[10:41:12] Command: --force --outdir /home/yquentin/work/wolbachia/prokka/wAu --addgenes --prefix wAu --locustag wAu --species Wolbachia endosymbiont --strain wAu --compliant --quiet /home/yquentin/work/wolbachia/prokka/wAu.fna
[10:41:12] Looking for 'aragorn' - found /usr/local/bioinfo/bin/aragorn
[10:41:12] Determined aragorn version is 1.2
[10:41:12] Looking for 'barrnap' - found /usr/local/bioinfo/bin/barrnap
[10:41:12] Determined barrnap version is 0.5
[10:41:12] Looking for 'blastp' - found /usr/local/bioinfo/src/NCBI_Blast+/ncbi-blast-2.6.0+/bin/blastp
[10:41:12] Determined blastp version is 2.6
[10:41:13] Looking for 'cmpress' - found /usr/local/bioinfo/src/PROKKA/prokka-1.10/bin/../binaries/linux/cmpress
[10:41:13] Determined cmpress version is 1.1
[10:41:13] Looking for 'cmscan' - found /usr/local/bioinfo/src/PROKKA/prokka-1.10/bin/../binaries/linux/cmscan
[10:41:13] Determined cmscan version is 1.1
[10:41:13] Looking for 'egrep' - found /bin/egrep
[10:41:13] Looking for 'find' - found /bin/find
[10:41:13] Looking for 'grep' - found /bin/grep
[10:41:13] Looking for 'hmmpress' - found /usr/local/bioinfo/bin/hmmpress
[10:41:13] Determined hmmpress version is 3.1
[10:41:13] Looking for 'hmmscan' - found /usr/local/bioinfo/bin/hmmscan
[10:41:13] Determined hmmscan version is 3.1
[10:41:13] Looking for 'less' - found /usr/bin/less
[10:41:13] Looking for 'makeblastdb' - found /usr/local/bioinfo/src/NCBI_Blast+/ncbi-blast-2.6.0+/bin/makeblastdb
[10:41:13] Determined makeblastdb version is 2.6
[10:41:13] Looking for 'minced' - found /usr/local/bioinfo/bin/minced
[10:41:13] Determined minced version is 1.6
[10:41:13] Looking for 'parallel' - found /usr/local/bioinfo/bin/parallel
[10:41:13] Determined parallel version is 20141022
[10:41:13] Looking for 'prodigal' - found /usr/local/bioinfo/bin/prodigal
[10:41:13] Determined prodigal version is 2.6
[10:41:14] Looking for 'rnammer' - found /usr/local/bioinfo/bin/rnammer
[10:41:14] Determined rnammer version is 1.2
[10:41:14] Looking for 'sed' - found /bin/sed
[10:41:14] Looking for 'signalp' - found /usr/local/bioinfo/bin/signalp
[10:41:14] Determined signalp version is 4.1
[10:41:14] Looking for 'tbl2asn' - found /home/yquentin/save/scripts/tbl2asn
[10:41:14] Determined tbl2asn version is 25.3
[10:41:14] Using genetic code table 11.
[10:41:14] Loading and checking input file: /home/yquentin/work/wolbachia/prokka/wAu.fna
[10:41:14] Wrote 1 contigs
[10:41:14] Predicting tRNAs and tmRNAs
[10:41:14] Running: aragorn -gc11  -w \/home\/yquentin\/work\/wolbachia\/prokka\/wAu\/wAu\.fna
[10:41:15] 1 tRNA-Leu [3028,3115] 35 (gag)
[10:41:15] 2 tRNA-Trp [17513,17586] 34 (cca)
[10:41:15] 3 tRNA-Arg c[43348,43425] 36 (acg)
[10:41:15] 4 tRNA-Arg c[85379,85455] 35 (cct)
[10:41:15] 5 tRNA-Ile c[101333,101409] 35 (gat)
[10:41:15] 6 tmRNA* [108813,109148] 195,245 ANDNFAAEDNVDAIAA*
[10:41:15] 7 tRNA-Thr c[141412,141485] 34 (tgt)
[10:41:15] 8 tRNA-Leu c[334335,334417] 35 (tag)
[10:41:15] 9 tRNA-Leu [375331,375414] 34 (caa)
[10:41:15] 10 tRNA-Leu [409935,410021] 35 (taa)
[10:41:15] 11 tRNA-Phe c[530488,530562] 34 (gaa)
[10:41:15] 12 tRNA-Asp [536212,536288] 35 (gtc)
[10:41:15] 13 tRNA-Gly c[579723,579794] 33 (tcc)
[10:41:15] 14 tRNA-Tyr c[579799,579881] 35 (gta)
[10:41:15] 15 tRNA-Ser [721548,721636] 36 (gga)
[10:41:15] 16 tRNA-Arg [746806,746880] 35 (ccg)
[10:41:15] 17 tRNA-Met [759072,759145] 34 (cat)
[10:41:15] 18 tRNA-Gln c[792669,792743] 33 (ttg)
[10:41:15] 19 tRNA-Asn [839692,839764] 33 (gtt)
[10:41:15] 20 tRNA-Arg c[883240,883314] 35 (tct)
[10:41:15] 21 tRNA-Ser c[903332,903420] 35 (tga)
[10:41:15] 22 tRNA-Lys c[909737,909810] 34 (ttt)
[10:41:15] 23 tRNA-Ala [910152,910227] 34 (tgc)
[10:41:15] 24 tRNA-Met c[955303,955379] 35 (cat)
[10:41:15] 25 tRNA-Gly [956673,956746] 34 (gcc)
[10:41:15] 26 tRNA-Val c[1038484,1038557] 34 (gac)
[10:41:15] 27 tRNA-His [1071493,1071568] 34 (gtg)
[10:41:15] 28 tRNA-Ser c[1085168,1085253] 35 (cag)
[10:41:15] 29 tRNA-Thr c[1105336,1105409] 34 (ggt)
[10:41:15] 30 tRNA-Met c[1107086,1107162] 35 (cat)
[10:41:15] 31 tRNA-Val c[1152112,1152184] 34 (tac)
[10:41:15] 32 tRNA-Pro c[1158565,1158640] 36 (tgg)
[10:41:15] 33 tRNA-Glu c[1159572,1159644] 34 (ttc)
[10:41:15] 34 tRNA-Cys [1186259,1186331] 34 (gca)
[10:41:15] 35 tRNA-Ser [1208809,1208901] 36 (gct)
[10:41:15] Found 35 tRNAs
[10:41:15] Predicting Ribosomal RNAs
[10:41:15] Running Barrnap with 8 threads
[10:41:16] 1 gnl|Prokka|wAu_contig000001 179494 23S ribosomal RNA
[10:41:16] 2 gnl|Prokka|wAu_contig000001 182324 5S ribosomal RNA
[10:41:16] 3 gnl|Prokka|wAu_contig000001 1167903 16S ribosomal RNA
[10:41:16] Found 3 rRNAs
[10:41:16] Skipping ncRNA search, enable with --rfam if desired.
[10:41:16] Total of 37 tRNA + rRNA features
[10:41:16] Searching for CRISPR repeats
[10:41:16] Found 0 CRISPRs
[10:41:16] Predicting coding sequences
[10:41:16] Contigs total 1268461 bp, so using single mode
[10:41:16] Running: prodigal -i \/home\/yquentin\/work\/wolbachia\/prokka\/wAu\/wAu\.fna -c -m -g 11 -p single -f sco -q
[10:41:18] Excluding CDS which overlaps existing RNA (tRNA) at gnl|Prokka|wAu_contig000001:334253..334411 on - strand
[10:41:18] Excluding CDS which overlaps existing RNA (tRNA) at gnl|Prokka|wAu_contig000001:757780..759072 on + strand
[10:41:18] Excluding CDS which overlaps existing RNA (tRNA) at gnl|Prokka|wAu_contig000001:792734..793069 on - strand
[10:41:19] Excluding CDS which overlaps existing RNA (tRNA) at gnl|Prokka|wAu_contig000001:883249..883659 on + strand
[10:41:19] Excluding CDS which overlaps existing RNA (tRNA) at gnl|Prokka|wAu_contig000001:1107126..1109387 on + strand
[10:41:19] Excluding CDS which overlaps existing RNA (rRNA) at gnl|Prokka|wAu_contig000001:1168339..1168461 on + strand
[10:41:19] Found 1276 CDS
[10:41:19] Connecting features back to sequences
[10:41:19] Option --gram not specified, will NOT check for signal peptides.
[10:41:19] Not using genus-specific database. Try --usegenus to enable it.
[10:41:19] Annotating CDS, please be patient.
[10:41:19] Will use 8 CPUs for similarity searching.
[10:41:20] There are still 1276 unannotated CDS left (started with 1276)
[10:41:20] Will use blast to search against /usr/local/bioinfo/src/PROKKA/prokka-1.10/bin/../db/kingdom/Bacteria/sprot with 8 CPUs
[10:41:20] Running: cat \/home\/yquentin\/work\/wolbachia\/prokka\/wAu\/proteins\.faa | parallel --gnu -j 8 --block 22757 --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\/wAu\/proteins\.bls 2> /dev/null
[10:41:31] Modify product: Probable transcriptional regulatory protein aq_1575 => putative transcriptional regulatory protein
[10:41:31] Modify product: Actin-binding protein Smlt3054 => Actin-binding protein
[10:41:31] Modify product: Actin-binding protein Smlt3054 => Actin-binding protein
[10:41:31] Modify product: Probable deoxyribonuclease RhsA => putative deoxyribonuclease RhsA
[10:41:32] Modify product: Probable GTP-binding protein EngB => putative GTP-binding protein EngB
[10:41:32] Modify product: N utilization substance protein B homolog => hypothetical protein
[10:41:32] Modify product: Bifunctional protein FolD => Bifunctional protein FolD protein
[10:41:32] Modify product: Transcription termination/antitermination protein NusG => hypothetical protein
[10:41:32] Modify product: Probable tRNA-dihydrouridine synthase => putative tRNA-dihydrouridine synthase
[10:41:32] Modify product: SCO1 protein homolog => hypothetical protein
[10:41:32] Modify product: Uncharacterized ABC transporter ATP-binding protein TM_0288 => putative ABC transporter ATP-binding protein
[10:41:32] Modify product: Uncharacterized oxidoreductase YciK => putative oxidoreductase YciK
[10:41:32] Modify product: Transcription termination/antitermination protein NusA => hypothetical protein
[10:41:32] Modify product: Probable glycerol-3-phosphate acyltransferase => putative glycerol-3-phosphate acyltransferase
[10:41:32] Modify product: Probable murein peptide carboxypeptidase => putative murein peptide carboxypeptidase
[10:41:32] Modify product: Probable acyltransferase YihG => putative acyltransferase YihG
[10:41:32] Modify product: Putative multidrug export ATP-binding/permease protein SAV1866 => Putative multidrug export ATP-binding/permease protein
[10:41:32] Modify product: Uncharacterized zinc protease Rv2782c => putative zinc protease
[10:41:32] Modify product: Probable protein kinase UbiB => putative protein kinase UbiB
[10:41:32] Modify product: Stringent starvation protein A homolog => hypothetical protein
[10:41:32] Modify product: Putative O-methyltransferase MSMEG_5073/MSMEI_4947 => Putative O-methyltransferase/MSMEI_4947
[10:41:32] Modify product: Uncharacterized metal-dependent hydrolase YcfH => putative metal-dependent hydrolase YcfH
[10:41:32] Modify product: Uncharacterized HIT-like protein HP_0404 => putative HIT-like protein
[10:41:32] Modify product: Probable ribonucleotide transport ATP-binding protein mkl => putative ribonucleotide transport ATP-binding protein mkl
[10:41:32] Modify product: Probable phospholipid ABC transporter permease protein MlaE => putative phospholipid ABC transporter permease protein MlaE
[10:41:32] Modify product: Co-chaperone protein HscB homolog => hypothetical protein
[10:41:32] Modify product: Probable peroxiredoxin => putative peroxiredoxin
[10:41:32] Modify product: Uncharacterized zinc protease Rv2782c => putative zinc protease
[10:41:32] Modify product: Uncharacterized zinc protease Rv2782c => putative zinc protease
[10:41:32] Modify product: Transcription termination factor Rho => hypothetical protein
[10:41:33] Modify product: Cytochrome b561 homolog 2 => hypothetical protein
[10:41:33] Modify product: Probable chromosome-partitioning protein ParB => putative chromosome-partitioning protein ParB
[10:41:33] Cleaned 32 /product names
[10:41:33] Deleting unwanted file: /home/yquentin/work/wolbachia/prokka/wAu/proteins.faa
[10:41:33] Deleting unwanted file: /home/yquentin/work/wolbachia/prokka/wAu/proteins.bls
[10:41:33] There are still 646 unannotated CDS left (started with 1276)
[10:41:33] Will use hmmer3 to search against /usr/local/bioinfo/src/PROKKA/prokka-1.10/bin/../db/hmm/HAMAP.hmm with 8 CPUs
[10:41:33] Running: cat \/home\/yquentin\/work\/wolbachia\/prokka\/wAu\/proteins\.faa | parallel --gnu -j 8 --block 8538 --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\/wAu\/proteins\.bls 2> /dev/null
[10:41:41] Deleting unwanted file: /home/yquentin/work/wolbachia/prokka/wAu/proteins.faa
[10:41:41] Deleting unwanted file: /home/yquentin/work/wolbachia/prokka/wAu/proteins.bls
[10:41:41] There are still 611 unannotated CDS left (started with 1276)
[10:41:41] Will use hmmer3 to search against /usr/local/bioinfo/src/PROKKA/prokka-1.10/bin/../db/hmm/CLUSTERS.hmm with 8 CPUs
[10:41:41] Running: cat \/home\/yquentin\/work\/wolbachia\/prokka\/wAu\/proteins\.faa | parallel --gnu -j 8 --block 7817 --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\/wAu\/proteins\.bls 2> /dev/null
[10:42:04] Deleting unwanted file: /home/yquentin/work/wolbachia/prokka/wAu/proteins.faa
[10:42:04] Deleting unwanted file: /home/yquentin/work/wolbachia/prokka/wAu/proteins.bls
[10:42:04] There are still 579 unannotated CDS left (started with 1276)
[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\/wAu\/proteins\.faa | parallel --gnu -j 8 --block 7252 --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\/wAu\/proteins\.bls 2> /dev/null
[10:42:31] Modify product: Phage capsid family => Phage capsid family protein
[10:42:31] Modify product: Transposase DDE domain => Transposase DDE domain protein
[10:42:31] Modify product: TrbC/VIRB2 family => TrbC/VIRB2 family protein
[10:42:31] Modify product: SPFH domain / Band 7 family => SPFH domain / Band 7 family protein
[10:42:31] Modify product: Transposase IS116/IS110/IS902 family => Transposase IS116/IS110/IS902 family protein
[10:42:31] Modify product: Transposase DDE domain => Transposase DDE domain protein
[10:42:31] Modify product: Transposase IS116/IS110/IS902 family => Transposase IS116/IS110/IS902 family protein
[10:42:31] Modify product: Transposase DDE domain => Transposase DDE domain protein
[10:42:31] Modify product: ParB-like nuclease domain => ParB-like nuclease domain protein
[10:42:31] Modify product: Ankyrin repeat => Ankyrin repeat protein
[10:42:31] Modify product: Sodium:dicarboxylate symporter family => Sodium:dicarboxylate symporter family protein
[10:42:31] Modify product: Transposase DDE domain => Transposase DDE domain protein
[10:42:31] Modify product: Transposase DDE domain => Transposase DDE domain protein
[10:42:31] Modify product: Transposase DDE domain => Transposase DDE domain protein
[10:42:31] Modify product: Transposase DDE domain => Transposase DDE domain protein
[10:42:31] Modify product: Transposase DDE domain => Transposase DDE domain protein
[10:42:31] Modify product: Acetyltransferase (GNAT) family => Acetyltransferase (GNAT) family protein
[10:42:31] Modify product: TrbC/VIRB2 family => TrbC/VIRB2 family protein
[10:42:31] Modify product: RDD family => RDD family protein
[10:42:31] Modify product: Transposase DDE domain => Transposase DDE domain protein
[10:42:31] Modify product: Na+/H+ antiporter family => Na+/H+ antiporter family protein
[10:42:31] Modify product: Zinc-finger domain => Zinc-finger domain protein
[10:42:31] Modify product: Transposase DDE domain => Transposase DDE domain protein
[10:42:31] Modify product: Transposase DDE domain => Transposase DDE domain protein
[10:42:31] Modify product: TrbC/VIRB2 family => TrbC/VIRB2 family protein
[10:42:31] Modify product: Piwi/Argonaute/Zwille siRNA-binding domain => Piwi/Argonaute/Zwille siRNA-binding domain protein
[10:42:31] Modify product: Ulp1 protease family, C-terminal catalytic domain => hypothetical protein
[10:42:31] Modify product: Piwi/Argonaute/Zwille siRNA-binding domain => Piwi/Argonaute/Zwille siRNA-binding domain protein
[10:42:31] Modify product: Integrase core domain => Integrase core domain protein
[10:42:31] Modify product: ETC complex I subunit conserved region => hypothetical protein
[10:42:31] Modify product: Uracil DNA glycosylase superfamily => Uracil DNA glycosylase superfamily protein
[10:42:31] Modify product: Transposase DDE domain => Transposase DDE domain protein
[10:42:31] Modify product: YGGT family => YGGT family protein
[10:42:31] Modify product: Transposase DDE domain => Transposase DDE domain protein
[10:42:31] Modify product: Tim44-like domain => Tim44-like domain protein
[10:42:31] Modify product: Integral membrane protein TerC family => Integral membrane protein TerC family protein
[10:42:31] Modify product: Transposase DDE domain => Transposase DDE domain protein
[10:42:31] Modify product: DnaJ domain => DnaJ domain protein
[10:42:31] Modify product: RDD family => RDD family protein
[10:42:31] Modify product: RDD family => RDD family protein
[10:42:31] Modify product: Transposase DDE domain => Transposase DDE domain protein
[10:42:31] Modify product: COQ9 => hypothetical protein
[10:42:31] Modify product: Transposase IS116/IS110/IS902 family => Transposase IS116/IS110/IS902 family protein
[10:42:31] Modify product: Alpha/beta hydrolase family => Alpha/beta hydrolase family protein
[10:42:31] Modify product: Transposase IS66 family => Transposase IS66 family protein
[10:42:31] Modify product: Terminase-like family => Terminase-like family protein
[10:42:31] Modify product: EVE domain => EVE domain protein
[10:42:31] Modify product: PAAR motif => PAAR motif protein
[10:42:31] Modify product: Transposase IS116/IS110/IS902 family => Transposase IS116/IS110/IS902 family protein
[10:42:31] Modify product: Transposase IS116/IS110/IS902 family => Transposase IS116/IS110/IS902 family protein
[10:42:31] Modify product: Transposase DDE domain => Transposase DDE domain protein
[10:42:31] Modify product: PAS domain => PAS domain protein
[10:42:31] Modify product: Transposase DDE domain => Transposase DDE domain protein
[10:42:31] Modify product: Transposase DDE domain => Transposase DDE domain protein
[10:42:31] Modify product: Transposase DDE domain => Transposase DDE domain protein
[10:42:31] Modify product: Transposase DDE domain => Transposase DDE domain protein
[10:42:31] Modify product: Major Facilitator Superfamily => Major Facilitator Superfamily protein
[10:42:31] Modify product: Terminase-like family => Terminase-like family protein
[10:42:31] Modify product: Bacterial SH3 domain => Bacterial SH3 domain protein
[10:42:31] Modify product: KAP family P-loop domain => KAP family P-loop domain protein
[10:42:31] Modify product: Transposase DDE domain => Transposase DDE domain protein
[10:42:31] Modify product: RDD family => RDD family protein
[10:42:31] Modify product: SURF1 family => SURF1 family protein
[10:42:31] Modify product: AhpC/TSA family => AhpC/TSA family protein
[10:42:31] Modify product: TrbC/VIRB2 family => TrbC/VIRB2 family protein
[10:42:31] Modify product: TrbC/VIRB2 family => TrbC/VIRB2 family protein
[10:42:31] Modify product: TrbC/VIRB2 family => TrbC/VIRB2 family protein
[10:42:31] Modify product: Terminase-like family => Terminase-like family protein
[10:42:31] Modify product: MgtE intracellular N domain => MgtE intracellular N domain protein
[10:42:31] Modify product: Transposase IS116/IS110/IS902 family => Transposase IS116/IS110/IS902 family protein
[10:42:31] Modify product: Transposase DDE domain => Transposase DDE domain protein
[10:42:31] Modify product: Transposase IS116/IS110/IS902 family => Transposase IS116/IS110/IS902 family protein
[10:42:31] Modify product: Transposase DDE domain => Transposase DDE domain protein
[10:42:31] Modify product: Transposase IS116/IS110/IS902 family => Transposase IS116/IS110/IS902 family protein
[10:42:31] Modify product: Transposase DDE domain => Transposase DDE domain protein
[10:42:31] Cleaned 75 /product names
[10:42:31] Deleting unwanted file: /home/yquentin/work/wolbachia/prokka/wAu/proteins.faa
[10:42:31] Deleting unwanted file: /home/yquentin/work/wolbachia/prokka/wAu/proteins.bls
[10:42:31] Labelling remaining 386 proteins as 'hypothetical protein'
[10:42:31] Possible /pseudo 'Exopolysaccharide synthesis, ExoD' at gnl|Prokka|wAu_contig000001 position 87586
[10:42:31] Possible /pseudo 'Aminopyrimidine aminohydrolase' at gnl|Prokka|wAu_contig000001 position 98374
[10:42:31] Possible /pseudo 'Quaternary ammonium compound-resistance protein SugE' at gnl|Prokka|wAu_contig000001 position 133932
[10:42:31] Possible /pseudo 'Ankyrin repeats (3 copies)' at gnl|Prokka|wAu_contig000001 position 406231
[10:42:31] Possible /pseudo 'ATP-dependent zinc metalloprotease FtsH' at gnl|Prokka|wAu_contig000001 position 493905
[10:42:31] Possible /pseudo 'Actin-binding protein' at gnl|Prokka|wAu_contig000001 position 596196
[10:42:31] Possible /pseudo 'Ankyrin repeats (3 copies)' at gnl|Prokka|wAu_contig000001 position 610790
[10:42:31] Possible /pseudo 'Ankyrin repeats (3 copies)' at gnl|Prokka|wAu_contig000001 position 615998
[10:42:31] Possible /pseudo 'Phage portal protein, lambda family' at gnl|Prokka|wAu_contig000001 position 627839
[10:42:31] Possible /pseudo 'L-allo-threonine aldolase' at gnl|Prokka|wAu_contig000001 position 656041
[10:42:31] Possible /pseudo 'putative zinc protease' at gnl|Prokka|wAu_contig000001 position 734706
[10:42:31] Possible /pseudo 'RDD family protein' at gnl|Prokka|wAu_contig000001 position 766098
[10:42:31] Possible /pseudo 'TrbL/VirB6 plasmid conjugal transfer protein' at gnl|Prokka|wAu_contig000001 position 819120
[10:42:31] Possible /pseudo 'TrbL/VirB6 plasmid conjugal transfer protein' at gnl|Prokka|wAu_contig000001 position 822095
[10:42:31] Possible /pseudo 'TrbL/VirB6 plasmid conjugal transfer protein' at gnl|Prokka|wAu_contig000001 position 824492
[10:42:31] Possible /pseudo 'Amino-acid carrier protein AlsT' at gnl|Prokka|wAu_contig000001 position 1033584
[10:42:31] Possible /pseudo 'TrbC/VIRB2 family protein' at gnl|Prokka|wAu_contig000001 position 1231524
[10:42:31] Possible /pseudo 'TrbC/VIRB2 family protein' at gnl|Prokka|wAu_contig000001 position 1231895
[10:42:31] Found 565 unique /gene codes.
[10:42:31] Fixed 36 colliding /gene names.
[10:42:31] Adding /locus_tag identifiers
[10:42:31] Assigned 1314 locus_tags to CDS and RNA features.
[10:42:31] Writing outputs to /home/yquentin/work/wolbachia/prokka/wAu/
[10:42:33] Generating annotation statistics file
[10:42:33] Generating Genbank and Sequin files
[10:42:33] 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\/wAu\/wAu\.err -i \/home\/yquentin\/work\/wolbachia\/prokka\/wAu\/wAu\.fsa 2> /dev/null
[10:42:36] Deleting unwanted file: /home/yquentin/work/wolbachia/prokka/wAu/errorsummary.val
[10:42:36] Deleting unwanted file: /home/yquentin/work/wolbachia/prokka/wAu/wAu.dr
[10:42:36] Deleting unwanted file: /home/yquentin/work/wolbachia/prokka/wAu/wAu.fixedproducts
[10:42:36] Deleting unwanted file: /home/yquentin/work/wolbachia/prokka/wAu/wAu.ecn
[10:42:36] Deleting unwanted file: /home/yquentin/work/wolbachia/prokka/wAu/wAu.val
[10:42:36] Output files:
[10:42:36] /home/yquentin/work/wolbachia/prokka/wAu/wAu.faa
[10:42:36] /home/yquentin/work/wolbachia/prokka/wAu/wAu.tbl
[10:42:36] /home/yquentin/work/wolbachia/prokka/wAu/wAu.gbk
[10:42:36] /home/yquentin/work/wolbachia/prokka/wAu/wAu.txt
[10:42:36] /home/yquentin/work/wolbachia/prokka/wAu/wAu.gff
[10:42:36] /home/yquentin/work/wolbachia/prokka/wAu/wAu.ffn
[10:42:36] /home/yquentin/work/wolbachia/prokka/wAu/wAu.log
[10:42:36] /home/yquentin/work/wolbachia/prokka/wAu/wAu.sqn
[10:42:36] /home/yquentin/work/wolbachia/prokka/wAu/wAu.fsa
[10:42:36] /home/yquentin/work/wolbachia/prokka/wAu/wAu.fna
[10:42:36] /home/yquentin/work/wolbachia/prokka/wAu/wAu.err
[10:42:36] Walltime used: 1.40 minutes
[10:42:36] If you use this result please cite the Prokka paper:
[10:42:36] Seemann T (2014) Prokka: rapid prokaryotic genome annotation. Bioinformatics. 30(14):2068-9.
[10:42:36] Type 'prokka --citation' for more details.
[10:42:36] Thank you, come again.