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:zap: :aquarius: Rapid prokaryotic genome annotation
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Could not run command: tbl2asn #463

Closed avonm closed 4 years ago

avonm commented 4 years ago

Hi,

I have installed the latest version of Prokka and I get the following error: [19:53:29] Could not run command: tbl2asn -V b -a r10k -l paired-ends -M n -N 1 -y 'Annotated using prokka 1.14.6 from https://github.com/tseemann/prokka' -Z E562_annotation\/E562_genome.err -i E562_annotation\/E562_genome.fsa 2> /dev/null (base) mib113392i:Unicycler avm$ prokka --version prokka 1.14.6

Complete log: [19:47:27] This is prokka 1.14.6 [19:47:27] Written by Torsten Seemann torsten.seemann@gmail.com [19:47:27] Homepage is https://github.com/tseemann/prokka [19:47:27] Local time is Thu Feb 20 19:47:27 2020 [19:47:27] You are avm [19:47:27] Operating system is darwin [19:47:27] You have BioPerl 1.007002 [19:47:28] System has 2 cores. [19:47:28] Option --cpu asked for 8 cores, but system only has 2 [19:47:28] Will use maximum of 2 cores. [19:47:28] Annotating as >>> Bacteria <<< [19:47:28] Generating locus_tag from 'E562_unicycler_assembly.fa' contents. [19:47:28] Setting --locustag JDMPMOBF from MD5 3d6968bffa78f20e6171f10ed7f4fb2f [19:47:28] Creating new output folder: E562_annotation [19:47:28] Running: mkdir -p E562_annotation [19:47:28] Using filename prefix: E562_genome.XXX [19:47:28] Setting HMMER_NCPU=1 [19:47:28] Writing log to: E562_annotation/E562_genome.log [19:47:28] Command: /Users/avm/anaconda3/bin/prokka --outdir E562_annotation --prefix E562_genome --species Escherichia coli E562_unicycler_assembly.fa [19:47:28] Appending to PATH: /Users/avm/anaconda3/bin [19:47:28] Looking for 'aragorn' - found /Users/avm/homebrew/bin/aragorn [19:47:28] Determined aragorn version is 001002 from 'ARAGORN v1.2.38 Dean Laslett' [19:47:28] Looking for 'barrnap' - found /Users/avm/homebrew/bin/barrnap [19:47:28] Determined barrnap version is 000009 from 'barrnap 0.9' [19:47:28] Looking for 'blastp' - found /Users/avm/homebrew/bin/blastp [19:47:28] Determined blastp version is 002009 from 'blastp: 2.9.0+' [19:47:28] Looking for 'cmpress' - found /Users/avm/homebrew/bin/cmpress [19:47:28] Determined cmpress version is 001001 from '# INFERNAL 1.1.2 (July 2016)' [19:47:28] Looking for 'cmscan' - found /Users/avm/homebrew/bin/cmscan [19:47:28] Determined cmscan version is 001001 from '# INFERNAL 1.1.2 (July 2016)' [19:47:28] Looking for 'egrep' - found /usr/bin/egrep [19:47:28] Looking for 'find' - found /usr/bin/find [19:47:28] Looking for 'grep' - found /usr/bin/grep [19:47:28] Looking for 'hmmpress' - found /Users/avm/homebrew/bin/hmmpress [19:47:28] Determined hmmpress version is 003002 from '# HMMER 3.2.1 (June 2018); http://hmmer.org/' [19:47:28] Looking for 'hmmscan' - found /Users/avm/homebrew/bin/hmmscan [19:47:28] Determined hmmscan version is 003002 from '# HMMER 3.2.1 (June 2018); http://hmmer.org/' [19:47:28] Looking for 'java' - found /Users/avm/anaconda3/bin/java [19:47:28] Looking for 'makeblastdb' - found /Users/avm/homebrew/bin/makeblastdb [19:47:28] Determined makeblastdb version is 002009 from 'makeblastdb: 2.9.0+' [19:47:28] Looking for 'minced' - found /Users/avm/homebrew/bin/minced [19:47:28] Determined minced version is 004000 from 'minced 0.4.0' [19:47:28] Looking for 'parallel' - found /Users/avm/homebrew/bin/parallel [19:47:29] Determined parallel version is 20190822 from 'GNU parallel 20190822' [19:47:29] Looking for 'prodigal' - found /Users/avm/homebrew/bin/prodigal [19:47:29] Determined prodigal version is 002006 from 'Prodigal V2.6.3: February, 2016' [19:47:29] Looking for 'prokka-genbank_to_fasta_db' - found /Users/avm/anaconda3/bin/prokka-genbank_to_fasta_db [19:47:29] Looking for 'sed' - found /usr/bin/sed [19:47:29] Looking for 'tbl2asn' - found /Users/avm/homebrew/bin/tbl2asn [19:47:29] Determined tbl2asn version is 025007 from 'tbl2asn 25.7 arguments:' [19:47:29] Using genetic code table 11. [19:47:29] Loading and checking input file: E562_unicycler_assembly.fa [19:47:29] Wrote 69 contigs totalling 5331471 bp. [19:47:29] Predicting tRNAs and tmRNAs [19:47:29] Running: aragorn -l -gc11 -w E562_annotation\/E562_genome.fna [19:47:32] 1 tRNA-Arg [186919,186995] 35 (tct) [19:47:32] 2 tRNA-Gln c[305560,305634] 33 (ctg) [19:47:32] 3 tRNA-Gln c[305672,305746] 33 (ctg) [19:47:32] 4 tRNA-Met c[305794,305870] 35 (cat) [19:47:32] 5 tRNA-Gln c[305886,305960] 33 (ttg) [19:47:32] 6 tRNA-Gln c[305995,306069] 33 (ttg) [19:47:32] 7 tRNA-Gln c[306104,306178] 33 (ttg) [19:47:32] 8 tRNA-Leu c[306202,306286] 35 (tag) [19:47:32] 9 tRNA-Met c[306295,306371] 35 (cat) [19:47:32] 10 tRNA-Lys [383928,384003] 34 (ttt) [19:47:32] 11 tRNA-Val [384140,384215] 34 (tac) [19:47:32] 12 tRNA-Lys [384220,384295] 34 (ttt) [19:47:32] 13 tRNA-Val [384347,384422] 34 (tac) [19:47:32] 14 tRNA-Lys [384427,384502] 34 (ttt) [19:47:32] 15 tRNA-Lys [384649,384724] 34 (ttt) [19:47:32] 16 tRNA-Lys [384857,384932] 34 (ttt) [19:47:32] 17 tRNA-Ser c[549126,549213] 35 (gga) [19:47:32] 18 tRNA-Ser c[655045,655132] 35 (tga) [19:47:32] 19 tRNA-Ser c[722616,722703] 35 (gga) [19:47:32] 20 tRNA-Tyr c[924377,924461] 35 (gta) [19:47:32] 21 tRNA-Tyr c[924496,924580] 35 (gta) [19:47:32] 22 tRNA-Met [966793,966868] 34 (cat) [19:47:32] 23 tRNA-Lys [966870,966946] 35 (ttt) [19:47:32] 24 tRNA-Thr [966949,967024] 34 (tgt) [19:47:32] 25 tRNA-Gly [967028,967102] 34 (tcc) [19:47:32] 26 tRNA-Val [1417954,1418030] 35 (gac) [19:47:32] 27 tRNA-Val [1418035,1418111] 35 (gac) [19:47:32] 28 tRNA-Leu c[1662071,1662157] 35 (taa) [19:47:32] 29 tRNA-Cys c[1662170,1662243] 33 (gca) [19:47:32] 30 tRNA-Gly c[1662298,1662373] 34 (gcc) [19:47:32] 31 tRNA-Ser c[1712716,1712805] 35 (cga) [19:47:32] 32 tRNA-Asn [1713797,1713872] 34 (gtt) [19:47:32] 33 tRNA-Asn c[1753691,1753766] 34 (gtt) [19:47:32] 34 tRNA-Asn [1755515,1755590] 34 (gtt) [19:47:32] 35 tRNA-Asn [1757924,1757999] 34 (gtt) [19:47:32] 36 tRNA-Pro [1995230,1995306] 35 (ggg) [19:47:32] 37 tRNA-Arg [2180242,2180316] 34 (cct) [19:47:32] 38 tRNA-Ala c[2229580,2229655] 34 (ggc) [19:47:32] 39 tRNA-Ala c[2229695,2229770] 34 (ggc) [19:47:32] 40 tRNA-Val [2232470,2232545] 34 (tac) [19:47:32] 41 tRNA-Val [2232592,2232667] 34 (tac) [19:47:32] 42 tRNA-Val [2232714,2232789] 34 (tac) [19:47:32] 43 tRNA-Lys [2232794,2232869] 34 (ttt) [19:47:32] 44 tRNA-Glu c[2427298,2427373] 35 (ttc) [19:47:32] 45 tmRNA [2453411,2453773] 90,125 ANDENYALAA** [19:47:32] 46 tRNA-Ser [2524476,2524568] 35 (gct) [19:47:32] 47 tRNA-Arg [2524572,2524648] 35 (acg) [19:47:32] 48 tRNA-Arg [2524847,2524923] 35 (acg) [19:47:32] 49 tRNA-Arg [2524986,2525062] 35 (acg) [19:47:32] 50 tRNA-Arg [2525261,2525337] 35 (acg) [19:47:32] 51 tRNA-Met [2557363,2557438] 34 (cat) [19:47:32] 52 tRNA-Met [2659877,2659953] 35 (cat) [19:47:32] 53 tRNA-Met [2659987,2660063] 35 (cat) [19:47:32] 54 tRNA-Met [2660097,2660173] 35 (cat) [19:47:32] 55 tRNA-Gly c[2719772,2719845] 33 (ccc) [19:47:32] 56 tRNA-Phe [2830984,2831059] 34 (gaa) [19:47:32] 57 tRNA-Met [2974543,2974618] 34 (cat) [19:47:32] 58 tRNA-Met c[3083979,3084055] 35 (cat) [19:47:32] 59 tRNA-Leu c[3087838,3087924] 35 (gag) [19:47:32] 60 tRNA-Thr c[3181733,3181808] 34 (ggt) [19:47:32] 61 tRNA-Ala c[3185111,3185186] 34 (tgc) [19:47:32] 62 tRNA-Ile c[3185229,3185305] 35 (gat) [19:47:32] 63 tRNA-Pro c[3502032,3502108] 35 (cgg) [19:47:32] 1 tRNA-SeC [88614,88708] 35 (tca) [19:47:32] 2 tRNA-Glu [195711,195786] 35 (ttc) [19:47:32] 3 tRNA-Asp [199148,199224] 35 (gtc) [19:47:32] 4 tRNA-Trp [199233,199308] 34 (cca) [19:47:32] 5 tRNA-Arg [234596,234672] 35 (ccg) [19:47:32] 6 tRNA-His [234731,234806] 34 (gtg) [19:47:32] 7 tRNA-Leu [234827,234913] 35 (cag) [19:47:32] 8 tRNA-Pro [234956,235032] 35 (tgg) [19:47:32] 9 tRNA-Ile [287479,287555] 35 (gat) [19:47:32] 10 tRNA-Ala [287598,287673] 34 (tgc) [19:47:32] 11 tRNA-Glu [455335,455410] 35 (ttc) [19:47:32] 12 tRNA-Thr [462183,462258] 34 (tgt) [19:47:32] 13 tRNA-Tyr [462267,462351] 35 (gta) [19:47:32] 14 tRNA-Gly [462468,462542] 34 (tcc) [19:47:32] 15 tRNA-Thr [462549,462624] 34 (ggt) [19:47:32] 16 tRNA-Glu [496548,496623] 35 (ttc) [19:47:32] 17 tRNA-Phe c[641991,642066] 34 (gaa) [19:47:32] 18 tRNA-Gly [671234,671309] 34 (gcc) [19:47:32] 19 tRNA-Gly [671467,671542] 34 (gcc) [19:47:32] 20 tRNA-Gly [671578,671653] 34 (gcc) [19:47:32] 1 tRNA-Thr c[44499,44574] 34 (cgt) [19:47:32] 2 tRNA-Asp c[84150,84226] 35 (gtc) [19:47:32] 3 tRNA-Asp c[92374,92450] 35 (gtc) [19:47:32] 4 tRNA-Ala c[95793,95868] 34 (tgc) [19:47:32] 5 tRNA-Ile c[95911,95987] 35 (gat) [19:47:32] 6 tRNA-Leu [359291,359377] 35 (cag) [19:47:32] 7 tRNA-Leu [359406,359492] 35 (cag) [19:47:32] 8 tRNA-Leu [359527,359613] 35 (cag) [19:47:32] 9 tRNA-Leu c[399680,399764] 35 (caa) [19:47:32] 1 tRNA-Ser [5298,5378] 38 (gga) [19:47:32] 1 tRNA-Thr [48634,48705] 34 (ggt) [19:47:32] Found 94 tRNAs [19:47:32] Predicting Ribosomal RNAs [19:47:32] Running Barrnap with 2 threads [19:47:36] 1 1 2423994 5S ribosomal RNA [19:47:36] 2 1 2424202 23S ribosomal RNA [19:47:36] 3 1 2427546 16S ribosomal RNA [19:47:36] 4 1 3181581 5S ribosomal RNA [19:47:36] 5 1 3181826 5S ribosomal RNA [19:47:36] 6 1 3182034 23S ribosomal RNA [19:47:36] 7 1 3185375 16S ribosomal RNA [19:47:36] 8 2 194087 16S ribosomal RNA [19:47:36] 9 2 195982 23S ribosomal RNA [19:47:36] 10 2 198980 5S ribosomal RNA [19:47:36] 11 2 285872 16S ribosomal RNA [19:47:36] 12 2 287859 23S ribosomal RNA [19:47:36] 13 2 290857 5S ribosomal RNA [19:47:36] 14 2 453711 16S ribosomal RNA [19:47:36] 15 2 455606 23S ribosomal RNA [19:47:36] 16 2 458604 5S ribosomal RNA [19:47:36] 17 2 494924 16S ribosomal RNA [19:47:36] 18 2 496819 23S ribosomal RNA [19:47:36] 19 2 499817 5S ribosomal RNA [19:47:36] 20 3 92508 5S ribosomal RNA [19:47:36] 21 3 92716 23S ribosomal RNA [19:47:36] 22 3 96057 16S ribosomal RNA [19:47:36] Found 22 rRNAs [19:47:36] Skipping ncRNA search, enable with --rfam if desired. [19:47:36] Total of 115 tRNA + rRNA features [19:47:36] Searching for CRISPR repeats [19:47:37] CRISPR1 1 2461833 with 12 spacers [19:47:37] CRISPR2 1 2616627 with 5 spacers [19:47:37] Found 2 CRISPRs [19:47:37] Predicting coding sequences [19:47:37] Contigs total 5331471 bp, so using single mode [19:47:37] Running: prodigal -i E562_annotation\/E562_genome.fna -c -m -g 11 -p single -f sco -q [19:47:47] Excluding CDS which overlaps existing RNA (tRNA) at 1:548605..549276 on + strand [19:47:48] Excluding CDS which overlaps existing RNA (tRNA) at 1:966695..966802 on + strand [19:47:49] Excluding CDS which overlaps existing RNA (rRNA) at 1:2427645..2427899 on - strand [19:47:50] Excluding CDS which overlaps existing RNA (tRNA) at 1:3181656..3181979 on + strand [19:47:50] Excluding CDS which overlaps existing RNA (rRNA) at 1:3185474..3185728 on - strand [19:47:50] Excluding CDS which overlaps existing RNA (rRNA) at 2:195271..195525 on + strand [19:47:50] Excluding CDS which overlaps existing RNA (rRNA) at 2:287056..287310 on + strand [19:47:51] Excluding CDS which overlaps existing RNA (rRNA) at 2:454895..455149 on + strand [19:47:51] Excluding CDS which overlaps existing RNA (rRNA) at 2:496108..496362 on + strand [19:47:51] Excluding CDS which overlaps existing RNA (rRNA) at 3:96156..96410 on - strand [19:47:51] Excluding CDS which overlaps existing RNA (tRNA) at 3:399661..399885 on + strand [19:47:51] Excluding CDS which overlaps existing RNA (tRNA) at 4:5368..5613 on + strand [19:47:51] Excluding CDS which overlaps existing RNA (tRNA) at 6:48082..49455 on - strand [19:47:51] Found 5076 CDS [19:47:51] Connecting features back to sequences [19:47:51] Not using genus-specific database. Try --usegenus to enable it. [19:47:51] Annotating CDS, please be patient. [19:47:51] Will use 2 CPUs for similarity searching. [19:47:52] There are still 5076 unannotated CDS left (started with 5076) [19:47:52] Will use blast to search against /Users/avm/anaconda3/db/kingdom/Bacteria/IS with 2 CPUs [19:47:52] Running: cat E562_annotation\/E562_genome.IS.tmp.5923.faa | parallel --gnu --plain -j 2 --block 393907 --recstart '>' --pipe blastp -query - -db /Users/avm/anaconda3/db/kingdom/Bacteria/IS -evalue 1e-30 -qcov_hsp_perc 90 -num_threads 1 -num_descriptions 1 -num_alignments 1 -seg no > E562_annotation\/E562_genome.IS.tmp.5923.blast 2> /dev/null [19:48:41] Deleting unwanted file: E562_annotation/E562_genome.IS.tmp.5923.faa [19:48:41] Deleting unwanted file: E562_annotation/E562_genome.IS.tmp.5923.blast [19:48:43] There are still 4932 unannotated CDS left (started with 5076) [19:48:43] Will use blast to search against /Users/avm/anaconda3/db/kingdom/Bacteria/AMR with 2 CPUs [19:48:43] Running: cat E562_annotation\/E562_genome.AMR.tmp.5923.faa | parallel --gnu --plain -j 2 --block 385667 --recstart '>' --pipe blastp -query - -db /Users/avm/anaconda3/db/kingdom/Bacteria/AMR -evalue 9.99999999999999e-301 -qcov_hsp_perc 90 -num_threads 1 -num_descriptions 1 -num_alignments 1 -seg no > E562_annotation\/E562_genome.AMR.tmp.5923.blast 2> /dev/null [19:49:22] Deleting unwanted file: E562_annotation/E562_genome.AMR.tmp.5923.faa [19:49:22] Deleting unwanted file: E562_annotation/E562_genome.AMR.tmp.5923.blast [19:49:24] There are still 4932 unannotated CDS left (started with 5076) [19:49:24] Will use blast to search against /Users/avm/anaconda3/db/kingdom/Bacteria/sprot with 2 CPUs [19:49:24] Running: cat E562_annotation\/E562_genome.sprot.tmp.5923.faa | parallel --gnu --plain -j 2 --block 385667 --recstart '>' --pipe blastp -query - -db /Users/avm/anaconda3/db/kingdom/Bacteria/sprot -evalue 1e-09 -qcov_hsp_perc 80 -num_threads 1 -num_descriptions 1 -num_alignments 1 -seg no > E562_annotation\/E562_genome.sprot.tmp.5923.blast 2> /dev/null [19:52:27] Modify product: Uncharacterized protein YdfR => putative protein YdfR [19:52:27] Modify product: UPF0060 membrane protein YnfA => hypothetical protein [19:52:27] Modify product: UPF0482 protein YnfB => hypothetical protein [19:52:27] Modify product: Uncharacterized protein YnfD => putative protein YnfD [19:52:27] Modify product: Probable dimethyl sulfoxide reductase chain YnfF => putative dimethyl sulfoxide reductase chain YnfF [19:52:27] Modify product: Uncharacterized oxidoreductase YdgJ => putative oxidoreductase YdgJ [19:52:27] Modify product: Uncharacterized protein YnhF => putative protein YnhF [19:52:27] Modify product: Uncharacterized HTH-type transcriptional regulator YahB => putative HTH-type transcriptional regulator YahB [19:52:27] Modify product: Uncharacterized protein YdhT => putative protein YdhT [19:52:27] Modify product: Uncharacterized ferredoxin-like protein YdhX => putative ferredoxin-like protein YdhX [19:52:27] Modify product: Uncharacterized protein YdhW => putative protein YdhW [19:52:27] Modify product: Uncharacterized oxidoreductase YdhV => putative oxidoreductase YdhV [19:52:27] Modify product: Uncharacterized ferredoxin-like protein YdhY => putative ferredoxin-like protein YdhY [19:52:27] Modify product: Probable L,D-transpeptidase YnhG => putative L,D-transpeptidase YnhG [19:52:27] Modify product: Probable ATP-dependent transporter SufC => putative ATP-dependent transporter SufC [19:52:27] Modify product: Uncharacterized protein HI_1163 => putative protein [19:52:27] Modify product: Uncharacterized protein YdiE => putative protein YdiE [19:52:27] Modify product: Uncharacterized protein YniD => putative protein YniD [19:52:27] Modify product: Probable ketoamine kinase lp_1983 => putative ketoamine kinase [19:52:27] Modify product: Uncharacterized HTH-type transcriptional regulator YdjF => putative HTH-type transcriptional regulator YdjF [19:52:27] Modify product: Uncharacterized sugar kinase YdjH => putative sugar kinase YdjH [19:52:27] Modify product: Uncharacterized protein YdjI => putative protein YdjI [19:52:27] Modify product: Uncharacterized zinc-type alcohol dehydrogenase-like protein YdjJ => putative zinc-type alcohol dehydrogenase-like protein YdjJ [19:52:27] Modify product: Stress response UPF0229 protein YhbH => hypothetical protein [19:52:27] Modify product: Probable diguanylate cyclase CdgI => putative diguanylate cyclase CdgI [19:52:27] Modify product: Probable diguanylate cyclase DgcJ => putative diguanylate cyclase DgcJ [19:52:27] Modify product: Uncharacterized protein YeaR => putative protein YeaR [19:52:27] Modify product: Probable ATP-dependent DNA helicase YoaA => putative ATP-dependent DNA helicase YoaA [19:52:27] Modify product: Probable cyclic di-GMP phosphodiesterase PdeD => putative cyclic di-GMP phosphodiesterase PdeD [19:52:27] Modify product: UPF0053 inner membrane protein YoaE => hypothetical protein [19:52:27] Modify product: UPF0266 membrane protein YobD => hypothetical protein [19:52:27] Modify product: Probable manganese efflux pump MntP => putative manganese efflux pump MntP [19:52:27] Modify product: Uncharacterized protein YebV => putative protein YebV [19:52:27] Modify product: Probable transcriptional regulatory protein YebC => putative transcriptional regulatory protein YebC [19:52:27] Modify product: UPF0394 inner membrane protein YedE => hypothetical protein [19:52:27] Modify product: Probable diguanylate cyclase DgcQ => putative diguanylate cyclase DgcQ [19:52:27] Modify product: Uncharacterized inner membrane transporter YedA => putative inner membrane transporter YedA [19:52:27] Modify product: Uncharacterized protein YedJ => putative protein YedJ [19:52:27] Modify product: Putative multidrug export ATP-binding/permease protein SAV1866 => Putative multidrug export ATP-binding/permease protein [19:52:27] Modify product: Probable transcriptional regulatory protein YeeN => putative transcriptional regulatory protein YeeN [19:52:27] Modify product: Probable FMN/FAD exporter YeeO => putative FMN/FAD exporter YeeO [19:52:27] Modify product: Probable L,D-transpeptidase ErfK/SrfK => putative L,D-transpeptidase ErfK/SrfK [19:52:27] Modify product: UPF0401 protein YkfF => hypothetical protein [19:52:27] Modify product: UPF0265 protein YeeX => hypothetical protein [19:52:27] Modify product: UPF0394 inner membrane protein YeeE => hypothetical protein [19:52:27] Modify product: UPF0053 inner membrane protein YoaE => hypothetical protein [19:52:27] Modify product: Probable diguanylate cyclase DgcE => putative diguanylate cyclase DgcE [19:52:27] Modify product: UPF0339 protein YegP => hypothetical protein [19:52:27] Modify product: 23S rRNA 5-hydroxycytidine C2501 synthase => 23S rRNA 5-hydroxycytidine synthase [19:52:27] Modify product: Uncharacterized fimbrial-like protein YehA => putative fimbrial-like protein YehA [19:52:27] Modify product: Probable fimbrial chaperone YehC => putative fimbrial chaperone YehC [19:52:27] Modify product: Uncharacterized fimbrial-like protein YehD => putative fimbrial-like protein YehD [19:52:27] Modify product: Uncharacterized protein YehL => putative protein YehL [19:52:27] Modify product: Uncharacterized lipoprotein YehR => putative lipoprotein YehR [19:52:27] Modify product: UPF0387 membrane protein YohO => hypothetical protein [19:52:27] Modify product: Uncharacterized oxidoreductase YohF => putative oxidoreductase YohF [19:52:27] Modify product: Uncharacterized oxidoreductase YohF => putative oxidoreductase YohF [19:52:27] Modify product: UPF0299 membrane protein YohJ => hypothetical protein [19:52:27] Modify product: UPF0324 inner membrane protein YeiH => hypothetical protein [19:52:27] Modify product: UPF0153 protein YeiW => hypothetical protein [19:52:27] Modify product: Probable cyclic di-GMP phosphodiesterase PdeN => putative cyclic di-GMP phosphodiesterase PdeN [19:52:27] Modify product: Uncharacterized ABC transporter ATP-binding protein YejF => putative ABC transporter ATP-binding protein YejF [19:52:27] Modify product: Uncharacterized protein YejG => putative protein YejG [19:52:27] Modify product: UPF0352 protein YejL => hypothetical protein [19:52:27] Modify product: Probable autotransporter ROD_p1121 => putative autotransporter [19:52:27] Modify product: Probable autotransporter YfaL => putative autotransporter YfaL [19:52:27] Modify product: Uncharacterized HTH-type transcriptional regulator RhmR => putative HTH-type transcriptional regulator RhmR [19:52:27] Modify product: Probable 4-deoxy-4-formamido-L-arabinose-phosphoundecaprenol deformylase ArnD => putative 4-deoxy-4-formamido-L-arabinose-phosphoundecaprenol deformylase ArnD [19:52:27] Modify product: Probable 4-amino-4-deoxy-L-arabinose-phosphoundecaprenol flippase subunit ArnE => putative 4-amino-4-deoxy-L-arabinose-phosphoundecaprenol flippase subunit ArnE [19:52:27] Modify product: Probable 4-amino-4-deoxy-L-arabinose-phosphoundecaprenol flippase subunit ArnF => putative 4-amino-4-deoxy-L-arabinose-phosphoundecaprenol flippase subunit ArnF [19:52:27] Modify product: UPF0304 protein YfbU => hypothetical protein [19:52:27] Modify product: UPF0208 membrane protein YfbV => hypothetical protein [19:52:27] Modify product: Uncharacterized Nudix hydrolase YfcD => putative Nudix hydrolase YfcD [19:52:27] Modify product: Epimerase family protein SA0724 => Epimerase family protein [19:52:27] Modify product: Uncharacterized MFS-type transporter YfcJ => putative MFS-type transporter YfcJ [19:52:27] Modify product: Probable membrane transporter protein YfcA => putative membrane transporter protein YfcA [19:52:27] Modify product: Uncharacterized protein YfcO => putative protein YfcO [19:52:27] Modify product: Uncharacterized fimbrial-like protein YfcP => putative fimbrial-like protein YfcP [19:52:27] Modify product: Uncharacterized fimbrial-like protein YfcQ => putative fimbrial-like protein YfcQ [19:52:27] Modify product: Uncharacterized fimbrial-like protein YfcR => putative fimbrial-like protein YfcR [19:52:27] Modify product: Probable fimbrial chaperone YfcS => putative fimbrial chaperone YfcS [19:52:27] Modify product: Uncharacterized fimbrial-like protein YfcV => putative fimbrial-like protein YfcV [19:52:27] Modify product: UPF0381 protein YiiS => hypothetical protein [19:52:27] Modify product: Probable multidrug resistance protein EmrY => putative multidrug resistance protein EmrY [19:52:27] Modify product: Probable multidrug resistance protein EmrK => putative multidrug resistance protein EmrK [19:52:28] Modify product: Probable cyclic di-GMP phosphodiesterase PdeA => putative cyclic di-GMP phosphodiesterase PdeA [19:52:28] Modify product: Uncharacterized protein YfeY => putative protein YfeY [19:52:28] Modify product: Uncharacterized protein Rv2575 => putative protein [19:52:28] Modify product: Probable formate transporter 2 => putative formate transporter 2 [19:52:28] Modify product: Uncharacterized protein YfgD => putative protein YfgD [19:52:28] Modify product: Uncharacterized protein YfgJ => putative protein YfgJ [19:52:28] Modify product: UPF0070 protein HI_0370 => hypothetical protein [19:52:28] Modify product: Uncharacterized protein Rv2307c => putative protein [19:52:28] Modify product: Probable 3-phenylpropionic acid transporter => putative 3-phenylpropionic acid transporter [19:52:28] Modify product: Uncharacterized protein YphB => putative protein YphB [19:52:28] Modify product: Uncharacterized tRNA/rRNA methyltransferase YfiF => putative tRNA/rRNA methyltransferase YfiF [19:52:28] Modify product: UPF0053 inner membrane protein YfjD => hypothetical protein [19:52:28] Modify product: UPF0125 protein RatB => hypothetical protein [19:52:28] Modify product: Probable UbiX-like flavin prenyltransferase => putative UbiX-like flavin prenyltransferase [19:52:28] Modify product: Probable transporter SCO4007 => putative transporter [19:52:28] Modify product: Uncharacterized protein YgaM => putative protein YgaM [19:52:28] Modify product: Probable HTH-type transcriptional regulator YgaV => putative HTH-type transcriptional regulator YgaV [19:52:28] Modify product: UPF0758 protein => hypothetical protein [19:52:28] Modify product: UPF0401 protein YkfF => hypothetical protein [19:52:28] Modify product: Probable diguanylate cyclase DgcC => putative diguanylate cyclase DgcC [19:52:28] Modify product: UPF0178 protein YaiI => hypothetical protein [19:52:28] Modify product: Uncharacterized protein YaiA => putative protein YaiA [19:52:28] Modify product: Uncharacterized lipoprotein YajI => putative lipoprotein YajI [19:52:28] Modify product: UPF0234 protein YajQ => hypothetical protein [19:52:28] Modify product: Uncharacterized protein HI_1008 => putative protein [19:52:28] Modify product: Probable multidrug resistance ABC transporter ATP-binding/permease protein YheI => putative multidrug resistance ABC transporter ATP-binding/permease protein YheI [19:52:28] Modify product: Uncharacterized lipoprotein YbaY => putative lipoprotein YbaY [19:52:28] Modify product: Uncharacterized protein YbaA => putative protein YbaA [19:52:28] Modify product: Probable cyclic di-GMP phosphodiesterase PdeB => putative cyclic di-GMP phosphodiesterase PdeB [19:52:28] Modify product: Uncharacterized HTH-type transcriptional regulator YbaQ => putative HTH-type transcriptional regulator YbaQ [19:52:28] Modify product: Probable iron export ATP-binding protein FetA => putative iron export ATP-binding protein FetA [19:52:28] Modify product: Probable iron export permease protein FetB => putative iron export permease protein FetB [19:52:28] Modify product: Uncharacterized protein YbcJ => putative protein YbcJ [19:52:28] Modify product: Bifunctional protein FolD => Bifunctional protein FolD protein [19:52:28] Modify product: Uncharacterized fimbrial-like protein SfmA => putative fimbrial-like protein SfmA [19:52:28] Modify product: Probable fimbrial chaperone SfmC => putative fimbrial chaperone SfmC [19:52:28] Modify product: Uncharacterized fimbrial-like protein SfmH => putative fimbrial-like protein SfmH [19:52:28] Modify product: Uncharacterized fimbrial-like protein SfmF => putative fimbrial-like protein SfmF [19:52:28] Modify product: Probable deoxyribonuclease RhsA => putative deoxyribonuclease RhsA [19:52:28] Modify product: Uncharacterized protein YbdM => putative protein YbdM [19:52:28] Modify product: Uncharacterized HTH-type transcriptional regulator YbdO => putative HTH-type transcriptional regulator YbdO [19:52:28] Modify product: Probable zinc-binding alcohol dehydrogenase Rv1895 => putative zinc-binding alcohol dehydrogenase [19:52:28] Modify product: Uncharacterized HTH-type transcriptional regulator YbdO => putative HTH-type transcriptional regulator YbdO [19:52:28] Modify product: UPF0250 protein YbeD => hypothetical protein [19:52:28] Modify product: Uncharacterized lipoprotein ChiQ => putative lipoprotein ChiQ [19:52:28] Modify product: Uncharacterized protein YbfE => putative protein YbfE [19:52:28] Modify product: GTP cyclohydrolase 1 type 2 homolog => GTP cyclohydrolase 1 type 2 [19:52:28] Modify product: Uncharacterized fimbrial-like protein YbgD => putative fimbrial-like protein YbgD [19:52:28] Modify product: UPF0098 protein YbhB => hypothetical protein [19:52:28] Modify product: Probable multidrug ABC transporter permease YbhR => putative multidrug ABC transporter permease YbhR [19:52:28] Modify product: Probable multidrug ABC transporter permease YbhS => putative multidrug ABC transporter permease YbhS [19:52:28] Modify product: Probable multidrug ABC transporter ATP-binding protein YbhF => putative multidrug ABC transporter ATP-binding protein YbhF [19:52:28] Modify product: UPF0194 membrane protein YbhG => hypothetical protein [19:52:28] Modify product: Uncharacterized protein YbiB => putative protein YbiB [19:52:28] Modify product: Uncharacterized protein YbiI => putative protein YbiI [19:52:28] Modify product: PKHD-type hydroxylase Sbal_3634 => PKHD-type hydroxylase [19:52:28] Modify product: Uncharacterized protein McbA => putative protein McbA [19:52:28] Modify product: Probable L,D-transpeptidase YbiS => putative L,D-transpeptidase YbiS [19:52:28] Modify product: Uncharacterized ABC transporter ATP-binding protein YbiT => putative ABC transporter ATP-binding protein YbiT [19:52:28] Modify product: Uncharacterized protein YbiU => putative protein YbiU [19:52:28] Modify product: Probable cyclic di-GMP phosphodiesterase PdeI => putative cyclic di-GMP phosphodiesterase PdeI [19:52:28] Modify product: Uncharacterized protein YbiI => putative protein YbiI [19:52:28] Modify product: Uncharacterized protein YbjN => putative protein YbjN [19:52:28] Modify product: Uncharacterized lipoprotein YbjP => putative lipoprotein YbjP [19:52:28] Modify product: UPF0145 protein YbjQ => hypothetical protein [19:52:28] Modify product: Probable ABC transporter ATP-binding/permease protein HI_0664 => putative ABC transporter ATP-binding/permease protein [19:52:28] Modify product: Probable hydrolase YcaC => putative hydrolase YcaC [19:52:28] Modify product: Uncharacterized MFS-type transporter YcaD => putative MFS-type transporter YcaD [19:52:28] Modify product: Probable formate transporter 1 => putative formate transporter 1 [19:52:28] Modify product: UPF0434 protein YcaR => hypothetical protein [19:52:29] Modify product: Probable L,D-transpeptidase YcbB => putative L,D-transpeptidase YcbB [19:52:29] Modify product: Probable fimbrial chaperone protein ElfD => putative fimbrial chaperone protein ElfD [19:52:29] Modify product: Probable outer membrane usher protein ElfC => putative outer membrane usher protein ElfC [19:52:29] Modify product: Uncharacterized fimbrial-like protein ElfG => putative fimbrial-like protein ElfG [19:52:29] Modify product: Uncharacterized fimbrial-like protein YcbU => putative fimbrial-like protein YcbU [19:52:29] Modify product: Uncharacterized fimbrial-like protein YcbV => putative fimbrial-like protein YcbV [19:52:29] Modify product: Uncharacterized fimbrial chaperone YcbF => putative fimbrial chaperone YcbF [19:52:29] Modify product: Uncharacterized protein YcbX => putative protein YcbX [19:52:29] Modify product: UPF0319 protein HI_1681 => hypothetical protein [19:52:29] Modify product: Uncharacterized protein YccU => putative protein YccU [19:52:29] Modify product: Probable Ni/Fe-hydrogenase 1 B-type cytochrome subunit => putative Ni/Fe-hydrogenase 1 B-type cytochrome subunit [19:52:29] Modify product: Uncharacterized lipoprotein GfcB => putative lipoprotein GfcB [19:52:29] Modify product: Uncharacterized protein YccJ => putative protein YccJ [19:52:29] Modify product: Probable malonic semialdehyde reductase RutE => putative malonic semialdehyde reductase RutE [19:52:29] Modify product: Probable diguanylate cyclase DgcT => putative diguanylate cyclase DgcT [19:52:29] Modify product: Probable phosphatase YcdX => putative phosphatase YcdX [19:52:29] Modify product: Uncharacterized protein YmdA => putative protein YmdA [19:52:29] Modify product: UPF0176 protein YceA => hypothetical protein [19:52:29] Modify product: Cytochrome b561 homolog 2 => Cytochrome b561 [19:52:29] Modify product: Uncharacterized protein YceO => putative protein YceO [19:52:29] Modify product: Uncharacterized lipoprotein YceB => putative lipoprotein YceB [19:52:29] Modify product: UPF0502 protein YceH => hypothetical protein [19:52:29] Modify product: Uncharacterized metal-dependent hydrolase YcfH => putative metal-dependent hydrolase YcfH [19:52:29] Modify product: UPF0227 protein YcfP => hypothetical protein [19:52:29] Modify product: Probable L,D-transpeptidase YcfS => putative L,D-transpeptidase YcfS [19:52:29] Modify product: Uncharacterized protein YdfO => putative protein YdfO [19:52:29] Modify product: Probable two-component-system connector protein YcgZ => putative two-component-system connector protein YcgZ [19:52:29] Modify product: Probable two-component-system connector protein AriR => putative two-component-system connector protein AriR [19:52:29] Modify product: Uncharacterized protein YmgC => putative protein YmgC [19:52:29] Modify product: Probable cyclic di-GMP phosphodiesterase PdeG => putative cyclic di-GMP phosphodiesterase PdeG [19:52:29] Modify product: Uncharacterized protein YmgD => putative protein YmgD [19:52:29] Modify product: UPF0757 protein YmgG => hypothetical protein [19:52:29] Modify product: Uncharacterized protein YcgM => putative protein YcgM [19:52:29] Modify product: UPF0225 protein YchJ => hypothetical protein [19:52:29] Modify product: Uncharacterized NTE family protein Rv1063c => putative NTE family protein [19:52:29] Modify product: UPF0056 inner membrane protein MarC => hypothetical protein [19:52:29] Modify product: UPF0263 protein YciU => hypothetical protein [19:52:29] Modify product: Uncharacterized acyl-CoA thioester hydrolase HI_0827 => putative acyl-CoA thioester hydrolase [19:52:29] Modify product: Probable intracellular septation protein A => putative intracellular septation protein A [19:52:29] Modify product: UPF0259 membrane protein YciC => hypothetical protein [19:52:29] Modify product: Uncharacterized protein YdfB => putative protein YdfB [19:52:29] Modify product: Uncharacterized protein YciO => putative protein YciO [19:52:29] Modify product: Uncharacterized oxidoreductase YciK => putative oxidoreductase YciK [19:52:29] Modify product: Probable protease SohB => putative protease SohB [19:52:29] Modify product: Uncharacterized protein YciH => putative protein YciH [19:52:29] Modify product: UPF0509 protein YciZ => hypothetical protein [19:52:29] Modify product: Uncharacterized protein HI_1162 => putative protein [19:52:29] Modify product: Uncharacterized protein YcjX => putative protein YcjX [19:52:29] Modify product: UPF0283 membrane protein YcjF => hypothetical protein [19:52:29] Modify product: Uncharacterized protein YcjY => putative protein YcjY [19:52:29] Modify product: Probable DNA endonuclease SmrA => putative DNA endonuclease SmrA [19:52:29] Modify product: Uncharacterized protein YnbC => putative protein YnbC [19:52:29] Modify product: Uncharacterized protein YnbD => putative protein YnbD [19:52:29] Modify product: Uncharacterized protein Rv3292 => putative protein [19:52:29] Modify product: 23S rRNA 5-hydroxycytidine C2501 synthase => 23S rRNA 5-hydroxycytidine synthase [19:52:29] Modify product: Probable mRNA interferase toxin HicA => putative mRNA interferase toxin HicA [19:52:29] Modify product: Uncharacterized protein YdcY => putative protein YdcY [19:52:29] Modify product: Uncharacterized protein YncE => putative protein YncE [19:52:29] Modify product: Uncharacterized isomerase YddE => putative isomerase YddE [19:52:29] Modify product: Probable nitrate reductase molybdenum cofactor assembly chaperone NarW => putative nitrate reductase molybdenum cofactor assembly chaperone NarW [19:52:29] Modify product: Uncharacterized HTH-type transcriptional regulator YddM => putative HTH-type transcriptional regulator YddM [19:52:29] Modify product: Probable D,D-dipeptide transport ATP-binding protein DdpF => putative D,D-dipeptide transport ATP-binding protein DdpF [19:52:29] Modify product: Probable D,D-dipeptide transport ATP-binding protein DdpD => putative D,D-dipeptide transport ATP-binding protein DdpD [19:52:29] Modify product: Probable D,D-dipeptide transport system permease protein DdpC => putative D,D-dipeptide transport system permease protein DdpC [19:52:29] Modify product: Probable D,D-dipeptide transport system permease protein DdpB => putative D,D-dipeptide transport system permease protein DdpB [19:52:29] Modify product: Probable D,D-dipeptide-binding periplasmic protein DdpA => putative D,D-dipeptide-binding periplasmic protein DdpA [19:52:29] Modify product: Probable glutamate/gamma-aminobutyrate antiporter => putative glutamate/gamma-aminobutyrate antiporter [19:52:29] Modify product: UPF0056 inner membrane protein MarC => hypothetical protein [19:52:29] Modify product: Probable amino-acid metabolite efflux pump => putative amino-acid metabolite efflux pump [19:52:29] Modify product: Uncharacterized protein YdfO => putative protein YdfO [19:52:29] Modify product: Uncharacterized protein YgcP => putative protein YgcP [19:52:29] Modify product: Uncharacterized protein YqcG => putative protein YqcG [19:52:29] Modify product: Probable glucarate transporter => putative glucarate transporter [19:52:29] Modify product: Uncharacterized protein PA3435 => putative protein [19:52:29] Modify product: Uncharacterized protein YqcC => putative protein YqcC [19:52:29] Modify product: Uncharacterized HTH-type transcriptional regulator YdjF => putative HTH-type transcriptional regulator YdjF [19:52:29] Modify product: UPF0382 inner membrane protein YgdD => hypothetical protein [19:52:29] Modify product: Uncharacterized lipoprotein YgdR => putative lipoprotein YgdR [19:52:29] Modify product: UPF0053 inner membrane protein YgdQ => hypothetical protein [19:52:29] Modify product: Uncharacterized lipoprotein YgdR => putative lipoprotein YgdR [19:52:29] Modify product: Uncharacterized response regulatory protein YgeK => putative response regulatory protein YgeK [19:52:29] Modify product: Uncharacterized protein YqfG => putative protein YqfG [19:52:29] Modify product: UPF0073 inner membrane protein YqfA => hypothetical protein [19:52:29] Modify product: UPF0267 protein YqfB => hypothetical protein [19:52:29] Modify product: Uncharacterized oxidoreductase YgfF => putative oxidoreductase YgfF [19:52:29] Modify product: UPF0149 protein HI_0817 => hypothetical protein [19:52:29] Modify product: UPF0301 protein YqgE => hypothetical protein [19:52:29] Modify product: Uncharacterized protein YggR => putative protein YggR [19:52:29] Modify product: UPF0235 protein YggU => hypothetical protein [19:52:29] Modify product: Uncharacterized protein HI_0341 => putative protein [19:52:29] Modify product: Probable Fe(2+)-trafficking protein => putative Fe(2+)-trafficking protein [19:52:29] Modify product: Uncharacterized FAD-linked oxidoreductase Rv2280 => putative FAD-linked oxidoreductase [19:52:29] Modify product: Uncharacterized protein YtfJ => putative protein YtfJ [19:52:29] Modify product: Probable Ni/Fe-hydrogenase 2 b-type cytochrome subunit => putative Ni/Fe-hydrogenase 2 b-type cytochrome subunit [19:52:29] Modify product: Uncharacterized oxidoreductase YghA => putative oxidoreductase YghA [19:52:29] Modify product: Probable deoxycholate-binding periplasmic protein YgiS => putative deoxycholate-binding periplasmic protein YgiS [19:52:29] Modify product: Probable quinol monooxygenase YgiN => putative quinol monooxygenase YgiN [19:52:30] Modify product: Uncharacterized fimbrial-like protein YbgD => putative fimbrial-like protein YbgD [19:52:30] Modify product: Probable glycerol-3-phosphate acyltransferase => putative glycerol-3-phosphate acyltransferase [19:52:30] Modify product: Uncharacterized protein YqjD => putative protein YqjD [19:52:30] Modify product: UPF0597 protein YhaM => hypothetical protein [19:52:30] Modify product: Probable serine transporter => putative serine transporter [19:52:30] Modify product: Probable galactarate transporter => putative galactarate transporter [19:52:30] Modify product: Uncharacterized fimbrial-like protein YraH => putative fimbrial-like protein YraH [19:52:30] Modify product: Probable fimbrial chaperone YraI => putative fimbrial chaperone YraI [19:52:30] Modify product: Uncharacterized fimbrial-like protein YraK => putative fimbrial-like protein YraK [19:52:30] Modify product: UPF0213 protein BH0048 => hypothetical protein [19:52:30] Modify product: Uncharacterized protease YhbU => putative protease YhbU [19:52:30] Modify product: Uncharacterized inner membrane transporter YhbE => putative inner membrane transporter YhbE [19:52:30] Modify product: Uncharacterized protein YrbL => putative protein YrbL [19:52:30] Modify product: Uncharacterized protein YhcH => putative protein YhcH [19:52:30] Modify product: Uncharacterized protein YhcO => putative protein YhcO [19:52:30] Modify product: Probable acrylyl-CoA reductase AcuI => putative acrylyl-CoA reductase AcuI [19:52:30] Modify product: Uncharacterized membrane protein YhdT => putative membrane protein YhdT [19:52:30] Modify product: Probable bifunctional chitinase/lysozyme => putative bifunctional chitinase/lysozyme [19:52:30] Modify product: Protein SlyX homolog => Protein SlyX [19:52:30] Modify product: Uncharacterized ABC transporter ATP-binding protein YheS => putative ABC transporter ATP-binding protein YheS [19:52:30] Modify product: UPF0270 protein PA3463 => hypothetical protein [19:52:30] Modify product: Probable protein adenylyltransferase Fic => putative protein adenylyltransferase Fic [19:52:30] Modify product: Uncharacterized protein YhfG => putative protein YhfG [19:52:30] Modify product: Probable fructoselysine/psicoselysine transporter FrlA => putative fructoselysine/psicoselysine transporter FrlA [19:52:30] Modify product: Probable fructoselysine utilization operon transcriptional repressor => putative fructoselysine utilization operon transcriptional repressor [19:52:30] Modify product: Uncharacterized protein YhfS => putative protein YhfS [19:52:30] Modify product: Uncharacterized protein YhfX => putative protein YhfX [19:52:30] Modify product: Putative membrane protein IgaA homolog => Putative membrane protein IgaA [19:52:30] Modify product: Probable [Fe-S]-dependent transcriptional repressor FeoC => putative [Fe-S]-dependent transcriptional repressor FeoC [19:52:30] Modify product: UPF0056 inner membrane protein YhgN => hypothetical protein [19:52:30] Modify product: Uncharacterized oxidoreductase YhhX => putative oxidoreductase YhhX [19:52:30] Modify product: Uncharacterized protein YhhA => putative protein YhhA [19:52:30] Modify product: Uncharacterized MFS-type transporter YhhS => putative MFS-type transporter YhhS [19:52:30] Modify product: Probable copper-binding protein PcoE => putative copper-binding protein PcoE [19:52:30] Modify product: Uncharacterized protein HI_0933 => putative protein [19:52:30] Modify product: Probable cyclic di-GMP phosphodiesterase PdeK => putative cyclic di-GMP phosphodiesterase PdeK [19:52:30] Modify product: Uncharacterized MFS-type transporter YhjX => putative MFS-type transporter YhjX [19:52:30] Modify product: Probable lipoprotein YiaD => putative lipoprotein YiaD [19:52:30] Modify product: Uncharacterized protein YhcH => putative protein YhcH [19:52:30] Modify product: Uncharacterized GST-like protein YibF => putative GST-like protein YibF [19:52:30] Modify product: Uncharacterized protein YibL => putative protein YibL [19:52:30] Modify product: Uncharacterized protein YibN => putative protein YibN [19:52:30] Modify product: Uncharacterized protein HI_0755 => putative protein [19:52:30] Modify product: UPF0758 protein SP_1088 => hypothetical protein [19:52:30] Modify product: UPF0701 protein YicC => hypothetical protein [19:52:30] Modify product: UPF0126 inner membrane protein YicG => hypothetical protein [19:52:30] Modify product: Uncharacterized inner membrane transporter YicL => putative inner membrane transporter YicL [19:52:30] Modify product: Uncharacterized symporter YidK => putative symporter YidK [19:52:30] Modify product: Probable 2-dehydro-3-deoxygalactonokinase DgoK1 => putative 2-dehydro-3-deoxygalactonokinase DgoK1 [19:52:30] Modify product: Probable glucosamine-6-phosphate deaminase 2 => putative glucosamine-6-phosphate deaminase 2 [19:52:30] Modify product: Probable transport protein HsrA => putative transport protein HsrA [19:52:30] Modify product: UPF0438 protein YifE => hypothetical protein [19:52:30] Modify product: Probable ECA polymerase => putative ECA polymerase [19:52:30] Modify product: Probable transport protein YifK => putative transport protein YifK [19:52:30] Modify product: Probable protein kinase UbiB => putative protein kinase UbiB [19:52:30] Modify product: Probable acyltransferase YihG => putative acyltransferase YihG [19:52:30] Modify product: Probable GTP-binding protein EngB => putative GTP-binding protein EngB [19:52:30] Modify product: Uncharacterized protein YshB => putative protein YshB [19:52:30] Modify product: Uncharacterized protein YihR => putative protein YihR [19:52:30] Modify product: UPF0761 membrane protein YihY => hypothetical protein [19:52:30] Modify product: UPF0381 protein YiiS => hypothetical protein [19:52:30] Modify product: Probable cystine transporter YijE => putative cystine transporter YijE [19:52:31] Modify product: Uncharacterized protein HI_0431 => putative protein [19:52:31] Modify product: Uncharacterized lipoprotein GfcB => putative lipoprotein GfcB [19:52:31] Modify product: UPF0337 protein YjbJ => hypothetical protein [19:52:31] Modify product: Uncharacterized protein YjbR => putative protein YjbR [19:52:31] Modify product: Probable cyclic di-GMP phosphodiesterase PdeC => putative cyclic di-GMP phosphodiesterase PdeC [19:52:31] Modify product: Uncharacterized ferredoxin-like protein YdhX => putative ferredoxin-like protein YdhX [19:52:31] Modify product: Probable transcriptional regulator PhnF => putative transcriptional regulator PhnF [19:52:31] Modify product: Uncharacterized protein YjdJ => putative protein YjdJ [19:52:31] Modify product: Probable cadaverine/lysine antiporter => putative cadaverine/lysine antiporter [19:52:31] Modify product: UPF0716 protein FxsA => hypothetical protein [19:52:31] Modify product: Protease HtpX homolog => Protease HtpX [19:52:31] Modify product: UPF0401 protein YkfF => hypothetical protein [19:52:31] Modify product: UPF0758 protein => hypothetical protein [19:52:31] Modify product: Prophage tail fiber assembly protein homolog TfaE => Prophage tail fiber assembly protein TfaE [19:52:31] Modify product: UPF0255 protein VV1_0328 => hypothetical protein [19:52:31] Modify product: Uncharacterized N-acetyltransferase YafP => putative N-acetyltransferase YafP [19:52:31] Modify product: Uncharacterized methyltransferase YcgJ => putative methyltransferase YcgJ [19:52:31] Modify product: Uncharacterized protein YaeQ => putative protein YaeQ [19:52:31] Modify product: UPF0253 protein YaeP => hypothetical protein [19:52:31] Modify product: UPF0126 inner membrane protein YadS => hypothetical protein [19:52:31] Modify product: Uncharacterized fimbrial-like protein YadN => putative fimbrial-like protein YadN [19:52:31] Modify product: Probable fimbrial chaperone YadV => putative fimbrial chaperone YadV [19:52:31] Modify product: Uncharacterized fimbrial-like protein YadM => putative fimbrial-like protein YadM [19:52:31] Modify product: Uncharacterized fimbrial-like protein YadL => putative fimbrial-like protein YadL [19:52:31] Modify product: Uncharacterized fimbrial-like protein YadK => putative fimbrial-like protein YadK [19:52:31] Modify product: Uncharacterized ABC transporter ATP-binding protein YadG => putative ABC transporter ATP-binding protein YadG [19:52:31] Modify product: UPF0231 protein YacL => hypothetical protein [19:52:31] Modify product: Probable peptidoglycan glycosyltransferase FtsW => putative peptidoglycan glycosyltransferase FtsW [19:52:31] Modify product: Uncharacterized tRNA/rRNA methyltransferase HI_0380 => putative tRNA/rRNA methyltransferase [19:52:31] Modify product: Probable inner membrane protein Smp => putative inner membrane protein Smp [19:52:31] Modify product: Uncharacterized protein YjjI => putative protein YjjI [19:52:31] Modify product: Uncharacterized metal-dependent hydrolase YjjV => putative metal-dependent hydrolase YjjV [19:52:31] Modify product: UPF0442 protein YjjB => hypothetical protein [19:52:31] Modify product: Probable HTH-type transcriptional regulator LgoR => putative HTH-type transcriptional regulator LgoR [19:52:31] Modify product: Probable L-galactonate transporter => putative L-galactonate transporter [19:52:31] Modify product: Uncharacterized protein YjgL => putative protein YjgL [19:52:31] Modify product: Probable RNA polymerase sigma factor FecI => putative RNA polymerase sigma factor FecI [19:52:31] Modify product: Probable 9-O-acetyl-N-acetylneuraminic acid deacetylase => putative 9-O-acetyl-N-acetylneuraminic acid deacetylase [19:52:31] Modify product: Probable N-acetylneuraminic acid outer membrane channel protein NanC => putative N-acetylneuraminic acid outer membrane channel protein NanC [19:52:31] Modify product: Probable major fimbrial subunit LpfA => putative major fimbrial subunit LpfA [19:52:31] Modify product: Probable RNA 2'-phosphotransferase => putative RNA 2'-phosphotransferase [19:52:31] Modify product: Uncharacterized protein YjiK => putative protein YjiK [19:52:31] Modify product: UPF0307 protein YjgA => hypothetical protein [19:52:31] Modify product: UPF0053 inner membrane protein YtfL => hypothetical protein [19:52:31] Modify product: Uncharacterized protein YtfJ => putative protein YtfJ [19:52:31] Modify product: Solute-binding protein Bamb_6123 => Solute-binding protein [19:52:31] Modify product: Probable L-ascorbate-6-phosphate lactonase UlaG => putative L-ascorbate-6-phosphate lactonase UlaG [19:52:31] Modify product: UPF0719 inner membrane protein YjfL => hypothetical protein [19:52:31] Modify product: Uncharacterized transporter YycB => putative transporter YycB [19:52:31] Modify product: Probable pyridine nucleotide-disulfide oxidoreductase RclA => putative pyridine nucleotide-disulfide oxidoreductase RclA [19:52:31] Modify product: Uncharacterized HTH-type transcriptional regulator YahB => putative HTH-type transcriptional regulator YahB [19:52:31] Modify product: Uncharacterized protein YggR => putative protein YggR [19:52:31] Modify product: Uncharacterized signaling protein PA1727 => putative signaling protein [19:52:32] Modify product: UPF0401 protein YkfF => hypothetical protein [19:52:32] Cleaned 368 /product names [19:52:32] Deleting unwanted file: E562_annotation/E562_genome.sprot.tmp.5923.faa [19:52:32] Deleting unwanted file: E562_annotation/E562_genome.sprot.tmp.5923.blast [19:52:32] There are still 1314 unannotated CDS left (started with 5076) [19:52:32] Will use hmmer3 to search against /Users/avm/anaconda3/db/hmm/HAMAP.hmm with 2 CPUs [19:52:32] Running: cat E562_annotation\/E562_genome.HAMAP.hmm.tmp.5923.faa | parallel --gnu --plain -j 2 --block 82842 --recstart '>' --pipe hmmscan --noali --notextw --acc -E 1e-09 --cpu 1 /Users/avm/anaconda3/db/hmm/HAMAP.hmm /dev/stdin > E562_annotation\/E562_genome.HAMAP.hmm.tmp.5923.hmmer3 2> /dev/null [19:53:10] Modify product: Uncharacterized Nudix hydrolase NudL => putative Nudix hydrolase NudL [19:53:10] Cleaned 1 /product names [19:53:10] Deleting unwanted file: E562_annotation/E562_genome.HAMAP.hmm.tmp.5923.faa [19:53:10] Deleting unwanted file: E562_annotation/E562_genome.HAMAP.hmm.tmp.5923.hmmer3 [19:53:10] Labelling remaining 1234 proteins as 'hypothetical protein' [19:53:10] Possible /pseudo 'IS3 family transposase IS2' at 1 position 20991 [19:53:10] Possible /pseudo 'Outer membrane usher protein SfmD' at 1 position 182714 [19:53:10] Possible /pseudo 'IS3 family transposase IS2' at 1 position 187700 [19:53:10] Possible /pseudo 'Protein RhsC' at 1 position 339930 [19:53:10] Possible /pseudo 'Oxygen-insensitive NADPH nitroreductase' at 1 position 513933 [19:53:10] Possible /pseudo 'Cold shock-like protein CspG' at 1 position 674104 [19:53:10] Possible /pseudo 'Hemolysin E, chromosomal' at 1 position 865254 [19:53:10] Possible /pseudo 'Small toxic polypeptide LdrA' at 1 position 907726 [19:53:10] Possible /pseudo 'Formate dehydrogenase, nitrate-inducible, major subunit' at 1 position 1201079 [19:53:10] Possible /pseudo 'IS3 family transposase IS2' at 1 position 1232105 [19:53:10] Possible /pseudo 'Serine/threonine-protein kinase toxin HipA' at 1 position 1249017 [19:53:10] Possible /pseudo 'IS30 family transposase IS30' at 1 position 1763678 [19:53:10] Possible /pseudo 'Protein kinase YegI' at 1 position 1861298 [19:53:10] Possible /pseudo 'D-tagatose-1,6-bisphosphate aldolase subunit GatZ' at 1 position 1885224 [19:53:10] Possible /pseudo 'putative oxidoreductase YohF' at 1 position 1936229 [19:53:10] Possible /pseudo 'Pseudouridine kinase' at 1 position 1968225 [19:53:10] Possible /pseudo 'IS3 family transposase IS2' at 1 position 2182050 [19:53:10] Possible /pseudo 'Acetyl-CoA:oxalate CoA-transferase' at 1 position 2201198 [19:53:10] Possible /pseudo 'Hydrogenase-4 component B' at 1 position 2303105 [19:53:10] Possible /pseudo 'Cyclic di-GMP phosphodiesterase PdeF' at 1 position 2325499 [19:53:10] Possible /pseudo 'IS3 family transposase IS2' at 1 position 2571306 [19:53:10] Possible /pseudo 'IS3 family transposase ISEc17' at 1 position 2575944 [19:53:10] Possible /pseudo 'Protein tas' at 1 position 2684349 [19:53:10] Possible /pseudo '8-amino-7-oxononanoate synthase' at 1 position 2884712 [19:53:10] Possible /pseudo 'N-acetylgalactosamine permease IIC component 1' at 1 position 3050959 [19:53:10] Possible /pseudo 'IS3 family transposase IS2' at 1 position 3421175 [19:53:10] Possible /pseudo 'Small toxic polypeptide LdrD' at 1 position 3492755 [19:53:10] Possible /pseudo 'Small toxic polypeptide LdrD' at 1 position 3493238 [19:53:10] Possible /pseudo 'Small toxic polypeptide LdrD' at 1 position 3493721 [19:53:10] Possible /pseudo 'Autotransporter adhesin EhaG' at 2 position 15170 [19:53:10] Possible /pseudo '6-phospho-alpha-glucosidase' at 2 position 113941 [19:53:10] Possible /pseudo 'Putative 2,3-dihydroxypropane-1-sulfonate exporter' at 2 position 315828 [19:53:10] Possible /pseudo 'Formate dehydrogenase-O major subunit' at 2 position 335254 [19:53:10] Possible /pseudo 'Isocitrate lyase' at 2 position 504596 [19:53:10] Possible /pseudo 'Formate dehydrogenase H' at 2 position 584164 [19:53:10] Possible /pseudo 'Aldehyde reductase Ahr' at 3 position 400847 [19:53:10] Possible /pseudo 'ISKra4 family transposase ISCep1' at 3 position 474588 [19:53:10] Possible /pseudo 'L-galactonate-5-dehydrogenase' at 4 position 63631 [19:53:10] Possible /pseudo 'IS3 family transposase IS2' at 5 position 41685 [19:53:10] Possible /pseudo 'IS1 family transposase IS1A' at 5 position 78734 [19:53:10] Possible /pseudo 'IS3 family transposase IS2' at 6 position 22451 [19:53:10] Possible /pseudo 'IS3 family transposase IS629' at 7 position 60749 [19:53:10] Possible /pseudo 'IS3 family transposase ISEc17' at 7 position 62615 [19:53:10] Possible /pseudo 'IS3 family transposase IS2' at 10 position 25933 [19:53:10] Found 3244 unique /gene codes. [19:53:10] Fixed 3 duplicate /gene - bioF_1 bioF_2 bioF_3 [19:53:10] Fixed 3 duplicate /gene - fabG_1 fabG_2 fabG_3 [19:53:10] Fixed 2 duplicate /gene - mipA_1 mipA_2 [19:53:10] Fixed 2 duplicate /gene - cfaE_1 cfaE_2 [19:53:10] Fixed 2 duplicate /gene - rbsK_1 rbsK_2 [19:53:10] Fixed 2 duplicate /gene - dncV_1 dncV_2 [19:53:10] Fixed 2 duplicate /gene - traA_1 traA_2 [19:53:10] Fixed 2 duplicate /gene - yhdJ_1 yhdJ_2 [19:53:10] Fixed 2 duplicate /gene - ompD_1 ompD_2 [19:53:10] Fixed 2 duplicate /gene - gstB_1 gstB_2 [19:53:10] Fixed 2 duplicate /gene - deoR_1 deoR_2 [19:53:10] Fixed 2 duplicate /gene - ygdR_1 ygdR_2 [19:53:10] Fixed 2 duplicate /gene - tmk_1 tmk_2 [19:53:10] Fixed 2 duplicate /gene - rob_1 rob_2 [19:53:10] Fixed 2 duplicate /gene - rbsC_1 rbsC_2 [19:53:10] Fixed 2 duplicate /gene - copA_1 copA_2 [19:53:10] Fixed 2 duplicate /gene - cutC_1 cutC_2 [19:53:10] Fixed 2 duplicate /gene - lsrK_1 lsrK_2 [19:53:10] Fixed 2 duplicate /gene - traC_1 traC_2 [19:53:10] Fixed 4 duplicate /gene - ldrD_1 ldrD_2 ldrD_3 ldrD_4 [19:53:10] Fixed 2 duplicate /gene - ydjF_1 ydjF_2 [19:53:10] Fixed 2 duplicate /gene - mhpD_1 mhpD_2 [19:53:10] Fixed 2 duplicate /gene - dam_1 dam_2 [19:53:10] Fixed 3 duplicate /gene - btuD_1 btuD_2 btuD_3 [19:53:10] Fixed 2 duplicate /gene - mhpC_1 mhpC_2 [19:53:10] Fixed 2 duplicate /gene - icd_1 icd_2 [19:53:10] Fixed 2 duplicate /gene - silE_1 silE_2 [19:53:10] Fixed 2 duplicate /gene - azoR_1 azoR_2 [19:53:10] Fixed 2 duplicate /gene - trxC_1 trxC_2 [19:53:10] Fixed 2 duplicate /gene - glpG_1 glpG_2 [19:53:10] Fixed 3 duplicate /gene - traD_1 traD_2 traD_3 [19:53:10] Fixed 6 duplicate /gene - xerC_1 xerC_2 xerC_3 xerC_4 xerC_5 xerC_6 [19:53:10] Fixed 2 duplicate /gene - ulaB_1 ulaB_2 [19:53:10] Fixed 2 duplicate /gene - yggR_1 yggR_2 [19:53:10] Fixed 2 duplicate /gene - murR_1 murR_2 [19:53:10] Fixed 3 duplicate /gene - ndhB_1 ndhB_2 ndhB_3 [19:53:10] Fixed 2 duplicate /gene - lutC_1 lutC_2 [19:53:10] Fixed 2 duplicate /gene - aaeB_1 aaeB_2 [19:53:10] Fixed 3 duplicate /gene - glnQ_1 glnQ_2 glnQ_3 [19:53:10] Fixed 6 duplicate /gene - intA_1 intA_2 intA_3 intA_4 intA_5 intA_6 [19:53:10] Fixed 2 duplicate /gene - dcuD_1 dcuD_2 [19:53:10] Fixed 2 duplicate /gene - ahr_1 ahr_2 [19:53:10] Fixed 4 duplicate /gene - potA_1 potA_2 potA_3 potA_4 [19:53:10] Fixed 2 duplicate /gene - bglF_1 bglF_2 [19:53:10] Fixed 3 duplicate /gene - manZ_1 manZ_2 manZ_3 [19:53:10] Fixed 3 duplicate /gene - fixX_1 fixX_2 fixX_3 [19:53:10] Fixed 2 duplicate /gene - por_1 por_2 [19:53:10] Fixed 2 duplicate /gene - aspT_1 aspT_2 [19:53:10] Fixed 2 duplicate /gene - fdoG_1 fdoG_2 [19:53:10] Fixed 2 duplicate /gene - mhpB_1 mhpB_2 [19:53:10] Fixed 2 duplicate /gene - manP_1 manP_2 [19:53:10] Fixed 4 duplicate /gene - rhaR_1 rhaR_2 rhaR_3 rhaR_4 [19:53:10] Fixed 2 duplicate /gene - fimD_1 fimD_2 [19:53:10] Fixed 2 duplicate /gene - mepM_1 mepM_2 [19:53:10] Fixed 4 duplicate /gene - parM_1 parM_2 parM_3 parM_4 [19:53:10] Fixed 2 duplicate /gene - ftnA_1 ftnA_2 [19:53:10] Fixed 2 duplicate /gene - fimG_1 fimG_2 [19:53:10] Fixed 2 duplicate /gene - lon_1 lon_2 [19:53:10] Fixed 2 duplicate /gene - yegI_1 yegI_2 [19:53:10] Fixed 2 duplicate /gene - ydhX_1 ydhX_2 [19:53:10] Fixed 2 duplicate /gene - melR_1 melR_2 [19:53:10] Fixed 2 duplicate /gene - cusB_1 cusB_2 [19:53:10] Fixed 2 duplicate /gene - ftsA_1 ftsA_2 [19:53:10] Fixed 3 duplicate /gene - agaC_1 agaC_2 agaC_3 [19:53:10] Fixed 2 duplicate /gene - purR_1 purR_2 [19:53:10] Fixed 2 duplicate /gene - nfsA_1 nfsA_2 [19:53:10] Fixed 3 duplicate /gene - malP_1 malP_2 malP_3 [19:53:10] Fixed 2 duplicate /gene - ybdO_1 ybdO_2 [19:53:10] Fixed 2 duplicate /gene - pdeF_1 pdeF_2 [19:53:10] Fixed 2 duplicate /gene - nanR_1 nanR_2 [19:53:10] Fixed 2 duplicate /gene - xdhA_1 xdhA_2 [19:53:10] Fixed 2 duplicate /gene - flu_1 flu_2 [19:53:10] Fixed 2 duplicate /gene - rlhA_1 rlhA_2 [19:53:10] Fixed 2 duplicate /gene - mtlA_1 mtlA_2 [19:53:10] Fixed 2 duplicate /gene - fdnH_1 fdnH_2 [19:53:10] Fixed 2 duplicate /gene - hha_1 hha_2 [19:53:10] Fixed 2 duplicate /gene - bglA_1 bglA_2 [19:53:10] Fixed 2 duplicate /gene - chbA_1 chbA_2 [19:53:10] Fixed 2 duplicate /gene - ccmH_1 ccmH_2 [19:53:10] Fixed 2 duplicate /gene - esiB_1 esiB_2 [19:53:10] Fixed 2 duplicate /gene - yahB_1 yahB_2 [19:53:10] Fixed 2 duplicate /gene - sbmC_1 sbmC_2 [19:53:10] Fixed 2 duplicate /gene - aglB_1 aglB_2 [19:53:10] Fixed 2 duplicate /gene - fucP_1 fucP_2 [19:53:10] Fixed 2 duplicate /gene - cusF_1 cusF_2 [19:53:10] Fixed 2 duplicate /gene - hipA_1 hipA_2 [19:53:10] Fixed 2 duplicate /gene - dmsC_1 dmsC_2 [19:53:10] Fixed 2 duplicate /gene - yhaJ_1 yhaJ_2 [19:53:10] Fixed 2 duplicate /gene - osmY_1 osmY_2 [19:53:10] Fixed 2 duplicate /gene - lptG_1 lptG_2 [19:53:10] Fixed 2 duplicate /gene - narL_1 narL_2 [19:53:10] Fixed 2 duplicate /gene - sapB_1 sapB_2 [19:53:10] Fixed 2 duplicate /gene - prs_1 prs_2 [19:53:10] Fixed 3 duplicate /gene - cynR_1 cynR_2 cynR_3 [19:53:10] Fixed 13 duplicate /gene - insK_1 insK_2 insK_3 insK_4 insK_5 insK_6 insK_7 insK_8 insK_9 insK_10 insK_11 insK_12 insK_13 [19:53:10] Fixed 2 duplicate /gene - fryA_1 fryA_2 [19:53:10] Fixed 2 duplicate /gene - fdhF_1 fdhF_2 [19:53:10] Fixed 2 duplicate /gene - caiT_1 caiT_2 [19:53:10] Fixed 2 duplicate /gene - acs_1 acs_2 [19:53:10] Fixed 2 duplicate /gene - ygiW_1 ygiW_2 [19:53:10] Fixed 2 duplicate /gene - arcC1_1 arcC1_2 [19:53:10] Fixed 2 duplicate /gene - gltC_1 gltC_2 [19:53:10] Fixed 2 duplicate /gene - chuR_1 chuR_2 [19:53:10] Fixed 2 duplicate /gene - yhcH_1 yhcH_2 [19:53:10] Fixed 2 duplicate /gene - xerD_1 xerD_2 [19:53:10] Fixed 2 duplicate /gene - cbtA_1 cbtA_2 [19:53:10] Fixed 2 duplicate /gene - fryB_1 fryB_2 [19:53:10] Fixed 2 duplicate /gene - deoB_1 deoB_2 [19:53:10] Fixed 2 duplicate /gene - ytfJ_1 ytfJ_2 [19:53:10] Fixed 2 duplicate /gene - coaA_1 coaA_2 [19:53:10] Fixed 2 duplicate /gene - chbC_1 chbC_2 [19:53:10] Fixed 2 duplicate /gene - nlpD_1 nlpD_2 [19:53:10] Fixed 4 duplicate /gene - era_1 era_2 era_3 era_4 [19:53:10] Fixed 2 duplicate /gene - rhtC_1 rhtC_2 [19:53:10] Fixed 2 duplicate /gene - lutB_1 lutB_2 [19:53:10] Fixed 2 duplicate /gene - gnsA_1 gnsA_2 [19:53:10] Fixed 2 duplicate /gene - mepS_1 mepS_2 [19:53:10] Fixed 2 duplicate /gene - dnaC_1 dnaC_2 [19:53:10] Fixed 2 duplicate /gene - ssuC_1 ssuC_2 [19:53:10] Fixed 3 duplicate /gene - tdh_1 tdh_2 tdh_3 [19:53:10] Fixed 2 duplicate /gene - cbeA_1 cbeA_2 [19:53:10] Fixed 2 duplicate /gene - ulaC_1 ulaC_2 [19:53:10] Fixed 3 duplicate /gene - psuK_1 psuK_2 psuK_3 [19:53:10] Fixed 2 duplicate /gene - ndhI_1 ndhI_2 [19:53:10] Fixed 2 duplicate /gene - ulaA_1 ulaA_2 [19:53:10] Fixed 3 duplicate /gene - bglH_1 bglH_2 bglH_3 [19:53:10] Fixed 2 duplicate /gene - ydfO_1 ydfO_2 [19:53:10] Fixed 2 duplicate /gene - yiaW_1 yiaW_2 [19:53:10] Fixed 2 duplicate /gene - cusR_1 cusR_2 [19:53:10] Fixed 2 duplicate /gene - yohF_1 yohF_2 [19:53:10] Fixed 2 duplicate /gene - melB_1 melB_2 [19:53:10] Fixed 2 duplicate /gene - epsF_1 epsF_2 [19:53:10] Fixed 2 duplicate /gene - ampG_1 ampG_2 [19:53:10] Fixed 2 duplicate /gene - yqiJ_1 yqiJ_2 [19:53:10] Fixed 2 duplicate /gene - cfaB_1 cfaB_2 [19:53:10] Fixed 2 duplicate /gene - dnaK_1 dnaK_2 [19:53:10] Fixed 2 duplicate /gene - bioD1_1 bioD1_2 [19:53:10] Fixed 3 duplicate /gene - papC_1 papC_2 papC_3 [19:53:10] Fixed 3 duplicate /gene - ydcV_1 ydcV_2 ydcV_3 [19:53:10] Fixed 2 duplicate /gene - hns_1 hns_2 [19:53:10] Fixed 2 duplicate /gene - topA_1 topA_2 [19:53:10] Fixed 2 duplicate /gene - yhhT_1 yhhT_2 [19:53:10] Fixed 2 duplicate /gene - cutD_1 cutD_2 [19:53:10] Fixed 2 duplicate /gene - hyfB_1 hyfB_2 [19:53:10] Fixed 2 duplicate /gene - ubiJ_1 ubiJ_2 [19:53:10] Fixed 2 duplicate /gene - artM_1 artM_2 [19:53:10] Fixed 2 duplicate /gene - srmB_1 srmB_2 [19:53:10] Fixed 2 duplicate /gene - gadX_1 gadX_2 [19:53:10] Fixed 2 duplicate /gene - spaS_1 spaS_2 [19:53:10] Fixed 2 duplicate /gene - hlyE_1 hlyE_2 [19:53:10] Fixed 2 duplicate /gene - argE_1 argE_2 [19:53:10] Fixed 2 duplicate /gene - tsr_1 tsr_2 [19:53:10] Fixed 2 duplicate /gene - gfcB_1 gfcB_2 [19:53:10] Fixed 2 duplicate /gene - nohA_1 nohA_2 [19:53:10] Fixed 2 duplicate /gene - oxyR_1 oxyR_2 [19:53:10] Fixed 4 duplicate /gene - srlR_1 srlR_2 srlR_3 srlR_4 [19:53:10] Fixed 2 duplicate /gene - ompN_1 ompN_2 [19:53:10] Fixed 2 duplicate /gene - cusA_1 cusA_2 [19:53:10] Fixed 2 duplicate /gene - dmsB_1 dmsB_2 [19:53:10] Fixed 2 duplicate /gene - mhpE_1 mhpE_2 [19:53:10] Fixed 2 duplicate /gene - pal_1 pal_2 [19:53:10] Fixed 2 duplicate /gene - psiB_1 psiB_2 [19:53:10] Fixed 4 duplicate /gene - def_1 def_2 def_3 def_4 [19:53:10] Fixed 3 duplicate /gene - lgoD_1 lgoD_2 lgoD_3 [19:53:10] Fixed 2 duplicate /gene - hdfR_1 hdfR_2 [19:53:10] Fixed 2 duplicate /gene - yihP_1 yihP_2 [19:53:10] Fixed 4 duplicate /gene - klcA_1 klcA_2 klcA_3 klcA_4 [19:53:10] Fixed 3 duplicate /gene - norR_1 norR_2 norR_3 [19:53:10] Fixed 2 duplicate /gene - ulaE_1 ulaE_2 [19:53:10] Fixed 2 duplicate /gene - pdhR_1 pdhR_2 [19:53:10] Fixed 2 duplicate /gene - acpP_1 acpP_2 [19:53:10] Fixed 2 duplicate /gene - mhpT_1 mhpT_2 [19:53:10] Fixed 3 duplicate /gene - hcpA_1 hcpA_2 hcpA_3 [19:53:10] Fixed 2 duplicate /gene - mglA_1 mglA_2 [19:53:10] Fixed 2 duplicate /gene - fdrA_1 fdrA_2 [19:53:10] Fixed 5 duplicate /gene - hyfA_1 hyfA_2 hyfA_3 hyfA_4 hyfA_5 [19:53:10] Fixed 2 duplicate /gene - fimF_1 fimF_2 [19:53:10] Fixed 2 duplicate /gene - traS_1 traS_2 [19:53:10] Fixed 2 duplicate /gene - umuD_1 umuD_2 [19:53:10] Fixed 2 duplicate /gene - aceA_1 aceA_2 [19:53:10] Fixed 2 duplicate /gene - gspA_1 gspA_2 [19:53:10] Fixed 2 duplicate /gene - pitA_1 pitA_2 [19:53:10] Fixed 2 duplicate /gene - gatZ_1 gatZ_2 [19:53:10] Fixed 2 duplicate /gene - mhpF_1 mhpF_2 [19:53:10] Fixed 2 duplicate /gene - ttdT_1 ttdT_2 [19:53:10] Fixed 2 duplicate /gene - vgrG1_1 vgrG1_2 [19:53:10] Fixed 2 duplicate /gene - oleD_1 oleD_2 [19:53:10] Fixed 2 duplicate /gene - ydiF_1 ydiF_2 [19:53:10] Fixed 3 duplicate /gene - cspG_1 cspG_2 cspG_3 [19:53:10] Fixed 2 duplicate /gene - cysE_1 cysE_2 [19:53:10] Fixed 2 duplicate /gene - traY_1 traY_2 [19:53:10] Fixed 3 duplicate /gene - rhsC_1 rhsC_2 rhsC_3 [19:53:10] Fixed 3 duplicate /gene - lutA_1 lutA_2 lutA_3 [19:53:10] Fixed 4 duplicate /gene - rhaS_1 rhaS_2 rhaS_3 rhaS_4 [19:53:10] Fixed 2 duplicate /gene - acrR_1 acrR_2 [19:53:10] Fixed 2 duplicate /gene - ais_1 ais_2 [19:53:10] Fixed 2 duplicate /gene - ylpA_1 ylpA_2 [19:53:10] Fixed 2 duplicate /gene - manX_1 manX_2 [19:53:10] Fixed 2 duplicate /gene - tsaR_1 tsaR_2 [19:53:10] Fixed 2 duplicate /gene - ydjE_1 ydjE_2 [19:53:10] Fixed 2 duplicate /gene - yfdE_1 yfdE_2 [19:53:10] Fixed 3 duplicate /gene - umuC_1 umuC_2 umuC_3 [19:53:10] Fixed 3 duplicate /gene - lexA_1 lexA_2 lexA_3 [19:53:10] Fixed 2 duplicate /gene - epsE_1 epsE_2 [19:53:10] Fixed 2 duplicate /gene - papD_1 papD_2 [19:53:10] Fixed 2 duplicate /gene - fimH_1 fimH_2 [19:53:10] Fixed 2 duplicate /gene - gspK_1 gspK_2 [19:53:10] Fixed 2 duplicate /gene - sgrR_1 sgrR_2 [19:53:10] Fixed 2 duplicate /gene - pspB_1 pspB_2 [19:53:10] Fixed 2 duplicate /gene - gntR_1 gntR_2 [19:53:10] Fixed 2 duplicate /gene - cfaD_1 cfaD_2 [19:53:10] Fixed 3 duplicate /gene - lolD_1 lolD_2 lolD_3 [19:53:10] Fixed 2 duplicate /gene - tas_1 tas_2 [19:53:10] Fixed 3 duplicate /gene - rfaH_1 rfaH_2 rfaH_3 [19:53:10] Fixed 2 duplicate /gene - pndA_1 pndA_2 [19:53:10] Fixed 2 duplicate /gene - fdnG_1 fdnG_2 [19:53:10] Fixed 2 duplicate /gene - ybiI_1 ybiI_2 [19:53:10] Fixed 2 duplicate /gene - vapC_1 vapC_2 [19:53:10] Fixed 2 duplicate /gene - pgrR_1 pgrR_2 [19:53:10] Fixed 2 duplicate /gene - ybgD_1 ybgD_2 [19:53:10] Fixed 2 duplicate /gene - finO_1 finO_2 [19:53:10] Fixed 2 duplicate /gene - repA_1 repA_2 [19:53:10] Fixed 2 duplicate /gene - yrdA_1 yrdA_2 [19:53:10] Fixed 2 duplicate /gene - leuC_1 leuC_2 [19:53:10] Fixed 2 duplicate /gene - gntP_1 gntP_2 [19:53:10] Fixed 2 duplicate /gene - ydgA_1 ydgA_2 [19:53:10] Fixed 2 duplicate /gene - mlc_1 mlc_2 [19:53:10] Fixed 2 duplicate /gene - lapB_1 lapB_2 [19:53:10] Fixed 2 duplicate /gene - flhA_1 flhA_2 [19:53:10] Fixed 2 duplicate /gene - yehB_1 yehB_2 [19:53:10] Fixed 2 duplicate /gene - lptB_1 lptB_2 [19:53:10] Fixed 2 duplicate /gene - fixB_1 fixB_2 [19:53:10] Fixed 2 duplicate /gene - ehaG_1 ehaG_2 [19:53:10] Fixed 2 duplicate /gene - sfmD_1 sfmD_2 [19:53:10] Fixed 2 duplicate /gene - dld_1 dld_2 [19:53:10] Fixed 2 duplicate /gene - acrB_1 acrB_2 [19:53:10] Fixed 2 duplicate /gene - bhsA_1 bhsA_2 [19:53:10] Fixed 2 duplicate /gene - aaeA_1 aaeA_2 [19:53:10] Fixed 2 duplicate /gene - kdgK_1 kdgK_2 [19:53:10] Fixed 2 duplicate /gene - mdh_1 mdh_2 [19:53:10] Fixed 2 duplicate /gene - mhpA_1 mhpA_2 [19:53:10] Fixed 5 duplicate /gene - dmlR_1 dmlR_2 dmlR_3 dmlR_4 dmlR_5 [19:53:10] Fixed 2 duplicate /gene - caiA_1 caiA_2 [19:53:10] Fixed 3 duplicate /gene - pncC_1 pncC_2 pncC_3 [19:53:10] Fixed 2 duplicate /gene - ldrA_1 ldrA_2 [19:53:10] Fixed 4 duplicate /gene - arnC_1 arnC_2 arnC_3 arnC_4 [19:53:10] Fixed 3 duplicate /gene - cusC_1 cusC_2 cusC_3 [19:53:10] Fixed 2 duplicate /gene - casA_1 casA_2 [19:53:10] Fixed 2 duplicate /gene - menE_1 menE_2 [19:53:10] Fixed 2 duplicate /gene - cusS_1 cusS_2 [19:53:10] Fixed 3 duplicate /gene - mngR_1 mngR_2 mngR_3 [19:53:10] Fixed 3 duplicate /gene - kefC_1 kefC_2 kefC_3 [19:53:10] Fixed 2 duplicate /gene - dadA_1 dadA_2 [19:53:10] Fixed 3 duplicate /gene - hcaR_1 hcaR_2 hcaR_3 [19:53:10] Fixed 2 duplicate /gene - fruA_1 fruA_2 [19:53:10] Fixed 2 duplicate /gene - proQ_1 proQ_2 [19:53:10] Fixed 2 duplicate /gene - proA_1 proA_2 [19:53:10] Fixed 2 duplicate /gene - fixA_1 fixA_2 [19:53:10] Fixed 2 duplicate /gene - ccmF_1 ccmF_2 [19:53:10] Fixed 2 duplicate /gene - lldR_1 lldR_2 [19:53:10] Fixed 2 duplicate /gene - nagB_1 nagB_2 [19:53:10] Fixed 2 duplicate /gene - yqiK_1 yqiK_2 [19:53:10] Fixed 3 duplicate /gene - traM_1 traM_2 traM_3 [19:53:10] Fixed 3 duplicate /gene - ompX_1 ompX_2 ompX_3 [19:53:10] Fixed 2 duplicate /gene - htpX_1 htpX_2 [19:53:10] Fixed 265 colliding /gene names. [19:53:10] Adding /locus_tag identifiers [19:53:11] Assigned 5192 locus_tags to CDS and RNA features. [19:53:11] Writing outputs to E562_annotation/ [19:53:17] Generating annotation statistics file [19:53:17] Generating Genbank and Sequin files [19:53:17] Running: tbl2asn -V b -a r10k -l paired-ends -M n -N 1 -y 'Annotated using prokka 1.14.6 from https://github.com/tseemann/prokka' -Z E562_annotation\/E562_genome.err -i E562_annotation\/E562_genome.fsa 2> /dev/null [19:53:29] Could not run command: tbl2asn -V b -a r10k -l paired-ends -M n -N 1 -y 'Annotated using prokka 1.14.6 from https://github.com/tseemann/prokka' -Z E562_annotation\/E562_genome.err -i E562_annotation\/E562_genome.fsa 2> /dev/null

Thanks in advance! /Astrid

tseemann commented 4 years ago

You still seem to have the old "expired" version of tbl2asn installed Determined tbl2asn version is 025007 from 'tbl2asn 25.7 arguments:' Please delete it and replace it with 25.8 (it's included in prokka/binaries/) Or upgrade your conda env (conda update prokka ?) or brew (brew update ; brew upgrade prokka)