[17:44:16] This is prokka 1.12
[17:44:16] Written by Torsten Seemann <torsten.seemann@gmail.com>
[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/Aaaf
[17:44:16] Running: mkdir -p \/share\/gsi2\/data\/www\/soap\-data\/M2BBS\/Phylogenomic\/Prochlorococcus\/prokka\/Aaaf
[17:44:16] Using filename prefix: AaafA01.XXX
[17:44:16] Setting HMMER_NCPU=1
[17:44:16] Writing log to: /share/gsi2/data/www/soap-data/M2BBS/Phylogenomic/Prochlorococcus/prokka/Aaaf/AaafA01.log
[17:44:16] Command: /share/gsi2/bin/prokka /share/gsi2/data/www/soap-data/M2BBS/Phylogenomic/Prochlorococcus/DNA/Aaaf/AaafA01.fas --compliant --addgenes --outdir /share/gsi2/data/www/soap-data/M2BBS/Phylogenomic/Prochlorococcus/prokka/Aaaf --prefix AaafA01 --locustag AaafA01.g --species ProchlorococcusmarinusstrAS9601 --strain ProchlorococcusmarinusstrAS9601 --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
[17:44:20] Determined hmmscan version is 3.1
[17:44:20] Looking for 'java' - found /usr/java/latest/bin/java
[17:44:20] Looking for 'less' - found /usr/bin/less
[17:44:20] Looking for 'makeblastdb' - found /share/gsi2/bin/makeblastdb
[17:44:20] Determined makeblastdb version is 2.7
[17:44:20] Looking for 'minced' - found /share/gsi2/bin/minced
[17:44:20] Determined minced version is 2.0
[17:44:20] Looking for 'parallel' - found /share/gsi2/software/prokka/bin/../binaries/linux/../common/parallel
[17:44:20] Determined parallel version is 20150122
[17:44:20] 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/Aaaf/AaafA01.fas
[17:44:21] Wrote 1 contigs totalling 1669886 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\/Aaaf\/AaafA01\.fna
[17:44:23] 1 tmRNA* c[67563,67872] 169,219 ANKIVSFSRQTAPVAA*
[17:44:23] 2 tRNA-Leu c[76716,76799] 36 (aag)
[17:44:23] 3 tRNA-Asn [133959,134032] 34 (gtt)
[17:44:23] 4 tRNA-Leu [239473,239555] 35 (tag)
[17:44:23] 5 tRNA-Arg c[259344,259419] 36 (acg)
[17:44:23] 6 tRNA-Met c[274475,274549] 35 (cat)
[17:44:23] 7 tRNA-Phe c[306351,306425] 34 (gaa)
[17:44:23] 8 tRNA-Thr c[315066,315137] 33 (tgt)
[17:44:23] 9 tRNA-Ile [324606,324681] 36 (gat)
[17:44:23] 10 tRNA-Ala [324693,324766] 34 (tgc)
[17:44:23] 11 tRNA-Thr c[356527,356599] 33 (ggt)
[17:44:23] 12 tRNA-Thr c[380826,380898] 33 (ggt)
[17:44:23] 13 tRNA-Tyr c[380908,380990] 35 (gta)
[17:44:23] 14 tRNA-Asp c[461205,461280] 36 (gtc)
[17:44:23] 15 tRNA-Trp c[461658,461732] 35 (cca)
[17:44:23] 16 tRNA-Leu [548164,548251] 36 (taa)
[17:44:23] 17 tRNA-Ser c[633339,633427] 36 (tga)
[17:44:23] 18 tRNA-Pro c[776995,777068] 35 (ggg)
[17:44:23] 19 tRNA-Ser [829984,830070] 35 (gga)
[17:44:23] 20 tRNA-Met [870778,870853] 36 (cat)
[17:44:23] 21 tRNA-Met [912293,912369] 35 (cat)
[17:44:23] 22 tRNA-Glu c[997777,997851] 36 (ttc)
[17:44:23] 23 tRNA-Lys [1041467,1041539] 33 (ttt)
[17:44:23] 24 tRNA-Pro [1049968,1050042] 35 (tgg)
[17:44:23] 25 tRNA-Ser c[1126407,1126493] 36 (cga)
[17:44:23] 26 tRNA-Arg [1155975,1156050] 36 (tct)
[17:44:23] 27 tRNA-Ala c[1201167,1201241] 35 (ggc)
[17:44:23] 28 tRNA-Leu [1282555,1282637] 35 (caa)
[17:44:23] 29 tRNA-His [1287814,1287887] 34 (gtg)
[17:44:23] 30 tRNA-Gly c[1304179,1304249] 33 (tcc)
[17:44:23] 31 tRNA-Val [1335754,1335825] 33 (gac)
[17:44:23] 32 tRNA-Thr [1444206,1444278] 33 (cgt)
[17:44:23] 33 tRNA-Ser c[1480450,1480540] 36 (gct)
[17:44:23] 34 tRNA-Gln [1500368,1500439] 33 (ttg)
[17:44:23] 35 tRNA-Arg [1513068,1513141] 35 (ccg)
[17:44:23] 36 tRNA-Cys [1527715,1527785] 33 (gca)
[17:44:23] 37 tRNA-Arg c[1546237,1546312] 36 (cct)
[17:44:23] 38 tRNA-Gly c[1582699,1582770] 33 (gcc)
[17:44:23] 39 tRNA-Val c[1629262,1629333] 33 (tac)
[17:44:23] Found 39 tRNAs
[17:44:23] Predicting Ribosomal RNAs
[17:44:23] Running Barrnap with 1 threads
[17:44:26] 1 gnl|Prokka|AaafA01.g_1 323001 16S ribosomal RNA
[17:44:26] 2 gnl|Prokka|AaafA01.g_1 325025 23S ribosomal RNA
[17:44:26] 3 gnl|Prokka|AaafA01.g_1 327965 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 1669886 bp, so using single mode
[17:44:26] Running: prodigal -i \/share\/gsi2\/data\/www\/soap\-data\/M2BBS\/Phylogenomic\/Prochlorococcus\/prokka\/Aaaf\/AaafA01\.fna -c -m -g 11 -p single -f sco -q
[17:44:33] Excluding CDS which overlaps existing RNA (tRNA) at gnl|Prokka|AaafA01.g_1:1282564..1283817 on + strand
[17:44:33] Excluding CDS which overlaps existing RNA (tRNA) at gnl|Prokka|AaafA01.g_1:1526443..1527855 on - strand
[17:44:33] Found 1889 CDS
[17:44:33] Connecting features back to sequences
[17:44:33] Not using genus-specific database. Try --usegenus to enable it.
[17:44:33] Annotating CDS, please be patient.
[17:44:33] Will use 1 CPUs for similarity searching.
[17:44:36] There are still 1889 unannotated CDS left (started with 1889)
[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\/Aaaf\/sprot\.faa | parallel --gnu --plain -j 1 --block 257931 --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\/Aaaf\/sprot\.blast 2> /dev/null
[17:47:15] Modify product: N utilization substance protein B homolog => N utilization substance protein B 
[17:47:15] Modify product: Probable cysteine desulfurase => putative cysteine desulfurase
[17:47:15] Modify product: Probable ATP-dependent transporter SufC => putative ATP-dependent transporter SufC
[17:47:15] Modify product: Uncharacterized transporter Rv2685 => putative transporter
[17:47:15] Modify product: Uncharacterized ABC transporter ATP-binding protein YheS => putative ABC transporter ATP-binding protein YheS
[17:47:15] Modify product: Vitamin K epoxide reductase homolog => Vitamin K epoxide reductase 
[17:47:15] Modify product: Epimerase family protein Rv2216 => Epimerase family protein
[17:47:15] Modify product: Probable glutaredoxin ssr2061 => putative glutaredoxin
[17:47:15] Modify product: Probable nicotinate-nucleotide pyrophosphorylase [carboxylating] => putative nicotinate-nucleotide pyrophosphorylase [carboxylating]
[17:47:15] Modify product: Probable protein kinase UbiB => putative protein kinase UbiB
[17:47:15] Modify product: Probable bifunctional SAT/APS kinase => putative bifunctional SAT/APS kinase
[17:47:15] Modify product: Probable ribonucleotide transport ATP-binding protein mkl => putative ribonucleotide transport ATP-binding protein mkl
[17:47:16] Modify product: Uncharacterized glycosyltransferase EpsJ => putative glycosyltransferase EpsJ
[17:47:16] Modify product: Uncharacterized ABC transporter ATP-binding protein YknY => putative ABC transporter ATP-binding protein YknY
[17:47:16] Modify product: Probable cytochrome c oxidase subunit 1 => putative cytochrome c oxidase subunit 1
[17:47:16] Modify product: Probable murein peptide carboxypeptidase => putative murein peptide carboxypeptidase
[17:47:16] Modify product: Thylakoid-associated single-stranded DNA-binding protein slr1034 => Thylakoid-associated single-stranded DNA-binding protein
[17:47:16] Modify product: Uncharacterized ABC transporter ATP-binding protein TM_0288 => putative ABC transporter ATP-binding protein
[17:47:16] Modify product: PGL/p-HBAD biosynthesis glycosyltransferase Rv2957 => PGL/p-HBAD biosynthesis glycosyltransferase
[17:47:16] Modify product: Uncharacterized ABC transporter ATP-binding protein HI_1470 => putative ABC transporter ATP-binding protein
[17:47:16] Modify product: Probable 2-phosphosulfolactate phosphatase => putative 2-phosphosulfolactate phosphatase
[17:47:16] Modify product: Probable trans-aconitate 2-methyltransferase => putative trans-aconitate 2-methyltransferase
[17:47:16] Modify product: Uncharacterized ABC transporter ATP-binding protein Rv0986 => putative ABC transporter ATP-binding protein
[17:47:16] Modify product: Uncharacterized zinc protease Rv2782c => putative zinc protease
[17:47:16] Modify product: Uncharacterized zinc protease Rv2782c => putative zinc protease
[17:47:16] Modify product: Uncharacterized ABC transporter ATP-binding protein Rv0986 => putative ABC transporter ATP-binding protein
[17:47:16] Modify product: GTP-binding protein TypA/BipA homolog => GTP-binding protein TypA/BipA 
[17:47:16] Modify product: Uncharacterized ABC transporter ATP-binding protein YlmA => putative ABC transporter ATP-binding protein YlmA
[17:47:16] Modify product: Probable multidrug resistance ABC transporter ATP-binding/permease protein YheI => putative multidrug resistance ABC transporter ATP-binding/permease protein YheI
[17:47:16] Modify product: Probable cystine transporter YijE => putative cystine transporter YijE
[17:47:16] Modify product: Vitamin K epoxide reductase homolog => Vitamin K epoxide reductase 
[17:47:16] Modify product: Probable peroxiredoxin => putative peroxiredoxin
[17:47:16] Modify product: Phosphorylated carbohydrates phosphatase TM_1254 => Phosphorylated carbohydrates phosphatase
[17:47:16] Modify product: Putative multidrug export ATP-binding/permease protein SA1683 => Putative multidrug export ATP-binding/permease protein
[17:47:16] Modify product: Uncharacterized peptidase Lmo0363 => putative peptidase
[17:47:16] Modify product: Probable tRNA-dihydrouridine synthase => putative tRNA-dihydrouridine synthase
[17:47:16] Modify product: Putative esterase aq_1494 => Putative esterase
[17:47:16] Modify product: Uncharacterized tRNA/rRNA methyltransferase HI_0380 => putative tRNA/rRNA methyltransferase
[17:47:16] Modify product: Uncharacterized oxidoreductase MSMEG_1603/MSMEI_1564 => putative oxidoreductase/MSMEI_1564
[17:47:16] Modify product: 1,4-alpha-glucan branching enzyme TTHA1902 => 1,4-alpha-glucan branching enzyme
[17:47:16] Modify product: Bifunctional protein FolD => Bifunctional protein FolD protein
[17:47:16] Modify product: Probable protein kinase UbiB => putative protein kinase UbiB
[17:47:17] Modify product: Putative multidrug export ATP-binding/permease protein SA1683 => Putative multidrug export ATP-binding/permease protein
[17:47:17] Modify product: Maf-like protein Rv3282 => Maf-like protein
[17:47:17] Modify product: Putative polysaccharide biosynthesis protein with aminopeptidase-like domain => Putative polysaccharide biosynthesis protein with aminopeptidase-like domain protein
[17:47:17] Modify product: PKHD-type hydroxylase Sbal_3634 => PKHD-type hydroxylase
[17:47:17] Modify product: Uncharacterized inner membrane transporter YedA => putative inner membrane transporter YedA
[17:47:17] Modify product: Probable undecaprenyl-phosphate N-acetylglucosaminyl 1-phosphate transferase => putative undecaprenyl-phosphate N-acetylglucosaminyl 1-phosphate transferase
[17:47:17] Modify product: PGL/p-HBAD biosynthesis glycosyltransferase Rv2957 => PGL/p-HBAD biosynthesis glycosyltransferase
[17:47:17] Modify product: Putative multidrug export ATP-binding/permease protein SA1683 => Putative multidrug export ATP-binding/permease protein
[17:47:17] Modify product: Probable undecaprenyl-phosphate N-acetylglucosaminyl 1-phosphate transferase => putative undecaprenyl-phosphate N-acetylglucosaminyl 1-phosphate transferase
[17:47:17] Modify product: Uncharacterized glycosyltransferase EpsJ => putative glycosyltransferase EpsJ
[17:47:17] Modify product: Uncharacterized FAD-linked oxidoreductase Rv2280 => putative FAD-linked oxidoreductase
[17:47:17] Modify product: Oxygen-independent coproporphyrinogen-III oxidase-like protein sll1917 => Oxygen-independent coproporphyrinogen-III oxidase-like protein
[17:47:17] Modify product: Uncharacterized PIN and TRAM-domain containing protein YacL => putative PIN and TRAM-domain containing protein YacL
[17:47:17] Modify product: Glycogen operon protein GlgX homolog => Glycogen operon protein GlgX 
[17:47:17] Modify product: Probable phospholipid ABC transporter permease protein MlaE => putative phospholipid ABC transporter permease protein MlaE
[17:47:17] Modify product: Probable 30S ribosomal protein PSRP-3 => putative 30S ribosomal protein PSRP-3
[17:47:17] Modify product: Probable peptidoglycan glycosyltransferase FtsW => putative peptidoglycan glycosyltransferase FtsW
[17:47:17] Modify product: Probable helicase HelY => putative helicase HelY
[17:47:17] Modify product: Probable dual-specificity RNA methyltransferase RlmN => putative dual-specificity RNA methyltransferase RlmN
[17:47:17] Modify product: Probable endopeptidase p60 => putative endopeptidase p60
[17:47:17] Modify product: Probable cobalt-factor III C(17)-methyltransferase => putative cobalt-factor III C(17)-methyltransferase
[17:47:17] Modify product: Probable adenylyltransferase/sulfurtransferase MoeZ => putative adenylyltransferase/sulfurtransferase MoeZ
[17:47:17] Modify product: Uncharacterized hydrolase YxeP => putative hydrolase YxeP
[17:47:17] Modify product: Inner membrane protein BB_0250 => Inner membrane protein
[17:47:17] Modify product: Probable branched-chain-amino-acid aminotransferase => putative branched-chain-amino-acid aminotransferase
[17:47:17] Modify product: Probable protein kinase UbiB => putative protein kinase UbiB
[17:47:17] Cleaned 68 /product names
[17:47:17] Deleting unwanted file: /share/gsi2/data/www/soap-data/M2BBS/Phylogenomic/Prochlorococcus/prokka/Aaaf/sprot.faa
[17:47:17] Deleting unwanted file: /share/gsi2/data/www/soap-data/M2BBS/Phylogenomic/Prochlorococcus/prokka/Aaaf/sprot.blast
[17:47:18] There are still 873 unannotated CDS left (started with 1889)
[17:47:18] Will use hmmer3 to search against /share/gsi2/software/prokka/bin/../db/hmm/HAMAP.hmm with 1 CPUs
[17:47:18] Running: cat \/share\/gsi2\/data\/www\/soap\-data\/M2BBS\/Phylogenomic\/Prochlorococcus\/prokka\/Aaaf\/HAMAP\.hmm\.faa | parallel --gnu --plain -j 1 --block 74145 --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\/Aaaf\/HAMAP\.hmm\.hmmer3 2> /dev/null
[17:48:37] Deleting unwanted file: /share/gsi2/data/www/soap-data/M2BBS/Phylogenomic/Prochlorococcus/prokka/Aaaf/HAMAP.hmm.faa
[17:48:37] Deleting unwanted file: /share/gsi2/data/www/soap-data/M2BBS/Phylogenomic/Prochlorococcus/prokka/Aaaf/HAMAP.hmm.hmmer3
[17:48:37] Labelling remaining 805 proteins as 'hypothetical protein'
[17:48:37] Possible /pseudo 'Ethanolamine utilization protein EutN' at gnl|Prokka|AaafA01.g_1 position 535222
[17:48:37] Possible /pseudo 'putative zinc protease' at gnl|Prokka|AaafA01.g_1 position 694842
[17:48:37] Possible /pseudo 'D-alanyl-D-alanine dipeptidase' at gnl|Prokka|AaafA01.g_1 position 706436
[17:48:37] Possible /pseudo 'ATP-dependent Clp protease proteolytic subunit' at gnl|Prokka|AaafA01.g_1 position 1296948
[17:48:37] Possible /pseudo 'Phosphoribosylaminoimidazole-succinocarboxamide synthase' at gnl|Prokka|AaafA01.g_1 position 1319801
[17:48:37] Possible /pseudo 'DNA-directed RNA polymerase subunit beta'' at gnl|Prokka|AaafA01.g_1 position 1428254
[17:48:37] Possible /pseudo '15,16-dihydrobiliverdin:ferredoxin oxidoreductase' at gnl|Prokka|AaafA01.g_1 position 1534556
[17:48:37] Possible /pseudo 'Putative fluoride ion transporter CrcB' at gnl|Prokka|AaafA01.g_1 position 1572576
[17:48:37] Found 921 unique /gene codes.
[17:48:37] Fixed 3 duplicate /gene - fcl_1 fcl_2 fcl_3
[17:48:37] Fixed 2 duplicate /gene - corC_1 corC_2
[17:48:37] Fixed 2 duplicate /gene - cobD_1 cobD_2
[17:48:37] Fixed 2 duplicate /gene - trxB_1 trxB_2
[17:48:37] Fixed 2 duplicate /gene - crtL_1 crtL_2
[17:48:37] Fixed 3 duplicate /gene - hisH_1 hisH_2 hisH_3
[17:48:37] Fixed 2 duplicate /gene - lexA_1 lexA_2
[17:48:37] Fixed 2 duplicate /gene - bshA_1 bshA_2
[17:48:37] Fixed 2 duplicate /gene - eutN_1 eutN_2
[17:48:37] Fixed 2 duplicate /gene - era_1 era_2
[17:48:37] Fixed 2 duplicate /gene - psbN_1 psbN_2
[17:48:37] Fixed 4 duplicate /gene - ligB_1 ligB_2 ligB_3 ligB_4
[17:48:37] Fixed 2 duplicate /gene - btuR_1 btuR_2
[17:48:37] Fixed 2 duplicate /gene - wfgD_1 wfgD_2
[17:48:37] Fixed 2 duplicate /gene - ppa_1 ppa_2
[17:48:37] Fixed 3 duplicate /gene - menG_1 menG_2 menG_3
[17:48:37] Fixed 2 duplicate /gene - nadK_1 nadK_2
[17:48:37] Fixed 2 duplicate /gene - arnT_1 arnT_2
[17:48:37] Fixed 2 duplicate /gene - bicA_1 bicA_2
[17:48:37] Fixed 2 duplicate /gene - crtI_1 crtI_2
[17:48:37] Fixed 2 duplicate /gene - ddpX_1 ddpX_2
[17:48:37] Fixed 4 duplicate /gene - clpP_1 clpP_2 clpP_3 clpP_4
[17:48:37] Fixed 3 duplicate /gene - bcp_1 bcp_2 bcp_3
[17:48:37] Fixed 2 duplicate /gene - cca_1 cca_2
[17:48:37] Fixed 2 duplicate /gene - rnr_1 rnr_2
[17:48:37] Fixed 2 duplicate /gene - iolC_1 iolC_2
[17:48:37] Fixed 2 duplicate /gene - rplU_1 rplU_2
[17:48:37] Fixed 2 duplicate /gene - dnaX_1 dnaX_2
[17:48:37] Fixed 2 duplicate /gene - fabG_1 fabG_2
[17:48:37] Fixed 2 duplicate /gene - bchI_1 bchI_2
[17:48:37] Fixed 2 duplicate /gene - ndhD1_1 ndhD1_2
[17:48:37] Fixed 2 duplicate /gene - der_1 der_2
[17:48:37] Fixed 2 duplicate /gene - dxs_1 dxs_2
[17:48:37] Fixed 3 duplicate /gene - yciC_1 yciC_2 yciC_3
[17:48:37] Fixed 2 duplicate /gene - galE_1 galE_2
[17:48:37] Fixed 2 duplicate /gene - cobN_1 cobN_2
[17:48:37] Fixed 2 duplicate /gene - hisF_1 hisF_2
[17:48:37] Fixed 2 duplicate /gene - purE_1 purE_2
[17:48:37] Fixed 2 duplicate /gene - hhoA_1 hhoA_2
[17:48:37] Fixed 2 duplicate /gene - psbA_1 psbA_2
[17:48:37] Fixed 2 duplicate /gene - pebA_1 pebA_2
[17:48:37] Fixed 2 duplicate /gene - gyrA_1 gyrA_2
[17:48:37] Fixed 2 duplicate /gene - phoP_1 phoP_2
[17:48:37] Fixed 2 duplicate /gene - rpsA_1 rpsA_2
[17:48:37] Fixed 2 duplicate /gene - hpf_1 hpf_2
[17:48:37] Fixed 2 duplicate /gene - trxA_1 trxA_2
[17:48:37] Fixed 3 duplicate /gene - petF_1 petF_2 petF_3
[17:48:37] Fixed 2 duplicate /gene - sasA_1 sasA_2
[17:48:37] Fixed 2 duplicate /gene - cugP_1 cugP_2
[17:48:37] Fixed 2 duplicate /gene - csgA_1 csgA_2
[17:48:37] Fixed 2 duplicate /gene - lpxB_1 lpxB_2
[17:48:37] Fixed 2 duplicate /gene - plsC_1 plsC_2
[17:48:37] Fixed 2 duplicate /gene - udk_1 udk_2
[17:48:37] Fixed 2 duplicate /gene - clpB1_1 clpB1_2
[17:48:37] Fixed 2 duplicate /gene - ubiG_1 ubiG_2
[17:48:37] Fixed 2 duplicate /gene - dnaK2_1 dnaK2_2
[17:48:37] Fixed 2 duplicate /gene - tagO_1 tagO_2
[17:48:37] Fixed 2 duplicate /gene - psbF_1 psbF_2
[17:48:37] Fixed 2 duplicate /gene - epsJ_1 epsJ_2
[17:48:37] Fixed 2 duplicate /gene - iscS_1 iscS_2
[17:48:37] Fixed 2 duplicate /gene - mntB_1 mntB_2
[17:48:37] Fixed 2 duplicate /gene - ycf3_1 ycf3_2
[17:48:37] Fixed 2 duplicate /gene - crcB_1 crcB_2
[17:48:37] Fixed 2 duplicate /gene - mnmC_1 mnmC_2
[17:48:37] Fixed 3 duplicate /gene - suhB_1 suhB_2 suhB_3
[17:48:37] Fixed 3 duplicate /gene - ubiB_1 ubiB_2 ubiB_3
[17:48:37] Fixed 2 duplicate /gene - lytB_1 lytB_2
[17:48:37] Fixed 2 duplicate /gene - speA_1 speA_2
[17:48:37] Fixed 2 duplicate /gene - glmM_1 glmM_2
[17:48:37] Fixed 3 duplicate /gene - sigA2_1 sigA2_2 sigA2_3
[17:48:37] Fixed 3 duplicate /gene - ftsH2_1 ftsH2_2 ftsH2_3
[17:48:37] Fixed 2 duplicate /gene - atpG_1 atpG_2
[17:48:37] Fixed 2 duplicate /gene - pds_1 pds_2
[17:48:37] Fixed 2 duplicate /gene - ilvE_1 ilvE_2
[17:48:37] Fixed 2 duplicate /gene - purC_1 purC_2
[17:48:37] Fixed 2 duplicate /gene - rpoC_1 rpoC_2
[17:48:37] Fixed 76 colliding /gene names.
[17:48:37] Adding /locus_tag identifiers
[17:48:38] Assigned 1931 locus_tags to CDS and RNA features.
[17:48:38] Writing outputs to /share/gsi2/data/www/soap-data/M2BBS/Phylogenomic/Prochlorococcus/prokka/Aaaf/
[17:48:43] Generating annotation statistics file
[17:48:43] Generating Genbank and Sequin files
[17:48:43] 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\/Aaaf\/AaafA01\.err -i \/share\/gsi2\/data\/www\/soap\-data\/M2BBS\/Phylogenomic\/Prochlorococcus\/prokka\/Aaaf\/AaafA01\.fsa 2> /dev/null
[17:48:50] Deleting unwanted file: /share/gsi2/data/www/soap-data/M2BBS/Phylogenomic/Prochlorococcus/prokka/Aaaf/errorsummary.val
[17:48:50] Deleting unwanted file: /share/gsi2/data/www/soap-data/M2BBS/Phylogenomic/Prochlorococcus/prokka/Aaaf/AaafA01.dr
[17:48:50] Deleting unwanted file: /share/gsi2/data/www/soap-data/M2BBS/Phylogenomic/Prochlorococcus/prokka/Aaaf/AaafA01.fixedproducts
[17:48:50] Deleting unwanted file: /share/gsi2/data/www/soap-data/M2BBS/Phylogenomic/Prochlorococcus/prokka/Aaaf/AaafA01.ecn
[17:48:50] Deleting unwanted file: /share/gsi2/data/www/soap-data/M2BBS/Phylogenomic/Prochlorococcus/prokka/Aaaf/AaafA01.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\/Aaaf\/AaafA01\.gbf > \/share\/gsi2\/data\/www\/soap\-data\/M2BBS\/Phylogenomic\/Prochlorococcus\/prokka\/Aaaf\/AaafA01\.gbk
[17:48:50] Deleting unwanted file: /share/gsi2/data/www/soap-data/M2BBS/Phylogenomic/Prochlorococcus/prokka/Aaaf/AaafA01.gbf
[17:48:50] Output files:
[17:48:50] /share/gsi2/data/www/soap-data/M2BBS/Phylogenomic/Prochlorococcus/prokka/Aaaf/AaafA01.log
[17:48:50] /share/gsi2/data/www/soap-data/M2BBS/Phylogenomic/Prochlorococcus/prokka/Aaaf/AaafA01.fna
[17:48:50] /share/gsi2/data/www/soap-data/M2BBS/Phylogenomic/Prochlorococcus/prokka/Aaaf/AaafA01.gff
[17:48:50] /share/gsi2/data/www/soap-data/M2BBS/Phylogenomic/Prochlorococcus/prokka/Aaaf/AaafA01.faa
[17:48:50] /share/gsi2/data/www/soap-data/M2BBS/Phylogenomic/Prochlorococcus/prokka/Aaaf/AaafA01.ffn
[17:48:50] /share/gsi2/data/www/soap-data/M2BBS/Phylogenomic/Prochlorococcus/prokka/Aaaf/AaafA01.tbl
[17:48:50] /share/gsi2/data/www/soap-data/M2BBS/Phylogenomic/Prochlorococcus/prokka/Aaaf/AaafA01.fsa
[17:48:50] /share/gsi2/data/www/soap-data/M2BBS/Phylogenomic/Prochlorococcus/prokka/Aaaf/AaafA01.tsv
[17:48:50] /share/gsi2/data/www/soap-data/M2BBS/Phylogenomic/Prochlorococcus/prokka/Aaaf/AaafA01.txt
[17:48:50] /share/gsi2/data/www/soap-data/M2BBS/Phylogenomic/Prochlorococcus/prokka/Aaaf/AaafA01.sqn
[17:48:50] /share/gsi2/data/www/soap-data/M2BBS/Phylogenomic/Prochlorococcus/prokka/Aaaf/AaafA01.err
[17:48:50] /share/gsi2/data/www/soap-data/M2BBS/Phylogenomic/Prochlorococcus/prokka/Aaaf/AaafA01.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.