aaao/Aaao.dr [09:24:34] Deleting unwanted file: prokka/Aaao/Aaao.fixedproducts [09:24:34] Deleting unwanted file: prokka/Aaao/Aaao.ecn [09:24:34] Deleting unwanted file: prokka/Aaao/Aaao.val [09:24:34] Repairing broken .GBK output that tbl2asn produces... [09:24:34] Running: sed 's/COORDINATES: profile/COORDINATES:profile/' < prokka\/Aaao\/Aaao\.gbf > prokka\/Aaao\/Aaao\.gbk [09:24:34] Deleting unwanted file: prokka/Aaao/Aaao.gbf [09:24:34] Output files: [09:24:34] prokka/Aaao/Aaao.faa [09:24:34] prokka/Aaao/Aaao.ffn [09:24:34] prokka/Aaao/Aaao.err [09:24:34] prokka/Aaao/Aaao.fna [09:24:34] prokka/Aaao/Aaao.fsa [09:24:34] prokka/Aaao/Aaao.tsv [09:24:34] prokka/Aaao/Aaao.sqn [09:24:34] prokka/Aaao/Aaao.gff [09:24:34] prokka/Aaao/Aaao.gbk [09:24:34] prokka/Aaao/Aaao.txt [09:24:34] prokka/Aaao/Aaao.log [09:24:34] prokka/Aaao/Aaao.tbl [09:24:34] Annotation finished successfully. [09:24:34] Walltime used: 5.95 minutes [09:24:34] If you use this result please cite the Prokka paper: [09:24:34] Seemann T (2014) Prokka: rapid prokaryotic genome annotation. Bioinformatics. 30(14):2068-9. [09:24:34] Type 'prokka --citation' for more details. [09:24:34] Share and enjoy!