[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/Aaag [17:44:16] Running: mkdir -p \/share\/gsi2\/data\/www\/soap\-data\/M2BBS\/Phylogenomic\/Prochlorococcus\/prokka\/Aaag [17:44:16] Using filename prefix: AaagA01.XXX [17:44:16] Setting HMMER_NCPU=1 [17:44:16] Writing log to: /share/gsi2/data/www/soap-data/M2BBS/Phylogenomic/Prochlorococcus/prokka/Aaag/AaagA01.log [17:44:16] Command: /share/gsi2/bin/prokka /share/gsi2/data/www/soap-data/M2BBS/Phylogenomic/Prochlorococcus/DNA/Aaag/AaagA01.fas --compliant --addgenes --outdir /share/gsi2/data/www/soap-data/M2BBS/Phylogenomic/Prochlorococcus/prokka/Aaag --prefix AaagA01 --locustag AaagA01.g --species ProchlorococcusmarinusstrMIT9515 --strain ProchlorococcusmarinusstrMIT9515 --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 [17:44:18] Determined blastp version is 2.7 [17:44:18] Looking for 'cmpress' - found /share/gsi2/software/prokka/bin/../binaries/linux/cmpress [17:44:18] Determined cmpress version is 1.1 [17:44:18] 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 [17:44:21] 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/Aaag/AaagA01.fas [17:44:22] Wrote 1 contigs totalling 1704176 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\/Aaag\/AaagA01\.fna [17:44:23] 1 tmRNA* c[65937,66247] 170,220 ANKIVSFSRQTAPVAA* [17:44:23] 2 tRNA-Leu c[75071,75154] 36 (aag) [17:44:23] 3 tRNA-Asn [132493,132566] 34 (gtt) [17:44:23] 4 tRNA-Leu [248726,248809] 36 (tag) [17:44:23] 5 tRNA-Arg c[268677,268752] 36 (acg) [17:44:23] 6 tRNA-Met c[283792,283864] 34 (cat) [17:44:23] 7 tRNA-Phe c[316364,316438] 34 (gaa) [17:44:23] 8 tRNA-Thr c[324454,324527] 34 (tgt) [17:44:23] 9 tRNA-Ile [334008,334083] 36 (gat) [17:44:23] 10 tRNA-Ala [334095,334168] 34 (tgc) [17:44:23] 11 tRNA-Thr c[400297,400369] 33 (ggt) [17:44:23] 12 tRNA-Tyr c[400380,400462] 35 (gta) [17:44:23] 13 tRNA-Asp c[480486,480561] 36 (gtc) [17:44:23] 14 tRNA-Trp c[480935,481009] 35 (cca) [17:44:23] 15 tRNA-Leu [569250,569337] 36 (taa) [17:44:23] 16 tRNA-Ser c[655783,655871] 36 (tga) [17:44:23] 17 tRNA-Met c[796700,796776] 35 (cat) [17:44:23] 18 tRNA-Met c[836600,836673] 35 (cat) [17:44:23] 19 tRNA-Ser c[877418,877506] 36 (gga) [17:44:23] 20 tRNA-Pro [930469,930542] 35 (ggg) [17:44:23] 21 tRNA-Glu c[1021433,1021507] 36 (ttc) [17:44:23] 22 tRNA-Lys [1066356,1066428] 33 (ttt) [17:44:23] 23 tRNA-Pro [1072522,1072596] 35 (tgg) [17:44:23] 24 tRNA-Ser c[1170556,1170642] 36 (cga) [17:44:23] 25 tRNA-Arg [1200397,1200470] 35 (tct) [17:44:23] 26 tRNA-Ala c[1254260,1254334] 35 (ggc) [17:44:23] 27 tRNA-Leu [1298197,1298279] 35 (caa) [17:44:23] 28 tRNA-His [1303467,1303540] 34 (gtg) [17:44:23] 29 tRNA-Gly c[1319859,1319929] 33 (tcc) [17:44:23] 30 tRNA-Val [1351472,1351543] 33 (gac) [17:44:23] 31 tRNA-Thr [1471568,1471639] 33 (cgt) [17:44:23] 32 tRNA-Ser c[1511078,1511168] 36 (gct) [17:44:23] 33 tRNA-Gln [1531023,1531096] 34 (ttg) [17:44:23] 34 tRNA-Arg [1546466,1546539] 35 (ccg) [17:44:23] 35 tRNA-Cys [1561134,1561204] 33 (gca) [17:44:23] 36 tRNA-Arg c[1577961,1578036] 36 (cct) [17:44:23] 37 tRNA-Gly c[1616911,1616982] 33 (gcc) [17:44:23] 38 tRNA-Val c[1663524,1663595] 33 (tac) [17:44:23] Found 38 tRNAs [17:44:23] Predicting Ribosomal RNAs [17:44:23] Running Barrnap with 1 threads [17:44:26] 1 gnl|Prokka|AaagA01.g_1 332405 16S ribosomal RNA [17:44:26] 2 gnl|Prokka|AaagA01.g_1 334436 23S ribosomal RNA [17:44:26] 3 gnl|Prokka|AaagA01.g_1 337377 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 40 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 1704176 bp, so using single mode [17:44:27] Running: prodigal -i \/share\/gsi2\/data\/www\/soap\-data\/M2BBS\/Phylogenomic\/Prochlorococcus\/prokka\/Aaag\/AaagA01\.fna -c -m -g 11 -p single -f sco -q [17:44:33] Excluding CDS which overlaps existing RNA (tRNA) at gnl|Prokka|AaagA01.g_1:1298206..1299459 on + strand [17:44:34] Excluding CDS which overlaps existing RNA (tRNA) at gnl|Prokka|AaagA01.g_1:1546397..1546546 on + strand [17:44:34] Excluding CDS which overlaps existing RNA (tRNA) at gnl|Prokka|AaagA01.g_1:1559862..1561274 on - strand [17:44:34] Found 1898 CDS [17:44:34] Connecting features back to sequences [17:44:34] Not using genus-specific database. Try --usegenus to enable it. [17:44:34] Annotating CDS, please be patient. [17:44:34] Will use 1 CPUs for similarity searching. [17:44:36] There are still 1898 unannotated CDS left (started with 1898) [17:44:36] Will use blast to search against /share/gsi2/software/prokka/bin/../db/kingdom/Bacteria/sprot with 1 CPUs [17:44:36] Running: cat \/share\/gsi2\/data\/www\/soap\-data\/M2BBS\/Phylogenomic\/Prochlorococcus\/prokka\/Aaag\/sprot\.faa | parallel --gnu --plain -j 1 --block 257034 --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\/Aaag\/sprot\.blast 2> /dev/null [17:47:12] Modify product: N utilization substance protein B homolog => N utilization substance protein B [17:47:12] Modify product: Probable peptidyl-prolyl cis-trans isomerase => putative peptidyl-prolyl cis-trans isomerase [17:47:13] Modify product: Uncharacterized oxidoreductase Rv2298 => putative oxidoreductase [17:47:13] Modify product: Probable cysteine desulfurase => putative cysteine desulfurase [17:47:13] Modify product: Probable ATP-dependent transporter SufC => putative ATP-dependent transporter SufC [17:47:13] Modify product: Uncharacterized AAA domain-containing protein Rv2559c => putative AAA domain-containing protein [17:47:13] Modify product: Uncharacterized transporter Rv2685 => putative transporter [17:47:13] Modify product: Uncharacterized ABC transporter ATP-binding protein YheS => putative ABC transporter ATP-binding protein YheS [17:47:13] Modify product: Vitamin K epoxide reductase homolog => Vitamin K epoxide reductase [17:47:13] Modify product: Epimerase family protein Rv2216 => Epimerase family protein [17:47:13] Modify product: Probable copper-transporting ATPase PacS => putative copper-transporting ATPase PacS [17:47:13] Modify product: Probable glutaredoxin ssr2061 => putative glutaredoxin [17:47:13] Modify product: Probable nicotinate-nucleotide pyrophosphorylase [carboxylating] => putative nicotinate-nucleotide pyrophosphorylase [carboxylating] [17:47:13] Modify product: Probable protein kinase UbiB => putative protein kinase UbiB [17:47:13] Modify product: Probable bifunctional SAT/APS kinase => putative bifunctional SAT/APS kinase [17:47:13] Modify product: Probable phospholipid import ATP-binding protein MlaF => putative phospholipid import ATP-binding protein MlaF [17:47:13] Modify product: Putative peroxiredoxin Rv1608c => Putative peroxiredoxin [17:47:13] Modify product: Uncharacterized glycosyltransferase EpsJ => putative glycosyltransferase EpsJ [17:47:13] Modify product: Uncharacterized ABC transporter ATP-binding protein YknY => putative ABC transporter ATP-binding protein YknY [17:47:13] Modify product: Probable cytochrome c oxidase subunit 1 => putative cytochrome c oxidase subunit 1 [17:47:13] Modify product: Probable doxorubicin resistance ABC transporter permease protein DrrC => putative doxorubicin resistance ABC transporter permease protein DrrC [17:47:13] Modify product: Probable murein peptide carboxypeptidase => putative murein peptide carboxypeptidase [17:47:13] Modify product: Thylakoid-associated single-stranded DNA-binding protein slr1034 => Thylakoid-associated single-stranded DNA-binding protein [17:47:13] Modify product: Probable oxidoreductase EphD => putative oxidoreductase EphD [17:47:13] Modify product: Probable multidrug resistance ABC transporter ATP-binding/permease protein YheH => putative multidrug resistance ABC transporter ATP-binding/permease protein YheH [17:47:14] Modify product: Uncharacterized ABC transporter ATP-binding protein HI_1470 => putative ABC transporter ATP-binding protein [17:47:14] Modify product: Probable 2-phosphosulfolactate phosphatase => putative 2-phosphosulfolactate phosphatase [17:47:14] Modify product: Uncharacterized glycosyltransferase sll0501 => putative glycosyltransferase [17:47:14] Modify product: Uncharacterized ABC transporter ATP-binding protein YlmA => putative ABC transporter ATP-binding protein YlmA [17:47:14] Modify product: GTP-binding protein TypA/BipA homolog => GTP-binding protein TypA/BipA [17:47:14] Modify product: Uncharacterized ABC transporter ATP-binding protein Rv0986 => putative ABC transporter ATP-binding protein [17:47:14] Modify product: Uncharacterized zinc protease Rv2782c => putative zinc protease [17:47:14] Modify product: Putative multidrug export ATP-binding/permease protein SA1683 => Putative multidrug export ATP-binding/permease protein [17:47:14] Modify product: Probable peroxiredoxin => putative peroxiredoxin [17:47:14] Modify product: Probable multidrug resistance ABC transporter ATP-binding/permease protein YheI => putative multidrug resistance ABC transporter ATP-binding/permease protein YheI [17:47:14] Modify product: Probable tRNA-dihydrouridine synthase => putative tRNA-dihydrouridine synthase [17:47:14] Modify product: Probable D,D-dipeptide-binding periplasmic protein DdpA => putative D,D-dipeptide-binding periplasmic protein DdpA [17:47:14] Modify product: Uncharacterized tRNA/rRNA methyltransferase HI_0380 => putative tRNA/rRNA methyltransferase [17:47:14] Modify product: Uncharacterized oxidoreductase MSMEG_1603/MSMEI_1564 => putative oxidoreductase/MSMEI_1564 [17:47:14] Modify product: 1,4-alpha-glucan branching enzyme TTHA1902 => 1,4-alpha-glucan branching enzyme [17:47:14] Modify product: Bifunctional protein FolD => Bifunctional protein FolD protein [17:47:14] Modify product: Probable protein kinase UbiB => putative protein kinase UbiB [17:47:14] Modify product: Probable glutamine ABC transporter permease protein GlnM => putative glutamine ABC transporter permease protein GlnM [17:47:14] Modify product: Probable cytochrome c oxidase subunit 1 => putative cytochrome c oxidase subunit 1 [17:47:14] Modify product: Maf-like protein Rv3282 => Maf-like protein [17:47:14] Modify product: PKHD-type hydroxylase Sbal_3634 => PKHD-type hydroxylase [17:47:14] Modify product: Probable undecaprenyl-phosphate N-acetylglucosaminyl 1-phosphate transferase => putative undecaprenyl-phosphate N-acetylglucosaminyl 1-phosphate transferase [17:47:14] Modify product: PGL/p-HBAD biosynthesis glycosyltransferase Rv2957 => PGL/p-HBAD biosynthesis glycosyltransferase [17:47:14] Modify product: Putative acetyltransferase SACOL2570 => Putative acetyltransferase [17:47:14] Modify product: Uncharacterized FAD-linked oxidoreductase Rv2280 => putative FAD-linked oxidoreductase [17:47:15] Modify product: Oxygen-independent coproporphyrinogen-III oxidase-like protein sll1917 => Oxygen-independent coproporphyrinogen-III oxidase-like protein [17:47:15] Modify product: Uncharacterized PIN and TRAM-domain containing protein YacL => putative PIN and TRAM-domain containing protein YacL [17:47:15] Modify product: Glycogen operon protein GlgX homolog => Glycogen operon protein GlgX [17:47:15] Modify product: Probable phospholipid ABC transporter permease protein MlaE => putative phospholipid ABC transporter permease protein MlaE [17:47:15] Modify product: Phosphorylated carbohydrates phosphatase TM_1254 => Phosphorylated carbohydrates phosphatase [17:47:15] Modify product: Probable 30S ribosomal protein PSRP-3 => putative 30S ribosomal protein PSRP-3 [17:47:15] Modify product: Probable peptidoglycan glycosyltransferase FtsW => putative peptidoglycan glycosyltransferase FtsW [17:47:15] Modify product: Probable helicase HelY => putative helicase HelY [17:47:15] Modify product: Probable dual-specificity RNA methyltransferase RlmN => putative dual-specificity RNA methyltransferase RlmN [17:47:15] Modify product: Probable cobalt-factor III C(17)-methyltransferase => putative cobalt-factor III C(17)-methyltransferase [17:47:15] Modify product: Probable adenylyltransferase/sulfurtransferase MoeZ => putative adenylyltransferase/sulfurtransferase MoeZ [17:47:15] Modify product: Uncharacterized hydrolase YxeP => putative hydrolase YxeP [17:47:15] Modify product: Inner membrane protein BB_0250 => Inner membrane protein [17:47:15] Modify product: Probable protein kinase UbiB => putative protein kinase UbiB [17:47:15] Cleaned 64 /product names [17:47:15] Deleting unwanted file: /share/gsi2/data/www/soap-data/M2BBS/Phylogenomic/Prochlorococcus/prokka/Aaag/sprot.faa [17:47:15] Deleting unwanted file: /share/gsi2/data/www/soap-data/M2BBS/Phylogenomic/Prochlorococcus/prokka/Aaag/sprot.blast [17:47:16] There are still 897 unannotated CDS left (started with 1898) [17:47:16] Will use hmmer3 to search against /share/gsi2/software/prokka/bin/../db/hmm/HAMAP.hmm with 1 CPUs [17:47:16] Running: cat \/share\/gsi2\/data\/www\/soap\-data\/M2BBS\/Phylogenomic\/Prochlorococcus\/prokka\/Aaag\/HAMAP\.hmm\.faa | parallel --gnu --plain -j 1 --block 76143 --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\/Aaag\/HAMAP\.hmm\.hmmer3 2> /dev/null [17:48:37] Deleting unwanted file: /share/gsi2/data/www/soap-data/M2BBS/Phylogenomic/Prochlorococcus/prokka/Aaag/HAMAP.hmm.faa [17:48:37] Deleting unwanted file: /share/gsi2/data/www/soap-data/M2BBS/Phylogenomic/Prochlorococcus/prokka/Aaag/HAMAP.hmm.hmmer3 [17:48:37] Labelling remaining 831 proteins as 'hypothetical protein' [17:48:37] Possible /pseudo 'Ethanolamine utilization protein EutN' at gnl|Prokka|AaagA01.g_1 position 555663 [17:48:37] Possible /pseudo 'D-alanyl-D-alanine dipeptidase' at gnl|Prokka|AaagA01.g_1 position 748582 [17:48:37] Possible /pseudo 'ATP-dependent Clp protease proteolytic subunit' at gnl|Prokka|AaagA01.g_1 position 1312603 [17:48:37] Possible /pseudo 'DNA-directed RNA polymerase subunit beta'' at gnl|Prokka|AaagA01.g_1 position 1455510 [17:48:37] Possible /pseudo '15,16-dihydrobiliverdin:ferredoxin oxidoreductase' at gnl|Prokka|AaagA01.g_1 position 1566267 [17:48:37] Possible /pseudo 'Putative fluoride ion transporter CrcB' at gnl|Prokka|AaagA01.g_1 position 1604326 [17:48:37] Found 905 unique /gene codes. [17:48:37] Fixed 2 duplicate /gene - crtL_1 crtL_2 [17:48:37] Fixed 2 duplicate /gene - ddpX_1 ddpX_2 [17:48:37] Fixed 2 duplicate /gene - kmo_1 kmo_2 [17:48:37] Fixed 2 duplicate /gene - psaM_1 psaM_2 [17:48:37] Fixed 2 duplicate /gene - pebA_1 pebA_2 [17:48:37] Fixed 2 duplicate /gene - bicA_1 bicA_2 [17:48:37] Fixed 2 duplicate /gene - resE_1 resE_2 [17:48:37] Fixed 2 duplicate /gene - ctaD_1 ctaD_2 [17:48:37] Fixed 2 duplicate /gene - lytB_1 lytB_2 [17:48:37] Fixed 4 duplicate /gene - dnaJ_1 dnaJ_2 dnaJ_3 dnaJ_4 [17:48:37] Fixed 2 duplicate /gene - fabG_1 fabG_2 [17:48:37] Fixed 2 duplicate /gene - coxM_1 coxM_2 [17:48:37] Fixed 2 duplicate /gene - lpxB_1 lpxB_2 [17:48:37] Fixed 2 duplicate /gene - dnaK2_1 dnaK2_2 [17:48:37] Fixed 2 duplicate /gene - corC_1 corC_2 [17:48:37] Fixed 2 duplicate /gene - menG_1 menG_2 [17:48:37] Fixed 2 duplicate /gene - der_1 der_2 [17:48:37] Fixed 2 duplicate /gene - csgA_1 csgA_2 [17:48:37] Fixed 2 duplicate /gene - ftsH4_1 ftsH4_2 [17:48:37] Fixed 2 duplicate /gene - clpB1_1 clpB1_2 [17:48:37] Fixed 2 duplicate /gene - ftsH2_1 ftsH2_2 [17:48:37] Fixed 2 duplicate /gene - bcp_1 bcp_2 [17:48:37] Fixed 2 duplicate /gene - lexA_1 lexA_2 [17:48:37] Fixed 2 duplicate /gene - iscS_1 iscS_2 [17:48:37] Fixed 2 duplicate /gene - ligA_1 ligA_2 [17:48:37] Fixed 2 duplicate /gene - cobN_1 cobN_2 [17:48:37] Fixed 2 duplicate /gene - trxA_1 trxA_2 [17:48:37] Fixed 2 duplicate /gene - mnmC_1 mnmC_2 [17:48:37] Fixed 4 duplicate /gene - clpP_1 clpP_2 clpP_3 clpP_4 [17:48:37] Fixed 2 duplicate /gene - psaA_1 psaA_2 [17:48:37] Fixed 2 duplicate /gene - ppa_1 ppa_2 [17:48:37] Fixed 2 duplicate /gene - gyrA_1 gyrA_2 [17:48:37] Fixed 2 duplicate /gene - ppiB_1 ppiB_2 [17:48:37] Fixed 2 duplicate /gene - crtI_1 crtI_2 [17:48:37] Fixed 2 duplicate /gene - rpsA_1 rpsA_2 [17:48:37] Fixed 2 duplicate /gene - dnaX_1 dnaX_2 [17:48:37] Fixed 2 duplicate /gene - hisH_1 hisH_2 [17:48:37] Fixed 2 duplicate /gene - atpG_1 atpG_2 [17:48:37] Fixed 2 duplicate /gene - psbF_1 psbF_2 [17:48:37] Fixed 2 duplicate /gene - eutN_1 eutN_2 [17:48:37] Fixed 2 duplicate /gene - gmd_1 gmd_2 [17:48:37] Fixed 2 duplicate /gene - pyrC_1 pyrC_2 [17:48:37] Fixed 2 duplicate /gene - bchI_1 bchI_2 [17:48:37] Fixed 2 duplicate /gene - nadK_1 nadK_2 [17:48:37] Fixed 2 duplicate /gene - suhB_1 suhB_2 [17:48:37] Fixed 2 duplicate /gene - carC_1 carC_2 [17:48:37] Fixed 2 duplicate /gene - pds_1 pds_2 [17:48:37] Fixed 4 duplicate /gene - fcl_1 fcl_2 fcl_3 fcl_4 [17:48:37] Fixed 2 duplicate /gene - colD_1 colD_2 [17:48:37] Fixed 2 duplicate /gene - iolC_1 iolC_2 [17:48:37] Fixed 3 duplicate /gene - mshA_1 mshA_2 mshA_3 [17:48:37] Fixed 2 duplicate /gene - psbA_1 psbA_2 [17:48:37] Fixed 2 duplicate /gene - cobD_1 cobD_2 [17:48:37] Fixed 2 duplicate /gene - glmU_1 glmU_2 [17:48:37] Fixed 3 duplicate /gene - yciC_1 yciC_2 yciC_3 [17:48:37] Fixed 2 duplicate /gene - ctaE_1 ctaE_2 [17:48:37] Fixed 2 duplicate /gene - fdhL_1 fdhL_2 [17:48:37] Fixed 2 duplicate /gene - crcB_1 crcB_2 [17:48:37] Fixed 3 duplicate /gene - ubiG_1 ubiG_2 ubiG_3 [17:48:37] Fixed 2 duplicate /gene - speA_1 speA_2 [17:48:37] Fixed 2 duplicate /gene - mnmE_1 mnmE_2 [17:48:37] Fixed 3 duplicate /gene - ubiB_1 ubiB_2 ubiB_3 [17:48:37] Fixed 2 duplicate /gene - purE_1 purE_2 [17:48:37] Fixed 2 duplicate /gene - rpoC_1 rpoC_2 [17:48:37] Fixed 2 duplicate /gene - bshA_1 bshA_2 [17:48:37] Fixed 2 duplicate /gene - plsC_1 plsC_2 [17:48:37] Fixed 2 duplicate /gene - rgtE_1 rgtE_2 [17:48:37] Fixed 3 duplicate /gene - sigA2_1 sigA2_2 sigA2_3 [17:48:37] Fixed 2 duplicate /gene - mntB_1 mntB_2 [17:48:37] Fixed 2 duplicate /gene - ydjZ_1 ydjZ_2 [17:48:37] Fixed 2 duplicate /gene - arnT_1 arnT_2 [17:48:37] Fixed 2 duplicate /gene - galE_1 galE_2 [17:48:37] Fixed 2 duplicate /gene - ndhD1_1 ndhD1_2 [17:48:37] Fixed 2 duplicate /gene - trxB_1 trxB_2 [17:48:37] Fixed 2 duplicate /gene - hhoA_1 hhoA_2 [17:48:37] Fixed 2 duplicate /gene - rnr_1 rnr_2 [17:48:37] Fixed 2 duplicate /gene - hpf_1 hpf_2 [17:48:37] Fixed 2 duplicate /gene - ntdC_1 ntdC_2 [17:48:37] Fixed 2 duplicate /gene - udk_1 udk_2 [17:48:37] Fixed 79 colliding /gene names. [17:48:37] Adding /locus_tag identifiers [17:48:37] Assigned 1939 locus_tags to CDS and RNA features. [17:48:37] Writing outputs to /share/gsi2/data/www/soap-data/M2BBS/Phylogenomic/Prochlorococcus/prokka/Aaag/ [17:48:42] Generating annotation statistics file [17:48:42] Generating Genbank and Sequin files [17:48:42] 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\/Aaag\/AaagA01\.err -i \/share\/gsi2\/data\/www\/soap\-data\/M2BBS\/Phylogenomic\/Prochlorococcus\/prokka\/Aaag\/AaagA01\.fsa 2> /dev/null [17:48:50] Deleting unwanted file: /share/gsi2/data/www/soap-data/M2BBS/Phylogenomic/Prochlorococcus/prokka/Aaag/errorsummary.val [17:48:50] Deleting unwanted file: /share/gsi2/data/www/soap-data/M2BBS/Phylogenomic/Prochlorococcus/prokka/Aaag/AaagA01.dr [17:48:50] Deleting unwanted file: /share/gsi2/data/www/soap-data/M2BBS/Phylogenomic/Prochlorococcus/prokka/Aaag/AaagA01.fixedproducts [17:48:50] Deleting unwanted file: /share/gsi2/data/www/soap-data/M2BBS/Phylogenomic/Prochlorococcus/prokka/Aaag/AaagA01.ecn [17:48:50] Deleting unwanted file: /share/gsi2/data/www/soap-data/M2BBS/Phylogenomic/Prochlorococcus/prokka/Aaag/AaagA01.val [17:48:50] Repairing broken .GBK output that tbl2asn produces... [17:48:50] Running: sed 's/COORDINATES: profile/COORDINATES:profile/' < \/share\/gsi2\/data\/www\/soap\-data\/M2BBS\/Phylogenomic\/Prochlorococcus\/prokka\/Aaag\/AaagA01\.gbf > \/share\/gsi2\/data\/www\/soap\-data\/M2BBS\/Phylogenomic\/Prochlorococcus\/prokka\/Aaag\/AaagA01\.gbk [17:48:50] Deleting unwanted file: /share/gsi2/data/www/soap-data/M2BBS/Phylogenomic/Prochlorococcus/prokka/Aaag/AaagA01.gbf [17:48:50] Output files: [17:48:50] /share/gsi2/data/www/soap-data/M2BBS/Phylogenomic/Prochlorococcus/prokka/Aaag/AaagA01.log [17:48:50] /share/gsi2/data/www/soap-data/M2BBS/Phylogenomic/Prochlorococcus/prokka/Aaag/AaagA01.fna [17:48:50] /share/gsi2/data/www/soap-data/M2BBS/Phylogenomic/Prochlorococcus/prokka/Aaag/AaagA01.gff [17:48:50] /share/gsi2/data/www/soap-data/M2BBS/Phylogenomic/Prochlorococcus/prokka/Aaag/AaagA01.faa [17:48:50] /share/gsi2/data/www/soap-data/M2BBS/Phylogenomic/Prochlorococcus/prokka/Aaag/AaagA01.ffn [17:48:50] /share/gsi2/data/www/soap-data/M2BBS/Phylogenomic/Prochlorococcus/prokka/Aaag/AaagA01.tbl [17:48:50] /share/gsi2/data/www/soap-data/M2BBS/Phylogenomic/Prochlorococcus/prokka/Aaag/AaagA01.fsa [17:48:50] /share/gsi2/data/www/soap-data/M2BBS/Phylogenomic/Prochlorococcus/prokka/Aaag/AaagA01.tsv [17:48:50] /share/gsi2/data/www/soap-data/M2BBS/Phylogenomic/Prochlorococcus/prokka/Aaag/AaagA01.txt [17:48:50] /share/gsi2/data/www/soap-data/M2BBS/Phylogenomic/Prochlorococcus/prokka/Aaag/AaagA01.sqn [17:48:50] /share/gsi2/data/www/soap-data/M2BBS/Phylogenomic/Prochlorococcus/prokka/Aaag/AaagA01.err [17:48:50] /share/gsi2/data/www/soap-data/M2BBS/Phylogenomic/Prochlorococcus/prokka/Aaag/AaagA01.gbk [17:48:50] Annotation finished successfully. [17:48:50] Walltime used: 4.57 minutes [17:48:50] If you use this result please cite the Prokka paper: [17:48:50] Seemann T (2014) Prokka: rapid prokaryotic genome annotation. Bioinformatics. 30(14):2068-9. [17:48:50] Type 'prokka --citation' for more details. [17:48:50] Thank you, come again.