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tseemann / prokka

:zap: :aquarius: Rapid prokaryotic genome annotation
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gbf file deleted #405

Closed olga216 closed 5 years ago

olga216 commented 5 years ago

Dear Torsten,

I run the Prokka’s version 1.13, but, the .gbf file was deleted. I installed Prokka on Ubuntu using the command "brew install brewsci/bio/prokka". I thought something was wrong with my tbl2asn version "25.7", but it seems to be the last version. Also, the fasta headers look like this:

c_001 c_002 c_003

I appreciate if someone could help me to find out what is causing that .gbf got deleted.

Bellow you will see the .log output.

[12:13:34] This is prokka 1.13 [12:13:34] Written by Torsten Seemann torsten.seemann@gmail.com [12:13:34] Homepage is https://github.com/tseemann/prokka [12:13:34] Local time is Thu Aug 8 12:13:34 2019 [12:13:34] You are olga [12:13:34] Operating system is linux [12:13:34] You have BioPerl 1.007002 [12:13:34] System has 28 cores. [12:13:34] Will use maximum of 8 cores. [12:13:34] Annotating as >>> Bacteria <<< [12:13:34] Generating locus_tag from 'M043S1.fasta' contents. [12:13:34] Setting --locustag MHEPLBDB from MD5 61e95bdbfefdc1e877873357a01c45f6 [12:13:34] Creating new output folder: M043S1 [12:13:34] Running: mkdir -p M043S1 [12:13:34] Using filename prefix: PROKKA_08082019.XXX [12:13:34] Setting HMMER_NCPU=1 [12:13:34] Writing log to: M043S1/PROKKA_08082019.log [12:13:34] Command: /home/linuxbrew/.linuxbrew/bin/prokka M043S1.fasta --kingdom Bacteria --outdir M043S1 [12:13:34] Appending to PATH: /home/linuxbrew/.linuxbrew/Cellar/prokka/1.13/bin [12:13:34] Looking for 'aragorn' - found /home/linuxbrew/.linuxbrew/bin/aragorn [12:13:34] Determined aragorn version is 1.2 [12:13:34] Looking for 'barrnap' - found /home/linuxbrew/.linuxbrew/bin/barrnap [12:13:35] Determined barrnap version is 0.9 [12:13:35] Looking for 'blastp' - found /home/linuxbrew/.linuxbrew/bin/blastp [12:13:35] Determined blastp version is 2.9 [12:13:35] Looking for 'cmpress' - found /home/linuxbrew/.linuxbrew/bin/cmpress [12:13:35] Determined cmpress version is 1.1 [12:13:35] Looking for 'cmscan' - found /home/linuxbrew/.linuxbrew/bin/cmscan [12:13:35] Determined cmscan version is 1.1 [12:13:35] Looking for 'egrep' - found /bin/egrep [12:13:35] Looking for 'find' - found /usr/bin/find [12:13:35] Looking for 'grep' - found /bin/grep [12:13:35] Looking for 'hmmpress' - found /home/linuxbrew/.linuxbrew/bin/hmmpress [12:13:35] Determined hmmpress version is 3.2 [12:13:35] Looking for 'hmmscan' - found /home/linuxbrew/.linuxbrew/bin/hmmscan [12:13:35] Determined hmmscan version is 3.2 [12:13:35] Looking for 'java' - found /usr/bin/java [12:13:35] Looking for 'less' - found /home/linuxbrew/.linuxbrew/bin/less [12:13:35] Looking for 'makeblastdb' - found /home/linuxbrew/.linuxbrew/bin/makeblastdb [12:13:35] Determined makeblastdb version is 2.9 [12:13:35] Looking for 'minced' - found /home/linuxbrew/.linuxbrew/bin/minced [12:13:35] Determined minced version is 4.0 [12:13:35] Looking for 'parallel' - found /home/linuxbrew/.linuxbrew/bin/parallel [12:13:35] Determined parallel version is 20190722 [12:13:35] Looking for 'prodigal' - found /home/linuxbrew/.linuxbrew/bin/prodigal [12:13:35] Determined prodigal version is 2.6 [12:13:35] Looking for 'prokka-genbank_to_fasta_db' - found /home/linuxbrew/.linuxbrew/bin/prokka-genbank_to_fasta_db [12:13:35] Looking for 'sed' - found /bin/sed [12:13:35] Looking for 'tbl2asn' - found /home/linuxbrew/.linuxbrew/bin/tbl2asn [12:13:35] Determined tbl2asn version is 25.7 [12:13:35] Using genetic code table 11. [12:13:35] Loading and checking input file: M043S1.fasta [12:13:35] Wrote 267 contigs totalling 4673225 bp. [12:13:35] Predicting tRNAs and tmRNAs [12:13:35] Running: aragorn -l -gc11 -w M043S1\/PROKKA_08082019.fna [12:13:36] 1 tRNA-Asp [1402,1482] 40 (atc) [12:13:36] 2 tRNA-Asp [1476,1556] 40 (atc) [12:13:36] 1 tRNA-Arg c[8823,8898] 35 (cct) [12:13:36] 2 tRNA-Val [48574,48645] 33 (tac) [12:13:36] 1 tRNA-Met [23938,24011] 35 (cat) [12:13:36] 1 tRNA-Leu [5993,6077] 36 (tag) [12:13:36] 1 tRNA-Val c[16002,16075] 35 (gac) [12:13:36] 1 tRNA-Asn [25297,25370] 34 (gtt) [12:13:36] 1 tRNA-Gly [46532,46602] 33 (tcc) [12:13:36] 1 tmRNA [7121,7508] 101,154 ANNIVPFARKAAPVAA** [12:13:36] 1 tRNA-Asn [3315,3407] 40 (att) [12:13:36] 1 tRNA-Ser c[41755,41849] 36 (gct) [12:13:36] 1 tRNA-Ala [72534,72606] 34 (tgc) [12:13:36] 1 tRNA-Asp c[1741,1822] 40 (atc) [12:13:36] 1 tRNA-Asp [23853,23931] 40 (atc) [12:13:36] 1 tRNA-Pro c[9784,9858] 35 (tgg) [12:13:36] 2 tRNA-Ser c[10520,10606] 36 (tga) [12:13:36] 1 tRNA-Ala [9901,9973] 34 (ggc) [12:13:36] 1 tRNA-Tyr [2841,2925] 35 (gta) [12:13:36] 2 tRNA-Thr [2934,3005] 33 (ggt) [12:13:36] 1 tRNA-Asp [12941,13022] 40 (atc) [12:13:36] 2 tRNA-Asn [13015,13096] 40 (att) [12:13:36] 1 tRNA-Glu [53458,53530] 35 (ttc) [12:13:36] 2 tRNA-Gly [56812,56883] 33 (ccc) [12:13:36] 1 tRNA-Thr [3849,3920] 33 (tgt) [12:13:36] 1 tRNA-Gln [5823,5895] 33 (ttg) [12:13:37] 1 tRNA-Asn [1218,1299] 40 (att) [12:13:37] 1 tRNA-Ser c[9172,9260] 36 (cga) [12:13:37] 2 tRNA-Leu c[38765,38850] 36 (cag) [12:13:37] 1 tRNA-Leu [6409,6494] 34 (taa) [12:13:37] 1 tRNA-His c[7084,7157] 34 (gtg) [12:13:37] 1 tRNA-Phe [5601,5673] 34 (gaa) [12:13:37] 1 tRNA-Trp [4120,4192] 34 (cca) [12:13:37] 1 tRNA-Asp [2545,2623] 40 (atc) [12:13:37] 2 tRNA-Asn [2616,2697] 40 (att) [12:13:37] 1 tRNA-Thr c[2156,2227] 33 (cgt) [12:13:37] 1 tRNA-Pyl c[14589,14677] 35 (cta) [12:13:37] 1 tRNA-Asn c[4510,4591] 40 (att) [12:13:37] 2 tRNA-Asn c[4584,4665] 40 (att) [12:13:37] 1 tRNA-Ser [3576,3664] 36 (gga) [12:13:37] 1 tRNA-Arg c[25887,25960] 35 (acg) [12:13:37] 1 tRNA-Met c[10890,10962] 34 (cat) [12:13:37] 1 tRNA-Met [17804,17877] 35 (cat) [12:13:37] 2 tRNA-Pro [20886,20961] 36 (ggg) [12:13:37] 1 tRNA-Asn [28,109] 40 (att) [12:13:37] 1 tRNA-Leu c[8898,8982] 35 (caa) [12:13:37] 2 tRNA-Lys c[23152,23223] 33 (ttt) [12:13:37] 3 tRNA-Arg [27463,27537] 35 (tct) [12:13:37] 1 tRNA-Pro c[3588,3663] 36 (cgg) [12:13:37] 1 tRNA-Leu c[989,1070] 35 (gag) [12:13:37] 1 tRNA-Asn c[52,133] 40 (att) [12:13:37] 1 tRNA-Ala c[194,268] 35 (cgc) [12:13:37] 2 tRNA-Gly c[5313,5384] 33 (gcc) [12:13:37] 1 tRNA-Asp [4380,4455] 36 (gtc) [12:13:37] 1 tRNA-Arg c[282,356] 35 (ccg) [12:13:37] Found 55 tRNAs [12:13:37] Predicting Ribosomal RNAs [12:13:37] Running Barrnap with 8 threads [12:13:38] Found 0 rRNAs [12:13:38] Skipping ncRNA search, enable with --rfam if desired. [12:13:38] Total of 54 tRNA + rRNA features [12:13:38] Searching for CRISPR repeats [12:13:39] Found 0 CRISPRs [12:13:39] Predicting coding sequences [12:13:39] Contigs total 4673225 bp, so using single mode [12:13:39] Running: prodigal -i M043S1\/PROKKA_08082019.fna -c -m -g 11 -p single -f sco -q [12:13:42] Excluding CDS which overlaps existing RNA (tRNA) at c_101:2817..2954 on + strand [12:13:42] Excluding CDS which overlaps existing RNA (tRNA) at c_231:8961..9836 on - strand [12:13:43] Excluding CDS which overlaps existing RNA (tRNA) at c_267:259..420 on + strand [12:13:43] Found 4329 CDS [12:13:43] Connecting features back to sequences [12:13:43] Not using genus-specific database. Try --usegenus to enable it. [12:13:43] Annotating CDS, please be patient. [12:13:43] Will use 8 CPUs for similarity searching. [12:13:43] There are still 4329 unannotated CDS left (started with 4329) [12:13:43] Will use blast to search against /home/linuxbrew/.linuxbrew/Cellar/prokka/1.13/bin/../db/kingdom/Bacteria/sprot with 8 CPUs [12:13:43] Running: cat M043S1\/sprot.faa | parallel --gnu --plain -j 8 --block 79917 --recstart '>' --pipe blastp -query - -db /home/linuxbrew/.linuxbrew/Cellar/prokka/1.13/bin/../db/kingdom/Bacteria/sprot -evalue 1e-06 -num_threads 1 -num_descriptions 1 -num_alignments 1 -seg no > M043S1\/sprot.blast 2> /dev/null [12:14:11] Modify product: Uncharacterized zinc protease Rv2782c => putative zinc protease [12:14:11] Modify product: Uncharacterized zinc protease Rv2782c => putative zinc protease [12:14:11] Modify product: Uncharacterized protein YciO => putative protein YciO [12:14:11] Modify product: Uncharacterized glycosyltransferase sll0501 => putative glycosyltransferase [12:14:11] Modify product: UPF0194 membrane protein YbhG => hypothetical protein [12:14:11] Modify product: Uncharacterized oxidoreductase Rv2298 => putative oxidoreductase [12:14:11] Modify product: Membrane-associated protein slr1513 => Membrane-associated protein [12:14:11] Modify product: Probable phospholipid ABC transporter permease protein MlaE => putative phospholipid ABC transporter permease protein MlaE [12:14:11] Modify product: Putative universal stress protein SA1532 => Putative universal stress protein [12:14:11] Modify product: Uncharacterized ABC transporter ATP-binding protein YknY => putative ABC transporter ATP-binding protein YknY [12:14:11] Modify product: Probable transcriptional regulatory protein aq_1575 => putative transcriptional regulatory protein [12:14:11] Modify product: Uncharacterized protein Rv1708 => putative protein [12:14:11] Modify product: Uncharacterized glycosyltransferase Rv0539 => putative glycosyltransferase [12:14:11] Modify product: Probable peptidyl-prolyl cis-trans isomerase => putative peptidyl-prolyl cis-trans isomerase [12:14:11] Modify product: Probable cytochrome c oxidase subunit 3 => putative cytochrome c oxidase subunit 3 [12:14:11] Modify product: Phycocyanobilin lyase CpcT homolog => Phycocyanobilin lyase CpcT [12:14:11] Modify product: Uncharacterized oxidoreductase SA2266 => putative oxidoreductase [12:14:11] Modify product: ABC transporter ATP-binding/permease protein Rv1747 => ABC transporter ATP-binding/permease protein [12:14:11] Modify product: Thylakoid-associated single-stranded DNA-binding protein slr1034 => Thylakoid-associated single-stranded DNA-binding protein [12:14:11] Modify product: UPF0754 membrane protein SA1664 => hypothetical protein [12:14:11] Modify product: Probable L,D-transpeptidase YnhG => putative L,D-transpeptidase YnhG [12:14:11] Modify product: Probable 2-phosphosulfolactate phosphatase => putative 2-phosphosulfolactate phosphatase [12:14:11] Modify product: Uncharacterized oxidoreductase Rv2298 => putative oxidoreductase [12:14:11] Modify product: Uncharacterized HTH-type transcriptional regulator YbaQ => putative HTH-type transcriptional regulator YbaQ [12:14:11] Modify product: Uncharacterized protein Rv2886c => putative protein [12:14:11] Modify product: Putative phosphoribosyl transferase MT0597 => Putative phosphoribosyl transferase [12:14:11] Modify product: Probable ribonucleotide transport ATP-binding protein mkl => putative ribonucleotide transport ATP-binding protein mkl [12:14:11] Modify product: UPF0053 inner membrane protein YoaE => hypothetical protein [12:14:11] Modify product: Uncharacterized protein Rv1829 => putative protein [12:14:11] Modify product: Probable glutaredoxin ssr2061 => putative glutaredoxin [12:14:11] Modify product: Probable type I restriction enzyme BthVORF4518P M protein => putative type I restriction enzymeP M protein [12:14:11] Modify product: Probable undecaprenyl-phosphate N-acetylglucosaminyl 1-phosphate transferase => putative undecaprenyl-phosphate N-acetylglucosaminyl 1-phosphate transferase [12:14:11] Modify product: Carbon dioxide-concentrating mechanism protein CcmK homolog 4 => Carbon dioxide-concentrating mechanism protein CcmK [12:14:11] Modify product: Putative lipoprotein NMB1126/NMB1164 => Putative lipoprotein/NMB1164 [12:14:11] Modify product: Ribonuclease TTHA0252 => Ribonuclease [12:14:11] Modify product: Probable ferredoxin/ferredoxin--NADP reductase => putative ferredoxin/ferredoxin--NADP reductase [12:14:11] Modify product: Uncharacterized sugar epimerase YhfK => putative sugar epimerase YhfK [12:14:11] Modify product: Epimerase family protein SA0724 => Epimerase family protein [12:14:11] Modify product: Uncharacterized glycosyltransferase sll0501 => putative glycosyltransferase [12:14:11] Modify product: Uncharacterized protein Rv2232 => putative protein [12:14:11] Modify product: Probable cysteine desulfurase => putative cysteine desulfurase [12:14:11] Modify product: Probable ATP-dependent transporter SufC => putative ATP-dependent transporter SufC [12:14:11] Modify product: Putative universal stress protein SA1532 => Putative universal stress protein [12:14:11] Modify product: Uncharacterized protein BHWA1_00569 => putative protein [12:14:11] Modify product: Uncharacterized oxidoreductase CzcO => putative oxidoreductase CzcO [12:14:11] Modify product: UPF0176 protein lpg2838 => hypothetical protein [12:14:11] Modify product: Uncharacterized glycosyltransferase sll0501 => putative glycosyltransferase [12:14:11] Modify product: Probable protein kinase UbiB => putative protein kinase UbiB [12:14:11] Modify product: Leu/Ile/Val-binding protein homolog 3 => Leu/Ile/Val-binding protein [12:14:11] Modify product: Probable molybdenum cofactor guanylyltransferase => putative molybdenum cofactor guanylyltransferase [12:14:11] Modify product: Uncharacterized FAD-linked oxidoreductase Rv2280 => putative FAD-linked oxidoreductase [12:14:11] Modify product: Uncharacterized HTH-type transcriptional regulator YbaQ => putative HTH-type transcriptional regulator YbaQ [12:14:11] Modify product: Uncharacterized protein Rv2102 => putative protein [12:14:11] Modify product: Uncharacterized protein HI_1162 => putative protein [12:14:11] Modify product: Putative cystathionine beta-synthase Rv1077 => Putative cystathionine beta-synthase [12:14:11] Modify product: Uncharacterized HTH-type transcriptional regulator YbaQ => putative HTH-type transcriptional regulator YbaQ [12:14:11] Modify product: Uncharacterized GTP-binding protein YjiA => putative GTP-binding protein YjiA [12:14:11] Modify product: Probable protein kinase UbiB => putative protein kinase UbiB [12:14:12] Modify product: Uncharacterized glycosyltransferase Rv0539 => putative glycosyltransferase [12:14:12] Modify product: Uncharacterized transporter Rv2685 => putative transporter [12:14:12] Modify product: Probable protein kinase UbiB => putative protein kinase UbiB [12:14:12] Modify product: Uncharacterized protein YacP => putative protein YacP [12:14:12] Modify product: Probable sulfate transporter Rv1739c => putative sulfate transporter [12:14:12] Modify product: Probable DNA double-strand break repair Rad50 ATPase => putative DNA double-strand break repair Rad50 ATPase [12:14:12] Modify product: Sulfurtransferase Alvin_2599 => Sulfurtransferase [12:14:12] Modify product: Uncharacterized zinc protease Rv2782c => putative zinc protease [12:14:12] Modify product: Phage shock protein A homolog => Phage shock protein A [12:14:12] Modify product: Uncharacterized oxidoreductase YdgJ => putative oxidoreductase YdgJ [12:14:12] Modify product: UPF0047 protein Rv2556c => hypothetical protein [12:14:12] Modify product: Uncharacterized glycosyltransferase Rv1514c => putative glycosyltransferase [12:14:12] Modify product: Probable adenylyltransferase/sulfurtransferase MoeZ => putative adenylyltransferase/sulfurtransferase MoeZ [12:14:12] Modify product: Uncharacterized membrane protein Rv3479 => putative membrane protein [12:14:12] Modify product: Uncharacterized ABC transporter ATP-binding protein YxlF => putative ABC transporter ATP-binding protein YxlF [12:14:12] Modify product: Vitamin K epoxide reductase homolog => Vitamin K epoxide reductase [12:14:12] Modify product: Probable dolichyl-phosphate-mannose--protein mannosyltransferase => putative dolichyl-phosphate-mannose--protein mannosyltransferase [12:14:12] Modify product: Maf-like protein Rv3282 => Maf-like protein [12:14:12] Modify product: Uncharacterized protein YcbX => putative protein YcbX [12:14:12] Modify product: Uncharacterized ABC transporter ATP-binding protein YxlF => putative ABC transporter ATP-binding protein YxlF [12:14:12] Modify product: Uncharacterized protein MT2060 => putative protein [12:14:12] Modify product: Uncharacterized signaling protein PA1727 => putative signaling protein [12:14:12] Modify product: Uncharacterized oxidoreductase MSMEG_1603/MSMEI_1564 => putative oxidoreductase/MSMEI_1564 [12:14:12] Modify product: Putative transport protein Rv0205 => Putative transport protein [12:14:12] Modify product: Bifunctional protein Rv2228c => Bifunctional protein [12:14:12] Modify product: Probable tRNA-dihydrouridine synthase => putative tRNA-dihydrouridine synthase [12:14:12] Modify product: Probable fused nickel transport protein LarMN => putative fused nickel transport protein LarMN [12:14:12] Modify product: Probable multidrug resistance ABC transporter ATP-binding/permease protein YheI => putative multidrug resistance ABC transporter ATP-binding/permease protein YheI [12:14:12] Modify product: Uncharacterized ABC transporter ATP-binding protein YxlF => putative ABC transporter ATP-binding protein YxlF [12:14:12] Modify product: Uncharacterized FAD-linked oxidoreductase Rv2280 => putative FAD-linked oxidoreductase [12:14:12] Modify product: Phosphate-specific transport system accessory protein PhoU homolog => Phosphate-specific transport system accessory protein PhoU [12:14:12] Modify product: Probable peptidoglycan glycosyltransferase FtsW => putative peptidoglycan glycosyltransferase FtsW [12:14:12] Modify product: Leu/Ile/Val-binding protein homolog 3 => Leu/Ile/Val-binding protein [12:14:12] Modify product: Uncharacterized ABC transporter ATP-binding protein YknY => putative ABC transporter ATP-binding protein YknY [12:14:12] Modify product: Putative anti-sigma factor antagonist TM_1442 => Putative anti-sigma factor antagonist [12:14:12] Modify product: Uncharacterized MFS-type transporter YhjX => putative MFS-type transporter YhjX [12:14:12] Modify product: Probable CtpA-like serine protease => putative CtpA-like serine protease [12:14:12] Modify product: Probable glutaredoxin ssr2061 => putative glutaredoxin [12:14:12] Modify product: Uncharacterized protein BHWA1_00569 => putative protein [12:14:12] Modify product: Uncharacterized methyltransferase YcgJ => putative methyltransferase YcgJ [12:14:12] Modify product: Putative O-methyltransferase MSMEG_5073/MSMEI_4947 => Putative O-methyltransferase/MSMEI_4947 [12:14:12] Modify product: Uncharacterized protein Rv2569c => putative protein [12:14:12] Modify product: Glycogen operon protein GlgX homolog => Glycogen operon protein GlgX [12:14:12] Modify product: Phycocyanobilin lyase CpcT homolog => Phycocyanobilin lyase CpcT [12:14:12] Modify product: Putative transport protein Rv0205 => Putative transport protein [12:14:12] Modify product: Oxygen-independent coproporphyrinogen-III oxidase-like protein sll1917 => Oxygen-independent coproporphyrinogen-III oxidase-like protein [12:14:12] Modify product: Uncharacterized PIN and TRAM-domain containing protein YacL => putative PIN and TRAM-domain containing protein YacL [12:14:12] Modify product: Uncharacterized glycosyltransferase sll0501 => putative glycosyltransferase [12:14:12] Modify product: Uncharacterized FAD-linked oxidoreductase Rv2280 => putative FAD-linked oxidoreductase [12:14:12] Modify product: UPF0758 protein YsxA => hypothetical protein [12:14:12] Modify product: Probable phospholipid ABC transporter permease protein MlaE => putative phospholipid ABC transporter permease protein MlaE [12:14:12] Modify product: Putative multidrug export ATP-binding/permease protein SA1683 => Putative multidrug export ATP-binding/permease protein [12:14:12] Modify product: Probable copper-transporting ATPase PacS => putative copper-transporting ATPase PacS [12:14:12] Modify product: Uncharacterized hydrolase YxeP => putative hydrolase YxeP [12:14:12] Modify product: Probable type I restriction enzyme BthVORF4518P M protein => putative type I restriction enzymeP M protein [12:14:12] Modify product: Uncharacterized protein Rv2569c => putative protein [12:14:12] Modify product: Uncharacterized protein Rv2567 => putative protein [12:14:12] Modify product: Uncharacterized protein Rv2411c => putative protein [12:14:12] Modify product: Uncharacterized protein YloA => putative protein YloA [12:14:12] Modify product: Uncharacterized protein YqeN => putative protein YqeN [12:14:12] Modify product: Thioredoxin-like protein slr0233 => Thioredoxin-like protein [12:14:12] Modify product: UPF0194 membrane protein YbhG => hypothetical protein [12:14:12] Modify product: Probable protein kinase UbiB => putative protein kinase UbiB [12:14:12] Modify product: Uncharacterized protein alr4550 => putative protein [12:14:12] Modify product: Probable multidrug ABC transporter permease YbhR => putative multidrug ABC transporter permease YbhR [12:14:12] Modify product: UPF0276 protein CCNA_03000 => hypothetical protein [12:14:12] Modify product: Transcriptional repressor SmtB homolog => Transcriptional repressor SmtB [12:14:12] Modify product: Probable helicase HelY => putative helicase HelY [12:14:12] Modify product: 1,4-alpha-glucan branching enzyme TTHA1902 => 1,4-alpha-glucan branching enzyme [12:14:12] Modify product: Uncharacterized glycosyltransferase sll0501 => putative glycosyltransferase [12:14:12] Modify product: Bifunctional protein FolD => Bifunctional protein FolD protein [12:14:12] Modify product: Uncharacterized zinc protease Rv2782c => putative zinc protease [12:14:12] Modify product: Uncharacterized protein alr4550 => putative protein [12:14:12] Modify product: Carbon dioxide-concentrating mechanism protein CcmK homolog 1 => Carbon dioxide-concentrating mechanism protein CcmK [12:14:12] Modify product: Carbon dioxide-concentrating mechanism protein CcmK homolog 2 => Carbon dioxide-concentrating mechanism protein CcmK [12:14:12] Modify product: Putative sulfur carrier protein TM_0983 => Putative sulfur carrier protein [12:14:12] Modify product: Uncharacterized protein YisK => putative protein YisK [12:14:12] Modify product: Uncharacterized zinc protease Rv2782c => putative zinc protease [12:14:12] Modify product: NADH dehydrogenase-like protein SA0802 => NADH dehydrogenase-like protein [12:14:12] Modify product: Probable murein peptide carboxypeptidase => putative murein peptide carboxypeptidase [12:14:12] Modify product: Probable nicotinate-nucleotide pyrophosphorylase [carboxylating] => putative nicotinate-nucleotide pyrophosphorylase [carboxylating] [12:14:12] Modify product: UPF0182 protein MSMEG_1959/MSMEI_1915 => hypothetical protein [12:14:12] Modify product: Uncharacterized ABC transporter ATP-binding protein YbiT => putative ABC transporter ATP-binding protein YbiT [12:14:12] Modify product: Uncharacterized ABC transporter ATP-binding protein TM_0288 => putative ABC transporter ATP-binding protein [12:14:12] Modify product: Probable iron export permease protein FetB => putative iron export permease protein FetB [12:14:12] Modify product: Universal stress protein A homolog 2 => Universal stress protein A [12:14:12] Modify product: Uncharacterized membrane protein Rv2637 => putative membrane protein [12:14:12] Modify product: Phage shock protein A homolog => Phage shock protein A [12:14:12] Modify product: Cyclic di-GMP phosphodiesterase PA4781 => Cyclic di-GMP phosphodiesterase [12:14:12] Modify product: UPF0053 protein Rv1842c => hypothetical protein [12:14:12] Modify product: Probable doxorubicin resistance ABC transporter permease protein DrrC => putative doxorubicin resistance ABC transporter permease protein DrrC [12:14:13] Modify product: UPF0102 protein RPA0323 => hypothetical protein [12:14:13] Modify product: Probable adenylyl-sulfate kinase => putative adenylyl-sulfate kinase [12:14:13] Modify product: Uncharacterized protein Rv0502 => putative protein [12:14:13] Modify product: Uncharacterized methyltransferase YcgJ => putative methyltransferase YcgJ [12:14:13] Modify product: Probable membrane transporter protein YfcA => putative membrane transporter protein YfcA [12:14:13] Modify product: Uncharacterized MscS family protein HI_0195.1 => putative MscS family protein.1 [12:14:13] Modify product: Uncharacterized HTH-type transcriptional regulator YddM => putative HTH-type transcriptional regulator YddM [12:14:13] Modify product: Probable dual-specificity RNA methyltransferase RlmN => putative dual-specificity RNA methyltransferase RlmN [12:14:13] Modify product: UPF0053 inner membrane protein YtfL => hypothetical protein [12:14:13] Modify product: Uncharacterized protein Rv2067c => putative protein [12:14:13] Modify product: Probable murein peptide carboxypeptidase => putative murein peptide carboxypeptidase [12:14:13] Modify product: Probable L,D-transpeptidase YnhG => putative L,D-transpeptidase YnhG [12:14:13] Modify product: Uncharacterized protein Rv0628c => putative protein [12:14:13] Modify product: Probable type I restriction enzyme BthVORF4518P M protein => putative type I restriction enzymeP M protein [12:14:13] Modify product: Uncharacterized protein slr1565 => putative protein [12:14:13] Modify product: Probable 30S ribosomal protein PSRP-3 => putative 30S ribosomal protein PSRP-3 [12:14:13] Modify product: Probable manganese efflux pump MntP => putative manganese efflux pump MntP [12:14:13] Modify product: Uncharacterized protein YciH => putative protein YciH [12:14:13] Modify product: Uncharacterized protein Rv1288 => putative protein [12:14:13] Modify product: Uncharacterized protein Rv2102 => putative protein [12:14:13] Modify product: Probable ABC transporter-binding protein DR_1571 => putative ABC transporter-binding protein [12:14:13] Modify product: Uncharacterized protein HI_0933 => putative protein [12:14:13] Modify product: Probable type I restriction enzyme BthVORF4518P M protein => putative type I restriction enzymeP M protein [12:14:13] Modify product: Probable sulfate transporter Rv1739c => putative sulfate transporter [12:14:13] Modify product: Probable protein kinase UbiB => putative protein kinase UbiB [12:14:13] Modify product: Probable type I restriction enzyme BthVORF4518P M protein => putative type I restriction enzymeP M protein [12:14:13] Modify product: Uncharacterized protein YccU => putative protein YccU [12:14:13] Modify product: Uncharacterized protein alr4550 => putative protein [12:14:13] Cleaned 177 /product names [12:14:13] Deleting unwanted file: M043S1/sprot.faa [12:14:13] Deleting unwanted file: M043S1/sprot.blast [12:14:13] There are still 2374 unannotated CDS left (started with 4329) [12:14:13] Will use hmmer3 to search against /home/linuxbrew/.linuxbrew/Cellar/prokka/1.13/bin/../db/hmm/HAMAP.hmm with 8 CPUs [12:14:13] Running: cat M043S1\/HAMAP.hmm.faa | parallel --gnu --plain -j 8 --block 33139 --recstart '>' --pipe hmmscan --noali --notextw --acc -E 1e-06 --cpu 1 /home/linuxbrew/.linuxbrew/Cellar/prokka/1.13/bin/../db/hmm/HAMAP.hmm /dev/stdin > M043S1\/HAMAP.hmm.hmmer3 2> /dev/null [12:14:26] Deleting unwanted file: M043S1/HAMAP.hmm.faa [12:14:26] Deleting unwanted file: M043S1/HAMAP.hmm.hmmer3 [12:14:26] Labelling remaining 2253 proteins as 'hypothetical protein' [12:14:26] Possible /pseudo 'Chaperone protein DnaK' at c_042 position 6935 [12:14:26] Possible /pseudo 'Serine/threonine-protein kinase pkn1' at c_047 position 27205 [12:14:26] Possible /pseudo 'putative zinc protease' at c_049 position 26685 [12:14:26] Possible /pseudo 'Phosphoserine phosphatase 1' at c_059 position 921 [12:14:26] Possible /pseudo 'Gas vesicle structural protein' at c_138 position 2298 [12:14:26] Possible /pseudo 'ATP-dependent Clp protease proteolytic subunit' at c_140 position 4851 [12:14:26] Possible /pseudo 'Carbon dioxide-concentrating mechanism protein CcmK ' at c_142 position 58483 [12:14:26] Possible /pseudo 'NAD(P) transhydrogenase subunit alpha' at c_160 position 4297 [12:14:26] Possible /pseudo 'putative protein' at c_182 position 1184 [12:14:26] Possible /pseudo 'putative protein' at c_182 position 2268 [12:14:26] Possible /pseudo 'Protein TolB' at c_195 position 7461 [12:14:26] Possible /pseudo 'Linear gramicidin synthase subunit D' at c_206 position 8000 [12:14:26] Possible /pseudo 'Linear gramicidin synthase subunit D' at c_206 position 15958 [12:14:26] Possible /pseudo 'Linear gramicidin synthase subunit D' at c_206 position 19200 [12:14:26] Possible /pseudo 'Putative fluoride ion transporter CrcB' at c_264 position 8174 [12:14:26] Found 1421 unique /gene codes. [12:14:26] Fixed 2 duplicate /gene - rpsA_1 rpsA_2 [12:14:26] Fixed 2 duplicate /gene - pyrD_1 pyrD_2 [12:14:26] Fixed 3 duplicate /gene - livF_1 livF_2 livF_3 [12:14:26] Fixed 2 duplicate /gene - pstB3_1 pstB3_2 [12:14:26] Fixed 2 duplicate /gene - tadA_1 tadA_2 [12:14:26] Fixed 2 duplicate /gene - sasA_1 sasA_2 [12:14:26] Fixed 2 duplicate /gene - cca_1 cca_2 [12:14:26] Fixed 2 duplicate /gene - ltxB_1 ltxB_2 [12:14:26] Fixed 2 duplicate /gene - folE_1 folE_2 [12:14:26] Fixed 10 duplicate /gene - smc_1 smc_2 smc_3 smc_4 smc_5 smc_6 smc_7 smc_8 smc_9 smc_10 [12:14:26] Fixed 3 duplicate /gene - queD_1 queD_2 queD_3 [12:14:26] Fixed 2 duplicate /gene - mdtA_1 mdtA_2 [12:14:26] Fixed 2 duplicate /gene - murC_1 murC_2 [12:14:26] Fixed 2 duplicate /gene - ltrA_1 ltrA_2 [12:14:26] Fixed 2 duplicate /gene - htpX_1 htpX_2 [12:14:26] Fixed 3 duplicate /gene - pyrE_1 pyrE_2 pyrE_3 [12:14:26] Fixed 2 duplicate /gene - cysE_1 cysE_2 [12:14:26] Fixed 3 duplicate /gene - cmpB_1 cmpB_2 cmpB_3 [12:14:26] Fixed 2 duplicate /gene - mlaE_1 mlaE_2 [12:14:26] Fixed 2 duplicate /gene - pta_1 pta_2 [12:14:26] Fixed 2 duplicate /gene - pstS_1 pstS_2 [12:14:26] Fixed 4 duplicate /gene - mshA_1 mshA_2 mshA_3 mshA_4 [12:14:26] Fixed 2 duplicate /gene - galE_1 galE_2 [12:14:26] Fixed 8 duplicate /gene - dnaJ_1 dnaJ_2 dnaJ_3 dnaJ_4 dnaJ_5 dnaJ_6 dnaJ_7 dnaJ_8 [12:14:26] Fixed 2 duplicate /gene - hhoA_1 hhoA_2 [12:14:26] Fixed 3 duplicate /gene - dapL_1 dapL_2 dapL_3 [12:14:26] Fixed 3 duplicate /gene - ntcA_1 ntcA_2 ntcA_3 [12:14:26] Fixed 3 duplicate /gene - dpnM_1 dpnM_2 dpnM_3 [12:14:26] Fixed 2 duplicate /gene - mnmE_1 mnmE_2 [12:14:26] Fixed 2 duplicate /gene - znuC_1 znuC_2 [12:14:26] Fixed 4 duplicate /gene - era_1 era_2 era_3 era_4 [12:14:26] Fixed 2 duplicate /gene - queE_1 queE_2 [12:14:26] Fixed 2 duplicate /gene - arsA_1 arsA_2 [12:14:26] Fixed 2 duplicate /gene - der_1 der_2 [12:14:26] Fixed 3 duplicate /gene - livH_1 livH_2 livH_3 [12:14:26] Fixed 3 duplicate /gene - relK_1 relK_2 relK_3 [12:14:26] Fixed 2 duplicate /gene - hisC_1 hisC_2 [12:14:26] Fixed 2 duplicate /gene - arsH_1 arsH_2 [12:14:26] Fixed 3 duplicate /gene - hsdR_1 hsdR_2 hsdR_3 [12:14:26] Fixed 2 duplicate /gene - yknY_1 yknY_2 [12:14:26] Fixed 4 duplicate /gene - clpP_1 clpP_2 clpP_3 clpP_4 [12:14:26] Fixed 2 duplicate /gene - lptD_1 lptD_2 [12:14:26] Fixed 3 duplicate /gene - glnQ_1 glnQ_2 glnQ_3 [12:14:26] Fixed 3 duplicate /gene - hrp1_1 hrp1_2 hrp1_3 [12:14:26] Fixed 9 duplicate /gene - pipB2_1 pipB2_2 pipB2_3 pipB2_4 pipB2_5 pipB2_6 pipB2_7 pipB2_8 pipB2_9 [12:14:26] Fixed 2 duplicate /gene - thrB_1 thrB_2 [12:14:26] Fixed 2 duplicate /gene - cphB_1 cphB_2 [12:14:26] Fixed 2 duplicate /gene - mscK_1 mscK_2 [12:14:26] Fixed 3 duplicate /gene - resE_1 resE_2 resE_3 [12:14:26] Fixed 2 duplicate /gene - cugP_1 cugP_2 [12:14:26] Fixed 2 duplicate /gene - ccmK_1 ccmK_2 [12:14:26] Fixed 2 duplicate /gene - ubiG_1 ubiG_2 [12:14:26] Fixed 2 duplicate /gene - braC_1 braC_2 [12:14:26] Fixed 4 duplicate /gene - bcp_1 bcp_2 bcp_3 bcp_4 [12:14:26] Fixed 3 duplicate /gene - kfoC_1 kfoC_2 kfoC_3 [12:14:26] Fixed 2 duplicate /gene - hhaIM_1 hhaIM_2 [12:14:26] Fixed 3 duplicate /gene - cobN_1 cobN_2 cobN_3 [12:14:26] Fixed 2 duplicate /gene - cefD_1 cefD_2 [12:14:26] Fixed 2 duplicate /gene - tkt_1 tkt_2 [12:14:26] Fixed 2 duplicate /gene - bchI_1 bchI_2 [12:14:26] Fixed 2 duplicate /gene - ecfT_1 ecfT_2 [12:14:26] Fixed 2 duplicate /gene - fbp_1 fbp_2 [12:14:26] Fixed 2 duplicate /gene - recJ_1 recJ_2 [12:14:26] Fixed 4 duplicate /gene - gltI_1 gltI_2 gltI_3 gltI_4 [12:14:26] Fixed 2 duplicate /gene - barA_1 barA_2 [12:14:26] Fixed 2 duplicate /gene - cmdD_1 cmdD_2 [12:14:26] Fixed 2 duplicate /gene - yecS_1 yecS_2 [12:14:26] Fixed 2 duplicate /gene - merA_1 merA_2 [12:14:26] Fixed 2 duplicate /gene - rimI_1 rimI_2 [12:14:26] Fixed 2 duplicate /gene - crtI_1 crtI_2 [12:14:26] Fixed 2 duplicate /gene - nasF_1 nasF_2 [12:14:26] Fixed 4 duplicate /gene - pipB_1 pipB_2 pipB_3 pipB_4 [12:14:26] Fixed 3 duplicate /gene - sigA2_1 sigA2_2 sigA2_3 [12:14:26] Fixed 2 duplicate /gene - amtB_1 amtB_2 [12:14:26] Fixed 2 duplicate /gene - metXA_1 metXA_2 [12:14:26] Fixed 2 duplicate /gene - mgtA_1 mgtA_2 [12:14:26] Fixed 3 duplicate /gene - gvpA_1 gvpA_2 gvpA_3 [12:14:26] Fixed 2 duplicate /gene - ydjZ_1 ydjZ_2 [12:14:26] Fixed 4 duplicate /gene - bacA_1 bacA_2 bacA_3 bacA_4 [12:14:26] Fixed 2 duplicate /gene - pcrA_1 pcrA_2 [12:14:26] Fixed 2 duplicate /gene - clpS_1 clpS_2 [12:14:26] Fixed 2 duplicate /gene - hspA_1 hspA_2 [12:14:26] Fixed 2 duplicate /gene - hpnP_1 hpnP_2 [12:14:26] Fixed 2 duplicate /gene - dauC_1 dauC_2 [12:14:26] Fixed 2 duplicate /gene - ligA_1 ligA_2 [12:14:26] Fixed 2 duplicate /gene - yodJ_1 yodJ_2 [12:14:26] Fixed 4 duplicate /gene - ftsH4_1 ftsH4_2 ftsH4_3 ftsH4_4 [12:14:26] Fixed 2 duplicate /gene - malP_1 malP_2 [12:14:26] Fixed 2 duplicate /gene - patA_1 patA_2 [12:14:26] Fixed 2 duplicate /gene - hisD_1 hisD_2 [12:14:26] Fixed 2 duplicate /gene - wcaJ_1 wcaJ_2 [12:14:26] Fixed 2 duplicate /gene - cheA_1 cheA_2 [12:14:26] Fixed 2 duplicate /gene - pds_1 pds_2 [12:14:26] Fixed 2 duplicate /gene - pntA_1 pntA_2 [12:14:26] Fixed 2 duplicate /gene - rnd_1 rnd_2 [12:14:26] Fixed 2 duplicate /gene - kaiC_1 kaiC_2 [12:14:26] Fixed 2 duplicate /gene - desV_1 desV_2 [12:14:26] Fixed 3 duplicate /gene - tldD_1 tldD_2 tldD_3 [12:14:26] Fixed 2 duplicate /gene - aroB_1 aroB_2 [12:14:26] Fixed 2 duplicate /gene - ubiE_1 ubiE_2 [12:14:26] Fixed 4 duplicate /gene - ftsH_1 ftsH_2 ftsH_3 ftsH_4 [12:14:26] Fixed 2 duplicate /gene - glgA_1 glgA_2 [12:14:26] Fixed 4 duplicate /gene - recF_1 recF_2 recF_3 recF_4 [12:14:26] Fixed 2 duplicate /gene - rip3_1 rip3_2 [12:14:26] Fixed 4 duplicate /gene - fabG_1 fabG_2 fabG_3 fabG_4 [12:14:26] Fixed 3 duplicate /gene - pstA_1 pstA_2 pstA_3 [12:14:26] Fixed 2 duplicate /gene - cpdA_1 cpdA_2 [12:14:26] Fixed 2 duplicate /gene - amiC_1 amiC_2 [12:14:26] Fixed 2 duplicate /gene - rsbW_1 rsbW_2 [12:14:26] Fixed 2 duplicate /gene - pcxA_1 pcxA_2 [12:14:26] Fixed 2 duplicate /gene - yhaV_1 yhaV_2 [12:14:26] Fixed 2 duplicate /gene - lpxD_1 lpxD_2 [12:14:26] Fixed 2 duplicate /gene - yefM_1 yefM_2 [12:14:26] Fixed 2 duplicate /gene - leuB_1 leuB_2 [12:14:26] Fixed 2 duplicate /gene - gmd_1 gmd_2 [12:14:26] Fixed 5 duplicate /gene - tolB_1 tolB_2 tolB_3 tolB_4 tolB_5 [12:14:26] Fixed 2 duplicate /gene - iscS_1 iscS_2 [12:14:26] Fixed 2 duplicate /gene - haeIIIM_1 haeIIIM_2 [12:14:26] Fixed 2 duplicate /gene - pyrC_1 pyrC_2 [12:14:26] Fixed 5 duplicate /gene - spkC_1 spkC_2 spkC_3 spkC_4 spkC_5 [12:14:26] Fixed 3 duplicate /gene - pspA_1 pspA_2 pspA_3 [12:14:26] Fixed 2 duplicate /gene - petE_1 petE_2 [12:14:26] Fixed 3 duplicate /gene - soj_1 soj_2 soj_3 [12:14:26] Fixed 2 duplicate /gene - apaH_1 apaH_2 [12:14:26] Fixed 3 duplicate /gene - carC_1 carC_2 carC_3 [12:14:26] Fixed 2 duplicate /gene - garA_1 garA_2 [12:14:26] Fixed 2 duplicate /gene - fbiC_1 fbiC_2 [12:14:26] Fixed 8 duplicate /gene - vapC_1 vapC_2 vapC_3 vapC_4 vapC_5 vapC_6 vapC_7 vapC_8 [12:14:26] Fixed 2 duplicate /gene - suhB_1 suhB_2 [12:14:26] Fixed 2 duplicate /gene - ycgJ_1 ycgJ_2 [12:14:26] Fixed 2 duplicate /gene - pimB_1 pimB_2 [12:14:26] Fixed 3 duplicate /gene - apcD_1 apcD_2 apcD_3 [12:14:26] Fixed 3 duplicate /gene - sbpA_1 sbpA_2 sbpA_3 [12:14:26] Fixed 2 duplicate /gene - speA_1 speA_2 [12:14:26] Fixed 3 duplicate /gene - lapB_1 lapB_2 lapB_3 [12:14:26] Fixed 2 duplicate /gene - higB2_1 higB2_2 [12:14:26] Fixed 2 duplicate /gene - spkF_1 spkF_2 [12:14:26] Fixed 3 duplicate /gene - kch_1 kch_2 kch_3 [12:14:26] Fixed 11 duplicate /gene - yrrB_1 yrrB_2 yrrB_3 yrrB_4 yrrB_5 yrrB_6 yrrB_7 yrrB_8 yrrB_9 yrrB_10 yrrB_11 [12:14:26] Fixed 2 duplicate /gene - act_1 act_2 [12:14:26] Fixed 2 duplicate /gene - nadK_1 nadK_2 [12:14:26] Fixed 2 duplicate /gene - walR_1 walR_2 [12:14:26] Fixed 2 duplicate /gene - plsC_1 plsC_2 [12:14:26] Fixed 2 duplicate /gene - mazF9_1 mazF9_2 [12:14:26] Fixed 4 duplicate /gene - cmpD_1 cmpD_2 cmpD_3 cmpD_4 [12:14:26] Fixed 3 duplicate /gene - sphX_1 sphX_2 sphX_3 [12:14:26] Fixed 13 duplicate /gene - pkn1_1 pkn1_2 pkn1_3 pkn1_4 pkn1_5 pkn1_6 pkn1_7 pkn1_8 pkn1_9 pkn1_10 pkn1_11 pkn1_12 pkn1_13 [12:14:26] Fixed 2 duplicate /gene - cpcS_1 cpcS_2 [12:14:26] Fixed 2 duplicate /gene - glgM_1 glgM_2 [12:14:26] Fixed 2 duplicate /gene - pstC_1 pstC_2 [12:14:26] Fixed 2 duplicate /gene - prpC_1 prpC_2 [12:14:26] Fixed 3 duplicate /gene - menG_1 menG_2 menG_3 [12:14:26] Fixed 3 duplicate /gene - higB_1 higB_2 higB_3 [12:14:26] Fixed 2 duplicate /gene - gsiA_1 gsiA_2 [12:14:26] Fixed 3 duplicate /gene - drrA_1 drrA_2 drrA_3 [12:14:26] Fixed 2 duplicate /gene - relJ_1 relJ_2 [12:14:26] Fixed 3 duplicate /gene - afsR_1 afsR_2 afsR_3 [12:14:26] Fixed 3 duplicate /gene - dfa5_1 dfa5_2 dfa5_3 [12:14:26] Fixed 7 duplicate /gene - spkB_1 spkB_2 spkB_3 spkB_4 spkB_5 spkB_6 spkB_7 [12:14:26] Fixed 3 duplicate /gene - bshA_1 bshA_2 bshA_3 [12:14:26] Fixed 2 duplicate /gene - pilT_1 pilT_2 [12:14:26] Fixed 3 duplicate /gene - algA_1 algA_2 algA_3 [12:14:26] Fixed 3 duplicate /gene - kaiB_1 kaiB_2 kaiB_3 [12:14:26] Fixed 2 duplicate /gene - pacL_1 pacL_2 [12:14:26] Fixed 2 duplicate /gene - ssuA_1 ssuA_2 [12:14:26] Fixed 4 duplicate /gene - dnaK_1 dnaK_2 dnaK_3 dnaK_4 [12:14:26] Fixed 2 duplicate /gene - hemB_1 hemB_2 [12:14:26] Fixed 2 duplicate /gene - walK_1 walK_2 [12:14:26] Fixed 2 duplicate /gene - hemH_1 hemH_2 [12:14:26] Fixed 2 duplicate /gene - spkA_1 spkA_2 [12:14:26] Fixed 2 duplicate /gene - nhaS3_1 nhaS3_2 [12:14:26] Fixed 2 duplicate /gene - cysA_1 cysA_2 [12:14:26] Fixed 2 duplicate /gene - rnr_1 rnr_2 [12:14:26] Fixed 2 duplicate /gene - garR_1 garR_2 [12:14:26] Fixed 3 duplicate /gene - wbbL_1 wbbL_2 wbbL_3 [12:14:26] Fixed 2 duplicate /gene - gcvT_1 gcvT_2 [12:14:26] Fixed 5 duplicate /gene - mprA_1 mprA_2 mprA_3 mprA_4 mprA_5 [12:14:26] Fixed 4 duplicate /gene - ppsA_1 ppsA_2 ppsA_3 ppsA_4 [12:14:26] Fixed 2 duplicate /gene - msrA_1 msrA_2 [12:14:26] Fixed 2 duplicate /gene - ykfA_1 ykfA_2 [12:14:26] Fixed 2 duplicate /gene - recQ_1 recQ_2 [12:14:26] Fixed 2 duplicate /gene - grpE_1 grpE_2 [12:14:26] Fixed 2 duplicate /gene - desA_1 desA_2 [12:14:26] Fixed 2 duplicate /gene - pyk_1 pyk_2 [12:14:26] Fixed 4 duplicate /gene - hsdS_1 hsdS_2 hsdS_3 hsdS_4 [12:14:26] Fixed 2 duplicate /gene - lnt_1 lnt_2 [12:14:26] Fixed 2 duplicate /gene - psbA_1 psbA_2 [12:14:26] Fixed 2 duplicate /gene - mepM_1 mepM_2 [12:14:26] Fixed 2 duplicate /gene - clpB1_1 clpB1_2 [12:14:26] Fixed 2 duplicate /gene - estB_1 estB_2 [12:14:26] Fixed 2 duplicate /gene - ilvE_1 ilvE_2 [12:14:26] Fixed 3 duplicate /gene - yxlF_1 yxlF_2 yxlF_3 [12:14:26] Fixed 2 duplicate /gene - rpoC_1 rpoC_2 [12:14:26] Fixed 9 duplicate /gene - ycf3_1 ycf3_2 ycf3_3 ycf3_4 ycf3_5 ycf3_6 ycf3_7 ycf3_8 ycf3_9 [12:14:26] Fixed 2 duplicate /gene - chlB_1 chlB_2 [12:14:26] Fixed 2 duplicate /gene - pglI_1 pglI_2 [12:14:26] Fixed 2 duplicate /gene - sipT_1 sipT_2 [12:14:26] Fixed 2 duplicate /gene - dnaK2_1 dnaK2_2 [12:14:26] Fixed 2 duplicate /gene - fabF_1 fabF_2 [12:14:26] Fixed 2 duplicate /gene - def_1 def_2 [12:14:26] Fixed 2 duplicate /gene - eryG_1 eryG_2 [12:14:26] Fixed 4 duplicate /gene - lptB_1 lptB_2 lptB_3 lptB_4 [12:14:26] Fixed 2 duplicate /gene - sppA_1 sppA_2 [12:14:26] Fixed 4 duplicate /gene - ndhD1_1 ndhD1_2 ndhD1_3 ndhD1_4 [12:14:26] Fixed 2 duplicate /gene - clpC_1 clpC_2 [12:14:26] Fixed 2 duplicate /gene - crcB_1 crcB_2 [12:14:26] Fixed 2 duplicate /gene - rfbD_1 rfbD_2 [12:14:26] Fixed 3 duplicate /gene - mdtC_1 mdtC_2 mdtC_3 [12:14:26] Fixed 3 duplicate /gene - sir_1 sir_2 sir_3 [12:14:26] Fixed 2 duplicate /gene - dppB_1 dppB_2 [12:14:26] Fixed 4 duplicate /gene - rapA_1 rapA_2 rapA_3 rapA_4 [12:14:26] Fixed 2 duplicate /gene - corA_1 corA_2 [12:14:26] Fixed 5 duplicate /gene - lgrD_1 lgrD_2 lgrD_3 lgrD_4 lgrD_5 [12:14:26] Fixed 2 duplicate /gene - macA_1 macA_2 [12:14:26] Fixed 2 duplicate /gene - map_1 map_2 [12:14:26] Fixed 2 duplicate /gene - cpcT2_1 cpcT2_2 [12:14:26] Fixed 2 duplicate /gene - trxB_1 trxB_2 [12:14:26] Fixed 2 duplicate /gene - lytC_1 lytC_2 [12:14:26] Fixed 3 duplicate /gene - yhhT_1 yhhT_2 yhhT_3 [12:14:26] Fixed 2 duplicate /gene - atpG_1 atpG_2 [12:14:26] Fixed 2 duplicate /gene - radD_1 radD_2 [12:14:26] Fixed 2 duplicate /gene - thrC_1 thrC_2 [12:14:26] Fixed 2 duplicate /gene - rnc_1 rnc_2 [12:14:26] Fixed 2 duplicate /gene - cysK1_1 cysK1_2 [12:14:26] Fixed 2 duplicate /gene - rfbE_1 rfbE_2 [12:14:26] Fixed 5 duplicate /gene - ubiB_1 ubiB_2 ubiB_3 ubiB_4 ubiB_5 [12:14:26] Fixed 2 duplicate /gene - gltB_1 gltB_2 [12:14:26] Fixed 5 duplicate /gene - yhdJ_1 yhdJ_2 yhdJ_3 yhdJ_4 yhdJ_5 [12:14:26] Fixed 2 duplicate /gene - nrtA_1 nrtA_2 [12:14:26] Fixed 2 duplicate /gene - psaA_1 psaA_2 [12:14:26] Fixed 2 duplicate /gene - hypA_1 hypA_2 [12:14:26] Fixed 2 duplicate /gene - cmpC_1 cmpC_2 [12:14:26] Fixed 2 duplicate /gene - dnaE_1 dnaE_2 [12:14:26] Fixed 2 duplicate /gene - dhbF_1 dhbF_2 [12:14:26] Fixed 2 duplicate /gene - fusA_1 fusA_2 [12:14:26] Fixed 2 duplicate /gene - rppH_1 rppH_2 [12:14:26] Fixed 2 duplicate /gene - cobD_1 cobD_2 [12:14:26] Fixed 2 duplicate /gene - nox_1 nox_2 [12:14:26] Fixed 2 duplicate /gene - dac_1 dac_2 [12:14:26] Fixed 2 duplicate /gene - hypB_1 hypB_2 [12:14:26] Fixed 2 duplicate /gene - ynhG_1 ynhG_2 [12:14:26] Fixed 4 duplicate /gene - trxA_1 trxA_2 trxA_3 trxA_4 [12:14:26] Fixed 2 duplicate /gene - crhR_1 crhR_2 [12:14:26] Fixed 2 duplicate /gene - ndbB_1 ndbB_2 [12:14:26] Fixed 2 duplicate /gene - gph_1 gph_2 [12:14:26] Fixed 2 duplicate /gene - sphR_1 sphR_2 [12:14:26] Fixed 2 duplicate /gene - glnA_1 glnA_2 [12:14:26] Fixed 3 duplicate /gene - mazF_1 mazF_2 mazF_3 [12:14:26] Fixed 3 duplicate /gene - higB-1_1 higB-1_2 higB-1_3 [12:14:26] Fixed 3 duplicate /gene - phoR_1 phoR_2 phoR_3 [12:14:26] Fixed 5 duplicate /gene - bepA_1 bepA_2 bepA_3 bepA_4 bepA_5 [12:14:26] Fixed 2 duplicate /gene - dnaX_1 dnaX_2 [12:14:26] Fixed 2 duplicate /gene - gyrA_1 gyrA_2 [12:14:26] Fixed 2 duplicate /gene - nuoL_1 nuoL_2 [12:14:26] Fixed 2 duplicate /gene - rluD_1 rluD_2 [12:14:26] Fixed 3 duplicate /gene - cmpR_1 cmpR_2 cmpR_3 [12:14:26] Fixed 4 duplicate /gene - macB_1 macB_2 macB_3 macB_4 [12:14:26] Fixed 2 duplicate /gene - uvrC_1 uvrC_2 [12:14:26] Fixed 2 duplicate /gene - lpxB_1 lpxB_2 [12:14:26] Fixed 3 duplicate /gene - ybaQ_1 ybaQ_2 ybaQ_3 [12:14:26] Fixed 2 duplicate /gene - rsbV_1 rsbV_2 [12:14:26] Fixed 3 duplicate /gene - petH_1 petH_2 petH_3 [12:14:26] Fixed 2 duplicate /gene - prkC_1 prkC_2 [12:14:26] Fixed 2 duplicate /gene - proA_1 proA_2 [12:14:26] Fixed 2 duplicate /gene - surA_1 surA_2 [12:14:26] Fixed 265 colliding /gene names. [12:14:26] Adding /locus_tag identifiers [12:14:26] Assigned 4384 locus_tags to CDS and RNA features. [12:14:26] Writing outputs to M043S1/ [12:14:27] Generating annotation statistics file [12:14:27] Generating Genbank and Sequin files [12:14:27] Running: tbl2asn -V b -a r10k -l paired-ends -M n -N 1 -y 'Annotated using prokka 1.13 from https://github.com/tseemann/prokka' -Z M043S1\/PROKKA_08082019.err -i M043S1\/PROKKA_08082019.fsa 2> /dev/null [12:14:33] Deleting unwanted file: M043S1/errorsummary.val [12:14:33] Deleting unwanted file: M043S1/PROKKA_08082019.dr [12:14:33] Deleting unwanted file: M043S1/PROKKA_08082019.fixedproducts [12:14:33] Deleting unwanted file: M043S1/PROKKA_08082019.ecn [12:14:33] Deleting unwanted file: M043S1/PROKKA_08082019.val [12:14:33] Repairing broken .GBK output that tbl2asn produces... [12:14:33] Running: sed 's/COORDINATES: profile/COORDINATES:profile/' < M043S1\/PROKKA_08082019.gbf > M043S1\/PROKKA_08082019.gbk [12:14:33] Deleting unwanted file: M043S1/PROKKA_08082019.gbf [12:14:33] Output files: [12:14:33] M043S1/PROKKA_08082019.faa [12:14:33] M043S1/PROKKA_08082019.sqn [12:14:33] M043S1/PROKKA_08082019.err [12:14:33] M043S1/PROKKA_08082019.gbk [12:14:33] M043S1/PROKKA_08082019.fsa [12:14:33] M043S1/PROKKA_08082019.ffn [12:14:33] M043S1/PROKKA_08082019.log [12:14:33] M043S1/PROKKA_08082019.gff [12:14:33] M043S1/PROKKA_08082019.tsv [12:14:33] M043S1/PROKKA_08082019.tbl [12:14:33] M043S1/PROKKA_08082019.txt [12:14:33] M043S1/PROKKA_08082019.fna [12:14:33] Annotation finished successfully. [12:14:33] Walltime used: 0.98 minutes [12:14:33] If you use this result please cite the Prokka paper: [12:14:33] Seemann T (2014) Prokka: rapid prokaryotic genome annotation. Bioinformatics. 30(14):2068-9. [12:14:33] Type 'prokka --citation' for more details. [12:14:33] Share and enjoy!

tseemann commented 5 years ago

The .gbf file is renamed to .gbk which is more standard. See M043S1/PROKKA_08082019.gbk