[17:44:15] This is prokka 1.12 [17:44:15] Written by Torsten Seemann [17:44:15] Homepage is https://github.com/tseemann/prokka [17:44:15] Local time is Thu Sep 6 17:44:15 2018 [17:44:15] You are gsi [17:44:15] Operating system is linux [17:44:15] You have BioPerl 1.007002 [17:44:15] System has 24 cores. [17:44:15] Will use maximum of 1 cores. [17:44:15] Annotating as >>> Bacteria <<< [17:44:15] Enabling options to ensure Genbank/ENA/DDJB submission compliance. [17:44:15] Creating new output folder: /share/gsi2/data/www/soap-data/M2BBS/Phylogenomic/Prochlorococcus/prokka/Aaal [17:44:15] Running: mkdir -p \/share\/gsi2\/data\/www\/soap\-data\/M2BBS\/Phylogenomic\/Prochlorococcus\/prokka\/Aaal [17:44:15] Using filename prefix: AaalA01.XXX [17:44:15] Setting HMMER_NCPU=1 [17:44:15] Writing log to: /share/gsi2/data/www/soap-data/M2BBS/Phylogenomic/Prochlorococcus/prokka/Aaal/AaalA01.log [17:44:15] Command: /share/gsi2/bin/prokka /share/gsi2/data/www/soap-data/M2BBS/Phylogenomic/Prochlorococcus/DNA/Aaal/AaalA01.fas --compliant --addgenes --outdir /share/gsi2/data/www/soap-data/M2BBS/Phylogenomic/Prochlorococcus/prokka/Aaal --prefix AaalA01 --locustag AaalA01.g --species ProchlorococcusmarinusstrMIT9303 --strain ProchlorococcusmarinusstrMIT9303 --kingdom bacteria --cpus 1 --force [17:44:15] Appending to PATH: /share/gsi2/software/prokka/bin/../binaries/linux [17:44:15] Appending to PATH: /share/gsi2/software/prokka/bin/../binaries/linux/../common [17:44:15] Appending to PATH: /share/gsi2/software/prokka/bin [17:44:15] Looking for 'aragorn' - found /share/gsi2/software/prokka/bin/../binaries/linux/aragorn [17:44:15] Determined aragorn version is 1.2 [17:44:15] Looking for 'barrnap' - found /share/gsi2/bin/barrnap [17:44:15] Determined barrnap version is 0.9 [17:44:15] Looking for 'blastp' - found /share/gsi2/bin/blastp [17:44:16] Determined blastp version is 2.7 [17:44:16] Looking for 'cmpress' - found /share/gsi2/software/prokka/bin/../binaries/linux/cmpress [17:44:16] Determined cmpress version is 1.1 [17:44:16] Looking for 'cmscan' - found /share/gsi2/software/prokka/bin/../binaries/linux/cmscan [17:44:16] Determined cmscan version is 1.1 [17:44:16] Looking for 'egrep' - found /bin/egrep [17:44:16] Looking for 'find' - found /bin/find [17:44:16] Looking for 'grep' - found /bin/grep [17:44:16] Looking for 'hmmpress' - found /share/gsi2/bin/hmmpress [17:44:16] Determined hmmpress version is 3.1 [17:44:16] Looking for 'hmmscan' - found /share/gsi2/bin/hmmscan [17:44:16] Determined hmmscan version is 3.1 [17:44:16] Looking for 'java' - found /usr/java/latest/bin/java [17:44:16] Looking for 'less' - found /usr/bin/less [17:44:16] Looking for 'makeblastdb' - found /share/gsi2/bin/makeblastdb [17:44:16] Determined makeblastdb version is 2.7 [17:44:16] Looking for 'minced' - found /share/gsi2/bin/minced [17:44:16] Determined minced version is 2.0 [17:44:16] Looking for 'parallel' - found /share/gsi2/software/prokka/bin/../binaries/linux/../common/parallel [17:44:16] Determined parallel version is 20150122 [17:44:16] Looking for 'prodigal' - found /share/gsi2/software/prokka/bin/../binaries/linux/prodigal [17:44:16] Determined prodigal version is 2.6 [17:44:16] Looking for 'prokka-genbank_to_fasta_db' - found /share/gsi2/software/prokka/bin/prokka-genbank_to_fasta_db [17:44:16] Looking for 'rnammer' - found /share/gsi2/bin/rnammer [17:44:16] Determined rnammer version is 1.2 [17:44:16] Looking for 'sed' - found /bin/sed [17:44:17] Looking for 'tbl2asn' - found /share/gsi2/bin/tbl2asn [17:44:18] Determined tbl2asn version is 25.6 [17:44:18] Using genetic code table 11. [17:44:18] Loading and checking input file: /share/gsi2/data/www/soap-data/M2BBS/Phylogenomic/Prochlorococcus/DNA/Aaal/AaalA01.fas [17:44:18] Wrote 1 contigs totalling 2682675 bp. [17:44:18] Predicting tRNAs and tmRNAs [17:44:18] Running: aragorn -l -gc11 -w \/share\/gsi2\/data\/www\/soap\-data\/M2BBS\/Phylogenomic\/Prochlorococcus\/prokka\/Aaal\/AaalA01\.fna [17:44:20] 1 tRNA-Gly c[42320,42391] 33 (ccc) [17:44:20] 2 tRNA-Gly [92543,92614] 33 (gcc) [17:44:20] 3 tRNA-Ile [245323,245398] 36 (gat) [17:44:20] 4 tRNA-Ala [245407,245480] 34 (tgc) [17:44:20] 5 tRNA-Leu [333962,334043] 35 (gag) [17:44:20] 6 tmRNA* [345302,345624] 182,232 ANNIVRFSRQPALVAA* [17:44:20] 7 tRNA-Thr c[410295,410369] 34 (cgt) [17:44:20] 8 tRNA-Val c[510289,510361] 33 (gac) [17:44:20] 9 tRNA-Gly [548075,548145] 33 (tcc) [17:44:20] 10 tRNA-Arg c[565241,565316] 36 (tct) [17:44:20] 11 tRNA-Val c[622849,622920] 33 (cac) [17:44:20] 12 tRNA-Asp c[637885,637960] 36 (gtc) [17:44:20] 13 tRNA-Trp c[638463,638539] 35 (cca) [17:44:20] 14 tRNA-Glu c[856723,856795] 35 (ttc) [17:44:20] 15 tRNA-Lys [918715,918787] 33 (ttt) [17:44:20] 16 tRNA-Pro [1083661,1083735] 35 (tgg) [17:44:20] 17 tRNA-Met c[1172940,1173013] 32 (cat) [17:44:20] 18 tRNA-Met c[1177575,1177651] 35 (cat) [17:44:20] 19 tRNA-Ser c[1209898,1209984] 35 (tga) [17:44:20] 20 tRNA-Met c[1261564,1261637] 35 (cat) [17:44:20] 21 tRNA-Ser c[1326369,1326457] 36 (gga) [17:44:20] 22 tRNA-Pro [1557100,1557173] 35 (ggg) [17:44:20] 23 tRNA-Leu c[1579797,1579883] 35 (taa) [17:44:20] 24 tRNA-Arg [1655286,1655360] 34 (gcg) [17:44:20] 25 tRNA-Ala c[1681296,1681370] 35 (ggc) [17:44:20] 26 tRNA-Leu c[1742617,1742700] 35 (cag) [17:44:20] 27 tRNA-Leu [1744188,1744270] 35 (caa) [17:44:20] 28 tRNA-His [1750832,1750905] 34 (gtg) [17:44:20] 29 tRNA-Ser c[1798728,1798814] 36 (cga) [17:44:20] 30 tRNA-Tyr [1920853,1920936] 35 (gta) [17:44:20] 31 tRNA-Thr [1920945,1921017] 33 (ggt) [17:44:20] 32 tRNA-Ala c[1938388,1938461] 34 (tgc) [17:44:20] 33 tRNA-Ile c[1938470,1938545] 36 (gat) [17:44:20] 34 tRNA-Thr [1956176,1956249] 34 (tgt) [17:44:20] 35 tRNA-Phe [1973037,1973109] 34 (gaa) [17:44:20] 36 tRNA-Cys c[1997145,1997215] 33 (gca) [17:44:20] 37 tRNA-Arg c[2013271,2013346] 36 (ccg) [17:44:20] 38 tRNA-Gln c[2030409,2030482] 34 (ttg) [17:44:20] 39 tRNA-Ser [2052755,2052845] 36 (gct) [17:44:20] 40 tRNA-Pro c[2072630,2072705] 36 (cgg) [17:44:20] 41 tRNA-Ala [2105618,2105692] 35 (cgc) [17:44:20] 42 tRNA-Leu c[2138369,2138454] 36 (tag) [17:44:20] 43 tRNA-Arg c[2174805,2174879] 35 (acg) [17:44:20] 44 tRNA-Met c[2192159,2192231] 34 (cat) [17:44:20] 45 tRNA-Arg c[2293384,2293459] 36 (cct) [17:44:20] 46 tRNA-Asn [2335558,2335629] 33 (gtt) [17:44:20] 47 tRNA-Val c[2597934,2598005] 33 (tac) [17:44:20] Found 47 tRNAs [17:44:20] Predicting Ribosomal RNAs [17:44:20] Running Barrnap with 1 threads [17:44:24] 1 gnl|Prokka|AaalA01.g_1 243658 16S ribosomal RNA [17:44:24] 2 gnl|Prokka|AaalA01.g_1 245972 23S ribosomal RNA [17:44:24] 3 gnl|Prokka|AaalA01.g_1 1935023 23S ribosomal RNA [17:44:24] 4 gnl|Prokka|AaalA01.g_1 1938731 16S ribosomal RNA [17:44:24] Found 4 rRNAs [17:44:24] Skipping ncRNA search, enable with --rfam if desired. [17:44:24] Total of 50 tRNA + rRNA features [17:44:24] Searching for CRISPR repeats [17:44:25] Found 0 CRISPRs [17:44:25] Predicting coding sequences [17:44:25] Contigs total 2682675 bp, so using single mode [17:44:25] Running: prodigal -i \/share\/gsi2\/data\/www\/soap\-data\/M2BBS\/Phylogenomic\/Prochlorococcus\/prokka\/Aaal\/AaalA01\.fna -c -m -g 11 -p single -f sco -q [17:44:36] Excluding CDS which overlaps existing RNA (rRNA) at gnl|Prokka|AaalA01.g_1:246031..246156 on - strand [17:44:36] Excluding CDS which overlaps existing RNA (rRNA) at gnl|Prokka|AaalA01.g_1:248382..248507 on - strand [17:44:37] Excluding CDS which overlaps existing RNA (tRNA) at gnl|Prokka|AaalA01.g_1:622784..622951 on + strand [17:44:38] Excluding CDS which overlaps existing RNA (tRNA) at gnl|Prokka|AaalA01.g_1:1655068..1656162 on + strand [17:44:38] Excluding CDS which overlaps existing RNA (tRNA) at gnl|Prokka|AaalA01.g_1:1744194..1745459 on + strand [17:44:38] Excluding CDS which overlaps existing RNA (tRNA) at gnl|Prokka|AaalA01.g_1:1750750..1750926 on + strand [17:44:38] Excluding CDS which overlaps existing RNA (rRNA) at gnl|Prokka|AaalA01.g_1:1935359..1935484 on + strand [17:44:38] Excluding CDS which overlaps existing RNA (rRNA) at gnl|Prokka|AaalA01.g_1:1937712..1937837 on + strand [17:44:38] Excluding CDS which overlaps existing RNA (tRNA) at gnl|Prokka|AaalA01.g_1:2013099..2013278 on - strand [17:44:38] Excluding CDS which overlaps existing RNA (tRNA) at gnl|Prokka|AaalA01.g_1:2072566..2072775 on + strand [17:44:38] Excluding CDS which overlaps existing RNA (tRNA) at gnl|Prokka|AaalA01.g_1:2174714..2174860 on + strand [17:44:39] Found 2732 CDS [17:44:39] Connecting features back to sequences [17:44:39] Not using genus-specific database. Try --usegenus to enable it. [17:44:39] Annotating CDS, please be patient. [17:44:39] Will use 1 CPUs for similarity searching. [17:44:44] There are still 2732 unannotated CDS left (started with 2732) [17:44:44] Will use blast to search against /share/gsi2/software/prokka/bin/../db/kingdom/Bacteria/sprot with 1 CPUs [17:44:44] Running: cat \/share\/gsi2\/data\/www\/soap\-data\/M2BBS\/Phylogenomic\/Prochlorococcus\/prokka\/Aaal\/sprot\.faa | parallel --gnu --plain -j 1 --block 380501 --recstart '>' --pipe blastp -query - -db /share/gsi2/software/prokka/bin/../db/kingdom/Bacteria/sprot -evalue 1e-06 -num_threads 1 -num_descriptions 1 -num_alignments 1 -seg no > \/share\/gsi2\/data\/www\/soap\-data\/M2BBS\/Phylogenomic\/Prochlorococcus\/prokka\/Aaal\/sprot\.blast 2> /dev/null [17:48:13] Modify product: N utilization substance protein B homolog => N utilization substance protein B [17:48:13] Modify product: Uncharacterized membrane protein Rv2637 => putative membrane protein [17:48:13] Modify product: Probable ABC transporter-binding protein DR_1438 => putative ABC transporter-binding protein [17:48:13] Modify product: Uncharacterized hydrolase YxeP => putative hydrolase YxeP [17:48:13] Modify product: Vitamin K epoxide reductase homolog => Vitamin K epoxide reductase [17:48:13] Modify product: Uncharacterized ABC transporter ATP-binding protein YheS => putative ABC transporter ATP-binding protein YheS [17:48:13] Modify product: Probable ATP-dependent transporter SufC => putative ATP-dependent transporter SufC [17:48:13] Modify product: Probable cysteine desulfurase => putative cysteine desulfurase [17:48:13] Modify product: Vitamin K epoxide reductase homolog => Vitamin K epoxide reductase [17:48:13] Modify product: Probable dual-specificity RNA methyltransferase RlmN => putative dual-specificity RNA methyltransferase RlmN [17:48:14] Modify product: Probable helicase HelY => putative helicase HelY [17:48:14] Modify product: Probable peptidoglycan glycosyltransferase FtsW => putative peptidoglycan glycosyltransferase FtsW [17:48:14] Modify product: Probable 30S ribosomal protein PSRP-3 => putative 30S ribosomal protein PSRP-3 [17:48:14] Modify product: Probable transcriptional regulatory protein aq_1575 => putative transcriptional regulatory protein [17:48:14] Modify product: Probable phospholipid ABC transporter permease protein MlaE => putative phospholipid ABC transporter permease protein MlaE [17:48:14] Modify product: Glycogen operon protein GlgX homolog => Glycogen operon protein GlgX [17:48:14] Modify product: Uncharacterized inner membrane transporter YedA => putative inner membrane transporter YedA [17:48:14] Modify product: Phage shock protein A homolog => Phage shock protein A [17:48:14] Modify product: Uncharacterized ABC transporter ATP-binding protein YknY => putative ABC transporter ATP-binding protein YknY [17:48:14] Modify product: Probable doxorubicin resistance ABC transporter permease protein DrrC => putative doxorubicin resistance ABC transporter permease protein DrrC [17:48:14] Modify product: Probable murein peptide carboxypeptidase => putative murein peptide carboxypeptidase [17:48:14] Modify product: Uncharacterized FAD-linked oxidoreductase Rv2280 => putative FAD-linked oxidoreductase [17:48:14] Modify product: Thylakoid-associated single-stranded DNA-binding protein slr1034 => Thylakoid-associated single-stranded DNA-binding protein [17:48:14] Modify product: Uncharacterized sugar kinase YdjH => putative sugar kinase YdjH [17:48:14] Modify product: Laccase domain protein Rv2149c => Laccase domain protein [17:48:14] Modify product: Uncharacterized oxidoreductase Rv1543 => putative oxidoreductase [17:48:14] Modify product: Uncharacterized ABC transporter ATP-binding protein TM_0288 => putative ABC transporter ATP-binding protein [17:48:14] Modify product: Putative peroxiredoxin sll1621 => Putative peroxiredoxin [17:48:14] Modify product: Maf-like protein Rv3282 => Maf-like protein [17:48:14] Modify product: Probable peptidyl-prolyl cis-trans isomerase => putative peptidyl-prolyl cis-trans isomerase [17:48:14] Modify product: Uncharacterized methyltransferase Rv3342 => putative methyltransferase [17:48:14] Modify product: Uncharacterized oxidoreductase MSMEG_1603/MSMEI_1564 => putative oxidoreductase/MSMEI_1564 [17:48:14] Modify product: 1,4-alpha-glucan branching enzyme TTHA1902 => 1,4-alpha-glucan branching enzyme [17:48:14] Modify product: Bifunctional protein FolD => Bifunctional protein FolD protein [17:48:14] Modify product: Putative multidrug export ATP-binding/permease protein SA1683 => Putative multidrug export ATP-binding/permease protein [17:48:14] Modify product: Probable protein kinase UbiB => putative protein kinase UbiB [17:48:14] Modify product: Cyclic nucleotide-gated potassium channel mll3241 => Cyclic nucleotide-gated potassium channel [17:48:14] Modify product: Probable chromate transport protein => putative chromate transport protein [17:48:14] Modify product: Probable glutamine ABC transporter permease protein GlnM => putative glutamine ABC transporter permease protein GlnM [17:48:14] Modify product: Probable isochorismatase => putative isochorismatase [17:48:14] Modify product: Uncharacterized MscS family protein YkuT => putative MscS family protein YkuT [17:48:14] Modify product: Putative multidrug export ATP-binding/permease protein SA1683 => Putative multidrug export ATP-binding/permease protein [17:48:14] Modify product: Uncharacterized ABC transporter ATP-binding protein Rv0986 => putative ABC transporter ATP-binding protein [17:48:14] Modify product: Probable ferredoxin/ferredoxin--NADP reductase => putative ferredoxin/ferredoxin--NADP reductase [17:48:14] Modify product: Probable ABC transporter-binding protein DR_1438 => putative ABC transporter-binding protein [17:48:15] Modify product: Uncharacterized ABC transporter ATP-binding protein YlmA => putative ABC transporter ATP-binding protein YlmA [17:48:15] Modify product: Probable multidrug resistance ABC transporter ATP-binding/permease protein YheI => putative multidrug resistance ABC transporter ATP-binding/permease protein YheI [17:48:15] Modify product: Uncharacterized zinc protease Rv2782c => putative zinc protease [17:48:15] Modify product: Uncharacterized zinc protease Rv2782c => putative zinc protease [17:48:15] Modify product: Uncharacterized ABC transporter ATP-binding protein Rv0986 => putative ABC transporter ATP-binding protein [17:48:15] Modify product: GTP-binding protein TypA/BipA homolog => GTP-binding protein TypA/BipA [17:48:15] Modify product: Probable murein peptide carboxypeptidase => putative murein peptide carboxypeptidase [17:48:15] Modify product: Uncharacterized sugar epimerase YhfK => putative sugar epimerase YhfK [17:48:15] Modify product: Probable L,D-transpeptidase YnhG => putative L,D-transpeptidase YnhG [17:48:15] Modify product: Probable 2-phosphosulfolactate phosphatase => putative 2-phosphosulfolactate phosphatase [17:48:15] Modify product: Phosphorylated carbohydrates phosphatase TM_1254 => Phosphorylated carbohydrates phosphatase [17:48:15] Modify product: Uncharacterized FAD-linked oxidoreductase Rv2280 => putative FAD-linked oxidoreductase [17:48:15] Modify product: Oxygen-independent coproporphyrinogen-III oxidase-like protein sll1917 => Oxygen-independent coproporphyrinogen-III oxidase-like protein [17:48:15] Modify product: Uncharacterized PIN and TRAM-domain containing protein YacL => putative PIN and TRAM-domain containing protein YacL [17:48:15] Modify product: PKHD-type hydroxylase Sbal_3634 => PKHD-type hydroxylase [17:48:15] Modify product: Uncharacterized methyltransferase YcgJ => putative methyltransferase YcgJ [17:48:15] Modify product: Probable sensor histidine kinase TcrY => putative sensor histidine kinase TcrY [17:48:15] Modify product: Cyclic nucleotide-gated potassium channel mll3241 => Cyclic nucleotide-gated potassium channel [17:48:15] Modify product: Uncharacterized MFS-type transporter Rv0037c => putative MFS-type transporter [17:48:15] Modify product: Probable tRNA-dihydrouridine synthase => putative tRNA-dihydrouridine synthase [17:48:15] Modify product: Probable septum site-determining protein MinC => putative septum site-determining protein MinC [17:48:15] Modify product: Putative esterase aq_1494 => Putative esterase [17:48:15] Modify product: Probable phycoerythrobilin lyase CpeT => putative phycoerythrobilin lyase CpeT [17:48:15] Modify product: Uncharacterized phycocyanin operon protein Z => putative phycocyanin operon protein Z [17:48:15] Modify product: Uncharacterized phycocyanin operon protein Z => putative phycocyanin operon protein Z [17:48:15] Modify product: Probable adenylyltransferase/sulfurtransferase MoeZ => putative adenylyltransferase/sulfurtransferase MoeZ [17:48:15] Modify product: Probable endopeptidase p60 => putative endopeptidase p60 [17:48:15] Modify product: Probable cobalt-factor III C(17)-methyltransferase => putative cobalt-factor III C(17)-methyltransferase [17:48:15] Modify product: Probable bifunctional SAT/APS kinase => putative bifunctional SAT/APS kinase [17:48:15] Modify product: NADH dehydrogenase-like protein SA0802 => NADH dehydrogenase-like protein [17:48:15] Modify product: Probable undecaprenyl-phosphate N-acetylglucosaminyl 1-phosphate transferase => putative undecaprenyl-phosphate N-acetylglucosaminyl 1-phosphate transferase [17:48:16] Modify product: Uncharacterized glycosyltransferase sll0501 => putative glycosyltransferase [17:48:16] Modify product: Uncharacterized FAD-linked oxidoreductase Rv2280 => putative FAD-linked oxidoreductase [17:48:16] Modify product: Stringent starvation protein A homolog => Stringent starvation protein A [17:48:16] Modify product: Epimerase family protein Rv2216 => Epimerase family protein [17:48:16] Modify product: Probable copper-transporting ATPase PacS => putative copper-transporting ATPase PacS [17:48:16] Modify product: Probable adenylyl-sulfate kinase => putative adenylyl-sulfate kinase [17:48:16] Modify product: Probable glutaredoxin ssr2061 => putative glutaredoxin [17:48:16] Modify product: Probable nicotinate-nucleotide pyrophosphorylase [carboxylating] => putative nicotinate-nucleotide pyrophosphorylase [carboxylating] [17:48:16] Modify product: Probable protein kinase UbiB => putative protein kinase UbiB [17:48:16] Modify product: Prophage bactoprenol glucosyl transferase homolog => Prophage bactoprenol glucosyl transferase [17:48:16] Modify product: Monocarboxylate 2-oxoacid-binding periplasmic protein all3028 => Monocarboxylate 2-oxoacid-binding periplasmic protein [17:48:16] Modify product: ABC transporter ATP-binding/permease protein Rv1747 => ABC transporter ATP-binding/permease protein [17:48:16] Modify product: Uncharacterized methyltransferase Rv3342 => putative methyltransferase [17:48:16] Modify product: Probable adenylyl-sulfate kinase => putative adenylyl-sulfate kinase [17:48:16] Modify product: Probable formate transporter 1 => putative formate transporter 1 [17:48:16] Modify product: Probable protein kinase UbiB => putative protein kinase UbiB [17:48:16] Cleaned 92 /product names [17:48:16] Deleting unwanted file: /share/gsi2/data/www/soap-data/M2BBS/Phylogenomic/Prochlorococcus/prokka/Aaal/sprot.faa [17:48:16] Deleting unwanted file: /share/gsi2/data/www/soap-data/M2BBS/Phylogenomic/Prochlorococcus/prokka/Aaal/sprot.blast [17:48:18] There are still 1424 unannotated CDS left (started with 2732) [17:48:18] Will use hmmer3 to search against /share/gsi2/software/prokka/bin/../db/hmm/HAMAP.hmm with 1 CPUs [17:48:18] Running: cat \/share\/gsi2\/data\/www\/soap\-data\/M2BBS\/Phylogenomic\/Prochlorococcus\/prokka\/Aaal\/HAMAP\.hmm\.faa | parallel --gnu --plain -j 1 --block 133620 --recstart '>' --pipe hmmscan --noali --notextw --acc -E 1e-06 --cpu 1 /share/gsi2/software/prokka/bin/../db/hmm/HAMAP.hmm /dev/stdin > \/share\/gsi2\/data\/www\/soap\-data\/M2BBS\/Phylogenomic\/Prochlorococcus\/prokka\/Aaal\/HAMAP\.hmm\.hmmer3 2> /dev/null [17:49:49] Deleting unwanted file: /share/gsi2/data/www/soap-data/M2BBS/Phylogenomic/Prochlorococcus/prokka/Aaal/HAMAP.hmm.faa [17:49:49] Deleting unwanted file: /share/gsi2/data/www/soap-data/M2BBS/Phylogenomic/Prochlorococcus/prokka/Aaal/HAMAP.hmm.hmmer3 [17:49:49] Labelling remaining 1348 proteins as 'hypothetical protein' [17:49:49] Possible /pseudo 'Putative fluoride ion transporter CrcB' at gnl|Prokka|AaalA01.g_1 position 177259 [17:49:49] Possible /pseudo 'Photosystem I assembly protein Ycf3' at gnl|Prokka|AaalA01.g_1 position 299748 [17:49:49] Possible /pseudo 'DNA-directed RNA polymerase subunit beta'' at gnl|Prokka|AaalA01.g_1 position 442268 [17:49:49] Possible /pseudo 'Long-chain acyl-[acyl-carrier-protein] reductase' at gnl|Prokka|AaalA01.g_1 position 717282 [17:49:49] Possible /pseudo 'Murein DD-endopeptidase MepM' at gnl|Prokka|AaalA01.g_1 position 1261676 [17:49:49] Possible /pseudo 'putative zinc protease' at gnl|Prokka|AaalA01.g_1 position 1446307 [17:49:49] Possible /pseudo 'ATP-dependent Clp protease proteolytic subunit' at gnl|Prokka|AaalA01.g_1 position 1760486 [17:49:49] Possible /pseudo 'Prophage integrase IntA' at gnl|Prokka|AaalA01.g_1 position 1792323 [17:49:49] Possible /pseudo 'putative phycocyanin operon protein Z' at gnl|Prokka|AaalA01.g_1 position 1980101 [17:49:49] Possible /pseudo 'TPR repeat-containing protein YrrB' at gnl|Prokka|AaalA01.g_1 position 2118119 [17:49:49] Possible /pseudo 'TPR repeat-containing protein YrrB' at gnl|Prokka|AaalA01.g_1 position 2126498 [17:49:49] Possible /pseudo 'TPR repeat-containing protein YrrB' at gnl|Prokka|AaalA01.g_1 position 2539765 [17:49:49] Possible /pseudo 'TPR repeat-containing protein YrrB' at gnl|Prokka|AaalA01.g_1 position 2540760 [17:49:49] Possible /pseudo 'TPR repeat-containing protein YrrB' at gnl|Prokka|AaalA01.g_1 position 2542584 [17:49:49] Possible /pseudo 'TPR repeat-containing protein YrrB' at gnl|Prokka|AaalA01.g_1 position 2543667 [17:49:49] Found 1103 unique /gene codes. [17:49:49] Fixed 6 duplicate /gene - ycf3_1 ycf3_2 ycf3_3 ycf3_4 ycf3_5 ycf3_6 [17:49:49] Fixed 2 duplicate /gene - hhoA_1 hhoA_2 [17:49:49] Fixed 3 duplicate /gene - hisF_1 hisF_2 hisF_3 [17:49:49] Fixed 2 duplicate /gene - gph_1 gph_2 [17:49:49] Fixed 2 duplicate /gene - rnr_1 rnr_2 [17:49:49] Fixed 2 duplicate /gene - phoC_1 phoC_2 [17:49:49] Fixed 5 duplicate /gene - ltxA_1 ltxA_2 ltxA_3 ltxA_4 ltxA_5 [17:49:49] Fixed 2 duplicate /gene - thiO_1 thiO_2 [17:49:49] Fixed 2 duplicate /gene - phnD_1 phnD_2 [17:49:49] Fixed 2 duplicate /gene - queD_1 queD_2 [17:49:49] Fixed 2 duplicate /gene - spkB_1 spkB_2 [17:49:49] Fixed 2 duplicate /gene - phnE_1 phnE_2 [17:49:49] Fixed 2 duplicate /gene - ykfA_1 ykfA_2 [17:49:49] Fixed 2 duplicate /gene - dapb3_1 dapb3_2 [17:49:49] Fixed 2 duplicate /gene - bfmBAB_1 bfmBAB_2 [17:49:49] Fixed 2 duplicate /gene - dapL_1 dapL_2 [17:49:49] Fixed 2 duplicate /gene - msrB_1 msrB_2 [17:49:49] Fixed 2 duplicate /gene - znuC_1 znuC_2 [17:49:49] Fixed 2 duplicate /gene - prtA_1 prtA_2 [17:49:49] Fixed 2 duplicate /gene - epsD_1 epsD_2 [17:49:49] Fixed 2 duplicate /gene - prfA_1 prfA_2 [17:49:49] Fixed 2 duplicate /gene - lexA_1 lexA_2 [17:49:49] Fixed 2 duplicate /gene - petJ_1 petJ_2 [17:49:49] Fixed 2 duplicate /gene - plsC_1 plsC_2 [17:49:49] Fixed 21 duplicate /gene - yrrB_1 yrrB_2 yrrB_3 yrrB_4 yrrB_5 yrrB_6 yrrB_7 yrrB_8 yrrB_9 yrrB_10 yrrB_11 yrrB_12 yrrB_13 yrrB_14 yrrB_15 yrrB_16 yrrB_17 yrrB_18 yrrB_19 yrrB_20 yrrB_21 [17:49:49] Fixed 2 duplicate /gene - mntB_1 mntB_2 [17:49:49] Fixed 2 duplicate /gene - btuR_1 btuR_2 [17:49:49] Fixed 2 duplicate /gene - tig_1 tig_2 [17:49:49] Fixed 2 duplicate /gene - ugpC_1 ugpC_2 [17:49:49] Fixed 2 duplicate /gene - aroB_1 aroB_2 [17:49:49] Fixed 2 duplicate /gene - hisH_1 hisH_2 [17:49:49] Fixed 2 duplicate /gene - ynaI_1 ynaI_2 [17:49:49] Fixed 3 duplicate /gene - bcp_1 bcp_2 bcp_3 [17:49:49] Fixed 2 duplicate /gene - mshA_1 mshA_2 [17:49:49] Fixed 2 duplicate /gene - gyrA_1 gyrA_2 [17:49:49] Fixed 2 duplicate /gene - pyrE_1 pyrE_2 [17:49:49] Fixed 4 duplicate /gene - dnaJ_1 dnaJ_2 dnaJ_3 dnaJ_4 [17:49:49] Fixed 4 duplicate /gene - slpA_1 slpA_2 slpA_3 slpA_4 [17:49:49] Fixed 2 duplicate /gene - vraR_1 vraR_2 [17:49:49] Fixed 2 duplicate /gene - carA_1 carA_2 [17:49:49] Fixed 2 duplicate /gene - sepF_1 sepF_2 [17:49:49] Fixed 2 duplicate /gene - dnaX_1 dnaX_2 [17:49:49] Fixed 2 duplicate /gene - cobD_1 cobD_2 [17:49:49] Fixed 3 duplicate /gene - mepM_1 mepM_2 mepM_3 [17:49:49] Fixed 2 duplicate /gene - pcyA_1 pcyA_2 [17:49:49] Fixed 2 duplicate /gene - hpf_1 hpf_2 [17:49:49] Fixed 3 duplicate /gene - hin_1 hin_2 hin_3 [17:49:49] Fixed 2 duplicate /gene - pilT_1 pilT_2 [17:49:49] Fixed 2 duplicate /gene - sir_1 sir_2 [17:49:49] Fixed 2 duplicate /gene - cyaA_1 cyaA_2 [17:49:49] Fixed 2 duplicate /gene - intQ_1 intQ_2 [17:49:49] Fixed 2 duplicate /gene - mnmC_1 mnmC_2 [17:49:49] Fixed 2 duplicate /gene - gatA_1 gatA_2 [17:49:49] Fixed 3 duplicate /gene - pds_1 pds_2 pds_3 [17:49:49] Fixed 2 duplicate /gene - clpS_1 clpS_2 [17:49:49] Fixed 2 duplicate /gene - msrR_1 msrR_2 [17:49:49] Fixed 2 duplicate /gene - aprA_1 aprA_2 [17:49:49] Fixed 2 duplicate /gene - psaB_1 psaB_2 [17:49:49] Fixed 3 duplicate /gene - pstS_1 pstS_2 pstS_3 [17:49:49] Fixed 2 duplicate /gene - speA_1 speA_2 [17:49:49] Fixed 2 duplicate /gene - ppa_1 ppa_2 [17:49:49] Fixed 2 duplicate /gene - def_1 def_2 [17:49:49] Fixed 3 duplicate /gene - mprA_1 mprA_2 mprA_3 [17:49:49] Fixed 2 duplicate /gene - iscS_1 iscS_2 [17:49:49] Fixed 2 duplicate /gene - era_1 era_2 [17:49:49] Fixed 2 duplicate /gene - dfa3_1 dfa3_2 [17:49:49] Fixed 2 duplicate /gene - ltxB_1 ltxB_2 [17:49:49] Fixed 2 duplicate /gene - suhB_1 suhB_2 [17:49:49] Fixed 3 duplicate /gene - algE7_1 algE7_2 algE7_3 [17:49:49] Fixed 2 duplicate /gene - atpG_1 atpG_2 [17:49:49] Fixed 3 duplicate /gene - glnQ_1 glnQ_2 glnQ_3 [17:49:49] Fixed 2 duplicate /gene - rmlD_1 rmlD_2 [17:49:49] Fixed 2 duplicate /gene - lip3_1 lip3_2 [17:49:49] Fixed 2 duplicate /gene - nuoL_1 nuoL_2 [17:49:49] Fixed 3 duplicate /gene - bepA_1 bepA_2 bepA_3 [17:49:49] Fixed 2 duplicate /gene - cca_1 cca_2 [17:49:49] Fixed 4 duplicate /gene - clpP_1 clpP_2 clpP_3 clpP_4 [17:49:49] Fixed 2 duplicate /gene - clcA_1 clcA_2 [17:49:49] Fixed 2 duplicate /gene - bchI_1 bchI_2 [17:49:49] Fixed 2 duplicate /gene - bepF_1 bepF_2 [17:49:49] Fixed 2 duplicate /gene - dnaK2_1 dnaK2_2 [17:49:49] Fixed 2 duplicate /gene - purE_1 purE_2 [17:49:49] Fixed 2 duplicate /gene - der_1 der_2 [17:49:49] Fixed 2 duplicate /gene - rpsA_1 rpsA_2 [17:49:49] Fixed 2 duplicate /gene - rapA_1 rapA_2 [17:49:49] Fixed 2 duplicate /gene - galE1_1 galE1_2 [17:49:49] Fixed 2 duplicate /gene - crcB_1 crcB_2 [17:49:49] Fixed 2 duplicate /gene - coaE_1 coaE_2 [17:49:49] Fixed 2 duplicate /gene - gltS_1 gltS_2 [17:49:49] Fixed 2 duplicate /gene - psbA_1 psbA_2 [17:49:49] Fixed 2 duplicate /gene - rpoC_1 rpoC_2 [17:49:49] Fixed 2 duplicate /gene - aspC_1 aspC_2 [17:49:49] Fixed 2 duplicate /gene - ftsH2_1 ftsH2_2 [17:49:49] Fixed 2 duplicate /gene - smc_1 smc_2 [17:49:49] Fixed 3 duplicate /gene - cugP_1 cugP_2 cugP_3 [17:49:49] Fixed 3 duplicate /gene - intA_1 intA_2 intA_3 [17:49:49] Fixed 2 duplicate /gene - ccmK_1 ccmK_2 [17:49:49] Fixed 2 duplicate /gene - degU_1 degU_2 [17:49:49] Fixed 2 duplicate /gene - acr1_1 acr1_2 [17:49:49] Fixed 2 duplicate /gene - trxA_1 trxA_2 [17:49:49] Fixed 2 duplicate /gene - menJ_1 menJ_2 [17:49:49] Fixed 2 duplicate /gene - pld_1 pld_2 [17:49:49] Fixed 3 duplicate /gene - menG_1 menG_2 menG_3 [17:49:49] Fixed 2 duplicate /gene - ndhD1_1 ndhD1_2 [17:49:49] Fixed 2 duplicate /gene - queE_1 queE_2 [17:49:49] Fixed 2 duplicate /gene - strE_1 strE_2 [17:49:49] Fixed 2 duplicate /gene - lpxB_1 lpxB_2 [17:49:49] Fixed 3 duplicate /gene - lytB_1 lytB_2 lytB_3 [17:49:49] Fixed 6 duplicate /gene - sigA2_1 sigA2_2 sigA2_3 sigA2_4 sigA2_5 sigA2_6 [17:49:49] Fixed 3 duplicate /gene - ubiB_1 ubiB_2 ubiB_3 [17:49:49] Fixed 2 duplicate /gene - novN_1 novN_2 [17:49:49] Fixed 2 duplicate /gene - tam_1 tam_2 [17:49:49] Fixed 2 duplicate /gene - corC_1 corC_2 [17:49:49] Fixed 2 duplicate /gene - cysC_1 cysC_2 [17:49:49] Fixed 2 duplicate /gene - ntcA_1 ntcA_2 [17:49:49] Fixed 3 duplicate /gene - fabG_1 fabG_2 fabG_3 [17:49:49] Fixed 2 duplicate /gene - psaA_1 psaA_2 [17:49:49] Fixed 2 duplicate /gene - tal_1 tal_2 [17:49:49] Fixed 2 duplicate /gene - ubiE_1 ubiE_2 [17:49:49] Fixed 3 duplicate /gene - yciC_1 yciC_2 yciC_3 [17:49:49] Fixed 2 duplicate /gene - pbsA1_1 pbsA1_2 [17:49:49] Fixed 2 duplicate /gene - acoA_1 acoA_2 [17:49:49] Fixed 2 duplicate /gene - cobN_1 cobN_2 [17:49:49] Fixed 2 duplicate /gene - clpB1_1 clpB1_2 [17:49:49] Fixed 2 duplicate /gene - ppiB_1 ppiB_2 [17:49:49] Fixed 2 duplicate /gene - pyrC_1 pyrC_2 [17:49:49] Fixed 2 duplicate /gene - crtL_1 crtL_2 [17:49:49] Fixed 2 duplicate /gene - sasA_1 sasA_2 [17:49:49] Fixed 128 colliding /gene names. [17:49:49] Adding /locus_tag identifiers [17:49:49] Assigned 2783 locus_tags to CDS and RNA features. [17:49:49] Writing outputs to /share/gsi2/data/www/soap-data/M2BBS/Phylogenomic/Prochlorococcus/prokka/Aaal/ [17:50:00] Generating annotation statistics file [17:50:00] Generating Genbank and Sequin files [17:50:00] 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 \/share\/gsi2\/data\/www\/soap\-data\/M2BBS\/Phylogenomic\/Prochlorococcus\/prokka\/Aaal\/AaalA01\.err -i \/share\/gsi2\/data\/www\/soap\-data\/M2BBS\/Phylogenomic\/Prochlorococcus\/prokka\/Aaal\/AaalA01\.fsa 2> /dev/null [17:50:08] Deleting unwanted file: /share/gsi2/data/www/soap-data/M2BBS/Phylogenomic/Prochlorococcus/prokka/Aaal/errorsummary.val [17:50:08] Deleting unwanted file: /share/gsi2/data/www/soap-data/M2BBS/Phylogenomic/Prochlorococcus/prokka/Aaal/AaalA01.dr [17:50:08] Deleting unwanted file: /share/gsi2/data/www/soap-data/M2BBS/Phylogenomic/Prochlorococcus/prokka/Aaal/AaalA01.fixedproducts [17:50:08] Deleting unwanted file: /share/gsi2/data/www/soap-data/M2BBS/Phylogenomic/Prochlorococcus/prokka/Aaal/AaalA01.ecn [17:50:08] Deleting unwanted file: /share/gsi2/data/www/soap-data/M2BBS/Phylogenomic/Prochlorococcus/prokka/Aaal/AaalA01.val [17:50:08] Repairing broken .GBK output that tbl2asn produces... [17:50:08] Running: sed 's/COORDINATES: profile/COORDINATES:profile/' < \/share\/gsi2\/data\/www\/soap\-data\/M2BBS\/Phylogenomic\/Prochlorococcus\/prokka\/Aaal\/AaalA01\.gbf > \/share\/gsi2\/data\/www\/soap\-data\/M2BBS\/Phylogenomic\/Prochlorococcus\/prokka\/Aaal\/AaalA01\.gbk [17:50:08] Deleting unwanted file: /share/gsi2/data/www/soap-data/M2BBS/Phylogenomic/Prochlorococcus/prokka/Aaal/AaalA01.gbf [17:50:08] Output files: [17:50:08] /share/gsi2/data/www/soap-data/M2BBS/Phylogenomic/Prochlorococcus/prokka/Aaal/AaalA01.log [17:50:08] /share/gsi2/data/www/soap-data/M2BBS/Phylogenomic/Prochlorococcus/prokka/Aaal/AaalA01.fna [17:50:08] /share/gsi2/data/www/soap-data/M2BBS/Phylogenomic/Prochlorococcus/prokka/Aaal/AaalA01.gff [17:50:08] /share/gsi2/data/www/soap-data/M2BBS/Phylogenomic/Prochlorococcus/prokka/Aaal/AaalA01.faa [17:50:08] /share/gsi2/data/www/soap-data/M2BBS/Phylogenomic/Prochlorococcus/prokka/Aaal/AaalA01.ffn [17:50:08] /share/gsi2/data/www/soap-data/M2BBS/Phylogenomic/Prochlorococcus/prokka/Aaal/AaalA01.tbl [17:50:08] /share/gsi2/data/www/soap-data/M2BBS/Phylogenomic/Prochlorococcus/prokka/Aaal/AaalA01.fsa [17:50:08] /share/gsi2/data/www/soap-data/M2BBS/Phylogenomic/Prochlorococcus/prokka/Aaal/AaalA01.tsv [17:50:08] /share/gsi2/data/www/soap-data/M2BBS/Phylogenomic/Prochlorococcus/prokka/Aaal/AaalA01.txt [17:50:08] /share/gsi2/data/www/soap-data/M2BBS/Phylogenomic/Prochlorococcus/prokka/Aaal/AaalA01.sqn [17:50:08] /share/gsi2/data/www/soap-data/M2BBS/Phylogenomic/Prochlorococcus/prokka/Aaal/AaalA01.err [17:50:08] /share/gsi2/data/www/soap-data/M2BBS/Phylogenomic/Prochlorococcus/prokka/Aaal/AaalA01.gbk [17:50:08] Annotation finished successfully. [17:50:08] Walltime used: 5.88 minutes [17:50:08] If you use this result please cite the Prokka paper: [17:50:08] Seemann T (2014) Prokka: rapid prokaryotic genome annotation. Bioinformatics. 30(14):2068-9. [17:50:08] Type 'prokka --citation' for more details. [17:50:08] Share and enjoy!