[17:44:14] This is prokka 1.12 [17:44:14] Written by Torsten Seemann [17:44:14] Homepage is https://github.com/tseemann/prokka [17:44:14] Local time is Thu Sep 6 17:44:14 2018 [17:44:14] You are gsi [17:44:14] Operating system is linux [17:44:14] You have BioPerl 1.007002 [17:44:14] System has 24 cores. [17:44:14] Will use maximum of 1 cores. [17:44:14] Annotating as >>> Bacteria <<< [17:44:14] Enabling options to ensure Genbank/ENA/DDJB submission compliance. [17:44:14] Creating new output folder: /share/gsi2/data/www/soap-data/M2BBS/Phylogenomic/Prochlorococcus/prokka/Aaak [17:44:14] Running: mkdir -p \/share\/gsi2\/data\/www\/soap\-data\/M2BBS\/Phylogenomic\/Prochlorococcus\/prokka\/Aaak [17:44:14] Using filename prefix: AaakA01.XXX [17:44:14] Setting HMMER_NCPU=1 [17:44:14] Writing log to: /share/gsi2/data/www/soap-data/M2BBS/Phylogenomic/Prochlorococcus/prokka/Aaak/AaakA01.log [17:44:14] Command: /share/gsi2/bin/prokka /share/gsi2/data/www/soap-data/M2BBS/Phylogenomic/Prochlorococcus/DNA/Aaak/AaakA01.fas --compliant --addgenes --outdir /share/gsi2/data/www/soap-data/M2BBS/Phylogenomic/Prochlorococcus/prokka/Aaak --prefix AaakA01 --locustag AaakA01.g --species ProchlorococcusmarinusstrMIT9215 --strain ProchlorococcusmarinusstrMIT9215 --kingdom bacteria --cpus 1 --force [17:44:14] Appending to PATH: /share/gsi2/software/prokka/bin/../binaries/linux [17:44:14] Appending to PATH: /share/gsi2/software/prokka/bin/../binaries/linux/../common [17:44:14] Appending to PATH: /share/gsi2/software/prokka/bin [17:44:14] Looking for 'aragorn' - found /share/gsi2/software/prokka/bin/../binaries/linux/aragorn [17:44:14] Determined aragorn version is 1.2 [17:44:14] Looking for 'barrnap' - found /share/gsi2/bin/barrnap [17:44:14] Determined barrnap version is 0.9 [17:44:14] Looking for 'blastp' - found /share/gsi2/bin/blastp [17:44:15] Determined blastp version is 2.7 [17:44:15] Looking for 'cmpress' - found /share/gsi2/software/prokka/bin/../binaries/linux/cmpress [17:44:15] Determined cmpress version is 1.1 [17:44:15] Looking for 'cmscan' - found /share/gsi2/software/prokka/bin/../binaries/linux/cmscan [17:44:15] Determined cmscan version is 1.1 [17:44:15] Looking for 'egrep' - found /bin/egrep [17:44:15] Looking for 'find' - found /bin/find [17:44:15] Looking for 'grep' - found /bin/grep [17:44:15] Looking for 'hmmpress' - found /share/gsi2/bin/hmmpress [17:44:15] Determined hmmpress version is 3.1 [17:44:15] Looking for 'hmmscan' - found /share/gsi2/bin/hmmscan [17:44:15] Determined hmmscan version is 3.1 [17:44:15] Looking for 'java' - found /usr/java/latest/bin/java [17:44:15] Looking for 'less' - found /usr/bin/less [17:44:15] 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 [17:44:16] Looking for 'tbl2asn' - found /share/gsi2/bin/tbl2asn [17:44:17] Determined tbl2asn version is 25.6 [17:44:17] Using genetic code table 11. [17:44:17] Loading and checking input file: /share/gsi2/data/www/soap-data/M2BBS/Phylogenomic/Prochlorococcus/DNA/Aaak/AaakA01.fas [17:44:17] Wrote 1 contigs totalling 1738790 bp. [17:44:17] Predicting tRNAs and tmRNAs [17:44:17] Running: aragorn -l -gc11 -w \/share\/gsi2\/data\/www\/soap\-data\/M2BBS\/Phylogenomic\/Prochlorococcus\/prokka\/Aaak\/AaakA01\.fna [17:44:18] 1 tmRNA* c[63642,63951] 169,219 ANKIVSFSRQAAPVAA* [17:44:18] 2 tRNA-Leu c[72796,72879] 36 (aag) [17:44:18] 3 tRNA-Asn [130026,130098] 33 (gtt) [17:44:18] 4 tRNA-Leu [236411,236493] 35 (tag) [17:44:18] 5 tRNA-Arg c[256260,256335] 36 (acg) [17:44:18] 6 tRNA-Met c[271389,271463] 35 (cat) [17:44:18] 7 tRNA-Phe c[303247,303321] 34 (gaa) [17:44:18] 8 tRNA-Thr c[311957,312030] 34 (tgt) [17:44:18] 9 tRNA-Ile [321501,321576] 36 (gat) [17:44:18] 10 tRNA-Ala [321588,321661] 34 (tgc) [17:44:18] 11 tRNA-Thr c[370616,370688] 33 (ggt) [17:44:18] 12 tRNA-Thr c[375405,375476] 32 (ggt) [17:44:18] 13 tRNA-Thr c[407093,407165] 33 (ggt) [17:44:18] 14 tRNA-Tyr c[407175,407257] 35 (gta) [17:44:18] 15 tRNA-Asp c[487223,487298] 36 (gtc) [17:44:18] 16 tRNA-Trp c[487677,487751] 35 (cca) [17:44:18] 17 tRNA-Leu [575552,575639] 36 (taa) [17:44:18] 18 tRNA-Ser c[661865,661953] 36 (tga) [17:44:18] 19 tRNA-Pro c[808659,808732] 35 (ggg) [17:44:18] 20 tRNA-Ser [861629,861715] 35 (gga) [17:44:18] 21 tRNA-Met [902394,902469] 36 (cat) [17:44:18] 22 tRNA-Met [943871,943947] 35 (cat) [17:44:18] 23 tRNA-Glu c[1029616,1029690] 36 (ttc) [17:44:18] 24 tRNA-Lys [1073305,1073377] 33 (ttt) [17:44:18] 25 tRNA-Pro [1085550,1085623] 35 (tgg) [17:44:18] 26 tRNA-Ser c[1169647,1169733] 36 (cga) [17:44:18] 27 tRNA-Arg [1199256,1199331] 36 (tct) [17:44:18] 28 tRNA-Ala c[1283535,1283607] 34 (ggc) [17:44:18] 29 tRNA-Leu [1323936,1324018] 35 (caa) [17:44:18] 30 tRNA-His [1329195,1329268] 34 (gtg) [17:44:18] 31 tRNA-Gly c[1345545,1345615] 33 (tcc) [17:44:18] 32 tRNA-Val [1377316,1377389] 34 (gac) [17:44:18] 33 tRNA-Thr [1513532,1513605] 34 (cgt) [17:44:18] 34 tRNA-Ser c[1550975,1551065] 36 (gct) [17:44:18] 35 tRNA-Gln [1570878,1570949] 33 (ttg) [17:44:18] 36 tRNA-Arg [1583582,1583655] 35 (ccg) [17:44:18] 37 tRNA-Cys [1598229,1598299] 33 (gca) [17:44:18] 38 tRNA-Arg c[1615206,1615281] 36 (cct) [17:44:18] 39 tRNA-Gly c[1651650,1651721] 33 (gcc) [17:44:18] 40 tRNA-Val c[1698190,1698261] 33 (tac) [17:44:18] Found 40 tRNAs [17:44:18] Predicting Ribosomal RNAs [17:44:18] Running Barrnap with 1 threads [17:44:21] 1 gnl|Prokka|AaakA01.g_1 319896 16S ribosomal RNA [17:44:21] 2 gnl|Prokka|AaakA01.g_1 321919 23S ribosomal RNA [17:44:21] 3 gnl|Prokka|AaakA01.g_1 324859 5S ribosomal RNA [17:44:21] Found 3 rRNAs [17:44:21] Skipping ncRNA search, enable with --rfam if desired. [17:44:21] Total of 42 tRNA + rRNA features [17:44:21] Searching for CRISPR repeats [17:44:22] Found 0 CRISPRs [17:44:22] Predicting coding sequences [17:44:22] Contigs total 1738790 bp, so using single mode [17:44:22] Running: prodigal -i \/share\/gsi2\/data\/www\/soap\-data\/M2BBS\/Phylogenomic\/Prochlorococcus\/prokka\/Aaak\/AaakA01\.fna -c -m -g 11 -p single -f sco -q [17:44:25] Excluding CDS which overlaps existing RNA (tRNA) at gnl|Prokka|AaakA01.g_1:71503..72894 on - strand [17:44:26] Excluding CDS which overlaps existing RNA (tRNA) at gnl|Prokka|AaakA01.g_1:375380..375562 on - strand [17:44:27] Excluding CDS which overlaps existing RNA (tRNA) at gnl|Prokka|AaakA01.g_1:1323945..1325198 on + strand [17:44:27] Excluding CDS which overlaps existing RNA (tRNA) at gnl|Prokka|AaakA01.g_1:1596957..1598369 on - strand [17:44:27] Found 1982 CDS [17:44:27] Connecting features back to sequences [17:44:27] Not using genus-specific database. Try --usegenus to enable it. [17:44:27] Annotating CDS, please be patient. [17:44:27] Will use 1 CPUs for similarity searching. [17:44:30] There are still 1982 unannotated CDS left (started with 1982) [17:44:30] Will use blast to search against /share/gsi2/software/prokka/bin/../db/kingdom/Bacteria/sprot with 1 CPUs [17:44:30] Running: cat \/share\/gsi2\/data\/www\/soap\-data\/M2BBS\/Phylogenomic\/Prochlorococcus\/prokka\/Aaak\/sprot\.faa | parallel --gnu --plain -j 1 --block 265028 --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\/Aaak\/sprot\.blast 2> /dev/null [17:46:51] Modify product: N utilization substance protein B homolog => N utilization substance protein B [17:46:51] Modify product: Uncharacterized oxidoreductase MSMEG_2408/MSMEI_2347 => putative oxidoreductase/MSMEI_2347 [17:46:51] Modify product: Probable cysteine desulfurase => putative cysteine desulfurase [17:46:51] Modify product: Probable ATP-dependent transporter SufC => putative ATP-dependent transporter SufC [17:46:51] Modify product: Uncharacterized AAA domain-containing protein Rv2559c => putative AAA domain-containing protein [17:46:51] Modify product: Uncharacterized transporter Rv2685 => putative transporter [17:46:51] Modify product: Uncharacterized ABC transporter ATP-binding protein YheS => putative ABC transporter ATP-binding protein YheS [17:46:51] Modify product: Vitamin K epoxide reductase homolog => Vitamin K epoxide reductase [17:46:51] Modify product: Epimerase family protein Rv2216 => Epimerase family protein [17:46:51] Modify product: Probable glutaredoxin ssr2061 => putative glutaredoxin [17:46:51] Modify product: Probable nicotinate-nucleotide pyrophosphorylase [carboxylating] => putative nicotinate-nucleotide pyrophosphorylase [carboxylating] [17:46:51] Modify product: Probable protein kinase UbiB => putative protein kinase UbiB [17:46:51] Modify product: Probable bifunctional SAT/APS kinase => putative bifunctional SAT/APS kinase [17:46:51] Modify product: Probable phospholipid import ATP-binding protein MlaF => putative phospholipid import ATP-binding protein MlaF [17:46:51] Modify product: Uncharacterized ABC transporter ATP-binding protein YknY => putative ABC transporter ATP-binding protein YknY [17:46:51] Modify product: Probable cytochrome c oxidase subunit 1 => putative cytochrome c oxidase subunit 1 [17:46:51] Modify product: Probable murein peptide carboxypeptidase => putative murein peptide carboxypeptidase [17:46:51] Modify product: Thylakoid-associated single-stranded DNA-binding protein slr1034 => Thylakoid-associated single-stranded DNA-binding protein [17:46:52] Modify product: Uncharacterized ABC transporter ATP-binding protein TM_0288 => putative ABC transporter ATP-binding protein [17:46:52] Modify product: PGL/p-HBAD biosynthesis glycosyltransferase Rv2957 => PGL/p-HBAD biosynthesis glycosyltransferase [17:46:52] Modify product: Uncharacterized ABC transporter ATP-binding protein HI_1470 => putative ABC transporter ATP-binding protein [17:46:52] Modify product: Probable 2-phosphosulfolactate phosphatase => putative 2-phosphosulfolactate phosphatase [17:46:52] Modify product: Probable trans-aconitate 2-methyltransferase => putative trans-aconitate 2-methyltransferase [17:46:52] Modify product: Uncharacterized zinc protease Rv2782c => putative zinc protease [17:46:52] Modify product: Uncharacterized zinc protease Rv2782c => putative zinc protease [17:46:52] Modify product: Uncharacterized ABC transporter ATP-binding protein Rv0986 => putative ABC transporter ATP-binding protein [17:46:52] Modify product: GTP-binding protein TypA/BipA homolog => GTP-binding protein TypA/BipA [17:46:52] Modify product: Uncharacterized ABC transporter ATP-binding protein YlmA => putative ABC transporter ATP-binding protein YlmA [17:46:52] Modify product: Probable multidrug resistance ABC transporter ATP-binding/permease protein YheI => putative multidrug resistance ABC transporter ATP-binding/permease protein YheI [17:46:52] Modify product: Probable cystine transporter YijE => putative cystine transporter YijE [17:46:52] Modify product: Vitamin K epoxide reductase homolog => Vitamin K epoxide reductase [17:46:52] Modify product: Probable peroxiredoxin => putative peroxiredoxin [17:46:52] Modify product: Putative multidrug export ATP-binding/permease protein SA1683 => Putative multidrug export ATP-binding/permease protein [17:46:52] Modify product: Uncharacterized peptidase Lmo0363 => putative peptidase [17:46:52] Modify product: Probable tRNA-dihydrouridine synthase => putative tRNA-dihydrouridine synthase [17:46:52] Modify product: Putative esterase aq_1494 => Putative esterase [17:46:52] Modify product: Uncharacterized tRNA/rRNA methyltransferase HI_0380 => putative tRNA/rRNA methyltransferase [17:46:52] Modify product: Uncharacterized oxidoreductase MSMEG_1603/MSMEI_1564 => putative oxidoreductase/MSMEI_1564 [17:46:52] Modify product: 1,4-alpha-glucan branching enzyme TTHA1902 => 1,4-alpha-glucan branching enzyme [17:46:52] Modify product: Bifunctional protein FolD => Bifunctional protein FolD protein [17:46:52] Modify product: Probable protein kinase UbiB => putative protein kinase UbiB [17:46:52] Modify product: Putative multidrug export ATP-binding/permease protein SA1683 => Putative multidrug export ATP-binding/permease protein [17:46:52] Modify product: Maf-like protein Rv3282 => Maf-like protein [17:46:52] Modify product: PKHD-type hydroxylase Sbal_3634 => PKHD-type hydroxylase [17:46:52] Modify product: Uncharacterized inner membrane transporter YedA => putative inner membrane transporter YedA [17:46:52] Modify product: Uncharacterized FAD-linked oxidoreductase Rv2280 => putative FAD-linked oxidoreductase [17:46:52] Modify product: Oxygen-independent coproporphyrinogen-III oxidase-like protein sll1917 => Oxygen-independent coproporphyrinogen-III oxidase-like protein [17:46:52] Modify product: Uncharacterized PIN and TRAM-domain containing protein YacL => putative PIN and TRAM-domain containing protein YacL [17:46:53] Modify product: Glycogen operon protein GlgX homolog => Glycogen operon protein GlgX [17:46:53] Modify product: Probable phospholipid ABC transporter permease protein MlaE => putative phospholipid ABC transporter permease protein MlaE [17:46:53] Modify product: Probable cytochrome c oxidase subunit 1 => putative cytochrome c oxidase subunit 1 [17:46:53] Modify product: Probable 30S ribosomal protein PSRP-3 => putative 30S ribosomal protein PSRP-3 [17:46:53] Modify product: Probable nicotinate-nucleotide adenylyltransferase => putative nicotinate-nucleotide adenylyltransferase [17:46:53] Modify product: Probable peptidoglycan glycosyltransferase FtsW => putative peptidoglycan glycosyltransferase FtsW [17:46:53] Modify product: Probable helicase HelY => putative helicase HelY [17:46:53] Modify product: Probable dual-specificity RNA methyltransferase RlmN => putative dual-specificity RNA methyltransferase RlmN [17:46:53] Modify product: Probable endopeptidase p60 => putative endopeptidase p60 [17:46:53] Modify product: Probable cobalt-factor III C(17)-methyltransferase => putative cobalt-factor III C(17)-methyltransferase [17:46:53] Modify product: Probable adenylyltransferase/sulfurtransferase MoeZ => putative adenylyltransferase/sulfurtransferase MoeZ [17:46:53] Modify product: Uncharacterized hydrolase YxeP => putative hydrolase YxeP [17:46:53] Modify product: Inner membrane protein BB_0250 => Inner membrane protein [17:46:53] Modify product: Probable branched-chain-amino-acid aminotransferase => putative branched-chain-amino-acid aminotransferase [17:46:53] Modify product: Probable protein kinase UbiB => putative protein kinase UbiB [17:46:53] Cleaned 63 /product names [17:46:53] Deleting unwanted file: /share/gsi2/data/www/soap-data/M2BBS/Phylogenomic/Prochlorococcus/prokka/Aaak/sprot.faa [17:46:53] Deleting unwanted file: /share/gsi2/data/www/soap-data/M2BBS/Phylogenomic/Prochlorococcus/prokka/Aaak/sprot.blast [17:46:54] There are still 952 unannotated CDS left (started with 1982) [17:46:54] Will use hmmer3 to search against /share/gsi2/software/prokka/bin/../db/hmm/HAMAP.hmm with 1 CPUs [17:46:54] Running: cat \/share\/gsi2\/data\/www\/soap\-data\/M2BBS\/Phylogenomic\/Prochlorococcus\/prokka\/Aaak\/HAMAP\.hmm\.faa | parallel --gnu --plain -j 1 --block 80526 --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\/Aaak\/HAMAP\.hmm\.hmmer3 2> /dev/null [17:47:58] Deleting unwanted file: /share/gsi2/data/www/soap-data/M2BBS/Phylogenomic/Prochlorococcus/prokka/Aaak/HAMAP.hmm.faa [17:47:58] Deleting unwanted file: /share/gsi2/data/www/soap-data/M2BBS/Phylogenomic/Prochlorococcus/prokka/Aaak/HAMAP.hmm.hmmer3 [17:47:58] Labelling remaining 883 proteins as 'hypothetical protein' [17:47:58] Possible /pseudo 'Photosystem II protein D1' at gnl|Prokka|AaakA01.g_1 position 224018 [17:47:58] Possible /pseudo 'Ethanolamine utilization protein EutN' at gnl|Prokka|AaakA01.g_1 position 561149 [17:47:58] Possible /pseudo 'putative zinc protease' at gnl|Prokka|AaakA01.g_1 position 727693 [17:47:58] Possible /pseudo 'UDP-glucose 4-epimerase' at gnl|Prokka|AaakA01.g_1 position 1203391 [17:47:58] Possible /pseudo 'ATP-dependent Clp protease proteolytic subunit' at gnl|Prokka|AaakA01.g_1 position 1338325 [17:47:58] Possible /pseudo 'DNA-directed RNA polymerase subunit beta'' at gnl|Prokka|AaakA01.g_1 position 1497609 [17:47:58] Possible /pseudo 'Putative fluoride ion transporter CrcB' at gnl|Prokka|AaakA01.g_1 position 1641535 [17:47:58] Found 923 unique /gene codes. [17:47:58] Fixed 2 duplicate /gene - dnaX_1 dnaX_2 [17:47:58] Fixed 2 duplicate /gene - ilvE_1 ilvE_2 [17:47:58] Fixed 2 duplicate /gene - legI_1 legI_2 [17:47:58] Fixed 2 duplicate /gene - suhB_1 suhB_2 [17:47:58] Fixed 2 duplicate /gene - rplU_1 rplU_2 [17:47:58] Fixed 2 duplicate /gene - cobN_1 cobN_2 [17:47:58] Fixed 2 duplicate /gene - fdhL_1 fdhL_2 [17:47:58] Fixed 2 duplicate /gene - ydjZ_1 ydjZ_2 [17:47:58] Fixed 2 duplicate /gene - trxB_1 trxB_2 [17:47:58] Fixed 2 duplicate /gene - novN_1 novN_2 [17:47:58] Fixed 2 duplicate /gene - ubiG_1 ubiG_2 [17:47:58] Fixed 2 duplicate /gene - cobD_1 cobD_2 [17:47:58] Fixed 2 duplicate /gene - yqgF_1 yqgF_2 [17:47:58] Fixed 2 duplicate /gene - psbF_1 psbF_2 [17:47:58] Fixed 2 duplicate /gene - ppa_1 ppa_2 [17:47:58] Fixed 2 duplicate /gene - rfbE_1 rfbE_2 [17:47:58] Fixed 2 duplicate /gene - glmM_1 glmM_2 [17:47:58] Fixed 2 duplicate /gene - crcB_1 crcB_2 [17:47:58] Fixed 2 duplicate /gene - ctpA_1 ctpA_2 [17:47:58] Fixed 2 duplicate /gene - hddC_1 hddC_2 [17:47:58] Fixed 2 duplicate /gene - bchI_1 bchI_2 [17:47:58] Fixed 2 duplicate /gene - iolC_1 iolC_2 [17:47:58] Fixed 2 duplicate /gene - dnaJ_1 dnaJ_2 [17:47:58] Fixed 2 duplicate /gene - lexA_1 lexA_2 [17:47:58] Fixed 2 duplicate /gene - mnmC_1 mnmC_2 [17:47:58] Fixed 2 duplicate /gene - dnaK2_1 dnaK2_2 [17:47:58] Fixed 3 duplicate /gene - sigA2_1 sigA2_2 sigA2_3 [17:47:58] Fixed 2 duplicate /gene - bicA_1 bicA_2 [17:47:58] Fixed 2 duplicate /gene - rpsA_1 rpsA_2 [17:47:58] Fixed 2 duplicate /gene - udk_1 udk_2 [17:47:58] Fixed 2 duplicate /gene - crtI_1 crtI_2 [17:47:58] Fixed 2 duplicate /gene - ndhD1_1 ndhD1_2 [17:47:58] Fixed 2 duplicate /gene - btuR_1 btuR_2 [17:47:58] Fixed 2 duplicate /gene - iscS_1 iscS_2 [17:47:58] Fixed 2 duplicate /gene - speA_1 speA_2 [17:47:58] Fixed 3 duplicate /gene - ftsH2_1 ftsH2_2 ftsH2_3 [17:47:58] Fixed 2 duplicate /gene - ribD_1 ribD_2 [17:47:58] Fixed 2 duplicate /gene - csgA_1 csgA_2 [17:47:58] Fixed 2 duplicate /gene - pds_1 pds_2 [17:47:58] Fixed 2 duplicate /gene - pcyA_1 pcyA_2 [17:47:58] Fixed 2 duplicate /gene - eutN_1 eutN_2 [17:47:58] Fixed 2 duplicate /gene - iolX_1 iolX_2 [17:47:58] Fixed 2 duplicate /gene - ctaE_1 ctaE_2 [17:47:58] Fixed 3 duplicate /gene - ubiB_1 ubiB_2 ubiB_3 [17:47:58] Fixed 2 duplicate /gene - rfbC_1 rfbC_2 [17:47:58] Fixed 3 duplicate /gene - yciC_1 yciC_2 yciC_3 [17:47:58] Fixed 2 duplicate /gene - pgmB_1 pgmB_2 [17:47:58] Fixed 3 duplicate /gene - ligB_1 ligB_2 ligB_3 [17:47:58] Fixed 2 duplicate /gene - lnpD_1 lnpD_2 [17:47:58] Fixed 2 duplicate /gene - ctaD_1 ctaD_2 [17:47:58] Fixed 3 duplicate /gene - psbA_1 psbA_2 psbA_3 [17:47:58] Fixed 3 duplicate /gene - bcp_1 bcp_2 bcp_3 [17:47:58] Fixed 2 duplicate /gene - petF_1 petF_2 [17:47:58] Fixed 4 duplicate /gene - clpP_1 clpP_2 clpP_3 clpP_4 [17:47:58] Fixed 2 duplicate /gene - mnmE_1 mnmE_2 [17:47:58] Fixed 2 duplicate /gene - crtL_1 crtL_2 [17:47:58] Fixed 2 duplicate /gene - asnB_1 asnB_2 [17:47:58] Fixed 2 duplicate /gene - hpf_1 hpf_2 [17:47:58] Fixed 2 duplicate /gene - pstB3_1 pstB3_2 [17:47:58] Fixed 2 duplicate /gene - lapB_1 lapB_2 [17:47:58] Fixed 2 duplicate /gene - plsC_1 plsC_2 [17:47:58] Fixed 2 duplicate /gene - hisH_1 hisH_2 [17:47:58] Fixed 2 duplicate /gene - purE_1 purE_2 [17:47:58] Fixed 2 duplicate /gene - fcl_1 fcl_2 [17:47:58] Fixed 2 duplicate /gene - clpB1_1 clpB1_2 [17:47:58] Fixed 4 duplicate /gene - menG_1 menG_2 menG_3 menG_4 [17:47:58] Fixed 2 duplicate /gene - hhoA_1 hhoA_2 [17:47:58] Fixed 2 duplicate /gene - gyrA_1 gyrA_2 [17:47:58] Fixed 2 duplicate /gene - mreB_1 mreB_2 [17:47:58] Fixed 2 duplicate /gene - rnr_1 rnr_2 [17:47:58] Fixed 2 duplicate /gene - murA_1 murA_2 [17:47:58] Fixed 2 duplicate /gene - apt_1 apt_2 [17:47:58] Fixed 2 duplicate /gene - atpG_1 atpG_2 [17:47:58] Fixed 2 duplicate /gene - rmd_1 rmd_2 [17:47:58] Fixed 2 duplicate /gene - mntB_1 mntB_2 [17:47:58] Fixed 2 duplicate /gene - trxA_1 trxA_2 [17:47:58] Fixed 2 duplicate /gene - ycf3_1 ycf3_2 [17:47:58] Fixed 2 duplicate /gene - rpoC_1 rpoC_2 [17:47:58] Fixed 2 duplicate /gene - dfa1_1 dfa1_2 [17:47:58] Fixed 2 duplicate /gene - arnT_1 arnT_2 [17:47:58] Fixed 2 duplicate /gene - lytB_1 lytB_2 [17:47:58] Fixed 2 duplicate /gene - era_1 era_2 [17:47:58] Fixed 2 duplicate /gene - psbN_1 psbN_2 [17:47:58] Fixed 2 duplicate /gene - corC_1 corC_2 [17:47:58] Fixed 2 duplicate /gene - ubiE_1 ubiE_2 [17:47:58] Fixed 3 duplicate /gene - fabG_1 fabG_2 fabG_3 [17:47:58] Fixed 2 duplicate /gene - sasA_1 sasA_2 [17:47:58] Fixed 2 duplicate /gene - nadK_1 nadK_2 [17:47:58] Fixed 88 colliding /gene names. [17:47:58] Adding /locus_tag identifiers [17:47:58] Assigned 2025 locus_tags to CDS and RNA features. [17:47:58] Writing outputs to /share/gsi2/data/www/soap-data/M2BBS/Phylogenomic/Prochlorococcus/prokka/Aaak/ [17:48:03] Generating annotation statistics file [17:48:03] Generating Genbank and Sequin files [17:48:03] 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\/Aaak\/AaakA01\.err -i \/share\/gsi2\/data\/www\/soap\-data\/M2BBS\/Phylogenomic\/Prochlorococcus\/prokka\/Aaak\/AaakA01\.fsa 2> /dev/null [17:48:09] Deleting unwanted file: /share/gsi2/data/www/soap-data/M2BBS/Phylogenomic/Prochlorococcus/prokka/Aaak/errorsummary.val [17:48:09] Deleting unwanted file: /share/gsi2/data/www/soap-data/M2BBS/Phylogenomic/Prochlorococcus/prokka/Aaak/AaakA01.dr [17:48:09] Deleting unwanted file: /share/gsi2/data/www/soap-data/M2BBS/Phylogenomic/Prochlorococcus/prokka/Aaak/AaakA01.fixedproducts [17:48:09] Deleting unwanted file: /share/gsi2/data/www/soap-data/M2BBS/Phylogenomic/Prochlorococcus/prokka/Aaak/AaakA01.ecn [17:48:09] Deleting unwanted file: /share/gsi2/data/www/soap-data/M2BBS/Phylogenomic/Prochlorococcus/prokka/Aaak/AaakA01.val [17:48:09] Repairing broken .GBK output that tbl2asn produces... [17:48:09] Running: sed 's/COORDINATES: profile/COORDINATES:profile/' < \/share\/gsi2\/data\/www\/soap\-data\/M2BBS\/Phylogenomic\/Prochlorococcus\/prokka\/Aaak\/AaakA01\.gbf > \/share\/gsi2\/data\/www\/soap\-data\/M2BBS\/Phylogenomic\/Prochlorococcus\/prokka\/Aaak\/AaakA01\.gbk [17:48:09] Deleting unwanted file: /share/gsi2/data/www/soap-data/M2BBS/Phylogenomic/Prochlorococcus/prokka/Aaak/AaakA01.gbf [17:48:09] Output files: [17:48:09] /share/gsi2/data/www/soap-data/M2BBS/Phylogenomic/Prochlorococcus/prokka/Aaak/AaakA01.log [17:48:09] /share/gsi2/data/www/soap-data/M2BBS/Phylogenomic/Prochlorococcus/prokka/Aaak/AaakA01.fna [17:48:09] /share/gsi2/data/www/soap-data/M2BBS/Phylogenomic/Prochlorococcus/prokka/Aaak/AaakA01.gff [17:48:09] /share/gsi2/data/www/soap-data/M2BBS/Phylogenomic/Prochlorococcus/prokka/Aaak/AaakA01.faa [17:48:09] /share/gsi2/data/www/soap-data/M2BBS/Phylogenomic/Prochlorococcus/prokka/Aaak/AaakA01.ffn [17:48:09] /share/gsi2/data/www/soap-data/M2BBS/Phylogenomic/Prochlorococcus/prokka/Aaak/AaakA01.tbl [17:48:09] /share/gsi2/data/www/soap-data/M2BBS/Phylogenomic/Prochlorococcus/prokka/Aaak/AaakA01.fsa [17:48:09] /share/gsi2/data/www/soap-data/M2BBS/Phylogenomic/Prochlorococcus/prokka/Aaak/AaakA01.tsv [17:48:09] /share/gsi2/data/www/soap-data/M2BBS/Phylogenomic/Prochlorococcus/prokka/Aaak/AaakA01.txt [17:48:09] /share/gsi2/data/www/soap-data/M2BBS/Phylogenomic/Prochlorococcus/prokka/Aaak/AaakA01.sqn [17:48:09] /share/gsi2/data/www/soap-data/M2BBS/Phylogenomic/Prochlorococcus/prokka/Aaak/AaakA01.err [17:48:09] /share/gsi2/data/www/soap-data/M2BBS/Phylogenomic/Prochlorococcus/prokka/Aaak/AaakA01.gbk [17:48:09] Annotation finished successfully. [17:48:09] Walltime used: 3.92 minutes [17:48:09] If you use this result please cite the Prokka paper: [17:48:09] Seemann T (2014) Prokka: rapid prokaryotic genome annotation. Bioinformatics. 30(14):2068-9. [17:48:09] Type 'prokka --citation' for more details. [17:48:09] Share and enjoy!