Thu Jan 21 09:22:34 2021 Start executionNamespace(clade_name='panplhan_clade', db_path='.', input='dummy', nprocs=7, output='trash6', tmp='trash6') [I] mmseqs is installed path: /home/andrespara/anaconda3/envs/panphlan/bin/mmseqs [I] diamond is installed path: /home/andrespara/anaconda3/envs/panphlan/bin/diamond [I] bowtie2 is installed path: /home/andrespara/anaconda3/envs/panphlan/bin/bowtie2 Thu Jan 21 09:22:34 2021 Creating temporal folders... Thu Jan 21 09:22:34 2021 Done. Thu Jan 21 09:22:34 2021 Checking PanPhlAn output directory... Thu Jan 21 09:22:34 2021 Done. Thu Jan 21 09:22:34 2021 Executing prokka...[09:22:34] This is prokka 1.13 [09:22:34] Written by Torsten Seemann [09:22:34] Homepage is https://github.com/tseemann/prokka [09:22:34] Local time is Thu Jan 21 09:22:34 2021 [09:22:34] You are andrespara [09:22:34] Operating system is linux [09:22:34] You have BioPerl 1.7.7 Argument "1.7.7" isn't numeric in numeric lt (<) at /home/andrespara/anaconda3/envs/panphlan/bin/prokka line 253. [09:22:34] System has 8 cores. [09:22:34] Will use maximum of 4 cores. [09:22:34] Annotating as >>> Bacteria <<< [09:22:34] Generating locus_tag from 'dummy/sample2.faa' contents. [09:22:34] Setting --locustag DIAHKAHI from MD5 d2a14a1207a59c7cf8c80bd584a98047 [09:22:34] Enabling options to ensure Genbank/ENA/DDJB submission compliance. [09:22:34] Re-using existing --outdir trash6/tmp/prokka/sample2 [09:22:34] Using filename prefix: sample2.XXX [09:22:34] Setting HMMER_NCPU=1 [09:22:34] Writing log to: trash6/tmp/prokka/sample2/sample2.log [09:22:34] Command: /home/andrespara/anaconda3/envs/panphlan/bin/prokka --outdir trash6/tmp/prokka/sample2 --prefix sample2 --centre X --compliant --force --cpus 4 dummy/sample2.faa [09:22:34] Appending to PATH: /home/andrespara/anaconda3/envs/panphlan/bin [09:22:34] Looking for 'aragorn' - found /home/andrespara/anaconda3/envs/panphlan/bin/aragorn [09:22:34] Determined aragorn version is 1.2 [09:22:34] Looking for 'barrnap' - found /home/andrespara/anaconda3/envs/panphlan/bin/barrnap [09:22:34] Determined barrnap version is 0.9 [09:22:34] Looking for 'blastp' - found /home/andrespara/anaconda3/envs/panphlan/bin/blastp [09:22:34] Determined blastp version is 2.9 [09:22:34] Looking for 'cmpress' - found /home/andrespara/anaconda3/envs/panphlan/bin/cmpress [09:22:34] Determined cmpress version is 1.1 [09:22:34] Looking for 'cmscan' - found /home/andrespara/anaconda3/envs/panphlan/bin/cmscan [09:22:34] Determined cmscan version is 1.1 [09:22:34] Looking for 'egrep' - found /usr/bin/egrep [09:22:34] Looking for 'find' - found /usr/bin/find [09:22:34] Looking for 'grep' - found /usr/bin/grep [09:22:34] Looking for 'hmmpress' - found /home/andrespara/anaconda3/envs/panphlan/bin/hmmpress [09:22:34] Determined hmmpress version is 3.3 [09:22:34] Looking for 'hmmscan' - found /home/andrespara/anaconda3/envs/panphlan/bin/hmmscan [09:22:34] Determined hmmscan version is 3.3 [09:22:34] Looking for 'java' - found /home/andrespara/anaconda3/envs/panphlan/bin/java [09:22:34] Looking for 'less' - found /usr/bin/less [09:22:34] Looking for 'makeblastdb' - found /home/andrespara/anaconda3/envs/panphlan/bin/makeblastdb [09:22:34] Determined makeblastdb version is 2.9 [09:22:34] Looking for 'minced' - found /home/andrespara/anaconda3/envs/panphlan/bin/minced [09:22:34] Determined minced version is 4.2 [09:22:34] Looking for 'parallel' - found /home/andrespara/anaconda3/envs/panphlan/bin/parallel [09:22:34] Determined parallel version is 20201122 [09:22:34] Looking for 'prodigal' - found /home/andrespara/anaconda3/envs/panphlan/bin/prodigal [09:22:34] Determined prodigal version is 2.6 [09:22:34] Looking for 'prokka-genbank_to_fasta_db' - found /home/andrespara/anaconda3/envs/panphlan/bin/prokka-genbank_to_fasta_db [09:22:34] Looking for 'sed' - found /usr/bin/sed [09:22:34] Looking for 'tbl2asn' - found /home/andrespara/anaconda3/envs/panphlan/bin/tbl2asn [tbl2asn] This copy of tbl2asn is more than a year old. Please download the current version. [09:22:34] Determined tbl2asn version is 25.7 [09:22:34] Using genetic code table 11. [09:22:34] Loading and checking input file: dummy/sample2.faa [09:22:34] Changing illegal '|' to '_' in sequence name: sample2|SC|contig000001 [09:22:34] Wrote 1 contigs totalling 4278057 bp. [09:22:34] Predicting tRNAs and tmRNAs [09:22:34] Running: aragorn -l -gc11 -w trash6\/tmp\/prokka\/sample2\/sample2\.fna [09:22:35] 1 tRNA-Asn [16142,16216] 33 (gtt) [09:22:35] tRNA [16222,16307] is a pseudo/wacky gene - skipping. [09:22:35] 3 tRNA-Ser [20818,20909] 35 (gga) [09:22:35] 4 tRNA-Tyr [26400,26484] 35 (gta) [09:22:35] 5 tRNA-Leu [26494,26577] 35 (tag) [09:22:35] 6 tRNA-Gly [26601,26675] 33 (gcc) [09:22:35] 7 tRNA-Pyl [26700,26776] 36 (cta) [09:22:35] 8 tRNA-Gln [26786,26861] 34 (ttg) [09:22:35] 9 tRNA-Lys [26870,26945] 34 (ttt) [09:22:35] 10 tRNA-Ser [26948,27036] 35 (tga) [09:22:35] 11 tRNA-Phe [27040,27115] 34 (gaa) [09:22:35] 12 tRNA-Met [27122,27196] 35 (cat) [09:22:35] 13 tRNA-Met [27210,27286] 35 (cat) [09:22:35] 14 tRNA-His [27304,27380] 35 (gtg) [09:22:35] 15 tRNA-Lys [27389,27464] 34 (ttt) [09:22:35] 16 tRNA-Cys [27472,27545] 33 (gca) [09:22:35] 17 tRNA-Arg [27553,27629] 35 (acg) [09:22:35] 18 tRNA-Val [27642,27717] 34 (tac) [09:22:35] 19 tRNA-Met [118669,118744] 34 (cat) [09:22:35] 20 tRNA-Glu [118752,118826] 34 (ttc) [09:22:35] 21 tRNA-Gly [118841,118914] 33 (tcc) [09:22:35] 22 tRNA-Val [118920,118995] 34 (tac) [09:22:35] 23 tRNA-Asp [119001,119077] 35 (gtc) [09:22:35] 24 tRNA-Gly [119088,119162] 33 (gcc) [09:22:35] 25 tRNA-Pyl [119171,119246] 37 (cta) [09:22:35] 26 tRNA-Ser [868709,868799] 35 (gct) [09:22:35] 27 tRNA-Gly [1114462,1114535] 33 (tcc) [09:22:35] 28 tRNA-Leu c[1196106,1196193] 35 (caa) [09:22:35] 29 tRNA-Leu [1786803,1786884] 35 (tag) [09:22:35] 30 tRNA-SeC c[2671299,2671395] 35 (tca) [09:22:35] 31 tRNA-Thr c[2962173,2962247] 33 (tgt) [09:22:35] 32 tmRNA c[3447367,3447716] 94,123 ADDNFAIAA* [09:22:35] 33 tRNA-Thr c[4025935,4026009] 33 (tgt) [09:22:35] 34 tRNA-Val c[4026043,4026118] 34 (tac) [09:22:35] 35 tRNA-Glu c[4026123,4026197] 34 (ttc) [09:22:35] 36 tRNA-Lys c[4026204,4026279] 34 (ttt) [09:22:35] 37 tRNA-Ile [4129743,4129816] 35 (tat) [09:22:35] 38 tRNA-Ser [4129825,4129915] 34 (gct) [09:22:35] 39 tRNA-Asn [4273344,4273418] 33 (gtt) [09:22:35] 40 tRNA-Leu [4273424,4273510] 35 (taa) [09:22:35] 41 tRNA-Met [4273525,4273600] 34 (cat) [09:22:35] 42 tRNA-Glu [4273608,4273682] 34 (ttc) [09:22:35] 43 tRNA-Gly [4273692,4273765] 33 (tcc) [09:22:35] 44 tRNA-Val [4273771,4273846] 34 (tac) [09:22:35] 45 tRNA-Asp [4273852,4273928] 35 (gtc) [09:22:35] 46 tRNA-Thr [4273938,4274012] 33 (tgt) [09:22:35] 47 tRNA-Tyr [4274027,4274111] 35 (gta) [09:22:35] 48 tRNA-Leu [4274121,4274204] 35 (tag) [09:22:35] 49 tRNA-Pyl [4274234,4274310] 36 (cta) [09:22:35] 50 tRNA-Gln [4274318,4274393] 34 (ttg) [09:22:35] 51 tRNA-Ser [4274482,4274570] 35 (tga) [09:22:35] 52 tRNA-Phe [4274574,4274649] 34 (gaa) [09:22:35] 53 tRNA-Met [4274656,4274730] 35 (cat) [09:22:35] 54 tRNA-Met [4274744,4274820] 35 (cat) [09:22:35] 55 tRNA-Pro [4274844,4274920] 35 (tgg) [09:22:35] 56 tRNA-His [4274928,4275004] 35 (gtg) [09:22:35] 57 tRNA-Lys [4275013,4275088] 34 (ttt) [09:22:35] 58 tRNA-Cys [4275096,4275169] 33 (gca) [09:22:35] 59 tRNA-Asn [4275176,4275250] 33 (gtt) [09:22:35] 60 tRNA-Asn [4275584,4275658] 33 (gtt) [09:22:35] 61 tRNA-Glu [4275663,4275737] 34 (ttc) [09:22:35] 62 tRNA-Val [4275743,4275818] 34 (tac) [09:22:35] 63 tRNA-Asp [4275824,4275900] 35 (gtc) [09:22:35] 64 tRNA-Thr [4275911,4275985] 33 (tgt) [09:22:35] 65 tRNA-Tyr [4276000,4276084] 35 (gta) [09:22:35] 66 tRNA-Gly [4276094,4276167] 33 (tcc) [09:22:35] 67 tRNA-Pyl [4276178,4276254] 36 (cta) [09:22:35] 68 tRNA-Gln [4276264,4276339] 34 (ttg) [09:22:35] 69 tRNA-Lys [4276351,4276426] 34 (ttt) [09:22:35] 70 tRNA-Ser [4276429,4276517] 35 (tga) [09:22:35] 71 tRNA-Ser [4276535,4276625] 35 (gct) [09:22:35] 72 tRNA-Pro [4276634,4276710] 35 (tgg) [09:22:35] 73 tRNA-Trp [4276796,4276871] 34 (cca) [09:22:35] 74 tRNA-Pro [4276932,4277008] 35 (tgg) [09:22:35] 75 tRNA-Ile [4277015,4277091] 35 (gat) [09:22:35] 76 tRNA-Phe [4277095,4277170] 34 (gaa) [09:22:35] 77 tRNA-Met [4277178,4277254] 35 (cat) [09:22:35] Found 76 tRNAs [09:22:35] Predicting Ribosomal RNAs [09:22:35] Running Barrnap with 4 threads [09:22:36] 1 gnl|X|DIAHKAHI_1 10814 16S ribosomal RNA [09:22:36] 2 gnl|X|DIAHKAHI_1 12995 23S ribosomal RNA [09:22:36] 3 gnl|X|DIAHKAHI_1 16025 5S ribosomal RNA [09:22:36] 4 gnl|X|DIAHKAHI_1 16674 5S ribosomal RNA [09:22:36] 5 gnl|X|DIAHKAHI_1 117842 16S ribosomal RNA (partial) [09:22:36] 6 gnl|X|DIAHKAHI_1 398913 16S ribosomal RNA (partial) [09:22:36] 7 gnl|X|DIAHKAHI_1 400313 5S ribosomal RNA [09:22:36] 8 gnl|X|DIAHKAHI_1 1114551 5S ribosomal RNA [09:22:36] 9 gnl|X|DIAHKAHI_1 2962779 16S ribosomal RNA (partial) [09:22:36] 10 gnl|X|DIAHKAHI_1 3776210 5S ribosomal RNA [09:22:36] 11 gnl|X|DIAHKAHI_1 3911987 5S ribosomal RNA [09:22:36] 12 gnl|X|DIAHKAHI_1 4267445 5S ribosomal RNA [09:22:36] 13 gnl|X|DIAHKAHI_1 4273227 5S ribosomal RNA [09:22:36] 14 gnl|X|DIAHKAHI_1 4275469 5S ribosomal RNA [09:22:36] Found 14 rRNAs [09:22:36] Skipping ncRNA search, enable with --rfam if desired. [09:22:36] Total of 89 tRNA + rRNA features [09:22:36] Searching for CRISPR repeats [09:22:36] Found 0 CRISPRs [09:22:36] Predicting coding sequences [09:22:36] Contigs total 4278057 bp, so using single mode [09:22:36] Running: prodigal -i trash6\/tmp\/prokka\/sample2\/sample2\.fna -c -m -g 11 -p single -f sco -q [09:22:40] Excluding CDS which overlaps existing RNA (rRNA) at gnl|X|DIAHKAHI_1:15161..15625 on + strand [09:22:40] Excluding CDS which overlaps existing RNA (tRNA) at gnl|X|DIAHKAHI_1:20832..21017 on + strand [09:22:43] Found 3908 CDS [09:22:43] Connecting features back to sequences [09:22:43] Not using genus-specific database. Try --usegenus to enable it. [09:22:43] Annotating CDS, please be patient. [09:22:43] Will use 4 CPUs for similarity searching. [09:22:45] There are still 3908 unannotated CDS left (started with 3908) [09:22:45] Will use blast to search against /home/andrespara/anaconda3/envs/panphlan/bin/../db/kingdom/Bacteria/sprot with 4 CPUs [09:22:45] Running: cat trash6\/tmp\/prokka\/sample2\/sprot\.faa | parallel --gnu --plain -j 4 --block 151430 --recstart '>' --pipe blastp -query - -db /home/andrespara/anaconda3/envs/panphlan/bin/../db/kingdom/Bacteria/sprot -evalue 1e-06 -num_threads 1 -num_descriptions 1 -num_alignments 1 -seg no > trash6\/tmp\/prokka\/sample2\/sprot\.blast 2> /dev/null [09:23:37] Modify product: Uncharacterized signaling protein PA1727 => putative signaling protein [09:23:37] Modify product: Acetyltransferase SACOL1063 => Acetyltransferase [09:23:37] Modify product: Uncharacterized ABC transporter ATP-binding protein YknY => putative ABC transporter ATP-binding protein YknY [09:23:37] Modify product: Dihydroorotate dehydrogenase B (NAD(+)), electron transfer subunit homolog => Dihydroorotate dehydrogenase B (NAD(+)), electron transfer subunit [09:23:37] Modify product: Uncharacterized signaling protein PA1727 => putative signaling protein [09:23:37] Modify product: UPF0073 inner membrane protein YqfA => hypothetical protein [09:23:37] Modify product: Probable xanthine dehydrogenase subunit A => putative xanthine dehydrogenase subunit A [09:23:37] Modify product: Probable manganese catalase => putative manganese catalase [09:23:37] Modify product: UPF0213 protein BH0048 => hypothetical protein [09:23:37] Modify product: Uncharacterized protein Rv2915c => putative protein [09:23:37] Modify product: Uncharacterized signaling protein PA1727 => putative signaling protein [09:23:37] Modify product: Probable L-galactonate transporter => putative L-galactonate transporter [09:23:37] Modify product: TelA-like protein SA1238 => TelA-like protein [09:23:37] Modify product: Probable siderophore transport system ATP-binding protein YusV => putative siderophore transport system ATP-binding protein YusV [09:23:37] Modify product: Uncharacterized ABC transporter solute-binding protein YclQ => putative ABC transporter solute-binding protein YclQ [09:23:37] Modify product: Uncharacterized signaling protein PA1727 => putative signaling protein [09:23:37] Modify product: Probable glycine dehydrogenase (decarboxylating) subunit 1 => putative glycine dehydrogenase (decarboxylating) subunit 1 [09:23:37] Modify product: Probable glycine dehydrogenase (decarboxylating) subunit 2 => putative glycine dehydrogenase (decarboxylating) subunit 2 [09:23:37] Modify product: Probable cation-transporting ATPase E => putative cation-transporting ATPase E [09:23:37] Modify product: Uncharacterized ABC transporter ATP-binding protein YxlF => putative ABC transporter ATP-binding protein YxlF [09:23:37] Modify product: Iron-sulfur flavoprotein CD630_04720 => Iron-sulfur flavoprotein [09:23:37] Modify product: Uncharacterized HTH-type transcriptional regulator YybR => putative HTH-type transcriptional regulator YybR [09:23:37] Modify product: Uncharacterized transporter Rv2685 => putative transporter [09:23:37] Modify product: Probable adenylyltransferase/sulfurtransferase MoeZ => putative adenylyltransferase/sulfurtransferase MoeZ [09:23:37] Modify product: UPF0145 protein BC_1012 => hypothetical protein [09:23:37] Modify product: Fluoroquinolones export ATP-binding protein Rv2688c => Fluoroquinolones export ATP-binding protein [09:23:37] Modify product: Fluoroquinolones export permease protein Rv2686c => Fluoroquinolones export permease protein [09:23:37] Modify product: Uncharacterized isomerase YddE => putative isomerase YddE [09:23:37] Modify product: Uncharacterized protein YjdF => putative protein YjdF [09:23:37] Modify product: UPF0702 transmembrane protein YetF => hypothetical protein [09:23:37] Modify product: Uncharacterized epimerase/dehydratase SA0511 => putative epimerase/dehydratase [09:23:37] Modify product: Uncharacterized protein HI_0933 => putative protein [09:23:37] Modify product: UPF0246 protein YaaA => hypothetical protein [09:23:37] Modify product: Uncharacterized HTH-type transcriptional regulator YusO => putative HTH-type transcriptional regulator YusO [09:23:37] Modify product: Uncharacterized signaling protein PA1727 => putative signaling protein [09:23:37] Modify product: Probable diguanylate cyclase DgcE => putative diguanylate cyclase DgcE [09:23:37] Modify product: Resolvase homolog YneB => Resolvase YneB [09:23:37] Modify product: Uncharacterized ABC transporter ATP-binding protein YxlF => putative ABC transporter ATP-binding protein YxlF [09:23:37] Modify product: Probable transcriptional regulatory protein pdtaR => putative transcriptional regulatory protein pdtaR [09:23:37] Modify product: Probable sensor histidine kinase pdtaS => putative sensor histidine kinase pdtaS [09:23:37] Modify product: Uncharacterized hydrolase YxeP => putative hydrolase YxeP [09:23:37] Modify product: Uncharacterized ABC transporter ATP-binding protein YknY => putative ABC transporter ATP-binding protein YknY [09:23:37] Modify product: Uncharacterized membrane protein YdfK => putative membrane protein YdfK [09:23:37] Modify product: Putative dipeptidase SACOL1801 => Putative dipeptidase [09:23:37] Modify product: Uncharacterized isomerase YddE => putative isomerase YddE [09:23:37] Modify product: Uncharacterized isomerase YddE => putative isomerase YddE [09:23:37] Modify product: Probable tryptophan transport protein => putative tryptophan transport protein [09:23:37] Modify product: Probable membrane transporter protein YfcA => putative membrane transporter protein YfcA [09:23:37] Modify product: Acetyltransferase Atu2258 => Acetyltransferase [09:23:37] Modify product: Probable amino-acid racemase => putative amino-acid racemase [09:23:37] Modify product: Iron-sulfur flavoprotein CD630_04720 => Iron-sulfur flavoprotein [09:23:37] Modify product: Probable multidrug ABC transporter ATP-binding protein YbhF => putative multidrug ABC transporter ATP-binding protein YbhF [09:23:37] Modify product: Uncharacterized ABC transporter ATP-binding protein YknY => putative ABC transporter ATP-binding protein YknY [09:23:37] Modify product: Putative multidrug export ATP-binding/permease protein SA1683 => Putative multidrug export ATP-binding/permease protein [09:23:37] Modify product: Uncharacterized signaling protein PA1727 => putative signaling protein [09:23:37] Modify product: Probable endonuclease 4 => putative endonuclease 4 [09:23:37] Modify product: UPF0754 membrane protein SA1664 => hypothetical protein [09:23:37] Modify product: Probable diguanylate cyclase DgcQ => putative diguanylate cyclase DgcQ [09:23:37] Modify product: Probable manganese/zinc-exporting P-type ATPase => putative manganese/zinc-exporting P-type ATPase [09:23:37] Modify product: Uncharacterized protein YbdM => putative protein YbdM [09:23:37] Modify product: Probable manganese catalase => putative manganese catalase [09:23:37] Modify product: Uncharacterized HTH-type transcriptional regulator SACOL2360 => putative HTH-type transcriptional regulator [09:23:37] Modify product: Uncharacterized protein YhaZ => putative protein YhaZ [09:23:37] Modify product: Uncharacterized N-acetyltransferase YvbK => putative N-acetyltransferase YvbK [09:23:37] Modify product: Uncharacterized ABC transporter ATP-binding protein YxlF => putative ABC transporter ATP-binding protein YxlF [09:23:37] Modify product: Probable metallo-hydrolase YflN => putative metallo-hydrolase YflN [09:23:37] Modify product: Probable HTH-type transcriptional repressor ExuR => putative HTH-type transcriptional repressor ExuR [09:23:37] Modify product: Uncharacterized oxidoreductase SA2266 => putative oxidoreductase [09:23:37] Modify product: Uncharacterized protease YdcP => putative protease YdcP [09:23:37] Modify product: Probable diguanylate cyclase DgcC => putative diguanylate cyclase DgcC [09:23:37] Modify product: Bifunctional protein FolD => Bifunctional protein FolD protein [09:23:37] Modify product: Uncharacterized signaling protein CC_0091 => putative signaling protein [09:23:37] Modify product: Probable tRNA sulfurtransferase => putative tRNA sulfurtransferase [09:23:37] Modify product: Uncharacterized signaling protein PA1727 => putative signaling protein [09:23:37] Modify product: Probable licABCH operon regulator => putative licABCH operon regulator [09:23:37] Modify product: N-acetylmuramoyl-L-alanine amidase Rv3717 => N-acetylmuramoyl-L-alanine amidase [09:23:37] Modify product: Uncharacterized ABC transporter ATP-binding protein YbiT => putative ABC transporter ATP-binding protein YbiT [09:23:37] Modify product: Probable HTH-type transcriptional repressor ExuR => putative HTH-type transcriptional repressor ExuR [09:23:37] Modify product: Uncharacterized signaling protein PA1727 => putative signaling protein [09:23:37] Modify product: Putative universal stress protein SA1532 => Putative universal stress protein [09:23:37] Modify product: Uncharacterized protein YisK => putative protein YisK [09:23:37] Modify product: Putative DNA-binding protein Rv0500A => Putative DNA-binding proteinA [09:23:37] Modify product: Uncharacterized protein Rv1488 => putative protein [09:23:37] Modify product: UPF0371 protein DIP2346 => hypothetical protein [09:23:37] Modify product: Probable cation efflux system protein Rv2025c => putative cation efflux system protein [09:23:37] Modify product: 30S ribosomal protein S1 homolog => 30S ribosomal protein S1 [09:23:37] Modify product: Probable phosphatase YcdX => putative phosphatase YcdX [09:23:37] Modify product: Probable diguanylate cyclase DgcE => putative diguanylate cyclase DgcE [09:23:37] Modify product: Uncharacterized signaling protein PA1727 => putative signaling protein [09:23:37] Modify product: Uncharacterized ABC transporter ATP-binding protein Rv1273c => putative ABC transporter ATP-binding protein [09:23:37] Modify product: Uncharacterized ABC transporter ATP-binding protein Rv1272c => putative ABC transporter ATP-binding protein [09:23:37] Modify product: UPF0053 protein HI_0107 => hypothetical protein [09:23:37] Modify product: UPF0291 protein YnzC => hypothetical protein [09:23:37] Modify product: Probable M18 family aminopeptidase 1 => putative M18 family aminopeptidase 1 [09:23:37] Modify product: Uncharacterized HTH-type transcriptional regulator YurK => putative HTH-type transcriptional regulator YurK [09:23:37] Modify product: Putative multidrug export ATP-binding/permease protein SA1683 => Putative multidrug export ATP-binding/permease protein [09:23:37] Modify product: Uncharacterized hydrolase YxeP => putative hydrolase YxeP [09:23:37] Modify product: UPF0758 protein YsxA => hypothetical protein [09:23:37] Modify product: Probable peptidoglycan glycosyltransferase FtsW => putative peptidoglycan glycosyltransferase FtsW [09:23:37] Modify product: RNA-binding protein HI_1333 => RNA-binding protein [09:23:37] Modify product: Uncharacterized FAD-linked oxidoreductase Rv2280 => putative FAD-linked oxidoreductase [09:23:37] Modify product: UPF0348 protein SP_1742 => hypothetical protein [09:23:37] Modify product: Uncharacterized protein Rv2926c => putative protein [09:23:37] Modify product: Probable diguanylate cyclase DgcC => putative diguanylate cyclase DgcC [09:23:37] Modify product: Putative glutamine amidotransferase Rv2859c => Putative glutamine amidotransferase [09:23:37] Modify product: Uncharacterized transporter Rv1979c => putative transporter [09:23:37] Modify product: Uncharacterized protein Spy1535 => putative protein [09:23:37] Modify product: Uncharacterized N-acetyltransferase YsnE => putative N-acetyltransferase YsnE [09:23:37] Modify product: Putative O-methyltransferase MSMEG_5073/MSMEI_4947 => Putative O-methyltransferase/MSMEI_4947 [09:23:37] Modify product: Uncharacterized protease YdcP => putative protease YdcP [09:23:37] Modify product: Oxygen-independent coproporphyrinogen-III oxidase-like protein LL1139 => Oxygen-independent coproporphyrinogen-III oxidase-like protein [09:23:37] Modify product: UPF0122 protein SP_1288 => hypothetical protein [09:23:37] Modify product: UPF0109 protein Rv2908c => hypothetical protein [09:23:37] Modify product: UPF0102 protein RPA0323 => hypothetical protein [09:23:37] Modify product: Uncharacterized AAA domain-containing protein Rv2559c => putative AAA domain-containing protein [09:23:37] Modify product: UPF0297 protein EF_1202 => hypothetical protein [09:23:37] Modify product: UPF0473 protein SP_0194 => hypothetical protein [09:23:37] Modify product: Uncharacterized spore protein YtfJ => putative spore protein YtfJ [09:23:37] Modify product: Probable ribosomal protein YlxQ => putative ribosomal protein YlxQ [09:23:37] Modify product: DegV domain-containing protein SA0704 => DegV domain-containing protein [09:23:37] Modify product: Uncharacterized zinc protease Rv2782c => putative zinc protease [09:23:37] Modify product: Uncharacterized signaling protein PA1727 => putative signaling protein [09:23:37] Modify product: Uncharacterized HTH-type transcriptional regulator Rv0880 => putative HTH-type transcriptional regulator [09:23:37] Modify product: Uncharacterized ABC transporter ATP-binding protein YxlF => putative ABC transporter ATP-binding protein YxlF [09:23:37] Modify product: Probable endopeptidase p60 => putative endopeptidase p60 [09:23:37] Modify product: UPF0271 protein TTHB195 => hypothetical protein [09:23:37] Modify product: Uncharacterized hydrolase YxeP => putative hydrolase YxeP [09:23:37] Modify product: Probable murein peptide carboxypeptidase => putative murein peptide carboxypeptidase [09:23:37] Modify product: Uncharacterized inner membrane transporter YicL => putative inner membrane transporter YicL [09:23:37] Modify product: Probable diguanylate cyclase DgcE => putative diguanylate cyclase DgcE [09:23:37] Modify product: Probable diguanylate cyclase DgcC => putative diguanylate cyclase DgcC [09:23:37] Modify product: Uncharacterized signaling protein PA1727 => putative signaling protein [09:23:37] Modify product: Uncharacterized HTH-type transcriptional regulator YybR => putative HTH-type transcriptional regulator YybR [09:23:37] Modify product: Probable ATP-dependent helicase DinG homolog => putative ATP-dependent helicase DinG [09:23:37] Modify product: GTP cyclohydrolase 1 type 2 homolog => GTP cyclohydrolase 1 type 2 [09:23:37] Modify product: Sulfurtransferase Alvin_2599 => Sulfurtransferase [09:23:37] Modify product: Uncharacterized ABC transporter ATP-binding protein Rv1273c => putative ABC transporter ATP-binding protein [09:23:37] Modify product: Uncharacterized ABC transporter ATP-binding protein TM_0288 => putative ABC transporter ATP-binding protein [09:23:37] Modify product: Uncharacterized signaling protein PA1727 => putative signaling protein [09:23:37] Modify product: Uncharacterized protein YpuA => putative protein YpuA [09:23:37] Modify product: Probable lipid II flippase MurJ => putative lipid II flippase MurJ [09:23:37] Modify product: Probable transcription repressor NiaR => putative transcription repressor NiaR [09:23:37] Modify product: Nucleoid-associated protein Cthe_2143 => Nucleoid-associated protein [09:23:37] Modify product: Uncharacterized PIN and TRAM-domain containing protein YacL => putative PIN and TRAM-domain containing protein YacL [09:23:37] Modify product: Uncharacterized protein YacP => putative protein YacP [09:23:38] Modify product: Uncharacterized protein BHWA1_00569 => putative protein [09:23:38] Modify product: Uncharacterized ABC transporter ATP-binding protein Rv0986 => putative ABC transporter ATP-binding protein [09:23:38] Modify product: Uncharacterized transporter Rv1979c => putative transporter [09:23:38] Modify product: Probable FMN/FAD exporter YeeO => putative FMN/FAD exporter YeeO [09:23:38] Modify product: Uncharacterized ABC transporter ATP-binding protein YheS => putative ABC transporter ATP-binding protein YheS [09:23:38] Modify product: UPF0324 inner membrane protein YeiH => hypothetical protein [09:23:38] Modify product: Uncharacterized protein YqbN => putative protein YqbN [09:23:38] Modify product: Uncharacterized protein YgaU => putative protein YgaU [09:23:38] Modify product: Probable licABCH operon regulator => putative licABCH operon regulator [09:23:38] Modify product: Probable ATP synthase YscN => putative ATP synthase YscN [09:23:38] Modify product: Uncharacterized HTH-type transcriptional regulator YybR => putative HTH-type transcriptional regulator YybR [09:23:38] Modify product: Probable phosphatase YcdX => putative phosphatase YcdX [09:23:38] Modify product: Putative dipeptidase SACOL1801 => Putative dipeptidase [09:23:38] Modify product: Uncharacterized ABC transporter ATP-binding protein YxlF => putative ABC transporter ATP-binding protein YxlF [09:23:38] Modify product: Uncharacterized transmembrane protein YxlG => putative transmembrane protein YxlG [09:23:38] Modify product: Transcriptional repressor SmtB homolog => Transcriptional repressor SmtB [09:23:38] Modify product: Probable M18 family aminopeptidase 2 => putative M18 family aminopeptidase 2 [09:23:38] Modify product: Uncharacterized ABC transporter ATP-binding protein YknY => putative ABC transporter ATP-binding protein YknY [09:23:38] Modify product: Probable metallo-hydrolase YflN => putative metallo-hydrolase YflN [09:23:38] Modify product: Nucleotidase CA_C3379 => Nucleotidase [09:23:38] Modify product: Uncharacterized RNA methyltransferase SP_1029 => putative RNA methyltransferase [09:23:38] Modify product: Probable metallo-hydrolase YflN => putative metallo-hydrolase YflN [09:23:38] Modify product: Putative phosphatase M6_Spy0533 => Putative phosphatase [09:23:38] Modify product: Probable formate transporter 1 => putative formate transporter 1 [09:23:38] Modify product: Probable cobalt-factor III C(17)-methyltransferase => putative cobalt-factor III C(17)-methyltransferase [09:23:38] Modify product: Probable licABCH operon regulator => putative licABCH operon regulator [09:23:38] Modify product: Uncharacterized protein YqgN => putative protein YqgN [09:23:38] Modify product: Uncharacterized protein HP_1423 => putative protein [09:23:38] Modify product: Probable type II secretion system protein HxcR => putative type II secretion system protein HxcR [09:23:38] Modify product: Uncharacterized protein HI_0131 => putative protein [09:23:38] Modify product: Uncharacterized protein HI_0131 => putative protein [09:23:38] Modify product: Uncharacterized metal-dependent hydrolase YcfH => putative metal-dependent hydrolase YcfH [09:23:38] Modify product: Probable tRNA-dihydrouridine synthase => putative tRNA-dihydrouridine synthase [09:23:38] Modify product: Uncharacterized aminopeptidase Rv1333 => putative aminopeptidase [09:23:38] Modify product: Probable D-xylose utilization operon transcriptional repressor => putative D-xylose utilization operon transcriptional repressor [09:23:38] Modify product: Deacetylase Oant_2987 => Deacetylase [09:23:38] Modify product: Probable FMN/FAD exporter YeeO => putative FMN/FAD exporter YeeO [09:23:38] Modify product: Uncharacterized N-acetyltransferase YjaB => putative N-acetyltransferase YjaB [09:23:38] Modify product: Deacetylase EF_0837 => Deacetylase [09:23:38] Modify product: Probable endopeptidase p60 => putative endopeptidase p60 [09:23:38] Modify product: Uncharacterized ABC transporter ATP-binding protein YbiT => putative ABC transporter ATP-binding protein YbiT [09:23:38] Modify product: Probable xanthine dehydrogenase subunit C => putative xanthine dehydrogenase subunit C [09:23:38] Modify product: Probable xanthine dehydrogenase subunit C => putative xanthine dehydrogenase subunit C [09:23:38] Modify product: Probable FMN/FAD exporter YeeO => putative FMN/FAD exporter YeeO [09:23:38] Modify product: Uncharacterized signaling protein PA1727 => putative signaling protein [09:23:38] Modify product: Iron-sulfur flavoprotein CD630_04720 => Iron-sulfur flavoprotein [09:23:38] Modify product: Uncharacterized ABC transporter ATP-binding protein Rv1272c => putative ABC transporter ATP-binding protein [09:23:38] Modify product: Uncharacterized ABC transporter ATP-binding protein Rv1273c => putative ABC transporter ATP-binding protein [09:23:38] Modify product: Uncharacterized HTH-type transcriptional regulator YusO => putative HTH-type transcriptional regulator YusO [09:23:38] Modify product: Uncharacterized HTH-type transcriptional regulator YbbH => putative HTH-type transcriptional regulator YbbH [09:23:38] Modify product: Aminopeptidase HP_1037 => Aminopeptidase [09:23:38] Modify product: Probable licABCH operon regulator => putative licABCH operon regulator [09:23:38] Modify product: Putative binding protein HI_1525 => Putative binding protein [09:23:38] Modify product: TelA-like protein SA1238 => TelA-like protein [09:23:38] Modify product: Putative phosphatase M6_Spy0533 => Putative phosphatase [09:23:38] Modify product: Putative permease Rv2963 => Putative permease [09:23:38] Modify product: Probable nicotinate-nucleotide pyrophosphorylase [carboxylating] => putative nicotinate-nucleotide pyrophosphorylase [carboxylating] [09:23:38] Modify product: Probable diguanylate cyclase DgcT => putative diguanylate cyclase DgcT [09:23:38] Modify product: Probable manganese catalase => putative manganese catalase [09:23:38] Modify product: Uncharacterized HTH-type transcriptional regulator YusO => putative HTH-type transcriptional regulator YusO [09:23:38] Modify product: Probable licABCH operon regulator => putative licABCH operon regulator [09:23:38] Modify product: Uncharacterized protein YqeY => putative protein YqeY [09:23:38] Modify product: Oxygen-independent coproporphyrinogen-III oxidase-like protein LL1139 => Oxygen-independent coproporphyrinogen-III oxidase-like protein [09:23:38] Modify product: Uncharacterized protein YqeN => putative protein YqeN [09:23:38] Modify product: Probable licABCH operon regulator => putative licABCH operon regulator [09:23:38] Modify product: Putative dipeptidase SACOL1801 => Putative dipeptidase [09:23:38] Modify product: Uncharacterized acyl--CoA ligase YhfT => putative acyl--CoA ligase YhfT [09:23:38] Modify product: Uncharacterized N-acetyltransferase YjaB => putative N-acetyltransferase YjaB [09:23:38] Modify product: Probable 2-dehydro-3-deoxy-D-pentonate aldolase YjhH => putative 2-dehydro-3-deoxy-D-pentonate aldolase YjhH [09:23:38] Modify product: Uncharacterized protein YisK => putative protein YisK [09:23:38] Modify product: Probable pyridine nucleotide-disulfide oxidoreductase RclA => putative pyridine nucleotide-disulfide oxidoreductase RclA [09:23:38] Modify product: Probable licABCH operon regulator => putative licABCH operon regulator [09:23:38] Modify product: Probable glucose uptake protein GlcU => putative glucose uptake protein GlcU [09:23:38] Modify product: Uncharacterized isomerase YddE => putative isomerase YddE [09:23:38] Modify product: Uncharacterized HTH-type transcriptional regulator YbbH => putative HTH-type transcriptional regulator YbbH [09:23:38] Modify product: Probable licABCH operon regulator => putative licABCH operon regulator [09:23:38] Modify product: Uncharacterized transporter Rv1979c => putative transporter [09:23:38] Modify product: Putative glutamine amidotransferase Rv2859c => Putative glutamine amidotransferase [09:23:38] Modify product: Putative dipeptidase SACOL1801 => Putative dipeptidase [09:23:38] Modify product: Probable licABCH operon regulator => putative licABCH operon regulator [09:23:38] Modify product: HTH-type transcriptional regulator Rv2034 => HTH-type transcriptional regulator [09:23:38] Modify product: Uncharacterized protease YdeA => putative protease YdeA [09:23:38] Modify product: Uncharacterized ABC transporter ATP-binding protein YxlF => putative ABC transporter ATP-binding protein YxlF [09:23:38] Modify product: Uncharacterized protein YhaZ => putative protein YhaZ [09:23:38] Modify product: UPF0098 protein CT_736 => hypothetical protein [09:23:38] Modify product: Virulence protein STM3117 => Virulence protein [09:23:38] Modify product: RutC family protein HI_0719 => RutC family protein [09:23:38] Modify product: Fluoroquinolones export ATP-binding protein Rv2688c => Fluoroquinolones export ATP-binding protein [09:23:38] Modify product: UPF0597 protein YhaM => hypothetical protein [09:23:38] Modify product: Phosphate-specific transport system accessory protein PhoU homolog => Phosphate-specific transport system accessory protein PhoU [09:23:38] Modify product: Uncharacterized protein YgaU => putative protein YgaU [09:23:38] Modify product: Uncharacterized protein YqbN => putative protein YqbN [09:23:38] Modify product: Probable type II secretion system protein HxcR => putative type II secretion system protein HxcR [09:23:38] Modify product: UPF0749 protein YlxW => hypothetical protein [09:23:38] Modify product: Probable GTP-binding protein EngB => putative GTP-binding protein EngB [09:23:38] Modify product: Probable chromate transport protein => putative chromate transport protein [09:23:38] Modify product: Probable chromate transport protein => putative chromate transport protein [09:23:38] Modify product: Putative metallophosphoesterase MG207 homolog => Putative metallophosphoesterase MG207 [09:23:38] Modify product: Uncharacterized MFS-type transporter YhjX => putative MFS-type transporter YhjX [09:23:38] Modify product: Uncharacterized ABC transporter ATP-binding protein YxlF => putative ABC transporter ATP-binding protein YxlF [09:23:38] Modify product: Uncharacterized protein SAV1875 => putative protein [09:23:38] Modify product: Uncharacterized ABC transporter ATP-binding protein YbiT => putative ABC transporter ATP-binding protein YbiT [09:23:38] Modify product: Calcium-transporting ATPase lmo0841 => Calcium-transporting ATPase [09:23:38] Modify product: Probable multidrug resistance protein EmrY => putative multidrug resistance protein EmrY [09:23:38] Modify product: Probable nicotinate-nucleotide adenylyltransferase => putative nicotinate-nucleotide adenylyltransferase [09:23:38] Modify product: Uncharacterized ABC transporter ATP-binding protein Rv0986 => putative ABC transporter ATP-binding protein [09:23:38] Modify product: UPF0309 protein BH3325 => hypothetical protein [09:23:38] Modify product: Uncharacterized protein Rv2927c => putative protein [09:23:38] Modify product: Uncharacterized protein SA1069 => putative protein [09:23:38] Modify product: Uncharacterized protein Spy1614 => putative protein [09:23:38] Modify product: Probable licABCH operon regulator => putative licABCH operon regulator [09:23:38] Modify product: Probable dual-specificity RNA methyltransferase RlmN => putative dual-specificity RNA methyltransferase RlmN [09:23:38] Modify product: UPF0701 protein HI_0467 => hypothetical protein [09:23:38] Modify product: Uncharacterized protein YloA => putative protein YloA [09:23:38] Modify product: Uncharacterized ABC transporter ATP-binding protein YheS => putative ABC transporter ATP-binding protein YheS [09:23:39] Modify product: Uncharacterized peptidase SA1530 => putative peptidase [09:23:39] Modify product: DegV domain-containing protein MW1315 => DegV domain-containing protein [09:23:39] Modify product: UPF0210 protein SP_0239 => hypothetical protein [09:23:39] Modify product: UPF0237 protein SP_0238 => hypothetical protein [09:23:39] Modify product: Uncharacterized peptidase SA1530 => putative peptidase [09:23:39] Modify product: UPF0749 protein YlxW => hypothetical protein [09:23:39] Modify product: UPF0749 protein Rv1825 => hypothetical protein [09:23:39] Modify product: Probable peptidoglycan glycosyltransferase FtsW => putative peptidoglycan glycosyltransferase FtsW [09:23:39] Modify product: Uncharacterized signaling protein PA1727 => putative signaling protein [09:23:39] Modify product: Uncharacterized protein HI_0933 => putative protein [09:23:39] Modify product: Uncharacterized hydrolase YxeP => putative hydrolase YxeP [09:23:39] Modify product: Uncharacterized protein Rv2581c => putative protein [09:23:39] Modify product: Probable protein kinase UbiB => putative protein kinase UbiB [09:23:39] Modify product: Uncharacterized signaling protein PA1727 => putative signaling protein [09:23:39] Modify product: PGL/p-HBAD biosynthesis glycosyltransferase Rv2957 => PGL/p-HBAD biosynthesis glycosyltransferase [09:23:39] Modify product: Probable lipid II flippase MurJ => putative lipid II flippase MurJ [09:23:39] Modify product: Probable D-xylose utilization operon transcriptional repressor => putative D-xylose utilization operon transcriptional repressor [09:23:39] Modify product: Uncharacterized ABC transporter ATP-binding protein Rv1272c => putative ABC transporter ATP-binding protein [09:23:39] Modify product: Uncharacterized ABC transporter ATP-binding protein Rv1273c => putative ABC transporter ATP-binding protein [09:23:39] Modify product: Uncharacterized hydrolase YxeP => putative hydrolase YxeP [09:23:39] Modify product: Uncharacterized response regulatory protein SACOL0201 => putative response regulatory protein [09:23:39] Modify product: Nitrilase blr3397 => Nitrilase [09:23:39] Modify product: Phosphorylated carbohydrates phosphatase TM_1254 => Phosphorylated carbohydrates phosphatase [09:23:39] Modify product: UPF0053 protein Rv1842c => hypothetical protein [09:23:39] Modify product: Uncharacterized signaling protein PA1727 => putative signaling protein [09:23:39] Modify product: Probable siderophore transport system ATP-binding protein YusV => putative siderophore transport system ATP-binding protein YusV [09:23:39] Modify product: Probable siderophore-binding lipoprotein YfiY => putative siderophore-binding lipoprotein YfiY [09:23:39] Modify product: Probable 6-phospho-beta-glucosidase => putative 6-phospho-beta-glucosidase [09:23:39] Modify product: Uncharacterized protein HI_0131 => putative protein [09:23:39] Modify product: Uncharacterized signaling protein PA1727 => putative signaling protein [09:23:39] Cleaned 290 /product names [09:23:39] Deleting unwanted file: trash6/tmp/prokka/sample2/sprot.faa [09:23:39] Deleting unwanted file: trash6/tmp/prokka/sample2/sprot.blast [09:23:40] There are still 1466 unannotated CDS left (started with 3908) [09:23:40] Will use hmmer3 to search against /home/andrespara/anaconda3/envs/panphlan/bin/../db/hmm/HAMAP.hmm with 4 CPUs [09:23:40] Running: cat trash6\/tmp\/prokka\/sample2\/HAMAP\.hmm\.faa | parallel --gnu --plain -j 4 --block 42303 --recstart '>' --pipe hmmscan --noali --notextw --acc -E 1e-06 --cpu 1 /home/andrespara/anaconda3/envs/panphlan/bin/../db/hmm/HAMAP.hmm /dev/stdin > trash6\/tmp\/prokka\/sample2\/HAMAP\.hmm\.hmmer3 2> /dev/null [09:23:49] Deleting unwanted file: trash6/tmp/prokka/sample2/HAMAP.hmm.faa [09:23:49] Deleting unwanted file: trash6/tmp/prokka/sample2/HAMAP.hmm.hmmer3 [09:23:49] Labelling remaining 1385 proteins as 'hypothetical protein' [09:23:49] Possible /pseudo 'Proline--tRNA ligase' at gnl|X|DIAHKAHI_1 position 68799 [09:23:49] Possible /pseudo 'Pyridinium-3,5-bisthiocarboxylic acid mononucleotide nickel insertion protein' at gnl|X|DIAHKAHI_1 position 225154 [09:23:49] Possible /pseudo 'Flagellar secretion chaperone FliS' at gnl|X|DIAHKAHI_1 position 317022 [09:23:49] Possible /pseudo 'Flagellar basal-body rod protein FlgG' at gnl|X|DIAHKAHI_1 position 352808 [09:23:49] Possible /pseudo 'HTH-type transcriptional regulator GlvR' at gnl|X|DIAHKAHI_1 position 515028 [09:23:49] Possible /pseudo 'Signal peptidase IB' at gnl|X|DIAHKAHI_1 position 613920 [09:23:49] Possible /pseudo 'Membrane lipoprotein TmpC' at gnl|X|DIAHKAHI_1 position 631309 [09:23:49] Possible /pseudo 'H(+)/Cl(-) exchange transporter ClcA' at gnl|X|DIAHKAHI_1 position 681945 [09:23:49] Possible /pseudo 'Dipeptidyl-peptidase 5' at gnl|X|DIAHKAHI_1 position 726815 [09:23:49] Possible /pseudo 'Toxin B' at gnl|X|DIAHKAHI_1 position 741532 [09:23:49] Possible /pseudo 'Trifunctional nucleotide phosphoesterase protein YfkN' at gnl|X|DIAHKAHI_1 position 794847 [09:23:49] Possible /pseudo 'Biotin synthase' at gnl|X|DIAHKAHI_1 position 856315 [09:23:49] Possible /pseudo 'PTS system glucitol/sorbitol-specific EIIB component' at gnl|X|DIAHKAHI_1 position 899213 [09:23:49] Possible /pseudo 'Iron hydrogenase 1' at gnl|X|DIAHKAHI_1 position 1036339 [09:23:49] Possible /pseudo 'putative ABC transporter ATP-binding protein' at gnl|X|DIAHKAHI_1 position 1092423 [09:23:49] Possible /pseudo 'N-acetylmuramoyl-L-alanine amidase LytC' at gnl|X|DIAHKAHI_1 position 1117457 [09:23:49] Possible /pseudo 'Branched-chain amino acid transport system 2 carrier protein' at gnl|X|DIAHKAHI_1 position 1332378 [09:23:49] Possible /pseudo 'putative ABC transporter ATP-binding protein' at gnl|X|DIAHKAHI_1 position 1574034 [09:23:49] Possible /pseudo 'Anti-sigma-V factor RsiV' at gnl|X|DIAHKAHI_1 position 1673943 [09:23:49] Possible /pseudo 'General stress protein 16U' at gnl|X|DIAHKAHI_1 position 1760852 [09:23:49] Possible /pseudo 'Cysteine synthase' at gnl|X|DIAHKAHI_1 position 1801020 [09:23:49] Possible /pseudo 'Glycine reductase complex component B subunit gamma' at gnl|X|DIAHKAHI_1 position 1878639 [09:23:49] Possible /pseudo 'Multidrug resistance protein MdtG' at gnl|X|DIAHKAHI_1 position 1953025 [09:23:49] Possible /pseudo 'putative isomerase YddE' at gnl|X|DIAHKAHI_1 position 2105262 [09:23:49] Possible /pseudo 'Uric acid permease PucK' at gnl|X|DIAHKAHI_1 position 2217600 [09:23:49] Possible /pseudo 'putative ABC transporter ATP-binding protein' at gnl|X|DIAHKAHI_1 position 2371921 [09:23:49] Possible /pseudo 'Glycine reductase complex component B subunit gamma' at gnl|X|DIAHKAHI_1 position 2530744 [09:23:49] Possible /pseudo 'putative protein' at gnl|X|DIAHKAHI_1 position 2771411 [09:23:49] Possible /pseudo 'Polyisoprenyl-teichoic acid--peptidoglycan teichoic acid transferase TagT' at gnl|X|DIAHKAHI_1 position 3019443 [09:23:49] Possible /pseudo 'N-acetylmuramoyl-L-alanine amidase LytC' at gnl|X|DIAHKAHI_1 position 3047050 [09:23:49] Possible /pseudo 'N-acetylmuramoyl-L-alanine amidase LytC' at gnl|X|DIAHKAHI_1 position 3060348 [09:23:49] Possible /pseudo 'N-acetylmuramoyl-L-alanine amidase LytC' at gnl|X|DIAHKAHI_1 position 3062165 [09:23:49] Possible /pseudo 'N-acetylmuramoyl-L-alanine amidase LytC' at gnl|X|DIAHKAHI_1 position 3064133 [09:23:49] Possible /pseudo 'N-acetylmuramoyl-L-alanine amidase LytC' at gnl|X|DIAHKAHI_1 position 3074432 [09:23:49] Possible /pseudo 'putative ABC transporter ATP-binding protein' at gnl|X|DIAHKAHI_1 position 3094224 [09:23:49] Possible /pseudo 'PTS system mannose-specific EIIAB component' at gnl|X|DIAHKAHI_1 position 3310380 [09:23:49] Possible /pseudo 'D-proline reductase proprotein PrdA' at gnl|X|DIAHKAHI_1 position 3556460 [09:23:49] Possible /pseudo 'D-proline reductase proprotein PrdA' at gnl|X|DIAHKAHI_1 position 3556942 [09:23:49] Possible /pseudo 'D-proline reductase subunit gamma' at gnl|X|DIAHKAHI_1 position 3558053 [09:23:49] Possible /pseudo 'putative chromate transport protein' at gnl|X|DIAHKAHI_1 position 3683254 [09:23:49] Possible /pseudo 'Formate dehydrogenase H' at gnl|X|DIAHKAHI_1 position 3699854 [09:23:49] Possible /pseudo 'Type 4 prepilin-like proteins leader peptide-processing enzyme' at gnl|X|DIAHKAHI_1 position 3862213 [09:23:49] Found 1550 unique /gene codes. [09:23:49] Fixed 2 duplicate /gene - yvoA_1 yvoA_2 [09:23:49] Fixed 3 duplicate /gene - cutC_1 cutC_2 cutC_3 [09:23:49] Fixed 2 duplicate /gene - ydcP_1 ydcP_2 [09:23:49] Fixed 2 duplicate /gene - metQ_1 metQ_2 [09:23:49] Fixed 2 duplicate /gene - lplJ_1 lplJ_2 [09:23:49] Fixed 2 duplicate /gene - yabJ_1 yabJ_2 [09:23:49] Fixed 3 duplicate /gene - hemN_1 hemN_2 hemN_3 [09:23:49] Fixed 2 duplicate /gene - yusV_1 yusV_2 [09:23:49] Fixed 2 duplicate /gene - sapB_1 sapB_2 [09:23:49] Fixed 2 duplicate /gene - sigV_1 sigV_2 [09:23:49] Fixed 2 duplicate /gene - porC_1 porC_2 [09:23:49] Fixed 2 duplicate /gene - pucC_1 pucC_2 [09:23:49] Fixed 2 duplicate /gene - ftsL_1 ftsL_2 [09:23:49] Fixed 2 duplicate /gene - malH_1 malH_2 [09:23:49] Fixed 2 duplicate /gene - rpe_1 rpe_2 [09:23:49] Fixed 3 duplicate /gene - tal_1 tal_2 tal_3 [09:23:49] Fixed 2 duplicate /gene - lysA_1 lysA_2 [09:23:49] Fixed 2 duplicate /gene - dnaB_1 dnaB_2 [09:23:49] Fixed 2 duplicate /gene - grdE_1 grdE_2 [09:23:49] Fixed 2 duplicate /gene - ftsH4_1 ftsH4_2 [09:23:49] Fixed 3 duplicate /gene - ndhI_1 ndhI_2 ndhI_3 [09:23:49] Fixed 6 duplicate /gene - ytrA_1 ytrA_2 ytrA_3 ytrA_4 ytrA_5 ytrA_6 [09:23:49] Fixed 3 duplicate /gene - secA_1 secA_2 secA_3 [09:23:49] Fixed 2 duplicate /gene - zupT_1 zupT_2 [09:23:49] Fixed 3 duplicate /gene - dapA_1 dapA_2 dapA_3 [09:23:49] Fixed 2 duplicate /gene - ssuA_1 ssuA_2 [09:23:49] Fixed 2 duplicate /gene - nrdD_1 nrdD_2 [09:23:49] Fixed 12 duplicate /gene - blaI_1 blaI_2 blaI_3 blaI_4 blaI_5 blaI_6 blaI_7 blaI_8 blaI_9 blaI_10 blaI_11 blaI_12 [09:23:49] Fixed 3 duplicate /gene - polC_1 polC_2 polC_3 [09:23:49] Fixed 2 duplicate /gene - pcrA_1 pcrA_2 [09:23:49] Fixed 4 duplicate /gene - prdA_1 prdA_2 prdA_3 prdA_4 [09:23:49] Fixed 2 duplicate /gene - nhaP_1 nhaP_2 [09:23:49] Fixed 2 duplicate /gene - prsA_1 prsA_2 [09:23:49] Fixed 2 duplicate /gene - adh1_1 adh1_2 [09:23:49] Fixed 5 duplicate /gene - grdB_1 grdB_2 grdB_3 grdB_4 grdB_5 [09:23:49] Fixed 6 duplicate /gene - xerC_1 xerC_2 xerC_3 xerC_4 xerC_5 xerC_6 [09:23:49] Fixed 2 duplicate /gene - pyrC_1 pyrC_2 [09:23:49] Fixed 2 duplicate /gene - hflX_1 hflX_2 [09:23:49] Fixed 2 duplicate /gene - lytG_1 lytG_2 [09:23:49] Fixed 2 duplicate /gene - hyfA_1 hyfA_2 [09:23:49] Fixed 2 duplicate /gene - tsaD_1 tsaD_2 [09:23:49] Fixed 2 duplicate /gene - rluD_1 rluD_2 [09:23:49] Fixed 3 duplicate /gene - ycsE_1 ycsE_2 ycsE_3 [09:23:49] Fixed 2 duplicate /gene - acpP_1 acpP_2 [09:23:49] Fixed 2 duplicate /gene - clsA_1 clsA_2 [09:23:49] Fixed 2 duplicate /gene - topB_1 topB_2 [09:23:49] Fixed 2 duplicate /gene - tuf_1 tuf_2 [09:23:49] Fixed 10 duplicate /gene - licR_1 licR_2 licR_3 licR_4 licR_5 licR_6 licR_7 licR_8 licR_9 licR_10 [09:23:49] Fixed 4 duplicate /gene - glvR_1 glvR_2 glvR_3 glvR_4 [09:23:49] Fixed 2 duplicate /gene - mobA_1 mobA_2 [09:23:49] Fixed 2 duplicate /gene - spoIVB_1 spoIVB_2 [09:23:49] Fixed 2 duplicate /gene - atpE_1 atpE_2 [09:23:49] Fixed 2 duplicate /gene - ftsW_1 ftsW_2 [09:23:49] Fixed 2 duplicate /gene - srlA_1 srlA_2 [09:23:49] Fixed 2 duplicate /gene - spoVD_1 spoVD_2 [09:23:49] Fixed 4 duplicate /gene - xdhA_1 xdhA_2 xdhA_3 xdhA_4 [09:23:49] Fixed 3 duplicate /gene - hin_1 hin_2 hin_3 [09:23:49] Fixed 2 duplicate /gene - dtpT_1 dtpT_2 [09:23:49] Fixed 2 duplicate /gene - gntR_1 gntR_2 [09:23:49] Fixed 2 duplicate /gene - ygaU_1 ygaU_2 [09:23:49] Fixed 2 duplicate /gene - mngA_1 mngA_2 [09:23:49] Fixed 2 duplicate /gene - lpxG_1 lpxG_2 [09:23:49] Fixed 2 duplicate /gene - fusA_1 fusA_2 [09:23:49] Fixed 3 duplicate /gene - cysW_1 cysW_2 cysW_3 [09:23:49] Fixed 2 duplicate /gene - clpP_1 clpP_2 [09:23:49] Fixed 2 duplicate /gene - pdaC_1 pdaC_2 [09:23:49] Fixed 2 duplicate /gene - hxcR_1 hxcR_2 [09:23:49] Fixed 3 duplicate /gene - flgG_1 flgG_2 flgG_3 [09:23:49] Fixed 2 duplicate /gene - ulaB_1 ulaB_2 [09:23:49] Fixed 2 duplicate /gene - alaS_1 alaS_2 [09:23:49] Fixed 3 duplicate /gene - smc_1 smc_2 smc_3 [09:23:49] Fixed 3 duplicate /gene - asrC_1 asrC_2 asrC_3 [09:23:49] Fixed 7 duplicate /gene - licC_1 licC_2 licC_3 licC_4 licC_5 licC_6 licC_7 [09:23:49] Fixed 2 duplicate /gene - rho_1 rho_2 [09:23:49] Fixed 2 duplicate /gene - rob_1 rob_2 [09:23:49] Fixed 2 duplicate /gene - mftC_1 mftC_2 [09:23:49] Fixed 2 duplicate /gene - iap_1 iap_2 [09:23:49] Fixed 3 duplicate /gene - pdaA_1 pdaA_2 pdaA_3 [09:23:49] Fixed 3 duplicate /gene - ssbA_1 ssbA_2 ssbA_3 [09:23:49] Fixed 2 duplicate /gene - ttcA_1 ttcA_2 [09:23:49] Fixed 2 duplicate /gene - yjjP_1 yjjP_2 [09:23:49] Fixed 3 duplicate /gene - yybR_1 yybR_2 yybR_3 [09:23:49] Fixed 3 duplicate /gene - dgcC_1 dgcC_2 dgcC_3 [09:23:49] Fixed 2 duplicate /gene - cmpR_1 cmpR_2 [09:23:49] Fixed 4 duplicate /gene - bglH_1 bglH_2 bglH_3 bglH_4 [09:23:49] Fixed 2 duplicate /gene - pip_1 pip_2 [09:23:49] Fixed 2 duplicate /gene - truA_1 truA_2 [09:23:49] Fixed 5 duplicate /gene - lysN_1 lysN_2 lysN_3 lysN_4 lysN_5 [09:23:49] Fixed 3 duplicate /gene - proX_1 proX_2 proX_3 [09:23:49] Fixed 6 duplicate /gene - immR_1 immR_2 immR_3 immR_4 immR_5 immR_6 [09:23:49] Fixed 2 duplicate /gene - arlR_1 arlR_2 [09:23:49] Fixed 7 duplicate /gene - resE_1 resE_2 resE_3 resE_4 resE_5 resE_6 resE_7 [09:23:49] Fixed 7 duplicate /gene - abgB_1 abgB_2 abgB_3 abgB_4 abgB_5 abgB_6 abgB_7 [09:23:49] Fixed 3 duplicate /gene - yxdM_1 yxdM_2 yxdM_3 [09:23:49] Fixed 5 duplicate /gene - licB_1 licB_2 licB_3 licB_4 licB_5 [09:23:49] Fixed 2 duplicate /gene - hom_1 hom_2 [09:23:49] Fixed 2 duplicate /gene - yisK_1 yisK_2 [09:23:49] Fixed 3 duplicate /gene - rsgA_1 rsgA_2 rsgA_3 [09:23:49] Fixed 2 duplicate /gene - srmB_1 srmB_2 [09:23:49] Fixed 2 duplicate /gene - mreB_1 mreB_2 [09:23:49] Fixed 2 duplicate /gene - ybaK_1 ybaK_2 [09:23:49] Fixed 2 duplicate /gene - adaA_1 adaA_2 [09:23:49] Fixed 2 duplicate /gene - pduL_1 pduL_2 [09:23:49] Fixed 3 duplicate /gene - appA_1 appA_2 appA_3 [09:23:49] Fixed 3 duplicate /gene - korB_1 korB_2 korB_3 [09:23:49] Fixed 2 duplicate /gene - bchE_1 bchE_2 [09:23:49] Fixed 3 duplicate /gene - dnaC_1 dnaC_2 dnaC_3 [09:23:49] Fixed 2 duplicate /gene - megL_1 megL_2 [09:23:49] Fixed 3 duplicate /gene - fldA_1 fldA_2 fldA_3 [09:23:49] Fixed 3 duplicate /gene - cysK_1 cysK_2 cysK_3 [09:23:49] Fixed 2 duplicate /gene - yknX_1 yknX_2 [09:23:49] Fixed 2 duplicate /gene - yodJ_1 yodJ_2 [09:23:49] Fixed 2 duplicate /gene - mscS_1 mscS_2 [09:23:49] Fixed 6 duplicate /gene - bglF_1 bglF_2 bglF_3 bglF_4 bglF_5 bglF_6 [09:23:49] Fixed 5 duplicate /gene - ssuC_1 ssuC_2 ssuC_3 ssuC_4 ssuC_5 [09:23:49] Fixed 3 duplicate /gene - feoB_1 feoB_2 feoB_3 [09:23:49] Fixed 2 duplicate /gene - betI_1 betI_2 [09:23:49] Fixed 2 duplicate /gene - dapB_1 dapB_2 [09:23:49] Fixed 2 duplicate /gene - glpK_1 glpK_2 [09:23:49] Fixed 3 duplicate /gene - gatB_1 gatB_2 gatB_3 [09:23:49] Fixed 2 duplicate /gene - nit1_1 nit1_2 [09:23:49] Fixed 4 duplicate /gene - kdpD_1 kdpD_2 kdpD_3 kdpD_4 [09:23:49] Fixed 2 duplicate /gene - xerD_1 xerD_2 [09:23:49] Fixed 3 duplicate /gene - bceB_1 bceB_2 bceB_3 [09:23:49] Fixed 4 duplicate /gene - tetD_1 tetD_2 tetD_3 tetD_4 [09:23:49] Fixed 2 duplicate /gene - nagC_1 nagC_2 [09:23:49] Fixed 2 duplicate /gene - topA_1 topA_2 [09:23:49] Fixed 2 duplicate /gene - mtlR_1 mtlR_2 [09:23:49] Fixed 2 duplicate /gene - mecR1_1 mecR1_2 [09:23:49] Fixed 5 duplicate /gene - manZ_1 manZ_2 manZ_3 manZ_4 manZ_5 [09:23:49] Fixed 3 duplicate /gene - ykfC_1 ykfC_2 ykfC_3 [09:23:49] Fixed 3 duplicate /gene - yeeO_1 yeeO_2 yeeO_3 [09:23:49] Fixed 2 duplicate /gene - sigK_1 sigK_2 [09:23:49] Fixed 3 duplicate /gene - tipA_1 tipA_2 tipA_3 [09:23:49] Fixed 2 duplicate /gene - fieF_1 fieF_2 [09:23:49] Fixed 2 duplicate /gene - uxaA_1 uxaA_2 [09:23:49] Fixed 7 duplicate /gene - regX3_1 regX3_2 regX3_3 regX3_4 regX3_5 regX3_6 regX3_7 [09:23:49] Fixed 3 duplicate /gene - ydbD_1 ydbD_2 ydbD_3 [09:23:49] Fixed 2 duplicate /gene - hmo_1 hmo_2 [09:23:49] Fixed 7 duplicate /gene - fruA_1 fruA_2 fruA_3 fruA_4 fruA_5 fruA_6 fruA_7 [09:23:49] Fixed 3 duplicate /gene - graS_1 graS_2 graS_3 [09:23:49] Fixed 2 duplicate /gene - pepF1_1 pepF1_2 [09:23:49] Fixed 2 duplicate /gene - aaaT_1 aaaT_2 [09:23:49] Fixed 4 duplicate /gene - gltC_1 gltC_2 gltC_3 gltC_4 [09:23:49] Fixed 2 duplicate /gene - treP_1 treP_2 [09:23:49] Fixed 2 duplicate /gene - marA_1 marA_2 [09:23:49] Fixed 3 duplicate /gene - natA_1 natA_2 natA_3 [09:23:49] Fixed 2 duplicate /gene - lacA_1 lacA_2 [09:23:49] Fixed 3 duplicate /gene - hisC_1 hisC_2 hisC_3 [09:23:49] Fixed 7 duplicate /gene - licT_1 licT_2 licT_3 licT_4 licT_5 licT_6 licT_7 [09:23:49] Fixed 2 duplicate /gene - hpf_1 hpf_2 [09:23:49] Fixed 3 duplicate /gene - yfkN_1 yfkN_2 yfkN_3 [09:23:49] Fixed 3 duplicate /gene - mepH_1 mepH_2 mepH_3 [09:23:49] Fixed 3 duplicate /gene - ugtP_1 ugtP_2 ugtP_3 [09:23:49] Fixed 6 duplicate /gene - walK_1 walK_2 walK_3 walK_4 walK_5 walK_6 [09:23:49] Fixed 2 duplicate /gene - osmV_1 osmV_2 [09:23:49] Fixed 2 duplicate /gene - kdgT_1 kdgT_2 [09:23:49] Fixed 2 duplicate /gene - dut_1 dut_2 [09:23:49] Fixed 2 duplicate /gene - lspA_1 lspA_2 [09:23:49] Fixed 3 duplicate /gene - puuR_1 puuR_2 puuR_3 [09:23:49] Fixed 2 duplicate /gene - yjjG_1 yjjG_2 [09:23:49] Fixed 4 duplicate /gene - dacF_1 dacF_2 dacF_3 dacF_4 [09:23:49] Fixed 2 duplicate /gene - larC_1 larC_2 [09:23:49] Fixed 4 duplicate /gene - uvrA_1 uvrA_2 uvrA_3 uvrA_4 [09:23:49] Fixed 2 duplicate /gene - iolS_1 iolS_2 [09:23:49] Fixed 4 duplicate /gene - comEC_1 comEC_2 comEC_3 comEC_4 [09:23:49] Fixed 2 duplicate /gene - aroE_1 aroE_2 [09:23:49] Fixed 2 duplicate /gene - isp_1 isp_2 [09:23:49] Fixed 2 duplicate /gene - hpt_1 hpt_2 [09:23:49] Fixed 2 duplicate /gene - atpF_1 atpF_2 [09:23:49] Fixed 2 duplicate /gene - rny_1 rny_2 [09:23:49] Fixed 2 duplicate /gene - dmdA_1 dmdA_2 [09:23:49] Fixed 2 duplicate /gene - kdgR_1 kdgR_2 [09:23:49] Fixed 2 duplicate /gene - sigF_1 sigF_2 [09:23:49] Fixed 2 duplicate /gene - dnaG_1 dnaG_2 [09:23:49] Fixed 7 duplicate /gene - dgaR_1 dgaR_2 dgaR_3 dgaR_4 dgaR_5 dgaR_6 dgaR_7 [09:23:49] Fixed 2 duplicate /gene - murK_1 murK_2 [09:23:49] Fixed 3 duplicate /gene - gatC_1 gatC_2 gatC_3 [09:23:49] Fixed 3 duplicate /gene - cobD_1 cobD_2 cobD_3 [09:23:49] Fixed 3 duplicate /gene - buk2_1 buk2_2 buk2_3 [09:23:49] Fixed 2 duplicate /gene - sdpR_1 sdpR_2 [09:23:49] Fixed 2 duplicate /gene - ndx1_1 ndx1_2 [09:23:49] Fixed 4 duplicate /gene - sgcG_1 sgcG_2 sgcG_3 sgcG_4 [09:23:49] Fixed 2 duplicate /gene - puuB_1 puuB_2 [09:23:49] Fixed 2 duplicate /gene - glpR_1 glpR_2 [09:23:49] Fixed 2 duplicate /gene - yihN_1 yihN_2 [09:23:49] Fixed 2 duplicate /gene - purH_1 purH_2 [09:23:49] Fixed 3 duplicate /gene - malP_1 malP_2 malP_3 [09:23:49] Fixed 2 duplicate /gene - rtcB_1 rtcB_2 [09:23:49] Fixed 2 duplicate /gene - purC_1 purC_2 [09:23:49] Fixed 3 duplicate /gene - yflN_1 yflN_2 yflN_3 [09:23:49] Fixed 3 duplicate /gene - brnQ_1 brnQ_2 brnQ_3 [09:23:49] Fixed 2 duplicate /gene - srrB_1 srrB_2 [09:23:49] Fixed 2 duplicate /gene - yjcD_1 yjcD_2 [09:23:49] Fixed 2 duplicate /gene - fprA1_1 fprA1_2 [09:23:49] Fixed 2 duplicate /gene - der_1 der_2 [09:23:49] Fixed 3 duplicate /gene - gatA_1 gatA_2 gatA_3 [09:23:49] Fixed 3 duplicate /gene - bmrR_1 bmrR_2 bmrR_3 [09:23:49] Fixed 2 duplicate /gene - gatD_1 gatD_2 [09:23:49] Fixed 2 duplicate /gene - oppD_1 oppD_2 [09:23:49] Fixed 3 duplicate /gene - yceD_1 yceD_2 yceD_3 [09:23:49] Fixed 2 duplicate /gene - dnaE_1 dnaE_2 [09:23:49] Fixed 2 duplicate /gene - motB_1 motB_2 [09:23:49] Fixed 2 duplicate /gene - dpp5_1 dpp5_2 [09:23:49] Fixed 5 duplicate /gene - xre_1 xre_2 xre_3 xre_4 xre_5 [09:23:49] Fixed 2 duplicate /gene - celA_1 celA_2 [09:23:49] Fixed 2 duplicate /gene - dmsB_1 dmsB_2 [09:23:49] Fixed 3 duplicate /gene - sinR_1 sinR_2 sinR_3 [09:23:49] Fixed 2 duplicate /gene - yycJ_1 yycJ_2 [09:23:49] Fixed 2 duplicate /gene - phnW_1 phnW_2 [09:23:49] Fixed 2 duplicate /gene - fliS_1 fliS_2 [09:23:49] Fixed 3 duplicate /gene - macB_1 macB_2 macB_3 [09:23:49] Fixed 2 duplicate /gene - serS_1 serS_2 [09:23:49] Fixed 2 duplicate /gene - mprA_1 mprA_2 [09:23:49] Fixed 2 duplicate /gene - yqbN_1 yqbN_2 [09:23:49] Fixed 3 duplicate /gene - pepT_1 pepT_2 pepT_3 [09:23:49] Fixed 2 duplicate /gene - ogt_1 ogt_2 [09:23:49] Fixed 2 duplicate /gene - pduA_1 pduA_2 [09:23:49] Fixed 3 duplicate /gene - srlE_1 srlE_2 srlE_3 [09:23:49] Fixed 2 duplicate /gene - lysC_1 lysC_2 [09:23:49] Fixed 2 duplicate /gene - prkC_1 prkC_2 [09:23:49] Fixed 3 duplicate /gene - ylmB_1 ylmB_2 ylmB_3 [09:23:49] Fixed 2 duplicate /gene - yheS_1 yheS_2 [09:23:49] Fixed 2 duplicate /gene - potA_1 potA_2 [09:23:49] Fixed 2 duplicate /gene - rbsB_1 rbsB_2 [09:23:49] Fixed 4 duplicate /gene - pdeR_1 pdeR_2 pdeR_3 pdeR_4 [09:23:49] Fixed 3 duplicate /gene - pta_1 pta_2 pta_3 [09:23:49] Fixed 2 duplicate /gene - prfB_1 prfB_2 [09:23:49] Fixed 2 duplicate /gene - nox_1 nox_2 [09:23:49] Fixed 8 duplicate /gene - mepA_1 mepA_2 mepA_3 mepA_4 mepA_5 mepA_6 mepA_7 mepA_8 [09:23:49] Fixed 2 duplicate /gene - proC_1 proC_2 [09:23:49] Fixed 2 duplicate /gene - gloB_1 gloB_2 [09:23:49] Fixed 2 duplicate /gene - pgsA_1 pgsA_2 [09:23:49] Fixed 31 duplicate /gene - lytC_1 lytC_2 lytC_3 lytC_4 lytC_5 lytC_6 lytC_7 lytC_8 lytC_9 lytC_10 lytC_11 lytC_12 lytC_13 lytC_14 lytC_15 lytC_16 lytC_17 lytC_18 lytC_19 lytC_20 lytC_21 lytC_22 lytC_23 lytC_24 lytC_25 lytC_26 lytC_27 lytC_28 lytC_29 lytC_30 lytC_31 [09:23:49] Fixed 3 duplicate /gene - korA_1 korA_2 korA_3 [09:23:49] Fixed 3 duplicate /gene - atzA_1 atzA_2 atzA_3 [09:23:49] Fixed 13 duplicate /gene - walR_1 walR_2 walR_3 walR_4 walR_5 walR_6 walR_7 walR_8 walR_9 walR_10 walR_11 walR_12 walR_13 [09:23:49] Fixed 2 duplicate /gene - toxB_1 toxB_2 [09:23:49] Fixed 6 duplicate /gene - blaR1_1 blaR1_2 blaR1_3 blaR1_4 blaR1_5 blaR1_6 [09:23:49] Fixed 2 duplicate /gene - aroF_1 aroF_2 [09:23:49] Fixed 6 duplicate /gene - yxdL_1 yxdL_2 yxdL_3 yxdL_4 yxdL_5 yxdL_6 [09:23:49] Fixed 2 duplicate /gene - araQ_1 araQ_2 [09:23:49] Fixed 2 duplicate /gene - rbr_1 rbr_2 [09:23:49] Fixed 3 duplicate /gene - cysA_1 cysA_2 cysA_3 [09:23:49] Fixed 2 duplicate /gene - asnB_1 asnB_2 [09:23:49] Fixed 2 duplicate /gene - cwlC_1 cwlC_2 [09:23:49] Fixed 2 duplicate /gene - ulaF_1 ulaF_2 [09:23:49] Fixed 8 duplicate /gene - atoC_1 atoC_2 atoC_3 atoC_4 atoC_5 atoC_6 atoC_7 atoC_8 [09:23:49] Fixed 4 duplicate /gene - bioB_1 bioB_2 bioB_3 bioB_4 [09:23:49] Fixed 5 duplicate /gene - lolD_1 lolD_2 lolD_3 lolD_4 lolD_5 [09:23:49] Fixed 2 duplicate /gene - ybbH_1 ybbH_2 [09:23:49] Fixed 3 duplicate /gene - dgcE_1 dgcE_2 dgcE_3 [09:23:49] Fixed 4 duplicate /gene - sutR_1 sutR_2 sutR_3 sutR_4 [09:23:49] Fixed 2 duplicate /gene - yjaB_1 yjaB_2 [09:23:49] Fixed 3 duplicate /gene - spsB_1 spsB_2 spsB_3 [09:23:49] Fixed 2 duplicate /gene - bglA_1 bglA_2 [09:23:49] Fixed 2 duplicate /gene - gmk_1 gmk_2 [09:23:49] Fixed 3 duplicate /gene - mleN_1 mleN_2 mleN_3 [09:23:49] Fixed 2 duplicate /gene - mutS2_1 mutS2_2 [09:23:49] Fixed 2 duplicate /gene - pgcA_1 pgcA_2 [09:23:49] Fixed 2 duplicate /gene - yjiG_1 yjiG_2 [09:23:49] Fixed 3 duplicate /gene - tadA_1 tadA_2 tadA_3 [09:23:49] Fixed 2 duplicate /gene - cinA_1 cinA_2 [09:23:49] Fixed 3 duplicate /gene - kstR2_1 kstR2_2 kstR2_3 [09:23:49] Fixed 2 duplicate /gene - nfo_1 nfo_2 [09:23:49] Fixed 2 duplicate /gene - metH_1 metH_2 [09:23:49] Fixed 2 duplicate /gene - manR_1 manR_2 [09:23:49] Fixed 3 duplicate /gene - fdhF_1 fdhF_2 fdhF_3 [09:23:49] Fixed 3 duplicate /gene - hisK_1 hisK_2 hisK_3 [09:23:49] Fixed 2 duplicate /gene - hosA_1 hosA_2 [09:23:49] Fixed 2 duplicate /gene - dpaL_1 dpaL_2 [09:23:49] Fixed 2 duplicate /gene - menH_1 menH_2 [09:23:49] Fixed 2 duplicate /gene - prdB_1 prdB_2 [09:23:49] Fixed 3 duplicate /gene - guaB_1 guaB_2 guaB_3 [09:23:49] Fixed 3 duplicate /gene - ybiT_1 ybiT_2 ybiT_3 [09:23:49] Fixed 4 duplicate /gene - crr_1 crr_2 crr_3 crr_4 [09:23:49] Fixed 2 duplicate /gene - nudF_1 nudF_2 [09:23:49] Fixed 2 duplicate /gene - purF_1 purF_2 [09:23:49] Fixed 7 duplicate /gene - yxlF_1 yxlF_2 yxlF_3 yxlF_4 yxlF_5 yxlF_6 yxlF_7 [09:23:49] Fixed 2 duplicate /gene - leuA_1 leuA_2 [09:23:49] Fixed 2 duplicate /gene - map_1 map_2 [09:23:49] Fixed 3 duplicate /gene - kdpE_1 kdpE_2 kdpE_3 [09:23:49] Fixed 2 duplicate /gene - corA_1 corA_2 [09:23:49] Fixed 2 duplicate /gene - sigA_1 sigA_2 [09:23:49] Fixed 2 duplicate /gene - artQ_1 artQ_2 [09:23:49] Fixed 2 duplicate /gene - yhaZ_1 yhaZ_2 [09:23:49] Fixed 2 duplicate /gene - alsT_1 alsT_2 [09:23:49] Fixed 2 duplicate /gene - tktA_1 tktA_2 [09:23:49] Fixed 2 duplicate /gene - mtrB_1 mtrB_2 [09:23:49] Fixed 4 duplicate /gene - rocR_1 rocR_2 rocR_3 rocR_4 [09:23:49] Fixed 4 duplicate /gene - murJ_1 murJ_2 murJ_3 murJ_4 [09:23:49] Fixed 4 duplicate /gene - hxlR_1 hxlR_2 hxlR_3 hxlR_4 [09:23:49] Fixed 2 duplicate /gene - iscS_1 iscS_2 [09:23:49] Fixed 2 duplicate /gene - ubiG_1 ubiG_2 [09:23:49] Fixed 2 duplicate /gene - yocH_1 yocH_2 [09:23:49] Fixed 2 duplicate /gene - axe1-6A_1 axe1-6A_2 [09:23:49] Fixed 2 duplicate /gene - patA_1 patA_2 [09:23:49] Fixed 2 duplicate /gene - rplL_1 rplL_2 [09:23:49] Fixed 5 duplicate /gene - manP_1 manP_2 manP_3 manP_4 manP_5 [09:23:49] Fixed 2 duplicate /gene - suyB_1 suyB_2 [09:23:49] Fixed 2 duplicate /gene - srpC_1 srpC_2 [09:23:49] Fixed 4 duplicate /gene - sorB_1 sorB_2 sorB_3 sorB_4 [09:23:49] Fixed 5 duplicate /gene - carE_1 carE_2 carE_3 carE_4 carE_5 [09:23:49] Fixed 2 duplicate /gene - cooS1_1 cooS1_2 [09:23:49] Fixed 2 duplicate /gene - sttH_1 sttH_2 [09:23:49] Fixed 2 duplicate /gene - dnaX_1 dnaX_2 [09:23:49] Fixed 3 duplicate /gene - rsxB_1 rsxB_2 rsxB_3 [09:23:49] Fixed 2 duplicate /gene - dppC_1 dppC_2 [09:23:49] Fixed 2 duplicate /gene - sunS_1 sunS_2 [09:23:49] Fixed 3 duplicate /gene - mngB_1 mngB_2 mngB_3 [09:23:49] Fixed 3 duplicate /gene - fryB_1 fryB_2 fryB_3 [09:23:49] Fixed 3 duplicate /gene - yusO_1 yusO_2 yusO_3 [09:23:49] Fixed 2 duplicate /gene - glyA_1 glyA_2 [09:23:49] Fixed 2 duplicate /gene - exuR_1 exuR_2 [09:23:49] Fixed 3 duplicate /gene - dan_1 dan_2 dan_3 [09:23:49] Fixed 2 duplicate /gene - uppS_1 uppS_2 [09:23:49] Fixed 5 duplicate /gene - yxeP_1 yxeP_2 yxeP_3 yxeP_4 yxeP_5 [09:23:49] Fixed 2 duplicate /gene - carA_1 carA_2 [09:23:49] Fixed 7 duplicate /gene - ytrF_1 ytrF_2 ytrF_3 ytrF_4 ytrF_5 ytrF_6 ytrF_7 [09:23:49] Fixed 3 duplicate /gene - ribZ_1 ribZ_2 ribZ_3 [09:23:49] Fixed 3 duplicate /gene - ypdB_1 ypdB_2 ypdB_3 [09:23:49] Fixed 4 duplicate /gene - xkdM_1 xkdM_2 xkdM_3 xkdM_4 [09:23:49] Fixed 2 duplicate /gene - pspA_1 pspA_2 [09:23:49] Fixed 2 duplicate /gene - comC_1 comC_2 [09:23:49] Fixed 2 duplicate /gene - queG_1 queG_2 [09:23:49] Fixed 2 duplicate /gene - epsF_1 epsF_2 [09:23:49] Fixed 2 duplicate /gene - rbr3A_1 rbr3A_2 [09:23:49] Fixed 5 duplicate /gene - carD_1 carD_2 carD_3 carD_4 carD_5 [09:23:49] Fixed 2 duplicate /gene - rimO_1 rimO_2 [09:23:49] Fixed 5 duplicate /gene - patB_1 patB_2 patB_3 patB_4 patB_5 [09:23:49] Fixed 2 duplicate /gene - ycdX_1 ycdX_2 [09:23:49] Fixed 2 duplicate /gene - zmp1_1 zmp1_2 [09:23:49] Fixed 2 duplicate /gene - uppP_1 uppP_2 [09:23:49] Fixed 2 duplicate /gene - carB_1 carB_2 [09:23:49] Fixed 2 duplicate /gene - nfrA2_1 nfrA2_2 [09:23:49] Fixed 5 duplicate /gene - pgdA_1 pgdA_2 pgdA_3 pgdA_4 pgdA_5 [09:23:49] Fixed 2 duplicate /gene - gtaB_1 gtaB_2 [09:23:49] Fixed 2 duplicate /gene - oppF_1 oppF_2 [09:23:49] Fixed 4 duplicate /gene - yddE_1 yddE_2 yddE_3 yddE_4 [09:23:49] Fixed 3 duplicate /gene - trxA_1 trxA_2 trxA_3 [09:23:49] Fixed 2 duplicate /gene - mta_1 mta_2 [09:23:49] Fixed 3 duplicate /gene - graR_1 graR_2 graR_3 [09:23:49] Fixed 2 duplicate /gene - tmpC_1 tmpC_2 [09:23:49] Fixed 4 duplicate /gene - ccpA_1 ccpA_2 ccpA_3 ccpA_4 [09:23:49] Fixed 2 duplicate /gene - flr_1 flr_2 [09:23:49] Fixed 2 duplicate /gene - thrZ_1 thrZ_2 [09:23:49] Fixed 2 duplicate /gene - glpQ_1 glpQ_2 [09:23:49] Fixed 3 duplicate /gene - sorC_1 sorC_2 sorC_3 [09:23:49] Fixed 2 duplicate /gene - mecI_1 mecI_2 [09:23:49] Fixed 3 duplicate /gene - bceA_1 bceA_2 bceA_3 [09:23:49] Fixed 5 duplicate /gene - manX_1 manX_2 manX_3 manX_4 manX_5 [09:23:49] Fixed 2 duplicate /gene - def1_1 def1_2 [09:23:49] Fixed 2 duplicate /gene - yhhT_1 yhhT_2 [09:23:49] Fixed 2 duplicate /gene - xylP_1 xylP_2 [09:23:49] Fixed 2 duplicate /gene - rnfC_1 rnfC_2 [09:23:49] Fixed 2 duplicate /gene - speA_1 speA_2 [09:23:49] Fixed 2 duplicate /gene - mutS_1 mutS_2 [09:23:49] Fixed 3 duplicate /gene - cspD_1 cspD_2 cspD_3 [09:23:49] Fixed 5 duplicate /gene - licA_1 licA_2 licA_3 licA_4 licA_5 [09:23:49] Fixed 2 duplicate /gene - ulaA_1 ulaA_2 [09:23:49] Fixed 3 duplicate /gene - trxB_1 trxB_2 trxB_3 [09:23:49] Fixed 2 duplicate /gene - thlA_1 thlA_2 [09:23:49] Fixed 2 duplicate /gene - rhaS_1 rhaS_2 [09:23:49] Fixed 2 duplicate /gene - gatY_1 gatY_2 [09:23:49] Fixed 2 duplicate /gene - fliN_1 fliN_2 [09:23:49] Fixed 2 duplicate /gene - agrB_1 agrB_2 [09:23:49] Fixed 2 duplicate /gene - rbsC_1 rbsC_2 [09:23:49] Fixed 3 duplicate /gene - dxs_1 dxs_2 dxs_3 [09:23:49] Fixed 3 duplicate /gene - ypdF_1 ypdF_2 ypdF_3 [09:23:49] Fixed 3 duplicate /gene - rsiV_1 rsiV_2 rsiV_3 [09:23:49] Fixed 2 duplicate /gene - codB_1 codB_2 [09:23:49] Fixed 4 duplicate /gene - yknY_1 yknY_2 yknY_3 yknY_4 [09:23:49] Fixed 2 duplicate /gene - srlB_1 srlB_2 [09:23:49] Fixed 2 duplicate /gene - ruvC_1 ruvC_2 [09:23:49] Fixed 2 duplicate /gene - yceC_1 yceC_2 [09:23:49] Fixed 2 duplicate /gene - pomA_1 pomA_2 [09:23:49] Fixed 2 duplicate /gene - thiH_1 thiH_2 [09:23:49] Fixed 4 duplicate /gene - srrA_1 srrA_2 srrA_3 srrA_4 [09:23:49] Fixed 2 duplicate /gene - hndD_1 hndD_2 [09:23:49] Fixed 3 duplicate /gene - ytrB_1 ytrB_2 ytrB_3 [09:23:49] Fixed 2 duplicate /gene - mdtG_1 mdtG_2 [09:23:49] Fixed 2 duplicate /gene - glmS_1 glmS_2 [09:23:49] Fixed 2 duplicate /gene - sglT_1 sglT_2 [09:23:49] Fixed 2 duplicate /gene - gap_1 gap_2 [09:23:49] Fixed 2 duplicate /gene - toxA_1 toxA_2 [09:23:49] Fixed 2 duplicate /gene - hadI_1 hadI_2 [09:23:49] Fixed 2 duplicate /gene - rhaR_1 rhaR_2 [09:23:49] Fixed 2 duplicate /gene - hhaIM_1 hhaIM_2 [09:23:49] Fixed 3 duplicate /gene - lacC_1 lacC_2 lacC_3 [09:23:49] Fixed 2 duplicate /gene - ftsZ_1 ftsZ_2 [09:23:49] Fixed 2 duplicate /gene - cysL_1 cysL_2 [09:23:49] Fixed 2 duplicate /gene - tilS_1 tilS_2 [09:23:49] Fixed 2 duplicate /gene - pyrD_1 pyrD_2 [09:23:49] Fixed 2 duplicate /gene - liaS_1 liaS_2 [09:23:49] Fixed 2 duplicate /gene - vanW_1 vanW_2 [09:23:49] Fixed 3 duplicate /gene - abgT_1 abgT_2 abgT_3 [09:23:49] Fixed 2 duplicate /gene - rsmH_1 rsmH_2 [09:23:49] Fixed 2 duplicate /gene - clcA_1 clcA_2 [09:23:49] Fixed 3 duplicate /gene - pucK_1 pucK_2 pucK_3 [09:23:49] Fixed 2 duplicate /gene - tagT_1 tagT_2 [09:23:49] Fixed 2 duplicate /gene - glnQ_1 glnQ_2 [09:23:49] Fixed 2 duplicate /gene - proS_1 proS_2 [09:23:49] Fixed 2 duplicate /gene - fabG_1 fabG_2 [09:23:49] Fixed 3 duplicate /gene - adhE_1 adhE_2 adhE_3 [09:23:49] Fixed 2 duplicate /gene - sufS_1 sufS_2 [09:23:49] Fixed 6 duplicate /gene - drrA_1 drrA_2 drrA_3 drrA_4 drrA_5 drrA_6 [09:23:49] Fixed 2 duplicate /gene - steT_1 steT_2 [09:23:49] Fixed 2 duplicate /gene - tuaG_1 tuaG_2 [09:23:49] Fixed 2 duplicate /gene - lytR_1 lytR_2 [09:23:49] Fixed 5 duplicate /gene - Int-Tn_1 Int-Tn_2 Int-Tn_3 Int-Tn_4 Int-Tn_5 [09:23:49] Fixed 2 duplicate /gene - nrdG_1 nrdG_2 [09:23:49] Fixed 2 duplicate /gene - natR_1 natR_2 [09:23:49] Fixed 9 duplicate /gene - phoR_1 phoR_2 phoR_3 phoR_4 phoR_5 phoR_6 phoR_7 phoR_8 phoR_9 [09:23:49] Fixed 5 duplicate /gene - ssuB_1 ssuB_2 ssuB_3 ssuB_4 ssuB_5 [09:23:49] Fixed 2 duplicate /gene - cheW_1 cheW_2 [09:23:49] Fixed 415 colliding /gene names. [09:23:49] Adding /locus_tag identifiers [09:23:49] Assigned 3998 locus_tags to CDS and RNA features. [09:23:49] Writing outputs to trash6/tmp/prokka/sample2/ [09:23:55] Generating annotation statistics file [09:23:55] Generating Genbank and Sequin files [09:23:55] Running: tbl2asn -V b -a r10k -l paired-ends -M n -N 1 -y 'Annotated using prokka 1.13 from https://github.com/tseemann/prokka' -Z trash6\/tmp\/prokka\/sample2\/sample2\.err -i trash6\/tmp\/prokka\/sample2\/sample2\.fsa 2> /dev/null [09:24:02] Could not run command: tbl2asn -V b -a r10k -l paired-ends -M n -N 1 -y 'Annotated using prokka 1.13 from https://github.com/tseemann/prokka' -Z trash6\/tmp\/prokka\/sample2\/sample2\.err -i trash6\/tmp\/prokka\/sample2\/sample2\.fsa 2> /dev/null [09:24:02] This is prokka 1.13 [09:24:02] Written by Torsten Seemann [09:24:02] Homepage is https://github.com/tseemann/prokka [09:24:02] Local time is Thu Jan 21 09:24:02 2021 [09:24:02] You are andrespara [09:24:02] Operating system is linux [09:24:02] You have BioPerl 1.7.7 Argument "1.7.7" isn't numeric in numeric lt (<) at /home/andrespara/anaconda3/envs/panphlan/bin/prokka line 253. [09:24:02] System has 8 cores. [09:24:02] Will use maximum of 4 cores. [09:24:02] Annotating as >>> Bacteria <<< [09:24:02] Generating locus_tag from 'dummy/sample1.faa' contents. [09:24:02] Setting --locustag NLPIPFPC from MD5 75929f9c9a855bc440f9a1d7212d1db6 [09:24:02] Enabling options to ensure Genbank/ENA/DDJB submission compliance. [09:24:02] Re-using existing --outdir trash6/tmp/prokka/sample1 [09:24:02] Using filename prefix: sample1.XXX [09:24:02] Setting HMMER_NCPU=1 [09:24:02] Writing log to: trash6/tmp/prokka/sample1/sample1.log [09:24:02] Command: /home/andrespara/anaconda3/envs/panphlan/bin/prokka --outdir trash6/tmp/prokka/sample1 --prefix sample1 --centre X --compliant --force --cpus 4 dummy/sample1.faa [09:24:02] Appending to PATH: /home/andrespara/anaconda3/envs/panphlan/bin [09:24:02] Looking for 'aragorn' - found /home/andrespara/anaconda3/envs/panphlan/bin/aragorn [09:24:02] Determined aragorn version is 1.2 [09:24:02] Looking for 'barrnap' - found /home/andrespara/anaconda3/envs/panphlan/bin/barrnap [09:24:02] Determined barrnap version is 0.9 [09:24:02] Looking for 'blastp' - found /home/andrespara/anaconda3/envs/panphlan/bin/blastp [09:24:02] Determined blastp version is 2.9 [09:24:02] Looking for 'cmpress' - found /home/andrespara/anaconda3/envs/panphlan/bin/cmpress [09:24:02] Determined cmpress version is 1.1 [09:24:02] Looking for 'cmscan' - found /home/andrespara/anaconda3/envs/panphlan/bin/cmscan [09:24:02] Determined cmscan version is 1.1 [09:24:02] Looking for 'egrep' - found /usr/bin/egrep [09:24:02] Looking for 'find' - found /usr/bin/find [09:24:02] Looking for 'grep' - found /usr/bin/grep [09:24:02] Looking for 'hmmpress' - found /home/andrespara/anaconda3/envs/panphlan/bin/hmmpress [09:24:02] Determined hmmpress version is 3.3 [09:24:02] Looking for 'hmmscan' - found /home/andrespara/anaconda3/envs/panphlan/bin/hmmscan [09:24:02] Determined hmmscan version is 3.3 [09:24:02] Looking for 'java' - found /home/andrespara/anaconda3/envs/panphlan/bin/java [09:24:02] Looking for 'less' - found /usr/bin/less [09:24:02] Looking for 'makeblastdb' - found /home/andrespara/anaconda3/envs/panphlan/bin/makeblastdb [09:24:02] Determined makeblastdb version is 2.9 [09:24:02] Looking for 'minced' - found /home/andrespara/anaconda3/envs/panphlan/bin/minced [09:24:02] Determined minced version is 4.2 [09:24:02] Looking for 'parallel' - found /home/andrespara/anaconda3/envs/panphlan/bin/parallel [09:24:02] Determined parallel version is 20201122 [09:24:02] Looking for 'prodigal' - found /home/andrespara/anaconda3/envs/panphlan/bin/prodigal [09:24:02] Determined prodigal version is 2.6 [09:24:02] Looking for 'prokka-genbank_to_fasta_db' - found /home/andrespara/anaconda3/envs/panphlan/bin/prokka-genbank_to_fasta_db [09:24:02] Looking for 'sed' - found /usr/bin/sed [09:24:02] Looking for 'tbl2asn' - found /home/andrespara/anaconda3/envs/panphlan/bin/tbl2asn [tbl2asn] This copy of tbl2asn is more than a year old. Please download the current version. [09:24:02] Determined tbl2asn version is 25.7 [09:24:02] Using genetic code table 11. [09:24:02] Loading and checking input file: dummy/sample1.faa [09:24:02] Changing illegal '|' to '_' in sequence name: sample1|SC|contig000001 [09:24:03] Wrote 1 contigs totalling 4047741 bp. [09:24:03] Predicting tRNAs and tmRNAs [09:24:03] Running: aragorn -l -gc11 -w trash6\/tmp\/prokka\/sample1\/sample1\.fna [09:24:03] 1 tRNA-Leu [15902,15990] 35 (taa) [09:24:03] 2 tRNA-Met [16002,16078] 35 (cat) [09:24:03] 3 tRNA-Ala [17740,17815] 34 (tgc) [09:24:03] 4 tRNA-Ser [25255,25346] 35 (gga) [09:24:03] 5 tRNA-Asn [35491,35565] 33 (gtt) [09:24:03] 6 tRNA-Leu [35572,35658] 35 (taa) [09:24:03] 7 tRNA-Met [35673,35748] 34 (cat) [09:24:03] 8 tRNA-Glu [35756,35830] 34 (ttc) [09:24:03] 9 tRNA-Gly [35840,35913] 33 (tcc) [09:24:03] 10 tRNA-Val [35919,35994] 34 (tac) [09:24:03] 11 tRNA-Asp [36000,36076] 35 (gtc) [09:24:03] 12 tRNA-Thr [36086,36160] 33 (tgt) [09:24:03] 13 tRNA-Tyr [36174,36258] 35 (gta) [09:24:03] 14 tRNA-Leu [36268,36351] 35 (tag) [09:24:03] 15 tRNA-Pyl [36380,36456] 36 (cta) [09:24:03] 16 tRNA-Gln [36464,36539] 34 (ttg) [09:24:03] 17 tRNA-Ser [36628,36716] 35 (tga) [09:24:03] 18 tRNA-Phe [36720,36795] 34 (gaa) [09:24:03] 19 tRNA-Met [36802,36876] 35 (cat) [09:24:03] 20 tRNA-Met [36890,36966] 35 (cat) [09:24:03] 21 tRNA-Pro [36990,37066] 35 (tgg) [09:24:03] 22 tRNA-His [37074,37150] 35 (gtg) [09:24:03] 23 tRNA-Lys [37159,37234] 34 (ttt) [09:24:03] 24 tRNA-Cys [37242,37315] 33 (gca) [09:24:03] 25 tRNA-Asn [37322,37396] 33 (gtt) [09:24:03] 26 tRNA-Leu [37403,37489] 35 (taa) [09:24:03] 27 tRNA-Met [37504,37579] 34 (cat) [09:24:03] 28 tRNA-Glu [37587,37661] 34 (ttc) [09:24:03] 29 tRNA-Gly [37671,37744] 33 (tcc) [09:24:03] 30 tRNA-Val [37750,37825] 34 (tac) [09:24:03] 31 tRNA-Asp [37831,37907] 35 (gtc) [09:24:03] 32 tRNA-Thr [37917,37991] 33 (tgt) [09:24:03] 33 tRNA-Tyr [38005,38089] 35 (gta) [09:24:03] 34 tRNA-Leu [38099,38182] 35 (tag) [09:24:03] 35 tRNA-Gly [38206,38280] 33 (gcc) [09:24:03] 36 tRNA-Pyl [38305,38381] 36 (cta) [09:24:03] 37 tRNA-Gln [38391,38466] 34 (ttg) [09:24:03] 38 tRNA-Lys [38478,38553] 34 (ttt) [09:24:03] 39 tRNA-Ser [38556,38644] 35 (tga) [09:24:03] 40 tRNA-Phe [38648,38723] 34 (gaa) [09:24:03] 41 tRNA-Met [38730,38804] 35 (cat) [09:24:03] 42 tRNA-Met [38818,38894] 35 (cat) [09:24:03] 43 tRNA-His [38912,38988] 35 (gtg) [09:24:03] 44 tRNA-Lys [38997,39072] 34 (ttt) [09:24:03] 45 tRNA-Cys [39080,39153] 33 (gca) [09:24:03] 46 tRNA-Arg [39161,39237] 35 (acg) [09:24:03] 47 tRNA-Val [39250,39325] 34 (tac) [09:24:03] 48 tRNA-Ala [134412,134487] 34 (tgc) [09:24:03] 49 tRNA-Asn [137949,138023] 33 (gtt) [09:24:03] 50 tRNA-Glu [138028,138102] 34 (ttc) [09:24:03] 51 tRNA-Val [138108,138183] 34 (tac) [09:24:03] 52 tRNA-Asp [138189,138265] 35 (gtc) [09:24:03] 53 tRNA-Thr [138277,138351] 33 (tgt) [09:24:03] 54 tRNA-Tyr [138365,138449] 35 (gta) [09:24:03] 55 tRNA-Gly [138459,138532] 33 (tcc) [09:24:03] 56 tRNA-Pyl [138543,138619] 36 (cta) [09:24:03] 57 tRNA-Gln [138629,138704] 34 (ttg) [09:24:03] 58 tRNA-Lys [138716,138791] 34 (ttt) [09:24:03] 59 tRNA-Ser [138794,138882] 35 (tga) [09:24:03] 60 tRNA-Ser [138899,138989] 35 (gct) [09:24:03] 61 tRNA-Pro [138998,139074] 35 (tgg) [09:24:03] 62 tRNA-Trp [139159,139234] 34 (cca) [09:24:03] 63 tRNA-Pro [139295,139371] 35 (tgg) [09:24:03] 64 tRNA-Ile [139378,139454] 35 (gat) [09:24:03] 65 tRNA-Phe [139458,139533] 34 (gaa) [09:24:03] 66 tRNA-Met [139541,139617] 35 (cat) [09:24:03] 67 tRNA-Ala [141291,141366] 34 (tgc) [09:24:03] 68 tRNA-Ala [151850,151925] 34 (tgc) [09:24:03] 69 tRNA-Asn [155346,155420] 33 (gtt) [09:24:03] 70 tRNA-Leu [155426,155512] 35 (taa) [09:24:03] 71 tRNA-Met [155527,155602] 34 (cat) [09:24:03] 72 tRNA-Glu [155610,155684] 34 (ttc) [09:24:03] 73 tRNA-Gly [155694,155767] 33 (tcc) [09:24:03] 74 tRNA-Val [155773,155848] 34 (tac) [09:24:03] 75 tRNA-Asp [155854,155930] 35 (gtc) [09:24:03] 76 tRNA-Gly [155941,156015] 33 (gcc) [09:24:03] 77 tRNA-Pyl [156024,156099] 37 (cta) [09:24:03] 78 tRNA-Ser [899558,899648] 35 (gct) [09:24:03] 79 tRNA-Gly [1152856,1152929] 33 (tcc) [09:24:03] 80 tRNA-Leu c[1236043,1236125] 35 (caa) [09:24:03] 81 tRNA-Leu [1813597,1813678] 35 (tag) [09:24:03] 82 tRNA-SeC c[2727013,2727109] 35 (tca) [09:24:03] 83 tRNA-Thr c[3017318,3017392] 33 (tgt) [09:24:03] 84 tmRNA c[3497378,3497727] 94,123 ADDNFAIAA* [09:24:03] 85 tRNA-Thr c[4023013,4023087] 33 (tgt) [09:24:03] 86 tRNA-Val c[4023121,4023196] 34 (tac) [09:24:03] 87 tRNA-Glu c[4023201,4023275] 34 (ttc) [09:24:03] 88 tRNA-Lys c[4023282,4023357] 34 (ttt) [09:24:03] Found 88 tRNAs [09:24:03] Predicting Ribosomal RNAs [09:24:03] Running Barrnap with 4 threads [09:24:05] 1 gnl|X|NLPIPFPC_1 10810 16S ribosomal RNA [09:24:05] 2 gnl|X|NLPIPFPC_1 12682 23S ribosomal RNA [09:24:05] 3 gnl|X|NLPIPFPC_1 15787 5S ribosomal RNA [09:24:05] 4 gnl|X|NLPIPFPC_1 16190 16S ribosomal RNA [09:24:05] 5 gnl|X|NLPIPFPC_1 18090 23S ribosomal RNA [09:24:05] 6 gnl|X|NLPIPFPC_1 21108 5S ribosomal RNA [09:24:05] 7 gnl|X|NLPIPFPC_1 30523 16S ribosomal RNA [09:24:05] 8 gnl|X|NLPIPFPC_1 32290 23S ribosomal RNA [09:24:05] 9 gnl|X|NLPIPFPC_1 35376 5S ribosomal RNA [09:24:05] 10 gnl|X|NLPIPFPC_1 132858 16S ribosomal RNA [09:24:05] 11 gnl|X|NLPIPFPC_1 134803 23S ribosomal RNA [09:24:05] 12 gnl|X|NLPIPFPC_1 137833 5S ribosomal RNA [09:24:05] 13 gnl|X|NLPIPFPC_1 139735 16S ribosomal RNA [09:24:05] 14 gnl|X|NLPIPFPC_1 141683 23S ribosomal RNA [09:24:05] 15 gnl|X|NLPIPFPC_1 144710 5S ribosomal RNA [09:24:05] 16 gnl|X|NLPIPFPC_1 150294 16S ribosomal RNA [09:24:05] 17 gnl|X|NLPIPFPC_1 152200 23S ribosomal RNA [09:24:05] 18 gnl|X|NLPIPFPC_1 155229 5S ribosomal RNA [09:24:05] 19 gnl|X|NLPIPFPC_1 351817 16S ribosomal RNA [09:24:05] 20 gnl|X|NLPIPFPC_1 353585 23S ribosomal RNA [09:24:05] 21 gnl|X|NLPIPFPC_1 356615 5S ribosomal RNA [09:24:05] 22 gnl|X|NLPIPFPC_1 1148105 16S ribosomal RNA [09:24:05] 23 gnl|X|NLPIPFPC_1 1149870 23S ribosomal RNA [09:24:05] 24 gnl|X|NLPIPFPC_1 1152945 5S ribosomal RNA [09:24:05] 25 gnl|X|NLPIPFPC_1 3017488 23S ribosomal RNA [09:24:05] 26 gnl|X|NLPIPFPC_1 3020711 16S ribosomal RNA [09:24:05] 27 gnl|X|NLPIPFPC_1 3770460 5S ribosomal RNA [09:24:05] 28 gnl|X|NLPIPFPC_1 3770701 23S ribosomal RNA [09:24:05] 29 gnl|X|NLPIPFPC_1 3773883 16S ribosomal RNA [09:24:05] 30 gnl|X|NLPIPFPC_1 3900898 5S ribosomal RNA [09:24:05] 31 gnl|X|NLPIPFPC_1 3901139 23S ribosomal RNA [09:24:05] 32 gnl|X|NLPIPFPC_1 3904362 16S ribosomal RNA [09:24:05] Found 32 rRNAs [09:24:05] Skipping ncRNA search, enable with --rfam if desired. [09:24:05] Total of 119 tRNA + rRNA features [09:24:05] Searching for CRISPR repeats [09:24:05] Found 0 CRISPRs [09:24:05] Predicting coding sequences [09:24:05] Contigs total 4047741 bp, so using single mode [09:24:05] Running: prodigal -i trash6\/tmp\/prokka\/sample1\/sample1\.fna -c -m -g 11 -p single -f sco -q [09:24:09] Excluding CDS which overlaps existing RNA (tRNA) at gnl|X|NLPIPFPC_1:25269..25454 on + strand [09:24:12] Found 3594 CDS [09:24:12] Connecting features back to sequences [09:24:12] Not using genus-specific database. Try --usegenus to enable it. [09:24:12] Annotating CDS, please be patient. [09:24:12] Will use 4 CPUs for similarity searching. [09:24:14] There are still 3594 unannotated CDS left (started with 3594) [09:24:14] Will use blast to search against /home/andrespara/anaconda3/envs/panphlan/bin/../db/kingdom/Bacteria/sprot with 4 CPUs [09:24:14] Running: cat trash6\/tmp\/prokka\/sample1\/sprot\.faa | parallel --gnu --plain -j 4 --block 141662 --recstart '>' --pipe blastp -query - -db /home/andrespara/anaconda3/envs/panphlan/bin/../db/kingdom/Bacteria/sprot -evalue 1e-06 -num_threads 1 -num_descriptions 1 -num_alignments 1 -seg no > trash6\/tmp\/prokka\/sample1\/sprot\.blast 2> /dev/null [09:25:02] Modify product: Uncharacterized protein Rv1488 => putative protein [09:25:02] Modify product: UPF0371 protein DIP2346 => hypothetical protein [09:25:02] Modify product: Probable cation efflux system protein Rv2025c => putative cation efflux system protein [09:25:02] Modify product: 30S ribosomal protein S1 homolog => 30S ribosomal protein S1 [09:25:02] Modify product: Probable phosphatase YcdX => putative phosphatase YcdX [09:25:02] Modify product: Probable diguanylate cyclase DgcE => putative diguanylate cyclase DgcE [09:25:02] Modify product: Uncharacterized signaling protein PA1727 => putative signaling protein [09:25:02] Modify product: Uncharacterized ABC transporter ATP-binding protein Rv1273c => putative ABC transporter ATP-binding protein [09:25:02] Modify product: Uncharacterized ABC transporter ATP-binding protein TM_0288 => putative ABC transporter ATP-binding protein [09:25:02] Modify product: UPF0053 protein HI_0107 => hypothetical protein [09:25:02] Modify product: UPF0291 protein YnzC => hypothetical protein [09:25:02] Modify product: Probable M18 family aminopeptidase 1 => putative M18 family aminopeptidase 1 [09:25:02] Modify product: Uncharacterized HTH-type transcriptional regulator YurK => putative HTH-type transcriptional regulator YurK [09:25:02] Modify product: Probable phosphotransferase enzyme IIB component M6_Spy0801 => putative phosphotransferase enzyme IIB component [09:25:02] Modify product: Putative multidrug export ATP-binding/permease protein SA1683 => Putative multidrug export ATP-binding/permease protein [09:25:02] Modify product: Uncharacterized hydrolase YxeP => putative hydrolase YxeP [09:25:02] Modify product: Uncharacterized protein YpbG => putative protein YpbG [09:25:02] Modify product: UPF0758 protein YsxA => hypothetical protein [09:25:02] Modify product: Probable peptidoglycan glycosyltransferase FtsW => putative peptidoglycan glycosyltransferase FtsW [09:25:02] Modify product: RNA-binding protein HI_1333 => RNA-binding protein [09:25:02] Modify product: Uncharacterized FAD-linked oxidoreductase Rv2280 => putative FAD-linked oxidoreductase [09:25:02] Modify product: UPF0348 protein SP_1742 => hypothetical protein [09:25:02] Modify product: Uncharacterized protein Rv2926c => putative protein [09:25:02] Modify product: Probable diguanylate cyclase DgcC => putative diguanylate cyclase DgcC [09:25:02] Modify product: Putative glutamine amidotransferase Rv2859c => Putative glutamine amidotransferase [09:25:02] Modify product: Uncharacterized transporter Rv1979c => putative transporter [09:25:02] Modify product: Uncharacterized protein Spy1535 => putative protein [09:25:02] Modify product: Uncharacterized N-acetyltransferase YsnE => putative N-acetyltransferase YsnE [09:25:02] Modify product: Putative O-methyltransferase MSMEG_5073/MSMEI_4947 => Putative O-methyltransferase/MSMEI_4947 [09:25:02] Modify product: Uncharacterized protease YdcP => putative protease YdcP [09:25:02] Modify product: Oxygen-independent coproporphyrinogen-III oxidase-like protein LL1139 => Oxygen-independent coproporphyrinogen-III oxidase-like protein [09:25:02] Modify product: UPF0122 protein SP_1288 => hypothetical protein [09:25:02] Modify product: UPF0109 protein Rv2908c => hypothetical protein [09:25:02] Modify product: Probable multidrug ABC transporter ATP-binding protein YbhF => putative multidrug ABC transporter ATP-binding protein YbhF [09:25:02] Modify product: UPF0102 protein RPA0323 => hypothetical protein [09:25:02] Modify product: Uncharacterized AAA domain-containing protein Rv2559c => putative AAA domain-containing protein [09:25:02] Modify product: UPF0297 protein EF_1202 => hypothetical protein [09:25:02] Modify product: UPF0473 protein SP_0194 => hypothetical protein [09:25:02] Modify product: Uncharacterized spore protein YtfJ => putative spore protein YtfJ [09:25:02] Modify product: Probable ribosomal protein YlxQ => putative ribosomal protein YlxQ [09:25:02] Modify product: DegV domain-containing protein SA0704 => DegV domain-containing protein [09:25:02] Modify product: Uncharacterized zinc protease Rv2782c => putative zinc protease [09:25:02] Modify product: Uncharacterized signaling protein PA1727 => putative signaling protein [09:25:02] Modify product: Uncharacterized HTH-type transcriptional regulator Rv0880 => putative HTH-type transcriptional regulator [09:25:02] Modify product: Uncharacterized ABC transporter ATP-binding protein YxlF => putative ABC transporter ATP-binding protein YxlF [09:25:02] Modify product: Probable endopeptidase p60 => putative endopeptidase p60 [09:25:02] Modify product: UPF0271 protein TTHB195 => hypothetical protein [09:25:02] Modify product: S-adenosyl-L-methionine-binding protein RPA0152 => S-adenosyl-L-methionine-binding protein [09:25:02] Modify product: Probable murein peptide carboxypeptidase => putative murein peptide carboxypeptidase [09:25:02] Modify product: Iron-sulfur flavoprotein CD630_04720 => Iron-sulfur flavoprotein [09:25:02] Modify product: Probable metallo-hydrolase YflN => putative metallo-hydrolase YflN [09:25:02] Modify product: Uncharacterized HTH-type transcriptional regulator YfiR => putative HTH-type transcriptional regulator YfiR [09:25:02] Modify product: Probable multidrug ABC transporter ATP-binding protein YbhF => putative multidrug ABC transporter ATP-binding protein YbhF [09:25:02] Modify product: Uncharacterized ABC transporter ATP-binding protein YknY => putative ABC transporter ATP-binding protein YknY [09:25:02] Modify product: Uncharacterized signaling protein PA1727 => putative signaling protein [09:25:02] Modify product: Probable endonuclease 4 => putative endonuclease 4 [09:25:02] Modify product: UPF0754 membrane protein SA1664 => hypothetical protein [09:25:02] Modify product: Uncharacterized signaling protein PA1727 => putative signaling protein [09:25:02] Modify product: Probable diguanylate cyclase DgcQ => putative diguanylate cyclase DgcQ [09:25:02] Modify product: Uncharacterized protein YbdM => putative protein YbdM [09:25:02] Modify product: Probable manganese catalase => putative manganese catalase [09:25:02] Modify product: Uncharacterized HTH-type transcriptional regulator SACOL2360 => putative HTH-type transcriptional regulator [09:25:02] Modify product: Uncharacterized N-acetyltransferase YvbK => putative N-acetyltransferase YvbK [09:25:02] Modify product: Probable multidrug ABC transporter ATP-binding protein YbhF => putative multidrug ABC transporter ATP-binding protein YbhF [09:25:02] Modify product: Uncharacterized ABC transporter ATP-binding protein YxlF => putative ABC transporter ATP-binding protein YxlF [09:25:02] Modify product: Probable metallo-hydrolase YflN => putative metallo-hydrolase YflN [09:25:02] Modify product: Uncharacterized oxidoreductase SA2266 => putative oxidoreductase [09:25:02] Modify product: Uncharacterized protease YdcP => putative protease YdcP [09:25:02] Modify product: Probable diguanylate cyclase DgcC => putative diguanylate cyclase DgcC [09:25:02] Modify product: Bifunctional protein FolD => Bifunctional protein FolD protein [09:25:02] Modify product: Probable tRNA sulfurtransferase => putative tRNA sulfurtransferase [09:25:02] Modify product: Probable licABCH operon regulator => putative licABCH operon regulator [09:25:02] Modify product: N-acetylmuramoyl-L-alanine amidase Rv3717 => N-acetylmuramoyl-L-alanine amidase [09:25:02] Modify product: Uncharacterized ABC transporter ATP-binding protein YbiT => putative ABC transporter ATP-binding protein YbiT [09:25:02] Modify product: Uncharacterized signaling protein PA1727 => putative signaling protein [09:25:02] Modify product: Putative universal stress protein SA1532 => Putative universal stress protein [09:25:02] Modify product: Uncharacterized protein YisK => putative protein YisK [09:25:02] Modify product: Putative DNA-binding protein Rv0500A => Putative DNA-binding proteinA [09:25:03] Modify product: Uncharacterized inner membrane transporter YicL => putative inner membrane transporter YicL [09:25:03] Modify product: Probable diguanylate cyclase DgcE => putative diguanylate cyclase DgcE [09:25:03] Modify product: Probable diguanylate cyclase DgcJ => putative diguanylate cyclase DgcJ [09:25:03] Modify product: Uncharacterized signaling protein PA1727 => putative signaling protein [09:25:03] Modify product: Probable ATP-dependent helicase DinG homolog => putative ATP-dependent helicase DinG [09:25:03] Modify product: GTP cyclohydrolase 1 type 2 homolog => GTP cyclohydrolase 1 type 2 [09:25:03] Modify product: Sulfurtransferase Alvin_2599 => Sulfurtransferase [09:25:03] Modify product: Uncharacterized ABC transporter ATP-binding protein Rv1273c => putative ABC transporter ATP-binding protein [09:25:03] Modify product: Uncharacterized ABC transporter ATP-binding protein TM_0288 => putative ABC transporter ATP-binding protein [09:25:03] Modify product: Uncharacterized signaling protein PA1727 => putative signaling protein [09:25:03] Modify product: Uncharacterized protein YpuA => putative protein YpuA [09:25:03] Modify product: Probable lipid II flippase MurJ => putative lipid II flippase MurJ [09:25:03] Modify product: Uncharacterized signaling protein PA1727 => putative signaling protein [09:25:03] Modify product: Acetyltransferase SACOL1063 => Acetyltransferase [09:25:03] Modify product: Uncharacterized ABC transporter ATP-binding protein YknY => putative ABC transporter ATP-binding protein YknY [09:25:03] Modify product: Dihydroorotate dehydrogenase B (NAD(+)), electron transfer subunit homolog => Dihydroorotate dehydrogenase B (NAD(+)), electron transfer subunit [09:25:03] Modify product: Uncharacterized signaling protein PA1727 => putative signaling protein [09:25:03] Modify product: UPF0073 inner membrane protein YqfA => hypothetical protein [09:25:03] Modify product: Probable xanthine dehydrogenase subunit A => putative xanthine dehydrogenase subunit A [09:25:03] Modify product: Probable manganese catalase => putative manganese catalase [09:25:03] Modify product: UPF0213 protein BH0048 => hypothetical protein [09:25:03] Modify product: Uncharacterized protein Rv2915c => putative protein [09:25:03] Modify product: Uncharacterized signaling protein PA1727 => putative signaling protein [09:25:03] Modify product: Probable L-galactonate transporter => putative L-galactonate transporter [09:25:03] Modify product: Uncharacterized protein YkoJ => putative protein YkoJ [09:25:03] Modify product: TelA-like protein SA1238 => TelA-like protein [09:25:03] Modify product: Probable siderophore transport system ATP-binding protein YusV => putative siderophore transport system ATP-binding protein YusV [09:25:03] Modify product: Uncharacterized ABC transporter solute-binding protein YclQ => putative ABC transporter solute-binding protein YclQ [09:25:03] Modify product: Uncharacterized signaling protein PA1727 => putative signaling protein [09:25:03] Modify product: Probable glycine dehydrogenase (decarboxylating) subunit 1 => putative glycine dehydrogenase (decarboxylating) subunit 1 [09:25:03] Modify product: Probable glycine dehydrogenase (decarboxylating) subunit 2 => putative glycine dehydrogenase (decarboxylating) subunit 2 [09:25:03] Modify product: Probable cation-transporting ATPase E => putative cation-transporting ATPase E [09:25:03] Modify product: Uncharacterized ABC transporter ATP-binding protein YxlF => putative ABC transporter ATP-binding protein YxlF [09:25:03] Modify product: Uncharacterized HTH-type transcriptional regulator YybR => putative HTH-type transcriptional regulator YybR [09:25:03] Modify product: Uncharacterized transporter Rv2685 => putative transporter [09:25:03] Modify product: Probable adenylyltransferase/sulfurtransferase MoeZ => putative adenylyltransferase/sulfurtransferase MoeZ [09:25:03] Modify product: UPF0145 protein BC_1012 => hypothetical protein [09:25:03] Modify product: Fluoroquinolones export ATP-binding protein Rv2688c => Fluoroquinolones export ATP-binding protein [09:25:03] Modify product: Fluoroquinolones export permease protein Rv2686c => Fluoroquinolones export permease protein [09:25:03] Modify product: Uncharacterized protein YjdF => putative protein YjdF [09:25:03] Modify product: UPF0702 transmembrane protein YetF => hypothetical protein [09:25:03] Modify product: Uncharacterized epimerase/dehydratase SA0511 => putative epimerase/dehydratase [09:25:03] Modify product: Uncharacterized protein HI_0933 => putative protein [09:25:03] Modify product: UPF0246 protein YaaA => hypothetical protein [09:25:03] Modify product: Uncharacterized HTH-type transcriptional regulator YusO => putative HTH-type transcriptional regulator YusO [09:25:03] Modify product: Uncharacterized signaling protein PA1727 => putative signaling protein [09:25:03] Modify product: Probable diguanylate cyclase DgcE => putative diguanylate cyclase DgcE [09:25:03] Modify product: Probable transcription repressor NiaR => putative transcription repressor NiaR [09:25:03] Modify product: Nucleoid-associated protein Cthe_2143 => Nucleoid-associated protein [09:25:03] Modify product: Uncharacterized PIN and TRAM-domain containing protein YacL => putative PIN and TRAM-domain containing protein YacL [09:25:03] Modify product: Uncharacterized protein YacP => putative protein YacP [09:25:03] Modify product: Uncharacterized protein BHWA1_00569 => putative protein [09:25:03] Modify product: Probable FMN/FAD exporter YeeO => putative FMN/FAD exporter YeeO [09:25:03] Modify product: Uncharacterized ABC transporter ATP-binding protein YheS => putative ABC transporter ATP-binding protein YheS [09:25:03] Modify product: UPF0324 inner membrane protein YeiH => hypothetical protein [09:25:03] Modify product: Probable licABCH operon regulator => putative licABCH operon regulator [09:25:03] Modify product: Uncharacterized HTH-type transcriptional regulator YybR => putative HTH-type transcriptional regulator YybR [09:25:03] Modify product: Probable phosphatase YcdX => putative phosphatase YcdX [09:25:03] Modify product: Putative dipeptidase SACOL1801 => Putative dipeptidase [09:25:03] Modify product: Uncharacterized ABC transporter ATP-binding protein YxlF => putative ABC transporter ATP-binding protein YxlF [09:25:03] Modify product: Uncharacterized transmembrane protein YxlG => putative transmembrane protein YxlG [09:25:03] Modify product: Transcriptional repressor SmtB homolog => Transcriptional repressor SmtB [09:25:03] Modify product: Probable M18 family aminopeptidase 2 => putative M18 family aminopeptidase 2 [09:25:03] Modify product: Uncharacterized ABC transporter ATP-binding protein YknY => putative ABC transporter ATP-binding protein YknY [09:25:03] Modify product: Probable metallo-hydrolase YflN => putative metallo-hydrolase YflN [09:25:03] Modify product: Nucleotidase CA_C3379 => Nucleotidase [09:25:03] Modify product: Uncharacterized RNA methyltransferase SP_1029 => putative RNA methyltransferase [09:25:03] Modify product: Probable endopeptidase p60 => putative endopeptidase p60 [09:25:03] Modify product: Probable transcriptional regulatory protein pdtaR => putative transcriptional regulatory protein pdtaR [09:25:03] Modify product: Probable sensor histidine kinase pdtaS => putative sensor histidine kinase pdtaS [09:25:03] Modify product: Uncharacterized ABC transporter ATP-binding protein YknY => putative ABC transporter ATP-binding protein YknY [09:25:03] Modify product: Uncharacterized membrane protein YdfK => putative membrane protein YdfK [09:25:03] Modify product: Putative dipeptidase SACOL1801 => Putative dipeptidase [09:25:03] Modify product: Uncharacterized isomerase YddE => putative isomerase YddE [09:25:03] Modify product: Probable tryptophan transport protein => putative tryptophan transport protein [09:25:03] Modify product: Probable membrane transporter protein YfcA => putative membrane transporter protein YfcA [09:25:03] Modify product: Probable membrane transporter protein YfcA => putative membrane transporter protein YfcA [09:25:03] Modify product: Uncharacterized HTH-type transcriptional regulator HI_0186 => putative HTH-type transcriptional regulator [09:25:03] Modify product: Probable endopeptidase p60 => putative endopeptidase p60 [09:25:03] Modify product: Acetyltransferase Atu2258 => Acetyltransferase [09:25:03] Modify product: Probable amino-acid racemase => putative amino-acid racemase [09:25:03] Modify product: Uncharacterized ABC transporter ATP-binding protein YbiT => putative ABC transporter ATP-binding protein YbiT [09:25:03] Modify product: Probable xanthine dehydrogenase subunit C => putative xanthine dehydrogenase subunit C [09:25:03] Modify product: Probable xanthine dehydrogenase subunit C => putative xanthine dehydrogenase subunit C [09:25:03] Modify product: Uncharacterized signaling protein PA1727 => putative signaling protein [09:25:03] Modify product: Uncharacterized signaling protein PA1727 => putative signaling protein [09:25:03] Modify product: Probable amino-acid import ATP-binding protein YxeO => putative amino-acid import ATP-binding protein YxeO [09:25:03] Modify product: Uncharacterized hydrolase YxeP => putative hydrolase YxeP [09:25:03] Modify product: Probable amino-acid-binding protein YxeM => putative amino-acid-binding protein YxeM [09:25:03] Modify product: Probable amino-acid permease protein YxeN => putative amino-acid permease protein YxeN [09:25:03] Modify product: Probable amino-acid-binding protein YxeM => putative amino-acid-binding protein YxeM [09:25:03] Modify product: Uncharacterized symporter YjmB => putative symporter YjmB [09:25:03] Modify product: Uncharacterized ABC transporter ATP-binding protein Rv1272c => putative ABC transporter ATP-binding protein [09:25:03] Modify product: Uncharacterized ABC transporter ATP-binding protein Rv1273c => putative ABC transporter ATP-binding protein [09:25:03] Modify product: Uncharacterized HTH-type transcriptional regulator YbbH => putative HTH-type transcriptional regulator YbbH [09:25:03] Modify product: Aminopeptidase HP_1037 => Aminopeptidase [09:25:03] Modify product: Probable licABCH operon regulator => putative licABCH operon regulator [09:25:03] Modify product: Putative binding protein HI_1525 => Putative binding protein [09:25:03] Modify product: Uncharacterized protein Rv2581c => putative protein [09:25:03] Modify product: Probable protein kinase UbiB => putative protein kinase UbiB [09:25:03] Modify product: Uncharacterized signaling protein PA1727 => putative signaling protein [09:25:03] Modify product: Uncharacterized glycosyltransferase EpsJ => putative glycosyltransferase EpsJ [09:25:03] Modify product: Probable lipid II flippase MurJ => putative lipid II flippase MurJ [09:25:03] Modify product: Probable D-xylose utilization operon transcriptional repressor => putative D-xylose utilization operon transcriptional repressor [09:25:03] Modify product: Uncharacterized ABC transporter ATP-binding protein Rv1272c => putative ABC transporter ATP-binding protein [09:25:03] Modify product: Uncharacterized ABC transporter ATP-binding protein Rv1273c => putative ABC transporter ATP-binding protein [09:25:03] Modify product: Uncharacterized protein YyaP => putative protein YyaP [09:25:03] Modify product: Uncharacterized hydrolase YxeP => putative hydrolase YxeP [09:25:03] Modify product: Uncharacterized response regulatory protein SACOL0201 => putative response regulatory protein [09:25:03] Modify product: Nitrilase blr3397 => Nitrilase [09:25:03] Modify product: Phosphorylated carbohydrates phosphatase TM_1254 => Phosphorylated carbohydrates phosphatase [09:25:03] Modify product: UPF0053 protein Rv1842c => hypothetical protein [09:25:03] Modify product: Uncharacterized signaling protein PA1727 => putative signaling protein [09:25:03] Modify product: Probable siderophore transport system ATP-binding protein YusV => putative siderophore transport system ATP-binding protein YusV [09:25:03] Modify product: Probable siderophore transport system permease protein YfhA => putative siderophore transport system permease protein YfhA [09:25:03] Modify product: Probable siderophore-binding lipoprotein YfiY => putative siderophore-binding lipoprotein YfiY [09:25:03] Modify product: Probable 6-phospho-beta-glucosidase => putative 6-phospho-beta-glucosidase [09:25:03] Modify product: Uncharacterized protein HI_0131 => putative protein [09:25:03] Modify product: Uncharacterized signaling protein PA1727 => putative signaling protein [09:25:03] Modify product: Uncharacterized acyl--CoA ligase YhfT => putative acyl--CoA ligase YhfT [09:25:03] Modify product: Uncharacterized N-acetyltransferase YjaB => putative N-acetyltransferase YjaB [09:25:03] Modify product: Probable 2-dehydro-3-deoxy-D-pentonate aldolase YjhH => putative 2-dehydro-3-deoxy-D-pentonate aldolase YjhH [09:25:03] Modify product: Uncharacterized protein YisK => putative protein YisK [09:25:03] Modify product: Probable pyridine nucleotide-disulfide oxidoreductase RclA => putative pyridine nucleotide-disulfide oxidoreductase RclA [09:25:03] Modify product: Probable licABCH operon regulator => putative licABCH operon regulator [09:25:03] Modify product: Probable glucose uptake protein GlcU => putative glucose uptake protein GlcU [09:25:03] Modify product: Uncharacterized isomerase YddE => putative isomerase YddE [09:25:03] Modify product: Uncharacterized HTH-type transcriptional regulator YbbH => putative HTH-type transcriptional regulator YbbH [09:25:03] Modify product: Uncharacterized transporter Rv1979c => putative transporter [09:25:03] Modify product: Putative glutamine amidotransferase Rv2859c => Putative glutamine amidotransferase [09:25:03] Modify product: Putative dipeptidase SACOL1801 => Putative dipeptidase [09:25:03] Modify product: Putative multidrug export ATP-binding/permease protein SA1683 => Putative multidrug export ATP-binding/permease protein [09:25:03] Modify product: Probable licABCH operon regulator => putative licABCH operon regulator [09:25:03] Modify product: Uncharacterized ABC transporter ATP-binding protein Rv0986 => putative ABC transporter ATP-binding protein [09:25:03] Modify product: Uncharacterized MFS-type transporter YhjX => putative MFS-type transporter YhjX [09:25:03] Modify product: Uncharacterized protein HI_0131 => putative protein [09:25:03] Modify product: Uncharacterized protease YdeA => putative protease YdeA [09:25:03] Modify product: Uncharacterized protein YhaZ => putative protein YhaZ [09:25:03] Modify product: UPF0098 protein CT_736 => hypothetical protein [09:25:03] Modify product: Virulence protein STM3117 => Virulence protein [09:25:03] Modify product: RutC family protein HI_0719 => RutC family protein [09:25:03] Modify product: TelA-like protein SA1238 => TelA-like protein [09:25:03] Modify product: Putative phosphatase M6_Spy0533 => Putative phosphatase [09:25:03] Modify product: Putative permease Rv2963 => Putative permease [09:25:03] Modify product: Probable nicotinate-nucleotide pyrophosphorylase [carboxylating] => putative nicotinate-nucleotide pyrophosphorylase [carboxylating] [09:25:03] Modify product: Probable diguanylate cyclase DgcT => putative diguanylate cyclase DgcT [09:25:04] Modify product: Probable manganese catalase => putative manganese catalase [09:25:04] Modify product: Uncharacterized HTH-type transcriptional regulator YusO => putative HTH-type transcriptional regulator YusO [09:25:04] Modify product: Probable licABCH operon regulator => putative licABCH operon regulator [09:25:04] Modify product: Uncharacterized protein YqeY => putative protein YqeY [09:25:04] Modify product: Oxygen-independent coproporphyrinogen-III oxidase-like protein LL1139 => Oxygen-independent coproporphyrinogen-III oxidase-like protein [09:25:04] Modify product: Uncharacterized protein YqeN => putative protein YqeN [09:25:04] Modify product: Probable licABCH operon regulator => putative licABCH operon regulator [09:25:04] Modify product: Putative dipeptidase SACOL1801 => Putative dipeptidase [09:25:04] Modify product: Calcium-transporting ATPase lmo0841 => Calcium-transporting ATPase [09:25:04] Modify product: Probable nicotinate-nucleotide adenylyltransferase => putative nicotinate-nucleotide adenylyltransferase [09:25:04] Modify product: Uncharacterized ABC transporter ATP-binding protein Rv0986 => putative ABC transporter ATP-binding protein [09:25:04] Modify product: Uncharacterized protein Rv2927c => putative protein [09:25:04] Modify product: Uncharacterized protein SA1069 => putative protein [09:25:04] Modify product: Uncharacterized protein Spy1614 => putative protein [09:25:04] Modify product: Probable licABCH operon regulator => putative licABCH operon regulator [09:25:04] Modify product: Probable dual-specificity RNA methyltransferase RlmN => putative dual-specificity RNA methyltransferase RlmN [09:25:04] Modify product: UPF0701 protein HI_0467 => hypothetical protein [09:25:04] Modify product: Uncharacterized protein YloA => putative protein YloA [09:25:04] Modify product: Uncharacterized peptidase SA1530 => putative peptidase [09:25:04] Modify product: DegV domain-containing protein MW1315 => DegV domain-containing protein [09:25:04] Modify product: UPF0210 protein SP_0239 => hypothetical protein [09:25:04] Modify product: UPF0237 protein SP_0238 => hypothetical protein [09:25:04] Modify product: UPF0749 protein YlxW => hypothetical protein [09:25:04] Modify product: UPF0749 protein YlxW => hypothetical protein [09:25:04] Modify product: Probable peptidoglycan glycosyltransferase FtsW => putative peptidoglycan glycosyltransferase FtsW [09:25:04] Modify product: Uncharacterized signaling protein PA1727 => putative signaling protein [09:25:04] Modify product: Iron-sulfur flavoprotein CD630_04720 => Iron-sulfur flavoprotein [09:25:04] Modify product: Uncharacterized protein HI_0933 => putative protein [09:25:04] Modify product: Fluoroquinolones export ATP-binding protein Rv2688c => Fluoroquinolones export ATP-binding protein [09:25:04] Modify product: UPF0597 protein YhaM => hypothetical protein [09:25:04] Modify product: Phosphate-specific transport system accessory protein PhoU homolog => Phosphate-specific transport system accessory protein PhoU [09:25:04] Modify product: Probable type II secretion system protein HxcR => putative type II secretion system protein HxcR [09:25:04] Modify product: UPF0749 protein YlxW => hypothetical protein [09:25:04] Modify product: Probable GTP-binding protein EngB => putative GTP-binding protein EngB [09:25:04] Modify product: Probable chromate transport protein => putative chromate transport protein [09:25:04] Modify product: Probable chromate transport protein => putative chromate transport protein [09:25:04] Modify product: Putative metallophosphoesterase MG207 homolog => Putative metallophosphoesterase MG207 [09:25:04] Modify product: Uncharacterized ABC transporter ATP-binding protein YbiT => putative ABC transporter ATP-binding protein YbiT [09:25:04] Modify product: Probable formate transporter 1 => putative formate transporter 1 [09:25:04] Modify product: Probable cobalt-factor III C(17)-methyltransferase => putative cobalt-factor III C(17)-methyltransferase [09:25:04] Modify product: Probable licABCH operon regulator => putative licABCH operon regulator [09:25:04] Modify product: Uncharacterized protein YqgN => putative protein YqgN [09:25:04] Modify product: Uncharacterized protein HP_1423 => putative protein [09:25:04] Modify product: Probable type II secretion system protein HxcR => putative type II secretion system protein HxcR [09:25:04] Modify product: Uncharacterized metal-dependent hydrolase YcfH => putative metal-dependent hydrolase YcfH [09:25:04] Modify product: Probable tRNA-dihydrouridine synthase => putative tRNA-dihydrouridine synthase [09:25:04] Modify product: Uncharacterized aminopeptidase Rv1333 => putative aminopeptidase [09:25:04] Modify product: Uncharacterized beta-barrel protein YwiB => putative beta-barrel protein YwiB [09:25:04] Modify product: Probable D-xylose utilization operon transcriptional repressor => putative D-xylose utilization operon transcriptional repressor [09:25:04] Modify product: Deacetylase Oant_2987 => Deacetylase [09:25:04] Modify product: Probable FMN/FAD exporter YeeO => putative FMN/FAD exporter YeeO [09:25:04] Modify product: Uncharacterized N-acetyltransferase YjaB => putative N-acetyltransferase YjaB [09:25:04] Modify product: Probable diguanylate cyclase DgcE => putative diguanylate cyclase DgcE [09:25:04] Modify product: Uncharacterized MFS-type transporter YhjX => putative MFS-type transporter YhjX [09:25:04] Modify product: Deacetylase EF_0837 => Deacetylase [09:25:04] Cleaned 279 /product names [09:25:04] Deleting unwanted file: trash6/tmp/prokka/sample1/sprot.faa [09:25:04] Deleting unwanted file: trash6/tmp/prokka/sample1/sprot.blast [09:25:05] There are still 1232 unannotated CDS left (started with 3594) [09:25:05] Will use hmmer3 to search against /home/andrespara/anaconda3/envs/panphlan/bin/../db/hmm/HAMAP.hmm with 4 CPUs [09:25:05] Running: cat trash6\/tmp\/prokka\/sample1\/HAMAP\.hmm\.faa | parallel --gnu --plain -j 4 --block 36249 --recstart '>' --pipe hmmscan --noali --notextw --acc -E 1e-06 --cpu 1 /home/andrespara/anaconda3/envs/panphlan/bin/../db/hmm/HAMAP.hmm /dev/stdin > trash6\/tmp\/prokka\/sample1\/HAMAP\.hmm\.hmmer3 2> /dev/null [09:25:13] Deleting unwanted file: trash6/tmp/prokka/sample1/HAMAP.hmm.faa [09:25:13] Deleting unwanted file: trash6/tmp/prokka/sample1/HAMAP.hmm.hmmer3 [09:25:13] Labelling remaining 1165 proteins as 'hypothetical protein' [09:25:13] Possible /pseudo 'Proline--tRNA ligase' at gnl|X|NLPIPFPC_1 position 83821 [09:25:13] Possible /pseudo 'Orotate phosphoribosyltransferase' at gnl|X|NLPIPFPC_1 position 236393 [09:25:13] Possible /pseudo 'Pyridinium-3,5-bisthiocarboxylic acid mononucleotide nickel insertion protein' at gnl|X|NLPIPFPC_1 position 246576 [09:25:13] Possible /pseudo 'Chromate transport protein' at gnl|X|NLPIPFPC_1 position 256233 [09:25:13] Possible /pseudo 'Flagellar secretion chaperone FliS' at gnl|X|NLPIPFPC_1 position 292963 [09:25:13] Possible /pseudo 'Signal peptidase IB' at gnl|X|NLPIPFPC_1 position 676247 [09:25:13] Possible /pseudo 'Dipeptidyl-peptidase 5' at gnl|X|NLPIPFPC_1 position 771370 [09:25:13] Possible /pseudo 'Trifunctional nucleotide phosphoesterase protein YfkN' at gnl|X|NLPIPFPC_1 position 826449 [09:25:13] Possible /pseudo 'Biotin synthase' at gnl|X|NLPIPFPC_1 position 887633 [09:25:13] Possible /pseudo 'PTS system glucitol/sorbitol-specific EIIB component' at gnl|X|NLPIPFPC_1 position 927172 [09:25:13] Possible /pseudo 'Iron hydrogenase 1' at gnl|X|NLPIPFPC_1 position 1064876 [09:25:13] Possible /pseudo 'putative ABC transporter ATP-binding protein' at gnl|X|NLPIPFPC_1 position 1126995 [09:25:13] Possible /pseudo 'Signal recognition particle protein' at gnl|X|NLPIPFPC_1 position 1361691 [09:25:13] Possible /pseudo 'Branched-chain amino acid transport system 2 carrier protein' at gnl|X|NLPIPFPC_1 position 1368379 [09:25:13] Possible /pseudo 'putative ABC transporter ATP-binding protein' at gnl|X|NLPIPFPC_1 position 1608362 [09:25:13] Possible /pseudo 'Anti-sigma-V factor RsiV' at gnl|X|NLPIPFPC_1 position 1712823 [09:25:13] Possible /pseudo 'General stress protein 16U' at gnl|X|NLPIPFPC_1 position 1787752 [09:25:13] Possible /pseudo 'Glycine reductase complex component B subunit gamma' at gnl|X|NLPIPFPC_1 position 1917015 [09:25:13] Possible /pseudo 'Multidrug resistance protein MdtG' at gnl|X|NLPIPFPC_1 position 1990957 [09:25:13] Possible /pseudo 'Multidrug resistance protein MdtG' at gnl|X|NLPIPFPC_1 position 1991244 [09:25:13] Possible /pseudo 'Calcium-transporting ATPase 1' at gnl|X|NLPIPFPC_1 position 2005639 [09:25:13] Possible /pseudo 'putative membrane transporter protein YfcA' at gnl|X|NLPIPFPC_1 position 2162626 [09:25:13] Possible /pseudo 'Uric acid permease PucK' at gnl|X|NLPIPFPC_1 position 2275137 [09:25:13] Possible /pseudo 'putative signaling protein' at gnl|X|NLPIPFPC_1 position 2345141 [09:25:13] Possible /pseudo 'putative ABC transporter ATP-binding protein' at gnl|X|NLPIPFPC_1 position 2437640 [09:25:13] Possible /pseudo 'Glycine reductase complex component B subunit gamma' at gnl|X|NLPIPFPC_1 position 2582314 [09:25:13] Possible /pseudo 'Regulatory protein RecX' at gnl|X|NLPIPFPC_1 position 2782618 [09:25:13] Possible /pseudo 'putative protein' at gnl|X|NLPIPFPC_1 position 2824994 [09:25:13] Possible /pseudo 'Polyisoprenyl-teichoic acid--peptidoglycan teichoic acid transferase TagT' at gnl|X|NLPIPFPC_1 position 3080090 [09:25:13] Possible /pseudo 'N-acetylmuramoyl-L-alanine amidase LytC' at gnl|X|NLPIPFPC_1 position 3107717 [09:25:13] Possible /pseudo 'N-acetylmuramoyl-L-alanine amidase LytC' at gnl|X|NLPIPFPC_1 position 3120706 [09:25:13] Possible /pseudo 'N-acetylmuramoyl-L-alanine amidase LytC' at gnl|X|NLPIPFPC_1 position 3122513 [09:25:13] Possible /pseudo 'N-acetylmuramoyl-L-alanine amidase LytC' at gnl|X|NLPIPFPC_1 position 3124627 [09:25:13] Possible /pseudo 'N-acetylmuramoyl-L-alanine amidase LytC' at gnl|X|NLPIPFPC_1 position 3126493 [09:25:13] Possible /pseudo 'putative ABC transporter ATP-binding protein' at gnl|X|NLPIPFPC_1 position 3148159 [09:25:13] Possible /pseudo 'PTS system mannose-specific EIIAB component' at gnl|X|NLPIPFPC_1 position 3378043 [09:25:13] Possible /pseudo 'D-proline reductase proprotein PrdA' at gnl|X|NLPIPFPC_1 position 3602949 [09:25:13] Possible /pseudo 'D-proline reductase proprotein PrdA' at gnl|X|NLPIPFPC_1 position 3603431 [09:25:13] Possible /pseudo 'D-proline reductase subunit gamma' at gnl|X|NLPIPFPC_1 position 3604542 [09:25:13] Possible /pseudo 'putative chromate transport protein' at gnl|X|NLPIPFPC_1 position 3678439 [09:25:13] Possible /pseudo 'Formate dehydrogenase H' at gnl|X|NLPIPFPC_1 position 3701073 [09:25:13] Possible /pseudo 'Type 4 prepilin-like proteins leader peptide-processing enzyme' at gnl|X|NLPIPFPC_1 position 3859393 [09:25:13] Found 1529 unique /gene codes. [09:25:13] Fixed 2 duplicate /gene - porC_1 porC_2 [09:25:13] Fixed 2 duplicate /gene - dtpA_1 dtpA_2 [09:25:13] Fixed 2 duplicate /gene - cysK_1 cysK_2 [09:25:13] Fixed 2 duplicate /gene - oppF_1 oppF_2 [09:25:13] Fixed 2 duplicate /gene - uppS_1 uppS_2 [09:25:13] Fixed 3 duplicate /gene - korA_1 korA_2 korA_3 [09:25:13] Fixed 2 duplicate /gene - rbr3A_1 rbr3A_2 [09:25:13] Fixed 3 duplicate /gene - srrB_1 srrB_2 srrB_3 [09:25:13] Fixed 2 duplicate /gene - mngB_1 mngB_2 [09:25:13] Fixed 3 duplicate /gene - trxA_1 trxA_2 trxA_3 [09:25:13] Fixed 2 duplicate /gene - artQ_1 artQ_2 [09:25:13] Fixed 2 duplicate /gene - recX_1 recX_2 [09:25:13] Fixed 2 duplicate /gene - steT_1 steT_2 [09:25:13] Fixed 2 duplicate /gene - macB_1 macB_2 [09:25:13] Fixed 3 duplicate /gene - xerC_1 xerC_2 xerC_3 [09:25:13] Fixed 3 duplicate /gene - pta_1 pta_2 pta_3 [09:25:13] Fixed 2 duplicate /gene - hadI_1 hadI_2 [09:25:13] Fixed 2 duplicate /gene - cspD_1 cspD_2 [09:25:13] Fixed 2 duplicate /gene - dnaX_1 dnaX_2 [09:25:13] Fixed 2 duplicate /gene - scpA_1 scpA_2 [09:25:13] Fixed 2 duplicate /gene - araQ_1 araQ_2 [09:25:13] Fixed 2 duplicate /gene - kdgT_1 kdgT_2 [09:25:13] Fixed 2 duplicate /gene - mutS2_1 mutS2_2 [09:25:13] Fixed 3 duplicate /gene - ugtP_1 ugtP_2 ugtP_3 [09:25:13] Fixed 4 duplicate /gene - comEC_1 comEC_2 comEC_3 comEC_4 [09:25:13] Fixed 3 duplicate /gene - fldA_1 fldA_2 fldA_3 [09:25:13] Fixed 2 duplicate /gene - rnfC_1 rnfC_2 [09:25:13] Fixed 2 duplicate /gene - yceC_1 yceC_2 [09:25:13] Fixed 2 duplicate /gene - aroF_1 aroF_2 [09:25:13] Fixed 2 duplicate /gene - hndD_1 hndD_2 [09:25:13] Fixed 3 duplicate /gene - brnQ_1 brnQ_2 brnQ_3 [09:25:13] Fixed 2 duplicate /gene - marA_1 marA_2 [09:25:13] Fixed 2 duplicate /gene - yabJ_1 yabJ_2 [09:25:13] Fixed 2 duplicate /gene - glnQ_1 glnQ_2 [09:25:13] Fixed 2 duplicate /gene - glpK_1 glpK_2 [09:25:13] Fixed 2 duplicate /gene - aaaT_1 aaaT_2 [09:25:13] Fixed 2 duplicate /gene - sinR_1 sinR_2 [09:25:13] Fixed 4 duplicate /gene - tetD_1 tetD_2 tetD_3 tetD_4 [09:25:13] Fixed 2 duplicate /gene - flr_1 flr_2 [09:25:13] Fixed 2 duplicate /gene - prsA_1 prsA_2 [09:25:13] Fixed 2 duplicate /gene - larC_1 larC_2 [09:25:13] Fixed 2 duplicate /gene - guaD_1 guaD_2 [09:25:13] Fixed 2 duplicate /gene - fur_1 fur_2 [09:25:13] Fixed 2 duplicate /gene - proC_1 proC_2 [09:25:13] Fixed 2 duplicate /gene - purF_1 purF_2 [09:25:13] Fixed 3 duplicate /gene - secA_1 secA_2 secA_3 [09:25:13] Fixed 2 duplicate /gene - lytG_1 lytG_2 [09:25:13] Fixed 3 duplicate /gene - yxdM_1 yxdM_2 yxdM_3 [09:25:13] Fixed 2 duplicate /gene - ogt_1 ogt_2 [09:25:13] Fixed 3 duplicate /gene - sorC_1 sorC_2 sorC_3 [09:25:13] Fixed 2 duplicate /gene - ycdX_1 ycdX_2 [09:25:13] Fixed 4 duplicate /gene - hxlR_1 hxlR_2 hxlR_3 hxlR_4 [09:25:13] Fixed 2 duplicate /gene - apt_1 apt_2 [09:25:13] Fixed 3 duplicate /gene - iap_1 iap_2 iap_3 [09:25:13] Fixed 3 duplicate /gene - cysL_1 cysL_2 cysL_3 [09:25:13] Fixed 6 duplicate /gene - lolD_1 lolD_2 lolD_3 lolD_4 lolD_5 lolD_6 [09:25:13] Fixed 5 duplicate /gene - regX3_1 regX3_2 regX3_3 regX3_4 regX3_5 [09:25:13] Fixed 2 duplicate /gene - rbr_1 rbr_2 [09:25:13] Fixed 4 duplicate /gene - patB_1 patB_2 patB_3 patB_4 [09:25:13] Fixed 2 duplicate /gene - mobA_1 mobA_2 [09:25:13] Fixed 3 duplicate /gene - bglH_1 bglH_2 bglH_3 [09:25:13] Fixed 2 duplicate /gene - phnW_1 phnW_2 [09:25:13] Fixed 2 duplicate /gene - nhaP_1 nhaP_2 [09:25:13] Fixed 2 duplicate /gene - mutS_1 mutS_2 [09:25:13] Fixed 3 duplicate /gene - clpP_1 clpP_2 clpP_3 [09:25:13] Fixed 3 duplicate /gene - queG_1 queG_2 queG_3 [09:25:13] Fixed 2 duplicate /gene - metQ_1 metQ_2 [09:25:13] Fixed 3 duplicate /gene - cysW_1 cysW_2 cysW_3 [09:25:13] Fixed 2 duplicate /gene - atpE_1 atpE_2 [09:25:13] Fixed 3 duplicate /gene - ylmB_1 ylmB_2 ylmB_3 [09:25:13] Fixed 2 duplicate /gene - dppC_1 dppC_2 [09:25:13] Fixed 3 duplicate /gene - ycsE_1 ycsE_2 ycsE_3 [09:25:13] Fixed 2 duplicate /gene - uppP_1 uppP_2 [09:25:13] Fixed 2 duplicate /gene - dapB_1 dapB_2 [09:25:13] Fixed 2 duplicate /gene - ftsW_1 ftsW_2 [09:25:13] Fixed 2 duplicate /gene - pgcA_1 pgcA_2 [09:25:13] Fixed 2 duplicate /gene - ndhS_1 ndhS_2 [09:25:13] Fixed 2 duplicate /gene - cinA_1 cinA_2 [09:25:13] Fixed 2 duplicate /gene - miaB_1 miaB_2 [09:25:13] Fixed 3 duplicate /gene - polC_1 polC_2 polC_3 [09:25:13] Fixed 4 duplicate /gene - pdaA_1 pdaA_2 pdaA_3 pdaA_4 [09:25:13] Fixed 2 duplicate /gene - alaS_1 alaS_2 [09:25:13] Fixed 2 duplicate /gene - kdpE_1 kdpE_2 [09:25:13] Fixed 2 duplicate /gene - def1_1 def1_2 [09:25:13] Fixed 2 duplicate /gene - tuf_1 tuf_2 [09:25:13] Fixed 2 duplicate /gene - rsxB_1 rsxB_2 [09:25:13] Fixed 2 duplicate /gene - ulaF_1 ulaF_2 [09:25:13] Fixed 3 duplicate /gene - ydbD_1 ydbD_2 ydbD_3 [09:25:13] Fixed 4 duplicate /gene - yknY_1 yknY_2 yknY_3 yknY_4 [09:25:13] Fixed 3 duplicate /gene - crr_1 crr_2 crr_3 [09:25:13] Fixed 4 duplicate /gene - yfkN_1 yfkN_2 yfkN_3 yfkN_4 [09:25:13] Fixed 2 duplicate /gene - pepF1_1 pepF1_2 [09:25:13] Fixed 2 duplicate /gene - hyfA_1 hyfA_2 [09:25:13] Fixed 2 duplicate /gene - hflX_1 hflX_2 [09:25:13] Fixed 2 duplicate /gene - srpC_1 srpC_2 [09:25:13] Fixed 2 duplicate /gene - suyB_1 suyB_2 [09:25:13] Fixed 2 duplicate /gene - der_1 der_2 [09:25:13] Fixed 2 duplicate /gene - adaA_1 adaA_2 [09:25:13] Fixed 3 duplicate /gene - gatA_1 gatA_2 gatA_3 [09:25:13] Fixed 5 duplicate /gene - grdB_1 grdB_2 grdB_3 grdB_4 grdB_5 [09:25:13] Fixed 3 duplicate /gene - pucK_1 pucK_2 pucK_3 [09:25:13] Fixed 2 duplicate /gene - mgtB_1 mgtB_2 [09:25:13] Fixed 2 duplicate /gene - osmV_1 osmV_2 [09:25:13] Fixed 2 duplicate /gene - rplL_1 rplL_2 [09:25:13] Fixed 2 duplicate /gene - rapA_1 rapA_2 [09:25:13] Fixed 2 duplicate /gene - acpP_1 acpP_2 [09:25:13] Fixed 2 duplicate /gene - carB_1 carB_2 [09:25:13] Fixed 2 duplicate /gene - malH_1 malH_2 [09:25:13] Fixed 2 duplicate /gene - ndx1_1 ndx1_2 [09:25:13] Fixed 2 duplicate /gene - treP_1 treP_2 [09:25:13] Fixed 4 duplicate /gene - Int-Tn_1 Int-Tn_2 Int-Tn_3 Int-Tn_4 [09:25:13] Fixed 5 duplicate /gene - ytrA_1 ytrA_2 ytrA_3 ytrA_4 ytrA_5 [09:25:13] Fixed 3 duplicate /gene - pepT_1 pepT_2 pepT_3 [09:25:13] Fixed 4 duplicate /gene - lysN_1 lysN_2 lysN_3 lysN_4 [09:25:13] Fixed 3 duplicate /gene - ccpA_1 ccpA_2 ccpA_3 [09:25:13] Fixed 2 duplicate /gene - ykfC_1 ykfC_2 [09:25:13] Fixed 2 duplicate /gene - pucC_1 pucC_2 [09:25:13] Fixed 2 duplicate /gene - ywlF_1 ywlF_2 [09:25:13] Fixed 4 duplicate /gene - prdA_1 prdA_2 prdA_3 prdA_4 [09:25:13] Fixed 2 duplicate /gene - sigV_1 sigV_2 [09:25:13] Fixed 2 duplicate /gene - hemN_1 hemN_2 [09:25:13] Fixed 3 duplicate /gene - hisK_1 hisK_2 hisK_3 [09:25:13] Fixed 6 duplicate /gene - bglF_1 bglF_2 bglF_3 bglF_4 bglF_5 bglF_6 [09:25:13] Fixed 4 duplicate /gene - mdtG_1 mdtG_2 mdtG_3 mdtG_4 [09:25:13] Fixed 2 duplicate /gene - rho_1 rho_2 [09:25:13] Fixed 2 duplicate /gene - pduL_1 pduL_2 [09:25:13] Fixed 2 duplicate /gene - yybR_1 yybR_2 [09:25:13] Fixed 3 duplicate /gene - yxeP_1 yxeP_2 yxeP_3 [09:25:13] Fixed 2 duplicate /gene - dnaI_1 dnaI_2 [09:25:13] Fixed 2 duplicate /gene - pdaC_1 pdaC_2 [09:25:13] Fixed 4 duplicate /gene - gltC_1 gltC_2 gltC_3 gltC_4 [09:25:13] Fixed 2 duplicate /gene - thiH_1 thiH_2 [09:25:13] Fixed 3 duplicate /gene - rhaS_1 rhaS_2 rhaS_3 [09:25:13] Fixed 3 duplicate /gene - cutC_1 cutC_2 cutC_3 [09:25:13] Fixed 4 duplicate /gene - isp_1 isp_2 isp_3 isp_4 [09:25:13] Fixed 4 duplicate /gene - cysA_1 cysA_2 cysA_3 cysA_4 [09:25:13] Fixed 2 duplicate /gene - yxeM_1 yxeM_2 [09:25:13] Fixed 5 duplicate /gene - carE_1 carE_2 carE_3 carE_4 carE_5 [09:25:13] Fixed 4 duplicate /gene - smc_1 smc_2 smc_3 smc_4 [09:25:13] Fixed 2 duplicate /gene - yocH_1 yocH_2 [09:25:13] Fixed 3 duplicate /gene - walK_1 walK_2 walK_3 [09:25:13] Fixed 3 duplicate /gene - mleN_1 mleN_2 mleN_3 [09:25:13] Fixed 2 duplicate /gene - rsgA_1 rsgA_2 [09:25:13] Fixed 2 duplicate /gene - speA_1 speA_2 [09:25:13] Fixed 2 duplicate /gene - carA_1 carA_2 [09:25:13] Fixed 9 duplicate /gene - licR_1 licR_2 licR_3 licR_4 licR_5 licR_6 licR_7 licR_8 licR_9 [09:25:13] Fixed 2 duplicate /gene - yusV_1 yusV_2 [09:25:13] Fixed 4 duplicate /gene - trxB_1 trxB_2 trxB_3 trxB_4 [09:25:13] Fixed 2 duplicate /gene - sigK_1 sigK_2 [09:25:13] Fixed 3 duplicate /gene - spsB_1 spsB_2 spsB_3 [09:25:13] Fixed 2 duplicate /gene - pspA_1 pspA_2 [09:25:13] Fixed 2 duplicate /gene - kstR2_1 kstR2_2 [09:25:13] Fixed 2 duplicate /gene - fliS_1 fliS_2 [09:25:13] Fixed 2 duplicate /gene - yisK_1 yisK_2 [09:25:13] Fixed 2 duplicate /gene - abgT_1 abgT_2 [09:25:13] Fixed 2 duplicate /gene - tmpC_1 tmpC_2 [09:25:13] Fixed 4 duplicate /gene - ribZ_1 ribZ_2 ribZ_3 ribZ_4 [09:25:13] Fixed 3 duplicate /gene - appA_1 appA_2 appA_3 [09:25:13] Fixed 2 duplicate /gene - dpaL_1 dpaL_2 [09:25:13] Fixed 2 duplicate /gene - mta_1 mta_2 [09:25:13] Fixed 6 duplicate /gene - atoC_1 atoC_2 atoC_3 atoC_4 atoC_5 atoC_6 [09:25:13] Fixed 2 duplicate /gene - asnB_1 asnB_2 [09:25:13] Fixed 3 duplicate /gene - graS_1 graS_2 graS_3 [09:25:13] Fixed 2 duplicate /gene - clsA_1 clsA_2 [09:25:13] Fixed 3 duplicate /gene - xre_1 xre_2 xre_3 [09:25:13] Fixed 3 duplicate /gene - malP_1 malP_2 malP_3 [09:25:13] Fixed 27 duplicate /gene - lytC_1 lytC_2 lytC_3 lytC_4 lytC_5 lytC_6 lytC_7 lytC_8 lytC_9 lytC_10 lytC_11 lytC_12 lytC_13 lytC_14 lytC_15 lytC_16 lytC_17 lytC_18 lytC_19 lytC_20 lytC_21 lytC_22 lytC_23 lytC_24 lytC_25 lytC_26 lytC_27 [09:25:13] Fixed 4 duplicate /gene - rocR_1 rocR_2 rocR_3 rocR_4 [09:25:13] Fixed 2 duplicate /gene - sapB_1 sapB_2 [09:25:13] Fixed 2 duplicate /gene - glpR_1 glpR_2 [09:25:13] Fixed 2 duplicate /gene - tktA_1 tktA_2 [09:25:13] Fixed 2 duplicate /gene - map_1 map_2 [09:25:13] Fixed 2 duplicate /gene - hpt_1 hpt_2 [09:25:13] Fixed 2 duplicate /gene - grdE_1 grdE_2 [09:25:13] Fixed 2 duplicate /gene - tilS_1 tilS_2 [09:25:13] Fixed 2 duplicate /gene - lysC_1 lysC_2 [09:25:13] Fixed 2 duplicate /gene - nudF_1 nudF_2 [09:25:13] Fixed 2 duplicate /gene - nfrA2_1 nfrA2_2 [09:25:13] Fixed 2 duplicate /gene - xerD_1 xerD_2 [09:25:13] Fixed 4 duplicate /gene - dacF_1 dacF_2 dacF_3 dacF_4 [09:25:13] Fixed 2 duplicate /gene - aadK_1 aadK_2 [09:25:13] Fixed 2 duplicate /gene - corA_1 corA_2 [09:25:13] Fixed 2 duplicate /gene - treA_1 treA_2 [09:25:13] Fixed 3 duplicate /gene - rsiV_1 rsiV_2 rsiV_3 [09:25:13] Fixed 3 duplicate /gene - dapA_1 dapA_2 dapA_3 [09:25:13] Fixed 3 duplicate /gene - ypdF_1 ypdF_2 ypdF_3 [09:25:13] Fixed 3 duplicate /gene - srlE_1 srlE_2 srlE_3 [09:25:13] Fixed 3 duplicate /gene - asrC_1 asrC_2 asrC_3 [09:25:13] Fixed 2 duplicate /gene - resA_1 resA_2 [09:25:13] Fixed 2 duplicate /gene - maa_1 maa_2 [09:25:13] Fixed 2 duplicate /gene - yusO_1 yusO_2 [09:25:13] Fixed 3 duplicate /gene - cobD_1 cobD_2 cobD_3 [09:25:13] Fixed 2 duplicate /gene - pyrE_1 pyrE_2 [09:25:13] Fixed 7 duplicate /gene - blaI_1 blaI_2 blaI_3 blaI_4 blaI_5 blaI_6 blaI_7 [09:25:13] Fixed 2 duplicate /gene - srlA_1 srlA_2 [09:25:13] Fixed 2 duplicate /gene - chrA_1 chrA_2 [09:25:13] Fixed 2 duplicate /gene - celA_1 celA_2 [09:25:13] Fixed 12 duplicate /gene - walR_1 walR_2 walR_3 walR_4 walR_5 walR_6 walR_7 walR_8 walR_9 walR_10 walR_11 walR_12 [09:25:13] Fixed 3 duplicate /gene - korB_1 korB_2 korB_3 [09:25:13] Fixed 4 duplicate /gene - licA_1 licA_2 licA_3 licA_4 [09:25:13] Fixed 2 duplicate /gene - zmp1_1 zmp1_2 [09:25:13] Fixed 4 duplicate /gene - drrA_1 drrA_2 drrA_3 drrA_4 [09:25:13] Fixed 6 duplicate /gene - licC_1 licC_2 licC_3 licC_4 licC_5 licC_6 [09:25:13] Fixed 6 duplicate /gene - immR_1 immR_2 immR_3 immR_4 immR_5 immR_6 [09:25:13] Fixed 3 duplicate /gene - thlA_1 thlA_2 thlA_3 [09:25:13] Fixed 3 duplicate /gene - natA_1 natA_2 natA_3 [09:25:13] Fixed 3 duplicate /gene - ytrB_1 ytrB_2 ytrB_3 [09:25:13] Fixed 2 duplicate /gene - fprA1_1 fprA1_2 [09:25:13] Fixed 2 duplicate /gene - cooS1_1 cooS1_2 [09:25:13] Fixed 7 duplicate /gene - licT_1 licT_2 licT_3 licT_4 licT_5 licT_6 licT_7 [09:25:13] Fixed 2 duplicate /gene - dmdA_1 dmdA_2 [09:25:13] Fixed 3 duplicate /gene - cph2_1 cph2_2 cph2_3 [09:25:13] Fixed 3 duplicate /gene - hisC_1 hisC_2 hisC_3 [09:25:13] Fixed 2 duplicate /gene - oppD_1 oppD_2 [09:25:13] Fixed 2 duplicate /gene - ybaK_1 ybaK_2 [09:25:13] Fixed 2 duplicate /gene - tipA_1 tipA_2 [09:25:13] Fixed 3 duplicate /gene - bceB_1 bceB_2 bceB_3 [09:25:13] Fixed 4 duplicate /gene - dgcE_1 dgcE_2 dgcE_3 dgcE_4 [09:25:13] Fixed 2 duplicate /gene - ybbH_1 ybbH_2 [09:25:13] Fixed 3 duplicate /gene - yflN_1 yflN_2 yflN_3 [09:25:13] Fixed 7 duplicate /gene - blaR1_1 blaR1_2 blaR1_3 blaR1_4 blaR1_5 blaR1_6 blaR1_7 [09:25:13] Fixed 4 duplicate /gene - adhE_1 adhE_2 adhE_3 adhE_4 [09:25:13] Fixed 2 duplicate /gene - metK_1 metK_2 [09:25:13] Fixed 3 duplicate /gene - fryB_1 fryB_2 fryB_3 [09:25:13] Fixed 2 duplicate /gene - proX_1 proX_2 [09:25:13] Fixed 2 duplicate /gene - rny_1 rny_2 [09:25:13] Fixed 2 duplicate /gene - cmpR_1 cmpR_2 [09:25:13] Fixed 2 duplicate /gene - purH_1 purH_2 [09:25:13] Fixed 5 duplicate /gene - ssuC_1 ssuC_2 ssuC_3 ssuC_4 ssuC_5 [09:25:13] Fixed 2 duplicate /gene - vanW_1 vanW_2 [09:25:13] Fixed 5 duplicate /gene - licB_1 licB_2 licB_3 licB_4 licB_5 [09:25:13] Fixed 2 duplicate /gene - zupT_1 zupT_2 [09:25:13] Fixed 2 duplicate /gene - lspA_1 lspA_2 [09:25:13] Fixed 2 duplicate /gene - dmsB_1 dmsB_2 [09:25:13] Fixed 2 duplicate /gene - ftsH4_1 ftsH4_2 [09:25:13] Fixed 2 duplicate /gene - yjaB_1 yjaB_2 [09:25:13] Fixed 2 duplicate /gene - yeeO_1 yeeO_2 [09:25:13] Fixed 2 duplicate /gene - gap_1 gap_2 [09:25:13] Fixed 2 duplicate /gene - kdgR_1 kdgR_2 [09:25:13] Fixed 2 duplicate /gene - ssbA_1 ssbA_2 [09:25:13] Fixed 2 duplicate /gene - npr_1 npr_2 [09:25:13] Fixed 2 duplicate /gene - hom_1 hom_2 [09:25:13] Fixed 2 duplicate /gene - ssuA_1 ssuA_2 [09:25:13] Fixed 5 duplicate /gene - ypdB_1 ypdB_2 ypdB_3 ypdB_4 ypdB_5 [09:25:13] Fixed 2 duplicate /gene - rimO_1 rimO_2 [09:25:13] Fixed 4 duplicate /gene - xdhA_1 xdhA_2 xdhA_3 xdhA_4 [09:25:13] Fixed 2 duplicate /gene - prkC_1 prkC_2 [09:25:13] Fixed 2 duplicate /gene - pyrC_1 pyrC_2 [09:25:13] Fixed 2 duplicate /gene - rpe_1 rpe_2 [09:25:13] Fixed 2 duplicate /gene - codB_1 codB_2 [09:25:13] Fixed 2 duplicate /gene - betI_1 betI_2 [09:25:13] Fixed 5 duplicate /gene - manZ_1 manZ_2 manZ_3 manZ_4 manZ_5 [09:25:13] Fixed 2 duplicate /gene - aroE_1 aroE_2 [09:25:13] Fixed 5 duplicate /gene - carD_1 carD_2 carD_3 carD_4 carD_5 [09:25:13] Fixed 8 duplicate /gene - abgB_1 abgB_2 abgB_3 abgB_4 abgB_5 abgB_6 abgB_7 abgB_8 [09:25:13] Fixed 2 duplicate /gene - ettA_1 ettA_2 [09:25:13] Fixed 7 duplicate /gene - fruA_1 fruA_2 fruA_3 fruA_4 fruA_5 fruA_6 fruA_7 [09:25:13] Fixed 4 duplicate /gene - sorB_1 sorB_2 sorB_3 sorB_4 [09:25:13] Fixed 2 duplicate /gene - cheW_1 cheW_2 [09:25:13] Fixed 2 duplicate /gene - metH_1 metH_2 [09:25:13] Fixed 2 duplicate /gene - hmo_1 hmo_2 [09:25:13] Fixed 2 duplicate /gene - manR_1 manR_2 [09:25:13] Fixed 2 duplicate /gene - cas1_1 cas1_2 [09:25:13] Fixed 3 duplicate /gene - buk2_1 buk2_2 buk2_3 [09:25:13] Fixed 2 duplicate /gene - yknX_1 yknX_2 [09:25:13] Fixed 2 duplicate /gene - pduA_1 pduA_2 [09:25:13] Fixed 7 duplicate /gene - srrA_1 srrA_2 srrA_3 srrA_4 srrA_5 srrA_6 srrA_7 [09:25:13] Fixed 2 duplicate /gene - mscS_1 mscS_2 [09:25:13] Fixed 2 duplicate /gene - hin_1 hin_2 [09:25:13] Fixed 3 duplicate /gene - pdeR_1 pdeR_2 pdeR_3 [09:25:13] Fixed 2 duplicate /gene - mreB_1 mreB_2 [09:25:13] Fixed 2 duplicate /gene - ffh_1 ffh_2 [09:25:13] Fixed 5 duplicate /gene - yxdL_1 yxdL_2 yxdL_3 yxdL_4 yxdL_5 [09:25:13] Fixed 2 duplicate /gene - mtrB_1 mtrB_2 [09:25:13] Fixed 2 duplicate /gene - pcrA_1 pcrA_2 [09:25:13] Fixed 3 duplicate /gene - dxs_1 dxs_2 dxs_3 [09:25:13] Fixed 2 duplicate /gene - agrB_1 agrB_2 [09:25:13] Fixed 2 duplicate /gene - glyA_1 glyA_2 [09:25:13] Fixed 3 duplicate /gene - potA_1 potA_2 potA_3 [09:25:13] Fixed 2 duplicate /gene - yjjP_1 yjjP_2 [09:25:13] Fixed 2 duplicate /gene - puuB_1 puuB_2 [09:25:13] Fixed 2 duplicate /gene - rsmH_1 rsmH_2 [09:25:13] Fixed 3 duplicate /gene - gatB_1 gatB_2 gatB_3 [09:25:13] Fixed 3 duplicate /gene - bmrR_1 bmrR_2 bmrR_3 [09:25:13] Fixed 2 duplicate /gene - fusA_1 fusA_2 [09:25:13] Fixed 2 duplicate /gene - yddE_1 yddE_2 [09:25:13] Fixed 2 duplicate /gene - fieF_1 fieF_2 [09:25:13] Fixed 5 duplicate /gene - ssuB_1 ssuB_2 ssuB_3 ssuB_4 ssuB_5 [09:25:13] Fixed 2 duplicate /gene - prdB_1 prdB_2 [09:25:13] Fixed 2 duplicate /gene - gntR_1 gntR_2 [09:25:13] Fixed 5 duplicate /gene - manX_1 manX_2 manX_3 manX_4 manX_5 [09:25:13] Fixed 2 duplicate /gene - dpp5_1 dpp5_2 [09:25:13] Fixed 4 duplicate /gene - sgcG_1 sgcG_2 sgcG_3 sgcG_4 [09:25:13] Fixed 2 duplicate /gene - yvoA_1 yvoA_2 [09:25:13] Fixed 2 duplicate /gene - ttcA_1 ttcA_2 [09:25:13] Fixed 4 duplicate /gene - yxlF_1 yxlF_2 yxlF_3 yxlF_4 [09:25:13] Fixed 2 duplicate /gene - glmS_1 glmS_2 [09:25:13] Fixed 2 duplicate /gene - pyrD_1 pyrD_2 [09:25:13] Fixed 2 duplicate /gene - yodJ_1 yodJ_2 [09:25:13] Fixed 2 duplicate /gene - glpQ_1 glpQ_2 [09:25:13] Fixed 2 duplicate /gene - treR_1 treR_2 [09:25:13] Fixed 2 duplicate /gene - megL_1 megL_2 [09:25:13] Fixed 2 duplicate /gene - spoVD_1 spoVD_2 [09:25:13] Fixed 3 duplicate /gene - tnpR_1 tnpR_2 tnpR_3 [09:25:13] Fixed 2 duplicate /gene - polA_1 polA_2 [09:25:13] Fixed 2 duplicate /gene - yfcA_1 yfcA_2 [09:25:13] Fixed 2 duplicate /gene - mepH_1 mepH_2 [09:25:13] Fixed 2 duplicate /gene - ftsL_1 ftsL_2 [09:25:13] Fixed 3 duplicate /gene - rluD_1 rluD_2 rluD_3 [09:25:13] Fixed 7 duplicate /gene - resE_1 resE_2 resE_3 resE_4 resE_5 resE_6 resE_7 [09:25:13] Fixed 10 duplicate /gene - phoR_1 phoR_2 phoR_3 phoR_4 phoR_5 phoR_6 phoR_7 phoR_8 phoR_9 phoR_10 [09:25:13] Fixed 2 duplicate /gene - dgcC_1 dgcC_2 [09:25:13] Fixed 3 duplicate /gene - ybiT_1 ybiT_2 ybiT_3 [09:25:13] Fixed 2 duplicate /gene - hxcR_1 hxcR_2 [09:25:13] Fixed 2 duplicate /gene - gtaB_1 gtaB_2 [09:25:13] Fixed 3 duplicate /gene - gatC_1 gatC_2 gatC_3 [09:25:13] Fixed 2 duplicate /gene - leuA_1 leuA_2 [09:25:13] Fixed 2 duplicate /gene - cas2_1 cas2_2 [09:25:13] Fixed 4 duplicate /gene - bglA_1 bglA_2 bglA_3 bglA_4 [09:25:13] Fixed 2 duplicate /gene - yhjX_1 yhjX_2 [09:25:13] Fixed 3 duplicate /gene - ndhI_1 ndhI_2 ndhI_3 [09:25:13] Fixed 2 duplicate /gene - comC_1 comC_2 [09:25:13] Fixed 8 duplicate /gene - mepA_1 mepA_2 mepA_3 mepA_4 mepA_5 mepA_6 mepA_7 mepA_8 [09:25:13] Fixed 3 duplicate /gene - dnaC_1 dnaC_2 dnaC_3 [09:25:13] Fixed 2 duplicate /gene - fdhF_1 fdhF_2 [09:25:13] Fixed 4 duplicate /gene - kdpD_1 kdpD_2 kdpD_3 kdpD_4 [09:25:13] Fixed 2 duplicate /gene - tagT_1 tagT_2 [09:25:13] Fixed 2 duplicate /gene - purC_1 purC_2 [09:25:13] Fixed 2 duplicate /gene - lplJ_1 lplJ_2 [09:25:13] Fixed 4 duplicate /gene - sutR_1 sutR_2 sutR_3 sutR_4 [09:25:13] Fixed 3 duplicate /gene - lacC_1 lacC_2 lacC_3 [09:25:13] Fixed 2 duplicate /gene - fabG_1 fabG_2 [09:25:13] Fixed 5 duplicate /gene - manP_1 manP_2 manP_3 manP_4 manP_5 [09:25:13] Fixed 3 duplicate /gene - feoB_1 feoB_2 feoB_3 [09:25:13] Fixed 2 duplicate /gene - yhhT_1 yhhT_2 [09:25:13] Fixed 4 duplicate /gene - uvrA_1 uvrA_2 uvrA_3 uvrA_4 [09:25:13] Fixed 4 duplicate /gene - topB_1 topB_2 topB_3 topB_4 [09:25:13] Fixed 2 duplicate /gene - ilvD_1 ilvD_2 [09:25:13] Fixed 3 duplicate /gene - patA_1 patA_2 patA_3 [09:25:13] Fixed 2 duplicate /gene - ydcP_1 ydcP_2 [09:25:13] Fixed 4 duplicate /gene - bioB_1 bioB_2 bioB_3 bioB_4 [09:25:13] Fixed 2 duplicate /gene - mprA_1 mprA_2 [09:25:13] Fixed 3 duplicate /gene - murJ_1 murJ_2 murJ_3 [09:25:13] Fixed 3 duplicate /gene - guaB_1 guaB_2 guaB_3 [09:25:13] Fixed 2 duplicate /gene - nagC_1 nagC_2 [09:25:13] Fixed 2 duplicate /gene - thrZ_1 thrZ_2 [09:25:13] Fixed 3 duplicate /gene - sdpR_1 sdpR_2 sdpR_3 [09:25:13] Fixed 3 duplicate /gene - graR_1 graR_2 graR_3 [09:25:13] Fixed 2 duplicate /gene - tsaD_1 tsaD_2 [09:25:13] Fixed 2 duplicate /gene - ftsZ_1 ftsZ_2 [09:25:13] Fixed 2 duplicate /gene - bamD_1 bamD_2 [09:25:13] Fixed 2 duplicate /gene - tuaG_1 tuaG_2 [09:25:13] Fixed 2 duplicate /gene - dan_1 dan_2 [09:25:13] Fixed 3 duplicate /gene - gatD_1 gatD_2 gatD_3 [09:25:13] Fixed 2 duplicate /gene - yjjG_1 yjjG_2 [09:25:13] Fixed 7 duplicate /gene - dgaR_1 dgaR_2 dgaR_3 dgaR_4 dgaR_5 dgaR_6 dgaR_7 [09:25:13] Fixed 2 duplicate /gene - alsT_1 alsT_2 [09:25:13] Fixed 2 duplicate /gene - proS_1 proS_2 [09:25:13] Fixed 2 duplicate /gene - kbaY_1 kbaY_2 [09:25:13] Fixed 3 duplicate /gene - atzA_1 atzA_2 atzA_3 [09:25:13] Fixed 3 duplicate /gene - puuR_1 puuR_2 puuR_3 [09:25:13] Fixed 2 duplicate /gene - sigA_1 sigA_2 [09:25:13] Fixed 2 duplicate /gene - hmuU_1 hmuU_2 [09:25:13] Fixed 2 duplicate /gene - truA_1 truA_2 [09:25:13] Fixed 2 duplicate /gene - uxaA_1 uxaA_2 [09:25:13] Fixed 3 duplicate /gene - yceD_1 yceD_2 yceD_3 [09:25:13] Fixed 2 duplicate /gene - srlB_1 srlB_2 [09:25:13] Fixed 4 duplicate /gene - bceA_1 bceA_2 bceA_3 bceA_4 [09:25:13] Fixed 2 duplicate /gene - xylP_1 xylP_2 [09:25:13] Fixed 3 duplicate /gene - ybhF_1 ybhF_2 ybhF_3 [09:25:13] Fixed 3 duplicate /gene - tal_1 tal_2 tal_3 [09:25:13] Fixed 7 duplicate /gene - ytrF_1 ytrF_2 ytrF_3 ytrF_4 ytrF_5 ytrF_6 ytrF_7 [09:25:13] Fixed 3 duplicate /gene - tadA_1 tadA_2 tadA_3 [09:25:13] Fixed 2 duplicate /gene - nfo_1 nfo_2 [09:25:13] Fixed 2 duplicate /gene - spoIVB_1 spoIVB_2 [09:25:13] Fixed 2 duplicate /gene - sunS_1 sunS_2 [09:25:13] Fixed 4 duplicate /gene - pgdA_1 pgdA_2 pgdA_3 pgdA_4 [09:25:13] Fixed 2 duplicate /gene - fepC_1 fepC_2 [09:25:13] Fixed 2 duplicate /gene - iscS_1 iscS_2 [09:25:13] Fixed 2 duplicate /gene - serS_1 serS_2 [09:25:13] Fixed 380 colliding /gene names. [09:25:13] Adding /locus_tag identifiers [09:25:13] Assigned 3714 locus_tags to CDS and RNA features. [09:25:13] Writing outputs to trash6/tmp/prokka/sample1/ [09:25:18] Generating annotation statistics file [09:25:18] Generating Genbank and Sequin files [09:25:18] Running: tbl2asn -V b -a r10k -l paired-ends -M n -N 1 -y 'Annotated using prokka 1.13 from https://github.com/tseemann/prokka' -Z trash6\/tmp\/prokka\/sample1\/sample1\.err -i trash6\/tmp\/prokka\/sample1\/sample1\.fsa 2> /dev/null [09:25:25] Could not run command: tbl2asn -V b -a r10k -l paired-ends -M n -N 1 -y 'Annotated using prokka 1.13 from https://github.com/tseemann/prokka' -Z trash6\/tmp\/prokka\/sample1\/sample1\.err -i trash6\/tmp\/prokka\/sample1\/sample1\.fsa 2> /dev/null ['prokka', '--outdir', 'trash6/tmp/prokka/sample2', '--prefix', 'sample2', '--centre', 'X', '--compliant', '--force', '--cpus', '4', 'dummy/sample2.faa'] ['prokka', '--outdir', 'trash6/tmp/prokka/sample1', '--prefix', 'sample1', '--centre', 'X', '--compliant', '--force', '--cpus', '4', 'dummy/sample1.faa'] Thu Jan 21 09:25:25 2021 Done. Thu Jan 21 09:25:25 2021 Executing uniref_annotator...Error: Database was built with a different version of diamond as is incompatible. Executing: /home/andrespara/anaconda3/envs/panphlan/bin/diamond blastp --db ./UniRef90_201906.dmnd --query trash6/tmp/prokka/sample2/sample2.faa --outfmt 6 qseqid sseqid pident qlen qstart qend slen sstart send evalue --tmpdir trash6/tmp/uniref/sample2/tmp --out trash6/tmp/uniref/sample2/tmp/sample2.faa.uniref90.hits --id 90 --evalue 1 --threads 4 Parsing results file: trash6/tmp/uniref/sample2/tmp/sample2.faa.uniref90.hits FAILED: The specified path is missing: trash6/tmp/uniref/sample2/tmp/sample2.faa.uniref90.hits Error: Database was built with a different version of diamond as is incompatible. Executing: /home/andrespara/anaconda3/envs/panphlan/bin/diamond blastp --db ./UniRef90_201906.dmnd --query trash6/tmp/prokka/sample1/sample1.faa --outfmt 6 qseqid sseqid pident qlen qstart qend slen sstart send evalue --tmpdir trash6/tmp/uniref/sample1/tmp --out trash6/tmp/uniref/sample1/tmp/sample1.faa.uniref90.hits --id 90 --evalue 1 --threads 4 Parsing results file: trash6/tmp/uniref/sample1/tmp/sample1.faa.uniref90.hits FAILED: The specified path is missing: trash6/tmp/uniref/sample1/tmp/sample1.faa.uniref90.hits ['/home/andrespara/andres/clostridium/Strains/panphlan/PanPhlAn_pangenome_exporter/uniref_annotator/uniref_annotator.py', '--out', 'trash6/tmp/uniref/sample2/sample2.faa', '--temp', 'trash6/tmp/uniref/sample2/tmp', '--seqtype', 'prot', '--diamond', '/home/andrespara/anaconda3/envs/panphlan/bin/diamond', '--uniref90db', './UniRef90_201906.dmnd', '--uniref50db', './UniRef50_201906.dmnd', '--diamond-options', '--threads 4', 'trash6/tmp/prokka/sample2/sample2.faa'] ['/home/andrespara/andres/clostridium/Strains/panphlan/PanPhlAn_pangenome_exporter/uniref_annotator/uniref_annotator.py', '--out', 'trash6/tmp/uniref/sample1/sample1.faa', '--temp', 'trash6/tmp/uniref/sample1/tmp', '--seqtype', 'prot', '--diamond', '/home/andrespara/anaconda3/envs/panphlan/bin/diamond', '--uniref90db', './UniRef90_201906.dmnd', '--uniref50db', './UniRef50_201906.dmnd', '--diamond-options', '--threads 4', 'trash6/tmp/prokka/sample1/sample1.faa'] Thu Jan 21 09:25:25 2021 Done. Thu Jan 21 09:25:25 2021 Clustering unnanotated proteins at UniRef90 level...Traceback (most recent call last): File "./panphlan_exporter.py", line 520, in panphlan_exporter(args.input, args.tmp, args.output, args.clade_name, args.nprocs, args.db_path) File "./panphlan_exporter.py", line 489, in panphlan_exporter get_unannotated_proteins(inputdir, tmp_dir, '90') File "./panphlan_exporter.py", line 135, in get_unannotated_proteins with open(os.path.join(outputdir, 'uniref', genome_name, genome_name + '.faa'), 'r') as read_fasta: FileNotFoundError: [Errno 2] No such file or directory: 'trash6/tmp/uniref/sample2/sample2.faa'