[17:44:20] This is prokka 1.12
[17:44:20] Written by Torsten Seemann <torsten.seemann@gmail.com>
[17:44:20] Homepage is https://github.com/tseemann/prokka
[17:44:20] Local time is Thu Sep  6 17:44:20 2018
[17:44:20] You are gsi
[17:44:20] Operating system is linux
[17:44:20] You have BioPerl 1.007002
[17:44:20] System has 24 cores.
[17:44:20] Will use maximum of 1 cores.
[17:44:20] Annotating as >>> Bacteria <<<
[17:44:20] Enabling options to ensure Genbank/ENA/DDJB submission compliance.
[17:44:20] Creating new output folder: /share/gsi2/data/www/soap-data/M2BBS/Phylogenomic/Prochlorococcus/prokka/Aaac
[17:44:20] Running: mkdir -p \/share\/gsi2\/data\/www\/soap\-data\/M2BBS\/Phylogenomic\/Prochlorococcus\/prokka\/Aaac
[17:44:20] Using filename prefix: AaacA01.XXX
[17:44:20] Setting HMMER_NCPU=1
[17:44:20] Writing log to: /share/gsi2/data/www/soap-data/M2BBS/Phylogenomic/Prochlorococcus/prokka/Aaac/AaacA01.log
[17:44:20] Command: /share/gsi2/bin/prokka /share/gsi2/data/www/soap-data/M2BBS/Phylogenomic/Prochlorococcus/DNA/Aaac/AaacA01.fas --compliant --addgenes --outdir /share/gsi2/data/www/soap-data/M2BBS/Phylogenomic/Prochlorococcus/prokka/Aaac --prefix AaacA01 --locustag AaacA01.g --species ProchlorococcusmarinusstrMIT9313 --strain ProchlorococcusmarinusstrMIT9313 --kingdom bacteria --cpus 1 --force
[17:44:20] Appending to PATH: /share/gsi2/software/prokka/bin/../binaries/linux
[17:44:20] Appending to PATH: /share/gsi2/software/prokka/bin/../binaries/linux/../common
[17:44:20] Appending to PATH: /share/gsi2/software/prokka/bin
[17:44:20] Looking for 'aragorn' - found /share/gsi2/software/prokka/bin/../binaries/linux/aragorn
[17:44:20] Determined aragorn version is 1.2
[17:44:20] Looking for 'barrnap' - found /share/gsi2/bin/barrnap
[17:44:20] Determined barrnap version is 0.9
[17:44:20] Looking for 'blastp' - found /share/gsi2/bin/blastp
[17:44:21] Determined blastp version is 2.7
[17:44:21] Looking for 'cmpress' - found /share/gsi2/software/prokka/bin/../binaries/linux/cmpress
[17:44:21] Determined cmpress version is 1.1
[17:44:21] Looking for 'cmscan' - found /share/gsi2/software/prokka/bin/../binaries/linux/cmscan
[17:44:21] Determined cmscan version is 1.1
[17:44:21] Looking for 'egrep' - found /bin/egrep
[17:44:21] Looking for 'find' - found /bin/find
[17:44:21] Looking for 'grep' - found /bin/grep
[17:44:21] Looking for 'hmmpress' - found /share/gsi2/bin/hmmpress
[17:44:21] Determined hmmpress version is 3.1
[17:44:21] Looking for 'hmmscan' - found /share/gsi2/bin/hmmscan
[17:44:21] Determined hmmscan version is 3.1
[17:44:21] Looking for 'java' - found /usr/java/latest/bin/java
[17:44:21] Looking for 'less' - found /usr/bin/less
[17:44:21] Looking for 'makeblastdb' - found /share/gsi2/bin/makeblastdb
[17:44:22] Determined makeblastdb version is 2.7
[17:44:22] Looking for 'minced' - found /share/gsi2/bin/minced
[17:44:22] Determined minced version is 2.0
[17:44:22] Looking for 'parallel' - found /share/gsi2/software/prokka/bin/../binaries/linux/../common/parallel
[17:44:23] Determined parallel version is 20150122
[17:44:23] Looking for 'prodigal' - found /share/gsi2/software/prokka/bin/../binaries/linux/prodigal
[17:44:23] Determined prodigal version is 2.6
[17:44:23] Looking for 'prokka-genbank_to_fasta_db' - found /share/gsi2/software/prokka/bin/prokka-genbank_to_fasta_db
[17:44:23] Looking for 'rnammer' - found /share/gsi2/bin/rnammer
[17:44:23] Determined rnammer version is 1.2
[17:44:23] Looking for 'sed' - found /bin/sed
[17:44:23] Looking for 'tbl2asn' - found /share/gsi2/bin/tbl2asn
[17:44:23] Determined tbl2asn version is 25.6
[17:44:23] Using genetic code table 11.
[17:44:23] Loading and checking input file: /share/gsi2/data/www/soap-data/M2BBS/Phylogenomic/Prochlorococcus/DNA/Aaac/AaacA01.fas
[17:44:23] Wrote 1 contigs totalling 2410873 bp.
[17:44:23] Predicting tRNAs and tmRNAs
[17:44:23] Running: aragorn -l -gc11  -w \/share\/gsi2\/data\/www\/soap\-data\/M2BBS\/Phylogenomic\/Prochlorococcus\/prokka\/Aaac\/AaacA01\.fna
[17:44:25] 1 tRNA-Gly c[42282,42353] 33 (ccc)
[17:44:25] 2 tRNA-Gly [87820,87891] 33 (gcc)
[17:44:25] 3 tRNA-Ile [210510,210585] 36 (gat)
[17:44:25] 4 tRNA-Ala [210594,210667] 34 (tgc)
[17:44:25] 5 tRNA-Thr c[227744,227817] 34 (ggt)
[17:44:25] 6 tRNA-Tyr c[227825,227908] 35 (gta)
[17:44:25] 7 tRNA-Ser [329017,329103] 36 (cga)
[17:44:25] 8 tRNA-His c[370809,370882] 34 (gtg)
[17:44:25] 9 tRNA-Leu c[379359,379441] 35 (caa)
[17:44:25] 10 tRNA-Leu [380928,381011] 35 (cag)
[17:44:25] 11 tRNA-Ala [430627,430701] 35 (ggc)
[17:44:25] 12 tRNA-Arg c[443167,443241] 34 (gcg)
[17:44:25] 13 tRNA-Leu [518780,518866] 35 (taa)
[17:44:25] 14 tRNA-Pro c[540453,540526] 35 (ggg)
[17:44:25] 15 tRNA-Ser [755234,755322] 36 (gga)
[17:44:25] 16 tRNA-Met [819958,820031] 35 (cat)
[17:44:25] 17 tRNA-Ser [871424,871510] 35 (tga)
[17:44:25] 18 tRNA-Met [904478,904553] 35 (cat)
[17:44:25] 19 tRNA-Pro [1002550,1002624] 35 (tgg)
[17:44:25] 20 tRNA-Lys c[1129198,1129270] 33 (ttt)
[17:44:25] 21 tRNA-Glu [1191237,1191309] 35 (ttc)
[17:44:25] 22 tRNA-Trp [1394721,1394797] 35 (cca)
[17:44:25] 23 tRNA-Asp [1395300,1395375] 36 (gtc)
[17:44:25] 24 tRNA-Val [1410332,1410403] 33 (cac)
[17:44:25] 25 tRNA-Arg [1466352,1466427] 36 (tct)
[17:44:25] 26 tRNA-Gly c[1484518,1484588] 33 (tcc)
[17:44:25] 27 tRNA-Val [1522156,1522228] 33 (gac)
[17:44:25] 28 tRNA-Thr [1623005,1623079] 34 (cgt)
[17:44:25] 29 tmRNA* c[1677611,1677933] 182,232 ANNIVRFSRQPALVAA*
[17:44:25] 30 tRNA-Leu c[1689824,1689905] 35 (gag)
[17:44:25] 31 tRNA-Ala c[1751821,1751894] 34 (tgc)
[17:44:25] 32 tRNA-Ile c[1751903,1751978] 36 (gat)
[17:44:25] 33 tRNA-Thr [1762099,1762172] 34 (tgt)
[17:44:25] 34 tRNA-Phe [1778675,1778747] 34 (gaa)
[17:44:25] 35 tRNA-Cys c[1800851,1800921] 33 (gca)
[17:44:25] 36 tRNA-Arg c[1816941,1817016] 36 (ccg)
[17:44:25] 37 tRNA-Gln c[1831861,1831934] 34 (ttg)
[17:44:25] 38 tRNA-Ser [1854200,1854290] 36 (gct)
[17:44:25] 39 tRNA-Pro c[1870396,1870471] 36 (cgg)
[17:44:25] 40 tRNA-Ala [1905154,1905228] 35 (cgc)
[17:44:25] 41 tRNA-Leu c[1921404,1921489] 36 (tag)
[17:44:25] 42 tRNA-Arg c[1956689,1956763] 35 (acg)
[17:44:25] 43 tRNA-Met c[1974076,1974148] 34 (cat)
[17:44:25] 44 tRNA-Arg c[2059322,2059397] 36 (cct)
[17:44:25] 45 tRNA-Asn [2101164,2101235] 33 (gtt)
[17:44:25] 46 tRNA-Val c[2336629,2336700] 33 (tac)
[17:44:25] Found 46 tRNAs
[17:44:25] Predicting Ribosomal RNAs
[17:44:25] Running Barrnap with 1 threads
[17:44:29] 1 gnl|Prokka|AaacA01.g_1 208847 16S ribosomal RNA
[17:44:29] 2 gnl|Prokka|AaacA01.g_1 211160 23S ribosomal RNA
[17:44:29] 3 gnl|Prokka|AaacA01.g_1 1748455 23S ribosomal RNA
[17:44:29] 4 gnl|Prokka|AaacA01.g_1 1752162 16S ribosomal RNA
[17:44:29] Found 4 rRNAs
[17:44:29] Skipping ncRNA search, enable with --rfam if desired.
[17:44:29] Total of 49 tRNA + rRNA features
[17:44:29] Searching for CRISPR repeats
[17:44:30] Found 0 CRISPRs
[17:44:30] Predicting coding sequences
[17:44:30] Contigs total 2410873 bp, so using single mode
[17:44:30] Running: prodigal -i \/share\/gsi2\/data\/www\/soap\-data\/M2BBS\/Phylogenomic\/Prochlorococcus\/prokka\/Aaac\/AaacA01\.fna -c -m -g 11 -p single -f sco -q
[17:44:41] Excluding CDS which overlaps existing RNA (rRNA) at gnl|Prokka|AaacA01.g_1:210024..210266 on + strand
[17:44:41] Excluding CDS which overlaps existing RNA (rRNA) at gnl|Prokka|AaacA01.g_1:211219..211344 on - strand
[17:44:41] Excluding CDS which overlaps existing RNA (rRNA) at gnl|Prokka|AaacA01.g_1:213572..213697 on - strand
[17:44:41] Excluding CDS which overlaps existing RNA (tRNA) at gnl|Prokka|AaacA01.g_1:370764..370964 on - strand
[17:44:41] Excluding CDS which overlaps existing RNA (tRNA) at gnl|Prokka|AaacA01.g_1:378170..379435 on - strand
[17:44:42] Excluding CDS which overlaps existing RNA (tRNA) at gnl|Prokka|AaacA01.g_1:430664..431248 on + strand
[17:44:42] Excluding CDS which overlaps existing RNA (tRNA) at gnl|Prokka|AaacA01.g_1:442365..443459 on - strand
[17:44:43] Excluding CDS which overlaps existing RNA (tRNA) at gnl|Prokka|AaacA01.g_1:1410301..1410468 on - strand
[17:44:43] Excluding CDS which overlaps existing RNA (rRNA) at gnl|Prokka|AaacA01.g_1:1748791..1748916 on + strand
[17:44:43] Excluding CDS which overlaps existing RNA (rRNA) at gnl|Prokka|AaacA01.g_1:1751144..1751269 on + strand
[17:44:43] Excluding CDS which overlaps existing RNA (rRNA) at gnl|Prokka|AaacA01.g_1:1752222..1752464 on - strand
[17:44:43] Excluding CDS which overlaps existing RNA (tRNA) at gnl|Prokka|AaacA01.g_1:1761822..1762109 on + strand
[17:44:43] Excluding CDS which overlaps existing RNA (tRNA) at gnl|Prokka|AaacA01.g_1:1800844..1802223 on + strand
[17:44:43] Excluding CDS which overlaps existing RNA (tRNA) at gnl|Prokka|AaacA01.g_1:1956598..1956744 on + strand
[17:44:44] Found 2552 CDS
[17:44:44] Connecting features back to sequences
[17:44:44] Not using genus-specific database. Try --usegenus to enable it.
[17:44:44] Annotating CDS, please be patient.
[17:44:44] Will use 1 CPUs for similarity searching.
[17:44:48] There are still 2552 unannotated CDS left (started with 2552)
[17:44:48] Will use blast to search against /share/gsi2/software/prokka/bin/../db/kingdom/Bacteria/sprot with 1 CPUs
[17:44:48] Running: cat \/share\/gsi2\/data\/www\/soap\-data\/M2BBS\/Phylogenomic\/Prochlorococcus\/prokka\/Aaac\/sprot\.faa | parallel --gnu --plain -j 1 --block 342064 --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\/Aaac\/sprot\.blast 2> /dev/null
[17:47:57] Modify product: N utilization substance protein B homolog => N utilization substance protein B 
[17:47:57] Modify product: Uncharacterized oxidoreductase MSMEG_2408/MSMEI_2347 => putative oxidoreductase/MSMEI_2347
[17:47:57] Modify product: Uncharacterized membrane protein Rv2637 => putative membrane protein
[17:47:57] Modify product: Probable ABC transporter-binding protein DR_1438 => putative ABC transporter-binding protein
[17:47:57] Modify product: Uncharacterized hydrolase YxeP => putative hydrolase YxeP
[17:47:57] Modify product: Vitamin K epoxide reductase homolog => Vitamin K epoxide reductase 
[17:47:57] Modify product: Probable tRNA-dihydrouridine synthase => putative tRNA-dihydrouridine synthase
[17:47:57] Modify product: Uncharacterized MFS-type transporter Rv0037c => putative MFS-type transporter
[17:47:57] Modify product: Cyclic nucleotide-gated potassium channel mll3241 => Cyclic nucleotide-gated potassium channel
[17:47:57] Modify product: PKHD-type hydroxylase Sbal_3634 => PKHD-type hydroxylase
[17:47:57] Modify product: Uncharacterized PIN and TRAM-domain containing protein YacL => putative PIN and TRAM-domain containing protein YacL
[17:47:57] Modify product: Oxygen-independent coproporphyrinogen-III oxidase-like protein sll1917 => Oxygen-independent coproporphyrinogen-III oxidase-like protein
[17:47:57] Modify product: Uncharacterized FAD-linked oxidoreductase Rv2280 => putative FAD-linked oxidoreductase
[17:47:58] Modify product: Phosphorylated carbohydrates phosphatase TM_1254 => Phosphorylated carbohydrates phosphatase
[17:47:58] Modify product: Probable 2-phosphosulfolactate phosphatase => putative 2-phosphosulfolactate phosphatase
[17:47:58] Modify product: Probable L,D-transpeptidase YnhG => putative L,D-transpeptidase YnhG
[17:47:58] Modify product: Uncharacterized sugar epimerase YhfK => putative sugar epimerase YhfK
[17:47:58] Modify product: Probable murein peptide carboxypeptidase => putative murein peptide carboxypeptidase
[17:47:58] Modify product: GTP-binding protein TypA/BipA homolog => GTP-binding protein TypA/BipA 
[17:47:58] Modify product: Uncharacterized zinc protease Rv2782c => putative zinc protease
[17:47:58] Modify product: Uncharacterized zinc protease Rv2782c => putative zinc protease
[17:47:58] Modify product: Probable multidrug resistance ABC transporter ATP-binding/permease protein YheI => putative multidrug resistance ABC transporter ATP-binding/permease protein YheI
[17:47:58] Modify product: Uncharacterized ABC transporter ATP-binding protein YlmA => putative ABC transporter ATP-binding protein YlmA
[17:47:58] Modify product: Probable ABC transporter-binding protein DR_1438 => putative ABC transporter-binding protein
[17:47:58] Modify product: Probable ferredoxin/ferredoxin--NADP reductase => putative ferredoxin/ferredoxin--NADP reductase
[17:47:58] Modify product: Uncharacterized ABC transporter ATP-binding protein Rv0986 => putative ABC transporter ATP-binding protein
[17:47:58] Modify product: Putative multidrug export ATP-binding/permease protein SA1683 => Putative multidrug export ATP-binding/permease protein
[17:47:58] Modify product: Uncharacterized MscS family protein YkuT => putative MscS family protein YkuT
[17:47:58] Modify product: Probable isochorismatase => putative isochorismatase
[17:47:58] Modify product: Probable glutamine ABC transporter permease protein GlnM => putative glutamine ABC transporter permease protein GlnM
[17:47:58] Modify product: Cyclic nucleotide-gated potassium channel mll3241 => Cyclic nucleotide-gated potassium channel
[17:47:58] Modify product: Probable protein kinase UbiB => putative protein kinase UbiB
[17:47:58] Modify product: Putative multidrug export ATP-binding/permease protein SA1683 => Putative multidrug export ATP-binding/permease protein
[17:47:58] Modify product: Bifunctional protein FolD => Bifunctional protein FolD protein
[17:47:58] Modify product: 1,4-alpha-glucan branching enzyme TTHA1902 => 1,4-alpha-glucan branching enzyme
[17:47:58] Modify product: Uncharacterized oxidoreductase MSMEG_1603/MSMEI_1564 => putative oxidoreductase/MSMEI_1564
[17:47:58] Modify product: Uncharacterized methyltransferase Rv3342 => putative methyltransferase
[17:47:58] Modify product: Maf-like protein Rv3282 => Maf-like protein
[17:47:58] Modify product: Putative peroxiredoxin sll1621 => Putative peroxiredoxin
[17:47:58] Modify product: Uncharacterized ABC transporter ATP-binding protein TM_0288 => putative ABC transporter ATP-binding protein
[17:47:58] Modify product: Uncharacterized oxidoreductase Rv0769 => putative oxidoreductase
[17:47:58] Modify product: Laccase domain protein Rv2149c => Laccase domain protein
[17:47:59] Modify product: Uncharacterized sugar kinase YdjH => putative sugar kinase YdjH
[17:47:59] Modify product: Thylakoid-associated single-stranded DNA-binding protein slr1034 => Thylakoid-associated single-stranded DNA-binding protein
[17:47:59] Modify product: Uncharacterized FAD-linked oxidoreductase Rv2280 => putative FAD-linked oxidoreductase
[17:47:59] Modify product: Probable murein peptide carboxypeptidase => putative murein peptide carboxypeptidase
[17:47:59] Modify product: Probable doxorubicin resistance ABC transporter permease protein DrrC => putative doxorubicin resistance ABC transporter permease protein DrrC
[17:47:59] Modify product: Probable cytochrome c oxidase subunit 1 => putative cytochrome c oxidase subunit 1
[17:47:59] Modify product: Uncharacterized ABC transporter ATP-binding protein YknY => putative ABC transporter ATP-binding protein YknY
[17:47:59] Modify product: Phage shock protein A homolog => Phage shock protein A 
[17:47:59] Modify product: Uncharacterized inner membrane transporter YedA => putative inner membrane transporter YedA
[17:47:59] Modify product: Glycogen operon protein GlgX homolog => Glycogen operon protein GlgX 
[17:47:59] Modify product: Probable phospholipid ABC transporter permease protein MlaE => putative phospholipid ABC transporter permease protein MlaE
[17:47:59] Modify product: Probable transcriptional regulatory protein aq_1575 => putative transcriptional regulatory protein
[17:47:59] Modify product: Probable 30S ribosomal protein PSRP-3 => putative 30S ribosomal protein PSRP-3
[17:47:59] Modify product: Probable peptidoglycan glycosyltransferase FtsW => putative peptidoglycan glycosyltransferase FtsW
[17:47:59] Modify product: Probable helicase HelY => putative helicase HelY
[17:47:59] Modify product: Probable dual-specificity RNA methyltransferase RlmN => putative dual-specificity RNA methyltransferase RlmN
[17:47:59] Modify product: Vitamin K epoxide reductase homolog => Vitamin K epoxide reductase 
[17:47:59] Modify product: Probable cysteine desulfurase => putative cysteine desulfurase
[17:47:59] Modify product: Probable ATP-dependent transporter SufC => putative ATP-dependent transporter SufC
[17:47:59] Modify product: Uncharacterized ABC transporter ATP-binding protein YheS => putative ABC transporter ATP-binding protein YheS
[17:47:59] Modify product: Probable septum site-determining protein MinC => putative septum site-determining protein MinC
[17:47:59] Modify product: Putative esterase aq_1494 => Putative esterase
[17:47:59] Modify product: Probable phycoerythrobilin lyase CpeT => putative phycoerythrobilin lyase CpeT
[17:47:59] Modify product: Uncharacterized phycocyanin operon protein Z => putative phycocyanin operon protein Z
[17:47:59] Modify product: Uncharacterized phycocyanin operon protein Z => putative phycocyanin operon protein Z
[17:47:59] Modify product: Probable adenylyltransferase/sulfurtransferase MoeZ => putative adenylyltransferase/sulfurtransferase MoeZ
[17:47:59] Modify product: Probable endopeptidase p60 => putative endopeptidase p60
[17:47:59] Modify product: Probable cobalt-factor III C(17)-methyltransferase => putative cobalt-factor III C(17)-methyltransferase
[17:47:59] Modify product: Probable bifunctional SAT/APS kinase => putative bifunctional SAT/APS kinase
[17:47:59] Modify product: NADH dehydrogenase-like protein SA0802 => NADH dehydrogenase-like protein
[17:47:59] Modify product: Probable undecaprenyl-phosphate N-acetylglucosaminyl 1-phosphate transferase => putative undecaprenyl-phosphate N-acetylglucosaminyl 1-phosphate transferase
[17:47:59] Modify product: Uncharacterized glycosyltransferase sll0501 => putative glycosyltransferase
[17:47:59] Modify product: Uncharacterized FAD-linked oxidoreductase Rv2280 => putative FAD-linked oxidoreductase
[17:47:59] Modify product: Stringent starvation protein A homolog => Stringent starvation protein A 
[17:47:59] Modify product: Epimerase family protein Rv2216 => Epimerase family protein
[17:47:59] Modify product: Probable copper-transporting ATPase PacS => putative copper-transporting ATPase PacS
[17:47:59] Modify product: Probable adenylyl-sulfate kinase => putative adenylyl-sulfate kinase
[17:47:59] Modify product: Uncharacterized oxidoreductase Rv2073c => putative oxidoreductase
[17:48:00] Modify product: Probable glutaredoxin ssr2061 => putative glutaredoxin
[17:48:00] Modify product: Probable nicotinate-nucleotide pyrophosphorylase [carboxylating] => putative nicotinate-nucleotide pyrophosphorylase [carboxylating]
[17:48:00] Modify product: Probable protein kinase UbiB => putative protein kinase UbiB
[17:48:00] Modify product: Cyclic nucleotide-gated potassium channel mll3241 => Cyclic nucleotide-gated potassium channel
[17:48:00] Modify product: Monocarboxylate 2-oxoacid-binding periplasmic protein all3028 => Monocarboxylate 2-oxoacid-binding periplasmic protein
[17:48:00] Modify product: Probable formate transporter 1 => putative formate transporter 1
[17:48:00] Modify product: Probable protein kinase UbiB => putative protein kinase UbiB
[17:48:00] Cleaned 87 /product names
[17:48:00] Deleting unwanted file: /share/gsi2/data/www/soap-data/M2BBS/Phylogenomic/Prochlorococcus/prokka/Aaac/sprot.faa
[17:48:00] Deleting unwanted file: /share/gsi2/data/www/soap-data/M2BBS/Phylogenomic/Prochlorococcus/prokka/Aaac/sprot.blast
[17:48:02] There are still 1332 unannotated CDS left (started with 2552)
[17:48:02] Will use hmmer3 to search against /share/gsi2/software/prokka/bin/../db/hmm/HAMAP.hmm with 1 CPUs
[17:48:02] Running: cat \/share\/gsi2\/data\/www\/soap\-data\/M2BBS\/Phylogenomic\/Prochlorococcus\/prokka\/Aaac\/HAMAP\.hmm\.faa | parallel --gnu --plain -j 1 --block 118583 --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\/Aaac\/HAMAP\.hmm\.hmmer3 2> /dev/null
[17:50:33] Deleting unwanted file: /share/gsi2/data/www/soap-data/M2BBS/Phylogenomic/Prochlorococcus/prokka/Aaac/HAMAP.hmm.faa
[17:50:33] Deleting unwanted file: /share/gsi2/data/www/soap-data/M2BBS/Phylogenomic/Prochlorococcus/prokka/Aaac/HAMAP.hmm.hmmer3
[17:50:33] Labelling remaining 1260 proteins as 'hypothetical protein'
[17:50:33] Possible /pseudo 'Putative fluoride ion transporter CrcB' at gnl|Prokka|AaacA01.g_1 position 141202
[17:50:33] Possible /pseudo 'ATP-dependent Clp protease proteolytic subunit' at gnl|Prokka|AaacA01.g_1 position 361312
[17:50:33] Possible /pseudo 'putative zinc protease' at gnl|Prokka|AaacA01.g_1 position 648977
[17:50:33] Possible /pseudo 'Methylenetetrahydrofolate--tRNA-(uracil-5-)-methyltransferase TrmFO' at gnl|Prokka|AaacA01.g_1 position 1130824
[17:50:33] Possible /pseudo 'DNA-directed RNA polymerase subunit beta'' at gnl|Prokka|AaacA01.g_1 position 1591304
[17:50:33] Possible /pseudo 'Competence protein ComM' at gnl|Prokka|AaacA01.g_1 position 1697431
[17:50:33] Possible /pseudo 'putative phycocyanin operon protein Z' at gnl|Prokka|AaacA01.g_1 position 1785737
[17:50:33] Possible /pseudo 'TPR repeat-containing protein YrrB' at gnl|Prokka|AaacA01.g_1 position 1911797
[17:50:33] Possible /pseudo 'TPR repeat-containing protein YrrB' at gnl|Prokka|AaacA01.g_1 position 1913984
[17:50:33] Found 1066 unique /gene codes.
[17:50:33] Fixed 4 duplicate /gene - dnaJ_1 dnaJ_2 dnaJ_3 dnaJ_4
[17:50:33] Fixed 2 duplicate /gene - suhB_1 suhB_2
[17:50:33] Fixed 3 duplicate /gene - ubiB_1 ubiB_2 ubiB_3
[17:50:33] Fixed 2 duplicate /gene - btuR_1 btuR_2
[17:50:33] Fixed 2 duplicate /gene - thiO_1 thiO_2
[17:50:33] Fixed 2 duplicate /gene - pstS_1 pstS_2
[17:50:33] Fixed 2 duplicate /gene - dapb3_1 dapb3_2
[17:50:33] Fixed 2 duplicate /gene - algE7_1 algE7_2
[17:50:33] Fixed 2 duplicate /gene - phoC_1 phoC_2
[17:50:33] Fixed 2 duplicate /gene - ccmK_1 ccmK_2
[17:50:33] Fixed 5 duplicate /gene - ycf3_1 ycf3_2 ycf3_3 ycf3_4 ycf3_5
[17:50:33] Fixed 2 duplicate /gene - mntB_1 mntB_2
[17:50:33] Fixed 2 duplicate /gene - lexA_1 lexA_2
[17:50:33] Fixed 2 duplicate /gene - gatA_1 gatA_2
[17:50:33] Fixed 2 duplicate /gene - purE_1 purE_2
[17:50:33] Fixed 3 duplicate /gene - pds_1 pds_2 pds_3
[17:50:33] Fixed 2 duplicate /gene - crtL_1 crtL_2
[17:50:33] Fixed 2 duplicate /gene - pilT_1 pilT_2
[17:50:33] Fixed 3 duplicate /gene - glnQ_1 glnQ_2 glnQ_3
[17:50:33] Fixed 7 duplicate /gene - yrrB_1 yrrB_2 yrrB_3 yrrB_4 yrrB_5 yrrB_6 yrrB_7
[17:50:33] Fixed 3 duplicate /gene - menG_1 menG_2 menG_3
[17:50:33] Fixed 2 duplicate /gene - hhoA_1 hhoA_2
[17:50:33] Fixed 2 duplicate /gene - spkB_1 spkB_2
[17:50:33] Fixed 2 duplicate /gene - rpsA_1 rpsA_2
[17:50:33] Fixed 2 duplicate /gene - petJ_1 petJ_2
[17:50:33] Fixed 2 duplicate /gene - sasA_1 sasA_2
[17:50:33] Fixed 2 duplicate /gene - kdsB_1 kdsB_2
[17:50:33] Fixed 2 duplicate /gene - cca_1 cca_2
[17:50:33] Fixed 2 duplicate /gene - yciC_1 yciC_2
[17:50:33] Fixed 2 duplicate /gene - hpf_1 hpf_2
[17:50:33] Fixed 2 duplicate /gene - sir_1 sir_2
[17:50:33] Fixed 2 duplicate /gene - resE_1 resE_2
[17:50:33] Fixed 2 duplicate /gene - fabG_1 fabG_2
[17:50:33] Fixed 2 duplicate /gene - degU_1 degU_2
[17:50:33] Fixed 2 duplicate /gene - aspC_1 aspC_2
[17:50:33] Fixed 2 duplicate /gene - bepA_1 bepA_2
[17:50:33] Fixed 2 duplicate /gene - cobN_1 cobN_2
[17:50:33] Fixed 2 duplicate /gene - hisH_1 hisH_2
[17:50:33] Fixed 3 duplicate /gene - apxIB_1 apxIB_2 apxIB_3
[17:50:33] Fixed 2 duplicate /gene - atpG_1 atpG_2
[17:50:33] Fixed 2 duplicate /gene - cobD_1 cobD_2
[17:50:33] Fixed 2 duplicate /gene - gyrA_1 gyrA_2
[17:50:33] Fixed 2 duplicate /gene - carA_1 carA_2
[17:50:33] Fixed 2 duplicate /gene - bepF_1 bepF_2
[17:50:33] Fixed 2 duplicate /gene - rpoC_1 rpoC_2
[17:50:33] Fixed 2 duplicate /gene - ynaI_1 ynaI_2
[17:50:33] Fixed 2 duplicate /gene - acr1_1 acr1_2
[17:50:33] Fixed 3 duplicate /gene - lytB_1 lytB_2 lytB_3
[17:50:33] Fixed 2 duplicate /gene - cyaA_1 cyaA_2
[17:50:33] Fixed 2 duplicate /gene - ubiE_1 ubiE_2
[17:50:33] Fixed 2 duplicate /gene - def_1 def_2
[17:50:33] Fixed 2 duplicate /gene - tam_1 tam_2
[17:50:33] Fixed 2 duplicate /gene - clcA_1 clcA_2
[17:50:33] Fixed 2 duplicate /gene - corC_1 corC_2
[17:50:33] Fixed 2 duplicate /gene - speA_1 speA_2
[17:50:33] Fixed 2 duplicate /gene - ugpC_1 ugpC_2
[17:50:33] Fixed 2 duplicate /gene - bchI_1 bchI_2
[17:50:33] Fixed 2 duplicate /gene - gph_1 gph_2
[17:50:33] Fixed 2 duplicate /gene - smc_1 smc_2
[17:50:33] Fixed 2 duplicate /gene - pyrC_1 pyrC_2
[17:50:33] Fixed 2 duplicate /gene - strE_1 strE_2
[17:50:33] Fixed 2 duplicate /gene - tal_1 tal_2
[17:50:33] Fixed 2 duplicate /gene - trmFO_1 trmFO_2
[17:50:33] Fixed 2 duplicate /gene - psaA_1 psaA_2
[17:50:33] Fixed 2 duplicate /gene - crcB_1 crcB_2
[17:50:33] Fixed 2 duplicate /gene - recD_1 recD_2
[17:50:33] Fixed 2 duplicate /gene - mepM_1 mepM_2
[17:50:33] Fixed 5 duplicate /gene - sigA2_1 sigA2_2 sigA2_3 sigA2_4 sigA2_5
[17:50:33] Fixed 2 duplicate /gene - msrB_1 msrB_2
[17:50:33] Fixed 2 duplicate /gene - der_1 der_2
[17:50:33] Fixed 5 duplicate /gene - slpA_1 slpA_2 slpA_3 slpA_4 slpA_5
[17:50:33] Fixed 2 duplicate /gene - dapL_1 dapL_2
[17:50:33] Fixed 2 duplicate /gene - ppa_1 ppa_2
[17:50:33] Fixed 2 duplicate /gene - sepF_1 sepF_2
[17:50:33] Fixed 2 duplicate /gene - dnaK2_1 dnaK2_2
[17:50:33] Fixed 2 duplicate /gene - trxA_1 trxA_2
[17:50:33] Fixed 2 duplicate /gene - dnaX_1 dnaX_2
[17:50:33] Fixed 2 duplicate /gene - psbA_1 psbA_2
[17:50:33] Fixed 2 duplicate /gene - ykfA_1 ykfA_2
[17:50:33] Fixed 3 duplicate /gene - bcp_1 bcp_2 bcp_3
[17:50:33] Fixed 2 duplicate /gene - plsC_1 plsC_2
[17:50:33] Fixed 2 duplicate /gene - pcyA_1 pcyA_2
[17:50:33] Fixed 2 duplicate /gene - lip3_1 lip3_2
[17:50:33] Fixed 2 duplicate /gene - comM_1 comM_2
[17:50:33] Fixed 2 duplicate /gene - rnr_1 rnr_2
[17:50:33] Fixed 2 duplicate /gene - clpB1_1 clpB1_2
[17:50:33] Fixed 2 duplicate /gene - mnmC_1 mnmC_2
[17:50:33] Fixed 2 duplicate /gene - hisF_1 hisF_2
[17:50:33] Fixed 2 duplicate /gene - msrR_1 msrR_2
[17:50:33] Fixed 2 duplicate /gene - epsD_1 epsD_2
[17:50:33] Fixed 2 duplicate /gene - yhcR_1 yhcR_2
[17:50:33] Fixed 2 duplicate /gene - hlyD_1 hlyD_2
[17:50:33] Fixed 3 duplicate /gene - mprA_1 mprA_2 mprA_3
[17:50:33] Fixed 2 duplicate /gene - tig_1 tig_2
[17:50:33] Fixed 2 duplicate /gene - pbsA1_1 pbsA1_2
[17:50:33] Fixed 2 duplicate /gene - ftsH2_1 ftsH2_2
[17:50:33] Fixed 2 duplicate /gene - lpxB_1 lpxB_2
[17:50:33] Fixed 2 duplicate /gene - lnt_1 lnt_2
[17:50:33] Fixed 2 duplicate /gene - macB_1 macB_2
[17:50:33] Fixed 2 duplicate /gene - clpS_1 clpS_2
[17:50:33] Fixed 2 duplicate /gene - prmC_1 prmC_2
[17:50:33] Fixed 4 duplicate /gene - clpP_1 clpP_2 clpP_3 clpP_4
[17:50:33] Fixed 2 duplicate /gene - era_1 era_2
[17:50:33] Fixed 2 duplicate /gene - menJ_1 menJ_2
[17:50:33] Fixed 2 duplicate /gene - rapA_1 rapA_2
[17:50:33] Fixed 2 duplicate /gene - ndhD1_1 ndhD1_2
[17:50:33] Fixed 2 duplicate /gene - nuoL_1 nuoL_2
[17:50:33] Fixed 2 duplicate /gene - hin_1 hin_2
[17:50:33] Fixed 2 duplicate /gene - murG_1 murG_2
[17:50:33] Fixed 2 duplicate /gene - psaB_1 psaB_2
[17:50:33] Fixed 2 duplicate /gene - dfa3_1 dfa3_2
[17:50:33] Fixed 111 colliding /gene names.
[17:50:33] Adding /locus_tag identifiers
[17:50:33] Assigned 2602 locus_tags to CDS and RNA features.
[17:50:33] Writing outputs to /share/gsi2/data/www/soap-data/M2BBS/Phylogenomic/Prochlorococcus/prokka/Aaac/
[17:50:42] Generating annotation statistics file
[17:50:42] Generating Genbank and Sequin files
[17:50:42] 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\/Aaac\/AaacA01\.err -i \/share\/gsi2\/data\/www\/soap\-data\/M2BBS\/Phylogenomic\/Prochlorococcus\/prokka\/Aaac\/AaacA01\.fsa 2> /dev/null
[17:50:51] Deleting unwanted file: /share/gsi2/data/www/soap-data/M2BBS/Phylogenomic/Prochlorococcus/prokka/Aaac/errorsummary.val
[17:50:51] Deleting unwanted file: /share/gsi2/data/www/soap-data/M2BBS/Phylogenomic/Prochlorococcus/prokka/Aaac/AaacA01.dr
[17:50:51] Deleting unwanted file: /share/gsi2/data/www/soap-data/M2BBS/Phylogenomic/Prochlorococcus/prokka/Aaac/AaacA01.fixedproducts
[17:50:51] Deleting unwanted file: /share/gsi2/data/www/soap-data/M2BBS/Phylogenomic/Prochlorococcus/prokka/Aaac/AaacA01.ecn
[17:50:51] Deleting unwanted file: /share/gsi2/data/www/soap-data/M2BBS/Phylogenomic/Prochlorococcus/prokka/Aaac/AaacA01.val
[17:50:51] Repairing broken .GBK output that tbl2asn produces...
[17:50:51] Running: sed 's/COORDINATES: profile/COORDINATES:profile/' < \/share\/gsi2\/data\/www\/soap\-data\/M2BBS\/Phylogenomic\/Prochlorococcus\/prokka\/Aaac\/AaacA01\.gbf > \/share\/gsi2\/data\/www\/soap\-data\/M2BBS\/Phylogenomic\/Prochlorococcus\/prokka\/Aaac\/AaacA01\.gbk
[17:50:51] Deleting unwanted file: /share/gsi2/data/www/soap-data/M2BBS/Phylogenomic/Prochlorococcus/prokka/Aaac/AaacA01.gbf
[17:50:51] Output files:
[17:50:51] /share/gsi2/data/www/soap-data/M2BBS/Phylogenomic/Prochlorococcus/prokka/Aaac/AaacA01.log
[17:50:51] /share/gsi2/data/www/soap-data/M2BBS/Phylogenomic/Prochlorococcus/prokka/Aaac/AaacA01.fna
[17:50:51] /share/gsi2/data/www/soap-data/M2BBS/Phylogenomic/Prochlorococcus/prokka/Aaac/AaacA01.gff
[17:50:51] /share/gsi2/data/www/soap-data/M2BBS/Phylogenomic/Prochlorococcus/prokka/Aaac/AaacA01.faa
[17:50:51] /share/gsi2/data/www/soap-data/M2BBS/Phylogenomic/Prochlorococcus/prokka/Aaac/AaacA01.ffn
[17:50:51] /share/gsi2/data/www/soap-data/M2BBS/Phylogenomic/Prochlorococcus/prokka/Aaac/AaacA01.tbl
[17:50:51] /share/gsi2/data/www/soap-data/M2BBS/Phylogenomic/Prochlorococcus/prokka/Aaac/AaacA01.fsa
[17:50:51] /share/gsi2/data/www/soap-data/M2BBS/Phylogenomic/Prochlorococcus/prokka/Aaac/AaacA01.tsv
[17:50:51] /share/gsi2/data/www/soap-data/M2BBS/Phylogenomic/Prochlorococcus/prokka/Aaac/AaacA01.txt
[17:50:51] /share/gsi2/data/www/soap-data/M2BBS/Phylogenomic/Prochlorococcus/prokka/Aaac/AaacA01.sqn
[17:50:51] /share/gsi2/data/www/soap-data/M2BBS/Phylogenomic/Prochlorococcus/prokka/Aaac/AaacA01.err
[17:50:51] /share/gsi2/data/www/soap-data/M2BBS/Phylogenomic/Prochlorococcus/prokka/Aaac/AaacA01.gbk
[17:50:51] Annotation finished successfully.
[17:50:51] Walltime used: 6.52 minutes
[17:50:51] If you use this result please cite the Prokka paper:
[17:50:51] Seemann T (2014) Prokka: rapid prokaryotic genome annotation. Bioinformatics. 30(14):2068-9.
[17:50:51] Type 'prokka --citation' for more details.
[17:50:51] Share and enjoy!