[10:41:17] Command: --force --outdir /home/yquentin/work/wolbachia/prokka/wBmal --addgenes --prefix wBmal --locustag wBmal --species Wolbachia endosymbiont strain TRS of  --strain wBmal --compliant --quiet /home/yquentin/work/wolbachia/prokka/wBmal.fna
[10:41:17] Looking for 'aragorn' - found /usr/local/bioinfo/bin/aragorn
[10:41:17] Determined aragorn version is 1.2
[10:41:17] Looking for 'barrnap' - found /usr/local/bioinfo/bin/barrnap
[10:41:17] Determined barrnap version is 0.5
[10:41:17] Looking for 'blastp' - found /usr/local/bioinfo/src/NCBI_Blast+/ncbi-blast-2.6.0+/bin/blastp
[10:41:17] Determined blastp version is 2.6
[10:41:17] Looking for 'cmpress' - found /usr/local/bioinfo/src/PROKKA/prokka-1.10/bin/../binaries/linux/cmpress
[10:41:17] Determined cmpress version is 1.1
[10:41:17] Looking for 'cmscan' - found /usr/local/bioinfo/src/PROKKA/prokka-1.10/bin/../binaries/linux/cmscan
[10:41:17] Determined cmscan version is 1.1
[10:41:17] Looking for 'egrep' - found /bin/egrep
[10:41:17] Looking for 'find' - found /bin/find
[10:41:17] Looking for 'grep' - found /bin/grep
[10:41:17] Looking for 'hmmpress' - found /usr/local/bioinfo/bin/hmmpress
[10:41:17] Determined hmmpress version is 3.1
[10:41:17] Looking for 'hmmscan' - found /usr/local/bioinfo/bin/hmmscan
[10:41:17] Determined hmmscan version is 3.1
[10:41:17] Looking for 'less' - found /usr/bin/less
[10:41:17] Looking for 'makeblastdb' - found /usr/local/bioinfo/src/NCBI_Blast+/ncbi-blast-2.6.0+/bin/makeblastdb
[10:41:17] Determined makeblastdb version is 2.6
[10:41:17] Looking for 'minced' - found /usr/local/bioinfo/bin/minced
[10:41:17] Determined minced version is 1.6
[10:41:17] Looking for 'parallel' - found /usr/local/bioinfo/bin/parallel
[10:41:17] Determined parallel version is 20141022
[10:41:17] Looking for 'prodigal' - found /usr/local/bioinfo/bin/prodigal
[10:41:18] Determined prodigal version is 2.6
[10:41:18] Looking for 'rnammer' - found /usr/local/bioinfo/bin/rnammer
[10:41:18] Determined rnammer version is 1.2
[10:41:18] Looking for 'sed' - found /bin/sed
[10:41:18] Looking for 'signalp' - found /usr/local/bioinfo/bin/signalp
[10:41:18] Determined signalp version is 4.1
[10:41:18] Looking for 'tbl2asn' - found /home/yquentin/save/scripts/tbl2asn
[10:41:18] Determined tbl2asn version is 25.3
[10:41:18] Using genetic code table 11.
[10:41:18] Loading and checking input file: /home/yquentin/work/wolbachia/prokka/wBmal.fna
[10:41:18] Wrote 1 contigs
[10:41:18] Predicting tRNAs and tmRNAs
[10:41:18] Running: aragorn -gc11  -w \/home\/yquentin\/work\/wolbachia\/prokka\/wBmal\/wBmal\.fna
[10:41:18] 1 tRNA-Ser [15358,15445] 36 (gga)
[10:41:18] 2 tRNA-Ser [43002,43090] 35 (tga)
[10:41:18] 3 tRNA-Ala c[81071,81143] 34 (tgc)
[10:41:18] 4 tRNA-Cys [121709,121781] 34 (gca)
[10:41:18] 5 tRNA-His [162060,162135] 35 (gtg)
[10:41:18] 6 tRNA-Arg c[283362,283437] 36 (ccg)
[10:41:18] 7 tRNA-Arg [306290,306364] 35 (tct)
[10:41:18] 8 tRNA-Leu [364005,364092] 35 (gag)
[10:41:18] 9 tRNA-Leu [396034,396117] 34 (caa)
[10:41:18] 10 tRNA-Val c[491142,491215] 34 (gac)
[10:41:18] 11 tRNA-Asn c[517357,517429] 33 (gtt)
[10:41:18] 12 tRNA-Val c[523698,523770] 34 (tac)
[10:41:18] 13 tRNA-Thr [528712,528785] 34 (tgt)
[10:41:18] 14 tRNA-Lys c[619706,619779] 34 (ttt)
[10:41:18] 15 tRNA-Met [656195,656268] 34 (cat)
[10:41:18] 16 tRNA-Pro c[678621,678696] 36 (tgg)
[10:41:18] 17 tRNA-Leu c[730695,730777] 35 (tag)
[10:41:18] 18 tRNA-Ser c[760370,760460] 35 (gct)
[10:41:18] 19 tRNA-Thr c[767033,767107] 35 (ggt)
[10:41:18] 20 tRNA-Met c[769449,769523] 35 (cat)
[10:41:18] 21 tRNA-Met c[798109,798183] 35 (cat)
[10:41:18] 22 tRNA-Gly [799444,799517] 34 (gcc)
[10:41:18] 23 tmRNA* c[841386,841717] 194,241 ANDNFAAEGDVAVAA*
[10:41:18] 24 tRNA-Trp c[853719,853792] 34 (cca)
[10:41:18] 25 tRNA-Gly c[855058,855130] 34 (tcc)
[10:41:18] 26 tRNA-Tyr c[855134,855217] 36 (gta)
[10:41:18] 27 tRNA-Leu c[863688,863774] 35 (taa)
[10:41:18] 28 tRNA-Arg c[884350,884423] 35 (cct)
[10:41:18] 29 tRNA-Ile c[910184,910260] 35 (gat)
[10:41:18] 30 tRNA-Glu c[921229,921302] 35 (ttc)
[10:41:18] 31 tRNA-Arg [929501,929576] 36 (acg)
[10:41:18] 32 tRNA-Ser [953875,953961] 35 (cag)
[10:41:18] 33 tRNA-Gln c[1006935,1007008] 33 (ttg)
[10:41:18] 34 tRNA-Phe c[1069732,1069805] 34 (gaa)
[10:41:18] 35 tRNA-Asp [1075386,1075460] 35 (gtc)
[10:41:18] Found 35 tRNAs
[10:41:18] Predicting Ribosomal RNAs
[10:41:18] Running Barrnap with 8 threads
[10:41:19] 1 gnl|Prokka|wBmal_contig000001 634570 16S ribosomal RNA
[10:41:19] 2 gnl|Prokka|wBmal_contig000001 899380 5S ribosomal RNA
[10:41:19] 3 gnl|Prokka|wBmal_contig000001 899555 23S ribosomal RNA
[10:41:19] Found 3 rRNAs
[10:41:19] Skipping ncRNA search, enable with --rfam if desired.
[10:41:19] Total of 37 tRNA + rRNA features
[10:41:19] Searching for CRISPR repeats
[10:41:20] Found 0 CRISPRs
[10:41:20] Predicting coding sequences
[10:41:20] Contigs total 1080084 bp, so using single mode
[10:41:20] Running: prodigal -i \/home\/yquentin\/work\/wolbachia\/prokka\/wBmal\/wBmal\.fna -c -m -g 11 -p single -f sco -q
[10:41:22] Excluding CDS which overlaps existing RNA (tRNA) at gnl|Prokka|wBmal_contig000001:654903..656195 on + strand
[10:41:22] Excluding CDS which overlaps existing RNA (tRNA) at gnl|Prokka|wBmal_contig000001:863647..863787 on - strand
[10:41:22] Excluding CDS which overlaps existing RNA (rRNA) at gnl|Prokka|wBmal_contig000001:901205..901477 on - strand
[10:41:22] Excluding CDS which overlaps existing RNA (tRNA) at gnl|Prokka|wBmal_contig000001:1006999..1007334 on - strand
[10:41:22] Found 1136 CDS
[10:41:22] Connecting features back to sequences
[10:41:22] Option --gram not specified, will NOT check for signal peptides.
[10:41:22] Not using genus-specific database. Try --usegenus to enable it.
[10:41:22] Annotating CDS, please be patient.
[10:41:22] Will use 8 CPUs for similarity searching.
[10:41:23] There are still 1136 unannotated CDS left (started with 1136)
[10:41:23] Will use blast to search against /usr/local/bioinfo/src/PROKKA/prokka-1.10/bin/../db/kingdom/Bacteria/sprot with 8 CPUs
[10:41:23] Running: cat \/home\/yquentin\/work\/wolbachia\/prokka\/wBmal\/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\/wBmal\/proteins\.bls 2> /dev/null
[10:41:33] Modify product: Probable UbiX-like flavin prenyltransferase => putative UbiX-like flavin prenyltransferase
[10:41:33] Modify product: Bifunctional protein FolD => Bifunctional protein FolD protein
[10:41:33] Modify product: Probable CtpA-like serine protease => putative CtpA-like serine protease
[10:41:33] Modify product: Uncharacterized zinc protease Rv2782c => putative zinc protease
[10:41:33] Modify product: Uncharacterized HIT-like protein HP_0404 => putative HIT-like protein
[10:41:33] Modify product: Uncharacterized metal-dependent hydrolase YcfH => putative metal-dependent hydrolase YcfH
[10:41:34] Modify product: Probable phospholipid ABC transporter-binding protein MlaD => putative phospholipid ABC transporter-binding protein MlaD
[10:41:34] Modify product: Probable ABC transporter ATP-binding protein HI_0664 => putative ABC transporter ATP-binding protein
[10:41:34] Modify product: Putative multidrug export ATP-binding/permease protein SAV1866 => Putative multidrug export ATP-binding/permease protein
[10:41:34] Modify product: N utilization substance protein B homolog => hypothetical protein
[10:41:34] Modify product: Uncharacterized ABC transporter ATP-binding protein TM_0288 => putative ABC transporter ATP-binding protein
[10:41:34] Modify product: Probable GTP-binding protein EngB => putative GTP-binding protein EngB
[10:41:34] Modify product: Uncharacterized zinc protease Rv2782c => putative zinc protease
[10:41:34] Modify product: Uncharacterized zinc protease Rv2782c => putative zinc protease
[10:41:34] Modify product: Stringent starvation protein A homolog => hypothetical protein
[10:41:34] Modify product: Putative O-methyltransferase MSMEG_5073/MSMEI_4947 => Putative O-methyltransferase/MSMEI_4947
[10:41:34] Modify product: Probable tRNA-dihydrouridine synthase => putative tRNA-dihydrouridine synthase
[10:41:34] Modify product: Uncharacterized oxidoreductase YciK => putative oxidoreductase YciK
[10:41:34] Modify product: Probable peroxiredoxin => putative peroxiredoxin
[10:41:34] Modify product: Probable phospholipid ABC transporter permease protein MlaE => putative phospholipid ABC transporter permease protein MlaE
[10:41:34] Modify product: Probable amino-acid import ATP-binding protein YxeO => putative amino-acid import ATP-binding protein YxeO
[10:41:34] Modify product: Probable transcriptional regulatory protein aq_1575 => putative transcriptional regulatory protein
[10:41:34] Modify product: Probable chromosome-partitioning protein ParB => putative chromosome-partitioning protein ParB
[10:41:34] Modify product: Probable protein kinase UbiB => putative protein kinase UbiB
[10:41:34] Modify product: Transcription termination/antitermination protein NusG => hypothetical protein
[10:41:34] Modify product: Probable acyltransferase YihG => putative acyltransferase YihG
[10:41:34] Modify product: Cytochrome b561 homolog 2 => hypothetical protein
[10:41:34] Modify product: Co-chaperone protein HscB homolog => hypothetical protein
[10:41:34] Modify product: Transcription termination factor Rho => hypothetical protein
[10:41:35] Modify product: Transcription termination/antitermination protein NusA => hypothetical protein
[10:41:35] Modify product: SCO1 protein homolog => hypothetical protein
[10:41:35] Cleaned 31 /product names
[10:41:35] Deleting unwanted file: /home/yquentin/work/wolbachia/prokka/wBmal/proteins.faa
[10:41:35] Deleting unwanted file: /home/yquentin/work/wolbachia/prokka/wBmal/proteins.bls
[10:41:35] There are still 581 unannotated CDS left (started with 1136)
[10:41:35] Will use hmmer3 to search against /usr/local/bioinfo/src/PROKKA/prokka-1.10/bin/../db/hmm/HAMAP.hmm with 8 CPUs
[10:41:35] Running: cat \/home\/yquentin\/work\/wolbachia\/prokka\/wBmal\/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\/wBmal\/proteins\.bls 2> /dev/null
[10:41:42] Deleting unwanted file: /home/yquentin/work/wolbachia/prokka/wBmal/proteins.faa
[10:41:42] Deleting unwanted file: /home/yquentin/work/wolbachia/prokka/wBmal/proteins.bls
[10:41:42] There are still 552 unannotated CDS left (started with 1136)
[10:41:42] Will use hmmer3 to search against /usr/local/bioinfo/src/PROKKA/prokka-1.10/bin/../db/hmm/CLUSTERS.hmm with 8 CPUs
[10:41:42] Running: cat \/home\/yquentin\/work\/wolbachia\/prokka\/wBmal\/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\/wBmal\/proteins\.bls 2> /dev/null
[10:42:03] Deleting unwanted file: /home/yquentin/work/wolbachia/prokka/wBmal/proteins.faa
[10:42:03] Deleting unwanted file: /home/yquentin/work/wolbachia/prokka/wBmal/proteins.bls
[10:42:04] There are still 527 unannotated CDS left (started with 1136)
[10:42:04] Will use hmmer3 to search against /usr/local/bioinfo/src/PROKKA/prokka-1.10/bin/../db/hmm/Pfam.hmm with 8 CPUs
[10:42:04] Running: cat \/home\/yquentin\/work\/wolbachia\/prokka\/wBmal\/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\/wBmal\/proteins\.bls 2> /dev/null
[10:42:23] Modify product: PD-(D/E)XK nuclease superfamily => PD-(D/E)XK nuclease superfamily protein
[10:42:23] Modify product: Ankyrin repeat => Ankyrin repeat protein
[10:42:23] Modify product: RDD family => RDD family protein
[10:42:23] Modify product: TrbC/VIRB2 family => TrbC/VIRB2 family protein
[10:42:23] Modify product: Alpha/beta hydrolase family => Alpha/beta hydrolase family protein
[10:42:23] Modify product: Integral membrane protein TerC family => Integral membrane protein TerC family protein
[10:42:23] Modify product: Uracil DNA glycosylase superfamily => Uracil DNA glycosylase superfamily protein
[10:42:23] Modify product: RDD family => RDD family protein
[10:42:23] Modify product: SURF1 family => SURF1 family protein
[10:42:23] Modify product: AhpC/TSA family => AhpC/TSA family protein
[10:42:23] Modify product: Zinc-finger domain => Zinc-finger domain protein
[10:42:23] Modify product: Sodium:dicarboxylate symporter family => Sodium:dicarboxylate symporter family protein
[10:42:23] Modify product: Bacterial SH3 domain => Bacterial SH3 domain protein
[10:42:23] Modify product: YGGT family => YGGT family protein
[10:42:23] Modify product: COQ9 => hypothetical protein
[10:42:23] Modify product: Nitroreductase family => Nitroreductase family protein
[10:42:23] Modify product: Tetratricopeptide repeat => Tetratricopeptide repeat protein
[10:42:23] Modify product: AcrB/AcrD/AcrF family => AcrB/AcrD/AcrF family protein
[10:42:23] Modify product: Tim44-like domain => Tim44-like domain protein
[10:42:23] Modify product: ETC complex I subunit conserved region => hypothetical protein
[10:42:23] Modify product: RmlD substrate binding domain => RmlD substrate binding domain protein
[10:42:23] Modify product: EVE domain => EVE domain protein
[10:42:23] Modify product: TENA/THI-4/PQQC family => TENA/THI-4/PQQC family protein
[10:42:23] Modify product: TrbC/VIRB2 family => TrbC/VIRB2 family protein
[10:42:23] Modify product: Phage capsid family => Phage capsid family protein
[10:42:23] Cleaned 25 /product names
[10:42:23] Deleting unwanted file: /home/yquentin/work/wolbachia/prokka/wBmal/proteins.faa
[10:42:23] Deleting unwanted file: /home/yquentin/work/wolbachia/prokka/wBmal/proteins.bls
[10:42:23] Labelling remaining 454 proteins as 'hypothetical protein'
[10:42:23] Possible /pseudo 'tRNA pseudouridine synthase B' at gnl|Prokka|wBmal_contig000001 position 29140
[10:42:23] Possible /pseudo 'Arginine/agmatine antiporter' at gnl|Prokka|wBmal_contig000001 position 57222
[10:42:23] Possible /pseudo 'ATP-dependent Clp protease ATP-binding subunit ClpA' at gnl|Prokka|wBmal_contig000001 position 118889
[10:42:23] Possible /pseudo 'putative zinc protease' at gnl|Prokka|wBmal_contig000001 position 545464
[10:42:23] Possible /pseudo 'Protein TolB' at gnl|Prokka|wBmal_contig000001 position 610076
[10:42:23] Possible /pseudo 'Alginate biosynthesis protein AlgA' at gnl|Prokka|wBmal_contig000001 position 631642
[10:42:23] Possible /pseudo 'Alginate biosynthesis protein AlgA' at gnl|Prokka|wBmal_contig000001 position 631860
[10:42:23] Possible /pseudo 'Outer membrane protein assembly factor BamB' at gnl|Prokka|wBmal_contig000001 position 736579
[10:42:23] Possible /pseudo 'Pyridoxine/pyridoxamine 5'-phosphate oxidase' at gnl|Prokka|wBmal_contig000001 position 768424
[10:42:23] Possible /pseudo 'Competence protein' at gnl|Prokka|wBmal_contig000001 position 770757
[10:42:23] Possible /pseudo 'DNA repair protein RadA' at gnl|Prokka|wBmal_contig000001 position 993791
[10:42:23] Possible /pseudo 'TrbL/VirB6 plasmid conjugal transfer protein' at gnl|Prokka|wBmal_contig000001 position 1055217
[10:42:23] Possible /pseudo 'TrbL/VirB6 plasmid conjugal transfer protein' at gnl|Prokka|wBmal_contig000001 position 1058336
[10:42:23] Possible /pseudo 'TrbL/VirB6 plasmid conjugal transfer protein' at gnl|Prokka|wBmal_contig000001 position 1060804
[10:42:23] Found 520 unique /gene codes.
[10:42:23] Fixed 23 colliding /gene names.
[10:42:23] Adding /locus_tag identifiers
[10:42:23] Assigned 1174 locus_tags to CDS and RNA features.
[10:42:23] Writing outputs to /home/yquentin/work/wolbachia/prokka/wBmal/
[10:42:24] Generating annotation statistics file
[10:42:24] Generating Genbank and Sequin files
[10:42:24] 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\/wBmal\/wBmal\.err -i \/home\/yquentin\/work\/wolbachia\/prokka\/wBmal\/wBmal\.fsa 2> /dev/null
[10:42:27] Deleting unwanted file: /home/yquentin/work/wolbachia/prokka/wBmal/errorsummary.val
[10:42:27] Deleting unwanted file: /home/yquentin/work/wolbachia/prokka/wBmal/wBmal.dr
[10:42:27] Deleting unwanted file: /home/yquentin/work/wolbachia/prokka/wBmal/wBmal.fixedproducts
[10:42:27] Deleting unwanted file: /home/yquentin/work/wolbachia/prokka/wBmal/wBmal.ecn
[10:42:27] Deleting unwanted file: /home/yquentin/work/wolbachia/prokka/wBmal/wBmal.val
[10:42:27] Output files:
[10:42:27] /home/yquentin/work/wolbachia/prokka/wBmal/wBmal.ffn
[10:42:27] /home/yquentin/work/wolbachia/prokka/wBmal/wBmal.tbl
[10:42:27] /home/yquentin/work/wolbachia/prokka/wBmal/wBmal.fsa
[10:42:27] /home/yquentin/work/wolbachia/prokka/wBmal/wBmal.faa
[10:42:27] /home/yquentin/work/wolbachia/prokka/wBmal/wBmal.sqn
[10:42:27] /home/yquentin/work/wolbachia/prokka/wBmal/wBmal.err
[10:42:27] /home/yquentin/work/wolbachia/prokka/wBmal/wBmal.gff
[10:42:27] /home/yquentin/work/wolbachia/prokka/wBmal/wBmal.txt
[10:42:27] /home/yquentin/work/wolbachia/prokka/wBmal/wBmal.gbk
[10:42:27] /home/yquentin/work/wolbachia/prokka/wBmal/wBmal.fna
[10:42:27] /home/yquentin/work/wolbachia/prokka/wBmal/wBmal.log
[10:42:27] Walltime used: 1.17 minutes
[10:42:27] If you use this result please cite the Prokka paper:
[10:42:27] Seemann T (2014) Prokka: rapid prokaryotic genome annotation. Bioinformatics. 30(14):2068-9.
[10:42:27] Type 'prokka --citation' for more details.
[10:42:27] Thank you, come again.