[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/Aaai [17:44:16] Running: mkdir -p \/share\/gsi2\/data\/www\/soap\-data\/M2BBS\/Phylogenomic\/Prochlorococcus\/prokka\/Aaai [17:44:16] Using filename prefix: AaaiA01.XXX [17:44:16] Setting HMMER_NCPU=1 [17:44:16] Writing log to: /share/gsi2/data/www/soap-data/M2BBS/Phylogenomic/Prochlorococcus/prokka/Aaai/AaaiA01.log [17:44:16] Command: /share/gsi2/bin/prokka /share/gsi2/data/www/soap-data/M2BBS/Phylogenomic/Prochlorococcus/DNA/Aaai/AaaiA01.fas --compliant --addgenes --outdir /share/gsi2/data/www/soap-data/M2BBS/Phylogenomic/Prochlorococcus/prokka/Aaai --prefix AaaiA01 --locustag AaaiA01.g --species ProchlorococcusmarinusstrNATL1A --strain ProchlorococcusmarinusstrNATL1A --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 [17:44:19] Determined makeblastdb version is 2.7 [17:44:19] Looking for 'minced' - found /share/gsi2/bin/minced [17:44:19] Determined minced version is 2.0 [17:44:19] Looking for 'parallel' - found /share/gsi2/software/prokka/bin/../binaries/linux/../common/parallel [17:44:20] Determined parallel version is 20150122 [17:44:20] Looking for 'prodigal' - found /share/gsi2/software/prokka/bin/../binaries/linux/prodigal [17:44:20] Determined prodigal version is 2.6 [17:44:20] Looking for 'prokka-genbank_to_fasta_db' - found /share/gsi2/software/prokka/bin/prokka-genbank_to_fasta_db [17:44:20] Looking for 'rnammer' - found /share/gsi2/bin/rnammer [17:44:20] Determined rnammer version is 1.2 [17:44:20] Looking for 'sed' - found /bin/sed [17:44:20] 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/Aaai/AaaiA01.fas [17:44:21] Wrote 1 contigs totalling 1864731 bp. [17:44:21] Predicting tRNAs and tmRNAs [17:44:21] Running: aragorn -l -gc11 -w \/share\/gsi2\/data\/www\/soap\-data\/M2BBS\/Phylogenomic\/Prochlorococcus\/prokka\/Aaai\/AaaiA01\.fna [17:44:22] 1 tmRNA* c[112467,112775] 168,218 ANNIVSFSRQTAPVAA* [17:44:22] 2 tRNA-Leu c[121740,121823] 36 (aag) [17:44:22] 3 tRNA-Asn [184995,185066] 33 (gtt) [17:44:22] 4 tRNA-Leu c[292934,293016] 35 (tag) [17:44:22] 5 tRNA-Arg c[311854,311929] 36 (acg) [17:44:22] 6 tRNA-Met c[327520,327594] 35 (cat) [17:44:22] 7 tRNA-Phe c[367429,367504] 34 (gaa) [17:44:22] 8 tRNA-Thr c[377709,377782] 34 (tgt) [17:44:22] 9 tRNA-Ile [387468,387543] 36 (gat) [17:44:22] 10 tRNA-Ala [387552,387625] 34 (tgc) [17:44:22] 11 tRNA-Thr c[402169,402240] 33 (ggt) [17:44:22] 12 tRNA-Tyr c[402252,402333] 35 (gta) [17:44:22] 13 tRNA-Asp c[481453,481528] 36 (gtc) [17:44:22] 14 tRNA-Trp c[481953,482027] 35 (cca) [17:44:22] 15 tRNA-Leu c[569394,569481] 36 (taa) [17:44:22] 16 tRNA-Ser c[659767,659855] 36 (tga) [17:44:22] 17 tRNA-Met c[825916,825992] 35 (cat) [17:44:22] 18 tRNA-Pro c[851006,851079] 35 (ggg) [17:44:22] 19 tRNA-Ser [900647,900733] 35 (gga) [17:44:22] 20 tRNA-Met [951623,951696] 35 (cat) [17:44:22] 21 tRNA-Gly [1092399,1092470] 33 (ccc) [17:44:22] 22 tRNA-Pro c[1164253,1164326] 35 (tgg) [17:44:22] 23 tRNA-Lys c[1173518,1173589] 33 (ttt) [17:44:22] 24 tRNA-Glu [1220977,1221051] 36 (ttc) [17:44:22] 25 tRNA-Ser c[1322000,1322087] 35 (cga) [17:44:22] 26 tRNA-Arg [1362132,1362207] 36 (tct) [17:44:22] 27 tRNA-Ala c[1365192,1365266] 35 (ggc) [17:44:22] 28 tRNA-Leu [1406107,1406189] 35 (caa) [17:44:22] 29 tRNA-His [1411489,1411562] 34 (gtg) [17:44:22] 30 tRNA-Gly c[1431885,1431955] 33 (tcc) [17:44:22] 31 tRNA-Val [1464793,1464864] 33 (gac) [17:44:22] 32 tRNA-Thr [1560859,1560932] 34 (cgt) [17:44:22] 33 tRNA-Ser c[1629145,1629235] 36 (gct) [17:44:22] 34 tRNA-Gln [1649641,1649712] 33 (ttg) [17:44:22] 35 tRNA-Arg [1662951,1663026] 36 (ccg) [17:44:22] 36 tRNA-Cys [1678924,1678994] 33 (gca) [17:44:22] 37 tRNA-Arg c[1698544,1698617] 35 (cct) [17:44:22] 38 tRNA-Gly c[1765039,1765110] 33 (gcc) [17:44:22] 39 tRNA-Val c[1813934,1814008] 34 (tac) [17:44:22] Found 39 tRNAs [17:44:22] Predicting Ribosomal RNAs [17:44:22] Running Barrnap with 1 threads [17:44:26] 1 gnl|Prokka|AaaiA01.g_1 385820 16S ribosomal RNA [17:44:26] 2 gnl|Prokka|AaaiA01.g_1 387937 23S ribosomal RNA [17:44:26] 3 gnl|Prokka|AaaiA01.g_1 390902 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 41 tRNA + rRNA features [17:44:26] Searching for CRISPR repeats [17:44:26] Found 0 CRISPRs [17:44:26] Predicting coding sequences [17:44:26] Contigs total 1864731 bp, so using single mode [17:44:26] Running: prodigal -i \/share\/gsi2\/data\/www\/soap\-data\/M2BBS\/Phylogenomic\/Prochlorococcus\/prokka\/Aaai\/AaaiA01\.fna -c -m -g 11 -p single -f sco -q [17:44:33] Excluding CDS which overlaps existing RNA (tRNA) at gnl|Prokka|AaaiA01.g_1:311929..312408 on + strand [17:44:33] Excluding CDS which overlaps existing RNA (rRNA) at gnl|Prokka|AaaiA01.g_1:387996..388487 on - strand [17:44:33] Excluding CDS which overlaps existing RNA (tRNA) at gnl|Prokka|AaaiA01.g_1:480002..481480 on - strand [17:44:34] Excluding CDS which overlaps existing RNA (tRNA) at gnl|Prokka|AaaiA01.g_1:1406116..1407378 on + strand [17:44:35] Excluding CDS which overlaps existing RNA (tRNA) at gnl|Prokka|AaaiA01.g_1:1560560..1560922 on - strand [17:44:35] Excluding CDS which overlaps existing RNA (tRNA) at gnl|Prokka|AaaiA01.g_1:1677646..1679070 on - strand [17:44:35] Found 2149 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 2149 unannotated CDS left (started with 2149) [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\/Aaai\/sprot\.faa | parallel --gnu --plain -j 1 --block 275770 --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\/Aaai\/sprot\.blast 2> /dev/null [17:47:29] Modify product: N utilization substance protein B homolog => N utilization substance protein B [17:47:29] Modify product: Cyclic nucleotide-gated potassium channel mll3241 => Cyclic nucleotide-gated potassium channel [17:47:30] Modify product: Probable cysteine desulfurase => putative cysteine desulfurase [17:47:30] Modify product: Uncharacterized ABC transporter ATP-binding protein YheS => putative ABC transporter ATP-binding protein YheS [17:47:30] Modify product: Vitamin K epoxide reductase homolog => Vitamin K epoxide reductase [17:47:30] Modify product: Epimerase family protein SA0724 => Epimerase family protein [17:47:30] Modify product: Probable adenylyl-sulfate kinase => putative adenylyl-sulfate kinase [17:47:30] Modify product: Probable glutaredoxin ssr2061 => putative glutaredoxin [17:47:30] Modify product: Probable nicotinate-nucleotide pyrophosphorylase [carboxylating] => putative nicotinate-nucleotide pyrophosphorylase [carboxylating] [17:47:30] Modify product: Probable protein kinase UbiB => putative protein kinase UbiB [17:47:30] Modify product: Probable bifunctional SAT/APS kinase => putative bifunctional SAT/APS kinase [17:47:30] Modify product: Probable lipid II flippase MurJ => putative lipid II flippase MurJ [17:47:30] Modify product: Probable phospholipid import ATP-binding protein MlaF => putative phospholipid import ATP-binding protein MlaF [17:47:30] Modify product: Uncharacterized phycocyanin operon protein Z => putative phycocyanin operon protein Z [17:47:30] Modify product: Probable phycoerythrobilin lyase CpeT => putative phycoerythrobilin lyase CpeT [17:47:30] Modify product: Probable tRNA-dihydrouridine synthase => putative tRNA-dihydrouridine synthase [17:47:30] Modify product: Probable cysteine desulfurase => putative cysteine desulfurase [17:47:30] Modify product: Phage shock protein A homolog => Phage shock protein A [17:47:30] Modify product: Uncharacterized ABC transporter ATP-binding protein YknY => putative ABC transporter ATP-binding protein YknY [17:47:30] Modify product: Probable cytochrome c oxidase subunit 1 => putative cytochrome c oxidase subunit 1 [17:47:30] Modify product: Thylakoid-associated single-stranded DNA-binding protein slr1034 => Thylakoid-associated single-stranded DNA-binding protein [17:47:30] Modify product: Probable multidrug resistance ABC transporter ATP-binding/permease protein YheH => putative multidrug resistance ABC transporter ATP-binding/permease protein YheH [17:47:30] Modify product: PGL/p-HBAD biosynthesis glycosyltransferase Rv2957 => PGL/p-HBAD biosynthesis glycosyltransferase [17:47:30] Modify product: Uncharacterized ABC transporter ATP-binding protein HI_1470 => putative ABC transporter ATP-binding protein [17:47:30] Modify product: Probable 2-phosphosulfolactate phosphatase => putative 2-phosphosulfolactate phosphatase [17:47:30] Modify product: Uncharacterized methyltransferase YcgJ => putative methyltransferase YcgJ [17:47:31] Modify product: Uncharacterized zinc protease Rv2782c => putative zinc protease [17:47:31] Modify product: Uncharacterized ABC transporter ATP-binding protein Rv0986 => putative ABC transporter ATP-binding protein [17:47:31] Modify product: Uncharacterized sugar epimerase YhfK => putative sugar epimerase YhfK [17:47:31] Modify product: Uncharacterized ABC transporter ATP-binding protein YlmA => putative ABC transporter ATP-binding protein YlmA [17:47:31] Modify product: Probable undecaprenyl-phosphate N-acetylglucosaminyl 1-phosphate transferase => putative undecaprenyl-phosphate N-acetylglucosaminyl 1-phosphate transferase [17:47:31] Modify product: Putative Rieske 2Fe-2S iron-sulfur protein Rv3818 => Putative Rieske 2Fe-2S iron-sulfur protein [17:47:31] Modify product: Probable multidrug resistance ABC transporter ATP-binding/permease protein YheI => putative multidrug resistance ABC transporter ATP-binding/permease protein YheI [17:47:31] Modify product: Segregation and condensation protein B homolog => Segregation and condensation protein B [17:47:31] Modify product: Probable peroxiredoxin => putative peroxiredoxin [17:47:31] Modify product: Putative multidrug export ATP-binding/permease protein SA1683 => Putative multidrug export ATP-binding/permease protein [17:47:31] Modify product: Probable chromate transport protein => putative chromate transport protein [17:47:31] Modify product: Vitamin K epoxide reductase homolog => Vitamin K epoxide reductase [17:47:31] Modify product: Probable glutamine ABC transporter permease protein GlnM => putative glutamine ABC transporter permease protein GlnM [17:47:31] Modify product: Uncharacterized ABC transporter ATP-binding protein TM_0288 => putative ABC transporter ATP-binding protein [17:47:31] Modify product: Probable protein kinase UbiB => putative protein kinase UbiB [17:47:31] Modify product: Bifunctional protein FolD => Bifunctional protein FolD protein [17:47:31] Modify product: 1,4-alpha-glucan branching enzyme TTHA1902 => 1,4-alpha-glucan branching enzyme [17:47:31] Modify product: Uncharacterized oxidoreductase MSMEG_1603/MSMEI_1564 => putative oxidoreductase/MSMEI_1564 [17:47:31] Modify product: Uncharacterized tRNA/rRNA methyltransferase HI_0380 => putative tRNA/rRNA methyltransferase [17:47:31] Modify product: Maf-like protein Rv3282 => Maf-like protein [17:47:31] Modify product: PKHD-type hydroxylase Sbal_3634 => PKHD-type hydroxylase [17:47:31] Modify product: Uncharacterized inner membrane transporter YedA => putative inner membrane transporter YedA [17:47:31] Modify product: Uncharacterized FAD-linked oxidoreductase Rv2280 => putative FAD-linked oxidoreductase [17:47:31] Modify product: Oxygen-independent coproporphyrinogen-III oxidase-like protein sll1917 => Oxygen-independent coproporphyrinogen-III oxidase-like protein [17:47:31] Modify product: Uncharacterized PIN and TRAM-domain containing protein YacL => putative PIN and TRAM-domain containing protein YacL [17:47:31] Modify product: Glycogen operon protein GlgX homolog => Glycogen operon protein GlgX [17:47:31] Modify product: Probable phospholipid ABC transporter permease protein MlaE => putative phospholipid ABC transporter permease protein MlaE [17:47:32] Modify product: Probable 30S ribosomal protein PSRP-3 => putative 30S ribosomal protein PSRP-3 [17:47:32] Modify product: Probable nicotinate-nucleotide adenylyltransferase => putative nicotinate-nucleotide adenylyltransferase [17:47:32] Modify product: Probable peptidoglycan glycosyltransferase FtsW => putative peptidoglycan glycosyltransferase FtsW [17:47:32] Modify product: Probable helicase HelY => putative helicase HelY [17:47:32] Modify product: Probable trans-aconitate 2-methyltransferase => putative trans-aconitate 2-methyltransferase [17:47:32] Modify product: Probable cobalt-factor III C(17)-methyltransferase => putative cobalt-factor III C(17)-methyltransferase [17:47:32] Modify product: Probable adenylyltransferase/sulfurtransferase MoeZ => putative adenylyltransferase/sulfurtransferase MoeZ [17:47:32] Modify product: Uncharacterized hydrolase YxeP => putative hydrolase YxeP [17:47:32] Modify product: Uncharacterized membrane protein Rv2637 => putative membrane protein [17:47:32] Modify product: Probable formate transporter 1 => putative formate transporter 1 [17:47:32] Modify product: Probable protein kinase UbiB => putative protein kinase UbiB [17:47:32] Cleaned 64 /product names [17:47:32] Deleting unwanted file: /share/gsi2/data/www/soap-data/M2BBS/Phylogenomic/Prochlorococcus/prokka/Aaai/sprot.faa [17:47:32] Deleting unwanted file: /share/gsi2/data/www/soap-data/M2BBS/Phylogenomic/Prochlorococcus/prokka/Aaai/sprot.blast [17:47:33] There are still 1113 unannotated CDS left (started with 2149) [17:47:33] Will use hmmer3 to search against /share/gsi2/software/prokka/bin/../db/hmm/HAMAP.hmm with 1 CPUs [17:47:33] Running: cat \/share\/gsi2\/data\/www\/soap\-data\/M2BBS\/Phylogenomic\/Prochlorococcus\/prokka\/Aaai\/HAMAP\.hmm\.faa | parallel --gnu --plain -j 1 --block 86832 --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\/Aaai\/HAMAP\.hmm\.hmmer3 2> /dev/null [17:49:12] Deleting unwanted file: /share/gsi2/data/www/soap-data/M2BBS/Phylogenomic/Prochlorococcus/prokka/Aaai/HAMAP.hmm.faa [17:49:12] Deleting unwanted file: /share/gsi2/data/www/soap-data/M2BBS/Phylogenomic/Prochlorococcus/prokka/Aaai/HAMAP.hmm.hmmer3 [17:49:12] Labelling remaining 1045 proteins as 'hypothetical protein' [17:49:12] Possible /pseudo 'NADH-quinone oxidoreductase subunit N' at gnl|Prokka|AaaiA01.g_1 position 444918 [17:49:12] Possible /pseudo 'Bifunctional protein GlmU' at gnl|Prokka|AaaiA01.g_1 position 615012 [17:49:12] Possible /pseudo 'ATP-dependent Clp protease proteolytic subunit' at gnl|Prokka|AaaiA01.g_1 position 1420814 [17:49:12] Possible /pseudo 'TPR repeat-containing protein YrrB' at gnl|Prokka|AaaiA01.g_1 position 1485867 [17:49:12] Possible /pseudo 'DNA-directed RNA polymerase subunit beta'' at gnl|Prokka|AaaiA01.g_1 position 1544451 [17:49:12] Possible /pseudo '15,16-dihydrobiliverdin:ferredoxin oxidoreductase' at gnl|Prokka|AaaiA01.g_1 position 1685827 [17:49:12] Possible /pseudo 'Putative fluoride ion transporter CrcB' at gnl|Prokka|AaaiA01.g_1 position 1728506 [17:49:12] Possible /pseudo 'Phosphatidyl-myo-inositol mannosyltransferase' at gnl|Prokka|AaaiA01.g_1 position 1748701 [17:49:12] Found 939 unique /gene codes. [17:49:12] Fixed 3 duplicate /gene - ubiG_1 ubiG_2 ubiG_3 [17:49:12] Fixed 2 duplicate /gene - bchI_1 bchI_2 [17:49:12] Fixed 2 duplicate /gene - rpoC_1 rpoC_2 [17:49:12] Fixed 2 duplicate /gene - cobD_1 cobD_2 [17:49:12] Fixed 2 duplicate /gene - msrA_1 msrA_2 [17:49:12] Fixed 2 duplicate /gene - atpG_1 atpG_2 [17:49:12] Fixed 2 duplicate /gene - lexA_1 lexA_2 [17:49:12] Fixed 2 duplicate /gene - hpf_1 hpf_2 [17:49:12] Fixed 2 duplicate /gene - purE_1 purE_2 [17:49:12] Fixed 2 duplicate /gene - gph_1 gph_2 [17:49:12] Fixed 2 duplicate /gene - era_1 era_2 [17:49:12] Fixed 2 duplicate /gene - pimA_1 pimA_2 [17:49:12] Fixed 2 duplicate /gene - gmd_1 gmd_2 [17:49:12] Fixed 2 duplicate /gene - pcbB_1 pcbB_2 [17:49:12] Fixed 2 duplicate /gene - ccmK_1 ccmK_2 [17:49:12] Fixed 2 duplicate /gene - queD_1 queD_2 [17:49:12] Fixed 2 duplicate /gene - bepA_1 bepA_2 [17:49:12] Fixed 2 duplicate /gene - csgA_1 csgA_2 [17:49:12] Fixed 2 duplicate /gene - sir_1 sir_2 [17:49:12] Fixed 2 duplicate /gene - ntcA_1 ntcA_2 [17:49:12] Fixed 2 duplicate /gene - ndhD1_1 ndhD1_2 [17:49:12] Fixed 2 duplicate /gene - mnmC_1 mnmC_2 [17:49:12] Fixed 2 duplicate /gene - psaA_1 psaA_2 [17:49:12] Fixed 2 duplicate /gene - udk_1 udk_2 [17:49:12] Fixed 2 duplicate /gene - cobN_1 cobN_2 [17:49:12] Fixed 2 duplicate /gene - der_1 der_2 [17:49:12] Fixed 2 duplicate /gene - mfpsA_1 mfpsA_2 [17:49:12] Fixed 4 duplicate /gene - yrrB_1 yrrB_2 yrrB_3 yrrB_4 [17:49:12] Fixed 2 duplicate /gene - pds_1 pds_2 [17:49:12] Fixed 2 duplicate /gene - dnaK2_1 dnaK2_2 [17:49:12] Fixed 2 duplicate /gene - lpxB_1 lpxB_2 [17:49:12] Fixed 3 duplicate /gene - yciC_1 yciC_2 yciC_3 [17:49:12] Fixed 2 duplicate /gene - ycf3_1 ycf3_2 [17:49:12] Fixed 2 duplicate /gene - hisH_1 hisH_2 [17:49:12] Fixed 2 duplicate /gene - csd_1 csd_2 [17:49:12] Fixed 2 duplicate /gene - rpsA_1 rpsA_2 [17:49:12] Fixed 2 duplicate /gene - speA_1 speA_2 [17:49:12] Fixed 2 duplicate /gene - iscS_1 iscS_2 [17:49:12] Fixed 2 duplicate /gene - gyrA_1 gyrA_2 [17:49:12] Fixed 2 duplicate /gene - trpC_1 trpC_2 [17:49:12] Fixed 2 duplicate /gene - mgl_1 mgl_2 [17:49:12] Fixed 2 duplicate /gene - lip1_1 lip1_2 [17:49:12] Fixed 2 duplicate /gene - hhoA_1 hhoA_2 [17:49:12] Fixed 2 duplicate /gene - hisF_1 hisF_2 [17:49:12] Fixed 3 duplicate /gene - psbA_1 psbA_2 psbA_3 [17:49:12] Fixed 2 duplicate /gene - sphR_1 sphR_2 [17:49:12] Fixed 2 duplicate /gene - crcB_1 crcB_2 [17:49:12] Fixed 2 duplicate /gene - glmU_1 glmU_2 [17:49:12] Fixed 2 duplicate /gene - plsC_1 plsC_2 [17:49:12] Fixed 2 duplicate /gene - tam_1 tam_2 [17:49:12] Fixed 4 duplicate /gene - bcp_1 bcp_2 bcp_3 bcp_4 [17:49:12] Fixed 2 duplicate /gene - mgtA_1 mgtA_2 [17:49:12] Fixed 2 duplicate /gene - bicA_1 bicA_2 [17:49:12] Fixed 2 duplicate /gene - clpS_1 clpS_2 [17:49:12] Fixed 2 duplicate /gene - btuR_1 btuR_2 [17:49:12] Fixed 4 duplicate /gene - clpP_1 clpP_2 clpP_3 clpP_4 [17:49:12] Fixed 2 duplicate /gene - pebA_1 pebA_2 [17:49:12] Fixed 4 duplicate /gene - sigA2_1 sigA2_2 sigA2_3 sigA2_4 [17:49:12] Fixed 2 duplicate /gene - ppiA_1 ppiA_2 [17:49:12] Fixed 2 duplicate /gene - carA_1 carA_2 [17:49:12] Fixed 2 duplicate /gene - mntB_1 mntB_2 [17:49:12] Fixed 2 duplicate /gene - arnT_1 arnT_2 [17:49:12] Fixed 2 duplicate /gene - trxA_1 trxA_2 [17:49:12] Fixed 2 duplicate /gene - sdh_1 sdh_2 [17:49:12] Fixed 2 duplicate /gene - suhB_1 suhB_2 [17:49:12] Fixed 2 duplicate /gene - clpB1_1 clpB1_2 [17:49:12] Fixed 2 duplicate /gene - rnr_1 rnr_2 [17:49:12] Fixed 2 duplicate /gene - ftsH2_1 ftsH2_2 [17:49:12] Fixed 2 duplicate /gene - cca_1 cca_2 [17:49:12] Fixed 2 duplicate /gene - ppa_1 ppa_2 [17:49:12] Fixed 2 duplicate /gene - crtI_1 crtI_2 [17:49:12] Fixed 2 duplicate /gene - dnaX_1 dnaX_2 [17:49:12] Fixed 2 duplicate /gene - dnaJ_1 dnaJ_2 [17:49:12] Fixed 2 duplicate /gene - sasA_1 sasA_2 [17:49:12] Fixed 2 duplicate /gene - crtL_1 crtL_2 [17:49:12] Fixed 3 duplicate /gene - ligA_1 ligA_2 ligA_3 [17:49:12] Fixed 2 duplicate /gene - lytB_1 lytB_2 [17:49:12] Fixed 2 duplicate /gene - cbpA_1 cbpA_2 [17:49:12] Fixed 3 duplicate /gene - ubiB_1 ubiB_2 ubiB_3 [17:49:12] Fixed 2 duplicate /gene - nuoN_1 nuoN_2 [17:49:12] Fixed 2 duplicate /gene - trxB_1 trxB_2 [17:49:12] Fixed 81 colliding /gene names. [17:49:12] Adding /locus_tag identifiers [17:49:12] Assigned 2191 locus_tags to CDS and RNA features. [17:49:12] Writing outputs to /share/gsi2/data/www/soap-data/M2BBS/Phylogenomic/Prochlorococcus/prokka/Aaai/ [17:49:18] Generating annotation statistics file [17:49:18] Generating Genbank and Sequin files [17:49:18] 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\/Aaai\/AaaiA01\.err -i \/share\/gsi2\/data\/www\/soap\-data\/M2BBS\/Phylogenomic\/Prochlorococcus\/prokka\/Aaai\/AaaiA01\.fsa 2> /dev/null [17:49:27] Deleting unwanted file: /share/gsi2/data/www/soap-data/M2BBS/Phylogenomic/Prochlorococcus/prokka/Aaai/errorsummary.val [17:49:27] Deleting unwanted file: /share/gsi2/data/www/soap-data/M2BBS/Phylogenomic/Prochlorococcus/prokka/Aaai/AaaiA01.dr [17:49:27] Deleting unwanted file: /share/gsi2/data/www/soap-data/M2BBS/Phylogenomic/Prochlorococcus/prokka/Aaai/AaaiA01.fixedproducts [17:49:27] Deleting unwanted file: /share/gsi2/data/www/soap-data/M2BBS/Phylogenomic/Prochlorococcus/prokka/Aaai/AaaiA01.ecn [17:49:27] Deleting unwanted file: /share/gsi2/data/www/soap-data/M2BBS/Phylogenomic/Prochlorococcus/prokka/Aaai/AaaiA01.val [17:49:27] Repairing broken .GBK output that tbl2asn produces... [17:49:27] Running: sed 's/COORDINATES: profile/COORDINATES:profile/' < \/share\/gsi2\/data\/www\/soap\-data\/M2BBS\/Phylogenomic\/Prochlorococcus\/prokka\/Aaai\/AaaiA01\.gbf > \/share\/gsi2\/data\/www\/soap\-data\/M2BBS\/Phylogenomic\/Prochlorococcus\/prokka\/Aaai\/AaaiA01\.gbk [17:49:27] Deleting unwanted file: /share/gsi2/data/www/soap-data/M2BBS/Phylogenomic/Prochlorococcus/prokka/Aaai/AaaiA01.gbf [17:49:27] Output files: [17:49:27] /share/gsi2/data/www/soap-data/M2BBS/Phylogenomic/Prochlorococcus/prokka/Aaai/AaaiA01.log [17:49:27] /share/gsi2/data/www/soap-data/M2BBS/Phylogenomic/Prochlorococcus/prokka/Aaai/AaaiA01.fna [17:49:27] /share/gsi2/data/www/soap-data/M2BBS/Phylogenomic/Prochlorococcus/prokka/Aaai/AaaiA01.gff [17:49:27] /share/gsi2/data/www/soap-data/M2BBS/Phylogenomic/Prochlorococcus/prokka/Aaai/AaaiA01.faa [17:49:27] /share/gsi2/data/www/soap-data/M2BBS/Phylogenomic/Prochlorococcus/prokka/Aaai/AaaiA01.ffn [17:49:27] /share/gsi2/data/www/soap-data/M2BBS/Phylogenomic/Prochlorococcus/prokka/Aaai/AaaiA01.tbl [17:49:27] /share/gsi2/data/www/soap-data/M2BBS/Phylogenomic/Prochlorococcus/prokka/Aaai/AaaiA01.fsa [17:49:27] /share/gsi2/data/www/soap-data/M2BBS/Phylogenomic/Prochlorococcus/prokka/Aaai/AaaiA01.tsv [17:49:27] /share/gsi2/data/www/soap-data/M2BBS/Phylogenomic/Prochlorococcus/prokka/Aaai/AaaiA01.txt [17:49:27] /share/gsi2/data/www/soap-data/M2BBS/Phylogenomic/Prochlorococcus/prokka/Aaai/AaaiA01.sqn [17:49:27] /share/gsi2/data/www/soap-data/M2BBS/Phylogenomic/Prochlorococcus/prokka/Aaai/AaaiA01.err [17:49:27] /share/gsi2/data/www/soap-data/M2BBS/Phylogenomic/Prochlorococcus/prokka/Aaai/AaaiA01.gbk [17:49:27] Annotation finished successfully. [17:49:27] Walltime used: 5.18 minutes [17:49:27] If you use this result please cite the Prokka paper: [17:49:27] Seemann T (2014) Prokka: rapid prokaryotic genome annotation. Bioinformatics. 30(14):2068-9. [17:49:27] Type 'prokka --citation' for more details. [17:49:27] Share and enjoy!