[21:30:27] This is prokka 1.12 [21:30:27] Written by Torsten Seemann [21:30:27] Homepage is https://github.com/tseemann/prokka [21:30:27] Local time is Mon Aug 18 21:30:27 2025 [21:30:27] You are pabloati [21:30:27] Operating system is linux [21:30:27] You have BioPerl 1.006924 [21:30:27] System has 8 cores. [21:30:27] Will use maximum of 8 cores. [21:30:27] Annotating as >>> Bacteria <<< [21:30:27] Generating locus_tag from 'results/bsubtilis/final_assembly.fasta' contents. [21:30:27] Setting --locustag GDDPFNLP from MD5 0dd9f75950d16b1b6bda605ad7a07a76 [21:30:27] Creating new output folder: results/bsubtilis/annotation [21:30:27] Running: mkdir -p results\/bsubtilis\/annotation [21:30:27] Using filename prefix: bsubtilis.XXX [21:30:27] Setting HMMER_NCPU=1 [21:30:27] Writing log to: results/bsubtilis/annotation/bsubtilis.log [21:30:27] Command: /home/pabloati/miniforge3/envs/pablo_course/bin/prokka --outdir results/bsubtilis/annotation --prefix bsubtilis --genus Bacillus --cpus 8 results/bsubtilis/final_assembly.fasta [21:30:27] Appending to PATH: /home/pabloati/miniforge3/envs/pablo_course/bin [21:30:27] Looking for 'aragorn' - found /home/pabloati/miniforge3/envs/pablo_course/bin/aragorn [21:30:27] Determined aragorn version is 1.2 [21:30:27] Looking for 'barrnap' - found /home/pabloati/miniforge3/envs/pablo_course/bin/barrnap [21:30:27] Determined barrnap version is 0.9 [21:30:27] Looking for 'blastp' - found /home/pabloati/miniforge3/envs/pablo_course/bin/blastp [21:30:27] Determined blastp version is 2.2 [21:30:27] Looking for 'cmpress' - found /home/pabloati/miniforge3/envs/pablo_course/bin/cmpress [21:30:27] Determined cmpress version is 1.1 [21:30:27] Looking for 'cmscan' - found /home/pabloati/miniforge3/envs/pablo_course/bin/cmscan [21:30:27] Determined cmscan version is 1.1 [21:30:27] Looking for 'egrep' - found /usr/bin/egrep [21:30:27] Looking for 'find' - found /home/pabloati/miniforge3/envs/pablo_course/bin/find [21:30:27] Looking for 'grep' - found /usr/bin/grep [21:30:27] Looking for 'hmmpress' - found /home/pabloati/miniforge3/envs/pablo_course/bin/hmmpress [21:30:28] Determined hmmpress version is 3.4 [21:30:28] Looking for 'hmmscan' - found /home/pabloati/miniforge3/envs/pablo_course/bin/hmmscan [21:30:28] Determined hmmscan version is 3.4 [21:30:28] Looking for 'java' - found /home/pabloati/miniforge3/envs/pablo_course/bin/java [21:30:28] Looking for 'less' - found /usr/bin/less [21:30:28] Looking for 'makeblastdb' - found /home/pabloati/miniforge3/envs/pablo_course/bin/makeblastdb [21:30:28] Determined makeblastdb version is 2.2 [21:30:28] Looking for 'minced' - found /home/pabloati/miniforge3/envs/pablo_course/bin/minced [21:30:28] Determined minced version is 4.2 [21:30:28] Looking for 'parallel' - found /home/pabloati/miniforge3/envs/pablo_course/bin/parallel [21:30:28] Determined parallel version is 20250622 [21:30:28] Looking for 'prodigal' - found /home/pabloati/miniforge3/envs/pablo_course/bin/prodigal [21:30:28] Determined prodigal version is 2.6 [21:30:28] Looking for 'prokka-genbank_to_fasta_db' - found /home/pabloati/miniforge3/envs/pablo_course/bin/prokka-genbank_to_fasta_db [21:30:28] Looking for 'sed' - found /home/pabloati/miniforge3/envs/pablo_course/bin/sed [21:30:28] Looking for 'tbl2asn' - found /home/pabloati/miniforge3/envs/pablo_course/bin/tbl2asn [21:30:28] Determined tbl2asn version is 25.8 [21:30:28] Using genetic code table 11. [21:30:28] Loading and checking input file: results/bsubtilis/final_assembly.fasta [21:30:28] Wrote 2 contigs totalling 4299847 bp. [21:30:28] Predicting tRNAs and tmRNAs [21:30:28] Running: aragorn -l -gc11 -w results\/bsubtilis\/annotation\/bsubtilis\.fna [21:30:29] 1 tRNA-Ile [11055,11131] 35 (gat) [21:30:29] 2 tRNA-Ala [11143,11218] 34 (tgc) [21:30:29] 3 tRNA-Ser [21883,21975] 37 (tga) [21:30:29] 4 tRNA-Ile [31523,31599] 35 (gat) [21:30:29] 5 tRNA-Ala [31611,31686] 34 (tgc) [21:30:29] 6 tRNA-Met [69772,69848] 35 (cat) [21:30:29] 7 tRNA-Glu [69857,69932] 35 (ttc) [21:30:29] 8 tRNA-Val [94966,95041] 34 (tac) [21:30:29] 9 tRNA-Thr [95046,95121] 34 (tgt) [21:30:29] 10 tRNA-Lys [95158,95233] 34 (ttt) [21:30:29] 11 tRNA-Leu [95240,95322] 35 (tag) [21:30:29] 12 tRNA-Gly [95363,95437] 33 (gcc) [21:30:29] 13 tRNA-Leu [95452,95537] 35 (taa) [21:30:29] 14 tRNA-Arg [95547,95623] 35 (acg) [21:30:29] 15 tRNA-Pro [95651,95727] 35 (tgg) [21:30:29] 16 tRNA-Ala [95737,95812] 34 (tgc) [21:30:29] 17 tRNA-Asn [165346,165420] 33 (gtt) [21:30:29] 18 tRNA-Thr [165423,165495] 34 (ggt) [21:30:29] 19 tRNA-Gly [165552,165626] 33 (gcc) [21:30:29] 20 tRNA-Arg [165658,165734] 35 (acg) [21:30:29] 21 tRNA-Pro [165762,165838] 35 (tgg) [21:30:29] 22 tRNA-Ala [165847,165922] 34 (tgc) [21:30:29] 23 tRNA-Glu [193804,193878] 34 (ttc) [21:30:29] 24 tRNA-Val [193882,193957] 34 (tac) [21:30:29] 25 tRNA-Thr [193962,194035] 34 (tgt) [21:30:29] 26 tRNA-Tyr [194057,194141] 35 (gta) [21:30:29] 27 tRNA-Gln [194145,194219] 34 (ttg) [21:30:29] 28 tRNA-Asn [528297,528371] 33 (gtt) [21:30:29] 29 tRNA-Ser [528376,528466] 35 (gct) [21:30:29] 30 tRNA-Glu [528496,528567] 34 (ttc) [21:30:29] 31 tRNA-Gln [528579,528653] 33 (ttg) [21:30:29] 32 tRNA-Lys [528680,528755] 34 (ttt) [21:30:29] 33 tRNA-Leu [528767,528849] 35 (tag) [21:30:29] 34 tRNA-Leu [528929,529012] 34 (gag) [21:30:29] 35 tRNA-Arg [634697,634773] 35 (acg) [21:30:29] 36 tRNA-Gly [634787,634860] 33 (tcc) [21:30:29] 37 tRNA-Met [639855,639931] 35 (cat) [21:30:29] 38 tRNA-Asp [639992,640068] 35 (gtc) [21:30:29] 39 tRNA-Asn [951169,951243] 33 (gtt) [21:30:29] 40 tRNA-Ser [951249,951340] 35 (gga) [21:30:29] 41 tRNA-Glu [951375,951446] 34 (ttc) [21:30:29] 42 tRNA-Val [951456,951531] 34 (tac) [21:30:29] 43 tRNA-Met [951541,951617] 35 (cat) [21:30:29] 44 tRNA-Asp [951629,951705] 35 (gtc) [21:30:29] 45 tRNA-Phe [951718,951793] 34 (gaa) [21:30:29] 46 tRNA-Thr [951799,951872] 34 (tgt) [21:30:29] 47 tRNA-Tyr [951894,951978] 35 (gta) [21:30:29] 48 tRNA-Trp [951984,952057] 33 (cca) [21:30:29] 49 tRNA-His [952082,952157] 34 (gtg) [21:30:29] 50 tRNA-Gln [952166,952240] 34 (ttg) [21:30:29] 51 tRNA-Gly [952288,952362] 33 (gcc) [21:30:29] 52 tRNA-Cys [952368,952438] 33 (gca) [21:30:29] 53 tRNA-Leu [952446,952534] 35 (taa) [21:30:29] 54 tRNA-Leu [952799,952882] 36 (caa) [21:30:29] 55 tRNA-Gly [966652,966725] 33 (tcc) [21:30:29] 56 tRNA-Val [1262378,1262452] 35 (gac) [21:30:29] 57 tRNA-Arg c[2002874,2002946] 34 (cct) [21:30:29] 58 tRNA-Asn c[2143687,2143783] 37 (gtt) [21:30:29] 59 tRNA-Gln [2563479,2563549] 33 (ttg) [21:30:29] 60 tRNA-Arg c[2899406,2899481] 36 (tct) [21:30:29] 61 tRNA-Glu c[3171471,3171542] 34 (ttc) [21:30:29] 62 tRNA-Ser c[3171568,3171658] 35 (gct) [21:30:29] 63 tRNA-Asn c[3171662,3171736] 33 (gtt) [21:30:29] 64 tRNA-Ile c[3171747,3171823] 35 (gat) [21:30:29] 65 tRNA-Gly c[3171839,3171912] 33 (tcc) [21:30:29] 66 tRNA-His c[3171923,3171998] 34 (gtg) [21:30:29] 67 tRNA-Phe c[3172016,3172091] 34 (gaa) [21:30:29] 68 tRNA-Asp c[3172104,3172180] 35 (gtc) [21:30:29] 69 tRNA-Met c[3172192,3172268] 35 (cat) [21:30:29] 70 tRNA-Ser c[3172286,3172378] 37 (tga) [21:30:29] 71 tRNA-Met c[3172385,3172461] 35 (cat) [21:30:29] 72 tRNA-Met c[3172464,3172540] 35 (cat) [21:30:29] 73 tRNA-Ala c[3172559,3172632] 34 (tgc) [21:30:29] 74 tRNA-Pro c[3172638,3172714] 35 (tgg) [21:30:29] 75 tRNA-Arg c[3172730,3172806] 35 (acg) [21:30:29] 76 tRNA-Leu c[3172816,3172901] 35 (taa) [21:30:29] 77 tRNA-Gly c[3172916,3172990] 33 (gcc) [21:30:29] 78 tRNA-Leu c[3172996,3173082] 35 (cag) [21:30:29] 79 tRNA-Lys c[3173093,3173168] 34 (ttt) [21:30:29] 80 tRNA-Thr c[3173206,3173281] 34 (tgt) [21:30:29] 81 tRNA-Val c[3173314,3173389] 34 (tac) [21:30:29] 82 tRNA-Ala c[3194047,3194119] 34 (ggc) [21:30:29] 83 tmRNA c[3450304,3450663] 87,134 GKTNSFNQNVALAA** [21:30:29] 84 tRNA-Arg c[3545478,3545558] 36 (ccg) [21:30:29] 85 tRNA-Phe c[4154402,4154475] 34 (gaa) [21:30:29] 86 tRNA-Asp c[4154511,4154587] 35 (gtc) [21:30:29] 87 tRNA-Glu c[4154669,4154740] 34 (ttc) [21:30:29] 88 tRNA-Lys c[4154750,4154825] 34 (ttt) [21:30:29] 1 tRNA-Trp c[36246,36319] 33 (cca) [21:30:29] 2 tRNA-Asn c[36321,36397] 35 (gtt) [21:30:29] Found 90 tRNAs [21:30:29] Predicting Ribosomal RNAs [21:30:29] Running Barrnap with 8 threads [21:30:31] 1 contig_1 9406 16S ribosomal RNA [21:30:31] 2 contig_1 11302 23S ribosomal RNA [21:30:31] 3 contig_1 14285 5S ribosomal RNA [21:30:31] 4 contig_1 29874 16S ribosomal RNA [21:30:31] 5 contig_1 31770 23S ribosomal RNA [21:30:31] 6 contig_1 34830 5S ribosomal RNA [21:30:31] 7 contig_1 90131 16S ribosomal RNA [21:30:31] 8 contig_1 91847 23S ribosomal RNA [21:30:31] 9 contig_1 94830 5S ribosomal RNA [21:30:31] 10 contig_1 95987 16S ribosomal RNA [21:30:31] 11 contig_1 97703 23S ribosomal RNA [21:30:31] 12 contig_1 100686 5S ribosomal RNA [21:30:31] 13 contig_1 160488 16S ribosomal RNA [21:30:31] 14 contig_1 162204 23S ribosomal RNA [21:30:31] 15 contig_1 165187 5S ribosomal RNA [21:30:31] 16 contig_1 166097 16S ribosomal RNA [21:30:31] 17 contig_1 167813 23S ribosomal RNA [21:30:31] 18 contig_1 170796 5S ribosomal RNA [21:30:31] 19 contig_1 171099 16S ribosomal RNA [21:30:31] 20 contig_1 172815 23S ribosomal RNA [21:30:31] 21 contig_1 175798 5S ribosomal RNA [21:30:31] 22 contig_1 635025 16S ribosomal RNA [21:30:31] 23 contig_1 636744 23S ribosomal RNA [21:30:31] 24 contig_1 639727 5S ribosomal RNA [21:30:31] 25 contig_1 946288 16S ribosomal RNA [21:30:31] 26 contig_1 948007 23S ribosomal RNA [21:30:31] 27 contig_1 951046 5S ribosomal RNA [21:30:31] 28 contig_1 3173415 5S ribosomal RNA [21:30:31] 29 contig_1 3173584 23S ribosomal RNA [21:30:31] 30 contig_1 3176681 16S ribosomal RNA [21:30:31] Found 30 rRNAs [21:30:31] Skipping ncRNA search, enable with --rfam if desired. [21:30:31] Total of 119 tRNA + rRNA features [21:30:31] Searching for CRISPR repeats [21:30:32] Found 0 CRISPRs [21:30:32] Predicting coding sequences [21:30:32] Contigs total 4299847 bp, so using single mode [21:30:32] Running: prodigal -i results\/bsubtilis\/annotation\/bsubtilis\.fna -c -m -g 11 -p single -f sco -q [21:30:38] Excluding CDS which overlaps existing RNA (rRNA) at contig_1:10597..10851 on + strand [21:30:38] Excluding CDS which overlaps existing RNA (rRNA) at contig_1:31065..31319 on + strand [21:30:38] Excluding CDS which overlaps existing RNA (rRNA) at contig_1:91322..91576 on + strand [21:30:38] Excluding CDS which overlaps existing RNA (rRNA) at contig_1:97178..97432 on + strand [21:30:38] Excluding CDS which overlaps existing RNA (rRNA) at contig_1:161679..161933 on + strand [21:30:38] Excluding CDS which overlaps existing RNA (rRNA) at contig_1:167288..167542 on + strand [21:30:38] Excluding CDS which overlaps existing RNA (rRNA) at contig_1:172290..172544 on + strand [21:30:39] Excluding CDS which overlaps existing RNA (tRNA) at contig_1:634736..634849 on - strand [21:30:39] Excluding CDS which overlaps existing RNA (rRNA) at contig_1:636216..636470 on + strand [21:30:39] Excluding CDS which overlaps existing RNA (rRNA) at contig_1:947479..947733 on + strand [21:30:41] Excluding CDS which overlaps existing RNA (tRNA) at contig_1:2143259..2143948 on - strand [21:30:42] Excluding CDS which overlaps existing RNA (rRNA) at contig_1:3176782..3177036 on - strand [21:30:43] Excluding CDS which overlaps existing RNA (tRNA) at contig_2:34515..36305 on - strand [21:30:43] Found 4312 CDS [21:30:43] Connecting features back to sequences [21:30:43] Not using genus-specific database. Try --usegenus to enable it. [21:30:43] Annotating CDS, please be patient. [21:30:43] Will use 8 CPUs for similarity searching. [21:30:46] There are still 4312 unannotated CDS left (started with 4312) [21:30:46] Will use blast to search against /home/pabloati/miniforge3/envs/pablo_course/bin/../db/kingdom/Bacteria/sprot with 8 CPUs [21:30:46] Running: cat results\/bsubtilis\/annotation\/sprot\.faa | parallel --gnu --plain -j 8 --block 80280 --recstart '>' --pipe blastp -query - -db /home/pabloati/miniforge3/envs/pablo_course/bin/../db/kingdom/Bacteria/sprot -evalue 1e-06 -num_threads 1 -num_descriptions 1 -num_alignments 1 -seg no > results\/bsubtilis\/annotation\/sprot\.blast 2> /dev/null [21:31:34] Modify product: Uncharacterized oxidoreductase YghA => putative oxidoreductase YghA [21:31:34] Modify product: Uncharacterized symporter YodF => putative symporter YodF [21:31:34] Modify product: Uncharacterized cysteine-rich protein YhjQ => putative cysteine-rich protein YhjQ [21:31:34] Modify product: Probable spore germination protein GerPF => putative spore germination protein GerPF [21:31:34] Modify product: Probable spore germination protein GerPE => putative spore germination protein GerPE [21:31:34] Modify product: Probable spore germination protein GerPD => putative spore germination protein GerPD [21:31:34] Modify product: Probable spore germination protein GerPC => putative spore germination protein GerPC [21:31:34] Modify product: Probable spore germination protein GerPB => putative spore germination protein GerPB [21:31:34] Modify product: Probable spore germination protein GerPA => putative spore germination protein GerPA [21:31:34] Modify product: Probable FMN/FAD exporter YeeO => putative FMN/FAD exporter YeeO [21:31:34] Modify product: Probable adenylyl-sulfate kinase => putative adenylyl-sulfate kinase [21:31:34] Modify product: Probable 2-phosphosulfolactate phosphatase => putative 2-phosphosulfolactate phosphatase [21:31:34] Modify product: Fatty acid-binding protein TM_1468 => Fatty acid-binding protein [21:31:34] Modify product: Purine-binding protein BAB2_0673 => Purine-binding protein [21:31:34] Modify product: Uncharacterized N-acetyltransferase YjcF => putative N-acetyltransferase YjcF [21:31:34] Modify product: Putative formate dehydrogenase SA2102 => Putative formate dehydrogenase [21:31:34] Modify product: Uncharacterized lipoprotein YjhA => putative lipoprotein YjhA [21:31:34] Modify product: Probable iron export permease protein FetB => putative iron export permease protein FetB [21:31:34] Modify product: Uncharacterized symporter YjmB => putative symporter YjmB [21:31:34] Modify product: Uncharacterized oxidoreductase YjmC => putative oxidoreductase YjmC [21:31:34] Modify product: Uncharacterized zinc-type alcohol dehydrogenase-like protein YjmD => putative zinc-type alcohol dehydrogenase-like protein YjmD [21:31:34] Modify product: Uncharacterized oxidoreductase UxuB => putative oxidoreductase UxuB [21:31:34] Modify product: Probable HTH-type transcriptional repressor ExuR => putative HTH-type transcriptional repressor ExuR [21:31:34] Modify product: Uncharacterized ATPase YjoB => putative ATPase YjoB [21:31:34] Modify product: Probable manganese catalase => putative manganese catalase [21:31:34] Modify product: Uncharacterized glycosyltransferase sll0501 => putative glycosyltransferase [21:31:34] Modify product: Probable murein peptide carboxypeptidase => putative murein peptide carboxypeptidase [21:31:34] Modify product: Uncharacterized acyl-CoA thioester hydrolase HI_0827 => putative acyl-CoA thioester hydrolase [21:31:34] Modify product: Nucleoid-associated protein Cthe_2143 => Nucleoid-associated protein [21:31:34] Modify product: TelA-like protein SA1238 => TelA-like protein [21:31:34] Modify product: Uncharacterized metal-dependent hydrolase YcfH => putative metal-dependent hydrolase YcfH [21:31:34] Modify product: Probable serine/threonine-protein kinase YabT => putative serine/threonine-protein kinase YabT [21:31:34] Modify product: Probable tRNA-dihydrouridine synthase => putative tRNA-dihydrouridine synthase [21:31:34] Modify product: Uncharacterized PIN and TRAM-domain containing protein YacL => putative PIN and TRAM-domain containing protein YacL [21:31:34] Modify product: Ribosome-associated protein L7Ae-like => Ribosome-associated protein L7Ae-like protein [21:31:34] Modify product: PTS system EIIBC component SA0186 => PTS system EIIBC component [21:31:34] Modify product: Uncharacterized HTH-type transcriptional regulator YbbH => putative HTH-type transcriptional regulator YbbH [21:31:34] Modify product: Probable serine/threonine-protein kinase YbdM => putative serine/threonine-protein kinase YbdM [21:31:34] Modify product: Probable transport protein YifK => putative transport protein YifK [21:31:34] Modify product: Probable beta-lactamase YbxI => putative beta-lactamase YbxI [21:31:34] Modify product: Uncharacterized inner membrane transporter YhbE => putative inner membrane transporter YhbE [21:31:34] Modify product: Uncharacterized membrane protein YbgB => putative membrane protein YbgB [21:31:34] Modify product: Probable 5-dehydro-4-deoxyglucarate dehydratase => putative 5-dehydro-4-deoxyglucarate dehydratase [21:31:34] Modify product: Probable glucarate transporter => putative glucarate transporter [21:31:34] Modify product: Uncharacterized ABC transporter ATP-binding protein YxlF => putative ABC transporter ATP-binding protein YxlF [21:31:34] Modify product: Probable cysteine desulfurase => putative cysteine desulfurase [21:31:34] Modify product: Probable multidrug resistance protein EmrY => putative multidrug resistance protein EmrY [21:31:34] Modify product: Uncharacterized HTH-type transcriptional regulator YxaF => putative HTH-type transcriptional regulator YxaF [21:31:34] Modify product: Uncharacterized lipoprotein YcdA => putative lipoprotein YcdA [21:31:34] Modify product: Probable deoxyuridine 5'-triphosphate nucleotidohydrolase YncF => putative deoxyuridine 5'-triphosphate nucleotidohydrolase YncF [21:31:34] Modify product: Resolvase homolog YneB => Resolvase YneB [21:31:34] Modify product: Putative esterase aq_1494 => Putative esterase [21:31:34] Modify product: Uncharacterized membrane protein Rv0364 => putative membrane protein [21:31:34] Modify product: Probable propionyl-CoA carboxylase beta chain 5 => putative propionyl-CoA carboxylase beta chain 5 [21:31:34] Modify product: Probable cystine transporter YijE => putative cystine transporter YijE [21:31:34] Modify product: Uncharacterized protease YdeA => putative protease YdeA [21:31:34] Modify product: Probable chaperone CsaA => putative chaperone CsaA [21:31:34] Modify product: Probable metallo-hydrolase M6_Spy0554 => putative metallo-hydrolase [21:31:34] Modify product: Probable N-acetyl-alpha-D-glucosaminyl L-malate deacetylase 2 => putative N-acetyl-alpha-D-glucosaminyl L-malate deacetylase 2 [21:31:34] Modify product: Uncharacterized symporter YodF => putative symporter YodF [21:31:35] Modify product: Probable succinyl-CoA:3-ketoacid coenzyme A transferase subunit B => putative succinyl-CoA:3-ketoacid coenzyme A transferase subunit B [21:31:35] Modify product: Probable aminotransferase Rv3329 => putative aminotransferase [21:31:35] Modify product: Uncharacterized glycosyltransferase YkoT => putative glycosyltransferase YkoT [21:31:35] Modify product: Uncharacterized signaling protein CC_0091 => putative signaling protein [21:31:35] Modify product: Uncharacterized HTH-type transcriptional regulator YtcD => putative HTH-type transcriptional regulator YtcD [21:31:35] Modify product: Uncharacterized peptidase SA1530 => putative peptidase [21:31:35] Modify product: Probable 2,4-dienoyl-CoA reductase => putative 2,4-dienoyl-CoA reductase [21:31:35] Modify product: Uncharacterized EAL-domain containing protein YkuI => putative EAL-domain containing protein YkuI [21:31:35] Modify product: Uncharacterized MscS family protein YkuT => putative MscS family protein YkuT [21:31:35] Modify product: Probable molybdenum cofactor guanylyltransferase => putative molybdenum cofactor guanylyltransferase [21:31:35] Modify product: Putative multidrug export ATP-binding/permease protein SA1683 => Putative multidrug export ATP-binding/permease protein [21:31:35] Modify product: Uncharacterized ABC transporter ATP-binding protein TM_0288 => putative ABC transporter ATP-binding protein [21:31:35] Modify product: Uncharacterized ABC transporter ATP-binding protein YknY => putative ABC transporter ATP-binding protein YknY [21:31:35] Modify product: Uncharacterized ABC transporter permease YknZ => putative ABC transporter permease YknZ [21:31:35] Modify product: Uncharacterized ABC transporter ATP-binding protein YbiT => putative ABC transporter ATP-binding protein YbiT [21:31:35] Modify product: Probable peptidoglycan glycosyltransferase FtsW => putative peptidoglycan glycosyltransferase FtsW [21:31:35] Modify product: Uncharacterized NTE family protein Rv1063c => putative NTE family protein [21:31:35] Modify product: Uncharacterized N-acetyltransferase YlbP => putative N-acetyltransferase YlbP [21:31:35] Modify product: Probable 2-dehydropantoate 2-reductase => putative 2-dehydropantoate 2-reductase [21:31:35] Modify product: Probable peptidoglycan glycosyltransferase FtsW => putative peptidoglycan glycosyltransferase FtsW [21:31:35] Modify product: Uncharacterized ABC transporter ATP-binding protein YlmA => putative ABC transporter ATP-binding protein YlmA [21:31:35] Modify product: Probable adenylyl-sulfate kinase => putative adenylyl-sulfate kinase [21:31:35] Modify product: Uncharacterized MFS-type transporter YcaD => putative MFS-type transporter YcaD [21:31:35] Modify product: Uncharacterized MscS family protein YfkC => putative MscS family protein YfkC [21:31:35] Modify product: Probable tRNA-dihydrouridine synthase => putative tRNA-dihydrouridine synthase [21:31:35] Modify product: Uncharacterized ABC transporter ATP-binding protein Rv1273c => putative ABC transporter ATP-binding protein [21:31:35] Modify product: Uncharacterized ABC transporter ATP-binding protein TM_0288 => putative ABC transporter ATP-binding protein [21:31:35] Modify product: Probable poly-beta-1,6-N-acetyl-D-glucosamine export protein => putative poly-beta-1,6-N-acetyl-D-glucosamine export protein [21:31:35] Modify product: Uncharacterized HTH-type transcriptional regulator YfiR => putative HTH-type transcriptional regulator YfiR [21:31:35] Modify product: Probable transport protein HsrA => putative transport protein HsrA [21:31:35] Modify product: Uncharacterized HTH-type transcriptional regulator YusO => putative HTH-type transcriptional regulator YusO [21:31:35] Modify product: Probable siderophore-binding lipoprotein YfiY => putative siderophore-binding lipoprotein YfiY [21:31:35] Modify product: Probable siderophore transport system permease protein YfiZ => putative siderophore transport system permease protein YfiZ [21:31:35] Modify product: Probable siderophore transport system permease protein YfhA => putative siderophore transport system permease protein YfhA [21:31:35] Modify product: Uncharacterized isomerase YddE => putative isomerase YddE [21:31:35] Modify product: Epimerase family protein SA0724 => Epimerase family protein [21:31:35] Modify product: Putative multidrug export ATP-binding/permease protein SA1683 => Putative multidrug export ATP-binding/permease protein [21:31:35] Modify product: Uncharacterized peptidase Lmo0363 => putative peptidase [21:31:35] Modify product: Uncharacterized FAD-linked oxidoreductase YvdP => putative FAD-linked oxidoreductase YvdP [21:31:35] Modify product: Stress response UPF0229 protein YhbH => hypothetical protein [21:31:35] Modify product: Probable multidrug resistance protein EmrK => putative multidrug resistance protein EmrK [21:31:35] Modify product: Uncharacterized ABC transporter ATP-binding protein YxlF => putative ABC transporter ATP-binding protein YxlF [21:31:35] Modify product: Probable diguanylate cyclase YedQ => putative diguanylate cyclase YedQ [21:31:35] Modify product: Probable peptidoglycan endopeptidase LytE => putative peptidoglycan endopeptidase LytE [21:31:35] Modify product: Uncharacterized amino acid permease YhdG => putative amino acid permease YhdG [21:31:35] Modify product: Probable anti-sigma-M factor YhdK => putative anti-sigma-M factor YhdK [21:31:35] Modify product: Probable anti-sigma-M factor YhdL => putative anti-sigma-M factor YhdL [21:31:35] Modify product: Probable multidrug resistance ABC transporter ATP-binding/permease protein YheI => putative multidrug resistance ABC transporter ATP-binding/permease protein YheI [21:31:35] Modify product: Probable multidrug resistance ABC transporter ATP-binding/permease protein YheH => putative multidrug resistance ABC transporter ATP-binding/permease protein YheH [21:31:35] Modify product: Uncharacterized metallophosphoesterase YhaO => putative metallophosphoesterase YhaO [21:31:35] Modify product: Probable tryptophan transport protein => putative tryptophan transport protein [21:31:35] Modify product: Uncharacterized HIT-like protein HP_0404 => putative HIT-like protein [21:31:35] Modify product: Uncharacterized sugar epimerase YhfK => putative sugar epimerase YhfK [21:31:35] Modify product: Uncharacterized acyl--CoA ligase YhfT => putative acyl--CoA ligase YhfT [21:31:35] Modify product: Probable biotin transporter BioY => putative biotin transporter BioY [21:31:35] Modify product: Uncharacterized HTH-type transcriptional regulator YybR => putative HTH-type transcriptional regulator YybR [21:31:35] Modify product: Probable transporter SCO4007 => putative transporter [21:31:35] Modify product: Uncharacterized HTH-type transcriptional regulator Rv1556 => putative HTH-type transcriptional regulator [21:31:35] Modify product: Uncharacterized inner membrane transporter YedA => putative inner membrane transporter YedA [21:31:35] Modify product: Uncharacterized carboxylesterase nap => putative carboxylesterase nap [21:31:35] Modify product: Uncharacterized membrane protein YdfK => putative membrane protein YdfK [21:31:35] Modify product: Uncharacterized N-acetyltransferase YycN => putative N-acetyltransferase YycN [21:31:35] Modify product: Uncharacterized ABC transporter ATP-binding protein YheS => putative ABC transporter ATP-binding protein YheS [21:31:35] Modify product: Probable mannose-6-phosphate isomerase GmuF => putative mannose-6-phosphate isomerase GmuF [21:31:35] Modify product: Probable manganese catalase => putative manganese catalase [21:31:35] Modify product: Probable manganese catalase => putative manganese catalase [21:31:35] Modify product: Uncharacterized ABC transporter ATP-binding protein YbiT => putative ABC transporter ATP-binding protein YbiT [21:31:35] Modify product: Probable BsuMI modification methylase subunit YdiO => putative BsuMI modification methylase subunit YdiO [21:31:35] Modify product: Probable BsuMI modification methylase subunit YdiP => putative BsuMI modification methylase subunit YdiP [21:31:35] Modify product: Phage shock protein A homolog => Phage shock protein A [21:31:35] Modify product: Probable cation efflux system protein Rv2025c => putative cation efflux system protein [21:31:35] Modify product: Probable antitoxin YezG => putative antitoxin YezG [21:31:35] Modify product: Probable transcriptional regulatory protein SA0624 => putative transcriptional regulatory protein [21:31:35] Modify product: Uncharacterized PhzA/B-like protein PA3332 => putative PhzA/B-like protein [21:31:35] Modify product: Uncharacterized response regulatory protein SA0215 => putative response regulatory protein [21:31:35] Modify product: Probable rhamnogalacturonan acetylesterase YesY => putative rhamnogalacturonan acetylesterase YesY [21:31:35] Modify product: Uncharacterized multiple-sugar transport system permease YteP => putative multiple-sugar transport system permease YteP [21:31:35] Modify product: Uncharacterized amino acid permease YhdG => putative amino acid permease YhdG [21:31:35] Modify product: Uncharacterized ABC transporter ATP-binding protein YbiT => putative ABC transporter ATP-binding protein YbiT [21:31:35] Modify product: Probable ATP-dependent RNA helicase YfmL => putative ATP-dependent RNA helicase YfmL [21:31:35] Modify product: Probable siderophore transport system ATP-binding protein YusV => putative siderophore transport system ATP-binding protein YusV [21:31:35] Modify product: Probable siderophore transport system permease protein YfiZ => putative siderophore transport system permease protein YfiZ [21:31:35] Modify product: Probable metallo-hydrolase YflN => putative metallo-hydrolase YflN [21:31:35] Modify product: Probable oligo-1,6-glucosidase 2 => putative oligo-1,6-glucosidase 2 [21:31:35] Modify product: TelA-like protein SA1238 => TelA-like protein [21:31:35] Modify product: Uncharacterized hydrolase YxeP => putative hydrolase YxeP [21:31:35] Modify product: Uncharacterized methyltransferase YcgJ => putative methyltransferase YcgJ [21:31:35] Modify product: Probable ABC transporter extracellular-binding protein YckB => putative ABC transporter extracellular-binding protein YckB [21:31:35] Modify product: Probable UbiX-like flavin prenyltransferase => putative UbiX-like flavin prenyltransferase [21:31:35] Modify product: Probable siderophore transport system ATP-binding protein YusV => putative siderophore transport system ATP-binding protein YusV [21:31:35] Modify product: Uncharacterized ABC transporter solute-binding protein YclQ => putative ABC transporter solute-binding protein YclQ [21:31:35] Modify product: Probable multidrug resistance protein EmrY => putative multidrug resistance protein EmrY [21:31:35] Modify product: Transcriptional repressor SmtB homolog => Transcriptional repressor SmtB [21:31:35] Modify product: Probable D-lyxose ketol-isomerase => putative D-lyxose ketol-isomerase [21:31:35] Modify product: Probable diguanylate cyclase AdrA => putative diguanylate cyclase AdrA [21:31:35] Modify product: Probable manganese catalase => putative manganese catalase [21:31:35] Modify product: Uncharacterized ABC transporter ATP-binding protein YxlF => putative ABC transporter ATP-binding protein YxlF [21:31:35] Modify product: Probable cation efflux system protein Rv2025c => putative cation efflux system protein [21:31:35] Modify product: Probable endopeptidase p60 => putative endopeptidase p60 [21:31:35] Modify product: Uncharacterized protease YdeA => putative protease YdeA [21:31:35] Modify product: Uncharacterized inner membrane transporter YicL => putative inner membrane transporter YicL [21:31:35] Modify product: Probable dual-specificity RNA methyltransferase RlmN => putative dual-specificity RNA methyltransferase RlmN [21:31:35] Modify product: Probable ATP synthase YscN => putative ATP synthase YscN [21:31:35] Modify product: Probable ribosomal protein YlxQ => putative ribosomal protein YlxQ [21:31:35] Modify product: Uncharacterized zinc protease Rv2782c => putative zinc protease [21:31:35] Modify product: Probable polyketide biosynthesis zinc-dependent hydrolase PksB => putative polyketide biosynthesis zinc-dependent hydrolase PksB [21:31:35] Modify product: Polyketide biosynthesis acyltransferase homolog PksD => Polyketide biosynthesis acyltransferase PksD [21:31:35] Modify product: Probable polyketide biosynthesis enoyl-CoA hydratase PksH => putative polyketide biosynthesis enoyl-CoA hydratase PksH [21:31:35] Modify product: Probable ribonuclease YokI => putative ribonuclease YokI [21:31:35] Modify product: Uncharacterized HTH-type transcriptional regulator YusO => putative HTH-type transcriptional regulator YusO [21:31:35] Modify product: SCO1 protein homolog => SCO1 protein [21:31:35] Modify product: Probable ATP-dependent helicase DinG homolog => putative ATP-dependent helicase DinG [21:31:36] Modify product: Probable ATP-dependent helicase DinG homolog => putative ATP-dependent helicase DinG [21:31:36] Modify product: 30S ribosomal protein S1 homolog => 30S ribosomal protein S1 [21:31:36] Modify product: Probable spore germination protein GerPF => putative spore germination protein GerPF [21:31:36] Modify product: Uncharacterized oxidoreductase SA2266 => putative oxidoreductase [21:31:36] Modify product: Probable 3-hydroxybutyryl-CoA dehydrogenase => putative 3-hydroxybutyryl-CoA dehydrogenase [21:31:36] Modify product: Uncharacterized oxidoreductase SpyM50865 => putative oxidoreductase [21:31:36] Modify product: Bifunctional protein FolD => Bifunctional protein FolD protein [21:31:36] Modify product: N utilization substance protein B homolog => N utilization substance protein B [21:31:36] Modify product: Uncharacterized NTE family protein Rv2565 => putative NTE family protein [21:31:36] Modify product: Probable adenylyltransferase/sulfurtransferase MoeZ => putative adenylyltransferase/sulfurtransferase MoeZ [21:31:36] Modify product: Probable glycine dehydrogenase (decarboxylating) subunit 2 => putative glycine dehydrogenase (decarboxylating) subunit 2 [21:31:36] Modify product: Probable glycine dehydrogenase (decarboxylating) subunit 1 => putative glycine dehydrogenase (decarboxylating) subunit 1 [21:31:36] Modify product: Probable metallo-hydrolase M6_Spy0554 => putative metallo-hydrolase [21:31:36] Modify product: Nucleotidase CA_C3379 => Nucleotidase [21:31:36] Modify product: Probable endonuclease 4 => putative endonuclease 4 [21:31:36] Modify product: GTP cyclohydrolase 1 type 2 homolog => GTP cyclohydrolase 1 type 2 [21:31:36] Modify product: RNA-binding protein HI_1333 => RNA-binding protein [21:31:36] Modify product: Uncharacterized oxidoreductase CzcO => putative oxidoreductase CzcO [21:31:36] Modify product: Uncharacterized hydrolase SA2367 => putative hydrolase [21:31:36] Modify product: Probable zinc-binding alcohol dehydrogenase Rv1895 => putative zinc-binding alcohol dehydrogenase [21:31:36] Modify product: Probable formaldehyde dehydrogenase AdhA => putative formaldehyde dehydrogenase AdhA [21:31:36] Modify product: Probable formate transporter 2 => putative formate transporter 2 [21:31:36] Modify product: Putative formate dehydrogenase SA2102 => Putative formate dehydrogenase [21:31:36] Modify product: Uncharacterized methyltransferase YrrT => putative methyltransferase YrrT [21:31:36] Modify product: Uncharacterized protease YdcP => putative protease YdcP [21:31:36] Modify product: Uncharacterized protease YdcP => putative protease YdcP [21:31:36] Modify product: Probable glutamine ABC transporter permease protein GlnM => putative glutamine ABC transporter permease protein GlnM [21:31:36] Modify product: Probable glutamine ABC transporter permease protein GlnP => putative glutamine ABC transporter permease protein GlnP [21:31:36] Modify product: Uncharacterized AAA domain-containing protein Rv2559c => putative AAA domain-containing protein [21:31:36] Modify product: Probable transcriptional regulatory protein YebC => putative transcriptional regulatory protein YebC [21:31:36] Modify product: Probable nicotinate-nucleotide pyrophosphorylase [carboxylating] => putative nicotinate-nucleotide pyrophosphorylase [carboxylating] [21:31:36] Modify product: Probable GTP-binding protein EngB => putative GTP-binding protein EngB [21:31:36] Modify product: Uncharacterized N-acetyltransferase YsnE => putative N-acetyltransferase YsnE [21:31:36] Modify product: Putative metallophosphoesterase MG207 homolog => Putative metallophosphoesterase MG207 [21:31:36] Modify product: Uncharacterized HTH-type transcriptional regulator YusO => putative HTH-type transcriptional regulator YusO [21:31:36] Modify product: Probable enoyl-CoA hydratase => putative enoyl-CoA hydratase [21:31:36] Modify product: Uncharacterized FAD-linked oxidoreductase Rv2280 => putative FAD-linked oxidoreductase [21:31:36] Modify product: Probable arabinose-binding protein => putative arabinose-binding protein [21:31:36] Modify product: Uncharacterized membrane protein YwnJ => putative membrane protein YwnJ [21:31:36] Modify product: Probable manganese efflux pump MntP => putative manganese efflux pump MntP [21:31:36] Modify product: Probable NAD-dependent malic enzyme 2 => putative NAD-dependent malic enzyme 2 [21:31:36] Modify product: Probable fructose-bisphosphate aldolase => putative fructose-bisphosphate aldolase [21:31:36] Modify product: Putative multidrug export ATP-binding/permease protein SA1683 => Putative multidrug export ATP-binding/permease protein [21:31:36] Modify product: Probable cardiolipin synthase YwiE => putative cardiolipin synthase YwiE [21:31:36] Modify product: Probable transcription regulator ArfM => putative transcription regulator ArfM [21:31:36] Modify product: Probable nitrate transporter NarT => putative nitrate transporter NarT [21:31:36] Modify product: Uncharacterized beta-barrel protein YwiB => putative beta-barrel protein YwiB [21:31:36] Modify product: Uncharacterized HTH-type transcriptional regulator YusO => putative HTH-type transcriptional regulator YusO [21:31:36] Modify product: Putative heme-dependent peroxidase GK3416 => Putative heme-dependent peroxidase [21:31:36] Modify product: Probable deferrochelatase/peroxidase EfeN => putative deferrochelatase/peroxidase EfeN [21:31:36] Modify product: Probable iron uptake system component EfeM => putative iron uptake system component EfeM [21:31:36] Modify product: Probable 6-phospho-beta-glucosidase => putative 6-phospho-beta-glucosidase [21:31:36] Modify product: Probable licABCH operon regulator => putative licABCH operon regulator [21:31:36] Modify product: Uncharacterized transmembrane protein YxlG => putative transmembrane protein YxlG [21:31:36] Modify product: Uncharacterized ABC transporter ATP-binding protein YxlF => putative ABC transporter ATP-binding protein YxlF [21:31:36] Modify product: Probable allantoin permease => putative allantoin permease [21:31:36] Modify product: Probable ABC transporter ATP-binding protein HI_0664 => putative ABC transporter ATP-binding protein [21:31:36] Modify product: Uncharacterized aldehyde dehydrogenase AldY => putative aldehyde dehydrogenase AldY [21:31:36] Modify product: Probable succinyl-CoA:3-ketoacid coenzyme A transferase subunit B => putative succinyl-CoA:3-ketoacid coenzyme A transferase subunit B [21:31:36] Modify product: Probable succinyl-CoA:3-ketoacid coenzyme A transferase subunit A => putative succinyl-CoA:3-ketoacid coenzyme A transferase subunit A [21:31:36] Modify product: Uncharacterized esterase YxiM => putative esterase YxiM [21:31:36] Modify product: Uncharacterized sugar transferase EpsL => putative sugar transferase EpsL [21:31:36] Modify product: Uncharacterized membrane protein EpsK => putative membrane protein EpsK [21:31:36] Modify product: Uncharacterized glycosyltransferase EpsJ => putative glycosyltransferase EpsJ [21:31:36] Modify product: Probable capsular polysaccharide biosynthesis protein YwqC => putative capsular polysaccharide biosynthesis protein YwqC [21:31:36] Modify product: Probable amino-acid racemase => putative amino-acid racemase [21:31:36] Modify product: Uncharacterized HTH-type transcriptional regulator YvdT => putative HTH-type transcriptional regulator YvdT [21:31:36] Modify product: Uncharacterized FAD-linked oxidoreductase YvdP => putative FAD-linked oxidoreductase YvdP [21:31:36] Modify product: Carbon storage regulator homolog => Carbon storage regulator [21:31:36] Modify product: DegV domain-containing protein SA0704 => DegV domain-containing protein [21:31:36] Modify product: Probable undecaprenyl-phosphate N-acetylglucosaminyl 1-phosphate transferase => putative undecaprenyl-phosphate N-acetylglucosaminyl 1-phosphate transferase [21:31:36] Modify product: Uncharacterized glycosyltransferase EpsJ => putative glycosyltransferase EpsJ [21:31:36] Modify product: Uncharacterized glycosyltransferase EpsJ => putative glycosyltransferase EpsJ [21:31:36] Modify product: Probable metabolite transport protein CsbC => putative metabolite transport protein CsbC [21:31:36] Modify product: Probable capsular polysaccharide biosynthesis protein YwqC => putative capsular polysaccharide biosynthesis protein YwqC [21:31:36] Modify product: Uncharacterized HTH-type transcriptional regulator BA_1941/GBAA_1941/BAS1801 => putative HTH-type transcriptional regulator/GBAA_1941/BAS1801 [21:31:36] Modify product: Probable allantoin permease => putative allantoin permease [21:31:36] Modify product: Uncharacterized HTH-type transcriptional regulator YtcD => putative HTH-type transcriptional regulator YtcD [21:31:36] Modify product: Uncharacterized oxidoreductase YtbE => putative oxidoreductase YtbE [21:31:36] Modify product: Uncharacterized hydrolase YxeP => putative hydrolase YxeP [21:31:36] Modify product: Uncharacterized N-acetyltransferase YtmI => putative N-acetyltransferase YtmI [21:31:36] Modify product: Probable thiol peroxidase => putative thiol peroxidase [21:31:36] Modify product: Uncharacterized spore protein YtfJ => putative spore protein YtfJ [21:31:36] Modify product: Probable tRNA sulfurtransferase => putative tRNA sulfurtransferase [21:31:36] Modify product: Probable HTH-type transcriptional regulator YttP => putative HTH-type transcriptional regulator YttP [21:31:36] Modify product: Probable diguanylate cyclase YdaM => putative diguanylate cyclase YdaM [21:31:36] Modify product: Probable NAD-dependent malic enzyme 2 => putative NAD-dependent malic enzyme 2 [21:31:36] Modify product: Probable quorum-quenching lactonase YtnP => putative quorum-quenching lactonase YtnP [21:31:36] Modify product: Putative dipeptidase SACOL1801 => Putative dipeptidase [21:31:36] Modify product: Uncharacterized HTH-type transcriptional regulator YtzE => putative HTH-type transcriptional regulator YtzE [21:31:36] Modify product: Uncharacterized multiple-sugar transport system permease YteP => putative multiple-sugar transport system permease YteP [21:31:36] Modify product: Uncharacterized membrane protein YttA => putative membrane protein YttA [21:31:36] Modify product: Probable ABC transporter permease YtrD => putative ABC transporter permease YtrD [21:31:36] Modify product: Probable ABC transporter permease YtrC => putative ABC transporter permease YtrC [21:31:36] Modify product: Uncharacterized membrane protein YuaF => putative membrane protein YuaF [21:31:37] Modify product: Cyclic nucleotide-gated potassium channel mll3241 => Cyclic nucleotide-gated potassium channel [21:31:37] Modify product: Uncharacterized hydrolase YxeP => putative hydrolase YxeP [21:31:37] Modify product: Probable amino-acid import ATP-binding protein YxeO => putative amino-acid import ATP-binding protein YxeO [21:31:37] Modify product: Probable amino-acid permease protein YxeN => putative amino-acid permease protein YxeN [21:31:37] Modify product: Probable amino-acid-binding protein YxeM => putative amino-acid-binding protein YxeM [21:31:37] Modify product: Uncharacterized N-acetyltransferase YtmI => putative N-acetyltransferase YtmI [21:31:37] Modify product: Probable metabolite transport protein CsbC => putative metabolite transport protein CsbC [21:31:37] Modify product: Desiccation/radiation resistance protein DR_1769 => Desiccation/radiation resistance protein [21:31:37] Modify product: Uncharacterized HTH-type transcriptional regulator YxaF => putative HTH-type transcriptional regulator YxaF [21:31:37] Modify product: Probable D-xylose utilization operon transcriptional repressor => putative D-xylose utilization operon transcriptional repressor [21:31:37] Modify product: Uncharacterized HTH-type transcriptional regulator YydK => putative HTH-type transcriptional regulator YydK [21:31:37] Modify product: Probable peptide export permease protein YydJ => putative peptide export permease protein YydJ [21:31:37] Modify product: Probable peptide export ATP-binding protein YydI => putative peptide export ATP-binding protein YydI [21:31:37] Modify product: Uncharacterized N-acetyltransferase YycN => putative N-acetyltransferase YycN [21:31:37] Modify product: Uncharacterized transporter YycB => putative transporter YycB [21:31:37] Modify product: Uncharacterized HTH-type transcriptional regulator YybR => putative HTH-type transcriptional regulator YybR [21:31:37] Modify product: Probable galactarate transporter => putative galactarate transporter [21:31:37] Modify product: Uncharacterized N-acetyltransferase YjcF => putative N-acetyltransferase YjcF [21:31:37] Modify product: Probable metallo-hydrolase YflN => putative metallo-hydrolase YflN [21:31:37] Modify product: Uncharacterized N-acetyltransferase YjcF => putative N-acetyltransferase YjcF [21:31:37] Modify product: Uncharacterized HTH-type transcriptional regulator HI_0186 => putative HTH-type transcriptional regulator [21:31:37] Modify product: Probable dimethyl sulfoxide reductase chain YnfF => putative dimethyl sulfoxide reductase chain YnfF [21:31:37] Modify product: Probable chromosome-partitioning protein ParB => putative chromosome-partitioning protein ParB [21:31:37] Modify product: Putative esterase HI_1161 => Putative esterase [21:31:37] Modify product: Probable spore germination protein GerPF => putative spore germination protein GerPF [21:31:37] Modify product: ESAT-6-like protein SAG1039 => ESAT-6-like protein [21:31:37] Modify product: NADH dehydrogenase-like protein SA0802 => NADH dehydrogenase-like protein [21:31:37] Modify product: Probable xanthine dehydrogenase subunit E => putative xanthine dehydrogenase subunit E [21:31:37] Modify product: Probable xanthine dehydrogenase subunit D => putative xanthine dehydrogenase subunit D [21:31:37] Modify product: Probable xanthine dehydrogenase subunit C => putative xanthine dehydrogenase subunit C [21:31:37] Modify product: Probable xanthine dehydrogenase subunit A => putative xanthine dehydrogenase subunit A [21:31:37] Modify product: Uncharacterized HTH-type transcriptional regulator YurK => putative HTH-type transcriptional regulator YurK [21:31:37] Modify product: Probable acyl-CoA dehydrogenase => putative acyl-CoA dehydrogenase [21:31:37] Modify product: Probable 3-hydroxyacyl-CoA dehydrogenase => putative 3-hydroxyacyl-CoA dehydrogenase [21:31:37] Modify product: Uncharacterized HTH-type transcriptional regulator YusO => putative HTH-type transcriptional regulator YusO [21:31:37] Modify product: Probable siderophore transport system ATP-binding protein YusV => putative siderophore transport system ATP-binding protein YusV [21:31:37] Modify product: Uncharacterized oxidoreductase Rv0484c => putative oxidoreductase [21:31:37] Modify product: Phage shock protein A homolog => Phage shock protein A [21:31:37] Modify product: Uncharacterized ABC transporter permease YknZ => putative ABC transporter permease YknZ [21:31:37] Modify product: Uncharacterized ABC transporter ATP-binding protein YknY => putative ABC transporter ATP-binding protein YknY [21:31:37] Modify product: Probable siderophore transport system ATP-binding protein YusV => putative siderophore transport system ATP-binding protein YusV [21:31:37] Modify product: Putative DNA-binding protein Rv0500A => Putative DNA-binding proteinA [21:31:37] Modify product: Probable protein-export membrane protein SecG => putative protein-export membrane protein SecG [21:31:37] Modify product: Uncharacterized N-acetyltransferase YvbK => putative N-acetyltransferase YvbK [21:31:37] Modify product: Probable amino-acid metabolite efflux pump => putative amino-acid metabolite efflux pump [21:31:37] Modify product: Uncharacterized amino acid permease YvbW => putative amino acid permease YvbW [21:31:37] Cleaned 313 /product names [21:31:37] Deleting unwanted file: results/bsubtilis/annotation/sprot.faa [21:31:37] Deleting unwanted file: results/bsubtilis/annotation/sprot.blast [21:31:38] There are still 1468 unannotated CDS left (started with 4312) [21:31:38] Will use hmmer3 to search against /home/pabloati/miniforge3/envs/pablo_course/bin/../db/hmm/HAMAP.hmm with 8 CPUs [21:31:38] Running: cat results\/bsubtilis\/annotation\/HAMAP\.hmm\.faa | parallel --gnu --plain -j 8 --block 17885 --recstart '>' --pipe hmmscan --noali --notextw --acc -E 1e-06 --cpu 1 /home/pabloati/miniforge3/envs/pablo_course/bin/../db/hmm/HAMAP.hmm /dev/stdin > results\/bsubtilis\/annotation\/HAMAP\.hmm\.hmmer3 2> /dev/null [21:31:50] Modify product: Protein SprT-like => Protein SprT-like protein [21:31:51] Cleaned 1 /product names [21:31:51] Deleting unwanted file: results/bsubtilis/annotation/HAMAP.hmm.faa [21:31:51] Deleting unwanted file: results/bsubtilis/annotation/HAMAP.hmm.hmmer3 [21:31:51] Labelling remaining 1397 proteins as 'hypothetical protein' [21:31:51] Possible /pseudo 'Stress response protein SCP2' at contig_1 position 312111 [21:31:51] Possible /pseudo 'General stress protein 16U' at contig_1 position 312994 [21:31:51] Possible /pseudo 'HTH-type transcriptional regulator LrpC' at contig_1 position 551645 [21:31:51] Possible /pseudo 'putative manganese catalase' at contig_1 position 634177 [21:31:51] Possible /pseudo 'putative ABC transporter ATP-binding protein' at contig_1 position 895206 [21:31:51] Possible /pseudo 'Putative fluoride ion transporter CrcB' at contig_1 position 1036892 [21:31:51] Possible /pseudo 'Endospore coat-associated protein YheD' at contig_1 position 1051748 [21:31:51] Possible /pseudo 'ATP-dependent helicase/deoxyribonuclease subunit B' at contig_1 position 1137847 [21:31:51] Possible /pseudo 'Spore protein YkvP' at contig_1 position 1444911 [21:31:51] Possible /pseudo 'Phosphate import ATP-binding protein PstB 3' at contig_1 position 2577593 [21:31:51] Possible /pseudo 'putative protease YdcP' at contig_1 position 2793738 [21:31:51] Possible /pseudo 'Manganese transport system membrane protein MntB' at contig_1 position 3142546 [21:31:51] Possible /pseudo 'Methyl-accepting chemotaxis protein McpA' at contig_1 position 3207872 [21:31:51] Possible /pseudo 'Long-chain-alcohol dehydrogenase 2' at contig_1 position 3223063 [21:31:51] Possible /pseudo 'HTH-type transcriptional repressor RghR' at contig_1 position 3456696 [21:31:51] Possible /pseudo 'Quaternary ammonium compound-resistance protein SugE' at contig_1 position 3541416 [21:31:51] Possible /pseudo 'putative glycosyltransferase EpsJ' at contig_1 position 3669653 [21:31:51] Possible /pseudo 'Chromate transport protein' at contig_1 position 3721623 [21:31:51] Possible /pseudo 'Flagellar basal-body rod protein FlgG' at contig_1 position 3745896 [21:31:51] Possible /pseudo 'Nitrate reductase-like protein NarX' at contig_1 position 3823844 [21:31:51] Possible /pseudo '5-methyltetrahydropteroyltriglutamate--homocysteine methyltransferase' at contig_1 position 3998967 [21:31:51] Found 2333 unique /gene codes. [21:31:51] Fixed 2 duplicate /gene - iscS_1 iscS_2 [21:31:51] Fixed 2 duplicate /gene - arsB_1 arsB_2 [21:31:51] Fixed 2 duplicate /gene - ugtP_1 ugtP_2 [21:31:51] Fixed 2 duplicate /gene - iolW_1 iolW_2 [21:31:51] Fixed 2 duplicate /gene - rhaS_1 rhaS_2 [21:31:51] Fixed 3 duplicate /gene - lacR_1 lacR_2 lacR_3 [21:31:51] Fixed 3 duplicate /gene - lutA_1 lutA_2 lutA_3 [21:31:51] Fixed 2 duplicate /gene - immR_1 immR_2 [21:31:51] Fixed 7 duplicate /gene - fabG_1 fabG_2 fabG_3 fabG_4 fabG_5 fabG_6 fabG_7 [21:31:51] Fixed 3 duplicate /gene - bacC_1 bacC_2 bacC_3 [21:31:51] Fixed 2 duplicate /gene - motB_1 motB_2 [21:31:51] Fixed 2 duplicate /gene - carA_1 carA_2 [21:31:51] Fixed 2 duplicate /gene - tdk_1 tdk_2 [21:31:51] Fixed 2 duplicate /gene - cotSA_1 cotSA_2 [21:31:51] Fixed 2 duplicate /gene - pksS_1 pksS_2 [21:31:51] Fixed 5 duplicate /gene - yusO_1 yusO_2 yusO_3 yusO_4 yusO_5 [21:31:51] Fixed 2 duplicate /gene - yceD_1 yceD_2 [21:31:51] Fixed 2 duplicate /gene - lipC_1 lipC_2 [21:31:51] Fixed 2 duplicate /gene - speA_1 speA_2 [21:31:51] Fixed 2 duplicate /gene - mntB_1 mntB_2 [21:31:51] Fixed 3 duplicate /gene - ydaD_1 ydaD_2 ydaD_3 [21:31:51] Fixed 3 duplicate /gene - dnaE_1 dnaE_2 dnaE_3 [21:31:51] Fixed 2 duplicate /gene - drrA_1 drrA_2 [21:31:51] Fixed 2 duplicate /gene - malF_1 malF_2 [21:31:51] Fixed 2 duplicate /gene - gyrB_1 gyrB_2 [21:31:51] Fixed 2 duplicate /gene - lytB_1 lytB_2 [21:31:51] Fixed 2 duplicate /gene - bacF_1 bacF_2 [21:31:51] Fixed 2 duplicate /gene - flhB_1 flhB_2 [21:31:51] Fixed 2 duplicate /gene - xkdM_1 xkdM_2 [21:31:51] Fixed 2 duplicate /gene - mgsR_1 mgsR_2 [21:31:51] Fixed 2 duplicate /gene - cysC_1 cysC_2 [21:31:51] Fixed 2 duplicate /gene - gloB_1 gloB_2 [21:31:51] Fixed 2 duplicate /gene - ypdA_1 ypdA_2 [21:31:51] Fixed 2 duplicate /gene - rsmH_1 rsmH_2 [21:31:51] Fixed 2 duplicate /gene - lipO_1 lipO_2 [21:31:51] Fixed 2 duplicate /gene - ccpA_1 ccpA_2 [21:31:51] Fixed 2 duplicate /gene - smc_1 smc_2 [21:31:51] Fixed 2 duplicate /gene - lytA_1 lytA_2 [21:31:51] Fixed 3 duplicate /gene - feuB_1 feuB_2 feuB_3 [21:31:51] Fixed 2 duplicate /gene - walK_1 walK_2 [21:31:51] Fixed 2 duplicate /gene - ywsB_1 ywsB_2 [21:31:51] Fixed 2 duplicate /gene - yodC_1 yodC_2 [21:31:51] Fixed 2 duplicate /gene - cotH_1 cotH_2 [21:31:51] Fixed 3 duplicate /gene - ydaF_1 ydaF_2 ydaF_3 [21:31:51] Fixed 2 duplicate /gene - malL_1 malL_2 [21:31:51] Fixed 2 duplicate /gene - ytmI_1 ytmI_2 [21:31:51] Fixed 2 duplicate /gene - gntT_1 gntT_2 [21:31:51] Fixed 2 duplicate /gene - licC_1 licC_2 [21:31:51] Fixed 2 duplicate /gene - stp_1 stp_2 [21:31:51] Fixed 2 duplicate /gene - yqcG_1 yqcG_2 [21:31:51] Fixed 4 duplicate /gene - liaS_1 liaS_2 liaS_3 liaS_4 [21:31:51] Fixed 2 duplicate /gene - yvdP_1 yvdP_2 [21:31:51] Fixed 2 duplicate /gene - alkA_1 alkA_2 [21:31:51] Fixed 2 duplicate /gene - wapI_1 wapI_2 [21:31:51] Fixed 2 duplicate /gene - sugE_1 sugE_2 [21:31:51] Fixed 4 duplicate /gene - cpdA_1 cpdA_2 cpdA_3 cpdA_4 [21:31:51] Fixed 2 duplicate /gene - xerD_1 xerD_2 [21:31:51] Fixed 2 duplicate /gene - emrY_1 emrY_2 [21:31:51] Fixed 2 duplicate /gene - dinG_1 dinG_2 [21:31:51] Fixed 3 duplicate /gene - priA_1 priA_2 priA_3 [21:31:51] Fixed 4 duplicate /gene - gltC_1 gltC_2 gltC_3 gltC_4 [21:31:51] Fixed 3 duplicate /gene - glpQ_1 glpQ_2 glpQ_3 [21:31:51] Fixed 2 duplicate /gene - yveA_1 yveA_2 [21:31:51] Fixed 3 duplicate /gene - wecD_1 wecD_2 wecD_3 [21:31:51] Fixed 2 duplicate /gene - rghR_1 rghR_2 [21:31:51] Fixed 3 duplicate /gene - gerPF_1 gerPF_2 gerPF_3 [21:31:51] Fixed 2 duplicate /gene - htrA_1 htrA_2 [21:31:51] Fixed 2 duplicate /gene - uvrC_1 uvrC_2 [21:31:51] Fixed 2 duplicate /gene - sacX_1 sacX_2 [21:31:51] Fixed 4 duplicate /gene - walR_1 walR_2 walR_3 walR_4 [21:31:51] Fixed 2 duplicate /gene - yndE_1 yndE_2 [21:31:51] Fixed 2 duplicate /gene - malG_1 malG_2 [21:31:51] Fixed 3 duplicate /gene - degU_1 degU_2 degU_3 [21:31:51] Fixed 2 duplicate /gene - rfnT_1 rfnT_2 [21:31:51] Fixed 2 duplicate /gene - sigM_1 sigM_2 [21:31:51] Fixed 2 duplicate /gene - spsA_1 spsA_2 [21:31:51] Fixed 3 duplicate /gene - opcR_1 opcR_2 opcR_3 [21:31:51] Fixed 3 duplicate /gene - rocC_1 rocC_2 rocC_3 [21:31:51] Fixed 2 duplicate /gene - yflN_1 yflN_2 [21:31:51] Fixed 2 duplicate /gene - nrdI_1 nrdI_2 [21:31:51] Fixed 2 duplicate /gene - addB_1 addB_2 [21:31:51] Fixed 3 duplicate /gene - ysdC_1 ysdC_2 ysdC_3 [21:31:51] Fixed 2 duplicate /gene - ydjF_1 ydjF_2 [21:31:51] Fixed 2 duplicate /gene - ydjA_1 ydjA_2 [21:31:51] Fixed 3 duplicate /gene - feuC_1 feuC_2 feuC_3 [21:31:51] Fixed 3 duplicate /gene - trxA_1 trxA_2 trxA_3 [21:31:51] Fixed 2 duplicate /gene - gmk_1 gmk_2 [21:31:51] Fixed 2 duplicate /gene - pucI_1 pucI_2 [21:31:51] Fixed 2 duplicate /gene - glnQ_1 glnQ_2 [21:31:51] Fixed 2 duplicate /gene - ywqC_1 ywqC_2 [21:31:51] Fixed 2 duplicate /gene - sdpA_1 sdpA_2 [21:31:51] Fixed 3 duplicate /gene - cwlA_1 cwlA_2 cwlA_3 [21:31:51] Fixed 2 duplicate /gene - dus_1 dus_2 [21:31:51] Fixed 2 duplicate /gene - ssuC_1 ssuC_2 [21:31:51] Fixed 2 duplicate /gene - rlmCD_1 rlmCD_2 [21:31:51] Fixed 3 duplicate /gene - slyA_1 slyA_2 slyA_3 [21:31:51] Fixed 2 duplicate /gene - epsF_1 epsF_2 [21:31:51] Fixed 2 duplicate /gene - cysK_1 cysK_2 [21:31:51] Fixed 2 duplicate /gene - znuC_1 znuC_2 [21:31:51] Fixed 3 duplicate /gene - rapF_1 rapF_2 rapF_3 [21:31:51] Fixed 2 duplicate /gene - yesS_1 yesS_2 [21:31:51] Fixed 3 duplicate /gene - yocK_1 yocK_2 yocK_3 [21:31:51] Fixed 2 duplicate /gene - brnQ_1 brnQ_2 [21:31:51] Fixed 2 duplicate /gene - ecsA_1 ecsA_2 [21:31:51] Fixed 3 duplicate /gene - pdaA_1 pdaA_2 pdaA_3 [21:31:51] Fixed 2 duplicate /gene - csbC_1 csbC_2 [21:31:51] Fixed 2 duplicate /gene - carB_1 carB_2 [21:31:51] Fixed 2 duplicate /gene - natA_1 natA_2 [21:31:51] Fixed 2 duplicate /gene - der_1 der_2 [21:31:51] Fixed 5 duplicate /gene - gabR_1 gabR_2 gabR_3 gabR_4 gabR_5 [21:31:51] Fixed 2 duplicate /gene - acsA_1 acsA_2 [21:31:51] Fixed 2 duplicate /gene - bioY_1 bioY_2 [21:31:51] Fixed 2 duplicate /gene - xkdW_1 xkdW_2 [21:31:51] Fixed 2 duplicate /gene - resE_1 resE_2 [21:31:51] Fixed 3 duplicate /gene - hrp1_1 hrp1_2 hrp1_3 [21:31:51] Fixed 2 duplicate /gene - ltaS1_1 ltaS1_2 [21:31:51] Fixed 2 duplicate /gene - ccpB_1 ccpB_2 [21:31:51] Fixed 3 duplicate /gene - graR_1 graR_2 graR_3 [21:31:51] Fixed 4 duplicate /gene - gltR_1 gltR_2 gltR_3 gltR_4 [21:31:51] Fixed 2 duplicate /gene - dapE_1 dapE_2 [21:31:51] Fixed 3 duplicate /gene - queE_1 queE_2 queE_3 [21:31:51] Fixed 4 duplicate /gene - gtaB_1 gtaB_2 gtaB_3 gtaB_4 [21:31:51] Fixed 2 duplicate /gene - sdpC_1 sdpC_2 [21:31:51] Fixed 2 duplicate /gene - resA_1 resA_2 [21:31:51] Fixed 2 duplicate /gene - alr_1 alr_2 [21:31:51] Fixed 2 duplicate /gene - phoR_1 phoR_2 [21:31:51] Fixed 3 duplicate /gene - lrp_1 lrp_2 lrp_3 [21:31:51] Fixed 6 duplicate /gene - araQ_1 araQ_2 araQ_3 araQ_4 araQ_5 araQ_6 [21:31:51] Fixed 2 duplicate /gene - pbpH_1 pbpH_2 [21:31:51] Fixed 2 duplicate /gene - srlR_1 srlR_2 [21:31:51] Fixed 2 duplicate /gene - narX_1 narX_2 [21:31:51] Fixed 2 duplicate /gene - xkdG_1 xkdG_2 [21:31:51] Fixed 3 duplicate /gene - liaR_1 liaR_2 liaR_3 [21:31:51] Fixed 2 duplicate /gene - dapH_1 dapH_2 [21:31:51] Fixed 2 duplicate /gene - sufB_1 sufB_2 [21:31:51] Fixed 2 duplicate /gene - yodB_1 yodB_2 [21:31:51] Fixed 2 duplicate /gene - yknX_1 yknX_2 [21:31:51] Fixed 2 duplicate /gene - sleB_1 sleB_2 [21:31:51] Fixed 3 duplicate /gene - mreB_1 mreB_2 mreB_3 [21:31:51] Fixed 3 duplicate /gene - metE_1 metE_2 metE_3 [21:31:51] Fixed 2 duplicate /gene - pip_1 pip_2 [21:31:51] Fixed 2 duplicate /gene - putR_1 putR_2 [21:31:51] Fixed 2 duplicate /gene - cdaR_1 cdaR_2 [21:31:51] Fixed 2 duplicate /gene - tusA_1 tusA_2 [21:31:51] Fixed 2 duplicate /gene - yknY_1 yknY_2 [21:31:51] Fixed 2 duplicate /gene - opuCA_1 opuCA_2 [21:31:51] Fixed 2 duplicate /gene - sdpB_1 sdpB_2 [21:31:51] Fixed 3 duplicate /gene - cysL_1 cysL_2 cysL_3 [21:31:51] Fixed 4 duplicate /gene - yusV_1 yusV_2 yusV_3 yusV_4 [21:31:51] Fixed 2 duplicate /gene - yceC_1 yceC_2 [21:31:51] Fixed 2 duplicate /gene - hxlR_1 hxlR_2 [21:31:51] Fixed 2 duplicate /gene - sigK_1 sigK_2 [21:31:51] Fixed 2 duplicate /gene - chrA_1 chrA_2 [21:31:51] Fixed 2 duplicate /gene - ppsA_1 ppsA_2 [21:31:51] Fixed 2 duplicate /gene - dppB_1 dppB_2 [21:31:51] Fixed 4 duplicate /gene - tetA_1 tetA_2 tetA_3 tetA_4 [21:31:51] Fixed 4 duplicate /gene - proC_1 proC_2 proC_3 proC_4 [21:31:51] Fixed 2 duplicate /gene - dnaI_1 dnaI_2 [21:31:51] Fixed 5 duplicate /gene - pbuE_1 pbuE_2 pbuE_3 pbuE_4 pbuE_5 [21:31:51] Fixed 2 duplicate /gene - speG_1 speG_2 [21:31:51] Fixed 3 duplicate /gene - lytC_1 lytC_2 lytC_3 [21:31:51] Fixed 2 duplicate /gene - nucB_1 nucB_2 [21:31:51] Fixed 2 duplicate /gene - iolE_1 iolE_2 [21:31:51] Fixed 3 duplicate /gene - oppD_1 oppD_2 oppD_3 [21:31:51] Fixed 2 duplicate /gene - albF_1 albF_2 [21:31:51] Fixed 2 duplicate /gene - cysE_1 cysE_2 [21:31:51] Fixed 3 duplicate /gene - ymfD_1 ymfD_2 ymfD_3 [21:31:51] Fixed 2 duplicate /gene - malP_1 malP_2 [21:31:51] Fixed 4 duplicate /gene - lrpC_1 lrpC_2 lrpC_3 lrpC_4 [21:31:51] Fixed 2 duplicate /gene - gyrA_1 gyrA_2 [21:31:51] Fixed 2 duplicate /gene - desR_1 desR_2 [21:31:51] Fixed 3 duplicate /gene - nrdF_1 nrdF_2 nrdF_3 [21:31:51] Fixed 2 duplicate /gene - pucK_1 pucK_2 [21:31:51] Fixed 2 duplicate /gene - gerAA_1 gerAA_2 [21:31:51] Fixed 2 duplicate /gene - folA_1 folA_2 [21:31:51] Fixed 3 duplicate /gene - yxeP_1 yxeP_2 yxeP_3 [21:31:51] Fixed 3 duplicate /gene - epsJ_1 epsJ_2 epsJ_3 [21:31:51] Fixed 2 duplicate /gene - yxdL_1 yxdL_2 [21:31:51] Fixed 2 duplicate /gene - yycN_1 yycN_2 [21:31:51] Fixed 2 duplicate /gene - yteP_1 yteP_2 [21:31:51] Fixed 2 duplicate /gene - sdpR_1 sdpR_2 [21:31:51] Fixed 2 duplicate /gene - epsH_1 epsH_2 [21:31:51] Fixed 2 duplicate /gene - crcB_1 crcB_2 [21:31:51] Fixed 2 duplicate /gene - dpp5_1 dpp5_2 [21:31:51] Fixed 2 duplicate /gene - lcfB_1 lcfB_2 [21:31:51] Fixed 2 duplicate /gene - pheT_1 pheT_2 [21:31:51] Fixed 2 duplicate /gene - gluP_1 gluP_2 [21:31:51] Fixed 2 duplicate /gene - yfiZ_1 yfiZ_2 [21:31:51] Fixed 2 duplicate /gene - ptsG_1 ptsG_2 [21:31:51] Fixed 2 duplicate /gene - yheD_1 yheD_2 [21:31:51] Fixed 2 duplicate /gene - ydeA_1 ydeA_2 [21:31:51] Fixed 2 duplicate /gene - mepA_1 mepA_2 [21:31:51] Fixed 2 duplicate /gene - murJ_1 murJ_2 [21:31:51] Fixed 4 duplicate /gene - yxlF_1 yxlF_2 yxlF_3 yxlF_4 [21:31:51] Fixed 2 duplicate /gene - sat_1 sat_2 [21:31:51] Fixed 4 duplicate /gene - xerC_1 xerC_2 xerC_3 xerC_4 [21:31:51] Fixed 2 duplicate /gene - rocR_1 rocR_2 [21:31:51] Fixed 2 duplicate /gene - lytR_1 lytR_2 [21:31:51] Fixed 3 duplicate /gene - pdhC_1 pdhC_2 pdhC_3 [21:31:51] Fixed 2 duplicate /gene - arsR_1 arsR_2 [21:31:51] Fixed 3 duplicate /gene - ydjZ_1 ydjZ_2 ydjZ_3 [21:31:51] Fixed 2 duplicate /gene - luxA_1 luxA_2 [21:31:51] Fixed 3 duplicate /gene - yedK_1 yedK_2 yedK_3 [21:31:51] Fixed 3 duplicate /gene - yjcF_1 yjcF_2 yjcF_3 [21:31:51] Fixed 2 duplicate /gene - dppC_1 dppC_2 [21:31:51] Fixed 2 duplicate /gene - yvoA_1 yvoA_2 [21:31:51] Fixed 2 duplicate /gene - mdtH_1 mdtH_2 [21:31:51] Fixed 2 duplicate /gene - tagD_1 tagD_2 [21:31:51] Fixed 2 duplicate /gene - cssS_1 cssS_2 [21:31:51] Fixed 2 duplicate /gene - ydcP_1 ydcP_2 [21:31:51] Fixed 2 duplicate /gene - btr_1 btr_2 [21:31:51] Fixed 2 duplicate /gene - pstB3_1 pstB3_2 [21:31:51] Fixed 4 duplicate /gene - gerBC_1 gerBC_2 gerBC_3 gerBC_4 [21:31:51] Fixed 2 duplicate /gene - sunI_1 sunI_2 [21:31:51] Fixed 2 duplicate /gene - khtT_1 khtT_2 [21:31:51] Fixed 2 duplicate /gene - albE_1 albE_2 [21:31:51] Fixed 2 duplicate /gene - yxdM_1 yxdM_2 [21:31:51] Fixed 3 duplicate /gene - xylB_1 xylB_2 xylB_3 [21:31:51] Fixed 2 duplicate /gene - spo0A_1 spo0A_2 [21:31:51] Fixed 3 duplicate /gene - htpX_1 htpX_2 htpX_3 [21:31:51] Fixed 5 duplicate /gene - yhdN_1 yhdN_2 yhdN_3 yhdN_4 yhdN_5 [21:31:51] Fixed 2 duplicate /gene - cccA_1 cccA_2 [21:31:51] Fixed 2 duplicate /gene - glpE_1 glpE_2 [21:31:51] Fixed 5 duplicate /gene - yocH_1 yocH_2 yocH_3 yocH_4 yocH_5 [21:31:51] Fixed 3 duplicate /gene - patA_1 patA_2 patA_3 [21:31:51] Fixed 2 duplicate /gene - dnaB_1 dnaB_2 [21:31:51] Fixed 2 duplicate /gene - mcpA_1 mcpA_2 [21:31:51] Fixed 2 duplicate /gene - cfiB_1 cfiB_2 [21:31:51] Fixed 2 duplicate /gene - ylmB_1 ylmB_2 [21:31:51] Fixed 2 duplicate /gene - fabZ_1 fabZ_2 [21:31:51] Fixed 2 duplicate /gene - mntH_1 mntH_2 [21:31:51] Fixed 2 duplicate /gene - sodA_1 sodA_2 [21:31:51] Fixed 2 duplicate /gene - cycA_1 cycA_2 [21:31:51] Fixed 2 duplicate /gene - sacY_1 sacY_2 [21:31:51] Fixed 2 duplicate /gene - proB_1 proB_2 [21:31:51] Fixed 2 duplicate /gene - adh2_1 adh2_2 [21:31:51] Fixed 2 duplicate /gene - nagB_1 nagB_2 [21:31:51] Fixed 2 duplicate /gene - bmrR_1 bmrR_2 [21:31:51] Fixed 2 duplicate /gene - ahpC_1 ahpC_2 [21:31:51] Fixed 2 duplicate /gene - yxaF_1 yxaF_2 [21:31:51] Fixed 2 duplicate /gene - ykvP_1 ykvP_2 [21:31:51] Fixed 5 duplicate /gene - rapA_1 rapA_2 rapA_3 rapA_4 rapA_5 [21:31:51] Fixed 4 duplicate /gene - dinB_1 dinB_2 dinB_3 dinB_4 [21:31:51] Fixed 2 duplicate /gene - rsbRD_1 rsbRD_2 [21:31:51] Fixed 4 duplicate /gene - iolT_1 iolT_2 iolT_3 iolT_4 [21:31:51] Fixed 2 duplicate /gene - ydhP_1 ydhP_2 [21:31:51] Fixed 3 duplicate /gene - rluD_1 rluD_2 rluD_3 [21:31:51] Fixed 3 duplicate /gene - bm3R1_1 bm3R1_2 bm3R1_3 [21:31:51] Fixed 2 duplicate /gene - rnhA_1 rnhA_2 [21:31:51] Fixed 2 duplicate /gene - sinR_1 sinR_2 [21:31:51] Fixed 2 duplicate /gene - lutR_1 lutR_2 [21:31:51] Fixed 3 duplicate /gene - pdhD_1 pdhD_2 pdhD_3 [21:31:51] Fixed 3 duplicate /gene - ydhD_1 ydhD_2 ydhD_3 [21:31:51] Fixed 2 duplicate /gene - mprA_1 mprA_2 [21:31:51] Fixed 2 duplicate /gene - yodF_1 yodF_2 [21:31:51] Fixed 4 duplicate /gene - ydbD_1 ydbD_2 ydbD_3 ydbD_4 [21:31:51] Fixed 2 duplicate /gene - recQ_1 recQ_2 [21:31:51] Fixed 2 duplicate /gene - tatAy_1 tatAy_2 [21:31:51] Fixed 2 duplicate /gene - ldh_1 ldh_2 [21:31:51] Fixed 2 duplicate /gene - murG_1 murG_2 [21:31:51] Fixed 2 duplicate /gene - norG_1 norG_2 [21:31:51] Fixed 2 duplicate /gene - msmE_1 msmE_2 [21:31:51] Fixed 2 duplicate /gene - araP_1 araP_2 [21:31:51] Fixed 3 duplicate /gene - mhqR_1 mhqR_2 mhqR_3 [21:31:51] Fixed 2 duplicate /gene - dnaA_1 dnaA_2 [21:31:51] Fixed 2 duplicate /gene - mtcA1_1 mtcA1_2 [21:31:51] Fixed 2 duplicate /gene - citN_1 citN_2 [21:31:51] Fixed 3 duplicate /gene - nrdE1_1 nrdE1_2 nrdE1_3 [21:31:51] Fixed 2 duplicate /gene - ytrA_1 ytrA_2 [21:31:51] Fixed 2 duplicate /gene - yybR_1 yybR_2 [21:31:51] Fixed 2 duplicate /gene - xkdH_1 xkdH_2 [21:31:51] Fixed 2 duplicate /gene - yugI_1 yugI_2 [21:31:51] Fixed 2 duplicate /gene - ethR_1 ethR_2 [21:31:51] Fixed 2 duplicate /gene - oleD_1 oleD_2 [21:31:51] Fixed 3 duplicate /gene - alsT_1 alsT_2 alsT_3 [21:31:51] Fixed 2 duplicate /gene - ktrB_1 ktrB_2 [21:31:51] Fixed 2 duplicate /gene - panS_1 panS_2 [21:31:51] Fixed 2 duplicate /gene - dcuS_1 dcuS_2 [21:31:51] Fixed 3 duplicate /gene - cmpR_1 cmpR_2 cmpR_3 [21:31:51] Fixed 2 duplicate /gene - rapI_1 rapI_2 [21:31:51] Fixed 4 duplicate /gene - mcpB_1 mcpB_2 mcpB_3 mcpB_4 [21:31:51] Fixed 3 duplicate /gene - graS_1 graS_2 graS_3 [21:31:51] Fixed 2 duplicate /gene - csoR_1 csoR_2 [21:31:51] Fixed 2 duplicate /gene - rsfA_1 rsfA_2 [21:31:51] Fixed 2 duplicate /gene - gutB_1 gutB_2 [21:31:51] Fixed 2 duplicate /gene - scoB_1 scoB_2 [21:31:51] Fixed 3 duplicate /gene - flgG_1 flgG_2 flgG_3 [21:31:51] Fixed 2 duplicate /gene - cimH_1 cimH_2 [21:31:51] Fixed 2 duplicate /gene - pepF1_1 pepF1_2 [21:31:51] Fixed 2 duplicate /gene - pepT_1 pepT_2 [21:31:51] Fixed 2 duplicate /gene - purR_1 purR_2 [21:31:51] Fixed 2 duplicate /gene - rnmV_1 rnmV_2 [21:31:51] Fixed 2 duplicate /gene - ybaK_1 ybaK_2 [21:31:51] Fixed 2 duplicate /gene - mntP_1 mntP_2 [21:31:51] Fixed 2 duplicate /gene - dnaG_1 dnaG_2 [21:31:51] Fixed 2 duplicate /gene - maeA_1 maeA_2 [21:31:51] Fixed 2 duplicate /gene - yorK_1 yorK_2 [21:31:51] Fixed 2 duplicate /gene - gltA_1 gltA_2 [21:31:51] Fixed 2 duplicate /gene - gerAB_1 gerAB_2 [21:31:51] Fixed 2 duplicate /gene - lacF_1 lacF_2 [21:31:51] Fixed 4 duplicate /gene - xre_1 xre_2 xre_3 xre_4 [21:31:51] Fixed 3 duplicate /gene - oppF_1 oppF_2 oppF_3 [21:31:51] Fixed 2 duplicate /gene - corA_1 corA_2 [21:31:51] Fixed 2 duplicate /gene - rsbRB_1 rsbRB_2 [21:31:51] Fixed 2 duplicate /gene - cysH_1 cysH_2 [21:31:51] Fixed 2 duplicate /gene - phnO_1 phnO_2 [21:31:51] Fixed 2 duplicate /gene - yumC_1 yumC_2 [21:31:51] Fixed 2 duplicate /gene - tadA_1 tadA_2 [21:31:51] Fixed 3 duplicate /gene - desK_1 desK_2 desK_3 [21:31:51] Fixed 3 duplicate /gene - ywrO_1 ywrO_2 ywrO_3 [21:31:51] Fixed 2 duplicate /gene - ytcD_1 ytcD_2 [21:31:51] Fixed 2 duplicate /gene - ccsA_1 ccsA_2 [21:31:51] Fixed 3 duplicate /gene - gerBA_1 gerBA_2 gerBA_3 [21:31:51] Fixed 2 duplicate /gene - ktrA_1 ktrA_2 [21:31:51] Fixed 2 duplicate /gene - pomA_1 pomA_2 [21:31:51] Fixed 3 duplicate /gene - ybiT_1 ybiT_2 ybiT_3 [21:31:51] Fixed 2 duplicate /gene - yhdG_1 yhdG_2 [21:31:51] Fixed 2 duplicate /gene - bdhA_1 bdhA_2 [21:31:51] Fixed 2 duplicate /gene - dcuR_1 dcuR_2 [21:31:51] Fixed 2 duplicate /gene - yknZ_1 yknZ_2 [21:31:51] Fixed 2 duplicate /gene - ykuD_1 ykuD_2 [21:31:51] Fixed 2 duplicate /gene - pta_1 pta_2 [21:31:51] Fixed 2 duplicate /gene - gltT_1 gltT_2 [21:31:51] Fixed 3 duplicate /gene - kinA_1 kinA_2 kinA_3 [21:31:51] Fixed 2 duplicate /gene - bioB_1 bioB_2 [21:31:51] Fixed 2 duplicate /gene - yjcA_1 yjcA_2 [21:31:51] Fixed 2 duplicate /gene - katA_1 katA_2 [21:31:51] Fixed 2 duplicate /gene - rapG_1 rapG_2 [21:31:51] Fixed 2 duplicate /gene - tetD_1 tetD_2 [21:31:51] Fixed 3 duplicate /gene - bmr3_1 bmr3_2 bmr3_3 [21:31:51] Fixed 2 duplicate /gene - estB_1 estB_2 [21:31:51] Fixed 3 duplicate /gene - cotF_1 cotF_2 cotF_3 [21:31:51] Fixed 3 duplicate /gene - corC_1 corC_2 corC_3 [21:31:51] Fixed 2 duplicate /gene - cheY_1 cheY_2 [21:31:51] Fixed 2 duplicate /gene - tlyC_1 tlyC_2 [21:31:51] Fixed 3 duplicate /gene - ribZ_1 ribZ_2 ribZ_3 [21:31:51] Fixed 2 duplicate /gene - srrA_1 srrA_2 [21:31:51] Fixed 2 duplicate /gene - czcD_1 czcD_2 [21:31:51] Fixed 2 duplicate /gene - coaE_1 coaE_2 [21:31:51] Fixed 2 duplicate /gene - dnaX_1 dnaX_2 [21:31:51] Fixed 2 duplicate /gene - ltaS2_1 ltaS2_2 [21:31:51] Fixed 2 duplicate /gene - cidA_1 cidA_2 [21:31:51] Fixed 2 duplicate /gene - metQ_1 metQ_2 [21:31:51] Fixed 2 duplicate /gene - ftsW_1 ftsW_2 [21:31:51] Fixed 344 colliding /gene names. [21:31:51] Adding /locus_tag identifiers [21:31:51] Assigned 4432 locus_tags to CDS and RNA features. [21:31:51] Writing outputs to results/bsubtilis/annotation/ [21:31:55] Generating annotation statistics file [21:31:55] Generating Genbank and Sequin files [21:31:55] Running: tbl2asn -V b -a r10k -l paired-ends -M n -N 1 -y 'Annotated using prokka 1.12 from https://github.com/tseemann/prokka' -Z results\/bsubtilis\/annotation\/bsubtilis\.err -i results\/bsubtilis\/annotation\/bsubtilis\.fsa 2> /dev/null [21:32:00] Deleting unwanted file: results/bsubtilis/annotation/errorsummary.val [21:32:00] Deleting unwanted file: results/bsubtilis/annotation/bsubtilis.dr [21:32:00] Deleting unwanted file: results/bsubtilis/annotation/bsubtilis.fixedproducts [21:32:00] Deleting unwanted file: results/bsubtilis/annotation/bsubtilis.ecn [21:32:00] Deleting unwanted file: results/bsubtilis/annotation/bsubtilis.val [21:32:00] Repairing broken .GBK output that tbl2asn produces... [21:32:00] Running: sed 's/COORDINATES: profile/COORDINATES:profile/' < results\/bsubtilis\/annotation\/bsubtilis\.gbf > results\/bsubtilis\/annotation\/bsubtilis\.gbk [21:32:01] Deleting unwanted file: results/bsubtilis/annotation/bsubtilis.gbf [21:32:01] Output files: [21:32:01] results/bsubtilis/annotation/bsubtilis.sqn [21:32:01] results/bsubtilis/annotation/bsubtilis.gbk [21:32:01] results/bsubtilis/annotation/bsubtilis.tbl [21:32:01] results/bsubtilis/annotation/bsubtilis.gff [21:32:01] results/bsubtilis/annotation/bsubtilis.ffn [21:32:01] results/bsubtilis/annotation/bsubtilis.fsa [21:32:01] results/bsubtilis/annotation/bsubtilis.fna [21:32:01] results/bsubtilis/annotation/bsubtilis.tsv [21:32:01] results/bsubtilis/annotation/bsubtilis.faa [21:32:01] results/bsubtilis/annotation/bsubtilis.txt [21:32:01] results/bsubtilis/annotation/bsubtilis.err [21:32:01] results/bsubtilis/annotation/bsubtilis.log [21:32:01] Annotation finished successfully. [21:32:01] Walltime used: 1.57 minutes [21:32:01] If you use this result please cite the Prokka paper: [21:32:01] Seemann T (2014) Prokka: rapid prokaryotic genome annotation. Bioinformatics. 30(14):2068-9. [21:32:01] Type 'prokka --citation' for more details. [21:32:01] Thank you, come again.