[10:41:12] Command: --force --outdir /home/yquentin/work/wolbachia/prokka/JHBwCquin --addgenes --prefix JHBwCquin --locustag JHBwCquin --species Wolbachia endosymbiont --strain JHBwCquin --compliant --quiet /home/yquentin/work/wolbachia/prokka/JHBwCquin.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/JHBwCquin.fna
[10:41:15] Wrote 16 contigs
[10:41:15] Predicting tRNAs and tmRNAs
[10:41:15] Running: aragorn -gc11  -w \/home\/yquentin\/work\/wolbachia\/prokka\/JHBwCquin\/JHBwCquin\.fna
[10:41:15] 1 tRNA-Thr [113244,113317] 34 (tgt)
[10:41:15] 2 tRNA-Gln c[119932,120004] 33 (ttg)
[10:41:15] 3 tRNA-Trp c[146923,146996] 34 (cca)
[10:41:15] 4 tRNA-Leu [154014,154096] 35 (tag)
[10:41:15] 5 tRNA-His c[248471,248546] 34 (gtg)
[10:41:15] 6 tRNA-Met c[259680,259752] 33 (cat)
[10:41:15] 7 tRNA-Asn [276069,276141] 33 (gtt)
[10:41:15] 8 tRNA-Met c[311437,311513] 35 (cat)
[10:41:15] 9 tRNA-Gly [312739,312812] 34 (gcc)
[10:41:15] 10 tRNA-Ser [319852,319939] 35 (gga)
[10:41:15] 11 tRNA-Ser [424211,424303] 36 (gct)
[10:41:15] 12 tRNA-Arg [435074,435149] 36 (ccg)
[10:41:15] 13 tRNA-Arg [464230,464305] 36 (tct)
[10:41:15] 14 tRNA-Thr [490895,490969] 35 (ggt)
[10:41:15] 15 tRNA-Met c[513992,514068] 35 (cat)
[10:41:15] 16 tRNA-Ser c[556786,556871] 35 (cag)
[10:41:15] 17 tRNA-Val c[563774,563846] 34 (tac)
[10:41:15] 18 tRNA-Pro c[570906,570981] 36 (tgg)
[10:41:15] 19 tRNA-Glu c[571830,571902] 34 (ttc)
[10:41:15] 20 tRNA-Ala c[611348,611423] 34 (tgc)
[10:41:15] 21 tRNA-Lys [611724,611797] 34 (ttt)
[10:41:15] 22 tRNA-Ser [617764,617849] 35 (tga)
[10:41:15] 23 tRNA-Cys [695199,695271] 34 (gca)
[10:41:15] 24 tRNA-Val c[736615,736688] 34 (gac)
[10:41:15] 25 tRNA-Ile [768174,768250] 35 (gat)
[10:41:15] 26 tRNA-Tyr [794455,794538] 36 (gta)
[10:41:15] 27 tRNA-Gly [794542,794613] 33 (tcc)
[10:41:15] 28 tRNA-Asp c[857759,857835] 35 (gtc)
[10:41:15] 29 tRNA-Leu [869390,869477] 35 (gag)
[10:41:15] 30 tRNA-Leu c[915555,915641] 35 (taa)
[10:41:15] 31 tRNA-Arg c[926987,927064] 36 (acg)
[10:41:15] 32 tmRNA* [948056,948388] 195,242 ANDNFAAEDNVALAA*
[10:41:15] 33 tRNA-Leu [1025032,1025115] 34 (caa)
[10:41:15] 34 tRNA-Arg [1089610,1089684] 35 (cct)
[10:41:15] 35 tRNA-Phe c[1179829,1179902] 34 (gaa)
[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|JHBwCquin_contig000003 678182 16S ribosomal RNA
[10:41:16] 2 gnl|Prokka|JHBwCquin_contig000003 778608 23S ribosomal RNA
[10:41:16] 3 gnl|Prokka|JHBwCquin_contig000003 781438 5S 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 1543661 bp, so using single mode
[10:41:16] Running: prodigal -i \/home\/yquentin\/work\/wolbachia\/prokka\/JHBwCquin\/JHBwCquin\.fna -c -m -g 11 -p single -f sco -q
[10:41:18] Excluding CDS which overlaps existing RNA (tRNA) at gnl|Prokka|JHBwCquin_contig000003:119995..120330 on - strand
[10:41:18] Excluding CDS which overlaps existing RNA (tRNA) at gnl|Prokka|JHBwCquin_contig000003:259743..261044 on - strand
[10:41:19] Excluding CDS which overlaps existing RNA (tRNA) at gnl|Prokka|JHBwCquin_contig000003:490866..491015 on + strand
[10:41:19] Excluding CDS which overlaps existing RNA (rRNA) at gnl|Prokka|JHBwCquin_contig000003:679328..679579 on + strand
[10:41:19] Found 1503 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 1503 unannotated CDS left (started with 1503)
[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\/JHBwCquin\/proteins\.faa | parallel --gnu -j 8 --block 28380 --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\/JHBwCquin\/proteins\.bls 2> /dev/null
[10:41:34] Modify product: Uncharacterized zinc protease Rv2782c => putative zinc protease
[10:41:34] Modify product: Uncharacterized zinc protease Rv2782c => putative zinc protease
[10:41:34] Modify product: Actin-binding protein Smlt3054 => Actin-binding protein
[10:41:34] Modify product: Transcription termination factor Rho => hypothetical protein
[10:41:34] Modify product: Probable tRNA-dihydrouridine synthase => putative tRNA-dihydrouridine synthase
[10:41:34] Modify product: Transcription termination/antitermination protein NusG => hypothetical protein
[10:41:35] Modify product: Probable chromosome-partitioning protein ParB => putative chromosome-partitioning protein ParB
[10:41:35] Modify product: Probable acyltransferase YihG => putative acyltransferase YihG
[10:41:35] Modify product: Probable phospholipid ABC transporter-binding protein MlaD => putative phospholipid ABC transporter-binding protein MlaD
[10:41:35] Modify product: Probable phospholipid ABC transporter permease protein MlaE => putative phospholipid ABC transporter permease protein MlaE
[10:41:35] Modify product: Probable ribonucleotide transport ATP-binding protein mkl => putative ribonucleotide transport ATP-binding protein mkl
[10:41:35] Modify product: Uncharacterized metal-dependent hydrolase YcfH => putative metal-dependent hydrolase YcfH
[10:41:35] Modify product: Actin-binding protein Smlt3054 => Actin-binding protein
[10:41:35] Modify product: Uncharacterized oxidoreductase YciK => putative oxidoreductase YciK
[10:41:35] Modify product: Stringent starvation protein A homolog => hypothetical protein
[10:41:35] Modify product: Putative O-methyltransferase MSMEG_5073/MSMEI_4947 => Putative O-methyltransferase/MSMEI_4947
[10:41:35] Modify product: Uncharacterized zinc protease Rv2782c => putative zinc protease
[10:41:35] Modify product: Cytochrome b561 homolog 2 => hypothetical protein
[10:41:35] Modify product: Probable murein peptide carboxypeptidase => putative murein peptide carboxypeptidase
[10:41:35] Modify product: Actin-binding protein Smlt3054 => Actin-binding protein
[10:41:35] Modify product: Bifunctional protein FolD => Bifunctional protein FolD protein
[10:41:35] Modify product: SCO1 protein homolog => hypothetical protein
[10:41:35] Modify product: Actin-binding protein Smlt3054 => Actin-binding protein
[10:41:35] Modify product: Transcription termination/antitermination protein NusA => hypothetical protein
[10:41:35] Modify product: N utilization substance protein B homolog => hypothetical protein
[10:41:35] Modify product: Probable GTP-binding protein EngB => putative GTP-binding protein EngB
[10:41:36] Modify product: Uncharacterized oxidoreductase Rv0945 => putative oxidoreductase
[10:41:36] Modify product: Probable transcriptional regulatory protein aq_1575 => putative transcriptional regulatory protein
[10:41:36] Modify product: Putative multidrug export ATP-binding/permease protein SAV1866 => Putative multidrug export ATP-binding/permease protein
[10:41:36] Modify product: Probable peroxiredoxin => putative peroxiredoxin
[10:41:36] Modify product: Probable protein kinase UbiB => putative protein kinase UbiB
[10:41:36] Modify product: Riboflavin biosynthesis protein VVA0006 => Riboflavin biosynthesis protein
[10:41:36] Modify product: Co-chaperone protein HscB homolog => hypothetical protein
[10:41:36] Cleaned 33 /product names
[10:41:36] Deleting unwanted file: /home/yquentin/work/wolbachia/prokka/JHBwCquin/proteins.faa
[10:41:36] Deleting unwanted file: /home/yquentin/work/wolbachia/prokka/JHBwCquin/proteins.bls
[10:41:36] There are still 875 unannotated CDS left (started with 1503)
[10:41:36] Will use hmmer3 to search against /usr/local/bioinfo/src/PROKKA/prokka-1.10/bin/../db/hmm/HAMAP.hmm with 8 CPUs
[10:41:36] Running: cat \/home\/yquentin\/work\/wolbachia\/prokka\/JHBwCquin\/proteins\.faa | parallel --gnu -j 8 --block 13422 --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\/JHBwCquin\/proteins\.bls 2> /dev/null
[10:41:46] Deleting unwanted file: /home/yquentin/work/wolbachia/prokka/JHBwCquin/proteins.faa
[10:41:46] Deleting unwanted file: /home/yquentin/work/wolbachia/prokka/JHBwCquin/proteins.bls
[10:41:47] There are still 841 unannotated CDS left (started with 1503)
[10:41:47] Will use hmmer3 to search against /usr/local/bioinfo/src/PROKKA/prokka-1.10/bin/../db/hmm/CLUSTERS.hmm with 8 CPUs
[10:41:47] Running: cat \/home\/yquentin\/work\/wolbachia\/prokka\/JHBwCquin\/proteins\.faa | parallel --gnu -j 8 --block 12615 --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\/JHBwCquin\/proteins\.bls 2> /dev/null
[10:42:16] Deleting unwanted file: /home/yquentin/work/wolbachia/prokka/JHBwCquin/proteins.faa
[10:42:16] Deleting unwanted file: /home/yquentin/work/wolbachia/prokka/JHBwCquin/proteins.bls
[10:42:16] There are still 790 unannotated CDS left (started with 1503)
[10:42:16] Will use hmmer3 to search against /usr/local/bioinfo/src/PROKKA/prokka-1.10/bin/../db/hmm/Pfam.hmm with 8 CPUs
[10:42:16] Running: cat \/home\/yquentin\/work\/wolbachia\/prokka\/JHBwCquin\/proteins\.faa | parallel --gnu -j 8 --block 11757 --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\/JHBwCquin\/proteins\.bls 2> /dev/null
[10:42:47] Modify product: Alpha/beta hydrolase family => Alpha/beta hydrolase family protein
[10:42:47] Modify product: Transposase DDE domain => Transposase DDE domain protein
[10:42:47] Modify product: Major Facilitator Superfamily => Major Facilitator Superfamily protein
[10:42:47] Modify product: Ankyrin repeat => Ankyrin repeat protein
[10:42:47] Modify product: KAP family P-loop domain => KAP family P-loop domain protein
[10:42:47] Modify product: Ankyrin repeat => Ankyrin repeat protein
[10:42:47] Modify product: RmlD substrate binding domain => RmlD substrate binding domain protein
[10:42:47] Modify product: Ankyrin repeat => Ankyrin repeat protein
[10:42:47] Modify product: Transposase DDE domain => Transposase DDE domain protein
[10:42:47] Modify product: PAS domain => PAS domain protein
[10:42:47] Modify product: Transposase IS116/IS110/IS902 family => Transposase IS116/IS110/IS902 family protein
[10:42:47] Modify product: Ankyrin repeat => Ankyrin repeat protein
[10:42:47] Modify product: DSBA-like thioredoxin domain => DSBA-like thioredoxin domain protein
[10:42:47] Modify product: Transposase DDE domain => Transposase DDE domain protein
[10:42:47] Modify product: COQ9 => hypothetical protein
[10:42:47] Modify product: Transposase DDE domain => Transposase DDE domain protein
[10:42:47] Modify product: DnaJ domain => DnaJ domain protein
[10:42:47] Modify product: RDD family => RDD family protein
[10:42:47] Modify product: Transposase DDE domain => Transposase DDE domain protein
[10:42:47] Modify product: EVE domain => EVE domain protein
[10:42:47] Modify product: Transposase DDE domain => Transposase DDE domain protein
[10:42:47] Modify product: Transposase DDE domain => Transposase DDE domain protein
[10:42:47] Modify product: Alpha/beta hydrolase family => Alpha/beta hydrolase family protein
[10:42:47] Modify product: Transposase DDE domain => Transposase DDE domain protein
[10:42:47] Modify product: Piwi/Argonaute/Zwille siRNA-binding domain => Piwi/Argonaute/Zwille siRNA-binding domain protein
[10:42:47] Modify product: Transposase DDE domain => Transposase DDE domain protein
[10:42:47] Modify product: Transposase DDE domain => Transposase DDE domain protein
[10:42:47] Modify product: Phosphotransferase enzyme family => Phosphotransferase enzyme family protein
[10:42:47] Modify product: AhpC/TSA family => AhpC/TSA family protein
[10:42:47] Modify product: Transposase DDE domain => Transposase DDE domain protein
[10:42:47] Modify product: TrbC/VIRB2 family => TrbC/VIRB2 family protein
[10:42:47] Modify product: Transposase DDE domain => Transposase DDE domain protein
[10:42:47] Modify product: Transposase IS116/IS110/IS902 family => Transposase IS116/IS110/IS902 family protein
[10:42:47] Modify product: Transposase IS200 like => Transposase IS200 like protein
[10:42:47] Modify product: Transposase DDE domain => Transposase DDE domain protein
[10:42:47] Modify product: Transposase DDE domain => Transposase DDE domain protein
[10:42:47] Modify product: Integral membrane protein TerC family => Integral membrane protein TerC family protein
[10:42:47] Modify product: Uracil DNA glycosylase superfamily => Uracil DNA glycosylase superfamily protein
[10:42:47] Modify product: Transposase DDE domain => Transposase DDE domain protein
[10:42:47] Modify product: ETC complex I subunit conserved region => hypothetical protein
[10:42:47] Modify product: Transposase DDE domain => Transposase DDE domain protein
[10:42:47] Modify product: Alpha/beta hydrolase family => Alpha/beta hydrolase family protein
[10:42:47] Modify product: MgtE intracellular N domain => MgtE intracellular N domain protein
[10:42:47] Modify product: Transposase DDE domain => Transposase DDE domain protein
[10:42:47] Modify product: Terminase-like family => Terminase-like family protein
[10:42:47] Modify product: Transposase DDE domain => Transposase DDE domain protein
[10:42:47] Modify product: Transposase DDE domain => Transposase DDE domain protein
[10:42:47] Modify product: Transposase DDE domain => Transposase DDE domain protein
[10:42:47] Modify product: Terminase-like family => Terminase-like family protein
[10:42:47] Modify product: Transposase DDE domain => Transposase DDE domain protein
[10:42:47] Modify product: Transposase IS116/IS110/IS902 family => Transposase IS116/IS110/IS902 family protein
[10:42:47] Modify product: PAAR motif => PAAR motif protein
[10:42:47] Modify product: Ankyrin repeat => Ankyrin repeat protein
[10:42:47] Modify product: Helix-turn-helix domain => Helix-turn-helix domain protein
[10:42:47] Modify product: Tim44-like domain => Tim44-like domain protein
[10:42:47] Modify product: Transposase DDE domain => Transposase DDE domain protein
[10:42:47] Modify product: Transposase DDE domain => Transposase DDE domain protein
[10:42:47] Modify product: Transposase DDE domain => Transposase DDE domain protein
[10:42:47] Modify product: Transposase DDE domain => Transposase DDE domain protein
[10:42:47] Modify product: Hepatic lectin, N-terminal domain => hypothetical protein
[10:42:47] Modify product: Transposase DDE domain => Transposase DDE domain protein
[10:42:47] Modify product: TrbC/VIRB2 family => TrbC/VIRB2 family protein
[10:42:47] Modify product: Transposase IS116/IS110/IS902 family => Transposase IS116/IS110/IS902 family protein
[10:42:47] Modify product: SPFH domain / Band 7 family => SPFH domain / Band 7 family protein
[10:42:47] Modify product: Transposase DDE domain => Transposase DDE domain protein
[10:42:47] Modify product: TrbC/VIRB2 family => TrbC/VIRB2 family protein
[10:42:47] Modify product: Ankyrin repeat => Ankyrin repeat protein
[10:42:47] Modify product: Transposase DDE domain => Transposase DDE domain protein
[10:42:47] Modify product: Transposase DDE domain => Transposase DDE domain protein
[10:42:47] Modify product: RDD family => RDD family protein
[10:42:47] Modify product: Transposase DDE domain => Transposase DDE domain protein
[10:42:47] Modify product: Ankyrin repeat => Ankyrin repeat protein
[10:42:47] Modify product: Transposase DDE domain => Transposase DDE domain protein
[10:42:47] Modify product: Transposase DDE domain => Transposase DDE domain protein
[10:42:47] Modify product: Phage capsid family => Phage capsid family protein
[10:42:47] Modify product: Transposase DDE domain => Transposase DDE domain protein
[10:42:47] Modify product: Transposase DDE domain => Transposase DDE domain protein
[10:42:47] Modify product: Transposase DDE domain => Transposase DDE domain protein
[10:42:47] Modify product: Transposase IS116/IS110/IS902 family => Transposase IS116/IS110/IS902 family protein
[10:42:48] Modify product: Transposase IS116/IS110/IS902 family => Transposase IS116/IS110/IS902 family protein
[10:42:48] Modify product: Transposase DDE domain => Transposase DDE domain protein
[10:42:48] Modify product: Glyoxalase-like domain => Glyoxalase-like domain protein
[10:42:48] Modify product: PAAR motif => PAAR motif protein
[10:42:48] Modify product: Ankyrin repeat => Ankyrin repeat protein
[10:42:48] Modify product: NB-ARC domain => NB-ARC domain protein
[10:42:48] Modify product: Transposase DDE domain => Transposase DDE domain protein
[10:42:48] Modify product: Transposase DDE domain => Transposase DDE domain protein
[10:42:48] Modify product: Transposase IS200 like => Transposase IS200 like protein
[10:42:48] Modify product: Transposase DDE domain => Transposase DDE domain protein
[10:42:48] Modify product: PD-(D/E)XK nuclease superfamily => PD-(D/E)XK nuclease superfamily protein
[10:42:48] Modify product: Transposase DDE domain => Transposase DDE domain protein
[10:42:48] Modify product: RDD family => RDD family protein
[10:42:48] Modify product: SURF1 family => SURF1 family protein
[10:42:48] Modify product: YGGT family => YGGT family protein
[10:42:48] Modify product: Sodium:dicarboxylate symporter family => Sodium:dicarboxylate symporter family protein
[10:42:48] Modify product: Na+/H+ antiporter family => Na+/H+ antiporter family protein
[10:42:48] Modify product: Transposase DDE domain => Transposase DDE domain protein
[10:42:48] Modify product: Transposase DDE domain => Transposase DDE domain protein
[10:42:48] Modify product: Piwi/Argonaute/Zwille siRNA-binding domain => Piwi/Argonaute/Zwille siRNA-binding domain protein
[10:42:48] Modify product: Transposase DDE domain => Transposase DDE domain protein
[10:42:48] Modify product: RDD family => RDD family protein
[10:42:48] Modify product: Transposase DDE domain => Transposase DDE domain protein
[10:42:48] Modify product: Transposase DDE domain => Transposase DDE domain protein
[10:42:48] Modify product: Na+/H+ antiporter family => Na+/H+ antiporter family protein
[10:42:48] Modify product: Transposase DDE domain => Transposase DDE domain protein
[10:42:48] Modify product: Transposase DDE domain => Transposase DDE domain protein
[10:42:48] Modify product: Transposase IS200 like => Transposase IS200 like protein
[10:42:48] Modify product: Transposase DDE domain => Transposase DDE domain protein
[10:42:48] Modify product: Transposase DDE domain => Transposase DDE domain protein
[10:42:48] Modify product: Transposase DDE domain => Transposase DDE domain protein
[10:42:48] Modify product: Ankyrin repeat => Ankyrin repeat protein
[10:42:48] Modify product: PAAR motif => PAAR motif protein
[10:42:48] Modify product: BRO family, N-terminal domain => hypothetical protein
[10:42:48] Modify product: Transposase IS66 family => Transposase IS66 family protein
[10:42:48] Modify product: CobQ/CobB/MinD/ParA nucleotide binding domain => CobQ/CobB/MinD/ParA nucleotide binding domain protein
[10:42:48] Modify product: Terminase-like family => Terminase-like family protein
[10:42:48] Modify product: PAAR motif => PAAR motif protein
[10:42:48] Modify product: Transposase DDE domain => Transposase DDE domain protein
[10:42:48] Modify product: Transposase DDE domain => Transposase DDE domain protein
[10:42:48] Modify product: Transposase DDE domain => Transposase DDE domain protein
[10:42:48] Cleaned 120 /product names
[10:42:48] Deleting unwanted file: /home/yquentin/work/wolbachia/prokka/JHBwCquin/proteins.faa
[10:42:48] Deleting unwanted file: /home/yquentin/work/wolbachia/prokka/JHBwCquin/proteins.bls
[10:42:48] Labelling remaining 501 proteins as 'hypothetical protein'
[10:42:48] Possible /pseudo 'DNA mismatch repair protein MutL' at gnl|Prokka|JHBwCquin_contig000001 position 40702
[10:42:48] Possible /pseudo 'anaerobic benzoate catabolism transcriptional regulator' at gnl|Prokka|JHBwCquin_contig000001 position 47566
[10:42:48] Possible /pseudo 'Phage terminase large subunit (GpA)' at gnl|Prokka|JHBwCquin_contig000002 position 664
[10:42:48] Possible /pseudo 'Transposase DDE domain protein' at gnl|Prokka|JHBwCquin_contig000003 position 66907
[10:42:48] Possible /pseudo 'putative zinc protease' at gnl|Prokka|JHBwCquin_contig000003 position 82161
[10:42:48] Possible /pseudo 'Transposase DDE domain protein' at gnl|Prokka|JHBwCquin_contig000003 position 182714
[10:42:48] Possible /pseudo 'TrbL/VirB6 plasmid conjugal transfer protein' at gnl|Prokka|JHBwCquin_contig000003 position 188329
[10:42:48] Possible /pseudo 'TrbL/VirB6 plasmid conjugal transfer protein' at gnl|Prokka|JHBwCquin_contig000003 position 191226
[10:42:48] Possible /pseudo 'TrbL/VirB6 plasmid conjugal transfer protein' at gnl|Prokka|JHBwCquin_contig000003 position 193616
[10:42:48] Possible /pseudo 'Dihydropteroate synthase' at gnl|Prokka|JHBwCquin_contig000003 position 307425
[10:42:48] Possible /pseudo 'Arginine/agmatine antiporter' at gnl|Prokka|JHBwCquin_contig000003 position 329102
[10:42:48] Possible /pseudo 'Ankyrin repeats (3 copies)' at gnl|Prokka|JHBwCquin_contig000003 position 336457
[10:42:48] Possible /pseudo 'Ankyrin repeats (3 copies)' at gnl|Prokka|JHBwCquin_contig000003 position 337770
[10:42:48] Possible /pseudo 'Transposase DDE domain protein' at gnl|Prokka|JHBwCquin_contig000003 position 635853
[10:42:48] Possible /pseudo 'Amino-acid carrier protein AlsT' at gnl|Prokka|JHBwCquin_contig000003 position 729801
[10:42:48] Possible /pseudo 'Transposase DDE domain protein' at gnl|Prokka|JHBwCquin_contig000003 position 732405
[10:42:48] Possible /pseudo 'Aminopyrimidine aminohydrolase' at gnl|Prokka|JHBwCquin_contig000003 position 770271
[10:42:48] Possible /pseudo 'Ankyrin repeats (3 copies)' at gnl|Prokka|JHBwCquin_contig000003 position 934755
[10:42:48] Possible /pseudo 'Transposase DDE domain protein' at gnl|Prokka|JHBwCquin_contig000003 position 1069044
[10:42:48] Possible /pseudo 'Exopolysaccharide synthesis, ExoD' at gnl|Prokka|JHBwCquin_contig000003 position 1087633
[10:42:48] Possible /pseudo 'Phosphocholine transferase AnkX' at gnl|Prokka|JHBwCquin_contig000003 position 1114789
[10:42:48] Possible /pseudo 'Transposase, Mutator family' at gnl|Prokka|JHBwCquin_contig000003 position 1324873
[10:42:48] Possible /pseudo 'Transposase, Mutator family' at gnl|Prokka|JHBwCquin_contig000003 position 1349373
[10:42:48] Possible /pseudo 'Phage terminase large subunit (GpA)' at gnl|Prokka|JHBwCquin_contig000003 position 1364476
[10:42:48] Possible /pseudo 'anaerobic benzoate catabolism transcriptional regulator' at gnl|Prokka|JHBwCquin_contig000003 position 1383238
[10:42:48] Possible /pseudo 'DNA mismatch repair protein MutL' at gnl|Prokka|JHBwCquin_contig000003 position 1388627
[10:42:48] Possible /pseudo 'Transposase DDE domain protein' at gnl|Prokka|JHBwCquin_contig000013 position 1470
[10:42:48] Found 547 unique /gene codes.
[10:42:48] Fixed 35 colliding /gene names.
[10:42:48] Adding /locus_tag identifiers
[10:42:48] Assigned 1541 locus_tags to CDS and RNA features.
[10:42:48] Writing outputs to /home/yquentin/work/wolbachia/prokka/JHBwCquin/
[10:42:49] Generating annotation statistics file
[10:42:49] Generating Genbank and Sequin files
[10:42:49] 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\/JHBwCquin\/JHBwCquin\.err -i \/home\/yquentin\/work\/wolbachia\/prokka\/JHBwCquin\/JHBwCquin\.fsa 2> /dev/null
[10:42:53] Deleting unwanted file: /home/yquentin/work/wolbachia/prokka/JHBwCquin/errorsummary.val
[10:42:53] Deleting unwanted file: /home/yquentin/work/wolbachia/prokka/JHBwCquin/JHBwCquin.dr
[10:42:53] Deleting unwanted file: /home/yquentin/work/wolbachia/prokka/JHBwCquin/JHBwCquin.fixedproducts
[10:42:53] Deleting unwanted file: /home/yquentin/work/wolbachia/prokka/JHBwCquin/JHBwCquin.ecn
[10:42:53] Deleting unwanted file: /home/yquentin/work/wolbachia/prokka/JHBwCquin/JHBwCquin.val
[10:42:53] Output files:
[10:42:53] /home/yquentin/work/wolbachia/prokka/JHBwCquin/JHBwCquin.gbk
[10:42:53] /home/yquentin/work/wolbachia/prokka/JHBwCquin/JHBwCquin.sqn
[10:42:53] /home/yquentin/work/wolbachia/prokka/JHBwCquin/JHBwCquin.gff
[10:42:53] /home/yquentin/work/wolbachia/prokka/JHBwCquin/JHBwCquin.log
[10:42:53] /home/yquentin/work/wolbachia/prokka/JHBwCquin/JHBwCquin.ffn
[10:42:53] /home/yquentin/work/wolbachia/prokka/JHBwCquin/JHBwCquin.txt
[10:42:53] /home/yquentin/work/wolbachia/prokka/JHBwCquin/JHBwCquin.fsa
[10:42:53] /home/yquentin/work/wolbachia/prokka/JHBwCquin/JHBwCquin.fna
[10:42:53] /home/yquentin/work/wolbachia/prokka/JHBwCquin/JHBwCquin.err
[10:42:53] /home/yquentin/work/wolbachia/prokka/JHBwCquin/JHBwCquin.tbl
[10:42:53] /home/yquentin/work/wolbachia/prokka/JHBwCquin/JHBwCquin.faa
[10:42:53] Walltime used: 1.68 minutes
[10:42:53] If you use this result please cite the Prokka paper:
[10:42:53] Seemann T (2014) Prokka: rapid prokaryotic genome annotation. Bioinformatics. 30(14):2068-9.
[10:42:53] Type 'prokka --citation' for more details.
[10:42:53] Share and enjoy!