[17:44:16] This is prokka 1.12 [17:44:16] Written by Torsten Seemann [17:44:16] Homepage is https://github.com/tseemann/prokka [17:44:16] Local time is Thu Sep 6 17:44:16 2018 [17:44:16] You are gsi [17:44:16] Operating system is linux [17:44:16] You have BioPerl 1.007002 [17:44:16] System has 16 cores. [17:44:16] Will use maximum of 1 cores. [17:44:16] Annotating as >>> Bacteria <<< [17:44:16] Enabling options to ensure Genbank/ENA/DDJB submission compliance. [17:44:16] Creating new output folder: /share/gsi2/data/www/soap-data/M2BBS/Phylogenomic/Prochlorococcus/prokka/Aaaa [17:44:16] Running: mkdir -p \/share\/gsi2\/data\/www\/soap\-data\/M2BBS\/Phylogenomic\/Prochlorococcus\/prokka\/Aaaa [17:44:16] Using filename prefix: AaaaA01.XXX [17:44:16] Setting HMMER_NCPU=1 [17:44:16] Writing log to: /share/gsi2/data/www/soap-data/M2BBS/Phylogenomic/Prochlorococcus/prokka/Aaaa/AaaaA01.log [17:44:16] Command: /share/gsi2/bin/prokka /share/gsi2/data/www/soap-data/M2BBS/Phylogenomic/Prochlorococcus/DNA/Aaaa/AaaaA01.fas --compliant --addgenes --outdir /share/gsi2/data/www/soap-data/M2BBS/Phylogenomic/Prochlorococcus/prokka/Aaaa --prefix AaaaA01 --locustag AaaaA01.g --species Prochlorococcusmarinussubsp --strain marinusstrCCMP1375 --kingdom bacteria --cpus 1 --force [17:44:16] Appending to PATH: /share/gsi2/software/prokka/bin/../binaries/linux [17:44:16] Appending to PATH: /share/gsi2/software/prokka/bin/../binaries/linux/../common [17:44:16] Appending to PATH: /share/gsi2/software/prokka/bin [17:44:16] Looking for 'aragorn' - found /share/gsi2/software/prokka/bin/../binaries/linux/aragorn [17:44:16] Determined aragorn version is 1.2 [17:44:16] Looking for 'barrnap' - found /share/gsi2/bin/barrnap [17:44:16] Determined barrnap version is 0.9 [17:44:16] Looking for 'blastp' - found /share/gsi2/bin/blastp [17:44:19] Determined blastp version is 2.7 [17:44:19] Looking for 'cmpress' - found /share/gsi2/software/prokka/bin/../binaries/linux/cmpress [17:44:19] Determined cmpress version is 1.1 [17:44:19] Looking for 'cmscan' - found /share/gsi2/software/prokka/bin/../binaries/linux/cmscan [17:44:19] Determined cmscan version is 1.1 [17:44:19] Looking for 'egrep' - found /bin/egrep [17:44:19] Looking for 'find' - found /bin/find [17:44:19] Looking for 'grep' - found /bin/grep [17:44:19] Looking for 'hmmpress' - found /share/gsi2/bin/hmmpress [17:44:19] Determined hmmpress version is 3.1 [17:44:19] Looking for 'hmmscan' - found /share/gsi2/bin/hmmscan [17:44:19] Determined hmmscan version is 3.1 [17:44:19] Looking for 'java' - found /usr/java/latest/bin/java [17:44:19] Looking for 'less' - found /usr/bin/less [17:44:19] Looking for 'makeblastdb' - found /share/gsi2/bin/makeblastdb [17:44:20] Determined makeblastdb version is 2.7 [17:44:20] Looking for 'minced' - found /share/gsi2/bin/minced [17:44:20] Determined minced version is 2.0 [17:44:20] Looking for 'parallel' - found /share/gsi2/software/prokka/bin/../binaries/linux/../common/parallel [17:44:21] Determined parallel version is 20150122 [17:44:21] Looking for 'prodigal' - found /share/gsi2/software/prokka/bin/../binaries/linux/prodigal [17:44:21] Determined prodigal version is 2.6 [17:44:21] Looking for 'prokka-genbank_to_fasta_db' - found /share/gsi2/software/prokka/bin/prokka-genbank_to_fasta_db [17:44:21] Looking for 'rnammer' - found /share/gsi2/bin/rnammer [17:44:21] Determined rnammer version is 1.2 [17:44:21] Looking for 'sed' - found /bin/sed [17:44:21] Looking for 'tbl2asn' - found /share/gsi2/bin/tbl2asn [17:44:21] Determined tbl2asn version is 25.6 [17:44:21] Using genetic code table 11. [17:44:21] Loading and checking input file: /share/gsi2/data/www/soap-data/M2BBS/Phylogenomic/Prochlorococcus/DNA/Aaaa/AaaaA01.fas [17:44:22] Wrote 1 contigs totalling 1751080 bp. [17:44:22] Predicting tRNAs and tmRNAs [17:44:22] Running: aragorn -l -gc11 -w \/share\/gsi2\/data\/www\/soap\-data\/M2BBS\/Phylogenomic\/Prochlorococcus\/prokka\/Aaaa\/AaaaA01\.fna [17:44:23] 1 tmRNA* c[75304,75615] 171,221 ANKIVSFSRQTAPVAA* [17:44:23] 2 tRNA-Leu c[84969,85052] 36 (aag) [17:44:23] 3 tRNA-Asn [146967,147038] 33 (gtt) [17:44:23] 4 tRNA-Leu c[262281,262362] 35 (tag) [17:44:23] 5 tRNA-Arg c[282703,282778] 36 (acg) [17:44:23] 6 tRNA-Met c[298481,298553] 34 (cat) [17:44:23] 7 tRNA-Phe c[334895,334970] 34 (gaa) [17:44:23] 8 tRNA-Thr c[345077,345151] 34 (tgt) [17:44:23] 9 tRNA-Ile [354972,355047] 36 (gat) [17:44:23] 10 tRNA-Ala [355056,355129] 34 (tgc) [17:44:23] 11 tRNA-Thr c[366468,366538] 33 (agt) [17:44:23] 12 tRNA-Thr c[370506,370578] 33 (ggt) [17:44:23] 13 tRNA-Tyr c[370587,370670] 35 (gta) [17:44:23] 14 tRNA-Asp c[451915,451990] 36 (gtc) [17:44:23] 15 tRNA-Trp c[452381,452455] 35 (cca) [17:44:23] 16 tRNA-Leu [544513,544600] 36 (taa) [17:44:23] 17 tRNA-Lys [554562,554635] 34 (ttt) [17:44:23] 18 tRNA-Pro [562384,562458] 35 (tgg) [17:44:23] 19 tRNA-SeC [600120,600192] 33 (tca) [17:44:23] 20 tRNA-Gly [651118,651189] 33 (ccc) [17:44:23] 21 tRNA-Pro c[670780,670855] 36 (ggg) [17:44:23] 22 tRNA-Ser c[736097,736185] 36 (tga) [17:44:23] 23 tRNA-Met c[811193,811269] 35 (cat) [17:44:23] 24 tRNA-Ser [852209,852295] 35 (gga) [17:44:23] 25 tRNA-Met [896720,896793] 35 (cat) [17:44:23] 26 tRNA-Glu [1049321,1049395] 36 (ttc) [17:44:23] 27 tRNA-Ser [1173899,1173985] 35 (cga) [17:44:23] 28 tRNA-Arg [1212078,1212151] 35 (tct) [17:44:23] 29 tRNA-Ala c[1237211,1237286] 35 (ggc) [17:44:23] 30 tRNA-Leu c[1275824,1275908] 36 (cag) [17:44:23] 31 tRNA-Leu [1277487,1277569] 35 (caa) [17:44:23] 32 tRNA-His [1282673,1282746] 34 (gtg) [17:44:23] 33 tRNA-Gly c[1304181,1304251] 33 (tcc) [17:44:23] 34 tRNA-Val [1337241,1337312] 33 (gac) [17:44:23] 35 tRNA-Thr [1510408,1510479] 33 (cgt) [17:44:23] 36 tRNA-Ser c[1546423,1546512] 35 (gct) [17:44:23] 37 tRNA-Gln [1566956,1567027] 33 (ttg) [17:44:23] 38 tRNA-Arg [1580264,1580339] 36 (ccg) [17:44:23] 39 tRNA-Cys [1595707,1595777] 33 (gca) [17:44:23] 40 tRNA-Arg c[1616669,1616744] 36 (cct) [17:44:23] 41 tRNA-Gly c[1656288,1656359] 33 (gcc) [17:44:23] 42 tRNA-Val c[1704853,1704924] 33 (tac) [17:44:23] Found 42 tRNAs [17:44:23] Predicting Ribosomal RNAs [17:44:23] Running Barrnap with 1 threads [17:44:26] 1 gnl|Prokka|AaaaA01.g_1 353314 16S ribosomal RNA [17:44:26] 2 gnl|Prokka|AaaaA01.g_1 355464 23S ribosomal RNA [17:44:26] 3 gnl|Prokka|AaaaA01.g_1 358433 5S ribosomal RNA [17:44:26] Found 3 rRNAs [17:44:26] Skipping ncRNA search, enable with --rfam if desired. [17:44:26] Total of 44 tRNA + rRNA features [17:44:26] Searching for CRISPR repeats [17:44:27] Found 0 CRISPRs [17:44:27] Predicting coding sequences [17:44:27] Contigs total 1751080 bp, so using single mode [17:44:27] Running: prodigal -i \/share\/gsi2\/data\/www\/soap\-data\/M2BBS\/Phylogenomic\/Prochlorococcus\/prokka\/Aaaa\/AaaaA01\.fna -c -m -g 11 -p single -f sco -q [17:44:33] Excluding CDS which overlaps existing RNA (rRNA) at gnl|Prokka|AaaaA01.g_1:353358..353756 on - strand [17:44:33] Excluding CDS which overlaps existing RNA (tRNA) at gnl|Prokka|AaaaA01.g_1:452157..452411 on - strand [17:44:34] Excluding CDS which overlaps existing RNA (tRNA) at gnl|Prokka|AaaaA01.g_1:544429..544614 on + strand [17:44:34] Excluding CDS which overlaps existing RNA (tRNA) at gnl|Prokka|AaaaA01.g_1:600113..600295 on + strand [17:44:34] Excluding CDS which overlaps existing RNA (tRNA) at gnl|Prokka|AaaaA01.g_1:1049395..1049916 on - strand [17:44:35] Excluding CDS which overlaps existing RNA (tRNA) at gnl|Prokka|AaaaA01.g_1:1277496..1278761 on + strand [17:44:35] Found 1902 CDS [17:44:35] Connecting features back to sequences [17:44:35] Not using genus-specific database. Try --usegenus to enable it. [17:44:35] Annotating CDS, please be patient. [17:44:35] Will use 1 CPUs for similarity searching. [17:44:38] There are still 1902 unannotated CDS left (started with 1902) [17:44:38] Will use blast to search against /share/gsi2/software/prokka/bin/../db/kingdom/Bacteria/sprot with 1 CPUs [17:44:38] Running: cat \/share\/gsi2\/data\/www\/soap\-data\/M2BBS\/Phylogenomic\/Prochlorococcus\/prokka\/Aaaa\/sprot\.faa | parallel --gnu --plain -j 1 --block 264784 --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\/Aaaa\/sprot\.blast 2> /dev/null [17:47:21] Modify product: N utilization substance protein B homolog => N utilization substance protein B [17:47:21] Modify product: Nucleoid-associated protein Cthe_2143 => Nucleoid-associated protein [17:47:21] Modify product: Probable cysteine desulfurase => putative cysteine desulfurase [17:47:21] Modify product: Uncharacterized transporter Rv2685 => putative transporter [17:47:21] Modify product: Uncharacterized ABC transporter ATP-binding protein YheS => putative ABC transporter ATP-binding protein YheS [17:47:21] Modify product: Vitamin K epoxide reductase homolog => Vitamin K epoxide reductase [17:47:21] Modify product: Epimerase family protein Rv2216 => Epimerase family protein [17:47:21] Modify product: Probable adenylyl-sulfate kinase => putative adenylyl-sulfate kinase [17:47:22] Modify product: Probable nicotinate-nucleotide pyrophosphorylase [carboxylating] => putative nicotinate-nucleotide pyrophosphorylase [carboxylating] [17:47:22] Modify product: Probable protein kinase UbiB => putative protein kinase UbiB [17:47:22] Modify product: Probable bifunctional SAT/APS kinase => putative bifunctional SAT/APS kinase [17:47:22] Modify product: Probable lipid II flippase MurJ => putative lipid II flippase MurJ [17:47:22] Modify product: Probable phospholipid import ATP-binding protein MlaF => putative phospholipid import ATP-binding protein MlaF [17:47:22] Modify product: Uncharacterized phycocyanin operon protein Z => putative phycocyanin operon protein Z [17:47:22] Modify product: Uncharacterized phycocyanin operon protein Z => putative phycocyanin operon protein Z [17:47:22] Modify product: Probable phycoerythrobilin lyase CpeT => putative phycoerythrobilin lyase CpeT [17:47:22] Modify product: Uncharacterized glycosyltransferase sll0501 => putative glycosyltransferase [17:47:22] Modify product: Uncharacterized ABC transporter ATP-binding protein YknY => putative ABC transporter ATP-binding protein YknY [17:47:22] Modify product: Probable cytochrome c oxidase subunit 1 => putative cytochrome c oxidase subunit 1 [17:47:22] Modify product: Probable murein peptide carboxypeptidase => putative murein peptide carboxypeptidase [17:47:22] Modify product: Thylakoid-associated single-stranded DNA-binding protein slr1034 => Thylakoid-associated single-stranded DNA-binding protein [17:47:22] Modify product: Uncharacterized sugar kinase YdjH => putative sugar kinase YdjH [17:47:22] Modify product: Probable multidrug resistance ABC transporter ATP-binding/permease protein YheH => putative multidrug resistance ABC transporter ATP-binding/permease protein YheH [17:47:22] Modify product: Uncharacterized glycosyltransferase Rv0539 => putative glycosyltransferase [17:47:22] Modify product: Probable undecaprenyl-phosphate N-acetylglucosaminyl 1-phosphate transferase => putative undecaprenyl-phosphate N-acetylglucosaminyl 1-phosphate transferase [17:47:22] Modify product: Probable multidrug resistance ABC transporter ATP-binding/permease protein YheI => putative multidrug resistance ABC transporter ATP-binding/permease protein YheI [17:47:22] Modify product: Probable trans-aconitate 2-methyltransferase => putative trans-aconitate 2-methyltransferase [17:47:22] Modify product: Uncharacterized zinc protease Rv2782c => putative zinc protease [17:47:22] Modify product: Uncharacterized ABC transporter ATP-binding protein Rv0986 => putative ABC transporter ATP-binding protein [17:47:22] Modify product: GTP-binding protein TypA/BipA homolog => GTP-binding protein TypA/BipA [17:47:22] Modify product: Putative multidrug export ATP-binding/permease protein SA1683 => Putative multidrug export ATP-binding/permease protein [17:47:23] Modify product: Probable ferredoxin/ferredoxin--NADP reductase => putative ferredoxin/ferredoxin--NADP reductase [17:47:23] Modify product: Probable peroxiredoxin => putative peroxiredoxin [17:47:23] Modify product: Phosphorylated carbohydrates phosphatase TM_1254 => Phosphorylated carbohydrates phosphatase [17:47:23] Modify product: Uncharacterized ABC transporter ATP-binding protein Rv0986 => putative ABC transporter ATP-binding protein [17:47:23] Modify product: Uncharacterized methyltransferase YcgJ => putative methyltransferase YcgJ [17:47:23] Modify product: Probable 2-phosphosulfolactate phosphatase => putative 2-phosphosulfolactate phosphatase [17:47:23] Modify product: Uncharacterized ABC transporter ATP-binding protein TM_0288 => putative ABC transporter ATP-binding protein [17:47:23] Modify product: Probable protein kinase UbiB => putative protein kinase UbiB [17:47:23] Modify product: Bifunctional protein FolD => Bifunctional protein FolD protein [17:47:23] Modify product: 1,4-alpha-glucan branching enzyme TTHA1902 => 1,4-alpha-glucan branching enzyme [17:47:23] Modify product: Uncharacterized oxidoreductase MSMEG_1603/MSMEI_1564 => putative oxidoreductase/MSMEI_1564 [17:47:23] Modify product: Probable peptidyl-prolyl cis-trans isomerase => putative peptidyl-prolyl cis-trans isomerase [17:47:23] Modify product: Maf-like protein Rv3282 => Maf-like protein [17:47:23] Modify product: Putative Rieske 2Fe-2S iron-sulfur protein MSMEG_6410/MSMEI_6242 => Putative Rieske 2Fe-2S iron-sulfur protein/MSMEI_6242 [17:47:23] Modify product: PKHD-type hydroxylase Sbal_3634 => PKHD-type hydroxylase [17:47:23] Modify product: Uncharacterized 33.6 kDa protein in fasciation locus => putative 33.6 kDa protein in fasciation locus [17:47:23] Modify product: Uncharacterized FAD-linked oxidoreductase Rv2280 => putative FAD-linked oxidoreductase [17:47:23] Modify product: Oxygen-independent coproporphyrinogen-III oxidase-like protein sll1917 => Oxygen-independent coproporphyrinogen-III oxidase-like protein [17:47:23] Modify product: Uncharacterized PIN and TRAM-domain containing protein YacL => putative PIN and TRAM-domain containing protein YacL [17:47:23] Modify product: Glycogen operon protein GlgX homolog => Glycogen operon protein GlgX [17:47:23] Modify product: Probable phospholipid ABC transporter permease protein MlaE => putative phospholipid ABC transporter permease protein MlaE [17:47:23] Modify product: Cyclic nucleotide-gated potassium channel mll3241 => Cyclic nucleotide-gated potassium channel [17:47:23] Modify product: Probable 30S ribosomal protein PSRP-3 => putative 30S ribosomal protein PSRP-3 [17:47:23] Modify product: Probable nicotinate-nucleotide adenylyltransferase => putative nicotinate-nucleotide adenylyltransferase [17:47:23] Modify product: Probable peptidoglycan glycosyltransferase FtsW => putative peptidoglycan glycosyltransferase FtsW [17:47:23] Modify product: Probable helicase HelY => putative helicase HelY [17:47:23] Modify product: Probable trans-aconitate 2-methyltransferase => putative trans-aconitate 2-methyltransferase [17:47:23] Modify product: Probable cobalt-factor III C(17)-methyltransferase => putative cobalt-factor III C(17)-methyltransferase [17:47:24] Modify product: Probable adenylyltransferase/sulfurtransferase MoeZ => putative adenylyltransferase/sulfurtransferase MoeZ [17:47:24] Modify product: Uncharacterized hydrolase YxeP => putative hydrolase YxeP [17:47:24] Modify product: Probable protein kinase UbiB => putative protein kinase UbiB [17:47:24] Cleaned 62 /product names [17:47:24] Deleting unwanted file: /share/gsi2/data/www/soap-data/M2BBS/Phylogenomic/Prochlorococcus/prokka/Aaaa/sprot.faa [17:47:24] Deleting unwanted file: /share/gsi2/data/www/soap-data/M2BBS/Phylogenomic/Prochlorococcus/prokka/Aaaa/sprot.blast [17:47:25] There are still 886 unannotated CDS left (started with 1902) [17:47:25] Will use hmmer3 to search against /share/gsi2/software/prokka/bin/../db/hmm/HAMAP.hmm with 1 CPUs [17:47:25] Running: cat \/share\/gsi2\/data\/www\/soap\-data\/M2BBS\/Phylogenomic\/Prochlorococcus\/prokka\/Aaaa\/HAMAP\.hmm\.faa | parallel --gnu --plain -j 1 --block 79750 --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\/Aaaa\/HAMAP\.hmm\.hmmer3 2> /dev/null [17:48:45] Deleting unwanted file: /share/gsi2/data/www/soap-data/M2BBS/Phylogenomic/Prochlorococcus/prokka/Aaaa/HAMAP.hmm.faa [17:48:45] Deleting unwanted file: /share/gsi2/data/www/soap-data/M2BBS/Phylogenomic/Prochlorococcus/prokka/Aaaa/HAMAP.hmm.hmmer3 [17:48:45] Labelling remaining 825 proteins as 'hypothetical protein' [17:48:45] Possible /pseudo 'putative phycocyanin operon protein Z' at gnl|Prokka|AaaaA01.g_1 position 328493 [17:48:45] Possible /pseudo 'UDP-glucose 4-epimerase' at gnl|Prokka|AaaaA01.g_1 position 1214631 [17:48:45] Possible /pseudo 'ATP-dependent Clp protease proteolytic subunit' at gnl|Prokka|AaaaA01.g_1 position 1291982 [17:48:45] Possible /pseudo 'DNA-directed RNA polymerase subunit beta'' at gnl|Prokka|AaaaA01.g_1 position 1494174 [17:48:45] Possible /pseudo 'Putative fluoride ion transporter CrcB' at gnl|Prokka|AaaaA01.g_1 position 1646465 [17:48:45] Found 922 unique /gene codes. [17:48:45] Fixed 2 duplicate /gene - gpgS_1 gpgS_2 [17:48:45] Fixed 2 duplicate /gene - ccmK_1 ccmK_2 [17:48:45] Fixed 2 duplicate /gene - bicA_1 bicA_2 [17:48:45] Fixed 3 duplicate /gene - sigA2_1 sigA2_2 sigA2_3 [17:48:45] Fixed 2 duplicate /gene - grxC_1 grxC_2 [17:48:45] Fixed 2 duplicate /gene - lytB_1 lytB_2 [17:48:45] Fixed 3 duplicate /gene - dnaJ_1 dnaJ_2 dnaJ_3 [17:48:45] Fixed 2 duplicate /gene - lpxB_1 lpxB_2 [17:48:45] Fixed 2 duplicate /gene - lip1_1 lip1_2 [17:48:45] Fixed 2 duplicate /gene - psaA_1 psaA_2 [17:48:45] Fixed 3 duplicate /gene - fabG_1 fabG_2 fabG_3 [17:48:45] Fixed 2 duplicate /gene - atpG_1 atpG_2 [17:48:45] Fixed 2 duplicate /gene - bchI_1 bchI_2 [17:48:45] Fixed 2 duplicate /gene - wfgD_1 wfgD_2 [17:48:45] Fixed 2 duplicate /gene - glnQ_1 glnQ_2 [17:48:45] Fixed 2 duplicate /gene - speA_1 speA_2 [17:48:45] Fixed 2 duplicate /gene - dnaX_1 dnaX_2 [17:48:45] Fixed 2 duplicate /gene - yqgF_1 yqgF_2 [17:48:45] Fixed 2 duplicate /gene - ilvE_1 ilvE_2 [17:48:45] Fixed 2 duplicate /gene - ppa_1 ppa_2 [17:48:45] Fixed 2 duplicate /gene - dnaK2_1 dnaK2_2 [17:48:45] Fixed 2 duplicate /gene - iscS_1 iscS_2 [17:48:45] Fixed 2 duplicate /gene - gloB_1 gloB_2 [17:48:45] Fixed 2 duplicate /gene - lexA_1 lexA_2 [17:48:45] Fixed 2 duplicate /gene - pds_1 pds_2 [17:48:45] Fixed 2 duplicate /gene - folE_1 folE_2 [17:48:45] Fixed 2 duplicate /gene - suhB_1 suhB_2 [17:48:45] Fixed 2 duplicate /gene - crtL_1 crtL_2 [17:48:45] Fixed 2 duplicate /gene - plsC_1 plsC_2 [17:48:45] Fixed 2 duplicate /gene - ntcA_1 ntcA_2 [17:48:45] Fixed 2 duplicate /gene - purE_1 purE_2 [17:48:45] Fixed 2 duplicate /gene - ppiB_1 ppiB_2 [17:48:45] Fixed 2 duplicate /gene - mgl_1 mgl_2 [17:48:45] Fixed 2 duplicate /gene - recF_1 recF_2 [17:48:45] Fixed 2 duplicate /gene - oatA_1 oatA_2 [17:48:45] Fixed 2 duplicate /gene - pstS_1 pstS_2 [17:48:45] Fixed 2 duplicate /gene - ftsH3_1 ftsH3_2 [17:48:45] Fixed 3 duplicate /gene - era_1 era_2 era_3 [17:48:45] Fixed 2 duplicate /gene - pcyA_1 pcyA_2 [17:48:45] Fixed 2 duplicate /gene - gyrA_1 gyrA_2 [17:48:45] Fixed 2 duplicate /gene - hhoA_1 hhoA_2 [17:48:45] Fixed 2 duplicate /gene - mnmC_1 mnmC_2 [17:48:45] Fixed 2 duplicate /gene - cugP_1 cugP_2 [17:48:45] Fixed 2 duplicate /gene - rpoC_1 rpoC_2 [17:48:45] Fixed 3 duplicate /gene - ubiB_1 ubiB_2 ubiB_3 [17:48:45] Fixed 2 duplicate /gene - msrA_1 msrA_2 [17:48:45] Fixed 2 duplicate /gene - corC_1 corC_2 [17:48:45] Fixed 2 duplicate /gene - fcl_1 fcl_2 [17:48:45] Fixed 2 duplicate /gene - tatAy_1 tatAy_2 [17:48:45] Fixed 2 duplicate /gene - btuR_1 btuR_2 [17:48:45] Fixed 2 duplicate /gene - cobN_1 cobN_2 [17:48:45] Fixed 2 duplicate /gene - ndhD1_1 ndhD1_2 [17:48:45] Fixed 2 duplicate /gene - clpS_1 clpS_2 [17:48:45] Fixed 2 duplicate /gene - rnr_1 rnr_2 [17:48:45] Fixed 2 duplicate /gene - sasA_1 sasA_2 [17:48:45] Fixed 2 duplicate /gene - bcp_1 bcp_2 [17:48:45] Fixed 2 duplicate /gene - thiO_1 thiO_2 [17:48:45] Fixed 3 duplicate /gene - phoP_1 phoP_2 phoP_3 [17:48:45] Fixed 2 duplicate /gene - guaA_1 guaA_2 [17:48:45] Fixed 4 duplicate /gene - yciC_1 yciC_2 yciC_3 yciC_4 [17:48:45] Fixed 2 duplicate /gene - murAA_1 murAA_2 [17:48:45] Fixed 2 duplicate /gene - tam_1 tam_2 [17:48:45] Fixed 2 duplicate /gene - cobD_1 cobD_2 [17:48:45] Fixed 2 duplicate /gene - crcB_1 crcB_2 [17:48:45] Fixed 2 duplicate /gene - arnT_1 arnT_2 [17:48:45] Fixed 3 duplicate /gene - recD_1 recD_2 recD_3 [17:48:45] Fixed 3 duplicate /gene - galE_1 galE_2 galE_3 [17:48:45] Fixed 2 duplicate /gene - gph_1 gph_2 [17:48:45] Fixed 2 duplicate /gene - trxA_1 trxA_2 [17:48:45] Fixed 2 duplicate /gene - trxB_1 trxB_2 [17:48:45] Fixed 2 duplicate /gene - clpB1_1 clpB1_2 [17:48:45] Fixed 2 duplicate /gene - hpf_1 hpf_2 [17:48:45] Fixed 2 duplicate /gene - cca_1 cca_2 [17:48:45] Fixed 2 duplicate /gene - mntB_1 mntB_2 [17:48:45] Fixed 4 duplicate /gene - clpP_1 clpP_2 clpP_3 clpP_4 [17:48:45] Fixed 2 duplicate /gene - rpsA_1 rpsA_2 [17:48:45] Fixed 2 duplicate /gene - pyrC_1 pyrC_2 [17:48:45] Fixed 77 colliding /gene names. [17:48:45] Adding /locus_tag identifiers [17:48:46] Assigned 1947 locus_tags to CDS and RNA features. [17:48:46] Writing outputs to /share/gsi2/data/www/soap-data/M2BBS/Phylogenomic/Prochlorococcus/prokka/Aaaa/ [17:48:51] Generating annotation statistics file [17:48:51] Generating Genbank and Sequin files [17:48:51] 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\/Aaaa\/AaaaA01\.err -i \/share\/gsi2\/data\/www\/soap\-data\/M2BBS\/Phylogenomic\/Prochlorococcus\/prokka\/Aaaa\/AaaaA01\.fsa 2> /dev/null [17:48:58] Deleting unwanted file: /share/gsi2/data/www/soap-data/M2BBS/Phylogenomic/Prochlorococcus/prokka/Aaaa/errorsummary.val [17:48:58] Deleting unwanted file: /share/gsi2/data/www/soap-data/M2BBS/Phylogenomic/Prochlorococcus/prokka/Aaaa/AaaaA01.dr [17:48:58] Deleting unwanted file: /share/gsi2/data/www/soap-data/M2BBS/Phylogenomic/Prochlorococcus/prokka/Aaaa/AaaaA01.fixedproducts [17:48:58] Deleting unwanted file: /share/gsi2/data/www/soap-data/M2BBS/Phylogenomic/Prochlorococcus/prokka/Aaaa/AaaaA01.ecn [17:48:58] Deleting unwanted file: /share/gsi2/data/www/soap-data/M2BBS/Phylogenomic/Prochlorococcus/prokka/Aaaa/AaaaA01.val [17:48:58] Repairing broken .GBK output that tbl2asn produces... [17:48:58] Running: sed 's/COORDINATES: profile/COORDINATES:profile/' < \/share\/gsi2\/data\/www\/soap\-data\/M2BBS\/Phylogenomic\/Prochlorococcus\/prokka\/Aaaa\/AaaaA01\.gbf > \/share\/gsi2\/data\/www\/soap\-data\/M2BBS\/Phylogenomic\/Prochlorococcus\/prokka\/Aaaa\/AaaaA01\.gbk [17:48:58] Deleting unwanted file: /share/gsi2/data/www/soap-data/M2BBS/Phylogenomic/Prochlorococcus/prokka/Aaaa/AaaaA01.gbf [17:48:58] Output files: [17:48:58] /share/gsi2/data/www/soap-data/M2BBS/Phylogenomic/Prochlorococcus/prokka/Aaaa/AaaaA01.log [17:48:58] /share/gsi2/data/www/soap-data/M2BBS/Phylogenomic/Prochlorococcus/prokka/Aaaa/AaaaA01.fna [17:48:58] /share/gsi2/data/www/soap-data/M2BBS/Phylogenomic/Prochlorococcus/prokka/Aaaa/AaaaA01.gff [17:48:58] /share/gsi2/data/www/soap-data/M2BBS/Phylogenomic/Prochlorococcus/prokka/Aaaa/AaaaA01.faa [17:48:58] /share/gsi2/data/www/soap-data/M2BBS/Phylogenomic/Prochlorococcus/prokka/Aaaa/AaaaA01.ffn [17:48:58] /share/gsi2/data/www/soap-data/M2BBS/Phylogenomic/Prochlorococcus/prokka/Aaaa/AaaaA01.tbl [17:48:58] /share/gsi2/data/www/soap-data/M2BBS/Phylogenomic/Prochlorococcus/prokka/Aaaa/AaaaA01.fsa [17:48:58] /share/gsi2/data/www/soap-data/M2BBS/Phylogenomic/Prochlorococcus/prokka/Aaaa/AaaaA01.tsv [17:48:58] /share/gsi2/data/www/soap-data/M2BBS/Phylogenomic/Prochlorococcus/prokka/Aaaa/AaaaA01.txt [17:48:58] /share/gsi2/data/www/soap-data/M2BBS/Phylogenomic/Prochlorococcus/prokka/Aaaa/AaaaA01.sqn [17:48:58] /share/gsi2/data/www/soap-data/M2BBS/Phylogenomic/Prochlorococcus/prokka/Aaaa/AaaaA01.err [17:48:58] /share/gsi2/data/www/soap-data/M2BBS/Phylogenomic/Prochlorococcus/prokka/Aaaa/AaaaA01.gbk [17:48:58] Annotation finished successfully. [17:48:58] Walltime used: 4.70 minutes [17:48:58] If you use this result please cite the Prokka paper: [17:48:58] Seemann T (2014) Prokka: rapid prokaryotic genome annotation. Bioinformatics. 30(14):2068-9. [17:48:58] Type 'prokka --citation' for more details. [17:48:58] Thank you, come again.