[09:22:47] Command: --force --outdir /home/yquentin/work/wolbachia/prokka/wDimm --addgenes --prefix wDimm --locustag wDimm --species Wolbachia endosymbiont --strain wDimm --compliant /home/formation/public_html/M2_Phylogenomique/data/Wolbachia/Additional/Dirofilaria_immitis_wolbachia_2.2.fna
[09:22:47] Looking for 'aragorn' - found /usr/local/bioinfo/bin/aragorn
[09:22:47] Determined aragorn version is 1.2
[09:22:47] Looking for 'barrnap' - found /usr/local/bioinfo/bin/barrnap
[09:22:47] Determined barrnap version is 0.5
[09:22:47] Looking for 'blastp' - found /usr/local/bioinfo/src/NCBI_Blast+/ncbi-blast-2.6.0+/bin/blastp
[09:22:47] Determined blastp version is 2.6
[09:22:47] Looking for 'cmpress' - found /usr/local/bioinfo/src/PROKKA/prokka-1.10/bin/../binaries/linux/cmpress
[09:22:47] Determined cmpress version is 1.1
[09:22:47] Looking for 'cmscan' - found /usr/local/bioinfo/src/PROKKA/prokka-1.10/bin/../binaries/linux/cmscan
[09:22:47] Determined cmscan version is 1.1
[09:22:47] Looking for 'egrep' - found /bin/egrep
[09:22:47] Looking for 'find' - found /bin/find
[09:22:47] Looking for 'grep' - found /bin/grep
[09:22:47] Looking for 'hmmpress' - found /usr/local/bioinfo/bin/hmmpress
[09:22:47] Determined hmmpress version is 3.1
[09:22:47] Looking for 'hmmscan' - found /usr/local/bioinfo/bin/hmmscan
[09:22:47] Determined hmmscan version is 3.1
[09:22:47] Looking for 'less' - found /usr/bin/less
[09:22:47] Looking for 'makeblastdb' - found /usr/local/bioinfo/src/NCBI_Blast+/ncbi-blast-2.6.0+/bin/makeblastdb
[09:22:47] Determined makeblastdb version is 2.6
[09:22:47] Looking for 'minced' - found /usr/local/bioinfo/bin/minced
[09:22:47] Determined minced version is 1.6
[09:22:47] Looking for 'parallel' - found /usr/local/bioinfo/bin/parallel
[09:22:47] Determined parallel version is 20141022
[09:22:47] Looking for 'prodigal' - found /usr/local/bioinfo/bin/prodigal
[09:22:47] Determined prodigal version is 2.6
[09:22:47] Looking for 'rnammer' - found /usr/local/bioinfo/bin/rnammer
[09:22:47] Determined rnammer version is 1.2
[09:22:47] Looking for 'sed' - found /bin/sed
[09:22:47] Looking for 'signalp' - found /usr/local/bioinfo/bin/signalp
[09:22:47] Determined signalp version is 4.1
[09:22:47] Looking for 'tbl2asn' - found /home/yquentin/save/scripts/tbl2asn
[09:22:47] Determined tbl2asn version is 25.3
[09:22:47] Using genetic code table 11.
[09:22:47] Loading and checking input file: /home/formation/public_html/M2_Phylogenomique/data/Wolbachia/Additional/Dirofilaria_immitis_wolbachia_2.2.fna
[09:22:48] Wrote 2 contigs
[09:22:48] Predicting tRNAs and tmRNAs
[09:22:48] Running: aragorn -gc11  -w \/home\/yquentin\/work\/wolbachia\/prokka\/wDimm\/wDimm\.fna
[09:22:48] 1 tmRNA* c[12128,12464] 196,246 ANNNFAADSNVMALAA*
[09:22:48] 2 tRNA-Val [32388,32461] 34 (gac)
[09:22:48] 3 tRNA-Lys c[52807,52882] 35 (ttt)
[09:22:48] 4 tRNA-Ala [53048,53122] 35 (tgc)
[09:22:48] 5 tRNA-Ser c[88872,88961] 36 (tga)
[09:22:48] 6 tRNA-Val [95369,95441] 34 (tac)
[09:22:48] 7 tRNA-Gly c[148933,149006] 34 (gcc)
[09:22:48] 8 tRNA-Met [150258,150332] 35 (cat)
[09:22:48] 9 tRNA-Pro c[154136,154210] 35 (tgg)
[09:22:48] 10 tRNA-Thr c[177022,177095] 34 (ggt)
[09:22:48] 11 tRNA-Met c[179328,179402] 35 (cat)
[09:22:48] 12 tRNA-His c[194142,194216] 34 (gtg)
[09:22:48] 13 tRNA-Trp c[225703,225776] 34 (cca)
[09:22:48] 14 tRNA-Arg [241261,241336] 36 (ccg)
[09:22:48] 15 tRNA-Arg [301905,301979] 35 (tct)
[09:22:48] 16 tRNA-Leu [343096,343183] 35 (gag)
[09:22:48] 17 tRNA-Leu [367548,367634] 35 (taa)
[09:22:48] 18 tRNA-Leu [385056,385138] 35 (tag)
[09:22:48] 19 tRNA-Met [415681,415756] 34 (cat)
[09:22:48] 20 tRNA-Ile [426514,426590] 35 (gat)
[09:22:48] 21 tRNA-Arg c[487109,487184] 36 (acg)
[09:22:48] 22 tRNA-Leu c[506311,506394] 34 (caa)
[09:22:48] 23 tRNA-Gln c[520374,520448] 33 (ttg)
[09:22:48] 24 tRNA-Ser c[534159,534244] 35 (cag)
[09:22:48] 25 tRNA-Phe c[616177,616250] 34 (gaa)
[09:22:48] 26 tRNA-Asp [621935,622009] 35 (gtc)
[09:22:48] 27 tRNA-Gly c[658086,658158] 34 (tcc)
[09:22:48] 28 tRNA-Tyr c[658162,658246] 36 (gta)
[09:22:48] 29 tRNA-Ser c[687362,687454] 36 (gct)
[09:22:48] 30 tRNA-Asn [693744,693818] 34 (gtt)
[09:22:48] 31 tRNA-Thr c[710070,710145] 36 (tgt)
[09:22:48] 32 tRNA-Arg c[728344,728418] 35 (cct)
[09:22:48] 33 tRNA-Ser c[760254,760340] 36 (gga)
[09:22:48] 34 tRNA-Cys [866170,866241] 34 (gca)
[09:22:48] 35 tRNA-Glu c[868827,868899] 34 (ttc)
[09:22:48] Found 35 tRNAs
[09:22:48] Predicting Ribosomal RNAs
[09:22:48] Running Barrnap with 8 threads
[09:22:49] 1 gnl|Prokka|wDimm_contig000001 636299 16S ribosomal RNA
[09:22:49] 2 gnl|Prokka|wDimm_contig000001 742404 5S ribosomal RNA
[09:22:49] 3 gnl|Prokka|wDimm_contig000001 743065 23S ribosomal RNA (partial)
[09:22:49] Found 3 rRNAs
[09:22:49] Skipping ncRNA search, enable with --rfam if desired.
[09:22:49] Total of 37 tRNA + rRNA features
[09:22:49] Searching for CRISPR repeats
[09:22:49] Found 0 CRISPRs
[09:22:49] Predicting coding sequences
[09:22:49] Contigs total 921012 bp, so using single mode
[09:22:49] Running: prodigal -i \/home\/yquentin\/work\/wolbachia\/prokka\/wDimm\/wDimm\.fna -c -m -g 11 -p single -f sco -q
[09:22:50] Excluding CDS which overlaps existing RNA (tRNA) at gnl|Prokka|wDimm_contig000001:385026..385151 on + strand
[09:22:50] Excluding CDS which overlaps existing RNA (tRNA) at gnl|Prokka|wDimm_contig000001:414389..415690 on + strand
[09:22:50] Excluding CDS which overlaps existing RNA (tRNA) at gnl|Prokka|wDimm_contig000001:520439..520774 on - strand
[09:22:51] Excluding CDS which overlaps existing RNA (rRNA) at gnl|Prokka|wDimm_contig000001:637240..637362 on - strand
[09:22:51] Excluding CDS which overlaps existing RNA (rRNA) at gnl|Prokka|wDimm_contig000001:744549..744674 on - strand
[09:22:51] Found 755 CDS
[09:22:51] Connecting features back to sequences
[09:22:51] Option --gram not specified, will NOT check for signal peptides.
[09:22:51] Not using genus-specific database. Try --usegenus to enable it.
[09:22:51] Annotating CDS, please be patient.
[09:22:51] Will use 8 CPUs for similarity searching.
[09:22:51] There are still 755 unannotated CDS left (started with 755)
[09:22:51] Will use blast to search against /usr/local/bioinfo/src/PROKKA/prokka-1.10/bin/../db/kingdom/Bacteria/sprot with 8 CPUs
[09:22:51] Running: cat \/home\/yquentin\/work\/wolbachia\/prokka\/wDimm\/proteins\.faa | parallel --gnu -j 8 --block 14095 --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\/wDimm\/proteins\.bls 2> /dev/null
[09:22:59] Modify product: Bifunctional protein FolD => Bifunctional protein FolD protein
[09:22:59] Modify product: Co-chaperone protein HscB homolog => hypothetical protein
[09:22:59] Modify product: Cytochrome b561 homolog 2 => hypothetical protein
[09:22:59] Modify product: Uncharacterized zinc protease Rv2782c => putative zinc protease
[09:22:59] Modify product: Transcription termination/antitermination protein NusG => hypothetical protein
[09:22:59] Modify product: Transcription termination/antitermination protein NusA => hypothetical protein
[09:22:59] Modify product: Transcription termination factor Rho => hypothetical protein
[09:22:59] Modify product: Probable dipeptidase PepE => putative dipeptidase PepE
[09:22:59] Modify product: Uncharacterized HIT-like protein HP_0404 => putative HIT-like protein
[09:22:59] Modify product: Uncharacterized metal-dependent hydrolase YcfH => putative metal-dependent hydrolase YcfH
[09:22:59] Modify product: Putative O-methyltransferase MSMEG_5073/MSMEI_4947 => Putative O-methyltransferase/MSMEI_4947
[09:22:59] Modify product: Stringent starvation protein A homolog => hypothetical protein
[09:22:59] Modify product: Riboflavin biosynthesis protein VVA0006 => Riboflavin biosynthesis protein
[09:22:59] Modify product: N utilization substance protein B homolog => hypothetical protein
[09:22:59] Modify product: SCO1 protein homolog => hypothetical protein
[09:22:59] Modify product: Putative NAD(P)H nitroreductase SA2311 => Putative NAD(P)H nitroreductase
[09:22:59] Modify product: Putative multidrug export ATP-binding/permease protein SAV1866 => Putative multidrug export ATP-binding/permease protein
[09:22:59] Modify product: GTP-binding protein TypA/BipA homolog => hypothetical protein
[09:22:59] Modify product: Probable protein kinase UbiB => putative protein kinase UbiB
[09:22:59] Modify product: Probable transcriptional regulatory protein aq_1575 => putative transcriptional regulatory protein
[09:22:59] Modify product: Uncharacterized oxidoreductase YciK => putative oxidoreductase YciK
[09:22:59] Modify product: Probable peroxiredoxin => putative peroxiredoxin
[09:23:00] Modify product: Probable GTP-binding protein EngB => putative GTP-binding protein EngB
[09:23:00] Modify product: Probable glycerol-3-phosphate acyltransferase => putative glycerol-3-phosphate acyltransferase
[09:23:00] Modify product: Uncharacterized zinc protease Rv2782c => putative zinc protease
[09:23:00] Modify product: Probable tRNA-dihydrouridine synthase => putative tRNA-dihydrouridine synthase
[09:23:00] Cleaned 26 /product names
[09:23:00] Deleting unwanted file: /home/yquentin/work/wolbachia/prokka/wDimm/proteins.faa
[09:23:00] Deleting unwanted file: /home/yquentin/work/wolbachia/prokka/wDimm/proteins.bls
[09:23:00] There are still 245 unannotated CDS left (started with 755)
[09:23:00] Will use hmmer3 to search against /usr/local/bioinfo/src/PROKKA/prokka-1.10/bin/../db/hmm/HAMAP.hmm with 8 CPUs
[09:23:00] Running: cat \/home\/yquentin\/work\/wolbachia\/prokka\/wDimm\/proteins\.faa | parallel --gnu -j 8 --block 2909 --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\/wDimm\/proteins\.bls 2> /dev/null
[09:23:02] Deleting unwanted file: /home/yquentin/work/wolbachia/prokka/wDimm/proteins.faa
[09:23:02] Deleting unwanted file: /home/yquentin/work/wolbachia/prokka/wDimm/proteins.bls
[09:23:02] There are still 227 unannotated CDS left (started with 755)
[09:23:02] Will use hmmer3 to search against /usr/local/bioinfo/src/PROKKA/prokka-1.10/bin/../db/hmm/CLUSTERS.hmm with 8 CPUs
[09:23:02] Running: cat \/home\/yquentin\/work\/wolbachia\/prokka\/wDimm\/proteins\.faa | parallel --gnu -j 8 --block 2612 --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\/wDimm\/proteins\.bls 2> /dev/null
[09:23:09] Deleting unwanted file: /home/yquentin/work/wolbachia/prokka/wDimm/proteins.faa
[09:23:09] Deleting unwanted file: /home/yquentin/work/wolbachia/prokka/wDimm/proteins.bls
[09:23:09] There are still 208 unannotated CDS left (started with 755)
[09:23:09] Will use hmmer3 to search against /usr/local/bioinfo/src/PROKKA/prokka-1.10/bin/../db/hmm/Pfam.hmm with 8 CPUs
[09:23:09] Running: cat \/home\/yquentin\/work\/wolbachia\/prokka\/wDimm\/proteins\.faa | parallel --gnu -j 8 --block 2382 --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\/wDimm\/proteins\.bls 2> /dev/null
[09:23:16] Modify product: RDD family => RDD family protein
[09:23:16] Modify product: Alpha/beta hydrolase family => Alpha/beta hydrolase family protein
[09:23:16] Modify product: PD-(D/E)XK nuclease superfamily => PD-(D/E)XK nuclease superfamily protein
[09:23:16] Modify product: KAP family P-loop domain => KAP family P-loop domain protein
[09:23:16] Modify product: AsmA family => AsmA family protein
[09:23:16] Modify product: Tim44-like domain => Tim44-like domain protein
[09:23:16] Modify product: BioY family => BioY family protein
[09:23:16] Modify product: ETC complex I subunit conserved region => hypothetical protein
[09:23:16] Modify product: RmlD substrate binding domain => RmlD substrate binding domain protein
[09:23:16] Modify product: Na+/H+ antiporter family => Na+/H+ antiporter family protein
[09:23:16] Modify product: TrbC/VIRB2 family => TrbC/VIRB2 family protein
[09:23:16] Modify product: AhpC/TSA family => AhpC/TSA family protein
[09:23:16] Modify product: SURF1 family => SURF1 family protein
[09:23:16] Modify product: Major Facilitator Superfamily => Major Facilitator Superfamily protein
[09:23:16] Modify product: RDD family => RDD family protein
[09:23:16] Modify product: Acetyltransferase (GNAT) family => Acetyltransferase (GNAT) family protein
[09:23:16] Modify product: Peptidase M16 inactive domain => Peptidase M16 inactive domain protein
[09:23:16] Modify product: Integral membrane protein TerC family => Integral membrane protein TerC family protein
[09:23:16] Modify product: Uracil DNA glycosylase superfamily => Uracil DNA glycosylase superfamily protein
[09:23:16] Cleaned 19 /product names
[09:23:16] Deleting unwanted file: /home/yquentin/work/wolbachia/prokka/wDimm/proteins.faa
[09:23:16] Deleting unwanted file: /home/yquentin/work/wolbachia/prokka/wDimm/proteins.bls
[09:23:16] Labelling remaining 162 proteins as 'hypothetical protein'
[09:23:16] Possible /pseudo '4-hydroxy-3-methylbut-2-enyl diphosphate reductase' at gnl|Prokka|wDimm_contig000001 position 71417
[09:23:16] Possible /pseudo 'Arginine/agmatine antiporter' at gnl|Prokka|wDimm_contig000001 position 73507
[09:23:16] Possible /pseudo '60 kDa chaperonin 5' at gnl|Prokka|wDimm_contig000001 position 518131
[09:23:16] Possible /pseudo 'Dephospho-CoA kinase' at gnl|Prokka|wDimm_contig000001 position 691946
[09:23:16] Possible /pseudo 'Exopolysaccharide synthesis, ExoD' at gnl|Prokka|wDimm_contig000001 position 730532
[09:23:16] Possible /pseudo 'TrbL/VirB6 plasmid conjugal transfer protein' at gnl|Prokka|wDimm_contig000001 position 783266
[09:23:16] Possible /pseudo 'TrbL/VirB6 plasmid conjugal transfer protein' at gnl|Prokka|wDimm_contig000001 position 785668
[09:23:16] Possible /pseudo 'TrbL/VirB6 plasmid conjugal transfer protein' at gnl|Prokka|wDimm_contig000001 position 788770
[09:23:16] Possible /pseudo 'Cell division protein FtsZ' at gnl|Prokka|wDimm_contig000001 position 830875
[09:23:16] Found 481 unique /gene codes.
[09:23:16] Fixed 17 colliding /gene names.
[09:23:16] Adding /locus_tag identifiers
[09:23:16] Assigned 793 locus_tags to CDS and RNA features.
[09:23:16] Writing outputs to /home/yquentin/work/wolbachia/prokka/wDimm/
[09:23:17] Generating annotation statistics file
[09:23:17] Generating Genbank and Sequin files
[09:23:17] 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\/wDimm\/wDimm\.err -i \/home\/yquentin\/work\/wolbachia\/prokka\/wDimm\/wDimm\.fsa 2> /dev/null
[09:23:19] Deleting unwanted file: /home/yquentin/work/wolbachia/prokka/wDimm/errorsummary.val
[09:23:19] Deleting unwanted file: /home/yquentin/work/wolbachia/prokka/wDimm/wDimm.dr
[09:23:19] Deleting unwanted file: /home/yquentin/work/wolbachia/prokka/wDimm/wDimm.fixedproducts
[09:23:19] Deleting unwanted file: /home/yquentin/work/wolbachia/prokka/wDimm/wDimm.ecn
[09:23:19] Deleting unwanted file: /home/yquentin/work/wolbachia/prokka/wDimm/wDimm.val
[09:23:19] Output files:
[09:23:19] /home/yquentin/work/wolbachia/prokka/wDimm/wDimm.gff
[09:23:19] /home/yquentin/work/wolbachia/prokka/wDimm/wDimm.err
[09:23:19] /home/yquentin/work/wolbachia/prokka/wDimm/wDimm.tbl
[09:23:19] /home/yquentin/work/wolbachia/prokka/wDimm/wDimm.txt
[09:23:19] /home/yquentin/work/wolbachia/prokka/wDimm/wDimm.gbk
[09:23:19] /home/yquentin/work/wolbachia/prokka/wDimm/wDimm.fna
[09:23:19] /home/yquentin/work/wolbachia/prokka/wDimm/wDimm.fsa
[09:23:19] /home/yquentin/work/wolbachia/prokka/wDimm/wDimm.faa
[09:23:19] /home/yquentin/work/wolbachia/prokka/wDimm/wDimm.sqn
[09:23:19] /home/yquentin/work/wolbachia/prokka/wDimm/wDimm.ffn
[09:23:19] /home/yquentin/work/wolbachia/prokka/wDimm/wDimm.log
[09:23:19] Walltime used: 0.53 minutes
[09:23:19] If you use this result please cite the Prokka paper:
[09:23:19] Seemann T (2014) Prokka: rapid prokaryotic genome annotation. Bioinformatics. 30(14):2068-9.
[09:23:19] Type 'prokka --citation' for more details.
[09:23:19] Thank you, come again.