[15:07:04] Command: --force --outdir /home/yquentin/work/wolbachia/prokka/wWb --addgenes --prefix wWb --locustag wWb --species Wolbachia endosymbiont --strain wWb --compliant --quiet /home/yquentin/work/wolbachia/prokka/wWb.fna
[15:07:04] Looking for 'aragorn' - found /usr/local/bioinfo/bin/aragorn
[15:07:04] Determined aragorn version is 1.2
[15:07:04] Looking for 'barrnap' - found /usr/local/bioinfo/bin/barrnap
[15:07:04] Determined barrnap version is 0.5
[15:07:04] Looking for 'blastp' - found /usr/local/bioinfo/src/NCBI_Blast+/ncbi-blast-2.6.0+/bin/blastp
[15:07:04] Determined blastp version is 2.6
[15:07:04] Looking for 'cmpress' - found /usr/local/bioinfo/src/PROKKA/prokka-1.10/bin/../binaries/linux/cmpress
[15:07:04] Determined cmpress version is 1.1
[15:07:04] Looking for 'cmscan' - found /usr/local/bioinfo/src/PROKKA/prokka-1.10/bin/../binaries/linux/cmscan
[15:07:04] Determined cmscan version is 1.1
[15:07:04] Looking for 'egrep' - found /bin/egrep
[15:07:04] Looking for 'find' - found /bin/find
[15:07:04] Looking for 'grep' - found /bin/grep
[15:07:04] Looking for 'hmmpress' - found /usr/local/bioinfo/bin/hmmpress
[15:07:04] Determined hmmpress version is 3.1
[15:07:04] Looking for 'hmmscan' - found /usr/local/bioinfo/bin/hmmscan
[15:07:04] Determined hmmscan version is 3.1
[15:07:04] Looking for 'less' - found /usr/bin/less
[15:07:04] Looking for 'makeblastdb' - found /usr/local/bioinfo/src/NCBI_Blast+/ncbi-blast-2.6.0+/bin/makeblastdb
[15:07:04] Determined makeblastdb version is 2.6
[15:07:04] Looking for 'minced' - found /usr/local/bioinfo/bin/minced
[15:07:04] Determined minced version is 1.6
[15:07:04] Looking for 'parallel' - found /usr/local/bioinfo/bin/parallel
[15:07:05] Determined parallel version is 20141022
[15:07:05] Looking for 'prodigal' - found /usr/local/bioinfo/bin/prodigal
[15:07:05] Determined prodigal version is 2.6
[15:07:05] Looking for 'rnammer' - found /usr/local/bioinfo/bin/rnammer
[15:07:05] Determined rnammer version is 1.2
[15:07:05] Looking for 'sed' - found /bin/sed
[15:07:05] Looking for 'signalp' - found /usr/local/bioinfo/bin/signalp
[15:07:05] Determined signalp version is 4.1
[15:07:05] Looking for 'tbl2asn' - found /home/yquentin/save/scripts/tbl2asn
[15:07:05] Determined tbl2asn version is 25.3
[15:07:05] Using genetic code table 11.
[15:07:05] Loading and checking input file: /home/yquentin/work/wolbachia/prokka/wWb.fna
[15:07:06] Wrote 100 contigs
[15:07:06] Predicting tRNAs and tmRNAs
[15:07:06] Running: aragorn -gc11  -w \/home\/yquentin\/work\/wolbachia\/prokka\/wWb\/wWb\.fna
[15:07:06] 1 tRNA-Leu c[13191,13273] 35 (tag)
[15:07:06] 2 tRNA-Ser c[42896,42987] 36 (gct)
[15:07:06] 3 tRNA-Thr c[49556,49630] 35 (ggt)
[15:07:06] 4 tRNA-Met c[51969,52043] 35 (cat)
[15:07:06] 1 tRNA-His c[2424,2499] 34 (gtg)
[15:07:06] 1 tRNA-Ala c[12582,12655] 34 (tgc)
[15:07:06] 1 tRNA-Asn c[6968,7040] 33 (gtt)
[15:07:06] 1 tRNA-Leu c[34650,34732] 34 (caa)
[15:07:06] 1 tRNA-Val c[20106,20179] 34 (gac)
[15:07:06] 2 tRNA-Ser [33638,33725] 36 (gga)
[15:07:06] 1 tRNA-Arg [9207,9281] 35 (tct)
[15:07:06] 1 tRNA-Ser [5607,5695] 35 (tga)
[15:07:06] 1 tRNA-Met [15795,15868] 34 (cat)
[15:07:06] 2 tRNA-Asp [24897,24971] 35 (gtc)
[15:07:06] 1 tRNA-Ile c[16525,16601] 35 (gat)
[15:07:06] 2 tRNA-Glu c[27547,27620] 35 (ttc)
[15:07:06] 3 tRNA-Arg [35795,35870] 36 (acg)
[15:07:06] 1 tRNA-Pro [21592,21667] 36 (tgg)
[15:07:06] 1 tRNA-Arg [8977,9050] 35 (cct)
[15:07:06] 1 tRNA-Ser c[10625,10711] 35 (cag)
[15:07:06] 1 tRNA-Leu c[12428,12515] 35 (gag)
[15:07:06] 1 tRNA-Val [6215,6287] 34 (tac)
[15:07:06] 1 tRNA-Tyr [6401,6484] 36 (gta)
[15:07:06] 2 tRNA-Gly [6488,6560] 34 (tcc)
[15:07:06] 1 tRNA-Gly [1862,1935] 34 (gcc)
[15:07:06] 2 tmRNA* c[43806,44137] 194,241 ANDNFAAEGDVAVAA*
[15:07:06] 3 tRNA-Trp c[56135,56208] 34 (cca)
[15:07:06] 1 tRNA-Arg c[2607,2682] 36 (ccg)
[15:07:06] Found 28 tRNAs
[15:07:06] Predicting Ribosomal RNAs
[15:07:06] Running Barrnap with 8 threads
[15:07:09] 1 gnl|Prokka|wWb_contig000021 5719 5S ribosomal RNA
[15:07:09] 2 gnl|Prokka|wWb_contig000021 5894 23S ribosomal RNA
[15:07:09] 3 gnl|Prokka|wWb_contig000069 14105 16S ribosomal RNA
[15:07:09] Found 3 rRNAs
[15:07:09] Skipping ncRNA search, enable with --rfam if desired.
[15:07:09] Total of 30 tRNA + rRNA features
[15:07:09] Searching for CRISPR repeats
[15:07:10] Found 0 CRISPRs
[15:07:10] Predicting coding sequences
[15:07:10] Contigs total 1060850 bp, so using single mode
[15:07:10] Running: prodigal -i \/home\/yquentin\/work\/wolbachia\/prokka\/wWb\/wWb\.fna -c -m -g 11 -p single -f sco -q
[15:07:12] Excluding CDS which overlaps existing RNA (tRNA) at gnl|Prokka|wWb_contig000020:14503..15795 on + strand
[15:07:12] Found 1121 CDS
[15:07:12] Connecting features back to sequences
[15:07:12] Option --gram not specified, will NOT check for signal peptides.
[15:07:12] Not using genus-specific database. Try --usegenus to enable it.
[15:07:12] Annotating CDS, please be patient.
[15:07:12] Will use 8 CPUs for similarity searching.
[15:07:14] There are still 1121 unannotated CDS left (started with 1121)
[15:07:14] Will use blast to search against /usr/local/bioinfo/src/PROKKA/prokka-1.10/bin/../db/kingdom/Bacteria/sprot with 8 CPUs
[15:07:14] Running: cat \/home\/yquentin\/work\/wolbachia\/prokka\/wWb\/proteins\.faa | parallel --gnu -j 8 --block 16768 --recstart '>' --pipe blastp -query - -db /usr/local/bioinfo/src/PROKKA/prokka-1.10/bin/../db/kingdom/Bacteria/sprot -evalue 1e-06 -num_threads 1 -num_descriptions 1 -num_alignments 1 -seg no > \/home\/yquentin\/work\/wolbachia\/prokka\/wWb\/proteins\.bls 2> /dev/null
[15:07:37] Modify product: Uncharacterized zinc protease Rv2782c => putative zinc protease
[15:07:37] Modify product: Uncharacterized zinc protease Rv2782c => putative zinc protease
[15:07:37] Modify product: Putative multidrug export ATP-binding/permease protein SAV1866 => Putative multidrug export ATP-binding/permease protein
[15:07:37] Modify product: Uncharacterized ABC transporter ATP-binding protein TM_0288 => putative ABC transporter ATP-binding protein
[15:07:37] Modify product: Uncharacterized HIT-like protein HP_0404 => putative HIT-like protein
[15:07:37] Modify product: Uncharacterized metal-dependent hydrolase YcfH => putative metal-dependent hydrolase YcfH
[15:07:38] Modify product: Probable GTP-binding protein EngB => putative GTP-binding protein EngB
[15:07:38] Modify product: Transcription termination/antitermination protein NusA => hypothetical protein
[15:07:38] Modify product: Transcription termination factor Rho => hypothetical protein
[15:07:38] Modify product: Probable peroxiredoxin => putative peroxiredoxin
[15:07:38] Modify product: Probable transcriptional regulatory protein aq_1575 => putative transcriptional regulatory protein
[15:07:38] Modify product: Probable acyltransferase YihG => putative acyltransferase YihG
[15:07:38] Modify product: Probable CtpA-like serine protease => putative CtpA-like serine protease
[15:07:38] Modify product: Probable protein kinase UbiB => putative protein kinase UbiB
[15:07:38] Modify product: Cytochrome b561 homolog 2 => hypothetical protein
[15:07:38] Modify product: Actin-binding protein Smlt3054 => Actin-binding protein
[15:07:39] Modify product: Uncharacterized ABC transporter ATP-binding protein TM_0288 => putative ABC transporter ATP-binding protein
[15:07:39] Modify product: SCO1 protein homolog => hypothetical protein
[15:07:39] Modify product: Co-chaperone protein HscB homolog => hypothetical protein
[15:07:39] Modify product: Probable phospholipid ABC transporter permease protein MlaE => putative phospholipid ABC transporter permease protein MlaE
[15:07:39] Modify product: Probable ribonucleotide transport ATP-binding protein mkl => putative ribonucleotide transport ATP-binding protein mkl
[15:07:39] Modify product: Uncharacterized oxidoreductase YciK => putative oxidoreductase YciK
[15:07:39] Modify product: Probable UbiX-like flavin prenyltransferase => putative UbiX-like flavin prenyltransferase
[15:07:39] Modify product: Bifunctional protein FolD => Bifunctional protein FolD protein
[15:07:39] Modify product: Putative O-methyltransferase MSMEG_5073/MSMEI_4947 => Putative O-methyltransferase/MSMEI_4947
[15:07:39] Modify product: Stringent starvation protein A homolog => hypothetical protein
[15:07:39] Modify product: Probable glycerol-3-phosphate acyltransferase => putative glycerol-3-phosphate acyltransferase
[15:07:40] Modify product: Probable phospholipid ABC transporter-binding protein MlaD => putative phospholipid ABC transporter-binding protein MlaD
[15:07:40] Modify product: Transcription termination/antitermination protein NusG => hypothetical protein
[15:07:40] Modify product: Probable tRNA-dihydrouridine synthase => putative tRNA-dihydrouridine synthase
[15:07:40] Modify product: N utilization substance protein B homolog => hypothetical protein
[15:07:40] Modify product: Uncharacterized zinc protease Rv2782c => putative zinc protease
[15:07:40] Cleaned 32 /product names
[15:07:40] Deleting unwanted file: /home/yquentin/work/wolbachia/prokka/wWb/proteins.faa
[15:07:40] Deleting unwanted file: /home/yquentin/work/wolbachia/prokka/wWb/proteins.bls
[15:07:40] There are still 565 unannotated CDS left (started with 1121)
[15:07:40] Will use hmmer3 to search against /usr/local/bioinfo/src/PROKKA/prokka-1.10/bin/../db/hmm/HAMAP.hmm with 8 CPUs
[15:07:40] Running: cat \/home\/yquentin\/work\/wolbachia\/prokka\/wWb\/proteins\.faa | parallel --gnu -j 8 --block 4937 --recstart '>' --pipe hmmscan --noali --notextw --acc -E 1e-06 --cpu 1 /usr/local/bioinfo/src/PROKKA/prokka-1.10/bin/../db/hmm/HAMAP.hmm /dev/stdin > \/home\/yquentin\/work\/wolbachia\/prokka\/wWb\/proteins\.bls 2> /dev/null
[15:07:57] Deleting unwanted file: /home/yquentin/work/wolbachia/prokka/wWb/proteins.faa
[15:07:57] Deleting unwanted file: /home/yquentin/work/wolbachia/prokka/wWb/proteins.bls
[15:07:58] There are still 538 unannotated CDS left (started with 1121)
[15:07:58] Will use hmmer3 to search against /usr/local/bioinfo/src/PROKKA/prokka-1.10/bin/../db/hmm/CLUSTERS.hmm with 8 CPUs
[15:07:58] Running: cat \/home\/yquentin\/work\/wolbachia\/prokka\/wWb\/proteins\.faa | parallel --gnu -j 8 --block 4533 --recstart '>' --pipe hmmscan --noali --notextw --acc -E 1e-06 --cpu 1 /usr/local/bioinfo/src/PROKKA/prokka-1.10/bin/../db/hmm/CLUSTERS.hmm /dev/stdin > \/home\/yquentin\/work\/wolbachia\/prokka\/wWb\/proteins\.bls 2> /dev/null
[15:08:41] Deleting unwanted file: /home/yquentin/work/wolbachia/prokka/wWb/proteins.faa
[15:08:41] Deleting unwanted file: /home/yquentin/work/wolbachia/prokka/wWb/proteins.bls
[15:08:42] There are still 512 unannotated CDS left (started with 1121)
[15:08:42] Will use hmmer3 to search against /usr/local/bioinfo/src/PROKKA/prokka-1.10/bin/../db/hmm/Pfam.hmm with 8 CPUs
[15:08:42] Running: cat \/home\/yquentin\/work\/wolbachia\/prokka\/wWb\/proteins\.faa | parallel --gnu -j 8 --block 4183 --recstart '>' --pipe hmmscan --noali --notextw --acc -E 1e-06 --cpu 1 /usr/local/bioinfo/src/PROKKA/prokka-1.10/bin/../db/hmm/Pfam.hmm /dev/stdin > \/home\/yquentin\/work\/wolbachia\/prokka\/wWb\/proteins\.bls 2> /dev/null
[15:09:22] Modify product: Phosphotransferase enzyme family => Phosphotransferase enzyme family protein
[15:09:22] Modify product: Tetratricopeptide repeat => Tetratricopeptide repeat protein
[15:09:22] Modify product: Nitroreductase family => Nitroreductase family protein
[15:09:22] Modify product: Sodium:dicarboxylate symporter family => Sodium:dicarboxylate symporter family protein
[15:09:22] Modify product: RDD family => RDD family protein
[15:09:22] Modify product: Zinc-finger domain => Zinc-finger domain protein
[15:09:22] Modify product: TrbC/VIRB2 family => TrbC/VIRB2 family protein
[15:09:22] Modify product: RDD family => RDD family protein
[15:09:22] Modify product: Ankyrin repeat => Ankyrin repeat protein
[15:09:22] Modify product: TrbC/VIRB2 family => TrbC/VIRB2 family protein
[15:09:22] Modify product: Phage capsid family => Phage capsid family protein
[15:09:22] Modify product: COQ9 => hypothetical protein
[15:09:22] Modify product: AcrB/AcrD/AcrF family => AcrB/AcrD/AcrF family protein
[15:09:22] Modify product: AhpC/TSA family => AhpC/TSA family protein
[15:09:22] Modify product: SURF1 family => SURF1 family protein
[15:09:22] Modify product: RDD family => RDD family protein
[15:09:22] Modify product: RmlD substrate binding domain => RmlD substrate binding domain protein
[15:09:22] Modify product: ETC complex I subunit conserved region => hypothetical protein
[15:09:22] Modify product: Tim44-like domain => Tim44-like domain protein
[15:09:22] Modify product: AcrB/AcrD/AcrF family => AcrB/AcrD/AcrF family protein
[15:09:22] Modify product: Major Facilitator Superfamily => Major Facilitator Superfamily protein
[15:09:22] Modify product: TrbC/VIRB2 family => TrbC/VIRB2 family protein
[15:09:22] Modify product: SPFH domain / Band 7 family => SPFH domain / Band 7 family protein
[15:09:22] Modify product: Porphobilinogen deaminase, C-terminal domain => hypothetical protein
[15:09:22] Modify product: PD-(D/E)XK nuclease superfamily => PD-(D/E)XK nuclease superfamily protein
[15:09:22] Modify product: Transposase DDE domain => Transposase DDE domain protein
[15:09:22] Modify product: Ankyrin repeat => Ankyrin repeat protein
[15:09:22] Modify product: Uracil DNA glycosylase superfamily => Uracil DNA glycosylase superfamily protein
[15:09:22] Modify product: TrbC/VIRB2 family => TrbC/VIRB2 family protein
[15:09:22] Modify product: Ankyrin repeat => Ankyrin repeat protein
[15:09:22] Modify product: EVE domain => EVE domain protein
[15:09:22] Modify product: Ankyrin repeat => Ankyrin repeat protein
[15:09:22] Modify product: PAS domain => PAS domain protein
[15:09:22] Modify product: Integral membrane protein TerC family => Integral membrane protein TerC family protein
[15:09:22] Modify product: Fic/DOC family => Fic/DOC family protein
[15:09:22] Modify product: Alpha/beta hydrolase family => Alpha/beta hydrolase family protein
[15:09:22] Modify product: YGGT family => YGGT family protein
[15:09:22] Modify product: Sodium:alanine symporter family => Sodium:alanine symporter family protein
[15:09:22] Modify product: Sodium:dicarboxylate symporter family => Sodium:dicarboxylate symporter family protein
[15:09:22] Modify product: Tetratricopeptide repeat => Tetratricopeptide repeat protein
[15:09:22] Cleaned 40 /product names
[15:09:22] Deleting unwanted file: /home/yquentin/work/wolbachia/prokka/wWb/proteins.faa
[15:09:22] Deleting unwanted file: /home/yquentin/work/wolbachia/prokka/wWb/proteins.bls
[15:09:22] Labelling remaining 431 proteins as 'hypothetical protein'
[15:09:22] Possible /pseudo '50S ribosomal protein L22' at gnl|Prokka|wWb_contig000013 position 3368
[15:09:22] Possible /pseudo 'putative zinc protease' at gnl|Prokka|wWb_contig000015 position 1380
[15:09:22] Possible /pseudo 'DNA mismatch repair protein MutS' at gnl|Prokka|wWb_contig000017 position 29221
[15:09:22] Possible /pseudo 'Arginine/agmatine antiporter' at gnl|Prokka|wWb_contig000018 position 19481
[15:09:22] Possible /pseudo 'TrbL/VirB6 plasmid conjugal transfer protein' at gnl|Prokka|wWb_contig000042 position 4934
[15:09:22] Possible /pseudo 'TrbL/VirB6 plasmid conjugal transfer protein' at gnl|Prokka|wWb_contig000042 position 8053
[15:09:22] Possible /pseudo 'TrbL/VirB6 plasmid conjugal transfer protein' at gnl|Prokka|wWb_contig000042 position 10521
[15:09:22] Possible /pseudo 'DNA gyrase subunit B' at gnl|Prokka|wWb_contig000053 position 1221
[15:09:22] Possible /pseudo 'UvrABC system protein B' at gnl|Prokka|wWb_contig000066 position 12061
[15:09:22] Possible /pseudo 'Cytochrome b' at gnl|Prokka|wWb_contig000066 position 15478
[15:09:22] Possible /pseudo 'ATP-dependent Clp protease ATP-binding subunit ClpA' at gnl|Prokka|wWb_contig000075 position 1536
[15:09:22] Possible /pseudo 'ATP-dependent Clp protease ATP-binding subunit ClpA' at gnl|Prokka|wWb_contig000075 position 1691
[15:09:22] Possible /pseudo 'ATP-dependent Clp protease ATP-binding subunit ClpA' at gnl|Prokka|wWb_contig000075 position 2278
[15:09:22] Possible /pseudo 'Valine--tRNA ligase' at gnl|Prokka|wWb_contig000076 position 4644
[15:09:22] Possible /pseudo 'Valine--tRNA ligase' at gnl|Prokka|wWb_contig000076 position 5048
[15:09:22] Possible /pseudo 'Valine--tRNA ligase' at gnl|Prokka|wWb_contig000076 position 5683
[15:09:22] Possible /pseudo 'Glutamate--tRNA ligase' at gnl|Prokka|wWb_contig000089 position 21008
[15:09:22] Possible /pseudo 'PD-(D/E)XK nuclease family transposase' at gnl|Prokka|wWb_contig000093 position 24229
[15:09:22] Found 522 unique /gene codes.
[15:09:22] Fixed 23 colliding /gene names.
[15:09:22] Adding /locus_tag identifiers
[15:09:22] Assigned 1152 locus_tags to CDS and RNA features.
[15:09:22] Writing outputs to /home/yquentin/work/wolbachia/prokka/wWb/
[15:09:24] Generating annotation statistics file
[15:09:24] Generating Genbank and Sequin files
[15:09:24] Running: tbl2asn -V b -a r10k -l paired-ends -M n -N 1 -y 'Annotated using prokka 1.10 from http://www.vicbioinformatics.com' -Z \/home\/yquentin\/work\/wolbachia\/prokka\/wWb\/wWb\.err -i \/home\/yquentin\/work\/wolbachia\/prokka\/wWb\/wWb\.fsa 2> /dev/null
[15:09:31] Deleting unwanted file: /home/yquentin/work/wolbachia/prokka/wWb/errorsummary.val
[15:09:31] Deleting unwanted file: /home/yquentin/work/wolbachia/prokka/wWb/wWb.dr
[15:09:31] Deleting unwanted file: /home/yquentin/work/wolbachia/prokka/wWb/wWb.fixedproducts
[15:09:31] Deleting unwanted file: /home/yquentin/work/wolbachia/prokka/wWb/wWb.ecn
[15:09:31] Deleting unwanted file: /home/yquentin/work/wolbachia/prokka/wWb/wWb.val
[15:09:31] Output files:
[15:09:31] /home/yquentin/work/wolbachia/prokka/wWb/wWb.tbl
[15:09:31] /home/yquentin/work/wolbachia/prokka/wWb/wWb.gbk
[15:09:31] /home/yquentin/work/wolbachia/prokka/wWb/wWb.fsa
[15:09:31] /home/yquentin/work/wolbachia/prokka/wWb/wWb.txt
[15:09:31] /home/yquentin/work/wolbachia/prokka/wWb/wWb.gff
[15:09:31] /home/yquentin/work/wolbachia/prokka/wWb/wWb.faa
[15:09:31] /home/yquentin/work/wolbachia/prokka/wWb/wWb.log
[15:09:31] /home/yquentin/work/wolbachia/prokka/wWb/wWb.fna
[15:09:31] /home/yquentin/work/wolbachia/prokka/wWb/wWb.err
[15:09:31] /home/yquentin/work/wolbachia/prokka/wWb/wWb.sqn
[15:09:31] /home/yquentin/work/wolbachia/prokka/wWb/wWb.ffn
[15:09:31] Walltime used: 2.45 minutes
[15:09:31] If you use this result please cite the Prokka paper:
[15:09:31] Seemann T (2014) Prokka: rapid prokaryotic genome annotation. Bioinformatics. 30(14):2068-9.
[15:09:31] Type 'prokka --citation' for more details.
[15:09:31] Share and enjoy!