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(bioinfo) [zhujiang@login1 example]$ prokka ./fasta_example_genomic.fna [19:52:08] This is prokka 1.13.3 [19:52:08] Written by Torsten Seemann [email protected] [19:52:08] Homepage is https://github.com/tseemann/prokka [19:52:08] Local time is Fri Apr 12 19:52:08 2024 [19:52:08] You are zhujiang [19:52:08] Operating system is linux [19:52:08] You have BioPerl 1.007002 [19:52:08] System has 52 cores. [19:52:08] Will use maximum of 8 cores. [19:52:08] Annotating as >>> Bacteria <<< [19:52:08] Generating locus_tag from './fasta_example_genomic.fna' contents. [19:52:08] Setting --locustag PICPPNBC from MD5 92c997bcd88e983ffdb21b2712ed3736 [19:52:08] Creating new output folder: PROKKA_04122024 [19:52:08] Running: mkdir -p PROKKA_04122024 [19:52:08] Using filename prefix: PROKKA_04122024.XXX [19:52:08] Setting HMMER_NCPU=1 [19:52:08] Writing log to: PROKKA_04122024/PROKKA_04122024.log [19:52:08] Command: /public/home/zhujiang/anaconda3/envs/bioinfo/bin/prokka ./fasta_example_genomic.fna [19:52:08] Appending to PATH: /public/home/zhujiang/anaconda3/envs/bioinfo/bin [19:52:08] Looking for 'aragorn' - found /public/home/zhujiang/anaconda3/envs/bioinfo/bin/aragorn [19:52:08] Determined aragorn version is 1.2 [19:52:08] Looking for 'barrnap' - found /public/home/zhujiang/anaconda3/envs/bioinfo/bin/barrnap [19:52:09] Determined barrnap version is 0.9 [19:52:09] Looking for 'blastp' - found /public/home/zhujiang/anaconda3/envs/bioinfo/bin/blastp [19:52:20] Determined blastp version is 2.15 [19:52:20] Prokka needs blastp 2.2 or higher. Please upgrade and try again. (bioinfo) [zhujiang@login1 example]$ export PATH=/public/home/zhujiang/crp/dede/ncbi-blast-2.2.30+/b (bioinfo) [zhujiang@login1 example]$ rm -rf PROKKA_04122024 (bioinfo) [zhujiang@login1 example]$ prokka ./fasta_example_genomic.fna [19:53:26] This is prokka 1.13.3 [19:53:26] Written by Torsten Seemann [email protected] [19:53:26] Homepage is https://github.com/tseemann/prokka [19:53:26] Local time is Fri Apr 12 19:53:26 2024 [19:53:26] You are zhujiang [19:53:26] Operating system is linux [19:53:26] You have BioPerl 1.007002 [19:53:26] System has 52 cores. [19:53:26] Will use maximum of 8 cores. [19:53:26] Annotating as >>> Bacteria <<< [19:53:26] Generating locus_tag from './fasta_example_genomic.fna' contents. [19:53:26] Setting --locustag PICPPNBC from MD5 92c997bcd88e983ffdb21b2712ed3736 [19:53:26] Creating new output folder: PROKKA_04122024 [19:53:26] Running: mkdir -p PROKKA_04122024 [19:53:26] Using filename prefix: PROKKA_04122024.XXX [19:53:26] Setting HMMER_NCPU=1 [19:53:26] Writing log to: PROKKA_04122024/PROKKA_04122024.log [19:53:26] Command: /public/home/zhujiang/anaconda3/envs/bioinfo/bin/prokka ./fasta_example_genomic. [19:53:26] Appending to PATH: /public/home/zhujiang/anaconda3/envs/bioinfo/bin [19:53:26] Looking for 'aragorn' - found /public/home/zhujiang/anaconda3/envs/bioinfo/bin/aragorn [19:53:26] Determined aragorn version is 1.2 [19:53:26] Looking for 'barrnap' - found /public/home/zhujiang/anaconda3/envs/bioinfo/bin/barrnap [19:53:26] Determined barrnap version is 0.9 [19:53:26] Looking for 'blastp' - found /public/home/zhujiang/crp/dede/ncbi-blast-2.2.30+/bin/blastp [19:53:26] Determined blastp version is 2.2 [19:53:26] Looking for 'cmpress' - found /public/home/zhujiang/anaconda3/envs/bioinfo/bin/cmpress [19:53:26] Determined cmpress version is 1.1 [19:53:26] Looking for 'cmscan' - found /public/home/zhujiang/anaconda3/envs/bioinfo/bin/cmscan [19:53:27] Determined cmscan version is 1.1 [19:53:27] Looking for 'egrep' - found /usr/bin/egrep [19:53:27] Looking for 'find' - found /usr/bin/find [19:53:27] Looking for 'grep' - found /usr/bin/grep [19:53:27] Looking for 'hmmpress' - found /public/home/zhujiang/anaconda3/envs/bioinfo/bin/hmmpress [19:53:27] Determined hmmpress version is 3.4 [19:53:27] Looking for 'hmmscan' - found /public/home/zhujiang/anaconda3/envs/bioinfo/bin/hmmscan [19:53:27] Determined hmmscan version is 3.4 [19:53:27] Looking for 'java' - found /public/home/zhujiang/anaconda3/envs/bioinfo/bin/java [19:53:27] Looking for 'less' - found /usr/bin/less [19:53:27] Looking for 'makeblastdb' - found /public/home/zhujiang/crp/dede/ncbi-blast-2.2.30+/bin/m [19:53:27] Determined makeblastdb version is 2.2 [19:53:27] Looking for 'minced' - found /public/home/zhujiang/anaconda3/envs/bioinfo/bin/minced [19:53:27] Determined minced version is 4.2 [19:53:27] Looking for 'parallel' - found /public/home/zhujiang/anaconda3/envs/bioinfo/bin/parallel [19:53:27] Determined parallel version is 20240322 [19:53:27] Looking for 'prodigal' - found /public/home/zhujiang/anaconda3/envs/bioinfo/bin/prodigal [19:53:27] Determined prodigal version is 2.6 [19:53:27] Looking for 'prokka-genbank_to_fasta_db' - found /public/home/zhujiang/anaconda3/envs/bio [19:53:27] Looking for 'sed' - found /usr/bin/sed [19:53:27] Looking for 'tbl2asn' - found /public/home/zhujiang/anaconda3/envs/bioinfo/bin/tbl2asn [19:53:27] Determined tbl2asn version is 25.8 [19:53:27] Using genetic code table 11. [19:53:27] Loading and checking input file: ./fasta_example_genomic.fna [19:53:28] Wrote 1 contigs totalling 4641652 bp. [19:53:28] Predicting tRNAs and tmRNAs [19:53:28] Running: aragorn -l -gc11 -w PROKKA_04122024/PROKKA_04122024.fna [19:53:29] 1 tRNA-Ile [225381,225457] 35 (gat) [19:53:29] 2 tRNA-Ala [225500,225575] 34 (tgc) [19:53:29] 3 tRNA-Asp [228928,229004] 35 (gtc) [19:53:29] 4 tRNA-Asp [236931,237007] 35 (gtc) [19:53:29] 5 tRNA-Thr [262871,262946] 34 (cgt) [19:53:29] 6 tRNA-Ser [345334,345414] 38 (gga) [19:53:29] 7 tRNA-Arg [564723,564799] 35 (tct) [19:53:29] 8 tRNA-Gln c[696430,696504] 33 (ctg) [19:53:29] 9 tRNA-Gln c[696542,696616] 33 (ctg) [19:53:29] 10 tRNA-Met c[696664,696740] 35 (cat) [19:53:29] 11 tRNA-Gln c[696756,696830] 33 (ttg) [19:53:29] 12 tRNA-Gln c[696865,696939] 33 (ttg) [19:53:29] 13 tRNA-Leu c[696963,697047] 35 (tag) [19:53:29] 14 tRNA-Met c[697057,697133] 35 (cat) [19:53:29] 15 tRNA-Lys [780554,780629] 34 (ttt) [19:53:29] 16 tRNA-Val [780765,780840] 34 (tac) [19:53:29] 17 tRNA-Lys [780843,780918] 34 (ttt) [19:53:29] 18 tRNA-Val [781068,781143] 34 (tac) [19:53:29] 19 tRNA-Lys [781147,781222] 34 (ttt) [19:53:29] 20 tRNA-Lys [781369,781444] 34 (ttt) [19:53:29] 21 tRNA-Lys [781577,781652] 34 (ttt) [19:53:29] 22 tRNA-Ser c[925884,925971] 35 (gga) [19:53:29] 23 tRNA-Ser c[1031625,1031712] 35 (tga) [19:53:29] 24 tRNA-Ser c[1097565,1097652] 35 (gga) [19:53:29] 25 tRNA-Tyr c[1287244,1287328] 35 (gta) [19:53:29] 26 tRNA-Tyr c[1287538,1287622] 35 (gta) [19:53:29] 27 tRNA-Val [1746435,1746511] 35 (gac) [19:53:29] 28 tRNA-Val [1746516,1746592] 35 (gac) [19:53:29] 29 tRNA-Leu c[1991815,1991901] 35 (taa) [19:53:29] 30 tRNA-Cys c[1991914,1991987] 33 (gca) [19:53:29] 31 tRNA-Gly c[1992042,1992117] 34 (gcc) [19:53:29] 32 tRNA-Ser c[2043468,2043557] 35 (cga) [19:53:29] 33 tRNA-Asn [2044549,2044624] 34 (gtt) [19:53:29] 34 tRNA-Asn c[2058027,2058102] 34 (gtt) [19:53:29] 35 tRNA-Asn [2059851,2059926] 34 (gtt) [19:53:29] 36 tRNA-Asn [2062260,2062335] 34 (gtt) [19:53:29] 37 tRNA-Pro [2286211,2286287] 35 (ggg) [19:53:29] 38 tRNA-Arg [2466309,2466383] 34 (cct) [19:53:29] 39 tRNA-Ala c[2518041,2518116] 34 (ggc) [19:53:29] 40 tRNA-Ala c[2518156,2518231] 34 (ggc) [19:53:29] 41 tRNA-Val [2520931,2521006] 34 (tac) [19:53:29] 42 tRNA-Val [2521051,2521126] 34 (tac) [19:53:29] 43 tRNA-Val [2521173,2521248] 34 (tac) [19:53:29] 44 tRNA-Lys [2521253,2521328] 34 (ttt) [19:53:29] 45 tRNA-Glu c[2729369,2729444] 35 (ttc) [19:53:29] 46 tmRNA [2755593,2755955] 90,125 ANDENYALAA** [19:53:29] 47 tRNA-Met c[2785762,2785837] 34 (cat) [19:53:29] 48 tRNA-Arg c[2817784,2817860] 35 (acg) [19:53:29] 49 tRNA-Arg c[2818059,2818135] 35 (acg) [19:53:29] 50 tRNA-Arg c[2818198,2818274] 35 (acg) [19:53:29] 51 tRNA-Arg [2818458,2818529] 34 (tcg) [19:53:29] 52 tRNA-Arg c[2818473,2818549] 35 (acg) [19:53:29] 53 tRNA-Ser c[2818553,2818645] 35 (gct) [19:53:29] 54 tRNA-Met [2947387,2947463] 35 (cat) [19:53:29] 55 tRNA-Met [2947497,2947573] 35 (cat) [19:53:29] 56 tRNA-Met [2947607,2947683] 35 (cat) [19:53:29] 57 tRNA-Gly c[2998984,2999057] 33 (ccc) [19:53:29] 58 tRNA-Phe [3110366,3110441] 34 (gaa) [19:53:29] 59 tRNA-Met [3215598,3215673] 34 (cat) [19:53:29] 60 tRNA-Met c[3318213,3318289] 35 (cat) [19:53:29] 61 tRNA-Leu c[3322072,3322158] 35 (gag) [19:53:29] 62 tRNA-Thr c[3423580,3423655] 34 (ggt) [19:53:29] 63 tRNA-Ala c[3426958,3427033] 34 (tgc) [19:53:29] 64 tRNA-Ile c[3427076,3427152] 35 (gat) [19:53:29] 65 tRNA-Pro c[3708616,3708692] 35 (cgg) [19:53:29] 66 tRNA-SeC [3836222,3836316] 35 (tca) [19:53:29] 67 tRNA-Glu [3943435,3943510] 35 (ttc) [19:53:29] 68 tRNA-Asp [3946872,3946948] 35 (gtc) [19:53:29] 69 tRNA-Trp [3946957,3947032] 34 (cca) [19:53:29] 70 tRNA-Arg [3982375,3982451] 35 (ccg) [19:53:29] 71 tRNA-His [3982510,3982585] 34 (gtg) [19:53:29] 72 tRNA-Leu [3982606,3982692] 35 (cag) [19:53:29] 73 tRNA-Pro [3982735,3982811] 35 (tgg) [19:53:29] 74 tRNA-Ile [4037141,4037217] 35 (gat) [19:53:29] 75 tRNA-Ala [4037260,4037335] 34 (tgc) [19:53:29] 76 tRNA-Glu [4168372,4168447] 35 (ttc) [19:53:29] 77 tRNA-Thr [4175388,4175463] 34 (tgt) [19:53:29] 78 tRNA-Tyr [4175472,4175556] 35 (gta) [19:53:29] 79 tRNA-Gly [4175673,4175747] 34 (tcc) [19:53:29] 80 tRNA-Thr [4175754,4175829] 34 (ggt) [19:53:29] 81 tRNA-Glu [4209774,4209849] 35 (ttc) [19:53:29] 82 tRNA-Phe c[4362551,4362626] 34 (gaa) [19:53:29] 83 tRNA-Gly [4392360,4392435] 34 (gcc) [19:53:29] 84 tRNA-Gly [4392472,4392547] 34 (gcc) [19:53:29] 85 tRNA-Gly [4392583,4392658] 34 (gcc) [19:53:29] 86 tRNA-Leu [4496405,4496489] 35 (caa) [19:53:29] 87 tRNA-Leu c[4606079,4606165] 35 (cag) [19:53:29] 88 tRNA-Leu c[4606200,4606286] 35 (cag) [19:53:29] 89 tRNA-Leu c[4606315,4606401] 35 (cag) [19:53:29] Found 89 tRNAs [19:53:29] Predicting Ribosomal RNAs [19:53:29] Running Barrnap with 8 threads [19:53:32] 1 NC_000913.3 223774 16S ribosomal RNA [19:53:32] 2 NC_000913.3 225761 23S ribosomal RNA [19:53:32] 3 NC_000913.3 228760 5S ribosomal RNA [19:53:32] 4 NC_000913.3 2726074 5S ribosomal RNA [19:53:32] 5 NC_000913.3 2726282 23S ribosomal RNA [19:53:32] 6 NC_000913.3 2729617 16S ribosomal RNA [19:53:32] 7 NC_000913.3 3423428 5S ribosomal RNA [19:53:32] 8 NC_000913.3 3423673 5S ribosomal RNA [19:53:32] 9 NC_000913.3 3423881 23S ribosomal RNA [19:53:32] 10 NC_000913.3 3427222 16S ribosomal RNA [19:53:32] 11 NC_000913.3 3941811 16S ribosomal RNA [19:53:32] 12 NC_000913.3 3943706 23S ribosomal RNA [19:53:32] 13 NC_000913.3 3946704 5S ribosomal RNA [19:53:32] 14 NC_000913.3 4035534 16S ribosomal RNA [19:53:32] 15 NC_000913.3 4037521 23S ribosomal RNA [19:53:32] 16 NC_000913.3 4040521 5S ribosomal RNA [19:53:32] 17 NC_000913.3 4166662 16S ribosomal RNA [19:53:32] 18 NC_000913.3 4168643 23S ribosomal RNA [19:53:32] 19 NC_000913.3 4171641 5S ribosomal RNA [19:53:32] 20 NC_000913.3 4208150 16S ribosomal RNA [19:53:32] 21 NC_000913.3 4210045 23S ribosomal RNA [19:53:32] 22 NC_000913.3 4213044 5S ribosomal RNA [19:53:32] Found 22 rRNAs [19:53:32] Skipping ncRNA search, enable with --rfam if desired. [19:53:32] Total of 110 tRNA + rRNA features [19:53:32] Searching for CRISPR repeats [19:53:32] CRISPR1 NC_000913.3 2877701 with 13 spacers [19:53:32] CRISPR2 NC_000913.3 2904014 with 7 spacers [19:53:32] Found 2 CRISPRs [19:53:32] Predicting coding sequences [19:53:32] Contigs total 4641652 bp, so using single mode [19:53:32] Running: prodigal -i PROKKA_04122024/PROKKA_04122024.fna -c -m -g 11 -p single -f sco - [19:53:41] Excluding CDS which overlaps existing RNA (rRNA) at NC_000913.3:224958..225212 on + stran [19:53:43] Excluding CDS which overlaps existing RNA (tRNA) at NC_000913.3:1287065..1287631 on + str [19:53:45] Excluding CDS which overlaps existing RNA (rRNA) at NC_000913.3:2727331..2727450 on - str [19:53:45] Excluding CDS which overlaps existing RNA (rRNA) at NC_000913.3:2729716..2729970 on - str [19:53:45] Excluding CDS which overlaps existing RNA (tRNA) at NC_000913.3:2817923..2818393 on + str [19:53:46] Excluding CDS which overlaps existing RNA (tRNA) at NC_000913.3:3423503..3423826 on + str [19:53:46] Excluding CDS which overlaps existing RNA (rRNA) at NC_000913.3:3427321..3427575 on - str [19:53:46] Excluding CDS which overlaps existing RNA (rRNA) at NC_000913.3:3942995..3943249 on + str [19:53:47] Excluding CDS which overlaps existing RNA (rRNA) at NC_000913.3:4036718..4036972 on + str [19:53:47] Excluding CDS which overlaps existing RNA (rRNA) at NC_000913.3:4167846..4168100 on + str [19:53:47] Excluding CDS which overlaps existing RNA (rRNA) at NC_000913.3:4170375..4170494 on + str [19:53:47] Excluding CDS which overlaps existing RNA (rRNA) at NC_000913.3:4209334..4209588 on + str [19:53:47] Excluding CDS which overlaps existing RNA (rRNA) at NC_000913.3:4211777..4211896 on + str [19:53:47] Found 4305 CDS [19:53:47] Connecting features back to sequences [19:53:47] Not using genus-specific database. Try --usegenus to enable it. [19:53:47] Annotating CDS, please be patient. [19:53:47] Will use 8 CPUs for similarity searching. [19:53:48] There are still 4305 unannotated CDS left (started with 4305) [19:53:48] Will use blast to search against /public/home/zhujiang/anaconda3/envs/bioinfo/db/kingdom/ [19:53:48] Running: cat PROKKA_04122024/IS.faa | parallel --gnu --plain -j 8 --block 86286 --recst teria/IS -evalue 1e-30 -qcov_hsp_perc 90 -num_threads 1 -num_descriptions 1 -num_alignments 1 -seg n [19:54:01] Deleting unwanted file: PROKKA_04122024/IS.faa [19:54:01] Deleting unwanted file: PROKKA_04122024/IS.blast [19:54:02] There are still 4229 unannotated CDS left (started with 4305) [19:54:02] Will use blast to search against /public/home/zhujiang/anaconda3/envs/bioinfo/db/kingdom/ [19:54:02] Running: cat PROKKA_04122024/AMR.faa | parallel --gnu --plain -j 8 --block 85153 --recs cteria/AMR -evalue 9.99999999999999e-301 -qcov_hsp_perc 90 -num_threads 1 -num_descriptions 1 -num_a [19:54:12] Deleting unwanted file: PROKKA_04122024/AMR.faa [19:54:12] Deleting unwanted file: PROKKA_04122024/AMR.blast [19:54:13] There are still 4229 unannotated CDS left (started with 4305) [19:54:13] Will use blast to search against /public/home/zhujiang/anaconda3/envs/bioinfo/db/kingdom/ [19:54:13] Running: cat PROKKA_04122024/sprot.faa | parallel --gnu --plain -j 8 --block 85153 --re Bacteria/sprot -evalue 1e-09 -qcov_hsp_perc 80 -num_threads 1 -num_descriptions 1 -num_alignments 1 [19:54:55] Could not run command: cat PROKKA_04122024/sprot.faa | parallel --gnu --plain -j 8 --bl fo/db/kingdom/Bacteria/sprot -evalue 1e-09 -qcov_hsp_perc 80 -num_threads 1 -num_descriptions 1 -num (bioinfo) [zhujiang@login1 example]$ ll total 4598 -rw-r--r-- 1 zhujiang lisuhua 4699745 Apr 1 22:52 fasta_example_genomic.fna drwxr-xr-x 2 zhujiang lisuhua 8192 Apr 12 19:54 PROKKA_04122024 (bioinfo) [zhujiang@login1 example]$ cat PROKKA_04122024/sprot.faa | parallel --gnu --plain -j 8 --b nfo/db/kingdom/Bacteria/sprot -evalue 1e-09 -qcov_hsp_perc 80 -num_threads 1 -num_descriptions 1 -nu (bioinfo) [zhujiang@login1 example]$ rm -rf PROKKA_04122024 (bioinfo) [zhujiang@login1 example]$ prokka ./fasta_example_genomic.fna [19:56:22] This is prokka 1.13.3 [19:56:22] Written by Torsten Seemann [email protected] [19:56:22] Homepage is https://github.com/tseemann/prokka [19:56:22] Local time is Fri Apr 12 19:56:22 2024 [19:56:22] You are zhujiang [19:56:22] Operating system is linux [19:56:22] You have BioPerl 1.007002 [19:56:22] System has 52 cores. [19:56:22] Will use maximum of 8 cores. [19:56:22] Annotating as >>> Bacteria <<< [19:56:22] Generating locus_tag from './fasta_example_genomic.fna' contents. [19:56:22] Setting --locustag PICPPNBC from MD5 92c997bcd88e983ffdb21b2712ed3736 [19:56:22] Creating new output folder: PROKKA_04122024 [19:56:22] Running: mkdir -p PROKKA_04122024 [19:56:22] Using filename prefix: PROKKA_04122024.XXX [19:56:22] Setting HMMER_NCPU=1 [19:56:22] Writing log to: PROKKA_04122024/PROKKA_04122024.log [19:56:22] Command: /public/home/zhujiang/anaconda3/envs/bioinfo/bin/prokka ./fasta_example_genomic. [19:56:22] Appending to PATH: /public/home/zhujiang/anaconda3/envs/bioinfo/bin [19:56:22] Looking for 'aragorn' - found /public/home/zhujiang/anaconda3/envs/bioinfo/bin/aragorn [19:56:22] Determined aragorn version is 1.2 [19:56:22] Looking for 'barrnap' - found /public/home/zhujiang/anaconda3/envs/bioinfo/bin/barrnap [19:56:23] Determined barrnap version is 0.9 [19:56:23] Looking for 'blastp' - found /public/home/zhujiang/crp/dede/ncbi-blast-2.2.30+/bin/blastp [19:56:23] Determined blastp version is 2.2 [19:56:23] Looking for 'cmpress' - found /public/home/zhujiang/anaconda3/envs/bioinfo/bin/cmpress [19:56:23] Determined cmpress version is 1.1 [19:56:23] Looking for 'cmscan' - found /public/home/zhujiang/anaconda3/envs/bioinfo/bin/cmscan [19:56:23] Determined cmscan version is 1.1 [19:56:23] Looking for 'egrep' - found /usr/bin/egrep [19:56:23] Looking for 'find' - found /usr/bin/find [19:56:23] Looking for 'grep' - found /usr/bin/grep [19:56:23] Looking for 'hmmpress' - found /public/home/zhujiang/anaconda3/envs/bioinfo/bin/hmmpress [19:56:23] Determined hmmpress version is 3.4 [19:56:23] Looking for 'hmmscan' - found /public/home/zhujiang/anaconda3/envs/bioinfo/bin/hmmscan [19:56:23] Determined hmmscan version is 3.4 [19:56:23] Looking for 'java' - found /public/home/zhujiang/anaconda3/envs/bioinfo/bin/java [19:56:23] Looking for 'less' - found /usr/bin/less [19:56:23] Looking for 'makeblastdb' - found /public/home/zhujiang/crp/dede/ncbi-blast-2.2.30+/bin/m [19:56:23] Determined makeblastdb version is 2.2 [19:56:23] Looking for 'minced' - found /public/home/zhujiang/anaconda3/envs/bioinfo/bin/minced [19:56:23] Determined minced version is 4.2 [19:56:23] Looking for 'parallel' - found /public/home/zhujiang/anaconda3/envs/bioinfo/bin/parallel [19:56:23] Determined parallel version is 20240322 [19:56:23] Looking for 'prodigal' - found /public/home/zhujiang/anaconda3/envs/bioinfo/bin/prodigal [19:56:23] Determined prodigal version is 2.6 [19:56:23] Looking for 'prokka-genbank_to_fasta_db' - found /public/home/zhujiang/anaconda3/envs/bio [19:56:23] Looking for 'sed' - found /usr/bin/sed [19:56:23] Looking for 'tbl2asn' - found /public/home/zhujiang/anaconda3/envs/bioinfo/bin/tbl2asn [19:56:23] Determined tbl2asn version is 25.8 [19:56:23] Using genetic code table 11. [19:56:23] Loading and checking input file: ./fasta_example_genomic.fna [19:56:23] Wrote 1 contigs totalling 4641652 bp. [19:56:23] Predicting tRNAs and tmRNAs [19:56:23] Running: aragorn -l -gc11 -w PROKKA_04122024/PROKKA_04122024.fna [19:56:25] 1 tRNA-Ile [225381,225457] 35 (gat) [19:56:25] 2 tRNA-Ala [225500,225575] 34 (tgc) [19:56:25] 3 tRNA-Asp [228928,229004] 35 (gtc) [19:56:25] 4 tRNA-Asp [236931,237007] 35 (gtc) [19:56:25] 5 tRNA-Thr [262871,262946] 34 (cgt) [19:56:25] 6 tRNA-Ser [345334,345414] 38 (gga) [19:56:25] 7 tRNA-Arg [564723,564799] 35 (tct) [19:56:25] 8 tRNA-Gln c[696430,696504] 33 (ctg) [19:56:25] 9 tRNA-Gln c[696542,696616] 33 (ctg) [19:56:25] 10 tRNA-Met c[696664,696740] 35 (cat) [19:56:25] 11 tRNA-Gln c[696756,696830] 33 (ttg) [19:56:25] 12 tRNA-Gln c[696865,696939] 33 (ttg) [19:56:25] 13 tRNA-Leu c[696963,697047] 35 (tag) [19:56:25] 14 tRNA-Met c[697057,697133] 35 (cat) [19:56:25] 15 tRNA-Lys [780554,780629] 34 (ttt) [19:56:25] 16 tRNA-Val [780765,780840] 34 (tac) [19:56:25] 17 tRNA-Lys [780843,780918] 34 (ttt) [19:56:25] 18 tRNA-Val [781068,781143] 34 (tac) [19:56:25] 19 tRNA-Lys [781147,781222] 34 (ttt) [19:56:25] 20 tRNA-Lys [781369,781444] 34 (ttt) [19:56:25] 21 tRNA-Lys [781577,781652] 34 (ttt) [19:56:25] 22 tRNA-Ser c[925884,925971] 35 (gga) [19:56:25] 23 tRNA-Ser c[1031625,1031712] 35 (tga) [19:56:25] 24 tRNA-Ser c[1097565,1097652] 35 (gga) [19:56:25] 25 tRNA-Tyr c[1287244,1287328] 35 (gta) [19:56:25] 26 tRNA-Tyr c[1287538,1287622] 35 (gta) [19:56:25] 27 tRNA-Val [1746435,1746511] 35 (gac) [19:56:25] 28 tRNA-Val [1746516,1746592] 35 (gac) [19:56:25] 29 tRNA-Leu c[1991815,1991901] 35 (taa) [19:56:25] 30 tRNA-Cys c[1991914,1991987] 33 (gca) [19:56:25] 31 tRNA-Gly c[1992042,1992117] 34 (gcc) [19:56:25] 32 tRNA-Ser c[2043468,2043557] 35 (cga) [19:56:25] 33 tRNA-Asn [2044549,2044624] 34 (gtt) [19:56:25] 34 tRNA-Asn c[2058027,2058102] 34 (gtt) [19:56:25] 35 tRNA-Asn [2059851,2059926] 34 (gtt) [19:56:25] 36 tRNA-Asn [2062260,2062335] 34 (gtt) [19:56:25] 37 tRNA-Pro [2286211,2286287] 35 (ggg) [19:56:25] 38 tRNA-Arg [2466309,2466383] 34 (cct) [19:56:25] 39 tRNA-Ala c[2518041,2518116] 34 (ggc) [19:56:25] 40 tRNA-Ala c[2518156,2518231] 34 (ggc) [19:56:25] 41 tRNA-Val [2520931,2521006] 34 (tac) [19:56:25] 42 tRNA-Val [2521051,2521126] 34 (tac) [19:56:25] 43 tRNA-Val [2521173,2521248] 34 (tac) [19:56:25] 44 tRNA-Lys [2521253,2521328] 34 (ttt) [19:56:25] 45 tRNA-Glu c[2729369,2729444] 35 (ttc) [19:56:25] 46 tmRNA [2755593,2755955] 90,125 ANDENYALAA** [19:56:25] 47 tRNA-Met c[2785762,2785837] 34 (cat) [19:56:25] 48 tRNA-Arg c[2817784,2817860] 35 (acg) [19:56:25] 49 tRNA-Arg c[2818059,2818135] 35 (acg) [19:56:25] 50 tRNA-Arg c[2818198,2818274] 35 (acg) [19:56:25] 51 tRNA-Arg [2818458,2818529] 34 (tcg) [19:56:25] 52 tRNA-Arg c[2818473,2818549] 35 (acg) [19:56:25] 53 tRNA-Ser c[2818553,2818645] 35 (gct) [19:56:25] 54 tRNA-Met [2947387,2947463] 35 (cat) [19:56:25] 55 tRNA-Met [2947497,2947573] 35 (cat) [19:56:25] 56 tRNA-Met [2947607,2947683] 35 (cat) [19:56:25] 57 tRNA-Gly c[2998984,2999057] 33 (ccc) [19:56:25] 58 tRNA-Phe [3110366,3110441] 34 (gaa) [19:56:25] 59 tRNA-Met [3215598,3215673] 34 (cat) [19:56:25] 60 tRNA-Met c[3318213,3318289] 35 (cat) [19:56:25] 61 tRNA-Leu c[3322072,3322158] 35 (gag) [19:56:25] 62 tRNA-Thr c[3423580,3423655] 34 (ggt) [19:56:25] 63 tRNA-Ala c[3426958,3427033] 34 (tgc) [19:56:25] 64 tRNA-Ile c[3427076,3427152] 35 (gat) [19:56:25] 65 tRNA-Pro c[3708616,3708692] 35 (cgg) [19:56:25] 66 tRNA-SeC [3836222,3836316] 35 (tca) [19:56:25] 67 tRNA-Glu [3943435,3943510] 35 (ttc) [19:56:25] 68 tRNA-Asp [3946872,3946948] 35 (gtc) [19:56:25] 69 tRNA-Trp [3946957,3947032] 34 (cca) [19:56:25] 70 tRNA-Arg [3982375,3982451] 35 (ccg) [19:56:25] 71 tRNA-His [3982510,3982585] 34 (gtg) [19:56:25] 72 tRNA-Leu [3982606,3982692] 35 (cag) [19:56:25] 73 tRNA-Pro [3982735,3982811] 35 (tgg) [19:56:25] 74 tRNA-Ile [4037141,4037217] 35 (gat) [19:56:25] 75 tRNA-Ala [4037260,4037335] 34 (tgc) [19:56:25] 76 tRNA-Glu [4168372,4168447] 35 (ttc) [19:56:25] 77 tRNA-Thr [4175388,4175463] 34 (tgt) [19:56:25] 78 tRNA-Tyr [4175472,4175556] 35 (gta) [19:56:25] 79 tRNA-Gly [4175673,4175747] 34 (tcc) [19:56:25] 80 tRNA-Thr [4175754,4175829] 34 (ggt) [19:56:25] 81 tRNA-Glu [4209774,4209849] 35 (ttc) [19:56:25] 82 tRNA-Phe c[4362551,4362626] 34 (gaa) [19:56:25] 83 tRNA-Gly [4392360,4392435] 34 (gcc) [19:56:25] 84 tRNA-Gly [4392472,4392547] 34 (gcc) [19:56:25] 85 tRNA-Gly [4392583,4392658] 34 (gcc) [19:56:25] 86 tRNA-Leu [4496405,4496489] 35 (caa) [19:56:25] 87 tRNA-Leu c[4606079,4606165] 35 (cag) [19:56:25] 88 tRNA-Leu c[4606200,4606286] 35 (cag) [19:56:25] 89 tRNA-Leu c[4606315,4606401] 35 (cag) [19:56:25] Found 89 tRNAs [19:56:25] Predicting Ribosomal RNAs [19:56:25] Running Barrnap with 8 threads [19:56:27] 1 NC_000913.3 223774 16S ribosomal RNA [19:56:27] 2 NC_000913.3 225761 23S ribosomal RNA [19:56:27] 3 NC_000913.3 228760 5S ribosomal RNA [19:56:27] 4 NC_000913.3 2726074 5S ribosomal RNA [19:56:27] 5 NC_000913.3 2726282 23S ribosomal RNA [19:56:27] 6 NC_000913.3 2729617 16S ribosomal RNA [19:56:27] 7 NC_000913.3 3423428 5S ribosomal RNA [19:56:27] 8 NC_000913.3 3423673 5S ribosomal RNA [19:56:27] 9 NC_000913.3 3423881 23S ribosomal RNA [19:56:27] 10 NC_000913.3 3427222 16S ribosomal RNA [19:56:27] 11 NC_000913.3 3941811 16S ribosomal RNA [19:56:27] 12 NC_000913.3 3943706 23S ribosomal RNA [19:56:27] 13 NC_000913.3 3946704 5S ribosomal RNA [19:56:27] 14 NC_000913.3 4035534 16S ribosomal RNA [19:56:27] 15 NC_000913.3 4037521 23S ribosomal RNA [19:56:27] 16 NC_000913.3 4040521 5S ribosomal RNA [19:56:27] 17 NC_000913.3 4166662 16S ribosomal RNA [19:56:27] 18 NC_000913.3 4168643 23S ribosomal RNA [19:56:27] 19 NC_000913.3 4171641 5S ribosomal RNA [19:56:27] 20 NC_000913.3 4208150 16S ribosomal RNA [19:56:27] 21 NC_000913.3 4210045 23S ribosomal RNA [19:56:27] 22 NC_000913.3 4213044 5S ribosomal RNA [19:56:27] Found 22 rRNAs [19:56:27] Skipping ncRNA search, enable with --rfam if desired. [19:56:27] Total of 110 tRNA + rRNA features [19:56:27] Searching for CRISPR repeats [19:56:28] CRISPR1 NC_000913.3 2877701 with 13 spacers [19:56:28] CRISPR2 NC_000913.3 2904014 with 7 spacers [19:56:28] Found 2 CRISPRs [19:56:28] Predicting coding sequences [19:56:28] Contigs total 4641652 bp, so using single mode [19:56:28] Running: prodigal -i PROKKA_04122024/PROKKA_04122024.fna -c -m -g 11 -p single -f sco - [19:56:37] Excluding CDS which overlaps existing RNA (rRNA) at NC_000913.3:224958..225212 on + stran [19:56:39] Excluding CDS which overlaps existing RNA (tRNA) at NC_000913.3:1287065..1287631 on + str [19:56:41] Excluding CDS which overlaps existing RNA (rRNA) at NC_000913.3:2727331..2727450 on - str [19:56:41] Excluding CDS which overlaps existing RNA (rRNA) at NC_000913.3:2729716..2729970 on - str [19:56:41] Excluding CDS which overlaps existing RNA (tRNA) at NC_000913.3:2817923..2818393 on + str [19:56:42] Excluding CDS which overlaps existing RNA (tRNA) at NC_000913.3:3423503..3423826 on + str [19:56:42] Excluding CDS which overlaps existing RNA (rRNA) at NC_000913.3:3427321..3427575 on - str [19:56:43] Excluding CDS which overlaps existing RNA (rRNA) at NC_000913.3:3942995..3943249 on + str [19:56:43] Excluding CDS which overlaps existing RNA (rRNA) at NC_000913.3:4036718..4036972 on + str [19:56:43] Excluding CDS which overlaps existing RNA (rRNA) at NC_000913.3:4167846..4168100 on + str [19:56:43] Excluding CDS which overlaps existing RNA (rRNA) at NC_000913.3:4170375..4170494 on + str [19:56:43] Excluding CDS which overlaps existing RNA (rRNA) at NC_000913.3:4209334..4209588 on + str [19:56:43] Excluding CDS which overlaps existing RNA (rRNA) at NC_000913.3:4211777..4211896 on + str [19:56:43] Found 4305 CDS [19:56:43] Connecting features back to sequences [19:56:43] Not using genus-specific database. Try --usegenus to enable it. [19:56:43] Annotating CDS, please be patient. [19:56:43] Will use 8 CPUs for similarity searching. [19:56:44] There are still 4305 unannotated CDS left (started with 4305) [19:56:44] Will use blast to search against /public/home/zhujiang/anaconda3/envs/bioinfo/db/kingdom/ [19:56:44] Running: cat PROKKA_04122024/IS.faa | parallel --gnu --plain -j 8 --block 86286 --recst teria/IS -evalue 1e-30 -qcov_hsp_perc 90 -num_threads 1 -num_descriptions 1 -num_alignments 1 -seg n [19:56:57] Deleting unwanted file: PROKKA_04122024/IS.faa [19:56:57] Deleting unwanted file: PROKKA_04122024/IS.blast [19:56:58] There are still 4229 unannotated CDS left (started with 4305) [19:56:58] Will use blast to search against /public/home/zhujiang/anaconda3/envs/bioinfo/db/kingdom/ [19:56:58] Running: cat PROKKA_04122024/AMR.faa | parallel --gnu --plain -j 8 --block 85153 --recs cteria/AMR -evalue 9.99999999999999e-301 -qcov_hsp_perc 90 -num_threads 1 -num_descriptions 1 -num_a [19:57:08] Deleting unwanted file: PROKKA_04122024/AMR.faa [19:57:08] Deleting unwanted file: PROKKA_04122024/AMR.blast [19:57:09] There are still 4229 unannotated CDS left (started with 4305) [19:57:09] Will use blast to search against /public/home/zhujiang/anaconda3/envs/bioinfo/db/kingdom/ [19:57:09] Running: cat PROKKA_04122024/sprot.faa | parallel --gnu --plain -j 8 --block 85153 --re Bacteria/sprot -evalue 1e-09 -qcov_hsp_perc 80 -num_threads 1 -num_descriptions 1 -num_alignments 1 [19:57:52] Could not run command: cat PROKKA_04122024/sprot.faa | parallel --gnu --plain -j 8 --bl fo/db/kingdom/Bacteria/sprot -evalue 1e-09 -qcov_hsp_perc 80 -num_threads 1 -num_descriptions 1 -num 求大神指导，跑着跑着出问题了
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(bioinfo) [zhujiang@login1 example]$ prokka ./fasta_example_genomic.fna
[19:52:08] This is prokka 1.13.3
[19:52:08] Written by Torsten Seemann [email protected]
[19:52:08] Homepage is https://github.com/tseemann/prokka
[19:52:08] Local time is Fri Apr 12 19:52:08 2024
[19:52:08] You are zhujiang
[19:52:08] Operating system is linux
[19:52:08] You have BioPerl 1.007002
[19:52:08] System has 52 cores.
[19:52:08] Will use maximum of 8 cores.
[19:52:08] Annotating as >>> Bacteria <<<
[19:52:08] Generating locus_tag from './fasta_example_genomic.fna' contents.
[19:52:08] Setting --locustag PICPPNBC from MD5 92c997bcd88e983ffdb21b2712ed3736
[19:52:08] Creating new output folder: PROKKA_04122024
[19:52:08] Running: mkdir -p PROKKA_04122024
[19:52:08] Using filename prefix: PROKKA_04122024.XXX
[19:52:08] Setting HMMER_NCPU=1
[19:52:08] Writing log to: PROKKA_04122024/PROKKA_04122024.log
[19:52:08] Command: /public/home/zhujiang/anaconda3/envs/bioinfo/bin/prokka ./fasta_example_genomic.fna
[19:52:08] Appending to PATH: /public/home/zhujiang/anaconda3/envs/bioinfo/bin
[19:52:08] Looking for 'aragorn' - found /public/home/zhujiang/anaconda3/envs/bioinfo/bin/aragorn
[19:52:08] Determined aragorn version is 1.2
[19:52:08] Looking for 'barrnap' - found /public/home/zhujiang/anaconda3/envs/bioinfo/bin/barrnap
[19:52:09] Determined barrnap version is 0.9
[19:52:09] Looking for 'blastp' - found /public/home/zhujiang/anaconda3/envs/bioinfo/bin/blastp
[19:52:20] Determined blastp version is 2.15
[19:52:20] Prokka needs blastp 2.2 or higher. Please upgrade and try again.
(bioinfo) [zhujiang@login1 example]$ export PATH=/public/home/zhujiang/crp/dede/ncbi-blast-2.2.30+/b
(bioinfo) [zhujiang@login1 example]$ rm -rf PROKKA_04122024
(bioinfo) [zhujiang@login1 example]$ prokka ./fasta_example_genomic.fna
[19:53:26] This is prokka 1.13.3
[19:53:26] Written by Torsten Seemann [email protected]
[19:53:26] Homepage is https://github.com/tseemann/prokka
[19:53:26] Local time is Fri Apr 12 19:53:26 2024
[19:53:26] You are zhujiang
[19:53:26] Operating system is linux
[19:53:26] You have BioPerl 1.007002
[19:53:26] System has 52 cores.
[19:53:26] Will use maximum of 8 cores.
[19:53:26] Annotating as >>> Bacteria <<<
[19:53:26] Generating locus_tag from './fasta_example_genomic.fna' contents.
[19:53:26] Setting --locustag PICPPNBC from MD5 92c997bcd88e983ffdb21b2712ed3736
[19:53:26] Creating new output folder: PROKKA_04122024
[19:53:26] Running: mkdir -p PROKKA_04122024
[19:53:26] Using filename prefix: PROKKA_04122024.XXX
[19:53:26] Setting HMMER_NCPU=1
[19:53:26] Writing log to: PROKKA_04122024/PROKKA_04122024.log
[19:53:26] Command: /public/home/zhujiang/anaconda3/envs/bioinfo/bin/prokka ./fasta_example_genomic.
[19:53:26] Appending to PATH: /public/home/zhujiang/anaconda3/envs/bioinfo/bin
[19:53:26] Looking for 'aragorn' - found /public/home/zhujiang/anaconda3/envs/bioinfo/bin/aragorn
[19:53:26] Determined aragorn version is 1.2
[19:53:26] Looking for 'barrnap' - found /public/home/zhujiang/anaconda3/envs/bioinfo/bin/barrnap
[19:53:26] Determined barrnap version is 0.9
[19:53:26] Looking for 'blastp' - found /public/home/zhujiang/crp/dede/ncbi-blast-2.2.30+/bin/blastp
[19:53:26] Determined blastp version is 2.2
[19:53:26] Looking for 'cmpress' - found /public/home/zhujiang/anaconda3/envs/bioinfo/bin/cmpress
[19:53:26] Determined cmpress version is 1.1
[19:53:26] Looking for 'cmscan' - found /public/home/zhujiang/anaconda3/envs/bioinfo/bin/cmscan
[19:53:27] Determined cmscan version is 1.1
[19:53:27] Looking for 'egrep' - found /usr/bin/egrep
[19:53:27] Looking for 'find' - found /usr/bin/find
[19:53:27] Looking for 'grep' - found /usr/bin/grep
[19:53:27] Looking for 'hmmpress' - found /public/home/zhujiang/anaconda3/envs/bioinfo/bin/hmmpress
[19:53:27] Determined hmmpress version is 3.4
[19:53:27] Looking for 'hmmscan' - found /public/home/zhujiang/anaconda3/envs/bioinfo/bin/hmmscan
[19:53:27] Determined hmmscan version is 3.4
[19:53:27] Looking for 'java' - found /public/home/zhujiang/anaconda3/envs/bioinfo/bin/java
[19:53:27] Looking for 'less' - found /usr/bin/less
[19:53:27] Looking for 'makeblastdb' - found /public/home/zhujiang/crp/dede/ncbi-blast-2.2.30+/bin/m
[19:53:27] Determined makeblastdb version is 2.2
[19:53:27] Looking for 'minced' - found /public/home/zhujiang/anaconda3/envs/bioinfo/bin/minced
[19:53:27] Determined minced version is 4.2
[19:53:27] Looking for 'parallel' - found /public/home/zhujiang/anaconda3/envs/bioinfo/bin/parallel
[19:53:27] Determined parallel version is 20240322
[19:53:27] Looking for 'prodigal' - found /public/home/zhujiang/anaconda3/envs/bioinfo/bin/prodigal
[19:53:27] Determined prodigal version is 2.6
[19:53:27] Looking for 'prokka-genbank_to_fasta_db' - found /public/home/zhujiang/anaconda3/envs/bio
[19:53:27] Looking for 'sed' - found /usr/bin/sed
[19:53:27] Looking for 'tbl2asn' - found /public/home/zhujiang/anaconda3/envs/bioinfo/bin/tbl2asn
[19:53:27] Determined tbl2asn version is 25.8
[19:53:27] Using genetic code table 11.
[19:53:27] Loading and checking input file: ./fasta_example_genomic.fna
[19:53:28] Wrote 1 contigs totalling 4641652 bp.
[19:53:28] Predicting tRNAs and tmRNAs
[19:53:28] Running: aragorn -l -gc11 -w PROKKA_04122024/PROKKA_04122024.fna
[19:53:29] 1 tRNA-Ile [225381,225457] 35 (gat)
[19:53:29] 2 tRNA-Ala [225500,225575] 34 (tgc)
[19:53:29] 3 tRNA-Asp [228928,229004] 35 (gtc)
[19:53:29] 4 tRNA-Asp [236931,237007] 35 (gtc)
[19:53:29] 5 tRNA-Thr [262871,262946] 34 (cgt)
[19:53:29] 6 tRNA-Ser [345334,345414] 38 (gga)
[19:53:29] 7 tRNA-Arg [564723,564799] 35 (tct)
[19:53:29] 8 tRNA-Gln c[696430,696504] 33 (ctg)
[19:53:29] 9 tRNA-Gln c[696542,696616] 33 (ctg)
[19:53:29] 10 tRNA-Met c[696664,696740] 35 (cat)
[19:53:29] 11 tRNA-Gln c[696756,696830] 33 (ttg)
[19:53:29] 12 tRNA-Gln c[696865,696939] 33 (ttg)
[19:53:29] 13 tRNA-Leu c[696963,697047] 35 (tag)
[19:53:29] 14 tRNA-Met c[697057,697133] 35 (cat)
[19:53:29] 15 tRNA-Lys [780554,780629] 34 (ttt)
[19:53:29] 16 tRNA-Val [780765,780840] 34 (tac)
[19:53:29] 17 tRNA-Lys [780843,780918] 34 (ttt)
[19:53:29] 18 tRNA-Val [781068,781143] 34 (tac)
[19:53:29] 19 tRNA-Lys [781147,781222] 34 (ttt)
[19:53:29] 20 tRNA-Lys [781369,781444] 34 (ttt)
[19:53:29] 21 tRNA-Lys [781577,781652] 34 (ttt)
[19:53:29] 22 tRNA-Ser c[925884,925971] 35 (gga)
[19:53:29] 23 tRNA-Ser c[1031625,1031712] 35 (tga)
[19:53:29] 24 tRNA-Ser c[1097565,1097652] 35 (gga)
[19:53:29] 25 tRNA-Tyr c[1287244,1287328] 35 (gta)
[19:53:29] 26 tRNA-Tyr c[1287538,1287622] 35 (gta)
[19:53:29] 27 tRNA-Val [1746435,1746511] 35 (gac)
[19:53:29] 28 tRNA-Val [1746516,1746592] 35 (gac)
[19:53:29] 29 tRNA-Leu c[1991815,1991901] 35 (taa)
[19:53:29] 30 tRNA-Cys c[1991914,1991987] 33 (gca)
[19:53:29] 31 tRNA-Gly c[1992042,1992117] 34 (gcc)
[19:53:29] 32 tRNA-Ser c[2043468,2043557] 35 (cga)
[19:53:29] 33 tRNA-Asn [2044549,2044624] 34 (gtt)
[19:53:29] 34 tRNA-Asn c[2058027,2058102] 34 (gtt)
[19:53:29] 35 tRNA-Asn [2059851,2059926] 34 (gtt)
[19:53:29] 36 tRNA-Asn [2062260,2062335] 34 (gtt)
[19:53:29] 37 tRNA-Pro [2286211,2286287] 35 (ggg)
[19:53:29] 38 tRNA-Arg [2466309,2466383] 34 (cct)
[19:53:29] 39 tRNA-Ala c[2518041,2518116] 34 (ggc)
[19:53:29] 40 tRNA-Ala c[2518156,2518231] 34 (ggc)
[19:53:29] 41 tRNA-Val [2520931,2521006] 34 (tac)
[19:53:29] 42 tRNA-Val [2521051,2521126] 34 (tac)
[19:53:29] 43 tRNA-Val [2521173,2521248] 34 (tac)
[19:53:29] 44 tRNA-Lys [2521253,2521328] 34 (ttt)
[19:53:29] 45 tRNA-Glu c[2729369,2729444] 35 (ttc)
[19:53:29] 46 tmRNA [2755593,2755955] 90,125 ANDENYALAA**
[19:53:29] 47 tRNA-Met c[2785762,2785837] 34 (cat)
[19:53:29] 48 tRNA-Arg c[2817784,2817860] 35 (acg)
[19:53:29] 49 tRNA-Arg c[2818059,2818135] 35 (acg)
[19:53:29] 50 tRNA-Arg c[2818198,2818274] 35 (acg)
[19:53:29] 51 tRNA-Arg [2818458,2818529] 34 (tcg)
[19:53:29] 52 tRNA-Arg c[2818473,2818549] 35 (acg)
[19:53:29] 53 tRNA-Ser c[2818553,2818645] 35 (gct)
[19:53:29] 54 tRNA-Met [2947387,2947463] 35 (cat)
[19:53:29] 55 tRNA-Met [2947497,2947573] 35 (cat)
[19:53:29] 56 tRNA-Met [2947607,2947683] 35 (cat)
[19:53:29] 57 tRNA-Gly c[2998984,2999057] 33 (ccc)
[19:53:29] 58 tRNA-Phe [3110366,3110441] 34 (gaa)
[19:53:29] 59 tRNA-Met [3215598,3215673] 34 (cat)
[19:53:29] 60 tRNA-Met c[3318213,3318289] 35 (cat)
[19:53:29] 61 tRNA-Leu c[3322072,3322158] 35 (gag)
[19:53:29] 62 tRNA-Thr c[3423580,3423655] 34 (ggt)
[19:53:29] 63 tRNA-Ala c[3426958,3427033] 34 (tgc)
[19:53:29] 64 tRNA-Ile c[3427076,3427152] 35 (gat)
[19:53:29] 65 tRNA-Pro c[3708616,3708692] 35 (cgg)
[19:53:29] 66 tRNA-SeC [3836222,3836316] 35 (tca)
[19:53:29] 67 tRNA-Glu [3943435,3943510] 35 (ttc)
[19:53:29] 68 tRNA-Asp [3946872,3946948] 35 (gtc)
[19:53:29] 69 tRNA-Trp [3946957,3947032] 34 (cca)
[19:53:29] 70 tRNA-Arg [3982375,3982451] 35 (ccg)
[19:53:29] 71 tRNA-His [3982510,3982585] 34 (gtg)
[19:53:29] 72 tRNA-Leu [3982606,3982692] 35 (cag)
[19:53:29] 73 tRNA-Pro [3982735,3982811] 35 (tgg)
[19:53:29] 74 tRNA-Ile [4037141,4037217] 35 (gat)
[19:53:29] 75 tRNA-Ala [4037260,4037335] 34 (tgc)
[19:53:29] 76 tRNA-Glu [4168372,4168447] 35 (ttc)
[19:53:29] 77 tRNA-Thr [4175388,4175463] 34 (tgt)
[19:53:29] 78 tRNA-Tyr [4175472,4175556] 35 (gta)
[19:53:29] 79 tRNA-Gly [4175673,4175747] 34 (tcc)
[19:53:29] 80 tRNA-Thr [4175754,4175829] 34 (ggt)
[19:53:29] 81 tRNA-Glu [4209774,4209849] 35 (ttc)
[19:53:29] 82 tRNA-Phe c[4362551,4362626] 34 (gaa)
[19:53:29] 83 tRNA-Gly [4392360,4392435] 34 (gcc)
[19:53:29] 84 tRNA-Gly [4392472,4392547] 34 (gcc)
[19:53:29] 85 tRNA-Gly [4392583,4392658] 34 (gcc)
[19:53:29] 86 tRNA-Leu [4496405,4496489] 35 (caa)
[19:53:29] 87 tRNA-Leu c[4606079,4606165] 35 (cag)
[19:53:29] 88 tRNA-Leu c[4606200,4606286] 35 (cag)
[19:53:29] 89 tRNA-Leu c[4606315,4606401] 35 (cag)
[19:53:29] Found 89 tRNAs
[19:53:29] Predicting Ribosomal RNAs
[19:53:29] Running Barrnap with 8 threads
[19:53:32] 1 NC_000913.3 223774 16S ribosomal RNA
[19:53:32] 2 NC_000913.3 225761 23S ribosomal RNA
[19:53:32] 3 NC_000913.3 228760 5S ribosomal RNA
[19:53:32] 4 NC_000913.3 2726074 5S ribosomal RNA
[19:53:32] 5 NC_000913.3 2726282 23S ribosomal RNA
[19:53:32] 6 NC_000913.3 2729617 16S ribosomal RNA
[19:53:32] 7 NC_000913.3 3423428 5S ribosomal RNA
[19:53:32] 8 NC_000913.3 3423673 5S ribosomal RNA
[19:53:32] 9 NC_000913.3 3423881 23S ribosomal RNA
[19:53:32] 10 NC_000913.3 3427222 16S ribosomal RNA
[19:53:32] 11 NC_000913.3 3941811 16S ribosomal RNA
[19:53:32] 12 NC_000913.3 3943706 23S ribosomal RNA
[19:53:32] 13 NC_000913.3 3946704 5S ribosomal RNA
[19:53:32] 14 NC_000913.3 4035534 16S ribosomal RNA
[19:53:32] 15 NC_000913.3 4037521 23S ribosomal RNA
[19:53:32] 16 NC_000913.3 4040521 5S ribosomal RNA
[19:53:32] 17 NC_000913.3 4166662 16S ribosomal RNA
[19:53:32] 18 NC_000913.3 4168643 23S ribosomal RNA
[19:53:32] 19 NC_000913.3 4171641 5S ribosomal RNA
[19:53:32] 20 NC_000913.3 4208150 16S ribosomal RNA
[19:53:32] 21 NC_000913.3 4210045 23S ribosomal RNA
[19:53:32] 22 NC_000913.3 4213044 5S ribosomal RNA
[19:53:32] Found 22 rRNAs
[19:53:32] Skipping ncRNA search, enable with --rfam if desired.
[19:53:32] Total of 110 tRNA + rRNA features
[19:53:32] Searching for CRISPR repeats
[19:53:32] CRISPR1 NC_000913.3 2877701 with 13 spacers
[19:53:32] CRISPR2 NC_000913.3 2904014 with 7 spacers
[19:53:32] Found 2 CRISPRs
[19:53:32] Predicting coding sequences
[19:53:32] Contigs total 4641652 bp, so using single mode
[19:53:32] Running: prodigal -i PROKKA_04122024/PROKKA_04122024.fna -c -m -g 11 -p single -f sco -
[19:53:41] Excluding CDS which overlaps existing RNA (rRNA) at NC_000913.3:224958..225212 on + stran
[19:53:43] Excluding CDS which overlaps existing RNA (tRNA) at NC_000913.3:1287065..1287631 on + str
[19:53:45] Excluding CDS which overlaps existing RNA (rRNA) at NC_000913.3:2727331..2727450 on - str
[19:53:45] Excluding CDS which overlaps existing RNA (rRNA) at NC_000913.3:2729716..2729970 on - str
[19:53:45] Excluding CDS which overlaps existing RNA (tRNA) at NC_000913.3:2817923..2818393 on + str
[19:53:46] Excluding CDS which overlaps existing RNA (tRNA) at NC_000913.3:3423503..3423826 on + str
[19:53:46] Excluding CDS which overlaps existing RNA (rRNA) at NC_000913.3:3427321..3427575 on - str
[19:53:46] Excluding CDS which overlaps existing RNA (rRNA) at NC_000913.3:3942995..3943249 on + str
[19:53:47] Excluding CDS which overlaps existing RNA (rRNA) at NC_000913.3:4036718..4036972 on + str
[19:53:47] Excluding CDS which overlaps existing RNA (rRNA) at NC_000913.3:4167846..4168100 on + str
[19:53:47] Excluding CDS which overlaps existing RNA (rRNA) at NC_000913.3:4170375..4170494 on + str
[19:53:47] Excluding CDS which overlaps existing RNA (rRNA) at NC_000913.3:4209334..4209588 on + str
[19:53:47] Excluding CDS which overlaps existing RNA (rRNA) at NC_000913.3:4211777..4211896 on + str
[19:53:47] Found 4305 CDS
[19:53:47] Connecting features back to sequences
[19:53:47] Not using genus-specific database. Try --usegenus to enable it.
[19:53:47] Annotating CDS, please be patient.
[19:53:47] Will use 8 CPUs for similarity searching.
[19:53:48] There are still 4305 unannotated CDS left (started with 4305)
[19:53:48] Will use blast to search against /public/home/zhujiang/anaconda3/envs/bioinfo/db/kingdom/
[19:53:48] Running: cat PROKKA_04122024/IS.faa | parallel --gnu --plain -j 8 --block 86286 --recst
teria/IS -evalue 1e-30 -qcov_hsp_perc 90 -num_threads 1 -num_descriptions 1 -num_alignments 1 -seg n
[19:54:01] Deleting unwanted file: PROKKA_04122024/IS.faa
[19:54:01] Deleting unwanted file: PROKKA_04122024/IS.blast
[19:54:02] There are still 4229 unannotated CDS left (started with 4305)
[19:54:02] Will use blast to search against /public/home/zhujiang/anaconda3/envs/bioinfo/db/kingdom/
[19:54:02] Running: cat PROKKA_04122024/AMR.faa | parallel --gnu --plain -j 8 --block 85153 --recs
cteria/AMR -evalue 9.99999999999999e-301 -qcov_hsp_perc 90 -num_threads 1 -num_descriptions 1 -num_a
[19:54:12] Deleting unwanted file: PROKKA_04122024/AMR.faa
[19:54:12] Deleting unwanted file: PROKKA_04122024/AMR.blast
[19:54:13] There are still 4229 unannotated CDS left (started with 4305)
[19:54:13] Will use blast to search against /public/home/zhujiang/anaconda3/envs/bioinfo/db/kingdom/
[19:54:13] Running: cat PROKKA_04122024/sprot.faa | parallel --gnu --plain -j 8 --block 85153 --re
Bacteria/sprot -evalue 1e-09 -qcov_hsp_perc 80 -num_threads 1 -num_descriptions 1 -num_alignments 1
[19:54:55] Could not run command: cat PROKKA_04122024/sprot.faa | parallel --gnu --plain -j 8 --bl
fo/db/kingdom/Bacteria/sprot -evalue 1e-09 -qcov_hsp_perc 80 -num_threads 1 -num_descriptions 1 -num
(bioinfo) [zhujiang@login1 example]$ ll
total 4598
-rw-r--r-- 1 zhujiang lisuhua 4699745 Apr 1 22:52 fasta_example_genomic.fna
drwxr-xr-x 2 zhujiang lisuhua 8192 Apr 12 19:54 PROKKA_04122024
(bioinfo) [zhujiang@login1 example]$ cat PROKKA_04122024/sprot.faa | parallel --gnu --plain -j 8 --b
nfo/db/kingdom/Bacteria/sprot -evalue 1e-09 -qcov_hsp_perc 80 -num_threads 1 -num_descriptions 1 -nu
(bioinfo) [zhujiang@login1 example]$ rm -rf PROKKA_04122024
(bioinfo) [zhujiang@login1 example]$ prokka ./fasta_example_genomic.fna
[19:56:22] This is prokka 1.13.3
[19:56:22] Written by Torsten Seemann [email protected]
[19:56:22] Homepage is https://github.com/tseemann/prokka
[19:56:22] Local time is Fri Apr 12 19:56:22 2024
[19:56:22] You are zhujiang
[19:56:22] Operating system is linux
[19:56:22] You have BioPerl 1.007002
[19:56:22] System has 52 cores.
[19:56:22] Will use maximum of 8 cores.
[19:56:22] Annotating as >>> Bacteria <<<
[19:56:22] Generating locus_tag from './fasta_example_genomic.fna' contents.
[19:56:22] Setting --locustag PICPPNBC from MD5 92c997bcd88e983ffdb21b2712ed3736
[19:56:22] Creating new output folder: PROKKA_04122024
[19:56:22] Running: mkdir -p PROKKA_04122024
[19:56:22] Using filename prefix: PROKKA_04122024.XXX
[19:56:22] Setting HMMER_NCPU=1
[19:56:22] Writing log to: PROKKA_04122024/PROKKA_04122024.log
[19:56:22] Command: /public/home/zhujiang/anaconda3/envs/bioinfo/bin/prokka ./fasta_example_genomic.
[19:56:22] Appending to PATH: /public/home/zhujiang/anaconda3/envs/bioinfo/bin
[19:56:22] Looking for 'aragorn' - found /public/home/zhujiang/anaconda3/envs/bioinfo/bin/aragorn
[19:56:22] Determined aragorn version is 1.2
[19:56:22] Looking for 'barrnap' - found /public/home/zhujiang/anaconda3/envs/bioinfo/bin/barrnap
[19:56:23] Determined barrnap version is 0.9
[19:56:23] Looking for 'blastp' - found /public/home/zhujiang/crp/dede/ncbi-blast-2.2.30+/bin/blastp
[19:56:23] Determined blastp version is 2.2
[19:56:23] Looking for 'cmpress' - found /public/home/zhujiang/anaconda3/envs/bioinfo/bin/cmpress
[19:56:23] Determined cmpress version is 1.1
[19:56:23] Looking for 'cmscan' - found /public/home/zhujiang/anaconda3/envs/bioinfo/bin/cmscan
[19:56:23] Determined cmscan version is 1.1
[19:56:23] Looking for 'egrep' - found /usr/bin/egrep
[19:56:23] Looking for 'find' - found /usr/bin/find
[19:56:23] Looking for 'grep' - found /usr/bin/grep
[19:56:23] Looking for 'hmmpress' - found /public/home/zhujiang/anaconda3/envs/bioinfo/bin/hmmpress
[19:56:23] Determined hmmpress version is 3.4
[19:56:23] Looking for 'hmmscan' - found /public/home/zhujiang/anaconda3/envs/bioinfo/bin/hmmscan
[19:56:23] Determined hmmscan version is 3.4
[19:56:23] Looking for 'java' - found /public/home/zhujiang/anaconda3/envs/bioinfo/bin/java
[19:56:23] Looking for 'less' - found /usr/bin/less
[19:56:23] Looking for 'makeblastdb' - found /public/home/zhujiang/crp/dede/ncbi-blast-2.2.30+/bin/m
[19:56:23] Determined makeblastdb version is 2.2
[19:56:23] Looking for 'minced' - found /public/home/zhujiang/anaconda3/envs/bioinfo/bin/minced
[19:56:23] Determined minced version is 4.2
[19:56:23] Looking for 'parallel' - found /public/home/zhujiang/anaconda3/envs/bioinfo/bin/parallel
[19:56:23] Determined parallel version is 20240322
[19:56:23] Looking for 'prodigal' - found /public/home/zhujiang/anaconda3/envs/bioinfo/bin/prodigal
[19:56:23] Determined prodigal version is 2.6
[19:56:23] Looking for 'prokka-genbank_to_fasta_db' - found /public/home/zhujiang/anaconda3/envs/bio
[19:56:23] Looking for 'sed' - found /usr/bin/sed
[19:56:23] Looking for 'tbl2asn' - found /public/home/zhujiang/anaconda3/envs/bioinfo/bin/tbl2asn
[19:56:23] Determined tbl2asn version is 25.8
[19:56:23] Using genetic code table 11.
[19:56:23] Loading and checking input file: ./fasta_example_genomic.fna
[19:56:23] Wrote 1 contigs totalling 4641652 bp.
[19:56:23] Predicting tRNAs and tmRNAs
[19:56:23] Running: aragorn -l -gc11 -w PROKKA_04122024/PROKKA_04122024.fna
[19:56:25] 1 tRNA-Ile [225381,225457] 35 (gat)
[19:56:25] 2 tRNA-Ala [225500,225575] 34 (tgc)
[19:56:25] 3 tRNA-Asp [228928,229004] 35 (gtc)
[19:56:25] 4 tRNA-Asp [236931,237007] 35 (gtc)
[19:56:25] 5 tRNA-Thr [262871,262946] 34 (cgt)
[19:56:25] 6 tRNA-Ser [345334,345414] 38 (gga)
[19:56:25] 7 tRNA-Arg [564723,564799] 35 (tct)
[19:56:25] 8 tRNA-Gln c[696430,696504] 33 (ctg)
[19:56:25] 9 tRNA-Gln c[696542,696616] 33 (ctg)
[19:56:25] 10 tRNA-Met c[696664,696740] 35 (cat)
[19:56:25] 11 tRNA-Gln c[696756,696830] 33 (ttg)
[19:56:25] 12 tRNA-Gln c[696865,696939] 33 (ttg)
[19:56:25] 13 tRNA-Leu c[696963,697047] 35 (tag)
[19:56:25] 14 tRNA-Met c[697057,697133] 35 (cat)
[19:56:25] 15 tRNA-Lys [780554,780629] 34 (ttt)
[19:56:25] 16 tRNA-Val [780765,780840] 34 (tac)
[19:56:25] 17 tRNA-Lys [780843,780918] 34 (ttt)
[19:56:25] 18 tRNA-Val [781068,781143] 34 (tac)
[19:56:25] 19 tRNA-Lys [781147,781222] 34 (ttt)
[19:56:25] 20 tRNA-Lys [781369,781444] 34 (ttt)
[19:56:25] 21 tRNA-Lys [781577,781652] 34 (ttt)
[19:56:25] 22 tRNA-Ser c[925884,925971] 35 (gga)
[19:56:25] 23 tRNA-Ser c[1031625,1031712] 35 (tga)
[19:56:25] 24 tRNA-Ser c[1097565,1097652] 35 (gga)
[19:56:25] 25 tRNA-Tyr c[1287244,1287328] 35 (gta)
[19:56:25] 26 tRNA-Tyr c[1287538,1287622] 35 (gta)
[19:56:25] 27 tRNA-Val [1746435,1746511] 35 (gac)
[19:56:25] 28 tRNA-Val [1746516,1746592] 35 (gac)
[19:56:25] 29 tRNA-Leu c[1991815,1991901] 35 (taa)
[19:56:25] 30 tRNA-Cys c[1991914,1991987] 33 (gca)
[19:56:25] 31 tRNA-Gly c[1992042,1992117] 34 (gcc)
[19:56:25] 32 tRNA-Ser c[2043468,2043557] 35 (cga)
[19:56:25] 33 tRNA-Asn [2044549,2044624] 34 (gtt)
[19:56:25] 34 tRNA-Asn c[2058027,2058102] 34 (gtt)
[19:56:25] 35 tRNA-Asn [2059851,2059926] 34 (gtt)
[19:56:25] 36 tRNA-Asn [2062260,2062335] 34 (gtt)
[19:56:25] 37 tRNA-Pro [2286211,2286287] 35 (ggg)
[19:56:25] 38 tRNA-Arg [2466309,2466383] 34 (cct)
[19:56:25] 39 tRNA-Ala c[2518041,2518116] 34 (ggc)
[19:56:25] 40 tRNA-Ala c[2518156,2518231] 34 (ggc)
[19:56:25] 41 tRNA-Val [2520931,2521006] 34 (tac)
[19:56:25] 42 tRNA-Val [2521051,2521126] 34 (tac)
[19:56:25] 43 tRNA-Val [2521173,2521248] 34 (tac)
[19:56:25] 44 tRNA-Lys [2521253,2521328] 34 (ttt)
[19:56:25] 45 tRNA-Glu c[2729369,2729444] 35 (ttc)
[19:56:25] 46 tmRNA [2755593,2755955] 90,125 ANDENYALAA**
[19:56:25] 47 tRNA-Met c[2785762,2785837] 34 (cat)
[19:56:25] 48 tRNA-Arg c[2817784,2817860] 35 (acg)
[19:56:25] 49 tRNA-Arg c[2818059,2818135] 35 (acg)
[19:56:25] 50 tRNA-Arg c[2818198,2818274] 35 (acg)
[19:56:25] 51 tRNA-Arg [2818458,2818529] 34 (tcg)
[19:56:25] 52 tRNA-Arg c[2818473,2818549] 35 (acg)
[19:56:25] 53 tRNA-Ser c[2818553,2818645] 35 (gct)
[19:56:25] 54 tRNA-Met [2947387,2947463] 35 (cat)
[19:56:25] 55 tRNA-Met [2947497,2947573] 35 (cat)
[19:56:25] 56 tRNA-Met [2947607,2947683] 35 (cat)
[19:56:25] 57 tRNA-Gly c[2998984,2999057] 33 (ccc)
[19:56:25] 58 tRNA-Phe [3110366,3110441] 34 (gaa)
[19:56:25] 59 tRNA-Met [3215598,3215673] 34 (cat)
[19:56:25] 60 tRNA-Met c[3318213,3318289] 35 (cat)
[19:56:25] 61 tRNA-Leu c[3322072,3322158] 35 (gag)
[19:56:25] 62 tRNA-Thr c[3423580,3423655] 34 (ggt)
[19:56:25] 63 tRNA-Ala c[3426958,3427033] 34 (tgc)
[19:56:25] 64 tRNA-Ile c[3427076,3427152] 35 (gat)
[19:56:25] 65 tRNA-Pro c[3708616,3708692] 35 (cgg)
[19:56:25] 66 tRNA-SeC [3836222,3836316] 35 (tca)
[19:56:25] 67 tRNA-Glu [3943435,3943510] 35 (ttc)
[19:56:25] 68 tRNA-Asp [3946872,3946948] 35 (gtc)
[19:56:25] 69 tRNA-Trp [3946957,3947032] 34 (cca)
[19:56:25] 70 tRNA-Arg [3982375,3982451] 35 (ccg)
[19:56:25] 71 tRNA-His [3982510,3982585] 34 (gtg)
[19:56:25] 72 tRNA-Leu [3982606,3982692] 35 (cag)
[19:56:25] 73 tRNA-Pro [3982735,3982811] 35 (tgg)
[19:56:25] 74 tRNA-Ile [4037141,4037217] 35 (gat)
[19:56:25] 75 tRNA-Ala [4037260,4037335] 34 (tgc)
[19:56:25] 76 tRNA-Glu [4168372,4168447] 35 (ttc)
[19:56:25] 77 tRNA-Thr [4175388,4175463] 34 (tgt)
[19:56:25] 78 tRNA-Tyr [4175472,4175556] 35 (gta)
[19:56:25] 79 tRNA-Gly [4175673,4175747] 34 (tcc)
[19:56:25] 80 tRNA-Thr [4175754,4175829] 34 (ggt)
[19:56:25] 81 tRNA-Glu [4209774,4209849] 35 (ttc)
[19:56:25] 82 tRNA-Phe c[4362551,4362626] 34 (gaa)
[19:56:25] 83 tRNA-Gly [4392360,4392435] 34 (gcc)
[19:56:25] 84 tRNA-Gly [4392472,4392547] 34 (gcc)
[19:56:25] 85 tRNA-Gly [4392583,4392658] 34 (gcc)
[19:56:25] 86 tRNA-Leu [4496405,4496489] 35 (caa)
[19:56:25] 87 tRNA-Leu c[4606079,4606165] 35 (cag)
[19:56:25] 88 tRNA-Leu c[4606200,4606286] 35 (cag)
[19:56:25] 89 tRNA-Leu c[4606315,4606401] 35 (cag)
[19:56:25] Found 89 tRNAs
[19:56:25] Predicting Ribosomal RNAs
[19:56:25] Running Barrnap with 8 threads
[19:56:27] 1 NC_000913.3 223774 16S ribosomal RNA
[19:56:27] 2 NC_000913.3 225761 23S ribosomal RNA
[19:56:27] 3 NC_000913.3 228760 5S ribosomal RNA
[19:56:27] 4 NC_000913.3 2726074 5S ribosomal RNA
[19:56:27] 5 NC_000913.3 2726282 23S ribosomal RNA
[19:56:27] 6 NC_000913.3 2729617 16S ribosomal RNA
[19:56:27] 7 NC_000913.3 3423428 5S ribosomal RNA
[19:56:27] 8 NC_000913.3 3423673 5S ribosomal RNA
[19:56:27] 9 NC_000913.3 3423881 23S ribosomal RNA
[19:56:27] 10 NC_000913.3 3427222 16S ribosomal RNA
[19:56:27] 11 NC_000913.3 3941811 16S ribosomal RNA
[19:56:27] 12 NC_000913.3 3943706 23S ribosomal RNA
[19:56:27] 13 NC_000913.3 3946704 5S ribosomal RNA
[19:56:27] 14 NC_000913.3 4035534 16S ribosomal RNA
[19:56:27] 15 NC_000913.3 4037521 23S ribosomal RNA
[19:56:27] 16 NC_000913.3 4040521 5S ribosomal RNA
[19:56:27] 17 NC_000913.3 4166662 16S ribosomal RNA
[19:56:27] 18 NC_000913.3 4168643 23S ribosomal RNA
[19:56:27] 19 NC_000913.3 4171641 5S ribosomal RNA
[19:56:27] 20 NC_000913.3 4208150 16S ribosomal RNA
[19:56:27] 21 NC_000913.3 4210045 23S ribosomal RNA
[19:56:27] 22 NC_000913.3 4213044 5S ribosomal RNA
[19:56:27] Found 22 rRNAs
[19:56:27] Skipping ncRNA search, enable with --rfam if desired.
[19:56:27] Total of 110 tRNA + rRNA features
[19:56:27] Searching for CRISPR repeats
[19:56:28] CRISPR1 NC_000913.3 2877701 with 13 spacers
[19:56:28] CRISPR2 NC_000913.3 2904014 with 7 spacers
[19:56:28] Found 2 CRISPRs
[19:56:28] Predicting coding sequences
[19:56:28] Contigs total 4641652 bp, so using single mode
[19:56:28] Running: prodigal -i PROKKA_04122024/PROKKA_04122024.fna -c -m -g 11 -p single -f sco -
[19:56:37] Excluding CDS which overlaps existing RNA (rRNA) at NC_000913.3:224958..225212 on + stran
[19:56:39] Excluding CDS which overlaps existing RNA (tRNA) at NC_000913.3:1287065..1287631 on + str
[19:56:41] Excluding CDS which overlaps existing RNA (rRNA) at NC_000913.3:2727331..2727450 on - str
[19:56:41] Excluding CDS which overlaps existing RNA (rRNA) at NC_000913.3:2729716..2729970 on - str
[19:56:41] Excluding CDS which overlaps existing RNA (tRNA) at NC_000913.3:2817923..2818393 on + str
[19:56:42] Excluding CDS which overlaps existing RNA (tRNA) at NC_000913.3:3423503..3423826 on + str
[19:56:42] Excluding CDS which overlaps existing RNA (rRNA) at NC_000913.3:3427321..3427575 on - str
[19:56:43] Excluding CDS which overlaps existing RNA (rRNA) at NC_000913.3:3942995..3943249 on + str
[19:56:43] Excluding CDS which overlaps existing RNA (rRNA) at NC_000913.3:4036718..4036972 on + str
[19:56:43] Excluding CDS which overlaps existing RNA (rRNA) at NC_000913.3:4167846..4168100 on + str
[19:56:43] Excluding CDS which overlaps existing RNA (rRNA) at NC_000913.3:4170375..4170494 on + str
[19:56:43] Excluding CDS which overlaps existing RNA (rRNA) at NC_000913.3:4209334..4209588 on + str
[19:56:43] Excluding CDS which overlaps existing RNA (rRNA) at NC_000913.3:4211777..4211896 on + str
[19:56:43] Found 4305 CDS
[19:56:43] Connecting features back to sequences
[19:56:43] Not using genus-specific database. Try --usegenus to enable it.
[19:56:43] Annotating CDS, please be patient.
[19:56:43] Will use 8 CPUs for similarity searching.
[19:56:44] There are still 4305 unannotated CDS left (started with 4305)
[19:56:44] Will use blast to search against /public/home/zhujiang/anaconda3/envs/bioinfo/db/kingdom/
[19:56:44] Running: cat PROKKA_04122024/IS.faa | parallel --gnu --plain -j 8 --block 86286 --recst
teria/IS -evalue 1e-30 -qcov_hsp_perc 90 -num_threads 1 -num_descriptions 1 -num_alignments 1 -seg n
[19:56:57] Deleting unwanted file: PROKKA_04122024/IS.faa
[19:56:57] Deleting unwanted file: PROKKA_04122024/IS.blast
[19:56:58] There are still 4229 unannotated CDS left (started with 4305)
[19:56:58] Will use blast to search against /public/home/zhujiang/anaconda3/envs/bioinfo/db/kingdom/
[19:56:58] Running: cat PROKKA_04122024/AMR.faa | parallel --gnu --plain -j 8 --block 85153 --recs
cteria/AMR -evalue 9.99999999999999e-301 -qcov_hsp_perc 90 -num_threads 1 -num_descriptions 1 -num_a
[19:57:08] Deleting unwanted file: PROKKA_04122024/AMR.faa
[19:57:08] Deleting unwanted file: PROKKA_04122024/AMR.blast
[19:57:09] There are still 4229 unannotated CDS left (started with 4305)
[19:57:09] Will use blast to search against /public/home/zhujiang/anaconda3/envs/bioinfo/db/kingdom/
[19:57:09] Running: cat PROKKA_04122024/sprot.faa | parallel --gnu --plain -j 8 --block 85153 --re
Bacteria/sprot -evalue 1e-09 -qcov_hsp_perc 80 -num_threads 1 -num_descriptions 1 -num_alignments 1
[19:57:52] Could not run command: cat PROKKA_04122024/sprot.faa | parallel --gnu --plain -j 8 --bl
fo/db/kingdom/Bacteria/sprot -evalue 1e-09 -qcov_hsp_perc 80 -num_threads 1 -num_descriptions 1 -num
求大神指导，跑着跑着出问题了
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