[15:07:04] Command: --force --outdir /home/yquentin/work/wolbachia/prokka/wViB --addgenes --prefix wViB --locustag wViB --species Wolbachia endosymbiont --strain wViB --compliant --quiet /home/yquentin/work/wolbachia/prokka/wViB.fna
[15:07:04] Looking for 'aragorn' - found /usr/local/bioinfo/bin/aragorn
[15:07:04] Determined aragorn version is 1.2
[15:07:04] Looking for 'barrnap' - found /usr/local/bioinfo/bin/barrnap
[15:07:04] Determined barrnap version is 0.5
[15:07:04] Looking for 'blastp' - found /usr/local/bioinfo/src/NCBI_Blast+/ncbi-blast-2.6.0+/bin/blastp
[15:07:04] Determined blastp version is 2.6
[15:07:04] Looking for 'cmpress' - found /usr/local/bioinfo/src/PROKKA/prokka-1.10/bin/../binaries/linux/cmpress
[15:07:04] Determined cmpress version is 1.1
[15:07:04] Looking for 'cmscan' - found /usr/local/bioinfo/src/PROKKA/prokka-1.10/bin/../binaries/linux/cmscan
[15:07:04] Determined cmscan version is 1.1
[15:07:04] Looking for 'egrep' - found /bin/egrep
[15:07:04] Looking for 'find' - found /bin/find
[15:07:04] Looking for 'grep' - found /bin/grep
[15:07:04] Looking for 'hmmpress' - found /usr/local/bioinfo/bin/hmmpress
[15:07:04] Determined hmmpress version is 3.1
[15:07:04] Looking for 'hmmscan' - found /usr/local/bioinfo/bin/hmmscan
[15:07:04] Determined hmmscan version is 3.1
[15:07:04] Looking for 'less' - found /usr/bin/less
[15:07:04] Looking for 'makeblastdb' - found /usr/local/bioinfo/src/NCBI_Blast+/ncbi-blast-2.6.0+/bin/makeblastdb
[15:07:04] Determined makeblastdb version is 2.6
[15:07:04] 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/wViB.fna
[15:07:06] Skipping short (<200 bp) contig: NZ_AERW01000022.1
[15:07:06] Skipping short (<200 bp) contig: NZ_AERW01000045.1
[15:07:06] Skipping short (<200 bp) contig: NZ_AERW01000065.1
[15:07:06] Skipping short (<200 bp) contig: NZ_AERW01000069.1
[15:07:06] Skipping short (<200 bp) contig: NZ_AERW01000080.1
[15:07:06] Skipping short (<200 bp) contig: NZ_AERW01000084.1
[15:07:06] Skipping short (<200 bp) contig: NZ_AERW01000090.1
[15:07:06] Skipping short (<200 bp) contig: NZ_AERW01000094.1
[15:07:06] Skipping short (<200 bp) contig: NZ_AERW01000104.1
[15:07:06] Skipping short (<200 bp) contig: NZ_AERW01000114.1
[15:07:06] Skipping short (<200 bp) contig: NZ_AERW01000123.1
[15:07:06] Skipping short (<200 bp) contig: NZ_AERW01000151.1
[15:07:06] Skipping short (<200 bp) contig: NZ_AERW01000166.1
[15:07:06] Skipping short (<200 bp) contig: NZ_AERW01000170.1
[15:07:06] Skipping short (<200 bp) contig: NZ_AERW01000179.1
[15:07:06] Skipping short (<200 bp) contig: NZ_AERW01000181.1
[15:07:06] Skipping short (<200 bp) contig: NZ_AERW01000182.1
[15:07:06] Skipping short (<200 bp) contig: NZ_AERW01000200.1
[15:07:06] Skipping short (<200 bp) contig: NZ_AERW01000201.1
[15:07:06] Skipping short (<200 bp) contig: NZ_AERW01000208.1
[15:07:06] Skipping short (<200 bp) contig: NZ_AERW01000218.1
[15:07:06] Skipping short (<200 bp) contig: NZ_AERW01000230.1
[15:07:06] Skipping short (<200 bp) contig: NZ_AERW01000260.1
[15:07:06] Skipping short (<200 bp) contig: NZ_AERW01000271.1
[15:07:06] Skipping short (<200 bp) contig: NZ_AERW01000299.1
[15:07:06] Skipping short (<200 bp) contig: NZ_AERW01000303.1
[15:07:06] Skipping short (<200 bp) contig: NZ_AERW01000305.1
[15:07:06] Skipping short (<200 bp) contig: NZ_AERW01000309.1
[15:07:06] Skipping short (<200 bp) contig: NZ_AERW01000339.1
[15:07:06] Skipping short (<200 bp) contig: NZ_AERW01000355.1
[15:07:06] Skipping short (<200 bp) contig: NZ_AERW01000358.1
[15:07:06] Skipping short (<200 bp) contig: NZ_AERW01000370.1
[15:07:06] Skipping short (<200 bp) contig: NZ_AERW01000379.1
[15:07:06] Skipping short (<200 bp) contig: NZ_AERW01000385.1
[15:07:06] Skipping short (<200 bp) contig: NZ_AERW01000395.1
[15:07:06] Skipping short (<200 bp) contig: NZ_AERW01000396.1
[15:07:06] Skipping short (<200 bp) contig: NZ_AERW01000398.1
[15:07:06] Skipping short (<200 bp) contig: NZ_AERW01000411.1
[15:07:06] Skipping short (<200 bp) contig: NZ_AERW01000419.1
[15:07:06] Skipping short (<200 bp) contig: NZ_AERW01000427.1
[15:07:06] Skipping short (<200 bp) contig: NZ_AERW01000446.1
[15:07:06] Skipping short (<200 bp) contig: NZ_AERW01000448.1
[15:07:06] Skipping short (<200 bp) contig: NZ_AERW01000449.1
[15:07:06] Skipping short (<200 bp) contig: NZ_AERW01000451.1
[15:07:06] Skipping short (<200 bp) contig: NZ_AERW01000453.1
[15:07:06] Skipping short (<200 bp) contig: NZ_AERW01000455.1
[15:07:06] Skipping short (<200 bp) contig: NZ_AERW01000457.1
[15:07:06] Skipping short (<200 bp) contig: NZ_AERW01000458.1
[15:07:06] Skipping short (<200 bp) contig: NZ_AERW01000459.1
[15:07:06] Skipping short (<200 bp) contig: NZ_AERW01000460.1
[15:07:06] Skipping short (<200 bp) contig: NZ_AERW01000462.1
[15:07:06] Skipping short (<200 bp) contig: NZ_AERW01000466.1
[15:07:06] Skipping short (<200 bp) contig: NZ_AERW01000467.1
[15:07:06] Skipping short (<200 bp) contig: NZ_AERW01000469.1
[15:07:06] Skipping short (<200 bp) contig: NZ_AERW01000470.1
[15:07:06] Skipping short (<200 bp) contig: NZ_AERW01000471.1
[15:07:06] Skipping short (<200 bp) contig: NZ_AERW01000477.1
[15:07:06] Skipping short (<200 bp) contig: NZ_AERW01000478.1
[15:07:06] Skipping short (<200 bp) contig: NZ_AERW01000480.1
[15:07:06] Skipping short (<200 bp) contig: NZ_AERW01000481.1
[15:07:06] Skipping short (<200 bp) contig: NZ_AERW01000484.1
[15:07:06] Skipping short (<200 bp) contig: NZ_AERW01000485.1
[15:07:06] Skipping short (<200 bp) contig: NZ_AERW01000488.1
[15:07:06] Skipping short (<200 bp) contig: NZ_AERW01000489.1
[15:07:06] Skipping short (<200 bp) contig: NZ_AERW01000491.1
[15:07:06] Skipping short (<200 bp) contig: NZ_AERW01000492.1
[15:07:06] Skipping short (<200 bp) contig: NZ_AERW01000493.1
[15:07:06] Skipping short (<200 bp) contig: NZ_AERW01000495.1
[15:07:06] Skipping short (<200 bp) contig: NZ_AERW01000500.1
[15:07:06] Skipping short (<200 bp) contig: NZ_AERW01000501.1
[15:07:06] Skipping short (<200 bp) contig: NZ_AERW01000502.1
[15:07:06] Skipping short (<200 bp) contig: NZ_AERW01000503.1
[15:07:06] Skipping short (<200 bp) contig: NZ_AERW01000504.1
[15:07:06] Skipping short (<200 bp) contig: NZ_AERW01000506.1
[15:07:06] Skipping short (<200 bp) contig: NZ_AERW01000509.1
[15:07:06] Skipping short (<200 bp) contig: NZ_AERW01000510.1
[15:07:06] Skipping short (<200 bp) contig: NZ_AERW01000511.1
[15:07:06] Skipping short (<200 bp) contig: NZ_AERW01000513.1
[15:07:06] Skipping short (<200 bp) contig: NZ_AERW01000514.1
[15:07:06] Skipping short (<200 bp) contig: NZ_AERW01000515.1
[15:07:06] Skipping short (<200 bp) contig: NZ_AERW01000516.1
[15:07:06] Skipping short (<200 bp) contig: NZ_AERW01000518.1
[15:07:06] Skipping short (<200 bp) contig: NZ_AERW01000519.1
[15:07:06] Wrote 343 contigs
[15:07:06] Predicting tRNAs and tmRNAs
[15:07:06] Running: aragorn -gc11  -w \/home\/yquentin\/work\/wolbachia\/prokka\/wViB\/wViB\.fna
[15:07:06] 1 tRNA-Phe c[2924,2997] 34 (gaa)
[15:07:06] 1 tRNA-Arg [4839,4916] 36 (acg)
[15:07:06] 1 tRNA-Thr [5152,5225] 34 (tgt)
[15:07:06] 1 tRNA-Trp c[11734,11807] 34 (cca)
[15:07:06] 1 tRNA-Ser [922,1009] 35 (gga)
[15:07:06] 1 tRNA-Ser [1703,1795] 36 (gct)
[15:07:06] 1 tRNA-Arg [5412,5487] 36 (ccg)
[15:07:06] 1 tRNA-Thr [7726,7800] 35 (ggt)
[15:07:07] 1 tRNA-Val c[3772,3844] 34 (tac)
[15:07:07] 1 tRNA-Pro c[3823,3898] 36 (tgg)
[15:07:07] 2 tRNA-Glu c[4750,4822] 34 (ttc)
[15:07:07] 1 tRNA-Ser [2073,2161] 35 (tga)
[15:07:07] 1 tRNA-Val c[2359,2432] 34 (gac)
[15:07:07] 1 tRNA-Tyr [4336,4419] 36 (gta)
[15:07:07] 2 tRNA-Gly [4423,4494] 33 (tcc)
[15:07:07] 1 tRNA-Asp c[4536,4612] 35 (gtc)
[15:07:07] 1 tRNA-Arg [7428,7503] 36 (tct)
[15:07:07] 1 tRNA-Leu c[2199,2285] 35 (taa)
[15:07:07] 1 tRNA-Leu c[7477,7564] 35 (gag)
[15:07:07] Found 19 tRNAs
[15:07:07] Predicting Ribosomal RNAs
[15:07:07] Running Barrnap with 8 threads
[15:07:09] 1 gnl|Prokka|wViB_contig000215 5180 23S ribosomal RNA
[15:07:09] 2 gnl|Prokka|wViB_contig000215 8010 5S ribosomal RNA
[15:07:09] Found 2 rRNAs
[15:07:09] Skipping ncRNA search, enable with --rfam if desired.
[15:07:09] Total of 21 tRNA + rRNA features
[15:07:09] Searching for CRISPR repeats
[15:07:10] Found 0 CRISPRs
[15:07:10] Predicting coding sequences
[15:07:10] Contigs total 1095411 bp, so using single mode
[15:07:10] Running: prodigal -i \/home\/yquentin\/work\/wolbachia\/prokka\/wViB\/wViB\.fna -c -m -g 11 -p single -f sco -q
[15:07:12] Excluding CDS which overlaps existing RNA (tRNA) at gnl|Prokka|wViB_contig000165:7697..7846 on + strand
[15:07:12] Excluding CDS which overlaps existing RNA (tRNA) at gnl|Prokka|wViB_contig000193:2079..2192 on + strand
[15:07:12] Excluding CDS which overlaps existing RNA (rRNA) at gnl|Prokka|wViB_contig000215:6011..6283 on + strand
[15:07:12] Found 1017 CDS
[15:07:12] Connecting features back to sequences
[15:07:12] Option --gram not specified, will NOT check for signal peptides.
[15:07:12] Not using genus-specific database. Try --usegenus to enable it.
[15:07:12] Annotating CDS, please be patient.
[15:07:12] Will use 8 CPUs for similarity searching.
[15:07:13] There are still 1017 unannotated CDS left (started with 1017)
[15:07:13] Will use blast to search against /usr/local/bioinfo/src/PROKKA/prokka-1.10/bin/../db/kingdom/Bacteria/sprot with 8 CPUs
[15:07:13] Running: cat \/home\/yquentin\/work\/wolbachia\/prokka\/wViB\/proteins\.faa | parallel --gnu -j 8 --block 18471 --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\/wViB\/proteins\.bls 2> /dev/null
[15:07:39] Modify product: Cytochrome b561 homolog 2 => hypothetical protein
[15:07:39] Modify product: Probable murein peptide carboxypeptidase => putative murein peptide carboxypeptidase
[15:07:39] Modify product: Probable protein kinase UbiB => putative protein kinase UbiB
[15:07:39] Modify product: Probable peroxiredoxin => putative peroxiredoxin
[15:07:40] Modify product: Uncharacterized zinc protease Rv2782c => putative zinc protease
[15:07:40] Modify product: Uncharacterized zinc protease Rv2782c => putative zinc protease
[15:07:40] Modify product: Actin-binding protein Smlt3054 => Actin-binding protein
[15:07:40] Modify product: Transcription termination factor Rho => hypothetical protein
[15:07:40] Modify product: Probable tRNA-dihydrouridine synthase => putative tRNA-dihydrouridine synthase
[15:07:40] Modify product: Transcription termination/antitermination protein NusG => hypothetical protein
[15:07:40] Modify product: N utilization substance protein B homolog => hypothetical protein
[15:07:40] Modify product: Probable GTP-binding protein EngB => putative GTP-binding protein EngB
[15:07:40] Modify product: Uncharacterized zinc protease Rv2782c => putative zinc protease
[15:07:40] Modify product: Uncharacterized metal-dependent hydrolase YcfH => putative metal-dependent hydrolase YcfH
[15:07:40] Modify product: Stringent starvation protein A homolog => hypothetical protein
[15:07:40] Modify product: Putative O-methyltransferase MSMEG_5073/MSMEI_4947 => Putative O-methyltransferase/MSMEI_4947
[15:07:40] Modify product: Probable chromosome-partitioning protein ParB => putative chromosome-partitioning protein ParB
[15:07:40] Modify product: Probable acyltransferase YihG => putative acyltransferase YihG
[15:07:41] Modify product: Probable phospholipid ABC transporter-binding protein MlaD => putative phospholipid ABC transporter-binding protein MlaD
[15:07:41] Modify product: Uncharacterized oxidoreductase Rv0945 => putative oxidoreductase
[15:07:41] Modify product: Putative multidrug export ATP-binding/permease protein SAV1866 => Putative multidrug export ATP-binding/permease protein
[15:07:41] Modify product: Bifunctional protein FolD => Bifunctional protein FolD protein
[15:07:41] Modify product: SCO1 protein homolog => hypothetical protein
[15:07:41] Modify product: Co-chaperone protein HscB homolog => hypothetical protein
[15:07:42] Modify product: Transcription termination/antitermination protein NusA => hypothetical protein
[15:07:42] Modify product: Probable ribonucleotide transport ATP-binding protein mkl => putative ribonucleotide transport ATP-binding protein mkl
[15:07:42] Modify product: Probable phospholipid ABC transporter permease protein MlaE => putative phospholipid ABC transporter permease protein MlaE
[15:07:42] Modify product: Probable transcriptional regulatory protein aq_1575 => putative transcriptional regulatory protein
[15:07:42] Modify product: Putative multidrug export ATP-binding/permease protein SAV1866 => Putative multidrug export ATP-binding/permease protein
[15:07:42] Modify product: Riboflavin biosynthesis protein VVA0006 => Riboflavin biosynthesis protein
[15:07:42] Modify product: Putative multidrug export ATP-binding/permease protein SAV1866 => Putative multidrug export ATP-binding/permease protein
[15:07:42] Modify product: Probable deoxyribonuclease RhsA => putative deoxyribonuclease RhsA
[15:07:42] Modify product: Riboflavin biosynthesis protein VVA0006 => Riboflavin biosynthesis protein
[15:07:42] Modify product: Actin-binding protein Smlt3054 => Actin-binding protein
[15:07:42] Modify product: Uncharacterized oxidoreductase YciK => putative oxidoreductase YciK
[15:07:42] Cleaned 35 /product names
[15:07:42] Deleting unwanted file: /home/yquentin/work/wolbachia/prokka/wViB/proteins.faa
[15:07:42] Deleting unwanted file: /home/yquentin/work/wolbachia/prokka/wViB/proteins.bls
[15:07:43] There are still 425 unannotated CDS left (started with 1017)
[15:07:43] Will use hmmer3 to search against /usr/local/bioinfo/src/PROKKA/prokka-1.10/bin/../db/hmm/HAMAP.hmm with 8 CPUs
[15:07:43] Running: cat \/home\/yquentin\/work\/wolbachia\/prokka\/wViB\/proteins\.faa | parallel --gnu -j 8 --block 5560 --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\/wViB\/proteins\.bls 2> /dev/null
[15:07:55] Deleting unwanted file: /home/yquentin/work/wolbachia/prokka/wViB/proteins.faa
[15:07:55] Deleting unwanted file: /home/yquentin/work/wolbachia/prokka/wViB/proteins.bls
[15:07:55] There are still 395 unannotated CDS left (started with 1017)
[15:07:55] Will use hmmer3 to search against /usr/local/bioinfo/src/PROKKA/prokka-1.10/bin/../db/hmm/CLUSTERS.hmm with 8 CPUs
[15:07:55] Running: cat \/home\/yquentin\/work\/wolbachia\/prokka\/wViB\/proteins\.faa | parallel --gnu -j 8 --block 5010 --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\/wViB\/proteins\.bls 2> /dev/null
[15:08:28] Deleting unwanted file: /home/yquentin/work/wolbachia/prokka/wViB/proteins.faa
[15:08:28] Deleting unwanted file: /home/yquentin/work/wolbachia/prokka/wViB/proteins.bls
[15:08:29] There are still 370 unannotated CDS left (started with 1017)
[15:08:29] Will use hmmer3 to search against /usr/local/bioinfo/src/PROKKA/prokka-1.10/bin/../db/hmm/Pfam.hmm with 8 CPUs
[15:08:29] Running: cat \/home\/yquentin\/work\/wolbachia\/prokka\/wViB\/proteins\.faa | parallel --gnu -j 8 --block 4658 --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\/wViB\/proteins\.bls 2> /dev/null
[15:09:01] Modify product: EVE domain => EVE domain protein
[15:09:01] Modify product: KAP family P-loop domain => KAP family P-loop domain protein
[15:09:01] Modify product: KAP family P-loop domain => KAP family P-loop domain protein
[15:09:01] Modify product: RmlD substrate binding domain => RmlD substrate binding domain protein
[15:09:01] Modify product: PAS domain => PAS domain protein
[15:09:01] Modify product: Transposase IS200 like => Transposase IS200 like protein
[15:09:01] Modify product: Integral membrane protein TerC family => Integral membrane protein TerC family protein
[15:09:01] Modify product: DSBA-like thioredoxin domain => DSBA-like thioredoxin domain protein
[15:09:01] Modify product: Transposase DDE domain => Transposase DDE domain protein
[15:09:01] Modify product: RDD family => RDD family protein
[15:09:01] Modify product: Sodium:dicarboxylate symporter family => Sodium:dicarboxylate symporter family protein
[15:09:01] Modify product: YGGT family => YGGT family protein
[15:09:01] Modify product: SURF1 family => SURF1 family protein
[15:09:01] Modify product: Alpha/beta hydrolase family => Alpha/beta hydrolase family protein
[15:09:01] Modify product: AhpC/TSA family => AhpC/TSA family protein
[15:09:01] Modify product: Uracil DNA glycosylase superfamily => Uracil DNA glycosylase superfamily protein
[15:09:01] Modify product: ETC complex I subunit conserved region => hypothetical protein
[15:09:01] Modify product: Terminase-like family => Terminase-like family protein
[15:09:01] Modify product: Terminase-like family => Terminase-like family protein
[15:09:01] Modify product: Tim44-like domain => Tim44-like domain protein
[15:09:01] Modify product: TrbC/VIRB2 family => TrbC/VIRB2 family protein
[15:09:01] Modify product: SPFH domain / Band 7 family => SPFH domain / Band 7 family protein
[15:09:01] Modify product: TrbC/VIRB2 family => TrbC/VIRB2 family protein
[15:09:01] Modify product: COQ9 => hypothetical protein
[15:09:01] Modify product: Transposase DDE domain => Transposase DDE domain protein
[15:09:01] Modify product: TrbC/VIRB2 family => TrbC/VIRB2 family protein
[15:09:01] Modify product: Ankyrin repeat => Ankyrin repeat protein
[15:09:01] Modify product: Na+/H+ antiporter family => Na+/H+ antiporter family protein
[15:09:01] Modify product: RmlD substrate binding domain => RmlD substrate binding domain protein
[15:09:01] Modify product: Ankyrin repeat => Ankyrin repeat protein
[15:09:01] Cleaned 30 /product names
[15:09:01] Deleting unwanted file: /home/yquentin/work/wolbachia/prokka/wViB/proteins.faa
[15:09:01] Deleting unwanted file: /home/yquentin/work/wolbachia/prokka/wViB/proteins.bls
[15:09:01] Labelling remaining 279 proteins as 'hypothetical protein'
[15:09:01] Possible /pseudo 'putative zinc protease' at gnl|Prokka|wViB_contig000088 position 6377
[15:09:01] Possible /pseudo 'TrbL/VirB6 plasmid conjugal transfer protein' at gnl|Prokka|wViB_contig000106 position 5449
[15:09:01] Possible /pseudo 'TrbL/VirB6 plasmid conjugal transfer protein' at gnl|Prokka|wViB_contig000106 position 8352
[15:09:01] Possible /pseudo 'Type IV secretion system protein virB4' at gnl|Prokka|wViB_contig000115 position 2379
[15:09:01] Possible /pseudo 'Arginine/agmatine antiporter' at gnl|Prokka|wViB_contig000133 position 8308
[15:09:01] Possible /pseudo 'Chaperone protein HtpG' at gnl|Prokka|wViB_contig000145 position 1795
[15:09:01] Possible /pseudo 'Amino-acid carrier protein AlsT' at gnl|Prokka|wViB_contig000205 position 12155
[15:09:01] Possible /pseudo '30S ribosomal protein S2' at gnl|Prokka|wViB_contig000227 position 5243
[15:09:01] Possible /pseudo 'L-allo-threonine aldolase' at gnl|Prokka|wViB_contig000251 position 4446
[15:09:01] Possible /pseudo 'Phage late control gene D protein (GPD)' at gnl|Prokka|wViB_contig000253 position 5172
[15:09:01] Possible /pseudo 'Dihydrofolate reductase' at gnl|Prokka|wViB_contig000264 position 1786
[15:09:01] Possible /pseudo 'L-allo-threonine aldolase' at gnl|Prokka|wViB_contig000267 position 1759
[15:09:01] Possible /pseudo 'L-allo-threonine aldolase' at gnl|Prokka|wViB_contig000267 position 2468
[15:09:01] Found 541 unique /gene codes.
[15:09:01] Fixed 28 colliding /gene names.
[15:09:01] Adding /locus_tag identifiers
[15:09:02] Assigned 1038 locus_tags to CDS and RNA features.
[15:09:02] Writing outputs to /home/yquentin/work/wolbachia/prokka/wViB/
[15:09:06] Generating annotation statistics file
[15:09:06] Generating Genbank and Sequin files
[15:09:06] 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\/wViB\/wViB\.err -i \/home\/yquentin\/work\/wolbachia\/prokka\/wViB\/wViB\.fsa 2> /dev/null
[15:09:13] Deleting unwanted file: /home/yquentin/work/wolbachia/prokka/wViB/errorsummary.val
[15:09:13] Deleting unwanted file: /home/yquentin/work/wolbachia/prokka/wViB/wViB.dr
[15:09:13] Deleting unwanted file: /home/yquentin/work/wolbachia/prokka/wViB/wViB.fixedproducts
[15:09:13] Deleting unwanted file: /home/yquentin/work/wolbachia/prokka/wViB/wViB.ecn
[15:09:13] Deleting unwanted file: /home/yquentin/work/wolbachia/prokka/wViB/wViB.val
[15:09:13] Output files:
[15:09:13] /home/yquentin/work/wolbachia/prokka/wViB/wViB.fsa
[15:09:13] /home/yquentin/work/wolbachia/prokka/wViB/wViB.sqn
[15:09:13] /home/yquentin/work/wolbachia/prokka/wViB/wViB.tbl
[15:09:13] /home/yquentin/work/wolbachia/prokka/wViB/wViB.ffn
[15:09:13] /home/yquentin/work/wolbachia/prokka/wViB/wViB.err
[15:09:13] /home/yquentin/work/wolbachia/prokka/wViB/wViB.gff
[15:09:13] /home/yquentin/work/wolbachia/prokka/wViB/wViB.faa
[15:09:13] /home/yquentin/work/wolbachia/prokka/wViB/wViB.fna
[15:09:13] /home/yquentin/work/wolbachia/prokka/wViB/wViB.gbk
[15:09:13] /home/yquentin/work/wolbachia/prokka/wViB/wViB.log
[15:09:13] /home/yquentin/work/wolbachia/prokka/wViB/wViB.txt
[15:09:13] Walltime used: 2.15 minutes
[15:09:13] If you use this result please cite the Prokka paper:
[15:09:13] Seemann T (2014) Prokka: rapid prokaryotic genome annotation. Bioinformatics. 30(14):2068-9.
[15:09:13] Type 'prokka --citation' for more details.
[15:09:13] Share and enjoy!