[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/Aaaj [17:44:16] Running: mkdir -p \/share\/gsi2\/data\/www\/soap\-data\/M2BBS\/Phylogenomic\/Prochlorococcus\/prokka\/Aaaj [17:44:16] Using filename prefix: AaajA01.XXX [17:44:16] Setting HMMER_NCPU=1 [17:44:16] Writing log to: /share/gsi2/data/www/soap-data/M2BBS/Phylogenomic/Prochlorococcus/prokka/Aaaj/AaajA01.log [17:44:16] Command: /share/gsi2/bin/prokka /share/gsi2/data/www/soap-data/M2BBS/Phylogenomic/Prochlorococcus/DNA/Aaaj/AaajA01.fas --compliant --addgenes --outdir /share/gsi2/data/www/soap-data/M2BBS/Phylogenomic/Prochlorococcus/prokka/Aaaj --prefix AaajA01 --locustag AaajA01.g --species ProchlorococcusmarinusstrMIT9301 --strain ProchlorococcusmarinusstrMIT9301 --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 [17:44:20] Determined minced version is 2.0 [17:44:20] Looking for 'parallel' - found /share/gsi2/software/prokka/bin/../binaries/linux/../common/parallel [17:44:20] 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 [17:44:21] 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/Aaaj/AaajA01.fas [17:44:21] Wrote 1 contigs totalling 1641879 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\/Aaaj\/AaajA01\.fna [17:44:22] 1 tmRNA* c[66363,66672] 169,219 ANKIVSFSRQTAPVAA* [17:44:22] 2 tRNA-Leu c[75525,75608] 36 (aag) [17:44:22] 3 tRNA-Asn [132757,132830] 34 (gtt) [17:44:22] 4 tRNA-Leu [240439,240521] 35 (tag) [17:44:22] 5 tRNA-Arg c[258921,258996] 36 (acg) [17:44:22] 6 tRNA-Met c[274057,274131] 35 (cat) [17:44:22] 7 tRNA-Phe c[305936,306010] 34 (gaa) [17:44:22] 8 tRNA-Thr c[314651,314722] 33 (tgt) [17:44:22] 9 tRNA-Ile [324199,324274] 36 (gat) [17:44:22] 10 tRNA-Ala [324286,324359] 34 (tgc) [17:44:22] 11 tRNA-Thr c[355255,355327] 33 (ggt) [17:44:22] 12 tRNA-Tyr c[355337,355419] 35 (gta) [17:44:22] 13 tRNA-Asp c[435677,435752] 36 (gtc) [17:44:22] 14 tRNA-Trp c[436130,436204] 35 (cca) [17:44:22] 15 tRNA-Leu [522597,522682] 35 (taa) [17:44:22] 16 tRNA-Ser c[610146,610234] 36 (tga) [17:44:22] 17 tRNA-Pro c[775451,775524] 35 (ggg) [17:44:22] 18 tRNA-Ser [828442,828528] 35 (gga) [17:44:22] 19 tRNA-Met [869242,869317] 36 (cat) [17:44:22] 20 tRNA-Met [910753,910829] 35 (cat) [17:44:22] 21 tRNA-Glu c[996625,996699] 36 (ttc) [17:44:22] 22 tRNA-Lys [1040313,1040385] 33 (ttt) [17:44:22] 23 tRNA-Pro [1045700,1045774] 35 (tgg) [17:44:22] 24 tRNA-Ser c[1134678,1134764] 36 (cga) [17:44:22] 25 tRNA-Arg [1164230,1164305] 36 (tct) [17:44:22] 26 tRNA-Ala c[1212953,1213025] 34 (ggc) [17:44:22] 27 tRNA-Leu [1255649,1255731] 35 (caa) [17:44:22] 28 tRNA-His [1260916,1260989] 34 (gtg) [17:44:22] 29 tRNA-Gly c[1277273,1277343] 33 (tcc) [17:44:22] 30 tRNA-Val [1308847,1308920] 34 (gac) [17:44:22] 31 tRNA-Thr [1419948,1420020] 33 (cgt) [17:44:22] 32 tRNA-Ser c[1454110,1454200] 36 (gct) [17:44:22] 33 tRNA-Gln [1474027,1474098] 33 (ttg) [17:44:22] 34 tRNA-Arg [1486727,1486800] 35 (ccg) [17:44:22] 35 tRNA-Cys [1501368,1501438] 33 (gca) [17:44:22] 36 tRNA-Arg c[1518206,1518281] 36 (cct) [17:44:22] 37 tRNA-Gly c[1554679,1554750] 33 (gcc) [17:44:22] 38 tRNA-Val c[1601255,1601326] 33 (tac) [17:44:22] Found 38 tRNAs [17:44:22] Predicting Ribosomal RNAs [17:44:22] Running Barrnap with 1 threads [17:44:25] 1 gnl|Prokka|AaajA01.g_1 322593 16S ribosomal RNA [17:44:25] 2 gnl|Prokka|AaajA01.g_1 324619 23S ribosomal RNA [17:44:25] 3 gnl|Prokka|AaajA01.g_1 327559 5S ribosomal RNA [17:44:25] Found 3 rRNAs [17:44:25] Skipping ncRNA search, enable with --rfam if desired. [17:44:25] Total of 40 tRNA + rRNA features [17:44:25] Searching for CRISPR repeats [17:44:26] Found 0 CRISPRs [17:44:26] Predicting coding sequences [17:44:26] Contigs total 1641879 bp, so using single mode [17:44:26] Running: prodigal -i \/share\/gsi2\/data\/www\/soap\-data\/M2BBS\/Phylogenomic\/Prochlorococcus\/prokka\/Aaaj\/AaajA01\.fna -c -m -g 11 -p single -f sco -q [17:44:32] Excluding CDS which overlaps existing RNA (tRNA) at gnl|Prokka|AaajA01.g_1:1255658..1256911 on + strand [17:44:32] Excluding CDS which overlaps existing RNA (tRNA) at gnl|Prokka|AaajA01.g_1:1500099..1501487 on - strand [17:44:32] Found 1873 CDS [17:44:32] Connecting features back to sequences [17:44:32] Not using genus-specific database. Try --usegenus to enable it. [17:44:32] Annotating CDS, please be patient. [17:44:32] Will use 1 CPUs for similarity searching. [17:44:35] There are still 1873 unannotated CDS left (started with 1873) [17:44:35] Will use blast to search against /share/gsi2/software/prokka/bin/../db/kingdom/Bacteria/sprot with 1 CPUs [17:44:35] Running: cat \/share\/gsi2\/data\/www\/soap\-data\/M2BBS\/Phylogenomic\/Prochlorococcus\/prokka\/Aaaj\/sprot\.faa | parallel --gnu --plain -j 1 --block 253385 --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\/Aaaj\/sprot\.blast 2> /dev/null [17:47:11] Modify product: N utilization substance protein B homolog => N utilization substance protein B [17:47:11] Modify product: Uncharacterized oxidoreductase Rv2298 => putative oxidoreductase [17:47:11] Modify product: Probable cysteine desulfurase => putative cysteine desulfurase [17:47:11] Modify product: Probable ATP-dependent transporter SufC => putative ATP-dependent transporter SufC [17:47:11] Modify product: Uncharacterized transporter Rv2685 => putative transporter [17:47:11] Modify product: Uncharacterized ABC transporter ATP-binding protein YheS => putative ABC transporter ATP-binding protein YheS [17:47:11] Modify product: Vitamin K epoxide reductase homolog => Vitamin K epoxide reductase [17:47:11] Modify product: Epimerase family protein Rv2216 => Epimerase family protein [17:47:11] Modify product: Probable adenylyl-sulfate kinase => putative adenylyl-sulfate kinase [17:47:11] Modify product: Probable glutaredoxin ssr2061 => putative glutaredoxin [17:47:11] Modify product: Probable nicotinate-nucleotide pyrophosphorylase [carboxylating] => putative nicotinate-nucleotide pyrophosphorylase [carboxylating] [17:47:11] Modify product: Probable protein kinase UbiB => putative protein kinase UbiB [17:47:11] Modify product: Probable bifunctional SAT/APS kinase => putative bifunctional SAT/APS kinase [17:47:12] Modify product: Probable ribonucleotide transport ATP-binding protein mkl => putative ribonucleotide transport ATP-binding protein mkl [17:47:12] Modify product: Probable septum site-determining protein MinC => putative septum site-determining protein MinC [17:47:12] Modify product: Uncharacterized ABC transporter ATP-binding protein YknY => putative ABC transporter ATP-binding protein YknY [17:47:12] Modify product: Probable cytochrome c oxidase subunit 1 => putative cytochrome c oxidase subunit 1 [17:47:12] Modify product: Probable murein peptide carboxypeptidase => putative murein peptide carboxypeptidase [17:47:12] Modify product: Thylakoid-associated single-stranded DNA-binding protein slr1034 => Thylakoid-associated single-stranded DNA-binding protein [17:47:12] Modify product: Uncharacterized ABC transporter ATP-binding protein TM_0288 => putative ABC transporter ATP-binding protein [17:47:12] Modify product: PGL/p-HBAD biosynthesis glycosyltransferase Rv2957 => PGL/p-HBAD biosynthesis glycosyltransferase [17:47:12] Modify product: Uncharacterized ABC transporter ATP-binding protein HI_1470 => putative ABC transporter ATP-binding protein [17:47:12] Modify product: Probable 2-phosphosulfolactate phosphatase => putative 2-phosphosulfolactate phosphatase [17:47:12] Modify product: Probable trans-aconitate 2-methyltransferase => putative trans-aconitate 2-methyltransferase [17:47:12] Modify product: Uncharacterized zinc protease Rv2782c => putative zinc protease [17:47:12] Modify product: Uncharacterized ABC transporter ATP-binding protein Rv0986 => putative ABC transporter ATP-binding protein [17:47:12] Modify product: GTP-binding protein TypA/BipA homolog => GTP-binding protein TypA/BipA [17:47:12] Modify product: Uncharacterized sugar epimerase YhfK => putative sugar epimerase YhfK [17:47:12] Modify product: Uncharacterized ABC transporter ATP-binding protein YlmA => putative ABC transporter ATP-binding protein YlmA [17:47:12] Modify product: Probable multidrug resistance ABC transporter ATP-binding/permease protein YheI => putative multidrug resistance ABC transporter ATP-binding/permease protein YheI [17:47:12] Modify product: Vitamin K epoxide reductase homolog => Vitamin K epoxide reductase [17:47:12] Modify product: Probable peroxiredoxin => putative peroxiredoxin [17:47:13] Modify product: Putative multidrug export ATP-binding/permease protein SA1683 => Putative multidrug export ATP-binding/permease protein [17:47:13] Modify product: Uncharacterized peptidase Lmo0363 => putative peptidase [17:47:13] Modify product: Probable tRNA-dihydrouridine synthase => putative tRNA-dihydrouridine synthase [17:47:13] Modify product: Putative esterase aq_1494 => Putative esterase [17:47:13] Modify product: Uncharacterized tRNA/rRNA methyltransferase HI_0380 => putative tRNA/rRNA methyltransferase [17:47:13] Modify product: Uncharacterized oxidoreductase MSMEG_1603/MSMEI_1564 => putative oxidoreductase/MSMEI_1564 [17:47:13] Modify product: 1,4-alpha-glucan branching enzyme TTHA1902 => 1,4-alpha-glucan branching enzyme [17:47:13] Modify product: Bifunctional protein FolD => Bifunctional protein FolD protein [17:47:13] Modify product: Probable protein kinase UbiB => putative protein kinase UbiB [17:47:13] Modify product: PKHD-type hydroxylase Sbal_3634 => PKHD-type hydroxylase [17:47:13] Modify product: Probable chromate transport protein => putative chromate transport protein [17:47:13] Modify product: Uncharacterized oxidoreductase CzcO => putative oxidoreductase CzcO [17:47:13] Modify product: Probable peptidyl-prolyl cis-trans isomerase => putative peptidyl-prolyl cis-trans isomerase [17:47:13] Modify product: Maf-like protein Rv3282 => Maf-like protein [17:47:13] Modify product: PKHD-type hydroxylase Sbal_3634 => PKHD-type hydroxylase [17:47:13] Modify product: Uncharacterized inner membrane transporter YedA => putative inner membrane transporter YedA [17:47:13] Modify product: Uncharacterized glycosyltransferase EpsJ => putative glycosyltransferase EpsJ [17:47:13] Modify product: Putative multidrug export ATP-binding/permease protein SA1683 => Putative multidrug export ATP-binding/permease protein [17:47:13] Modify product: Probable undecaprenyl-phosphate N-acetylglucosaminyl 1-phosphate transferase => putative undecaprenyl-phosphate N-acetylglucosaminyl 1-phosphate transferase [17:47:13] Modify product: Uncharacterized FAD-linked oxidoreductase Rv2280 => putative FAD-linked oxidoreductase [17:47:13] Modify product: Oxygen-independent coproporphyrinogen-III oxidase-like protein sll1917 => Oxygen-independent coproporphyrinogen-III oxidase-like protein [17:47:13] Modify product: Uncharacterized PIN and TRAM-domain containing protein YacL => putative PIN and TRAM-domain containing protein YacL [17:47:13] Modify product: Glycogen operon protein GlgX homolog => Glycogen operon protein GlgX [17:47:13] Modify product: Probable phospholipid ABC transporter permease protein MlaE => putative phospholipid ABC transporter permease protein MlaE [17:47:13] Modify product: Probable 30S ribosomal protein PSRP-3 => putative 30S ribosomal protein PSRP-3 [17:47:13] Modify product: Probable peptidoglycan glycosyltransferase FtsW => putative peptidoglycan glycosyltransferase FtsW [17:47:13] Modify product: Probable helicase HelY => putative helicase HelY [17:47:13] Modify product: Probable dual-specificity RNA methyltransferase RlmN => putative dual-specificity RNA methyltransferase RlmN [17:47:13] Modify product: Probable endopeptidase p60 => putative endopeptidase p60 [17:47:13] Modify product: Probable cobalt-factor III C(17)-methyltransferase => putative cobalt-factor III C(17)-methyltransferase [17:47:13] Modify product: Probable adenylyltransferase/sulfurtransferase MoeZ => putative adenylyltransferase/sulfurtransferase MoeZ [17:47:13] Modify product: Uncharacterized hydrolase YxeP => putative hydrolase YxeP [17:47:14] Modify product: Probable branched-chain-amino-acid aminotransferase => putative branched-chain-amino-acid aminotransferase [17:47:14] Modify product: Probable protein kinase UbiB => putative protein kinase UbiB [17:47:14] Cleaned 66 /product names [17:47:14] Deleting unwanted file: /share/gsi2/data/www/soap-data/M2BBS/Phylogenomic/Prochlorococcus/prokka/Aaaj/sprot.faa [17:47:14] Deleting unwanted file: /share/gsi2/data/www/soap-data/M2BBS/Phylogenomic/Prochlorococcus/prokka/Aaaj/sprot.blast [17:47:15] There are still 859 unannotated CDS left (started with 1873) [17:47:15] Will use hmmer3 to search against /share/gsi2/software/prokka/bin/../db/hmm/HAMAP.hmm with 1 CPUs [17:47:15] Running: cat \/share\/gsi2\/data\/www\/soap\-data\/M2BBS\/Phylogenomic\/Prochlorococcus\/prokka\/Aaaj\/HAMAP\.hmm\.faa | parallel --gnu --plain -j 1 --block 72430 --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\/Aaaj\/HAMAP\.hmm\.hmmer3 2> /dev/null [17:48:32] Deleting unwanted file: /share/gsi2/data/www/soap-data/M2BBS/Phylogenomic/Prochlorococcus/prokka/Aaaj/HAMAP.hmm.faa [17:48:32] Deleting unwanted file: /share/gsi2/data/www/soap-data/M2BBS/Phylogenomic/Prochlorococcus/prokka/Aaaj/HAMAP.hmm.hmmer3 [17:48:32] Labelling remaining 793 proteins as 'hypothetical protein' [17:48:32] Possible /pseudo 'Ethanolamine utilization protein EutN' at gnl|Prokka|AaajA01.g_1 position 509654 [17:48:32] Possible /pseudo 'ATP-dependent Clp protease proteolytic subunit' at gnl|Prokka|AaajA01.g_1 position 1270054 [17:48:32] Possible /pseudo 'DNA-directed RNA polymerase subunit beta'' at gnl|Prokka|AaajA01.g_1 position 1404027 [17:48:32] Possible /pseudo '15,16-dihydrobiliverdin:ferredoxin oxidoreductase' at gnl|Prokka|AaajA01.g_1 position 1506525 [17:48:32] Possible /pseudo 'Putative fluoride ion transporter CrcB' at gnl|Prokka|AaajA01.g_1 position 1544560 [17:48:32] Found 928 unique /gene codes. [17:48:32] Fixed 3 duplicate /gene - yciC_1 yciC_2 yciC_3 [17:48:32] Fixed 2 duplicate /gene - dnaK2_1 dnaK2_2 [17:48:32] Fixed 3 duplicate /gene - hisH_1 hisH_2 hisH_3 [17:48:32] Fixed 3 duplicate /gene - ycf3_1 ycf3_2 ycf3_3 [17:48:32] Fixed 2 duplicate /gene - cobN_1 cobN_2 [17:48:32] Fixed 2 duplicate /gene - suhB_1 suhB_2 [17:48:32] Fixed 2 duplicate /gene - hhoA_1 hhoA_2 [17:48:32] Fixed 2 duplicate /gene - csgA_1 csgA_2 [17:48:32] Fixed 3 duplicate /gene - ubiG_1 ubiG_2 ubiG_3 [17:48:32] Fixed 2 duplicate /gene - clpB1_1 clpB1_2 [17:48:32] Fixed 2 duplicate /gene - bicA_1 bicA_2 [17:48:32] Fixed 2 duplicate /gene - mnmC_1 mnmC_2 [17:48:32] Fixed 2 duplicate /gene - pds_1 pds_2 [17:48:32] Fixed 4 duplicate /gene - ligB_1 ligB_2 ligB_3 ligB_4 [17:48:32] Fixed 3 duplicate /gene - era_1 era_2 era_3 [17:48:32] Fixed 2 duplicate /gene - rpoC_1 rpoC_2 [17:48:32] Fixed 2 duplicate /gene - lpxB_1 lpxB_2 [17:48:32] Fixed 3 duplicate /gene - ftsH2_1 ftsH2_2 ftsH2_3 [17:48:32] Fixed 2 duplicate /gene - plsC_1 plsC_2 [17:48:32] Fixed 3 duplicate /gene - bcp_1 bcp_2 bcp_3 [17:48:32] Fixed 2 duplicate /gene - rpsA_1 rpsA_2 [17:48:32] Fixed 2 duplicate /gene - ctpA_1 ctpA_2 [17:48:32] Fixed 2 duplicate /gene - atpG_1 atpG_2 [17:48:32] Fixed 2 duplicate /gene - crtL_1 crtL_2 [17:48:32] Fixed 2 duplicate /gene - pstS_1 pstS_2 [17:48:32] Fixed 2 duplicate /gene - phnE_1 phnE_2 [17:48:32] Fixed 2 duplicate /gene - iscS_1 iscS_2 [17:48:32] Fixed 2 duplicate /gene - sasA_1 sasA_2 [17:48:32] Fixed 2 duplicate /gene - phnD_1 phnD_2 [17:48:32] Fixed 2 duplicate /gene - nadK_1 nadK_2 [17:48:32] Fixed 2 duplicate /gene - iolC_1 iolC_2 [17:48:32] Fixed 2 duplicate /gene - crcB_1 crcB_2 [17:48:32] Fixed 2 duplicate /gene - ilvE_1 ilvE_2 [17:48:32] Fixed 3 duplicate /gene - galE_1 galE_2 galE_3 [17:48:32] Fixed 2 duplicate /gene - arnT_1 arnT_2 [17:48:32] Fixed 2 duplicate /gene - dfa3_1 dfa3_2 [17:48:32] Fixed 2 duplicate /gene - ppiB_1 ppiB_2 [17:48:32] Fixed 2 duplicate /gene - lytB_1 lytB_2 [17:48:32] Fixed 2 duplicate /gene - hpf_1 hpf_2 [17:48:32] Fixed 2 duplicate /gene - corC_1 corC_2 [17:48:32] Fixed 2 duplicate /gene - dnaX_1 dnaX_2 [17:48:32] Fixed 3 duplicate /gene - ubiB_1 ubiB_2 ubiB_3 [17:48:32] Fixed 2 duplicate /gene - ppa_1 ppa_2 [17:48:32] Fixed 3 duplicate /gene - menG_1 menG_2 menG_3 [17:48:32] Fixed 2 duplicate /gene - trxA_1 trxA_2 [17:48:32] Fixed 2 duplicate /gene - eutN_1 eutN_2 [17:48:32] Fixed 2 duplicate /gene - bchI_1 bchI_2 [17:48:32] Fixed 2 duplicate /gene - thiL_1 thiL_2 [17:48:32] Fixed 2 duplicate /gene - trxB_1 trxB_2 [17:48:32] Fixed 4 duplicate /gene - clpP_1 clpP_2 clpP_3 clpP_4 [17:48:32] Fixed 2 duplicate /gene - crtI_1 crtI_2 [17:48:32] Fixed 2 duplicate /gene - mntB_1 mntB_2 [17:48:32] Fixed 2 duplicate /gene - lexA_1 lexA_2 [17:48:32] Fixed 2 duplicate /gene - purE_1 purE_2 [17:48:32] Fixed 2 duplicate /gene - cobD_1 cobD_2 [17:48:32] Fixed 3 duplicate /gene - sigA2_1 sigA2_2 sigA2_3 [17:48:32] Fixed 2 duplicate /gene - cugP_1 cugP_2 [17:48:32] Fixed 2 duplicate /gene - gyrA_1 gyrA_2 [17:48:32] Fixed 2 duplicate /gene - udk_1 udk_2 [17:48:32] Fixed 2 duplicate /gene - pebA_1 pebA_2 [17:48:32] Fixed 2 duplicate /gene - rnr_1 rnr_2 [17:48:32] Fixed 3 duplicate /gene - petF_1 petF_2 petF_3 [17:48:32] Fixed 2 duplicate /gene - glmM_1 glmM_2 [17:48:32] Fixed 2 duplicate /gene - rplU_1 rplU_2 [17:48:32] Fixed 2 duplicate /gene - hisF_1 hisF_2 [17:48:32] Fixed 2 duplicate /gene - speA_1 speA_2 [17:48:32] Fixed 2 duplicate /gene - ndhD1_1 ndhD1_2 [17:48:32] Fixed 67 colliding /gene names. [17:48:32] Adding /locus_tag identifiers [17:48:32] Assigned 1914 locus_tags to CDS and RNA features. [17:48:32] Writing outputs to /share/gsi2/data/www/soap-data/M2BBS/Phylogenomic/Prochlorococcus/prokka/Aaaj/ [17:48:37] Generating annotation statistics file [17:48:37] Generating Genbank and Sequin files [17:48:37] 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\/Aaaj\/AaajA01\.err -i \/share\/gsi2\/data\/www\/soap\-data\/M2BBS\/Phylogenomic\/Prochlorococcus\/prokka\/Aaaj\/AaajA01\.fsa 2> /dev/null [17:48:44] Deleting unwanted file: /share/gsi2/data/www/soap-data/M2BBS/Phylogenomic/Prochlorococcus/prokka/Aaaj/errorsummary.val [17:48:44] Deleting unwanted file: /share/gsi2/data/www/soap-data/M2BBS/Phylogenomic/Prochlorococcus/prokka/Aaaj/AaajA01.dr [17:48:44] Deleting unwanted file: /share/gsi2/data/www/soap-data/M2BBS/Phylogenomic/Prochlorococcus/prokka/Aaaj/AaajA01.fixedproducts [17:48:44] Deleting unwanted file: /share/gsi2/data/www/soap-data/M2BBS/Phylogenomic/Prochlorococcus/prokka/Aaaj/AaajA01.ecn [17:48:44] Deleting unwanted file: /share/gsi2/data/www/soap-data/M2BBS/Phylogenomic/Prochlorococcus/prokka/Aaaj/AaajA01.val [17:48:44] Repairing broken .GBK output that tbl2asn produces... [17:48:44] Running: sed 's/COORDINATES: profile/COORDINATES:profile/' < \/share\/gsi2\/data\/www\/soap\-data\/M2BBS\/Phylogenomic\/Prochlorococcus\/prokka\/Aaaj\/AaajA01\.gbf > \/share\/gsi2\/data\/www\/soap\-data\/M2BBS\/Phylogenomic\/Prochlorococcus\/prokka\/Aaaj\/AaajA01\.gbk [17:48:44] Deleting unwanted file: /share/gsi2/data/www/soap-data/M2BBS/Phylogenomic/Prochlorococcus/prokka/Aaaj/AaajA01.gbf [17:48:44] Output files: [17:48:44] /share/gsi2/data/www/soap-data/M2BBS/Phylogenomic/Prochlorococcus/prokka/Aaaj/AaajA01.log [17:48:44] /share/gsi2/data/www/soap-data/M2BBS/Phylogenomic/Prochlorococcus/prokka/Aaaj/AaajA01.fna [17:48:44] /share/gsi2/data/www/soap-data/M2BBS/Phylogenomic/Prochlorococcus/prokka/Aaaj/AaajA01.gff [17:48:44] /share/gsi2/data/www/soap-data/M2BBS/Phylogenomic/Prochlorococcus/prokka/Aaaj/AaajA01.faa [17:48:44] /share/gsi2/data/www/soap-data/M2BBS/Phylogenomic/Prochlorococcus/prokka/Aaaj/AaajA01.ffn [17:48:44] /share/gsi2/data/www/soap-data/M2BBS/Phylogenomic/Prochlorococcus/prokka/Aaaj/AaajA01.tbl [17:48:44] /share/gsi2/data/www/soap-data/M2BBS/Phylogenomic/Prochlorococcus/prokka/Aaaj/AaajA01.fsa [17:48:44] /share/gsi2/data/www/soap-data/M2BBS/Phylogenomic/Prochlorococcus/prokka/Aaaj/AaajA01.tsv [17:48:44] /share/gsi2/data/www/soap-data/M2BBS/Phylogenomic/Prochlorococcus/prokka/Aaaj/AaajA01.txt [17:48:44] /share/gsi2/data/www/soap-data/M2BBS/Phylogenomic/Prochlorococcus/prokka/Aaaj/AaajA01.sqn [17:48:44] /share/gsi2/data/www/soap-data/M2BBS/Phylogenomic/Prochlorococcus/prokka/Aaaj/AaajA01.err [17:48:44] /share/gsi2/data/www/soap-data/M2BBS/Phylogenomic/Prochlorococcus/prokka/Aaaj/AaajA01.gbk [17:48:44] Annotation finished successfully. [17:48:44] Walltime used: 4.47 minutes [17:48:44] If you use this result please cite the Prokka paper: [17:48:44] Seemann T (2014) Prokka: rapid prokaryotic genome annotation. Bioinformatics. 30(14):2068-9. [17:48:44] Type 'prokka --citation' for more details. [17:48:44] Thank you, come again.