prokka
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tseemann
I want to reopen this issue: "Issue with annotating CDS/ blast step #367 "
(base) lrt@lrt-VirtualBox:/tmp$ prokka --compliant --centre X --locustag 9249 --outdir /home/lrt/Documentos/9249_todo/prokka_output_9249 --force --prefix 9249 --addgenes --rfam /home/lrt/Documentos/9249_todo/filtrado.fasta [14:20:14] This is prokka 1.14.6 [14:20:14] Written by Torsten Seemann [email protected] [14:20:14] Homepage is https://github.com/tseemann/prokka [14:20:14] Local time is Mon Jun 7 14:20:14 2021 [14:20:14] You are lrt [14:20:14] Operating system is linux [14:20:14] You have BioPerl 1.007002 [14:20:14] System has 2 cores. [14:20:14] Option --cpu asked for 8 cores, but system only has 2 [14:20:14] Will use maximum of 2 cores. [14:20:14] Annotating as >>> Bacteria <<< [14:20:14] Enabling options to ensure Genbank/ENA/DDJB submission compliance. [14:20:14] Creating new output folder: /home/lrt/Documentos/9249_todo/prokka_output_9249 [14:20:14] Running: mkdir -p /home/lrt/Documentos/9249_todo/prokka_output_9249 [14:20:14] Using filename prefix: 9249.XXX [14:20:14] Setting HMMER_NCPU=1 [14:20:14] Writing log to: /home/lrt/Documentos/9249_todo/prokka_output_9249/9249.log [14:20:14] Command: /home/lrt/anaconda3/bin/prokka --compliant --centre X --locustag 9249 --outdir /home/lrt/Documentos/9249_todo/prokka_output_9249 --force --prefix 9249 --addgenes --rfam /home/lrt/Documentos/9249_todo/filtrado.fasta [14:20:14] Appending to PATH: /home/lrt/anaconda3/bin [14:20:14] Looking for 'aragorn' - found /home/lrt/anaconda3/bin/aragorn [14:20:14] Determined aragorn version is 001002 from 'ARAGORN v1.2.38 Dean Laslett' [14:20:14] Looking for 'barrnap' - found /home/lrt/anaconda3/bin/barrnap [14:20:14] Determined barrnap version is 000008 from 'barrnap 0.8' [14:20:14] Looking for 'blastp' - found /home/lrt/anaconda3/bin/blastp [14:20:15] Determined blastp version is 002009 from 'blastp: 2.9.0+' [14:20:15] Looking for 'cmpress' - found /home/lrt/anaconda3/bin/cmpress [14:20:15] Determined cmpress version is 001001 from '# INFERNAL 1.1.3 (Nov 2019)' [14:20:15] Looking for 'cmscan' - found /home/lrt/anaconda3/bin/cmscan [14:20:15] Determined cmscan version is 001001 from '# INFERNAL 1.1.3 (Nov 2019)' [14:20:15] Looking for 'egrep' - found /usr/bin/egrep [14:20:15] Looking for 'find' - found /usr/bin/find [14:20:15] Looking for 'grep' - found /usr/bin/grep [14:20:15] Looking for 'hmmpress' - found /home/lrt/anaconda3/bin/hmmpress [14:20:15] Determined hmmpress version is 003003 from '# HMMER 3.3.2 (Nov 2020); http://hmmer.org/' [14:20:15] Looking for 'hmmscan' - found /home/lrt/anaconda3/bin/hmmscan [14:20:15] Determined hmmscan version is 003003 from '# HMMER 3.3.2 (Nov 2020); http://hmmer.org/' [14:20:15] Looking for 'java' - found /home/lrt/anaconda3/bin/java [14:20:15] Looking for 'makeblastdb' - found /home/lrt/anaconda3/bin/makeblastdb [14:20:15] Determined makeblastdb version is 002009 from 'makeblastdb: 2.9.0+' [14:20:15] Looking for 'minced' - found /home/lrt/anaconda3/bin/minced [14:20:15] Determined minced version is 004002 from 'minced 0.4.2' [14:20:15] Looking for 'parallel' - found /home/lrt/anaconda3/bin/parallel [14:20:15] Determined parallel version is 20210422 from 'GNU parallel 20210422' [14:20:15] Looking for 'prodigal' - found /home/lrt/anaconda3/bin/prodigal [14:20:15] Determined prodigal version is 002006 from 'Prodigal V2.6.3: February, 2016' [14:20:15] Looking for 'prokka-genbank_to_fasta_db' - found /home/lrt/anaconda3/bin/prokka-genbank_to_fasta_db [14:20:15] Looking for 'sed' - found /usr/bin/sed [14:20:15] Looking for 'tbl2asn' - found /home/lrt/anaconda3/bin/tbl2asn [14:20:15] Determined tbl2asn version is 025007 from 'tbl2asn 25.7 arguments:' [14:20:15] Using genetic code table 11. [14:20:15] Loading and checking input file: /home/lrt/Documentos/9249_todo/filtrado.fasta [14:20:16] Wrote 120 contigs totalling 5939131 bp. [14:20:16] Predicting tRNAs and tmRNAs [14:20:16] Running: aragorn -l -gc11 -w /home/lrt/Documentos/9249_todo/prokka_output_9249/9249.fna [14:20:26] 1 tRNA-Leu c[15483,15569] 35 (cag) [14:20:26] 2 tRNA-Ala c[180906,180981] 34 (ggc) [14:20:26] 3 tRNA-Pro [387253,387329] 35 (tgg) [14:20:26] 4 tRNA-Gly [387341,387414] 33 (tcc) [14:20:26] 1 tRNA-Asn [270,345] 34 (gtt) [14:20:26] 2 tRNA-Ser [350,440] 35 (gga) [14:20:26] 3 tRNA-Glu [447,521] 34 (ttc) [14:20:26] 4 tRNA-Val [608,683] 34 (tac) [14:20:26] 5 tRNA-Met [694,770] 35 (cat) [14:20:26] 6 tRNA-Asp [780,856] 35 (gtc) [14:20:26] 7 tRNA-Phe [877,952] 34 (gaa) [14:20:26] 8 tRNA-Thr [969,1044] 34 (tgt) [14:20:26] 9 tRNA-Tyr [1058,1143] 35 (gta) [14:20:26] 10 tRNA-Trp [1158,1231] 33 (cca) [14:20:26] 11 tRNA-His [1255,1330] 34 (gtg) [14:20:26] 12 tRNA-Gln [1345,1419] 33 (ttg) [14:20:26] 13 tRNA-Gly [1424,1498] 33 (gcc) [14:20:26] 14 tRNA-Cys [1506,1579] 33 (gca) [14:20:26] 15 tRNA-Leu [1593,1681] 35 (taa) [14:20:26] 16 tRNA-Arg [1692,1768] 35 (acg) [14:20:26] 17 tRNA-Leu [1849,1931] 35 (caa) [14:20:26] 1 tRNA-Arg [197890,197966] 35 (tct) [14:20:26] 1 tRNA-Met [8924,9000] 35 (cat) [14:20:26] 2 tRNA-Met [9031,9107] 35 (cat) [14:20:26] 3 tRNA-Val [9247,9322] 34 (gac) [14:20:26] 1 tRNA-Pro [55023,55099] 35 (cgg) [14:20:26] 1 tRNA-Thr c[11919,11993] 33 (cgt) [14:20:26] 1 tmRNA c[46220,46586] 95,133 GKQQNNFALAA** [14:20:26] 1 tRNA-Ser c[20692,20782] 35 (cga) [14:20:26] 1 tRNA-Gly [10129,10222] 34 (acc) [14:20:26] 2 tRNA-Arg c[31061,31135] 34 (ccg) [14:20:26] 1 tRNA-Pro [25945,26021] 35 (ggg) [14:20:26] 1 tRNA-Glu [3898,3972] 34 (ttc) [14:20:26] 2 tRNA-Lys [4025,4100] 34 (ttt) [14:20:26] 3 tRNA-Leu [4122,4207] 34 (gag) [14:20:26] 1 tRNA-Pyl [19771,19863] 35 (cta) [14:20:26] 1 tRNA-Ala [8208,8293] 32 (tgc) [14:20:26] 2 tRNA-Asn [24070,24145] 34 (gtt) [14:20:26] 3 tRNA-Ser [24154,24245] 36 (gct) [14:20:26] 1 tRNA-Gly c[364,437] 33 (tcc) [14:20:27] 2 tRNA-Pro c[449,525] 35 (tgg) [14:20:27] 3 tRNA-Arg c[563,639] 35 (acg) [14:20:27] 4 tRNA-Gly c[664,738] 33 (gcc) [14:20:27] 5 tRNA-Leu c[22069,22151] 35 (tag) [14:20:27] 6 tRNA-Lys c[22170,22245] 34 (ttt) [14:20:27] 7 tRNA-Gln c[22271,22345] 33 (ttg) [14:20:27] 8 tRNA-Thr c[22389,22464] 34 (tgt) [14:20:27] 9 tRNA-Val c[22487,22562] 34 (tac) [14:20:27] 10 tRNA-Glu c[22633,22707] 34 (ttc) [14:20:27] 11 tRNA-Thr c[22735,22810] 34 (ggt) [14:20:27] 12 tRNA-Asn c[22814,22889] 34 (gtt) [14:20:27] 1 tRNA-Leu c[13550,13633] 34 (caa) [14:20:27] 2 tRNA-Arg c[13647,13723] 35 (acg) [14:20:27] 3 tRNA-Leu c[13734,13822] 35 (taa) [14:20:27] 4 tRNA-Gly c[13835,13909] 33 (gcc) [14:20:27] 5 tRNA-Leu c[13916,13998] 35 (tag) [14:20:27] 6 tRNA-Lys c[14017,14092] 34 (ttt) [14:20:27] 7 tRNA-Gln c[14102,14176] 33 (ttg) [14:20:27] 8 tRNA-His c[14192,14267] 34 (gtg) [14:20:27] 9 tRNA-Thr c[14318,14393] 34 (tgt) [14:20:27] 10 tRNA-Met c[14410,14486] 35 (cat) [14:20:27] 11 tRNA-Asp c[14562,14638] 35 (gtc) [14:20:27] 12 tRNA-Met c[14650,14726] 35 (cat) [14:20:27] 1 tRNA-Ser [8571,8659] 36 (tga) [14:20:27] 1 tRNA-Lys [171,246] 34 (ttt) [14:20:27] 1 tRNA-Ser [157,248] 36 (gct) [14:20:27] 2 tRNA-Met [274,350] 35 (cat) [14:20:27] 3 tRNA-Val [355,430] 34 (tac) [14:20:27] 4 tRNA-Asp [456,532] 35 (gtc) [14:20:27] 5 tRNA-Phe [625,700] 34 (gaa) [14:20:27] 6 tRNA-Tyr [710,795] 35 (gta) [14:20:27] 7 tRNA-Lys [804,879] 34 (ttt) [14:20:27] 1 tRNA-Ile [295,371] 35 (gat) [14:20:27] 2 tRNA-Ala [400,475] 34 (tgc) [14:20:27] 1 tRNA-Val c[52,127] 34 (tac) [14:20:27] 2 tRNA-Glu c[197,271] 34 (ttc) [14:20:27] 3 tRNA-Asn c[275,350] 34 (gtt) [14:20:27] 4 tRNA-Ile c[362,438] 35 (gat) [14:20:27] Found 78 tRNAs [14:20:27] Predicting Ribosomal RNAs [14:20:27] Running Barrnap with 2 threads [14:20:39] 1 gnl|X|9249_104 14 16S ribosomal RNA [14:20:39] 2 gnl|X|9249_111 155 5S ribosomal RNA [14:20:39] 3 gnl|X|9249_117 512 5S ribosomal RNA [14:20:39] 4 gnl|X|9249_20 91605 5S ribosomal RNA [14:20:39] 5 gnl|X|9249_22 83219 5S ribosomal RNA [14:20:39] 6 gnl|X|9249_65 22919 5S ribosomal RNA [14:20:39] 7 gnl|X|9249_67 5 5S ribosomal RNA [14:20:39] 8 gnl|X|9249_79 3 5S ribosomal RNA [14:20:39] Found 8 rRNAs [14:20:39] Scanning for ncRNAs... please be patient. [14:20:39] Running: cmscan -Z 11.878262 --cut_ga --rfam --nohmmonly --fmt 2 --cpu 2 --tblout /dev/stdout -o /dev/null --noali /home/lrt/anaconda3/db/cm/Bacteria /home/lrt/Documentos/9249_todo/prokka_output_9249/9249.fna [14:27:45] 1 ncRNA 1 gnl|X|9249_1 1..224 [14:27:45] 2 ncRNA 2 gnl|X|9249_1 1..138 [14:27:45] 3 ncRNA 3 gnl|X|9249_1 1..108 [14:27:45] 4 ncRNA 4 gnl|X|9249_1 1..188 [14:27:45] 5 ncRNA 5 gnl|X|9249_1 1..138 [14:27:45] 6 ncRNA 1 gnl|X|9249_2 1..191 [14:27:45] 7 ncRNA 2 gnl|X|9249_2 1..91 [14:27:45] 8 ncRNA 1 gnl|X|9249_3 1..169 [14:27:45] 9 ncRNA 2 gnl|X|9249_3 1..224 [14:27:45] 10 ncRNA 3 gnl|X|9249_3 1..108 [14:27:45] 11 ncRNA 4 gnl|X|9249_3 1..105 [14:27:45] 12 ncRNA 5 gnl|X|9249_3 1..105 [14:27:45] 13 ncRNA 1 gnl|X|9249_4 1..616 [14:27:45] 14 ncRNA 2 gnl|X|9249_4 1..169 [14:27:45] 15 ncRNA 3 gnl|X|9249_4 1..224 [14:35:41] 16 ncRNA 4 gnl|X|9249_4 1..140 [14:35:41] 17 ncRNA 5 gnl|X|9249_4 1..87 [14:35:41] 18 ncRNA 6 gnl|X|9249_4 1..93 [14:35:41] 19 ncRNA 1 gnl|X|9249_5 1..68 [14:35:41] 20 ncRNA 2 gnl|X|9249_5 1..150 [14:35:41] 21 ncRNA 1 gnl|X|9249_6 1..224 [14:35:41] 22 ncRNA 1 gnl|X|9249_8 1..191 [14:35:41] 23 ncRNA 2 gnl|X|9249_8 1..183 [14:35:41] 24 ncRNA 3 gnl|X|9249_8 1..117 [14:35:41] 25 ncRNA 4 gnl|X|9249_8 1..259 [14:35:41] 26 ncRNA 1 gnl|X|9249_9 1..94 [14:35:41] 27 ncRNA 1 gnl|X|9249_10 1..367 [14:35:41] 28 ncRNA 1 gnl|X|9249_11 1..224 [14:35:41] 29 ncRNA 2 gnl|X|9249_11 1..87 [14:35:41] 30 ncRNA 3 gnl|X|9249_11 1..87 [14:35:41] 31 ncRNA 1 gnl|X|9249_12 1..99 [14:35:41] 32 ncRNA 1 gnl|X|9249_14 1..259 [14:35:41] 33 ncRNA 1 gnl|X|9249_15 1..102 [14:44:46] 34 ncRNA 1 gnl|X|9249_16 1..87 [14:44:46] 35 ncRNA 2 gnl|X|9249_16 1..87 [14:44:46] 36 ncRNA 1 gnl|X|9249_17 1..98 [14:44:46] 37 ncRNA 2 gnl|X|9249_17 1..93 [14:44:46] 38 ncRNA 1 gnl|X|9249_20 1..102 [14:44:46] 39 ncRNA 1 gnl|X|9249_22 1..139 [14:44:46] 40 ncRNA 1 gnl|X|9249_23 1..136 [14:44:46] 41 ncRNA 1 gnl|X|9249_24 1..87 [14:44:46] 42 ncRNA 1 gnl|X|9249_26 1..224 [14:44:46] 43 ncRNA 1 gnl|X|9249_32 1..87 [14:44:46] 44 ncRNA 1 gnl|X|9249_33 1..136 [14:44:46] 45 ncRNA 1 gnl|X|9249_35 1..191 [14:44:46] 46 ncRNA 1 gnl|X|9249_38 1..93 [14:44:46] 47 ncRNA 1 gnl|X|9249_39 1..169 [14:44:46] 48 ncRNA 1 gnl|X|9249_42 1..136 [14:44:46] 49 ncRNA 1 gnl|X|9249_46 1..224 [14:44:46] 50 ncRNA 1 gnl|X|9249_47 1..136 [14:48:48] 51 ncRNA 1 gnl|X|9249_48 1..127 [14:48:48] 52 ncRNA 1 gnl|X|9249_51 1..122 [14:48:48] 53 ncRNA 1 gnl|X|9249_53 1..105 [14:48:48] 54 ncRNA 2 gnl|X|9249_53 1..93 [14:48:48] 55 ncRNA 1 gnl|X|9249_54 1..224 [14:48:48] 56 ncRNA 1 gnl|X|9249_57 1..87 [14:48:48] 57 ncRNA 1 gnl|X|9249_63 1..99 [14:48:48] 58 ncRNA 2 gnl|X|9249_63 1..105 [14:48:48] 59 ncRNA 1 gnl|X|9249_65 1..136 [14:48:48] 60 ncRNA 1 gnl|X|9249_66 1..224 [14:48:48] 61 ncRNA 2 gnl|X|9249_66 1..126 [14:48:48] 62 ncRNA 1 gnl|X|9249_75 1..171 [14:48:48] 63 ncRNA 1 gnl|X|9249_76 1..98 [14:48:48] 64 ncRNA 1 gnl|X|9249_79 1..97 [14:48:48] 65 ncRNA 1 gnl|X|9249_81 1..255 [14:48:48] 66 ncRNA 1 gnl|X|9249_82 1..93 [14:49:17] 67 ncRNA 1 gnl|X|9249_88 1..87 [14:49:17] 68 ncRNA 2 gnl|X|9249_88 1..87 [14:49:17] 69 ncRNA 1 gnl|X|9249_89 1..93 [14:49:17] 70 ncRNA 1 gnl|X|9249_96 1..171 [14:49:17] 71 ncRNA 2 gnl|X|9249_96 1..68 [14:49:17] 72 ncRNA 3 gnl|X|9249_96 1..84 [14:49:17] 73 ncRNA 4 gnl|X|9249_96 1..93 [14:49:17] 74 ncRNA 1 gnl|X|9249_97 1..102 [14:49:17] 75 ncRNA 1 gnl|X|9249_99 1..138 [14:49:17] Found 75 ncRNAs. [14:49:17] Total of 85 tRNA + rRNA features [14:49:17] Searching for CRISPR repeats [14:49:19] CRISPR1 gnl|X|9249_45 14807 with 50 spacers [14:49:19] CRISPR2 gnl|X|9249_45 26414 with 61 spacers [14:49:19] CRISPR3 gnl|X|9249_50 4013 with 107 spacers [14:49:19] Found 3 CRISPRs [14:49:19] Predicting coding sequences [14:49:19] Contigs total 5939131 bp, so using single mode [14:49:19] Running: prodigal -i /home/lrt/Documentos/9249_todo/prokka_output_9249/9249.fna -c -m -g 11 -p single -f sco -q [14:50:07] Excluding CDS which overlaps existing RNA (repeat_region) at gnl|X|9249_45:14682..15041 on + strand [14:50:07] Excluding CDS which overlaps existing RNA (repeat_region) at gnl|X|9249_45:26861..27733 on - strand [14:50:07] Excluding CDS which overlaps existing RNA (repeat_region) at gnl|X|9249_45:30345..30530 on - strand [14:50:08] Excluding CDS which overlaps existing RNA (tRNA) at gnl|X|9249_49:10075..10710 on + strand [14:50:08] Excluding CDS which overlaps existing RNA (repeat_region) at gnl|X|9249_50:3306..4055 on - strand [14:50:08] Excluding CDS which overlaps existing RNA (repeat_region) at gnl|X|9249_50:4209..4487 on - strand [14:50:08] Excluding CDS which overlaps existing RNA (repeat_region) at gnl|X|9249_50:7026..7115 on - strand [14:50:08] Excluding CDS which overlaps existing RNA (repeat_region) at gnl|X|9249_50:7273..7551 on - strand [14:50:09] Excluding CDS which overlaps existing RNA (tRNA) at gnl|X|9249_58:19445..21124 on + strand [14:50:09] Excluding CDS which overlaps existing RNA (tRNA) at gnl|X|9249_63:7994..8722 on + strand [14:50:10] Excluding CDS which overlaps existing RNA (tRNA) at gnl|X|9249_65:174..446 on + strand [14:50:11] Excluding CDS which overlaps existing RNA (rRNA) at gnl|X|9249_104:689..1309 on + strand [14:50:11] Found 5287 CDS [14:50:11] Connecting features back to sequences [14:50:11] Not using genus-specific database. Try --usegenus to enable it. [14:50:11] Annotating CDS, please be patient. [14:50:11] Will use 2 CPUs for similarity searching. [14:50:16] There are still 5287 unannotated CDS left (started with 5287) [14:50:16] Will use blast to search against /home/lrt/anaconda3/db/kingdom/Bacteria/IS with 2 CPUs [14:50:16] Running: cat /home/lrt/Documentos/9249_todo/prokka_output_9249/9249.IS.tmp.42827.faa | parallel --gnu --plain -j 2 --block 433955 --recstart '>' --pipe blastp -query - -db /home/lrt/anaconda3/db/kingdom/Bacteria/IS -evalue 1e-30 -qcov_hsp_perc 90 -num_threads 1 -num_descriptions 1 -num_alignments 1 -seg no > /home/lrt/Documentos/9249_todo/prokka_output_9249/9249.IS.tmp.42827.blast 2> /dev/null [14:51:27] Could not run command: cat /home/lrt/Documentos/9249_todo/prokka_output_9249/9249.IS.tmp.42827.faa | parallel --gnu --plain -j 2 --block 433955 --recstart '>' --pipe blastp -query - -db /home/lrt/anaconda3/db/kingdom/Bacteria/IS -evalue 1e-30 -qcov_hsp_perc 90 -num_threads 1 -num_descriptions 1 -num_alignments 1 -seg no > /home/lrt/Documentos/9249_todo/prokka_output_9249/9249.IS.tmp.42827.blast 2> /dev/null
Please, can you help me to solve this?
Hi,
So we had this issue too. It seems the tbl2asn stage was causing a problem, as this executable requires periodic updating, and will fail if it detects an old version. It worked for us once we updated this file.
