[10:41:32] Command: --force --outdir /home/yquentin/work/wolbachia/prokka/wRi --addgenes --prefix wRi --locustag wRi --species Wolbachia sp. wRi --strain wRi --compliant --quiet /home/yquentin/work/wolbachia/prokka/wRi.fna [10:41:32] Looking for 'aragorn' - found /usr/local/bioinfo/bin/aragorn [10:41:32] Determined aragorn version is 1.2 [10:41:32] Looking for 'barrnap' - found /usr/local/bioinfo/bin/barrnap [10:41:32] Determined barrnap version is 0.5 [10:41:32] Looking for 'blastp' - found /usr/local/bioinfo/src/NCBI_Blast+/ncbi-blast-2.6.0+/bin/blastp [10:41:32] Determined blastp version is 2.6 [10:41:32] Looking for 'cmpress' - found /usr/local/bioinfo/src/PROKKA/prokka-1.10/bin/../binaries/linux/cmpress [10:41:32] Determined cmpress version is 1.1 [10:41:32] Looking for 'cmscan' - found /usr/local/bioinfo/src/PROKKA/prokka-1.10/bin/../binaries/linux/cmscan [10:41:32] Determined cmscan version is 1.1 [10:41:32] Looking for 'egrep' - found /bin/egrep [10:41:32] Looking for 'find' - found /bin/find [10:41:32] Looking for 'grep' - found /bin/grep [10:41:32] Looking for 'hmmpress' - found /usr/local/bioinfo/bin/hmmpress [10:41:32] Determined hmmpress version is 3.1 [10:41:32] Looking for 'hmmscan' - found /usr/local/bioinfo/bin/hmmscan [10:41:32] Determined hmmscan version is 3.1 [10:41:32] Looking for 'less' - found /usr/bin/less [10:41:32] Looking for 'makeblastdb' - found /usr/local/bioinfo/src/NCBI_Blast+/ncbi-blast-2.6.0+/bin/makeblastdb [10:41:33] Determined makeblastdb version is 2.6 [10:41:33] Looking for 'minced' - found /usr/local/bioinfo/bin/minced [10:41:33] Determined minced version is 1.6 [10:41:33] Looking for 'parallel' - found /usr/local/bioinfo/bin/parallel [10:41:33] Determined parallel version is 20141022 [10:41:33] Looking for 'prodigal' - found /usr/local/bioinfo/bin/prodigal [10:41:33] Determined prodigal version is 2.6 [10:41:33] Looking for 'rnammer' - found /usr/local/bioinfo/bin/rnammer [10:41:33] Determined rnammer version is 1.2 [10:41:33] Looking for 'sed' - found /bin/sed [10:41:33] Looking for 'signalp' - found /usr/local/bioinfo/bin/signalp [10:41:33] Determined signalp version is 4.1 [10:41:33] Looking for 'tbl2asn' - found /home/yquentin/save/scripts/tbl2asn [10:41:33] Determined tbl2asn version is 25.3 [10:41:33] Using genetic code table 11. [10:41:33] Loading and checking input file: /home/yquentin/work/wolbachia/prokka/wRi.fna [10:41:33] Wrote 1 contigs [10:41:33] Predicting tRNAs and tmRNAs [10:41:33] Running: aragorn -gc11 -w \/home\/yquentin\/work\/wolbachia\/prokka\/wRi\/wRi\.fna [10:41:34] 1 tRNA-Leu [3028,3115] 35 (gag) [10:41:34] 2 tRNA-Trp [17582,17655] 34 (cca) [10:41:34] 3 tRNA-Arg c[44965,45042] 36 (acg) [10:41:34] 4 tRNA-Arg c[100390,100466] 35 (cct) [10:41:34] 5 tRNA-Ile c[118707,118783] 35 (gat) [10:41:34] 6 tmRNA* [126380,126708] 194,238 ANDNFAAEEYRVAA* [10:41:34] 7 tRNA-Thr c[161019,161092] 34 (tgt) [10:41:34] 8 tRNA-Phe c[366232,366306] 34 (gaa) [10:41:34] 9 tRNA-Asp [371956,372029] 35 (gtc) [10:41:34] 10 tRNA-Leu c[428327,428413] 35 (taa) [10:41:34] 11 tRNA-Leu c[464241,464324] 34 (caa) [10:41:34] 12 tRNA-Leu c[512977,513059] 35 (tag) [10:41:34] 13 tRNA-Gly c[554228,554299] 33 (tcc) [10:41:34] 14 tRNA-Tyr c[554304,554386] 35 (gta) [10:41:34] 15 tRNA-Arg [664416,664490] 35 (ccg) [10:41:34] 16 tRNA-Met [676778,676851] 34 (cat) [10:41:34] 17 tRNA-Ser c[789221,789309] 36 (gga) [10:41:34] 18 tRNA-Gln c[853833,853907] 33 (ttg) [10:41:34] 19 tRNA-Asn [904522,904594] 33 (gtt) [10:41:34] 20 tRNA-Met c[934886,934962] 35 (cat) [10:41:34] 21 tRNA-Gly [936238,936311] 34 (gcc) [10:41:34] 22 tRNA-Ala c[994816,994892] 34 (tgc) [10:41:34] 23 tRNA-Lys [995213,995286] 34 (ttt) [10:41:34] 24 tRNA-Ser [1002805,1002893] 35 (tga) [10:41:34] 25 tRNA-Ser [1019795,1019880] 35 (cag) [10:41:34] 26 tRNA-His c[1033523,1033598] 34 (gtg) [10:41:34] 27 tRNA-Val [1168180,1168253] 34 (gac) [10:41:34] 28 tRNA-Thr c[1221998,1222071] 34 (ggt) [10:41:34] 29 tRNA-Met c[1223629,1223705] 35 (cat) [10:41:34] 30 tRNA-Val c[1274331,1274403] 34 (tac) [10:41:34] 31 tRNA-Pro c[1280784,1280859] 36 (tgg) [10:41:34] 32 tRNA-Glu c[1281791,1281863] 34 (ttc) [10:41:34] 33 tRNA-Cys [1306976,1307048] 34 (gca) [10:41:34] 34 tRNA-Ser [1329700,1329792] 36 (gct) [10:41:34] 35 tRNA-Arg c[1388376,1388450] 35 (tct) [10:41:34] Found 35 tRNAs [10:41:34] Predicting Ribosomal RNAs [10:41:34] Running Barrnap with 8 threads [10:41:35] 1 gnl|Prokka|wRi_contig000001 188533 23S ribosomal RNA [10:41:35] 2 gnl|Prokka|wRi_contig000001 191363 5S ribosomal RNA [10:41:35] 3 gnl|Prokka|wRi_contig000001 1289972 16S ribosomal RNA [10:41:35] Found 3 rRNAs [10:41:35] Skipping ncRNA search, enable with --rfam if desired. [10:41:35] Total of 37 tRNA + rRNA features [10:41:35] Searching for CRISPR repeats [10:41:35] CRISPR1 gnl|Prokka|wRi_contig000001 418918 with 6 spacers [10:41:35] Found 1 CRISPRs [10:41:35] Predicting coding sequences [10:41:35] Contigs total 1445873 bp, so using single mode [10:41:35] Running: prodigal -i \/home\/yquentin\/work\/wolbachia\/prokka\/wRi\/wRi\.fna -c -m -g 11 -p single -f sco -q [10:41:38] Excluding CDS which overlaps existing RNA (tRNA) at gnl|Prokka|wRi_contig000001:512895..513053 on - strand [10:41:38] Excluding CDS which overlaps existing RNA (tRNA) at gnl|Prokka|wRi_contig000001:675486..676778 on + strand [10:41:38] Excluding CDS which overlaps existing RNA (tRNA) at gnl|Prokka|wRi_contig000001:853898..854155 on - strand [10:41:38] Excluding CDS which overlaps existing RNA (tRNA) at gnl|Prokka|wRi_contig000001:1223669..1225921 on + strand [10:41:38] Excluding CDS which overlaps existing RNA (rRNA) at gnl|Prokka|wRi_contig000001:1290408..1290530 on + strand [10:41:38] Excluding CDS which overlaps existing RNA (tRNA) at gnl|Prokka|wRi_contig000001:1388385..1388795 on + strand [10:41:38] Found 1396 CDS [10:41:38] Connecting features back to sequences [10:41:38] Option --gram not specified, will NOT check for signal peptides. [10:41:38] Not using genus-specific database. Try --usegenus to enable it. [10:41:38] Annotating CDS, please be patient. [10:41:38] Will use 8 CPUs for similarity searching. [10:41:39] There are still 1396 unannotated CDS left (started with 1396) [10:41:39] Will use blast to search against /usr/local/bioinfo/src/PROKKA/prokka-1.10/bin/../db/kingdom/Bacteria/sprot with 8 CPUs [10:41:39] Running: cat \/home\/yquentin\/work\/wolbachia\/prokka\/wRi\/proteins\.faa | parallel --gnu -j 8 --block 26024 --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\/wRi\/proteins\.bls 2> /dev/null [10:41:53] Modify product: Transcription termination/antitermination protein NusG => hypothetical protein [10:41:53] Modify product: Probable tRNA-dihydrouridine synthase => putative tRNA-dihydrouridine synthase [10:41:53] Modify product: SCO1 protein homolog => hypothetical protein [10:41:53] Modify product: Bifunctional protein FolD => Bifunctional protein FolD protein [10:41:53] Modify product: Uncharacterized ABC transporter ATP-binding protein TM_0288 => putative ABC transporter ATP-binding protein [10:41:53] Modify product: Actin-binding protein Smlt3054 => Actin-binding protein [10:41:53] Modify product: Probable deoxyribonuclease RhsA => putative deoxyribonuclease RhsA [10:41:53] Modify product: Putative multidrug export ATP-binding/permease protein SAV1866 => Putative multidrug export ATP-binding/permease protein [10:41:53] Modify product: Probable peroxiredoxin => putative peroxiredoxin [10:41:53] Modify product: Uncharacterized zinc protease Rv2782c => putative zinc protease [10:41:53] Modify product: Uncharacterized zinc protease Rv2782c => putative zinc protease [10:41:53] Modify product: Transcription termination factor Rho => hypothetical protein [10:41:53] Modify product: Putative multidrug export ATP-binding/permease protein SAV1866 => Putative multidrug export ATP-binding/permease protein [10:41:53] Modify product: N utilization substance protein B homolog => hypothetical protein [10:41:53] Modify product: Probable GTP-binding protein EngB => putative GTP-binding protein EngB [10:41:53] Modify product: Probable transcriptional regulatory protein aq_1575 => putative transcriptional regulatory protein [10:41:53] Modify product: Probable phospholipid ABC transporter permease protein MlaE => putative phospholipid ABC transporter permease protein MlaE [10:41:53] Modify product: Probable ribonucleotide transport ATP-binding protein mkl => putative ribonucleotide transport ATP-binding protein mkl [10:41:53] Modify product: Probable murein peptide carboxypeptidase => putative murein peptide carboxypeptidase [10:41:53] Modify product: Probable acyltransferase YihG => putative acyltransferase YihG [10:41:53] Modify product: Putative O-methyltransferase MSMEG_5073/MSMEI_4947 => Putative O-methyltransferase/MSMEI_4947 [10:41:53] Modify product: Stringent starvation protein A homolog => hypothetical protein [10:41:53] Modify product: Cytochrome b561 homolog 2 => hypothetical protein [10:41:54] Modify product: Probable deoxyribonuclease RhsA => putative deoxyribonuclease RhsA [10:41:54] Modify product: Putative multidrug export ATP-binding/permease protein SAV1866 => Putative multidrug export ATP-binding/permease protein [10:41:54] Modify product: Probable transport protein HsrA => putative transport protein HsrA [10:41:54] Modify product: Probable glycerol-3-phosphate acyltransferase => putative glycerol-3-phosphate acyltransferase [10:41:54] Modify product: Co-chaperone protein HscB homolog => hypothetical protein [10:41:54] Modify product: Probable protein kinase UbiB => putative protein kinase UbiB [10:41:54] Modify product: Actin-binding protein Smlt3054 => Actin-binding protein [10:41:54] Modify product: Probable deoxyribonuclease RhsA => putative deoxyribonuclease RhsA [10:41:54] Modify product: Uncharacterized zinc protease Rv2782c => putative zinc protease [10:41:54] Modify product: Probable chromosome-partitioning protein ParB => putative chromosome-partitioning protein ParB [10:41:54] Modify product: Actin-binding protein Smlt3054 => Actin-binding protein [10:41:54] Modify product: Probable phospholipid ABC transporter-binding protein MlaD => putative phospholipid ABC transporter-binding protein MlaD [10:41:54] Modify product: Uncharacterized metal-dependent hydrolase YcfH => putative metal-dependent hydrolase YcfH [10:41:54] Modify product: Uncharacterized HIT-like protein HP_0404 => putative HIT-like protein [10:41:54] Modify product: Uncharacterized oxidoreductase YciK => putative oxidoreductase YciK [10:41:54] Modify product: Transcription termination/antitermination protein NusA => hypothetical protein [10:41:54] Cleaned 39 /product names [10:41:54] Deleting unwanted file: /home/yquentin/work/wolbachia/prokka/wRi/proteins.faa [10:41:54] Deleting unwanted file: /home/yquentin/work/wolbachia/prokka/wRi/proteins.bls [10:41:54] There are still 751 unannotated CDS left (started with 1396) [10:41:54] Will use hmmer3 to search against /usr/local/bioinfo/src/PROKKA/prokka-1.10/bin/../db/hmm/HAMAP.hmm with 8 CPUs [10:41:54] Running: cat \/home\/yquentin\/work\/wolbachia\/prokka\/wRi\/proteins\.faa | parallel --gnu -j 8 --block 11241 --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\/wRi\/proteins\.bls 2> /dev/null [10:42:04] Deleting unwanted file: /home/yquentin/work/wolbachia/prokka/wRi/proteins.faa [10:42:04] Deleting unwanted file: /home/yquentin/work/wolbachia/prokka/wRi/proteins.bls [10:42:04] There are still 689 unannotated CDS left (started with 1396) [10:42:04] Will use hmmer3 to search against /usr/local/bioinfo/src/PROKKA/prokka-1.10/bin/../db/hmm/CLUSTERS.hmm with 8 CPUs [10:42:04] Running: cat \/home\/yquentin\/work\/wolbachia\/prokka\/wRi\/proteins\.faa | parallel --gnu -j 8 --block 9776 --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\/wRi\/proteins\.bls 2> /dev/null [10:42:32] Deleting unwanted file: /home/yquentin/work/wolbachia/prokka/wRi/proteins.faa [10:42:32] Deleting unwanted file: /home/yquentin/work/wolbachia/prokka/wRi/proteins.bls [10:42:32] There are still 648 unannotated CDS left (started with 1396) [10:42:32] Will use hmmer3 to search against /usr/local/bioinfo/src/PROKKA/prokka-1.10/bin/../db/hmm/Pfam.hmm with 8 CPUs [10:42:32] Running: cat \/home\/yquentin\/work\/wolbachia\/prokka\/wRi\/proteins\.faa | parallel --gnu -j 8 --block 9116 --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\/wRi\/proteins\.bls 2> /dev/null [10:42:59] Modify product: Transposase IS116/IS110/IS902 family => Transposase IS116/IS110/IS902 family protein [10:42:59] Modify product: Ankyrin repeat => Ankyrin repeat protein [10:42:59] Modify product: Transposase IS66 family => Transposase IS66 family protein [10:42:59] Modify product: Ankyrin repeat => Ankyrin repeat protein [10:42:59] Modify product: Transposase DDE domain => Transposase DDE domain protein [10:42:59] Modify product: Transposase DDE domain => Transposase DDE domain protein [10:42:59] Modify product: Ankyrin repeat => Ankyrin repeat protein [10:43:00] Modify product: Transposase DDE domain => Transposase DDE domain protein [10:43:00] Modify product: Transposase IS66 family => Transposase IS66 family protein [10:43:00] Modify product: Transposase IS116/IS110/IS902 family => Transposase IS116/IS110/IS902 family protein [10:43:00] Modify product: SPFH domain / Band 7 family => SPFH domain / Band 7 family protein [10:43:00] Modify product: Transposase IS116/IS110/IS902 family => Transposase IS116/IS110/IS902 family protein [10:43:00] Modify product: Phage capsid family => Phage capsid family protein [10:43:00] Modify product: TrbC/VIRB2 family => TrbC/VIRB2 family protein [10:43:00] Modify product: Transposase IS66 family => Transposase IS66 family protein [10:43:00] Modify product: RDD family => RDD family protein [10:43:00] Modify product: TrbC/VIRB2 family => TrbC/VIRB2 family protein [10:43:00] Modify product: Transposase DDE domain => Transposase DDE domain protein [10:43:00] Modify product: Transposase IS116/IS110/IS902 family => Transposase IS116/IS110/IS902 family protein [10:43:00] Modify product: Transposase IS116/IS110/IS902 family => Transposase IS116/IS110/IS902 family protein [10:43:00] Modify product: Transposase IS116/IS110/IS902 family => Transposase IS116/IS110/IS902 family protein [10:43:00] Modify product: Transposase IS116/IS110/IS902 family => Transposase IS116/IS110/IS902 family protein [10:43:00] Modify product: Transposase DDE domain => Transposase DDE domain protein [10:43:00] Modify product: TrbC/VIRB2 family => TrbC/VIRB2 family protein [10:43:00] Modify product: Transposase IS116/IS110/IS902 family => Transposase IS116/IS110/IS902 family protein [10:43:00] Modify product: Transposase IS116/IS110/IS902 family => Transposase IS116/IS110/IS902 family protein [10:43:00] Modify product: RDD family => RDD family protein [10:43:00] Modify product: RDD family => RDD family protein [10:43:00] Modify product: Transposase IS116/IS110/IS902 family => Transposase IS116/IS110/IS902 family protein [10:43:00] Modify product: Transposase IS116/IS110/IS902 family => Transposase IS116/IS110/IS902 family protein [10:43:00] Modify product: Integrase core domain => Integrase core domain protein [10:43:00] Modify product: Alpha/beta hydrolase family => Alpha/beta hydrolase family protein [10:43:00] Modify product: Transposase IS66 family => Transposase IS66 family protein [10:43:00] Modify product: Terminase-like family => Terminase-like family protein [10:43:00] Modify product: Piwi/Argonaute/Zwille siRNA-binding domain => Piwi/Argonaute/Zwille siRNA-binding domain protein [10:43:00] Modify product: Transposase IS116/IS110/IS902 family => Transposase IS116/IS110/IS902 family protein [10:43:00] Modify product: Transposase DDE domain => Transposase DDE domain protein [10:43:00] Modify product: Ankyrin repeat => Ankyrin repeat protein [10:43:00] Modify product: Integrase core domain => Integrase core domain protein [10:43:00] Modify product: Transposase DDE domain => Transposase DDE domain protein [10:43:00] Modify product: Integrase core domain => Integrase core domain protein [10:43:00] Modify product: ETC complex I subunit conserved region => hypothetical protein [10:43:00] Modify product: Uracil DNA glycosylase superfamily => Uracil DNA glycosylase superfamily protein [10:43:00] Modify product: Na+/H+ antiporter family => Na+/H+ antiporter family protein [10:43:00] Modify product: Zinc-finger domain => Zinc-finger domain protein [10:43:00] Modify product: Transposase DDE domain => Transposase DDE domain protein [10:43:00] Modify product: Transposase DDE domain => Transposase DDE domain protein [10:43:00] Modify product: Integrase core domain => Integrase core domain protein [10:43:00] Modify product: Integrase core domain => Integrase core domain protein [10:43:00] Modify product: Transposase IS116/IS110/IS902 family => Transposase IS116/IS110/IS902 family protein [10:43:00] Modify product: Transposase DDE domain => Transposase DDE domain protein [10:43:00] Modify product: Transposase DDE domain => Transposase DDE domain protein [10:43:00] Modify product: Transposase IS116/IS110/IS902 family => Transposase IS116/IS110/IS902 family protein [10:43:00] Modify product: Transposase IS116/IS110/IS902 family => Transposase IS116/IS110/IS902 family protein [10:43:00] Modify product: Tim44-like domain => Tim44-like domain protein [10:43:00] Modify product: Integral membrane protein TerC family => Integral membrane protein TerC family protein [10:43:00] Modify product: Transposase IS116/IS110/IS902 family => Transposase IS116/IS110/IS902 family protein [10:43:00] Modify product: Transposase IS116/IS110/IS902 family => Transposase IS116/IS110/IS902 family protein [10:43:00] Modify product: Sodium:dicarboxylate symporter family => Sodium:dicarboxylate symporter family protein [10:43:00] Modify product: Transposase DDE domain => Transposase DDE domain protein [10:43:00] Modify product: Transposase IS116/IS110/IS902 family => Transposase IS116/IS110/IS902 family protein [10:43:00] Modify product: EVE domain => EVE domain protein [10:43:00] Modify product: Transposase DDE domain => Transposase DDE domain protein [10:43:00] Modify product: Ankyrin repeat => Ankyrin repeat protein [10:43:00] Modify product: Transposase IS116/IS110/IS902 family => Transposase IS116/IS110/IS902 family protein [10:43:00] Modify product: Transposase DDE domain => Transposase DDE domain protein [10:43:00] Modify product: Transposase IS66 family => Transposase IS66 family protein [10:43:00] Modify product: Transposase DDE domain => Transposase DDE domain protein [10:43:00] Modify product: Transposase DDE domain => Transposase DDE domain protein [10:43:00] Modify product: COQ9 => hypothetical protein [10:43:00] Modify product: Transposase IS66 family => Transposase IS66 family protein [10:43:00] Modify product: Transposase IS66 family => Transposase IS66 family protein [10:43:00] Modify product: PAS domain => PAS domain protein [10:43:00] Modify product: Transposase IS66 family => Transposase IS66 family protein [10:43:00] Modify product: Transposase DDE domain => Transposase DDE domain protein [10:43:00] Modify product: Transposase DDE domain => Transposase DDE domain protein [10:43:00] Modify product: Transposase DDE domain => Transposase DDE domain protein [10:43:00] Modify product: PD-(D/E)XK nuclease superfamily => PD-(D/E)XK nuclease superfamily protein [10:43:00] Modify product: Integrase core domain => Integrase core domain protein [10:43:00] Modify product: Transposase IS116/IS110/IS902 family => Transposase IS116/IS110/IS902 family protein [10:43:00] Modify product: Transposase IS116/IS110/IS902 family => Transposase IS116/IS110/IS902 family protein [10:43:00] Modify product: Transposase DDE domain => Transposase DDE domain protein [10:43:00] Modify product: Integrase core domain => Integrase core domain protein [10:43:00] Modify product: Transposase DDE domain => Transposase DDE domain protein [10:43:00] Modify product: MgtE intracellular N domain => MgtE intracellular N domain protein [10:43:00] Modify product: Transposase IS66 family => Transposase IS66 family protein [10:43:00] Modify product: Transposase DDE domain => Transposase DDE domain protein [10:43:00] Modify product: Terminase-like family => Terminase-like family protein [10:43:00] Modify product: Transposase IS116/IS110/IS902 family => Transposase IS116/IS110/IS902 family protein [10:43:00] Modify product: Terminase-like family => Terminase-like family protein [10:43:00] Modify product: Transposase IS116/IS110/IS902 family => Transposase IS116/IS110/IS902 family protein [10:43:00] Modify product: Major Facilitator Superfamily => Major Facilitator Superfamily protein [10:43:00] Modify product: Transposase IS116/IS110/IS902 family => Transposase IS116/IS110/IS902 family protein [10:43:00] Modify product: Transposase IS116/IS110/IS902 family => Transposase IS116/IS110/IS902 family protein [10:43:00] Modify product: Transposase DDE domain => Transposase DDE domain protein [10:43:00] Modify product: Transposase DDE domain => Transposase DDE domain protein [10:43:00] Modify product: Bacterial SH3 domain => Bacterial SH3 domain protein [10:43:00] Modify product: KAP family P-loop domain => KAP family P-loop domain protein [10:43:00] Modify product: Transposase IS116/IS110/IS902 family => Transposase IS116/IS110/IS902 family protein [10:43:00] Modify product: Transposase DDE domain => Transposase DDE domain protein [10:43:00] Modify product: RDD family => RDD family protein [10:43:00] Modify product: SURF1 family => SURF1 family protein [10:43:00] Modify product: AhpC/TSA family => AhpC/TSA family protein [10:43:00] Modify product: Transposase DDE domain => Transposase DDE domain protein [10:43:00] Modify product: Transposase IS116/IS110/IS902 family => Transposase IS116/IS110/IS902 family protein [10:43:00] Modify product: TrbC/VIRB2 family => TrbC/VIRB2 family protein [10:43:00] Modify product: TrbC/VIRB2 family => TrbC/VIRB2 family protein [10:43:00] Modify product: TrbC/VIRB2 family => TrbC/VIRB2 family protein [10:43:00] Modify product: Transposase IS116/IS110/IS902 family => Transposase IS116/IS110/IS902 family protein [10:43:00] Cleaned 109 /product names [10:43:00] Deleting unwanted file: /home/yquentin/work/wolbachia/prokka/wRi/proteins.faa [10:43:00] Deleting unwanted file: /home/yquentin/work/wolbachia/prokka/wRi/proteins.bls [10:43:00] Labelling remaining 413 proteins as 'hypothetical protein' [10:43:00] Possible /pseudo 'Exopolysaccharide synthesis, ExoD' at gnl|Prokka|wRi_contig000001 position 102597 [10:43:00] Possible /pseudo 'Aminopyrimidine aminohydrolase' at gnl|Prokka|wRi_contig000001 position 116667 [10:43:00] Possible /pseudo 'Quaternary ammonium compound-resistance protein SugE' at gnl|Prokka|wRi_contig000001 position 153480 [10:43:00] Possible /pseudo 'Transposase IS116/IS110/IS902 family protein' at gnl|Prokka|wRi_contig000001 position 197304 [10:43:00] Possible /pseudo 'Transposase IS116/IS110/IS902 family protein' at gnl|Prokka|wRi_contig000001 position 492670 [10:43:00] Possible /pseudo 'L-allo-threonine aldolase' at gnl|Prokka|wRi_contig000001 position 623406 [10:43:00] Possible /pseudo 'anaerobic benzoate catabolism transcriptional regulator' at gnl|Prokka|wRi_contig000001 position 629456 [10:43:00] Possible /pseudo 'Phosphomannomutase/phosphoglucomutase' at gnl|Prokka|wRi_contig000001 position 640782 [10:43:00] Possible /pseudo 'putative zinc protease' at gnl|Prokka|wRi_contig000001 position 650846 [10:43:00] Possible /pseudo 'RDD family protein' at gnl|Prokka|wRi_contig000001 position 685251 [10:43:00] Possible /pseudo 'anaerobic benzoate catabolism transcriptional regulator' at gnl|Prokka|wRi_contig000001 position 716265 [10:43:00] Possible /pseudo 'Phosphocholine transferase AnkX' at gnl|Prokka|wRi_contig000001 position 741777 [10:43:00] Possible /pseudo 'Transposase IS66 family protein' at gnl|Prokka|wRi_contig000001 position 878027 [10:43:00] Possible /pseudo 'TrbL/VirB6 plasmid conjugal transfer protein' at gnl|Prokka|wRi_contig000001 position 884124 [10:43:00] Possible /pseudo 'TrbL/VirB6 plasmid conjugal transfer protein' at gnl|Prokka|wRi_contig000001 position 887066 [10:43:00] Possible /pseudo 'TrbL/VirB6 plasmid conjugal transfer protein' at gnl|Prokka|wRi_contig000001 position 889463 [10:43:00] Possible /pseudo 'Transposase IS116/IS110/IS902 family protein' at gnl|Prokka|wRi_contig000001 position 972137 [10:43:00] Possible /pseudo 'L-allo-threonine aldolase' at gnl|Prokka|wRi_contig000001 position 1129865 [10:43:00] Possible /pseudo 'anaerobic benzoate catabolism transcriptional regulator' at gnl|Prokka|wRi_contig000001 position 1135915 [10:43:00] Possible /pseudo 'Amino-acid carrier protein AlsT' at gnl|Prokka|wRi_contig000001 position 1173231 [10:43:00] Possible /pseudo 'TrbC/VIRB2 family protein' at gnl|Prokka|wRi_contig000001 position 1403579 [10:43:00] Possible /pseudo 'TrbC/VIRB2 family protein' at gnl|Prokka|wRi_contig000001 position 1403953 [10:43:00] Possible /pseudo 'Initiation-control protein YabA' at gnl|Prokka|wRi_contig000001 position 1432784 [10:43:00] Possible /pseudo 'Initiation-control protein YabA' at gnl|Prokka|wRi_contig000001 position 1434125 [10:43:00] Found 565 unique /gene codes. [10:43:00] Fixed 40 colliding /gene names. [10:43:00] Adding /locus_tag identifiers [10:43:00] Assigned 1434 locus_tags to CDS and RNA features. [10:43:00] Writing outputs to /home/yquentin/work/wolbachia/prokka/wRi/ [10:43:01] Generating annotation statistics file [10:43:01] Generating Genbank and Sequin files [10:43:01] 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\/wRi\/wRi\.err -i \/home\/yquentin\/work\/wolbachia\/prokka\/wRi\/wRi\.fsa 2> /dev/null [10:43:05] Deleting unwanted file: /home/yquentin/work/wolbachia/prokka/wRi/errorsummary.val [10:43:05] Deleting unwanted file: /home/yquentin/work/wolbachia/prokka/wRi/wRi.dr [10:43:05] Deleting unwanted file: /home/yquentin/work/wolbachia/prokka/wRi/wRi.fixedproducts [10:43:05] Deleting unwanted file: /home/yquentin/work/wolbachia/prokka/wRi/wRi.ecn [10:43:05] Deleting unwanted file: /home/yquentin/work/wolbachia/prokka/wRi/wRi.val [10:43:05] Output files: [10:43:05] /home/yquentin/work/wolbachia/prokka/wRi/wRi.gff [10:43:05] /home/yquentin/work/wolbachia/prokka/wRi/wRi.tbl [10:43:05] /home/yquentin/work/wolbachia/prokka/wRi/wRi.sqn [10:43:05] /home/yquentin/work/wolbachia/prokka/wRi/wRi.txt [10:43:05] /home/yquentin/work/wolbachia/prokka/wRi/wRi.ffn [10:43:05] /home/yquentin/work/wolbachia/prokka/wRi/wRi.gbk [10:43:05] /home/yquentin/work/wolbachia/prokka/wRi/wRi.err [10:43:05] /home/yquentin/work/wolbachia/prokka/wRi/wRi.log [10:43:05] /home/yquentin/work/wolbachia/prokka/wRi/wRi.faa [10:43:05] /home/yquentin/work/wolbachia/prokka/wRi/wRi.fsa [10:43:05] /home/yquentin/work/wolbachia/prokka/wRi/wRi.fna [10:43:05] Walltime used: 1.55 minutes [10:43:05] If you use this result please cite the Prokka paper: [10:43:05] Seemann T (2014) Prokka: rapid prokaryotic genome annotation. Bioinformatics. 30(14):2068-9. [10:43:05] Type 'prokka --citation' for more details. [10:43:05] Share and enjoy!