[15:07:05] Command: --force --outdir /home/yquentin/work/wolbachia/prokka/wPpe --addgenes --prefix wPpe --locustag wPpe --species Wolbachia pipientis --strain wPpe --compliant --quiet /home/yquentin/work/wolbachia/prokka/wPpe.fna
[15:07:05] Looking for 'aragorn' - found /usr/local/bioinfo/bin/aragorn
[15:07:05] Determined aragorn version is 1.2
[15:07:05] Looking for 'barrnap' - found /usr/local/bioinfo/bin/barrnap
[15:07:05] Determined barrnap version is 0.5
[15:07:05] Looking for 'blastp' - found /usr/local/bioinfo/src/NCBI_Blast+/ncbi-blast-2.6.0+/bin/blastp
[15:07:05] Determined blastp version is 2.6
[15:07:05] Looking for 'cmpress' - found /usr/local/bioinfo/src/PROKKA/prokka-1.10/bin/../binaries/linux/cmpress
[15:07:05] Determined cmpress version is 1.1
[15:07:05] Looking for 'cmscan' - found /usr/local/bioinfo/src/PROKKA/prokka-1.10/bin/../binaries/linux/cmscan
[15:07:05] Determined cmscan version is 1.1
[15:07:05] Looking for 'egrep' - found /bin/egrep
[15:07:05] Looking for 'find' - found /bin/find
[15:07:05] Looking for 'grep' - found /bin/grep
[15:07:05] Looking for 'hmmpress' - found /usr/local/bioinfo/bin/hmmpress
[15:07:05] Determined hmmpress version is 3.1
[15:07:05] Looking for 'hmmscan' - found /usr/local/bioinfo/bin/hmmscan
[15:07:05] Determined hmmscan version is 3.1
[15:07:05] Looking for 'less' - found /usr/bin/less
[15:07:05] Looking for 'makeblastdb' - found /usr/local/bioinfo/src/NCBI_Blast+/ncbi-blast-2.6.0+/bin/makeblastdb
[15:07:05] Determined makeblastdb version is 2.6
[15:07:05] Looking for 'minced' - found /usr/local/bioinfo/bin/minced
[15:07:05] Determined minced version is 1.6
[15:07:05] 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
[15:07:06] Determined signalp version is 4.1
[15:07:06] Looking for 'tbl2asn' - found /home/yquentin/save/scripts/tbl2asn
[15:07:06] Determined tbl2asn version is 25.3
[15:07:06] Using genetic code table 11.
[15:07:06] Loading and checking input file: /home/yquentin/work/wolbachia/prokka/wPpe.fna
[15:07:06] Wrote 12 contigs
[15:07:06] Predicting tRNAs and tmRNAs
[15:07:06] Running: aragorn -gc11  -w \/home\/yquentin\/work\/wolbachia\/prokka\/wPpe\/wPpe\.fna
[15:07:06] 1 tRNA-Gly c[145,217] 34 (tcc)
[15:07:06] 2 tRNA-Tyr c[223,307] 35 (gta)
[15:07:06] 3 tRNA-Thr c[479,552] 34 (ggt)
[15:07:06] 4 tRNA-Asn [49801,49873] 33 (gtt)
[15:07:06] 5 tRNA-His [100505,100578] 34 (gtg)
[15:07:06] 6 tRNA-Ser c[135496,135588] 35 (gct)
[15:07:06] 7 tRNA-Arg [163271,163345] 35 (ccg)
[15:07:06] 8 tRNA-Leu c[223613,223697] 35 (taa)
[15:07:06] 9 tRNA-Val c[261899,261973] 35 (tac)
[15:07:06] 10 tRNA-Glu [272331,272403] 34 (ttc)
[15:07:06] 11 tRNA-Val [284786,284859] 34 (gac)
[15:07:06] 1 tRNA-Gly c[4197,4270] 34 (gcc)
[15:07:06] 2 tRNA-Asp c[14094,14168] 35 (gtc)
[15:07:06] 3 tRNA-Phe [19477,19551] 34 (gaa)
[15:07:06] 4 tRNA-Trp [58785,58858] 34 (cca)
[15:07:06] 5 tRNA-Leu c[89466,89552] 35 (gag)
[15:07:06] 6 tRNA-Ser c[93129,93219] 35 (tga)
[15:07:06] 7 tRNA-Ile [95292,95368] 35 (gat)
[15:07:06] 1 tRNA-Met [13687,13759] 33 (cat)
[15:07:06] 2 tRNA-Leu [14515,14598] 35 (tag)
[15:07:06] 3 tRNA-Lys [26131,26204] 34 (ctt)
[15:07:06] 4 tRNA-Ser [35664,35753] 35 (gga)
[15:07:06] 5 tRNA-Leu c[65423,65506] 34 (caa)
[15:07:06] 6 tRNA-Cys c[84500,84572] 34 (gca)
[15:07:06] 1 tRNA-Arg [351,425] 35 (tct)
[15:07:06] 2 tRNA-Ser c[23339,23424] 35 (cag)
[15:07:06] 3 tRNA-Ala c[32691,32766] 34 (tgc)
[15:07:06] 1 tRNA-Lys [18153,18226] 34 (ttt)
[15:07:06] 2 tRNA-Arg [34159,34234] 36 (acg)
[15:07:06] 3 tRNA-Thr c[44278,44351] 34 (tgt)
[15:07:06] 1 tRNA-Arg c[7152,7228] 35 (cct)
[15:07:06] 2 tmRNA* [12978,13302] 184,234 ANDNFAADSNELSLAA*
[15:07:06] 3 tRNA-Pro c[56905,56981] 37 (tgg)
[15:07:06] 4 tRNA-Met [68176,68250] 35 (cat)
[15:07:06] 1 tRNA-Gln c[4549,4621] 33 (ttg)
[15:07:06] 2 tRNA-Met [21324,21398] 35 (cat)
[15:07:06] Found 36 tRNAs
[15:07:06] Predicting Ribosomal RNAs
[15:07:06] Running Barrnap with 8 threads
[15:07:08] 1 gnl|Prokka|wPpe_contig000007 69716 16S ribosomal RNA
[15:07:08] 2 gnl|Prokka|wPpe_contig000010 32396 23S ribosomal RNA
[15:07:08] 3 gnl|Prokka|wPpe_contig000010 35239 5S ribosomal RNA
[15:07:08] Found 3 rRNAs
[15:07:08] Skipping ncRNA search, enable with --rfam if desired.
[15:07:08] Total of 38 tRNA + rRNA features
[15:07:08] Searching for CRISPR repeats
[15:07:08] Found 0 CRISPRs
[15:07:08] Predicting coding sequences
[15:07:08] Contigs total 975127 bp, so using single mode
[15:07:08] Running: prodigal -i \/home\/yquentin\/work\/wolbachia\/prokka\/wPpe\/wPpe\.fna -c -m -g 11 -p single -f sco -q
[15:07:10] Excluding CDS which overlaps existing RNA (tRNA) at gnl|Prokka|wPpe_contig000001:284822..285730 on + strand
[15:07:10] Excluding CDS which overlaps existing RNA (tRNA) at gnl|Prokka|wPpe_contig000005:3393..4259 on + strand
[15:07:10] Excluding CDS which overlaps existing RNA (tRNA) at gnl|Prokka|wPpe_contig000006:12404..13696 on + strand
[15:07:10] Excluding CDS which overlaps existing RNA (tRNA) at gnl|Prokka|wPpe_contig000006:35510..35842 on - strand
[15:07:10] Excluding CDS which overlaps existing RNA (tRNA) at gnl|Prokka|wPpe_contig000006:65449..67044 on + strand
[15:07:10] Excluding CDS which overlaps existing RNA (tRNA) at gnl|Prokka|wPpe_contig000007:342..1646 on - strand
[15:07:10] Excluding CDS which overlaps existing RNA (tRNA) at gnl|Prokka|wPpe_contig000010:4612..4926 on - strand
[15:07:10] Found 962 CDS
[15:07:10] Connecting features back to sequences
[15:07:10] Option --gram not specified, will NOT check for signal peptides.
[15:07:10] Not using genus-specific database. Try --usegenus to enable it.
[15:07:10] Annotating CDS, please be patient.
[15:07:10] Will use 8 CPUs for similarity searching.
[15:07:11] There are still 962 unannotated CDS left (started with 962)
[15:07:11] Will use blast to search against /usr/local/bioinfo/src/PROKKA/prokka-1.10/bin/../db/kingdom/Bacteria/sprot with 8 CPUs
[15:07:11] Running: cat \/home\/yquentin\/work\/wolbachia\/prokka\/wPpe\/proteins\.faa | parallel --gnu -j 8 --block 17702 --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\/wPpe\/proteins\.bls 2> /dev/null
[15:07:31] Modify product: Probable transcriptional regulatory protein aq_1575 => putative transcriptional regulatory protein
[15:07:31] Modify product: Probable glycerol-3-phosphate acyltransferase => putative glycerol-3-phosphate acyltransferase
[15:07:31] Modify product: Probable phospholipid ABC transporter permease protein MlaE => putative phospholipid ABC transporter permease protein MlaE
[15:07:31] Modify product: Uncharacterized zinc protease Rv2782c => putative zinc protease
[15:07:31] Modify product: Probable phospholipid ABC transporter-binding protein MlaD => putative phospholipid ABC transporter-binding protein MlaD
[15:07:31] Modify product: Actin-binding protein Smlt3054 => Actin-binding protein
[15:07:31] Modify product: Probable murein peptide carboxypeptidase => putative murein peptide carboxypeptidase
[15:07:31] Modify product: Probable GTP-binding protein EngB => putative GTP-binding protein EngB
[15:07:31] Modify product: Transcription termination/antitermination protein NusA => hypothetical protein
[15:07:31] Modify product: Putative multidrug export ATP-binding/permease protein SAV1866 => Putative multidrug export ATP-binding/permease protein
[15:07:31] Modify product: Bifunctional protein FolD => Bifunctional protein FolD protein
[15:07:32] Modify product: Transcription termination/antitermination protein NusG => hypothetical protein
[15:07:32] Modify product: Uncharacterized HIT-like protein HP_0404 => putative HIT-like protein
[15:07:32] Modify product: Putative O-methyltransferase MSMEG_5073/MSMEI_4947 => Putative O-methyltransferase/MSMEI_4947
[15:07:32] Modify product: Probable protein kinase UbiB => putative protein kinase UbiB
[15:07:32] Modify product: Putative multidrug export ATP-binding/permease protein SAV1866 => Putative multidrug export ATP-binding/permease protein
[15:07:32] Modify product: Putative multidrug export ATP-binding/permease protein SAV1866 => Putative multidrug export ATP-binding/permease protein
[15:07:32] Modify product: Bifunctional protein FolD => Bifunctional protein FolD protein
[15:07:32] Modify product: Uncharacterized metal-dependent hydrolase YcfH => putative metal-dependent hydrolase YcfH
[15:07:32] Modify product: Probable dipeptidase PepE => putative dipeptidase PepE
[15:07:32] Modify product: Uncharacterized zinc protease Rv2782c => putative zinc protease
[15:07:32] Modify product: Actin-binding protein Smlt3054 => Actin-binding protein
[15:07:32] Modify product: Probable chromosome-partitioning protein ParB => putative chromosome-partitioning protein ParB
[15:07:32] Modify product: N utilization substance protein B homolog => hypothetical protein
[15:07:32] Modify product: Putative phosphoribosyl transferase Rv0571c => Putative phosphoribosyl transferase
[15:07:32] Modify product: Transcription termination factor Rho => hypothetical protein
[15:07:33] Modify product: SCO1 protein homolog => hypothetical protein
[15:07:33] Modify product: Probable peroxiredoxin => putative peroxiredoxin
[15:07:33] Modify product: Uncharacterized oxidoreductase YciK => putative oxidoreductase YciK
[15:07:33] Cleaned 29 /product names
[15:07:33] Deleting unwanted file: /home/yquentin/work/wolbachia/prokka/wPpe/proteins.faa
[15:07:33] Deleting unwanted file: /home/yquentin/work/wolbachia/prokka/wPpe/proteins.bls
[15:07:34] There are still 404 unannotated CDS left (started with 962)
[15:07:34] Will use hmmer3 to search against /usr/local/bioinfo/src/PROKKA/prokka-1.10/bin/../db/hmm/HAMAP.hmm with 8 CPUs
[15:07:34] Running: cat \/home\/yquentin\/work\/wolbachia\/prokka\/wPpe\/proteins\.faa | parallel --gnu -j 8 --block 5992 --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\/wPpe\/proteins\.bls 2> /dev/null
[15:07:42] Deleting unwanted file: /home/yquentin/work/wolbachia/prokka/wPpe/proteins.faa
[15:07:42] Deleting unwanted file: /home/yquentin/work/wolbachia/prokka/wPpe/proteins.bls
[15:07:42] There are still 380 unannotated CDS left (started with 962)
[15:07:42] Will use hmmer3 to search against /usr/local/bioinfo/src/PROKKA/prokka-1.10/bin/../db/hmm/CLUSTERS.hmm with 8 CPUs
[15:07:42] Running: cat \/home\/yquentin\/work\/wolbachia\/prokka\/wPpe\/proteins\.faa | parallel --gnu -j 8 --block 5547 --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\/wPpe\/proteins\.bls 2> /dev/null
[15:08:02] Deleting unwanted file: /home/yquentin/work/wolbachia/prokka/wPpe/proteins.faa
[15:08:02] Deleting unwanted file: /home/yquentin/work/wolbachia/prokka/wPpe/proteins.bls
[15:08:02] There are still 357 unannotated CDS left (started with 962)
[15:08:02] Will use hmmer3 to search against /usr/local/bioinfo/src/PROKKA/prokka-1.10/bin/../db/hmm/Pfam.hmm with 8 CPUs
[15:08:02] Running: cat \/home\/yquentin\/work\/wolbachia\/prokka\/wPpe\/proteins\.faa | parallel --gnu -j 8 --block 5154 --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\/wPpe\/proteins\.bls 2> /dev/null
[15:08:22] Modify product: TrbC/VIRB2 family => TrbC/VIRB2 family protein
[15:08:22] Modify product: Acetyltransferase (GNAT) family => Acetyltransferase (GNAT) family protein
[15:08:22] Modify product: Ankyrin repeat => Ankyrin repeat protein
[15:08:22] Modify product: PQ loop repeat => PQ loop repeat protein
[15:08:22] Modify product: Alpha/beta hydrolase family => Alpha/beta hydrolase family protein
[15:08:22] Modify product: Ankyrin repeat => Ankyrin repeat protein
[15:08:22] Modify product: Ankyrin repeat => Ankyrin repeat protein
[15:08:22] Modify product: Ankyrin repeat => Ankyrin repeat protein
[15:08:22] Modify product: Peptidase M16 inactive domain => Peptidase M16 inactive domain protein
[15:08:22] Modify product: Zinc-finger domain => Zinc-finger domain protein
[15:08:22] Modify product: KAP family P-loop domain => KAP family P-loop domain protein
[15:08:22] Modify product: Sodium:dicarboxylate symporter family => Sodium:dicarboxylate symporter family protein
[15:08:22] Modify product: RDD family => RDD family protein
[15:08:22] Modify product: Alpha/beta hydrolase family => Alpha/beta hydrolase family protein
[15:08:22] Modify product: RmuC family => RmuC family protein
[15:08:22] Modify product: NUDIX domain => NUDIX domain protein
[15:08:22] Modify product: Ankyrin repeat => Ankyrin repeat protein
[15:08:22] Modify product: SPFH domain / Band 7 family => SPFH domain / Band 7 family protein
[15:08:22] Modify product: RDD family => RDD family protein
[15:08:22] Modify product: SURF1 family => SURF1 family protein
[15:08:22] Modify product: PD-(D/E)XK nuclease superfamily => PD-(D/E)XK nuclease superfamily protein
[15:08:22] Modify product: RDD family => RDD family protein
[15:08:22] Modify product: HSCB C-terminal oligomerisation domain => hypothetical protein
[15:08:22] Modify product: Tetratricopeptide repeat => Tetratricopeptide repeat protein
[15:08:22] Modify product: ETC complex I subunit conserved region => hypothetical protein
[15:08:22] Modify product: COQ9 => hypothetical protein
[15:08:22] Modify product: Major Facilitator Superfamily => Major Facilitator Superfamily protein
[15:08:22] Modify product: DSBA-like thioredoxin domain => DSBA-like thioredoxin domain protein
[15:08:22] Modify product: Integral membrane protein TerC family => Integral membrane protein TerC family protein
[15:08:22] Modify product: AhpC/TSA family => AhpC/TSA family protein
[15:08:22] Modify product: Tim44-like domain => Tim44-like domain protein
[15:08:22] Modify product: Uracil DNA glycosylase superfamily => Uracil DNA glycosylase superfamily protein
[15:08:22] Cleaned 32 /product names
[15:08:22] Deleting unwanted file: /home/yquentin/work/wolbachia/prokka/wPpe/proteins.faa
[15:08:22] Deleting unwanted file: /home/yquentin/work/wolbachia/prokka/wPpe/proteins.bls
[15:08:22] Labelling remaining 276 proteins as 'hypothetical protein'
[15:08:22] Possible /pseudo 'PD-(D/E)XK nuclease family transposase' at gnl|Prokka|wPpe_contig000001 position 98141
[15:08:22] Possible /pseudo 'UDP-N-acetylenolpyruvoylglucosamine reductase' at gnl|Prokka|wPpe_contig000001 position 150884
[15:08:22] Possible /pseudo 'TrbL/VirB6 plasmid conjugal transfer protein' at gnl|Prokka|wPpe_contig000001 position 214689
[15:08:22] Possible /pseudo 'TrbL/VirB6 plasmid conjugal transfer protein' at gnl|Prokka|wPpe_contig000001 position 217061
[15:08:22] Possible /pseudo 'Ankyrin repeat protein' at gnl|Prokka|wPpe_contig000001 position 228026
[15:08:22] Possible /pseudo 'Ankyrin repeat protein' at gnl|Prokka|wPpe_contig000001 position 228204
[15:08:22] Possible /pseudo 'Ankyrin repeats (3 copies)' at gnl|Prokka|wPpe_contig000002 position 21524
[15:08:22] Possible /pseudo 'Holliday junction ATP-dependent DNA helicase RuvB' at gnl|Prokka|wPpe_contig000005 position 27306
[15:08:22] Possible /pseudo 'Trigger factor' at gnl|Prokka|wPpe_contig000006 position 16048
[15:08:22] Possible /pseudo 'ATP-dependent Clp protease proteolytic subunit' at gnl|Prokka|wPpe_contig000006 position 16808
[15:08:22] Possible /pseudo 'ATP-dependent Clp protease proteolytic subunit' at gnl|Prokka|wPpe_contig000006 position 16985
[15:08:22] Possible /pseudo '3-oxoacyl-[acyl-carrier-protein] synthase 2' at gnl|Prokka|wPpe_contig000008 position 75578
[15:08:22] Possible /pseudo 'Valine--tRNA ligase' at gnl|Prokka|wPpe_contig000009 position 9922
[15:08:22] Found 507 unique /gene codes.
[15:08:22] Fixed 37 colliding /gene names.
[15:08:22] Adding /locus_tag identifiers
[15:08:23] Assigned 1001 locus_tags to CDS and RNA features.
[15:08:23] Writing outputs to /home/yquentin/work/wolbachia/prokka/wPpe/
[15:08:25] Generating annotation statistics file
[15:08:25] Generating Genbank and Sequin files
[15:08:25] 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\/wPpe\/wPpe\.err -i \/home\/yquentin\/work\/wolbachia\/prokka\/wPpe\/wPpe\.fsa 2> /dev/null
[15:08:29] Deleting unwanted file: /home/yquentin/work/wolbachia/prokka/wPpe/errorsummary.val
[15:08:29] Deleting unwanted file: /home/yquentin/work/wolbachia/prokka/wPpe/wPpe.dr
[15:08:29] Deleting unwanted file: /home/yquentin/work/wolbachia/prokka/wPpe/wPpe.fixedproducts
[15:08:29] Deleting unwanted file: /home/yquentin/work/wolbachia/prokka/wPpe/wPpe.ecn
[15:08:29] Deleting unwanted file: /home/yquentin/work/wolbachia/prokka/wPpe/wPpe.val
[15:08:29] Output files:
[15:08:29] /home/yquentin/work/wolbachia/prokka/wPpe/wPpe.tbl
[15:08:29] /home/yquentin/work/wolbachia/prokka/wPpe/wPpe.err
[15:08:29] /home/yquentin/work/wolbachia/prokka/wPpe/wPpe.txt
[15:08:29] /home/yquentin/work/wolbachia/prokka/wPpe/wPpe.fna
[15:08:29] /home/yquentin/work/wolbachia/prokka/wPpe/wPpe.faa
[15:08:29] /home/yquentin/work/wolbachia/prokka/wPpe/wPpe.sqn
[15:08:29] /home/yquentin/work/wolbachia/prokka/wPpe/wPpe.log
[15:08:29] /home/yquentin/work/wolbachia/prokka/wPpe/wPpe.gff
[15:08:29] /home/yquentin/work/wolbachia/prokka/wPpe/wPpe.ffn
[15:08:29] /home/yquentin/work/wolbachia/prokka/wPpe/wPpe.gbk
[15:08:29] /home/yquentin/work/wolbachia/prokka/wPpe/wPpe.fsa
[15:08:29] Walltime used: 1.40 minutes
[15:08:29] If you use this result please cite the Prokka paper:
[15:08:29] Seemann T (2014) Prokka: rapid prokaryotic genome annotation. Bioinformatics. 30(14):2068-9.
[15:08:29] Type 'prokka --citation' for more details.
[15:08:29] Thank you, come again.