[15:06:39] Command: --force --outdir /home/yquentin/work/wolbachia/prokka/wCqu --addgenes --prefix wCqu --locustag wCqu --species Wolbachia endosymbiont --strain wCqu --compliant --quiet /home/yquentin/work/wolbachia/prokka/wCqu.fna
[15:06:39] Looking for 'aragorn' - found /usr/local/bioinfo/bin/aragorn
[15:06:39] Determined aragorn version is 1.2
[15:06:39] Looking for 'barrnap' - found /usr/local/bioinfo/bin/barrnap
[15:06:39] Determined barrnap version is 0.5
[15:06:39] Looking for 'blastp' - found /usr/local/bioinfo/src/NCBI_Blast+/ncbi-blast-2.6.0+/bin/blastp
[15:06:39] Determined blastp version is 2.6
[15:06:39] Looking for 'cmpress' - found /usr/local/bioinfo/src/PROKKA/prokka-1.10/bin/../binaries/linux/cmpress
[15:06:39] Determined cmpress version is 1.1
[15:06:39] Looking for 'cmscan' - found /usr/local/bioinfo/src/PROKKA/prokka-1.10/bin/../binaries/linux/cmscan
[15:06:39] Determined cmscan version is 1.1
[15:06:39] Looking for 'egrep' - found /bin/egrep
[15:06:39] Looking for 'find' - found /bin/find
[15:06:39] Looking for 'grep' - found /bin/grep
[15:06:39] Looking for 'hmmpress' - found /usr/local/bioinfo/bin/hmmpress
[15:06:39] Determined hmmpress version is 3.1
[15:06:39] Looking for 'hmmscan' - found /usr/local/bioinfo/bin/hmmscan
[15:06:39] Determined hmmscan version is 3.1
[15:06:39] Looking for 'less' - found /usr/bin/less
[15:06:39] Looking for 'makeblastdb' - found /usr/local/bioinfo/src/NCBI_Blast+/ncbi-blast-2.6.0+/bin/makeblastdb
[15:06:40] Determined makeblastdb version is 2.6
[15:06:40] Looking for 'minced' - found /usr/local/bioinfo/bin/minced
[15:06:40] Determined minced version is 1.6
[15:06:40] Looking for 'parallel' - found /usr/local/bioinfo/bin/parallel
[15:06:40] Determined parallel version is 20141022
[15:06:40] Looking for 'prodigal' - found /usr/local/bioinfo/bin/prodigal
[15:06:40] Determined prodigal version is 2.6
[15:06:40] Looking for 'rnammer' - found /usr/local/bioinfo/bin/rnammer
[15:06:40] Determined rnammer version is 1.2
[15:06:40] Looking for 'sed' - found /bin/sed
[15:06:40] Looking for 'signalp' - found /usr/local/bioinfo/bin/signalp
[15:06:41] Determined signalp version is 4.1
[15:06:41] Looking for 'tbl2asn' - found /home/yquentin/save/scripts/tbl2asn
[15:06:41] Determined tbl2asn version is 25.3
[15:06:41] Using genetic code table 11.
[15:06:41] Loading and checking input file: /home/yquentin/work/wolbachia/prokka/wCqu.fna
[15:06:41] Wrote 16 contigs
[15:06:41] Predicting tRNAs and tmRNAs
[15:06:41] Running: aragorn -gc11  -w \/home\/yquentin\/work\/wolbachia\/prokka\/wCqu\/wCqu\.fna
[15:06:42] 1 tRNA-Thr [113244,113317] 34 (tgt)
[15:06:42] 2 tRNA-Gln c[119932,120004] 33 (ttg)
[15:06:42] 3 tRNA-Trp c[146923,146996] 34 (cca)
[15:06:42] 4 tRNA-Leu [154014,154096] 35 (tag)
[15:06:42] 5 tRNA-His c[248471,248546] 34 (gtg)
[15:06:42] 6 tRNA-Met c[259680,259752] 33 (cat)
[15:06:42] 7 tRNA-Asn [276069,276141] 33 (gtt)
[15:06:42] 8 tRNA-Met c[311437,311513] 35 (cat)
[15:06:42] 9 tRNA-Gly [312739,312812] 34 (gcc)
[15:06:42] 10 tRNA-Ser [319852,319939] 35 (gga)
[15:06:42] 11 tRNA-Ser [424211,424303] 36 (gct)
[15:06:42] 12 tRNA-Arg [435074,435149] 36 (ccg)
[15:06:42] 13 tRNA-Arg [464230,464305] 36 (tct)
[15:06:42] 14 tRNA-Thr [490895,490969] 35 (ggt)
[15:06:42] 15 tRNA-Met c[513992,514068] 35 (cat)
[15:06:42] 16 tRNA-Ser c[556786,556871] 35 (cag)
[15:06:42] 17 tRNA-Val c[563774,563846] 34 (tac)
[15:06:42] 18 tRNA-Pro c[570906,570981] 36 (tgg)
[15:06:42] 19 tRNA-Glu c[571830,571902] 34 (ttc)
[15:06:42] 20 tRNA-Ala c[611348,611423] 34 (tgc)
[15:06:42] 21 tRNA-Lys [611724,611797] 34 (ttt)
[15:06:42] 22 tRNA-Ser [617764,617849] 35 (tga)
[15:06:42] 23 tRNA-Cys [695199,695271] 34 (gca)
[15:06:42] 24 tRNA-Val c[736615,736688] 34 (gac)
[15:06:42] 25 tRNA-Ile [768174,768250] 35 (gat)
[15:06:42] 26 tRNA-Tyr [794455,794538] 36 (gta)
[15:06:42] 27 tRNA-Gly [794542,794613] 33 (tcc)
[15:06:42] 28 tRNA-Asp c[857759,857835] 35 (gtc)
[15:06:42] 29 tRNA-Leu [869390,869477] 35 (gag)
[15:06:42] 30 tRNA-Leu c[915555,915641] 35 (taa)
[15:06:42] 31 tRNA-Arg c[926987,927064] 36 (acg)
[15:06:42] 32 tmRNA* [948056,948388] 195,242 ANDNFAAEDNVALAA*
[15:06:42] 33 tRNA-Leu [1025032,1025115] 34 (caa)
[15:06:42] 34 tRNA-Arg [1089610,1089684] 35 (cct)
[15:06:42] 35 tRNA-Phe c[1179829,1179902] 34 (gaa)
[15:06:42] Found 35 tRNAs
[15:06:42] Predicting Ribosomal RNAs
[15:06:42] Running Barrnap with 8 threads
[15:06:43] 1 gnl|Prokka|wCqu_contig000003 678182 16S ribosomal RNA
[15:06:43] 2 gnl|Prokka|wCqu_contig000003 778608 23S ribosomal RNA
[15:06:43] 3 gnl|Prokka|wCqu_contig000003 781438 5S ribosomal RNA
[15:06:43] Found 3 rRNAs
[15:06:43] Skipping ncRNA search, enable with --rfam if desired.
[15:06:43] Total of 37 tRNA + rRNA features
[15:06:43] Searching for CRISPR repeats
[15:06:44] Found 0 CRISPRs
[15:06:44] Predicting coding sequences
[15:06:44] Contigs total 1543661 bp, so using single mode
[15:06:44] Running: prodigal -i \/home\/yquentin\/work\/wolbachia\/prokka\/wCqu\/wCqu\.fna -c -m -g 11 -p single -f sco -q
[15:06:48] Excluding CDS which overlaps existing RNA (tRNA) at gnl|Prokka|wCqu_contig000003:119995..120330 on - strand
[15:06:48] Excluding CDS which overlaps existing RNA (tRNA) at gnl|Prokka|wCqu_contig000003:259743..261044 on - strand
[15:06:48] Excluding CDS which overlaps existing RNA (tRNA) at gnl|Prokka|wCqu_contig000003:490866..491015 on + strand
[15:06:49] Excluding CDS which overlaps existing RNA (rRNA) at gnl|Prokka|wCqu_contig000003:679328..679579 on + strand
[15:06:49] Found 1503 CDS
[15:06:49] Connecting features back to sequences
[15:06:49] Option --gram not specified, will NOT check for signal peptides.
[15:06:49] Not using genus-specific database. Try --usegenus to enable it.
[15:06:49] Annotating CDS, please be patient.
[15:06:49] Will use 8 CPUs for similarity searching.
[15:06:50] There are still 1503 unannotated CDS left (started with 1503)
[15:06:50] Will use blast to search against /usr/local/bioinfo/src/PROKKA/prokka-1.10/bin/../db/kingdom/Bacteria/sprot with 8 CPUs
[15:06:50] Running: cat \/home\/yquentin\/work\/wolbachia\/prokka\/wCqu\/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\/wCqu\/proteins\.bls 2> /dev/null
[15:07:24] Modify product: Uncharacterized metal-dependent hydrolase YcfH => putative metal-dependent hydrolase YcfH
[15:07:25] Modify product: Actin-binding protein Smlt3054 => Actin-binding protein
[15:07:25] Modify product: Uncharacterized oxidoreductase YciK => putative oxidoreductase YciK
[15:07:25] Modify product: Stringent starvation protein A homolog => hypothetical protein
[15:07:25] Modify product: Putative O-methyltransferase MSMEG_5073/MSMEI_4947 => Putative O-methyltransferase/MSMEI_4947
[15:07:25] Modify product: Probable chromosome-partitioning protein ParB => putative chromosome-partitioning protein ParB
[15:07:25] Modify product: Probable acyltransferase YihG => putative acyltransferase YihG
[15:07:25] Modify product: Probable phospholipid ABC transporter-binding protein MlaD => putative phospholipid ABC transporter-binding protein MlaD
[15:07:25] Modify product: Probable phospholipid ABC transporter permease protein MlaE => putative phospholipid ABC transporter permease protein MlaE
[15:07:25] Modify product: Probable ribonucleotide transport ATP-binding protein mkl => putative ribonucleotide transport ATP-binding protein mkl
[15:07:25] Modify product: Uncharacterized zinc protease Rv2782c => putative zinc protease
[15:07:25] Modify product: Uncharacterized zinc protease Rv2782c => putative zinc protease
[15:07:25] Modify product: Actin-binding protein Smlt3054 => Actin-binding protein
[15:07:25] Modify product: Transcription termination factor Rho => hypothetical protein
[15:07:25] Modify product: Probable tRNA-dihydrouridine synthase => putative tRNA-dihydrouridine synthase
[15:07:25] Modify product: Transcription termination/antitermination protein NusG => hypothetical protein
[15:07:26] Modify product: Uncharacterized zinc protease Rv2782c => putative zinc protease
[15:07:26] Modify product: Cytochrome b561 homolog 2 => hypothetical protein
[15:07:26] Modify product: Probable murein peptide carboxypeptidase => putative murein peptide carboxypeptidase
[15:07:26] Modify product: Actin-binding protein Smlt3054 => Actin-binding protein
[15:07:26] Modify product: Bifunctional protein FolD => Bifunctional protein FolD protein
[15:07:26] Modify product: SCO1 protein homolog => hypothetical protein
[15:07:26] Modify product: Actin-binding protein Smlt3054 => Actin-binding protein
[15:07:27] Modify product: Riboflavin biosynthesis protein VVA0006 => Riboflavin biosynthesis protein
[15:07:27] Modify product: Co-chaperone protein HscB homolog => hypothetical protein
[15:07:27] Modify product: Probable GTP-binding protein EngB => putative GTP-binding protein EngB
[15:07:27] Modify product: Uncharacterized oxidoreductase Rv0945 => putative oxidoreductase
[15:07:27] Modify product: Probable transcriptional regulatory protein aq_1575 => putative transcriptional regulatory protein
[15:07:27] Modify product: Putative multidrug export ATP-binding/permease protein SAV1866 => Putative multidrug export ATP-binding/permease protein
[15:07:28] Modify product: Probable peroxiredoxin => putative peroxiredoxin
[15:07:28] Modify product: Probable protein kinase UbiB => putative protein kinase UbiB
[15:07:28] Modify product: Transcription termination/antitermination protein NusA => hypothetical protein
[15:07:28] Modify product: N utilization substance protein B homolog => hypothetical protein
[15:07:28] Cleaned 33 /product names
[15:07:28] Deleting unwanted file: /home/yquentin/work/wolbachia/prokka/wCqu/proteins.faa
[15:07:28] Deleting unwanted file: /home/yquentin/work/wolbachia/prokka/wCqu/proteins.bls
[15:07:29] There are still 875 unannotated CDS left (started with 1503)
[15:07:29] Will use hmmer3 to search against /usr/local/bioinfo/src/PROKKA/prokka-1.10/bin/../db/hmm/HAMAP.hmm with 8 CPUs
[15:07:29] Running: cat \/home\/yquentin\/work\/wolbachia\/prokka\/wCqu\/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\/wCqu\/proteins\.bls 2> /dev/null
[15:07:50] Deleting unwanted file: /home/yquentin/work/wolbachia/prokka/wCqu/proteins.faa
[15:07:50] Deleting unwanted file: /home/yquentin/work/wolbachia/prokka/wCqu/proteins.bls
[15:07:51] There are still 841 unannotated CDS left (started with 1503)
[15:07:51] Will use hmmer3 to search against /usr/local/bioinfo/src/PROKKA/prokka-1.10/bin/../db/hmm/CLUSTERS.hmm with 8 CPUs
[15:07:51] Running: cat \/home\/yquentin\/work\/wolbachia\/prokka\/wCqu\/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\/wCqu\/proteins\.bls 2> /dev/null
[15:08:55] Deleting unwanted file: /home/yquentin/work/wolbachia/prokka/wCqu/proteins.faa
[15:08:55] Deleting unwanted file: /home/yquentin/work/wolbachia/prokka/wCqu/proteins.bls
[15:08:57] There are still 790 unannotated CDS left (started with 1503)
[15:08:57] Will use hmmer3 to search against /usr/local/bioinfo/src/PROKKA/prokka-1.10/bin/../db/hmm/Pfam.hmm with 8 CPUs
[15:08:57] Running: cat \/home\/yquentin\/work\/wolbachia\/prokka\/wCqu\/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\/wCqu\/proteins\.bls 2> /dev/null
[15:09:37] Modify product: Alpha/beta hydrolase family => Alpha/beta hydrolase family protein
[15:09:37] Modify product: Transposase DDE domain => Transposase DDE domain protein
[15:09:37] Modify product: Major Facilitator Superfamily => Major Facilitator Superfamily protein
[15:09:37] Modify product: Ankyrin repeat => Ankyrin repeat protein
[15:09:37] Modify product: KAP family P-loop domain => KAP family P-loop domain protein
[15:09:37] Modify product: Ankyrin repeat => Ankyrin repeat protein
[15:09:37] Modify product: RmlD substrate binding domain => RmlD substrate binding domain protein
[15:09:37] Modify product: Ankyrin repeat => Ankyrin repeat protein
[15:09:37] Modify product: Transposase DDE domain => Transposase DDE domain protein
[15:09:37] Modify product: PAS domain => PAS domain protein
[15:09:37] Modify product: DSBA-like thioredoxin domain => DSBA-like thioredoxin domain protein
[15:09:37] Modify product: Transposase DDE domain => Transposase DDE domain protein
[15:09:37] Modify product: COQ9 => hypothetical protein
[15:09:37] Modify product: Transposase DDE domain => Transposase DDE domain protein
[15:09:37] Modify product: DnaJ domain => DnaJ domain protein
[15:09:37] Modify product: RDD family => RDD family protein
[15:09:37] Modify product: Transposase DDE domain => Transposase DDE domain protein
[15:09:37] Modify product: EVE domain => EVE domain protein
[15:09:37] Modify product: Transposase DDE domain => Transposase DDE domain protein
[15:09:37] Modify product: Transposase DDE domain => Transposase DDE domain protein
[15:09:37] Modify product: Transposase IS116/IS110/IS902 family => Transposase IS116/IS110/IS902 family protein
[15:09:37] Modify product: Ankyrin repeat => Ankyrin repeat protein
[15:09:37] Modify product: Alpha/beta hydrolase family => Alpha/beta hydrolase family protein
[15:09:37] Modify product: Transposase DDE domain => Transposase DDE domain protein
[15:09:37] Modify product: Piwi/Argonaute/Zwille siRNA-binding domain => Piwi/Argonaute/Zwille siRNA-binding domain protein
[15:09:37] Modify product: Transposase DDE domain => Transposase DDE domain protein
[15:09:37] Modify product: Transposase DDE domain => Transposase DDE domain protein
[15:09:37] Modify product: Phosphotransferase enzyme family => Phosphotransferase enzyme family protein
[15:09:37] Modify product: AhpC/TSA family => AhpC/TSA family protein
[15:09:37] Modify product: Transposase DDE domain => Transposase DDE domain protein
[15:09:37] Modify product: TrbC/VIRB2 family => TrbC/VIRB2 family protein
[15:09:37] Modify product: Transposase DDE domain => Transposase DDE domain protein
[15:09:37] Modify product: Transposase IS116/IS110/IS902 family => Transposase IS116/IS110/IS902 family protein
[15:09:37] Modify product: Transposase IS200 like => Transposase IS200 like protein
[15:09:37] Modify product: Transposase DDE domain => Transposase DDE domain protein
[15:09:37] Modify product: Transposase DDE domain => Transposase DDE domain protein
[15:09:37] Modify product: Integral membrane protein TerC family => Integral membrane protein TerC family protein
[15:09:37] Modify product: Uracil DNA glycosylase superfamily => Uracil DNA glycosylase superfamily protein
[15:09:37] Modify product: Transposase DDE domain => Transposase DDE domain protein
[15:09:37] Modify product: ETC complex I subunit conserved region => hypothetical protein
[15:09:37] Modify product: Transposase DDE domain => Transposase DDE domain protein
[15:09:37] Modify product: Alpha/beta hydrolase family => Alpha/beta hydrolase family protein
[15:09:37] Modify product: MgtE intracellular N domain => MgtE intracellular N domain protein
[15:09:37] Modify product: Transposase DDE domain => Transposase DDE domain protein
[15:09:37] Modify product: Terminase-like family => Terminase-like family protein
[15:09:37] Modify product: Transposase DDE domain => Transposase DDE domain protein
[15:09:37] Modify product: Transposase DDE domain => Transposase DDE domain protein
[15:09:37] Modify product: Transposase DDE domain => Transposase DDE domain protein
[15:09:37] Modify product: Terminase-like family => Terminase-like family protein
[15:09:37] Modify product: Transposase DDE domain => Transposase DDE domain protein
[15:09:37] Modify product: Transposase IS116/IS110/IS902 family => Transposase IS116/IS110/IS902 family protein
[15:09:37] Modify product: PAAR motif => PAAR motif protein
[15:09:37] Modify product: Ankyrin repeat => Ankyrin repeat protein
[15:09:37] Modify product: Helix-turn-helix domain => Helix-turn-helix domain protein
[15:09:37] Modify product: Tim44-like domain => Tim44-like domain protein
[15:09:37] Modify product: Transposase DDE domain => Transposase DDE domain protein
[15:09:37] Modify product: Transposase DDE domain => Transposase DDE domain protein
[15:09:37] Modify product: Transposase DDE domain => Transposase DDE domain protein
[15:09:37] Modify product: Transposase DDE domain => Transposase DDE domain protein
[15:09:37] Modify product: Hepatic lectin, N-terminal domain => hypothetical protein
[15:09:37] Modify product: Transposase DDE domain => Transposase DDE domain protein
[15:09:37] Modify product: RDD family => RDD family protein
[15:09:37] Modify product: Transposase DDE domain => Transposase DDE domain protein
[15:09:37] Modify product: Ankyrin repeat => Ankyrin repeat protein
[15:09:37] Modify product: Transposase DDE domain => Transposase DDE domain protein
[15:09:37] Modify product: Transposase DDE domain => Transposase DDE domain protein
[15:09:37] Modify product: Phage capsid family => Phage capsid family protein
[15:09:37] Modify product: Transposase DDE domain => Transposase DDE domain protein
[15:09:37] Modify product: Transposase DDE domain => Transposase DDE domain protein
[15:09:37] Modify product: Transposase DDE domain => Transposase DDE domain protein
[15:09:37] Modify product: TrbC/VIRB2 family => TrbC/VIRB2 family protein
[15:09:37] Modify product: Transposase IS116/IS110/IS902 family => Transposase IS116/IS110/IS902 family protein
[15:09:37] Modify product: SPFH domain / Band 7 family => SPFH domain / Band 7 family protein
[15:09:37] Modify product: Transposase DDE domain => Transposase DDE domain protein
[15:09:37] Modify product: TrbC/VIRB2 family => TrbC/VIRB2 family protein
[15:09:37] Modify product: Ankyrin repeat => Ankyrin repeat protein
[15:09:37] Modify product: Transposase DDE domain => Transposase DDE domain protein
[15:09:37] Modify product: Transposase DDE domain => Transposase DDE domain protein
[15:09:37] Modify product: NB-ARC domain => NB-ARC domain protein
[15:09:37] Modify product: Transposase DDE domain => Transposase DDE domain protein
[15:09:37] Modify product: Transposase DDE domain => Transposase DDE domain protein
[15:09:37] Modify product: Transposase IS200 like => Transposase IS200 like protein
[15:09:37] Modify product: Transposase DDE domain => Transposase DDE domain protein
[15:09:37] Modify product: Transposase IS116/IS110/IS902 family => Transposase IS116/IS110/IS902 family protein
[15:09:37] Modify product: Transposase IS116/IS110/IS902 family => Transposase IS116/IS110/IS902 family protein
[15:09:37] Modify product: Transposase DDE domain => Transposase DDE domain protein
[15:09:37] Modify product: Glyoxalase-like domain => Glyoxalase-like domain protein
[15:09:37] Modify product: PAAR motif => PAAR motif protein
[15:09:37] Modify product: Ankyrin repeat => Ankyrin repeat protein
[15:09:37] Modify product: PD-(D/E)XK nuclease superfamily => PD-(D/E)XK nuclease superfamily protein
[15:09:37] Modify product: Transposase DDE domain => Transposase DDE domain protein
[15:09:37] Modify product: RDD family => RDD family protein
[15:09:37] Modify product: SURF1 family => SURF1 family protein
[15:09:37] Modify product: YGGT family => YGGT family protein
[15:09:37] Modify product: Sodium:dicarboxylate symporter family => Sodium:dicarboxylate symporter family protein
[15:09:37] Modify product: Na+/H+ antiporter family => Na+/H+ antiporter family protein
[15:09:37] Modify product: Transposase DDE domain => Transposase DDE domain protein
[15:09:37] Modify product: Transposase DDE domain => Transposase DDE domain protein
[15:09:37] Modify product: Piwi/Argonaute/Zwille siRNA-binding domain => Piwi/Argonaute/Zwille siRNA-binding domain protein
[15:09:37] Modify product: Transposase DDE domain => Transposase DDE domain protein
[15:09:37] Modify product: RDD family => RDD family protein
[15:09:37] Modify product: Transposase DDE domain => Transposase DDE domain protein
[15:09:37] Modify product: Transposase DDE domain => Transposase DDE domain protein
[15:09:37] Modify product: Na+/H+ antiporter family => Na+/H+ antiporter family protein
[15:09:37] Modify product: Transposase DDE domain => Transposase DDE domain protein
[15:09:37] Modify product: Transposase DDE domain => Transposase DDE domain protein
[15:09:37] Modify product: Transposase IS200 like => Transposase IS200 like protein
[15:09:37] Modify product: Transposase DDE domain => Transposase DDE domain protein
[15:09:37] Modify product: Transposase DDE domain => Transposase DDE domain protein
[15:09:37] Modify product: Transposase DDE domain => Transposase DDE domain protein
[15:09:37] Modify product: Ankyrin repeat => Ankyrin repeat protein
[15:09:37] Modify product: PAAR motif => PAAR motif protein
[15:09:37] Modify product: BRO family, N-terminal domain => hypothetical protein
[15:09:37] Modify product: Transposase IS66 family => Transposase IS66 family protein
[15:09:37] Modify product: CobQ/CobB/MinD/ParA nucleotide binding domain => CobQ/CobB/MinD/ParA nucleotide binding domain protein
[15:09:37] Modify product: Terminase-like family => Terminase-like family protein
[15:09:37] Modify product: PAAR motif => PAAR motif protein
[15:09:37] Modify product: Transposase DDE domain => Transposase DDE domain protein
[15:09:37] Modify product: Transposase DDE domain => Transposase DDE domain protein
[15:09:37] Modify product: Transposase DDE domain => Transposase DDE domain protein
[15:09:37] Cleaned 120 /product names
[15:09:37] Deleting unwanted file: /home/yquentin/work/wolbachia/prokka/wCqu/proteins.faa
[15:09:37] Deleting unwanted file: /home/yquentin/work/wolbachia/prokka/wCqu/proteins.bls
[15:09:37] Labelling remaining 501 proteins as 'hypothetical protein'
[15:09:37] Possible /pseudo 'DNA mismatch repair protein MutL' at gnl|Prokka|wCqu_contig000001 position 40702
[15:09:37] Possible /pseudo 'anaerobic benzoate catabolism transcriptional regulator' at gnl|Prokka|wCqu_contig000001 position 47566
[15:09:37] Possible /pseudo 'Phage terminase large subunit (GpA)' at gnl|Prokka|wCqu_contig000002 position 664
[15:09:37] Possible /pseudo 'Transposase DDE domain protein' at gnl|Prokka|wCqu_contig000003 position 66907
[15:09:37] Possible /pseudo 'putative zinc protease' at gnl|Prokka|wCqu_contig000003 position 82161
[15:09:37] Possible /pseudo 'Transposase DDE domain protein' at gnl|Prokka|wCqu_contig000003 position 182714
[15:09:37] Possible /pseudo 'TrbL/VirB6 plasmid conjugal transfer protein' at gnl|Prokka|wCqu_contig000003 position 188329
[15:09:37] Possible /pseudo 'TrbL/VirB6 plasmid conjugal transfer protein' at gnl|Prokka|wCqu_contig000003 position 191226
[15:09:37] Possible /pseudo 'TrbL/VirB6 plasmid conjugal transfer protein' at gnl|Prokka|wCqu_contig000003 position 193616
[15:09:37] Possible /pseudo 'Dihydropteroate synthase' at gnl|Prokka|wCqu_contig000003 position 307425
[15:09:37] Possible /pseudo 'Arginine/agmatine antiporter' at gnl|Prokka|wCqu_contig000003 position 329102
[15:09:37] Possible /pseudo 'Ankyrin repeats (3 copies)' at gnl|Prokka|wCqu_contig000003 position 336457
[15:09:37] Possible /pseudo 'Ankyrin repeats (3 copies)' at gnl|Prokka|wCqu_contig000003 position 337770
[15:09:37] Possible /pseudo 'Transposase DDE domain protein' at gnl|Prokka|wCqu_contig000003 position 635853
[15:09:37] Possible /pseudo 'Amino-acid carrier protein AlsT' at gnl|Prokka|wCqu_contig000003 position 729801
[15:09:37] Possible /pseudo 'Transposase DDE domain protein' at gnl|Prokka|wCqu_contig000003 position 732405
[15:09:37] Possible /pseudo 'Aminopyrimidine aminohydrolase' at gnl|Prokka|wCqu_contig000003 position 770271
[15:09:37] Possible /pseudo 'Ankyrin repeats (3 copies)' at gnl|Prokka|wCqu_contig000003 position 934755
[15:09:37] Possible /pseudo 'Transposase DDE domain protein' at gnl|Prokka|wCqu_contig000003 position 1069044
[15:09:37] Possible /pseudo 'Exopolysaccharide synthesis, ExoD' at gnl|Prokka|wCqu_contig000003 position 1087633
[15:09:37] Possible /pseudo 'Phosphocholine transferase AnkX' at gnl|Prokka|wCqu_contig000003 position 1114789
[15:09:37] Possible /pseudo 'Transposase, Mutator family' at gnl|Prokka|wCqu_contig000003 position 1324873
[15:09:37] Possible /pseudo 'Transposase, Mutator family' at gnl|Prokka|wCqu_contig000003 position 1349373
[15:09:37] Possible /pseudo 'Phage terminase large subunit (GpA)' at gnl|Prokka|wCqu_contig000003 position 1364476
[15:09:37] Possible /pseudo 'anaerobic benzoate catabolism transcriptional regulator' at gnl|Prokka|wCqu_contig000003 position 1383238
[15:09:37] Possible /pseudo 'DNA mismatch repair protein MutL' at gnl|Prokka|wCqu_contig000003 position 1388627
[15:09:37] Possible /pseudo 'Transposase DDE domain protein' at gnl|Prokka|wCqu_contig000013 position 1470
[15:09:37] Found 547 unique /gene codes.
[15:09:37] Fixed 35 colliding /gene names.
[15:09:37] Adding /locus_tag identifiers
[15:09:38] Assigned 1541 locus_tags to CDS and RNA features.
[15:09:38] Writing outputs to /home/yquentin/work/wolbachia/prokka/wCqu/
[15:09:39] Generating annotation statistics file
[15:09:39] Generating Genbank and Sequin files
[15:09:39] 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\/wCqu\/wCqu\.err -i \/home\/yquentin\/work\/wolbachia\/prokka\/wCqu\/wCqu\.fsa 2> /dev/null
[15:09:46] Deleting unwanted file: /home/yquentin/work/wolbachia/prokka/wCqu/errorsummary.val
[15:09:46] Deleting unwanted file: /home/yquentin/work/wolbachia/prokka/wCqu/wCqu.dr
[15:09:46] Deleting unwanted file: /home/yquentin/work/wolbachia/prokka/wCqu/wCqu.fixedproducts
[15:09:46] Deleting unwanted file: /home/yquentin/work/wolbachia/prokka/wCqu/wCqu.ecn
[15:09:46] Deleting unwanted file: /home/yquentin/work/wolbachia/prokka/wCqu/wCqu.val
[15:09:46] Output files:
[15:09:46] /home/yquentin/work/wolbachia/prokka/wCqu/wCqu.tbl
[15:09:46] /home/yquentin/work/wolbachia/prokka/wCqu/wCqu.fna
[15:09:46] /home/yquentin/work/wolbachia/prokka/wCqu/wCqu.gff
[15:09:46] /home/yquentin/work/wolbachia/prokka/wCqu/wCqu.err
[15:09:46] /home/yquentin/work/wolbachia/prokka/wCqu/wCqu.faa
[15:09:46] /home/yquentin/work/wolbachia/prokka/wCqu/wCqu.log
[15:09:46] /home/yquentin/work/wolbachia/prokka/wCqu/wCqu.txt
[15:09:46] /home/yquentin/work/wolbachia/prokka/wCqu/wCqu.sqn
[15:09:46] /home/yquentin/work/wolbachia/prokka/wCqu/wCqu.ffn
[15:09:46] /home/yquentin/work/wolbachia/prokka/wCqu/wCqu.fsa
[15:09:46] /home/yquentin/work/wolbachia/prokka/wCqu/wCqu.gbk
[15:09:46] Walltime used: 3.12 minutes
[15:09:46] If you use this result please cite the Prokka paper:
[15:09:46] Seemann T (2014) Prokka: rapid prokaryotic genome annotation. Bioinformatics. 30(14):2068-9.
[15:09:46] Type 'prokka --citation' for more details.
[15:09:46] Share and enjoy!