[10:41:24] Command: --force --outdir /home/yquentin/work/wolbachia/prokka/wHa --addgenes --prefix wHa --locustag wHa --species Wolbachia endosymbiont --strain wHa --compliant --quiet /home/yquentin/work/wolbachia/prokka/wHa.fna
[10:41:24] Looking for 'aragorn' - found /usr/local/bioinfo/bin/aragorn
[10:41:24] Determined aragorn version is 1.2
[10:41:24] Looking for 'barrnap' - found /usr/local/bioinfo/bin/barrnap
[10:41:24] Determined barrnap version is 0.5
[10:41:24] Looking for 'blastp' - found /usr/local/bioinfo/src/NCBI_Blast+/ncbi-blast-2.6.0+/bin/blastp
[10:41:24] Determined blastp version is 2.6
[10:41:24] Looking for 'cmpress' - found /usr/local/bioinfo/src/PROKKA/prokka-1.10/bin/../binaries/linux/cmpress
[10:41:24] Determined cmpress version is 1.1
[10:41:24] Looking for 'cmscan' - found /usr/local/bioinfo/src/PROKKA/prokka-1.10/bin/../binaries/linux/cmscan
[10:41:24] Determined cmscan version is 1.1
[10:41:24] Looking for 'egrep' - found /bin/egrep
[10:41:24] Looking for 'find' - found /bin/find
[10:41:24] Looking for 'grep' - found /bin/grep
[10:41:24] Looking for 'hmmpress' - found /usr/local/bioinfo/bin/hmmpress
[10:41:24] Determined hmmpress version is 3.1
[10:41:24] Looking for 'hmmscan' - found /usr/local/bioinfo/bin/hmmscan
[10:41:24] Determined hmmscan version is 3.1
[10:41:24] Looking for 'less' - found /usr/bin/less
[10:41:24] Looking for 'makeblastdb' - found /usr/local/bioinfo/src/NCBI_Blast+/ncbi-blast-2.6.0+/bin/makeblastdb
[10:41:25] Determined makeblastdb version is 2.6
[10:41:25] Looking for 'minced' - found /usr/local/bioinfo/bin/minced
[10:41:25] Determined minced version is 1.6
[10:41:25] Looking for 'parallel' - found /usr/local/bioinfo/bin/parallel
[10:41:26] Determined parallel version is 20141022
[10:41:26] Looking for 'prodigal' - found /usr/local/bioinfo/bin/prodigal
[10:41:26] Determined prodigal version is 2.6
[10:41:26] Looking for 'rnammer' - found /usr/local/bioinfo/bin/rnammer
[10:41:26] Determined rnammer version is 1.2
[10:41:26] Looking for 'sed' - found /bin/sed
[10:41:26] Looking for 'signalp' - found /usr/local/bioinfo/bin/signalp
[10:41:26] Determined signalp version is 4.1
[10:41:26] Looking for 'tbl2asn' - found /home/yquentin/save/scripts/tbl2asn
[10:41:26] Determined tbl2asn version is 25.3
[10:41:26] Using genetic code table 11.
[10:41:26] Loading and checking input file: /home/yquentin/work/wolbachia/prokka/wHa.fna
[10:41:26] Wrote 1 contigs
[10:41:26] Predicting tRNAs and tmRNAs
[10:41:26] Running: aragorn -gc11  -w \/home\/yquentin\/work\/wolbachia\/prokka\/wHa\/wHa\.fna
[10:41:27] 1 tRNA-Leu [3028,3115] 35 (gag)
[10:41:27] 2 tRNA-Trp [17536,17609] 34 (cca)
[10:41:27] 3 tRNA-Arg c[44582,44659] 36 (acg)
[10:41:27] 4 tRNA-Ile [65288,65364] 35 (gat)
[10:41:27] 5 tRNA-Arg [80410,80486] 35 (cct)
[10:41:27] 6 tmRNA* [121049,121377] 194,238 ANDNFAAEEYPVAA*
[10:41:27] 7 tRNA-Thr c[153461,153534] 34 (tgt)
[10:41:27] 8 tRNA-Phe c[506990,507064] 34 (gaa)
[10:41:27] 9 tRNA-Asp [512714,512790] 35 (gtc)
[10:41:27] 10 tRNA-Leu c[556288,556374] 35 (taa)
[10:41:27] 11 tRNA-Leu c[588939,589022] 34 (caa)
[10:41:27] 12 tRNA-Leu c[635355,635437] 35 (tag)
[10:41:27] 13 tRNA-Gly c[693077,693148] 33 (tcc)
[10:41:27] 14 tRNA-Tyr c[693153,693235] 35 (gta)
[10:41:27] 15 tRNA-Ser [755428,755516] 36 (gga)
[10:41:27] 16 tRNA-Arg [780999,781073] 35 (ccg)
[10:41:27] 17 tRNA-Met [793401,793474] 34 (cat)
[10:41:27] 18 tRNA-Gln c[826729,826803] 33 (ttg)
[10:41:27] 19 tRNA-Asn [892001,892073] 33 (gtt)
[10:41:27] 20 tRNA-Met c[909303,909379] 35 (cat)
[10:41:27] 21 tRNA-Gly [910656,910729] 34 (gcc)
[10:41:27] 22 tRNA-Ala c[967442,967517] 34 (tgc)
[10:41:27] 23 tRNA-Lys [967845,967918] 34 (ttt)
[10:41:27] 24 tRNA-Ser [974069,974157] 35 (tga)
[10:41:27] 25 tRNA-Ser [986376,986461] 35 (cag)
[10:41:27] 26 tRNA-His c[1000064,1000139] 34 (gtg)
[10:41:27] 27 tRNA-Val [1031265,1031338] 34 (gac)
[10:41:27] 28 tRNA-Arg c[1109354,1109428] 35 (tct)
[10:41:27] 29 tRNA-Thr c[1132920,1132993] 34 (ggt)
[10:41:27] 30 tRNA-Met c[1134670,1134746] 35 (cat)
[10:41:27] 31 tRNA-Val c[1179432,1179504] 34 (tac)
[10:41:27] 32 tRNA-Pro c[1186220,1186295] 36 (tgg)
[10:41:27] 33 tRNA-Glu c[1187218,1187290] 34 (ttc)
[10:41:27] 34 tRNA-Cys [1212592,1212664] 34 (gca)
[10:41:27] 35 tRNA-Ser [1235125,1235217] 36 (gct)
[10:41:27] Found 35 tRNAs
[10:41:27] Predicting Ribosomal RNAs
[10:41:27] Running Barrnap with 8 threads
[10:41:28] 1 gnl|Prokka|wHa_contig000001 179816 23S ribosomal RNA
[10:41:28] 2 gnl|Prokka|wHa_contig000001 182646 5S ribosomal RNA
[10:41:28] 3 gnl|Prokka|wHa_contig000001 1196642 16S ribosomal RNA
[10:41:28] Found 3 rRNAs
[10:41:28] Skipping ncRNA search, enable with --rfam if desired.
[10:41:28] Total of 37 tRNA + rRNA features
[10:41:28] Searching for CRISPR repeats
[10:41:29] Found 0 CRISPRs
[10:41:29] Predicting coding sequences
[10:41:29] Contigs total 1295804 bp, so using single mode
[10:41:29] Running: prodigal -i \/home\/yquentin\/work\/wolbachia\/prokka\/wHa\/wHa\.fna -c -m -g 11 -p single -f sco -q
[10:41:32] Excluding CDS which overlaps existing RNA (tRNA) at gnl|Prokka|wHa_contig000001:635273..635431 on - strand
[10:41:32] Excluding CDS which overlaps existing RNA (tRNA) at gnl|Prokka|wHa_contig000001:792136..793401 on + strand
[10:41:32] Excluding CDS which overlaps existing RNA (tRNA) at gnl|Prokka|wHa_contig000001:826794..827129 on - strand
[10:41:32] Excluding CDS which overlaps existing RNA (tRNA) at gnl|Prokka|wHa_contig000001:1109363..1109773 on + strand
[10:41:32] Excluding CDS which overlaps existing RNA (rRNA) at gnl|Prokka|wHa_contig000001:1197078..1197200 on + strand
[10:41:33] Found 1235 CDS
[10:41:33] Connecting features back to sequences
[10:41:33] Option --gram not specified, will NOT check for signal peptides.
[10:41:33] Not using genus-specific database. Try --usegenus to enable it.
[10:41:33] Annotating CDS, please be patient.
[10:41:33] Will use 8 CPUs for similarity searching.
[10:41:33] There are still 1235 unannotated CDS left (started with 1235)
[10:41:33] Will use blast to search against /usr/local/bioinfo/src/PROKKA/prokka-1.10/bin/../db/kingdom/Bacteria/sprot with 8 CPUs
[10:41:33] Running: cat \/home\/yquentin\/work\/wolbachia\/prokka\/wHa\/proteins\.faa | parallel --gnu -j 8 --block 23198 --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\/wHa\/proteins\.bls 2> /dev/null
[10:41:49] Modify product: Actin-binding protein Smlt3054 => Actin-binding protein
[10:41:49] Modify product: Transcription termination/antitermination protein NusG => hypothetical protein
[10:41:49] Modify product: Probable tRNA-dihydrouridine synthase => putative tRNA-dihydrouridine synthase
[10:41:49] Modify product: SCO1 protein homolog => hypothetical protein
[10:41:49] Modify product: Probable transcriptional regulatory protein aq_1575 => putative transcriptional regulatory protein
[10:41:50] Modify product: Probable GTP-binding protein EngB => putative GTP-binding protein EngB
[10:41:50] Modify product: N utilization substance protein B homolog => hypothetical protein
[10:41:50] Modify product: Putative multidrug export ATP-binding/permease protein SAV1866 => Putative multidrug export ATP-binding/permease protein
[10:41:50] Modify product: Actin-binding protein Smlt3054 => Actin-binding protein
[10:41:50] Modify product: Bifunctional protein FolD => Bifunctional protein FolD protein
[10:41:50] Modify product: Uncharacterized ABC transporter ATP-binding protein TM_0288 => putative ABC transporter ATP-binding protein
[10:41:50] Modify product: Uncharacterized zinc protease Rv2782c => putative zinc protease
[10:41:50] Modify product: Probable peroxiredoxin => putative peroxiredoxin
[10:41:50] Modify product: Uncharacterized zinc protease Rv2782c => putative zinc protease
[10:41:50] Modify product: Uncharacterized zinc protease Rv2782c => putative zinc protease
[10:41:50] Modify product: Transcription termination factor Rho => hypothetical protein
[10:41:50] Modify product: Co-chaperone protein HscB homolog => hypothetical protein
[10:41:50] Modify product: Actin-binding protein Smlt3054 => Actin-binding protein
[10:41:50] Modify product: Actin-binding protein Smlt3054 => Actin-binding protein
[10:41:50] Modify product: Actin-binding protein Smlt3054 => Actin-binding protein
[10:41:50] Modify product: Probable phospholipid ABC transporter-binding protein MlaD => putative phospholipid ABC transporter-binding protein MlaD
[10:41:50] Modify product: Uncharacterized metal-dependent hydrolase YcfH => putative metal-dependent hydrolase YcfH
[10:41:50] Modify product: Uncharacterized HIT-like protein HP_0404 => putative HIT-like protein
[10:41:50] Modify product: Probable acyltransferase YihG => putative acyltransferase YihG
[10:41:50] Modify product: Probable phospholipid ABC transporter permease protein MlaE => putative phospholipid ABC transporter permease protein MlaE
[10:41:50] Modify product: Probable ribonucleotide transport ATP-binding protein mkl => putative ribonucleotide transport ATP-binding protein mkl
[10:41:50] Modify product: Probable murein peptide carboxypeptidase => putative murein peptide carboxypeptidase
[10:41:50] Modify product: Probable transport protein HsrA => putative transport protein HsrA
[10:41:50] Modify product: Probable glycerol-3-phosphate acyltransferase => putative glycerol-3-phosphate acyltransferase
[10:41:50] Modify product: Putative O-methyltransferase MSMEG_5073/MSMEI_4947 => Putative O-methyltransferase/MSMEI_4947
[10:41:50] Modify product: Probable protein kinase UbiB => putative protein kinase UbiB
[10:41:51] Modify product: Uncharacterized oxidoreductase YciK => putative oxidoreductase YciK
[10:41:51] Modify product: Transcription termination/antitermination protein NusA => hypothetical protein
[10:41:51] Modify product: Cytochrome b561 homolog 2 => hypothetical protein
[10:41:51] Modify product: Probable chromosome-partitioning protein ParB => putative chromosome-partitioning protein ParB
[10:41:51] Cleaned 35 /product names
[10:41:51] Deleting unwanted file: /home/yquentin/work/wolbachia/prokka/wHa/proteins.faa
[10:41:51] Deleting unwanted file: /home/yquentin/work/wolbachia/prokka/wHa/proteins.bls
[10:41:51] There are still 610 unannotated CDS left (started with 1235)
[10:41:51] Will use hmmer3 to search against /usr/local/bioinfo/src/PROKKA/prokka-1.10/bin/../db/hmm/HAMAP.hmm with 8 CPUs
[10:41:51] Running: cat \/home\/yquentin\/work\/wolbachia\/prokka\/wHa\/proteins\.faa | parallel --gnu -j 8 --block 9046 --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\/wHa\/proteins\.bls 2> /dev/null
[10:42:01] Deleting unwanted file: /home/yquentin/work/wolbachia/prokka/wHa/proteins.faa
[10:42:01] Deleting unwanted file: /home/yquentin/work/wolbachia/prokka/wHa/proteins.bls
[10:42:01] There are still 571 unannotated CDS left (started with 1235)
[10:42:01] Will use hmmer3 to search against /usr/local/bioinfo/src/PROKKA/prokka-1.10/bin/../db/hmm/CLUSTERS.hmm with 8 CPUs
[10:42:01] Running: cat \/home\/yquentin\/work\/wolbachia\/prokka\/wHa\/proteins\.faa | parallel --gnu -j 8 --block 8014 --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\/wHa\/proteins\.bls 2> /dev/null
[10:42:27] Deleting unwanted file: /home/yquentin/work/wolbachia/prokka/wHa/proteins.faa
[10:42:27] Deleting unwanted file: /home/yquentin/work/wolbachia/prokka/wHa/proteins.bls
[10:42:27] There are still 544 unannotated CDS left (started with 1235)
[10:42:27] Will use hmmer3 to search against /usr/local/bioinfo/src/PROKKA/prokka-1.10/bin/../db/hmm/Pfam.hmm with 8 CPUs
[10:42:27] Running: cat \/home\/yquentin\/work\/wolbachia\/prokka\/wHa\/proteins\.faa | parallel --gnu -j 8 --block 7537 --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\/wHa\/proteins\.bls 2> /dev/null
[10:42:57] Modify product: Sodium:dicarboxylate symporter family => Sodium:dicarboxylate symporter family protein
[10:42:57] Modify product: Transposase DDE domain => Transposase DDE domain protein
[10:42:57] Modify product: Integrase core domain => Integrase core domain protein
[10:42:57] Modify product: Transposase DDE domain => Transposase DDE domain protein
[10:42:57] Modify product: SPFH domain / Band 7 family => SPFH domain / Band 7 family protein
[10:42:57] Modify product: Transposase DDE domain => Transposase DDE domain protein
[10:42:57] Modify product: TrbC/VIRB2 family => TrbC/VIRB2 family protein
[10:42:57] Modify product: Phage capsid family => Phage capsid family protein
[10:42:57] Modify product: Ankyrin repeat => Ankyrin repeat protein
[10:42:57] Modify product: Transposase IS116/IS110/IS902 family => Transposase IS116/IS110/IS902 family protein
[10:42:57] Modify product: Transposase DDE domain => Transposase DDE domain protein
[10:42:57] Modify product: Na+/H+ antiporter family => Na+/H+ antiporter family protein
[10:42:57] Modify product: Zinc-finger domain => Zinc-finger domain protein
[10:42:57] Modify product: Transposase IS116/IS110/IS902 family => Transposase IS116/IS110/IS902 family protein
[10:42:57] Modify product: Transposase IS116/IS110/IS902 family => Transposase IS116/IS110/IS902 family protein
[10:42:57] Modify product: Piwi/Argonaute/Zwille siRNA-binding domain => Piwi/Argonaute/Zwille siRNA-binding domain protein
[10:42:57] Modify product: NB-ARC domain => NB-ARC domain protein
[10:42:57] Modify product: Integrase core domain => Integrase core domain protein
[10:42:57] Modify product: RDD family => RDD family protein
[10:42:57] Modify product: TrbC/VIRB2 family => TrbC/VIRB2 family protein
[10:42:57] Modify product: Piwi/Argonaute/Zwille siRNA-binding domain => Piwi/Argonaute/Zwille siRNA-binding domain protein
[10:42:57] Modify product: Transposase IS116/IS110/IS902 family => Transposase IS116/IS110/IS902 family protein
[10:42:57] Modify product: Uracil DNA glycosylase superfamily => Uracil DNA glycosylase superfamily protein
[10:42:57] Modify product: ETC complex I subunit conserved region => hypothetical protein
[10:42:57] Modify product: Integrase core domain => Integrase core domain protein
[10:42:57] Modify product: Tim44-like domain => Tim44-like domain protein
[10:42:57] Modify product: Integral membrane protein TerC family => Integral membrane protein TerC family protein
[10:42:57] Modify product: Transposase DDE domain => Transposase DDE domain protein
[10:42:57] Modify product: Transposase DDE domain => Transposase DDE domain protein
[10:42:57] Modify product: Transposase DDE domain => Transposase DDE domain protein
[10:42:57] Modify product: COQ9 => hypothetical protein
[10:42:57] Modify product: PAS domain => PAS domain protein
[10:42:57] Modify product: RDD family => RDD family protein
[10:42:57] Modify product: RDD family => RDD family protein
[10:42:57] Modify product: Transposase DDE domain => Transposase DDE domain protein
[10:42:57] Modify product: Transposase DDE domain => Transposase DDE domain protein
[10:42:57] Modify product: Terminase-like family => Terminase-like family protein
[10:42:57] Modify product: TrbC/VIRB2 family => TrbC/VIRB2 family protein
[10:42:57] Modify product: Transposase IS116/IS110/IS902 family => Transposase IS116/IS110/IS902 family protein
[10:42:57] Modify product: Alpha/beta hydrolase family => Alpha/beta hydrolase family protein
[10:42:57] Modify product: Transposase IS66 family => Transposase IS66 family protein
[10:42:57] Modify product: Terminase-like family => Terminase-like family protein
[10:42:57] Modify product: EVE domain => EVE domain protein
[10:42:57] Modify product: Transposase DDE domain => Transposase DDE domain protein
[10:42:57] Modify product: Transposase IS116/IS110/IS902 family => Transposase IS116/IS110/IS902 family protein
[10:42:57] Modify product: Transposase IS116/IS110/IS902 family => Transposase IS116/IS110/IS902 family protein
[10:42:57] Modify product: Transposase IS116/IS110/IS902 family => Transposase IS116/IS110/IS902 family protein
[10:42:57] Modify product: Transposase DDE domain => Transposase DDE domain protein
[10:42:57] Modify product: Transposase IS116/IS110/IS902 family => Transposase IS116/IS110/IS902 family protein
[10:42:57] Modify product: Terminase-like family => Terminase-like family protein
[10:42:57] Modify product: Transposase DDE domain => Transposase DDE domain protein
[10:42:57] Modify product: Transposase IS66 family => Transposase IS66 family protein
[10:42:57] Modify product: PD-(D/E)XK nuclease superfamily => PD-(D/E)XK nuclease superfamily protein
[10:42:57] Modify product: Transposase DDE domain => Transposase DDE domain protein
[10:42:57] Modify product: Transposase IS116/IS110/IS902 family => Transposase IS116/IS110/IS902 family protein
[10:42:57] Modify product: Transposase IS116/IS110/IS902 family => Transposase IS116/IS110/IS902 family protein
[10:42:57] Modify product: MgtE intracellular N domain => MgtE intracellular N domain protein
[10:42:57] Modify product: Transposase DDE domain => Transposase DDE domain protein
[10:42:57] Modify product: RDD family => RDD family protein
[10:42:57] Modify product: SURF1 family => SURF1 family protein
[10:42:57] Modify product: AhpC/TSA family => AhpC/TSA family protein
[10:42:57] Modify product: TrbC/VIRB2 family => TrbC/VIRB2 family protein
[10:42:57] Modify product: TrbC/VIRB2 family => TrbC/VIRB2 family protein
[10:42:57] Modify product: TrbC/VIRB2 family => TrbC/VIRB2 family protein
[10:42:57] Modify product: Transposase DDE domain => Transposase DDE domain protein
[10:42:57] Modify product: Terminase-like family => Terminase-like family protein
[10:42:57] Modify product: Bacterial SH3 domain => Bacterial SH3 domain protein
[10:42:57] Modify product: KAP family P-loop domain => KAP family P-loop domain protein
[10:42:57] Cleaned 68 /product names
[10:42:57] Deleting unwanted file: /home/yquentin/work/wolbachia/prokka/wHa/proteins.faa
[10:42:57] Deleting unwanted file: /home/yquentin/work/wolbachia/prokka/wHa/proteins.bls
[10:42:57] Labelling remaining 370 proteins as 'hypothetical protein'
[10:42:57] Possible /pseudo 'Aminopyrimidine aminohydrolase' at gnl|Prokka|wHa_contig000001 position 67449
[10:42:57] Possible /pseudo 'Exopolysaccharide synthesis, ExoD' at gnl|Prokka|wHa_contig000001 position 78370
[10:42:57] Possible /pseudo 'Quaternary ammonium compound-resistance protein SugE' at gnl|Prokka|wHa_contig000001 position 145850
[10:42:57] Possible /pseudo 'L-allo-threonine aldolase' at gnl|Prokka|wHa_contig000001 position 241032
[10:42:57] Possible /pseudo 'Phage portal protein, lambda family' at gnl|Prokka|wHa_contig000001 position 293734
[10:42:57] Possible /pseudo 'Ankyrin repeats (3 copies)' at gnl|Prokka|wHa_contig000001 position 305718
[10:42:57] Possible /pseudo 'Ankyrin repeats (3 copies)' at gnl|Prokka|wHa_contig000001 position 310613
[10:42:57] Possible /pseudo 'Phosphocholine transferase AnkX' at gnl|Prokka|wHa_contig000001 position 316758
[10:42:57] Possible /pseudo 'Chromosome partition protein Smc' at gnl|Prokka|wHa_contig000001 position 379884
[10:42:57] Possible /pseudo 'Chromosome partition protein Smc' at gnl|Prokka|wHa_contig000001 position 380688
[10:42:57] Possible /pseudo 'anaerobic benzoate catabolism transcriptional regulator' at gnl|Prokka|wHa_contig000001 position 448995
[10:42:57] Possible /pseudo 'Protein translocase subunit SecA' at gnl|Prokka|wHa_contig000001 position 467613
[10:42:57] Possible /pseudo 'Transposase IS116/IS110/IS902 family protein' at gnl|Prokka|wHa_contig000001 position 617903
[10:42:57] Possible /pseudo 'Actin-binding protein' at gnl|Prokka|wHa_contig000001 position 666327
[10:42:57] Possible /pseudo 'putative zinc protease' at gnl|Prokka|wHa_contig000001 position 768608
[10:42:57] Possible /pseudo 'RDD family protein' at gnl|Prokka|wHa_contig000001 position 799088
[10:42:57] Possible /pseudo 'TrbL/VirB6 plasmid conjugal transfer protein' at gnl|Prokka|wHa_contig000001 position 872154
[10:42:57] Possible /pseudo 'TrbL/VirB6 plasmid conjugal transfer protein' at gnl|Prokka|wHa_contig000001 position 875096
[10:42:57] Possible /pseudo 'TrbL/VirB6 plasmid conjugal transfer protein' at gnl|Prokka|wHa_contig000001 position 877493
[10:42:57] Possible /pseudo 'Transposase IS116/IS110/IS902 family protein' at gnl|Prokka|wHa_contig000001 position 949081
[10:42:57] Possible /pseudo 'Amino-acid carrier protein AlsT' at gnl|Prokka|wHa_contig000001 position 1036454
[10:42:57] Possible /pseudo 'TrbC/VIRB2 family protein' at gnl|Prokka|wHa_contig000001 position 1257933
[10:42:57] Possible /pseudo 'TrbC/VIRB2 family protein' at gnl|Prokka|wHa_contig000001 position 1258310
[10:42:57] Found 566 unique /gene codes.
[10:42:57] Fixed 32 colliding /gene names.
[10:42:57] Adding /locus_tag identifiers
[10:42:57] Assigned 1273 locus_tags to CDS and RNA features.
[10:42:57] Writing outputs to /home/yquentin/work/wolbachia/prokka/wHa/
[10:42:59] Generating annotation statistics file
[10:42:59] Generating Genbank and Sequin files
[10:42:59] 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\/wHa\/wHa\.err -i \/home\/yquentin\/work\/wolbachia\/prokka\/wHa\/wHa\.fsa 2> /dev/null
[10:43:03] Deleting unwanted file: /home/yquentin/work/wolbachia/prokka/wHa/errorsummary.val
[10:43:03] Deleting unwanted file: /home/yquentin/work/wolbachia/prokka/wHa/wHa.dr
[10:43:03] Deleting unwanted file: /home/yquentin/work/wolbachia/prokka/wHa/wHa.fixedproducts
[10:43:03] Deleting unwanted file: /home/yquentin/work/wolbachia/prokka/wHa/wHa.ecn
[10:43:03] Deleting unwanted file: /home/yquentin/work/wolbachia/prokka/wHa/wHa.val
[10:43:03] Output files:
[10:43:03] /home/yquentin/work/wolbachia/prokka/wHa/wHa.ffn
[10:43:03] /home/yquentin/work/wolbachia/prokka/wHa/wHa.tbl
[10:43:03] /home/yquentin/work/wolbachia/prokka/wHa/wHa.gbk
[10:43:03] /home/yquentin/work/wolbachia/prokka/wHa/wHa.log
[10:43:03] /home/yquentin/work/wolbachia/prokka/wHa/wHa.sqn
[10:43:03] /home/yquentin/work/wolbachia/prokka/wHa/wHa.fna
[10:43:03] /home/yquentin/work/wolbachia/prokka/wHa/wHa.gff
[10:43:03] /home/yquentin/work/wolbachia/prokka/wHa/wHa.faa
[10:43:03] /home/yquentin/work/wolbachia/prokka/wHa/wHa.fsa
[10:43:03] /home/yquentin/work/wolbachia/prokka/wHa/wHa.txt
[10:43:03] /home/yquentin/work/wolbachia/prokka/wHa/wHa.err
[10:43:03] Walltime used: 1.65 minutes
[10:43:03] If you use this result please cite the Prokka paper:
[10:43:03] Seemann T (2014) Prokka: rapid prokaryotic genome annotation. Bioinformatics. 30(14):2068-9.
[10:43:03] Type 'prokka --citation' for more details.
[10:43:03] Share and enjoy!