[15:06:39] Command: --force --outdir /home/yquentin/work/wolbachia/prokka/wBma --addgenes --prefix wBma --locustag wBma --species Wolbachia endosymbiont strain TRS of  --strain wBma --compliant --quiet /home/yquentin/work/wolbachia/prokka/wBma.fna
[15:06:39] Looking for 'aragorn' - found /usr/local/bioinfo/bin/aragorn
[15:06:39] Determined aragorn version is 1.2
[15:06:39] Looking for 'barrnap' - found /usr/local/bioinfo/bin/barrnap
[15:06:39] Determined barrnap version is 0.5
[15:06:39] Looking for 'blastp' - found /usr/local/bioinfo/src/NCBI_Blast+/ncbi-blast-2.6.0+/bin/blastp
[15:06:39] Determined blastp version is 2.6
[15:06:39] Looking for 'cmpress' - found /usr/local/bioinfo/src/PROKKA/prokka-1.10/bin/../binaries/linux/cmpress
[15:06:39] Determined cmpress version is 1.1
[15:06:39] Looking for 'cmscan' - found /usr/local/bioinfo/src/PROKKA/prokka-1.10/bin/../binaries/linux/cmscan
[15:06:39] Determined cmscan version is 1.1
[15:06:39] Looking for 'egrep' - found /bin/egrep
[15:06:39] Looking for 'find' - found /bin/find
[15:06:39] Looking for 'grep' - found /bin/grep
[15:06:39] Looking for 'hmmpress' - found /usr/local/bioinfo/bin/hmmpress
[15:06:39] Determined hmmpress version is 3.1
[15:06:39] Looking for 'hmmscan' - found /usr/local/bioinfo/bin/hmmscan
[15:06:39] Determined hmmscan version is 3.1
[15:06:39] Looking for 'less' - found /usr/bin/less
[15:06:39] Looking for 'makeblastdb' - found /usr/local/bioinfo/src/NCBI_Blast+/ncbi-blast-2.6.0+/bin/makeblastdb
[15:06:39] Determined makeblastdb version is 2.6
[15:06:39] Looking for 'minced' - found /usr/local/bioinfo/bin/minced
[15:06:39] Determined minced version is 1.6
[15:06:39] Looking for 'parallel' - found /usr/local/bioinfo/bin/parallel
[15:06:40] Determined parallel version is 20141022
[15:06:40] Looking for 'prodigal' - found /usr/local/bioinfo/bin/prodigal
[15:06:40] Determined prodigal version is 2.6
[15:06:40] Looking for 'rnammer' - found /usr/local/bioinfo/bin/rnammer
[15:06:40] Determined rnammer version is 1.2
[15:06:40] Looking for 'sed' - found /bin/sed
[15:06:40] Looking for 'signalp' - found /usr/local/bioinfo/bin/signalp
[15:06:40] Determined signalp version is 4.1
[15:06:40] Looking for 'tbl2asn' - found /home/yquentin/save/scripts/tbl2asn
[15:06:40] Determined tbl2asn version is 25.3
[15:06:40] Using genetic code table 11.
[15:06:40] Loading and checking input file: /home/yquentin/work/wolbachia/prokka/wBma.fna
[15:06:40] Wrote 1 contigs
[15:06:40] Predicting tRNAs and tmRNAs
[15:06:40] Running: aragorn -gc11  -w \/home\/yquentin\/work\/wolbachia\/prokka\/wBma\/wBma\.fna
[15:06:41] 1 tRNA-Ser [15358,15445] 36 (gga)
[15:06:41] 2 tRNA-Ser [43002,43090] 35 (tga)
[15:06:41] 3 tRNA-Ala c[81071,81143] 34 (tgc)
[15:06:41] 4 tRNA-Cys [121709,121781] 34 (gca)
[15:06:41] 5 tRNA-His [162060,162135] 35 (gtg)
[15:06:41] 6 tRNA-Arg c[283362,283437] 36 (ccg)
[15:06:41] 7 tRNA-Arg [306290,306364] 35 (tct)
[15:06:41] 8 tRNA-Leu [364005,364092] 35 (gag)
[15:06:41] 9 tRNA-Leu [396034,396117] 34 (caa)
[15:06:41] 10 tRNA-Val c[491142,491215] 34 (gac)
[15:06:41] 11 tRNA-Asn c[517357,517429] 33 (gtt)
[15:06:41] 12 tRNA-Val c[523698,523770] 34 (tac)
[15:06:41] 13 tRNA-Thr [528712,528785] 34 (tgt)
[15:06:41] 14 tRNA-Lys c[619706,619779] 34 (ttt)
[15:06:41] 15 tRNA-Met [656195,656268] 34 (cat)
[15:06:41] 16 tRNA-Pro c[678621,678696] 36 (tgg)
[15:06:41] 17 tRNA-Leu c[730695,730777] 35 (tag)
[15:06:41] 18 tRNA-Ser c[760370,760460] 35 (gct)
[15:06:41] 19 tRNA-Thr c[767033,767107] 35 (ggt)
[15:06:41] 20 tRNA-Met c[769449,769523] 35 (cat)
[15:06:41] 21 tRNA-Met c[798109,798183] 35 (cat)
[15:06:41] 22 tRNA-Gly [799444,799517] 34 (gcc)
[15:06:41] 23 tmRNA* c[841386,841717] 194,241 ANDNFAAEGDVAVAA*
[15:06:41] 24 tRNA-Trp c[853719,853792] 34 (cca)
[15:06:41] 25 tRNA-Gly c[855058,855130] 34 (tcc)
[15:06:41] 26 tRNA-Tyr c[855134,855217] 36 (gta)
[15:06:41] 27 tRNA-Leu c[863688,863774] 35 (taa)
[15:06:41] 28 tRNA-Arg c[884350,884423] 35 (cct)
[15:06:41] 29 tRNA-Ile c[910184,910260] 35 (gat)
[15:06:41] 30 tRNA-Glu c[921229,921302] 35 (ttc)
[15:06:41] 31 tRNA-Arg [929501,929576] 36 (acg)
[15:06:41] 32 tRNA-Ser [953875,953961] 35 (cag)
[15:06:41] 33 tRNA-Gln c[1006935,1007008] 33 (ttg)
[15:06:41] 34 tRNA-Phe c[1069732,1069805] 34 (gaa)
[15:06:41] 35 tRNA-Asp [1075386,1075460] 35 (gtc)
[15:06:41] Found 35 tRNAs
[15:06:41] Predicting Ribosomal RNAs
[15:06:41] Running Barrnap with 8 threads
[15:06:42] 1 gnl|Prokka|wBma_contig000001 634570 16S ribosomal RNA
[15:06:42] 2 gnl|Prokka|wBma_contig000001 899380 5S ribosomal RNA
[15:06:42] 3 gnl|Prokka|wBma_contig000001 899555 23S ribosomal RNA
[15:06:42] Found 3 rRNAs
[15:06:42] Skipping ncRNA search, enable with --rfam if desired.
[15:06:42] Total of 37 tRNA + rRNA features
[15:06:42] Searching for CRISPR repeats
[15:06:42] Found 0 CRISPRs
[15:06:42] Predicting coding sequences
[15:06:42] Contigs total 1080084 bp, so using single mode
[15:06:42] Running: prodigal -i \/home\/yquentin\/work\/wolbachia\/prokka\/wBma\/wBma\.fna -c -m -g 11 -p single -f sco -q
[15:06:46] Excluding CDS which overlaps existing RNA (tRNA) at gnl|Prokka|wBma_contig000001:654903..656195 on + strand
[15:06:47] Excluding CDS which overlaps existing RNA (tRNA) at gnl|Prokka|wBma_contig000001:863647..863787 on - strand
[15:06:47] Excluding CDS which overlaps existing RNA (rRNA) at gnl|Prokka|wBma_contig000001:901205..901477 on - strand
[15:06:47] Excluding CDS which overlaps existing RNA (tRNA) at gnl|Prokka|wBma_contig000001:1006999..1007334 on - strand
[15:06:47] Found 1136 CDS
[15:06:47] Connecting features back to sequences
[15:06:47] Option --gram not specified, will NOT check for signal peptides.
[15:06:47] Not using genus-specific database. Try --usegenus to enable it.
[15:06:47] Annotating CDS, please be patient.
[15:06:47] Will use 8 CPUs for similarity searching.
[15:06:48] There are still 1136 unannotated CDS left (started with 1136)
[15:06:48] Will use blast to search against /usr/local/bioinfo/src/PROKKA/prokka-1.10/bin/../db/kingdom/Bacteria/sprot with 8 CPUs
[15:06:48] Running: cat \/home\/yquentin\/work\/wolbachia\/prokka\/wBma\/proteins\.faa | parallel --gnu -j 8 --block 17030 --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\/wBma\/proteins\.bls 2> /dev/null
[15:07:03] Modify product: N utilization substance protein B homolog => hypothetical protein
[15:07:03] Modify product: Uncharacterized ABC transporter ATP-binding protein TM_0288 => putative ABC transporter ATP-binding protein
[15:07:03] Modify product: Probable UbiX-like flavin prenyltransferase => putative UbiX-like flavin prenyltransferase
[15:07:03] Modify product: Bifunctional protein FolD => Bifunctional protein FolD protein
[15:07:03] Modify product: Probable CtpA-like serine protease => putative CtpA-like serine protease
[15:07:03] Modify product: Probable phospholipid ABC transporter-binding protein MlaD => putative phospholipid ABC transporter-binding protein MlaD
[15:07:03] Modify product: Uncharacterized zinc protease Rv2782c => putative zinc protease
[15:07:03] Modify product: Uncharacterized HIT-like protein HP_0404 => putative HIT-like protein
[15:07:03] Modify product: Uncharacterized metal-dependent hydrolase YcfH => putative metal-dependent hydrolase YcfH
[15:07:04] Modify product: Probable GTP-binding protein EngB => putative GTP-binding protein EngB
[15:07:04] Modify product: Probable ABC transporter ATP-binding protein HI_0664 => putative ABC transporter ATP-binding protein
[15:07:04] Modify product: Putative multidrug export ATP-binding/permease protein SAV1866 => Putative multidrug export ATP-binding/permease protein
[15:07:04] Modify product: Uncharacterized zinc protease Rv2782c => putative zinc protease
[15:07:04] Modify product: Uncharacterized zinc protease Rv2782c => putative zinc protease
[15:07:04] Modify product: Stringent starvation protein A homolog => hypothetical protein
[15:07:04] Modify product: Putative O-methyltransferase MSMEG_5073/MSMEI_4947 => Putative O-methyltransferase/MSMEI_4947
[15:07:04] Modify product: Probable tRNA-dihydrouridine synthase => putative tRNA-dihydrouridine synthase
[15:07:04] Modify product: Uncharacterized oxidoreductase YciK => putative oxidoreductase YciK
[15:07:04] Modify product: Probable peroxiredoxin => putative peroxiredoxin
[15:07:04] Modify product: Probable phospholipid ABC transporter permease protein MlaE => putative phospholipid ABC transporter permease protein MlaE
[15:07:04] Modify product: Probable amino-acid import ATP-binding protein YxeO => putative amino-acid import ATP-binding protein YxeO
[15:07:05] Modify product: Transcription termination/antitermination protein NusG => hypothetical protein
[15:07:05] Modify product: Transcription termination factor Rho => hypothetical protein
[15:07:05] Modify product: Transcription termination/antitermination protein NusA => hypothetical protein
[15:07:05] Modify product: SCO1 protein homolog => hypothetical protein
[15:07:05] Modify product: Probable transcriptional regulatory protein aq_1575 => putative transcriptional regulatory protein
[15:07:05] Modify product: Probable chromosome-partitioning protein ParB => putative chromosome-partitioning protein ParB
[15:07:05] Modify product: Probable protein kinase UbiB => putative protein kinase UbiB
[15:07:05] Modify product: Probable acyltransferase YihG => putative acyltransferase YihG
[15:07:05] Modify product: Cytochrome b561 homolog 2 => hypothetical protein
[15:07:05] Modify product: Co-chaperone protein HscB homolog => hypothetical protein
[15:07:05] Cleaned 31 /product names
[15:07:05] Deleting unwanted file: /home/yquentin/work/wolbachia/prokka/wBma/proteins.faa
[15:07:05] Deleting unwanted file: /home/yquentin/work/wolbachia/prokka/wBma/proteins.bls
[15:07:05] There are still 581 unannotated CDS left (started with 1136)
[15:07:05] Will use hmmer3 to search against /usr/local/bioinfo/src/PROKKA/prokka-1.10/bin/../db/hmm/HAMAP.hmm with 8 CPUs
[15:07:05] Running: cat \/home\/yquentin\/work\/wolbachia\/prokka\/wBma\/proteins\.faa | parallel --gnu -j 8 --block 5043 --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\/wBma\/proteins\.bls 2> /dev/null
[15:07:14] Deleting unwanted file: /home/yquentin/work/wolbachia/prokka/wBma/proteins.faa
[15:07:14] Deleting unwanted file: /home/yquentin/work/wolbachia/prokka/wBma/proteins.bls
[15:07:14] There are still 552 unannotated CDS left (started with 1136)
[15:07:14] Will use hmmer3 to search against /usr/local/bioinfo/src/PROKKA/prokka-1.10/bin/../db/hmm/CLUSTERS.hmm with 8 CPUs
[15:07:14] Running: cat \/home\/yquentin\/work\/wolbachia\/prokka\/wBma\/proteins\.faa | parallel --gnu -j 8 --block 4627 --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\/wBma\/proteins\.bls 2> /dev/null
[15:07:35] Deleting unwanted file: /home/yquentin/work/wolbachia/prokka/wBma/proteins.faa
[15:07:35] Deleting unwanted file: /home/yquentin/work/wolbachia/prokka/wBma/proteins.bls
[15:07:36] There are still 527 unannotated CDS left (started with 1136)
[15:07:36] Will use hmmer3 to search against /usr/local/bioinfo/src/PROKKA/prokka-1.10/bin/../db/hmm/Pfam.hmm with 8 CPUs
[15:07:36] Running: cat \/home\/yquentin\/work\/wolbachia\/prokka\/wBma\/proteins\.faa | parallel --gnu -j 8 --block 4273 --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\/wBma\/proteins\.bls 2> /dev/null
[15:07:59] Modify product: PD-(D/E)XK nuclease superfamily => PD-(D/E)XK nuclease superfamily protein
[15:07:59] Modify product: Ankyrin repeat => Ankyrin repeat protein
[15:07:59] Modify product: RDD family => RDD family protein
[15:07:59] Modify product: TrbC/VIRB2 family => TrbC/VIRB2 family protein
[15:07:59] Modify product: Alpha/beta hydrolase family => Alpha/beta hydrolase family protein
[15:07:59] Modify product: Integral membrane protein TerC family => Integral membrane protein TerC family protein
[15:07:59] Modify product: Uracil DNA glycosylase superfamily => Uracil DNA glycosylase superfamily protein
[15:07:59] Modify product: RDD family => RDD family protein
[15:07:59] Modify product: SURF1 family => SURF1 family protein
[15:07:59] Modify product: AhpC/TSA family => AhpC/TSA family protein
[15:07:59] Modify product: Zinc-finger domain => Zinc-finger domain protein
[15:07:59] Modify product: Sodium:dicarboxylate symporter family => Sodium:dicarboxylate symporter family protein
[15:07:59] Modify product: Bacterial SH3 domain => Bacterial SH3 domain protein
[15:07:59] Modify product: YGGT family => YGGT family protein
[15:07:59] Modify product: ETC complex I subunit conserved region => hypothetical protein
[15:07:59] Modify product: RmlD substrate binding domain => RmlD substrate binding domain protein
[15:07:59] Modify product: EVE domain => EVE domain protein
[15:07:59] Modify product: COQ9 => hypothetical protein
[15:07:59] Modify product: Nitroreductase family => Nitroreductase family protein
[15:07:59] Modify product: Tetratricopeptide repeat => Tetratricopeptide repeat protein
[15:07:59] Modify product: AcrB/AcrD/AcrF family => AcrB/AcrD/AcrF family protein
[15:07:59] Modify product: Tim44-like domain => Tim44-like domain protein
[15:07:59] Modify product: TENA/THI-4/PQQC family => TENA/THI-4/PQQC family protein
[15:07:59] Modify product: TrbC/VIRB2 family => TrbC/VIRB2 family protein
[15:07:59] Modify product: Phage capsid family => Phage capsid family protein
[15:07:59] Cleaned 25 /product names
[15:07:59] Deleting unwanted file: /home/yquentin/work/wolbachia/prokka/wBma/proteins.faa
[15:07:59] Deleting unwanted file: /home/yquentin/work/wolbachia/prokka/wBma/proteins.bls
[15:07:59] Labelling remaining 454 proteins as 'hypothetical protein'
[15:07:59] Possible /pseudo 'tRNA pseudouridine synthase B' at gnl|Prokka|wBma_contig000001 position 29140
[15:07:59] Possible /pseudo 'Arginine/agmatine antiporter' at gnl|Prokka|wBma_contig000001 position 57222
[15:07:59] Possible /pseudo 'ATP-dependent Clp protease ATP-binding subunit ClpA' at gnl|Prokka|wBma_contig000001 position 118889
[15:07:59] Possible /pseudo 'putative zinc protease' at gnl|Prokka|wBma_contig000001 position 545464
[15:07:59] Possible /pseudo 'Protein TolB' at gnl|Prokka|wBma_contig000001 position 610076
[15:07:59] Possible /pseudo 'Alginate biosynthesis protein AlgA' at gnl|Prokka|wBma_contig000001 position 631642
[15:07:59] Possible /pseudo 'Alginate biosynthesis protein AlgA' at gnl|Prokka|wBma_contig000001 position 631860
[15:07:59] Possible /pseudo 'Outer membrane protein assembly factor BamB' at gnl|Prokka|wBma_contig000001 position 736579
[15:07:59] Possible /pseudo 'Pyridoxine/pyridoxamine 5'-phosphate oxidase' at gnl|Prokka|wBma_contig000001 position 768424
[15:07:59] Possible /pseudo 'Competence protein' at gnl|Prokka|wBma_contig000001 position 770757
[15:07:59] Possible /pseudo 'DNA repair protein RadA' at gnl|Prokka|wBma_contig000001 position 993791
[15:07:59] Possible /pseudo 'TrbL/VirB6 plasmid conjugal transfer protein' at gnl|Prokka|wBma_contig000001 position 1055217
[15:07:59] Possible /pseudo 'TrbL/VirB6 plasmid conjugal transfer protein' at gnl|Prokka|wBma_contig000001 position 1058336
[15:07:59] Possible /pseudo 'TrbL/VirB6 plasmid conjugal transfer protein' at gnl|Prokka|wBma_contig000001 position 1060804
[15:07:59] Found 520 unique /gene codes.
[15:07:59] Fixed 23 colliding /gene names.
[15:07:59] Adding /locus_tag identifiers
[15:07:59] Assigned 1174 locus_tags to CDS and RNA features.
[15:07:59] Writing outputs to /home/yquentin/work/wolbachia/prokka/wBma/
[15:08:01] Generating annotation statistics file
[15:08:01] Generating Genbank and Sequin files
[15:08:01] 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\/wBma\/wBma\.err -i \/home\/yquentin\/work\/wolbachia\/prokka\/wBma\/wBma\.fsa 2> /dev/null
[15:08:05] Deleting unwanted file: /home/yquentin/work/wolbachia/prokka/wBma/errorsummary.val
[15:08:05] Deleting unwanted file: /home/yquentin/work/wolbachia/prokka/wBma/wBma.dr
[15:08:05] Deleting unwanted file: /home/yquentin/work/wolbachia/prokka/wBma/wBma.fixedproducts
[15:08:05] Deleting unwanted file: /home/yquentin/work/wolbachia/prokka/wBma/wBma.ecn
[15:08:05] Deleting unwanted file: /home/yquentin/work/wolbachia/prokka/wBma/wBma.val
[15:08:05] Output files:
[15:08:05] /home/yquentin/work/wolbachia/prokka/wBma/wBma.txt
[15:08:05] /home/yquentin/work/wolbachia/prokka/wBma/wBma.err
[15:08:05] /home/yquentin/work/wolbachia/prokka/wBma/wBma.gff
[15:08:05] /home/yquentin/work/wolbachia/prokka/wBma/wBma.faa
[15:08:05] /home/yquentin/work/wolbachia/prokka/wBma/wBma.tbl
[15:08:05] /home/yquentin/work/wolbachia/prokka/wBma/wBma.ffn
[15:08:05] /home/yquentin/work/wolbachia/prokka/wBma/wBma.log
[15:08:05] /home/yquentin/work/wolbachia/prokka/wBma/wBma.fna
[15:08:05] /home/yquentin/work/wolbachia/prokka/wBma/wBma.sqn
[15:08:05] /home/yquentin/work/wolbachia/prokka/wBma/wBma.fsa
[15:08:05] /home/yquentin/work/wolbachia/prokka/wBma/wBma.gbk
[15:08:05] Walltime used: 1.43 minutes
[15:08:05] If you use this result please cite the Prokka paper:
[15:08:05] Seemann T (2014) Prokka: rapid prokaryotic genome annotation. Bioinformatics. 30(14):2068-9.
[15:08:05] Type 'prokka --citation' for more details.
[15:08:05] Thank you, come again.