[15:07:07] 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
[15:07:07] Looking for 'aragorn' - found /usr/local/bioinfo/bin/aragorn
[15:07:07] Determined aragorn version is 1.2
[15:07:07] Looking for 'barrnap' - found /usr/local/bioinfo/bin/barrnap
[15:07:07] Determined barrnap version is 0.5
[15:07:07] Looking for 'blastp' - found /usr/local/bioinfo/src/NCBI_Blast+/ncbi-blast-2.6.0+/bin/blastp
[15:07:07] Determined blastp version is 2.6
[15:07:07] Looking for 'cmpress' - found /usr/local/bioinfo/src/PROKKA/prokka-1.10/bin/../binaries/linux/cmpress
[15:07:07] Determined cmpress version is 1.1
[15:07:07] Looking for 'cmscan' - found /usr/local/bioinfo/src/PROKKA/prokka-1.10/bin/../binaries/linux/cmscan
[15:07:07] Determined cmscan version is 1.1
[15:07:07] Looking for 'egrep' - found /bin/egrep
[15:07:07] Looking for 'find' - found /bin/find
[15:07:07] Looking for 'grep' - found /bin/grep
[15:07:07] Looking for 'hmmpress' - found /usr/local/bioinfo/bin/hmmpress
[15:07:07] Determined hmmpress version is 3.1
[15:07:07] Looking for 'hmmscan' - found /usr/local/bioinfo/bin/hmmscan
[15:07:07] Determined hmmscan version is 3.1
[15:07:07] Looking for 'less' - found /usr/bin/less
[15:07:07] Looking for 'makeblastdb' - found /usr/local/bioinfo/src/NCBI_Blast+/ncbi-blast-2.6.0+/bin/makeblastdb
[15:07:07] Determined makeblastdb version is 2.6
[15:07:07] Looking for 'minced' - found /usr/local/bioinfo/bin/minced
[15:07:08] Determined minced version is 1.6
[15:07:08] Looking for 'parallel' - found /usr/local/bioinfo/bin/parallel
[15:07:08] Determined parallel version is 20141022
[15:07:08] Looking for 'prodigal' - found /usr/local/bioinfo/bin/prodigal
[15:07:08] Determined prodigal version is 2.6
[15:07:08] Looking for 'rnammer' - found /usr/local/bioinfo/bin/rnammer
[15:07:08] Determined rnammer version is 1.2
[15:07:08] Looking for 'sed' - found /bin/sed
[15:07:08] Looking for 'signalp' - found /usr/local/bioinfo/bin/signalp
[15:07:08] Determined signalp version is 4.1
[15:07:08] Looking for 'tbl2asn' - found /home/yquentin/save/scripts/tbl2asn
[15:07:08] Determined tbl2asn version is 25.3
[15:07:08] Using genetic code table 11.
[15:07:08] Loading and checking input file: /home/yquentin/work/wolbachia/prokka/wRi.fna
[15:07:09] Wrote 1 contigs
[15:07:09] Predicting tRNAs and tmRNAs
[15:07:09] Running: aragorn -gc11  -w \/home\/yquentin\/work\/wolbachia\/prokka\/wRi\/wRi\.fna
[15:07:09] 1 tRNA-Leu [3028,3115] 35 (gag)
[15:07:09] 2 tRNA-Trp [17582,17655] 34 (cca)
[15:07:09] 3 tRNA-Arg c[44965,45042] 36 (acg)
[15:07:09] 4 tRNA-Arg c[100390,100466] 35 (cct)
[15:07:09] 5 tRNA-Ile c[118707,118783] 35 (gat)
[15:07:09] 6 tmRNA* [126380,126708] 194,238 ANDNFAAEEYRVAA*
[15:07:09] 7 tRNA-Thr c[161019,161092] 34 (tgt)
[15:07:09] 8 tRNA-Phe c[366232,366306] 34 (gaa)
[15:07:09] 9 tRNA-Asp [371956,372029] 35 (gtc)
[15:07:09] 10 tRNA-Leu c[428327,428413] 35 (taa)
[15:07:09] 11 tRNA-Leu c[464241,464324] 34 (caa)
[15:07:09] 12 tRNA-Leu c[512977,513059] 35 (tag)
[15:07:09] 13 tRNA-Gly c[554228,554299] 33 (tcc)
[15:07:09] 14 tRNA-Tyr c[554304,554386] 35 (gta)
[15:07:09] 15 tRNA-Arg [664416,664490] 35 (ccg)
[15:07:09] 16 tRNA-Met [676778,676851] 34 (cat)
[15:07:09] 17 tRNA-Ser c[789221,789309] 36 (gga)
[15:07:09] 18 tRNA-Gln c[853833,853907] 33 (ttg)
[15:07:09] 19 tRNA-Asn [904522,904594] 33 (gtt)
[15:07:09] 20 tRNA-Met c[934886,934962] 35 (cat)
[15:07:09] 21 tRNA-Gly [936238,936311] 34 (gcc)
[15:07:09] 22 tRNA-Ala c[994816,994892] 34 (tgc)
[15:07:09] 23 tRNA-Lys [995213,995286] 34 (ttt)
[15:07:09] 24 tRNA-Ser [1002805,1002893] 35 (tga)
[15:07:09] 25 tRNA-Ser [1019795,1019880] 35 (cag)
[15:07:09] 26 tRNA-His c[1033523,1033598] 34 (gtg)
[15:07:09] 27 tRNA-Val [1168180,1168253] 34 (gac)
[15:07:09] 28 tRNA-Thr c[1221998,1222071] 34 (ggt)
[15:07:09] 29 tRNA-Met c[1223629,1223705] 35 (cat)
[15:07:09] 30 tRNA-Val c[1274331,1274403] 34 (tac)
[15:07:09] 31 tRNA-Pro c[1280784,1280859] 36 (tgg)
[15:07:09] 32 tRNA-Glu c[1281791,1281863] 34 (ttc)
[15:07:09] 33 tRNA-Cys [1306976,1307048] 34 (gca)
[15:07:09] 34 tRNA-Ser [1329700,1329792] 36 (gct)
[15:07:09] 35 tRNA-Arg c[1388376,1388450] 35 (tct)
[15:07:09] Found 35 tRNAs
[15:07:09] Predicting Ribosomal RNAs
[15:07:09] Running Barrnap with 8 threads
[15:07:10] 1 gnl|Prokka|wRi_contig000001 188533 23S ribosomal RNA
[15:07:10] 2 gnl|Prokka|wRi_contig000001 191363 5S ribosomal RNA
[15:07:10] 3 gnl|Prokka|wRi_contig000001 1289972 16S ribosomal RNA
[15:07:10] Found 3 rRNAs
[15:07:10] Skipping ncRNA search, enable with --rfam if desired.
[15:07:10] Total of 37 tRNA + rRNA features
[15:07:10] Searching for CRISPR repeats
[15:07:11] CRISPR1 gnl|Prokka|wRi_contig000001 418918 with 6 spacers
[15:07:11] Found 1 CRISPRs
[15:07:11] Predicting coding sequences
[15:07:11] Contigs total 1445873 bp, so using single mode
[15:07:11] Running: prodigal -i \/home\/yquentin\/work\/wolbachia\/prokka\/wRi\/wRi\.fna -c -m -g 11 -p single -f sco -q
[15:07:16] Excluding CDS which overlaps existing RNA (tRNA) at gnl|Prokka|wRi_contig000001:512895..513053 on - strand
[15:07:16] Excluding CDS which overlaps existing RNA (tRNA) at gnl|Prokka|wRi_contig000001:675486..676778 on + strand
[15:07:17] Excluding CDS which overlaps existing RNA (tRNA) at gnl|Prokka|wRi_contig000001:853898..854155 on - strand
[15:07:17] Excluding CDS which overlaps existing RNA (tRNA) at gnl|Prokka|wRi_contig000001:1223669..1225921 on + strand
[15:07:17] Excluding CDS which overlaps existing RNA (rRNA) at gnl|Prokka|wRi_contig000001:1290408..1290530 on + strand
[15:07:17] Excluding CDS which overlaps existing RNA (tRNA) at gnl|Prokka|wRi_contig000001:1388385..1388795 on + strand
[15:07:17] Found 1396 CDS
[15:07:17] Connecting features back to sequences
[15:07:17] Option --gram not specified, will NOT check for signal peptides.
[15:07:17] Not using genus-specific database. Try --usegenus to enable it.
[15:07:17] Annotating CDS, please be patient.
[15:07:17] Will use 8 CPUs for similarity searching.
[15:07:19] There are still 1396 unannotated CDS left (started with 1396)
[15:07:19] Will use blast to search against /usr/local/bioinfo/src/PROKKA/prokka-1.10/bin/../db/kingdom/Bacteria/sprot with 8 CPUs
[15:07:19] 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
[15:07:46] Modify product: SCO1 protein homolog => hypothetical protein
[15:07:46] Modify product: N utilization substance protein B homolog => hypothetical protein
[15:07:46] Modify product: Probable GTP-binding protein EngB => putative GTP-binding protein EngB
[15:07:46] Modify product: Probable transcriptional regulatory protein aq_1575 => putative transcriptional regulatory protein
[15:07:47] Modify product: Bifunctional protein FolD => Bifunctional protein FolD protein
[15:07:47] Modify product: Uncharacterized ABC transporter ATP-binding protein TM_0288 => putative ABC transporter ATP-binding protein
[15:07:47] Modify product: Actin-binding protein Smlt3054 => Actin-binding protein
[15:07:47] Modify product: Probable deoxyribonuclease RhsA => putative deoxyribonuclease RhsA
[15:07:47] Modify product: Putative multidrug export ATP-binding/permease protein SAV1866 => Putative multidrug export ATP-binding/permease protein
[15:07:47] Modify product: Transcription termination/antitermination protein NusG => hypothetical protein
[15:07:47] Modify product: Probable tRNA-dihydrouridine synthase => putative tRNA-dihydrouridine synthase
[15:07:47] Modify product: Putative multidrug export ATP-binding/permease protein SAV1866 => Putative multidrug export ATP-binding/permease protein
[15:07:47] Modify product: Probable peroxiredoxin => putative peroxiredoxin
[15:07:47] Modify product: Uncharacterized zinc protease Rv2782c => putative zinc protease
[15:07:48] Modify product: Uncharacterized zinc protease Rv2782c => putative zinc protease
[15:07:48] Modify product: Transcription termination factor Rho => hypothetical protein
[15:07:48] Modify product: Probable phospholipid ABC transporter permease protein MlaE => putative phospholipid ABC transporter permease protein MlaE
[15:07:48] Modify product: Probable ribonucleotide transport ATP-binding protein mkl => putative ribonucleotide transport ATP-binding protein mkl
[15:07:48] Modify product: Probable murein peptide carboxypeptidase => putative murein peptide carboxypeptidase
[15:07:48] Modify product: Probable acyltransferase YihG => putative acyltransferase YihG
[15:07:48] Modify product: Co-chaperone protein HscB homolog => hypothetical protein
[15:07:49] Modify product: Probable protein kinase UbiB => putative protein kinase UbiB
[15:07:49] Modify product: Actin-binding protein Smlt3054 => Actin-binding protein
[15:07:49] Modify product: Probable deoxyribonuclease RhsA => putative deoxyribonuclease RhsA
[15:07:49] Modify product: Uncharacterized zinc protease Rv2782c => putative zinc protease
[15:07:49] Modify product: Probable deoxyribonuclease RhsA => putative deoxyribonuclease RhsA
[15:07:49] Modify product: Putative multidrug export ATP-binding/permease protein SAV1866 => Putative multidrug export ATP-binding/permease protein
[15:07:49] Modify product: Probable transport protein HsrA => putative transport protein HsrA
[15:07:49] Modify product: Probable glycerol-3-phosphate acyltransferase => putative glycerol-3-phosphate acyltransferase
[15:07:49] Modify product: Putative O-methyltransferase MSMEG_5073/MSMEI_4947 => Putative O-methyltransferase/MSMEI_4947
[15:07:49] Modify product: Stringent starvation protein A homolog => hypothetical protein
[15:07:49] Modify product: Cytochrome b561 homolog 2 => hypothetical protein
[15:07:49] Modify product: Probable chromosome-partitioning protein ParB => putative chromosome-partitioning protein ParB
[15:07:50] Modify product: Actin-binding protein Smlt3054 => Actin-binding protein
[15:07:50] Modify product: Probable phospholipid ABC transporter-binding protein MlaD => putative phospholipid ABC transporter-binding protein MlaD
[15:07:50] Modify product: Uncharacterized metal-dependent hydrolase YcfH => putative metal-dependent hydrolase YcfH
[15:07:50] Modify product: Uncharacterized HIT-like protein HP_0404 => putative HIT-like protein
[15:07:50] Modify product: Uncharacterized oxidoreductase YciK => putative oxidoreductase YciK
[15:07:50] Modify product: Transcription termination/antitermination protein NusA => hypothetical protein
[15:07:50] Cleaned 39 /product names
[15:07:50] Deleting unwanted file: /home/yquentin/work/wolbachia/prokka/wRi/proteins.faa
[15:07:50] Deleting unwanted file: /home/yquentin/work/wolbachia/prokka/wRi/proteins.bls
[15:07:51] There are still 751 unannotated CDS left (started with 1396)
[15:07:51] Will use hmmer3 to search against /usr/local/bioinfo/src/PROKKA/prokka-1.10/bin/../db/hmm/HAMAP.hmm with 8 CPUs
[15:07:51] 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
[15:08:05] Deleting unwanted file: /home/yquentin/work/wolbachia/prokka/wRi/proteins.faa
[15:08:05] Deleting unwanted file: /home/yquentin/work/wolbachia/prokka/wRi/proteins.bls
[15:08:05] There are still 689 unannotated CDS left (started with 1396)
[15:08:05] Will use hmmer3 to search against /usr/local/bioinfo/src/PROKKA/prokka-1.10/bin/../db/hmm/CLUSTERS.hmm with 8 CPUs
[15:08:05] 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
[15:08:38] Deleting unwanted file: /home/yquentin/work/wolbachia/prokka/wRi/proteins.faa
[15:08:38] Deleting unwanted file: /home/yquentin/work/wolbachia/prokka/wRi/proteins.bls
[15:08:38] There are still 648 unannotated CDS left (started with 1396)
[15:08:38] Will use hmmer3 to search against /usr/local/bioinfo/src/PROKKA/prokka-1.10/bin/../db/hmm/Pfam.hmm with 8 CPUs
[15:08:38] 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
[15:09:05] Modify product: Transposase IS116/IS110/IS902 family => Transposase IS116/IS110/IS902 family protein
[15:09:05] Modify product: Ankyrin repeat => Ankyrin repeat protein
[15:09:05] Modify product: Transposase IS66 family => Transposase IS66 family protein
[15:09:05] Modify product: Ankyrin repeat => Ankyrin repeat protein
[15:09:05] Modify product: Transposase DDE domain => Transposase DDE domain protein
[15:09:05] Modify product: Transposase DDE domain => Transposase DDE domain protein
[15:09:05] Modify product: Ankyrin repeat => Ankyrin repeat protein
[15:09:05] Modify product: Transposase DDE domain => Transposase DDE domain protein
[15:09:05] Modify product: Transposase IS66 family => Transposase IS66 family protein
[15:09:05] Modify product: Transposase IS116/IS110/IS902 family => Transposase IS116/IS110/IS902 family protein
[15:09:05] Modify product: SPFH domain / Band 7 family => SPFH domain / Band 7 family protein
[15:09:05] Modify product: Transposase IS116/IS110/IS902 family => Transposase IS116/IS110/IS902 family protein
[15:09:05] Modify product: Phage capsid family => Phage capsid family protein
[15:09:05] Modify product: TrbC/VIRB2 family => TrbC/VIRB2 family protein
[15:09:05] Modify product: Transposase IS66 family => Transposase IS66 family protein
[15:09:05] Modify product: Transposase IS116/IS110/IS902 family => Transposase IS116/IS110/IS902 family protein
[15:09:05] Modify product: Transposase IS116/IS110/IS902 family => Transposase IS116/IS110/IS902 family protein
[15:09:05] Modify product: RDD family => RDD family protein
[15:09:05] Modify product: RDD family => RDD family protein
[15:09:05] Modify product: Transposase IS116/IS110/IS902 family => Transposase IS116/IS110/IS902 family protein
[15:09:05] Modify product: Transposase IS116/IS110/IS902 family => Transposase IS116/IS110/IS902 family protein
[15:09:05] Modify product: Integrase core domain => Integrase core domain protein
[15:09:05] Modify product: Alpha/beta hydrolase family => Alpha/beta hydrolase family protein
[15:09:05] Modify product: Transposase IS66 family => Transposase IS66 family protein
[15:09:05] Modify product: Terminase-like family => Terminase-like family protein
[15:09:05] Modify product: RDD family => RDD family protein
[15:09:05] Modify product: TrbC/VIRB2 family => TrbC/VIRB2 family protein
[15:09:05] Modify product: Transposase DDE domain => Transposase DDE domain protein
[15:09:05] Modify product: Transposase IS116/IS110/IS902 family => Transposase IS116/IS110/IS902 family protein
[15:09:05] Modify product: Transposase IS116/IS110/IS902 family => Transposase IS116/IS110/IS902 family protein
[15:09:05] Modify product: Transposase IS116/IS110/IS902 family => Transposase IS116/IS110/IS902 family protein
[15:09:05] Modify product: Transposase IS116/IS110/IS902 family => Transposase IS116/IS110/IS902 family protein
[15:09:05] Modify product: Transposase DDE domain => Transposase DDE domain protein
[15:09:05] Modify product: TrbC/VIRB2 family => TrbC/VIRB2 family protein
[15:09:05] Modify product: Piwi/Argonaute/Zwille siRNA-binding domain => Piwi/Argonaute/Zwille siRNA-binding domain protein
[15:09:05] Modify product: Transposase IS116/IS110/IS902 family => Transposase IS116/IS110/IS902 family protein
[15:09:05] Modify product: Transposase DDE domain => Transposase DDE domain protein
[15:09:05] Modify product: Ankyrin repeat => Ankyrin repeat protein
[15:09:05] Modify product: Integrase core domain => Integrase core domain protein
[15:09:05] Modify product: Transposase DDE domain => Transposase DDE domain protein
[15:09:05] Modify product: Integrase core domain => Integrase core domain protein
[15:09:05] Modify product: ETC complex I subunit conserved region => hypothetical protein
[15:09:05] Modify product: Uracil DNA glycosylase superfamily => Uracil DNA glycosylase superfamily protein
[15:09:05] Modify product: Na+/H+ antiporter family => Na+/H+ antiporter family protein
[15:09:05] Modify product: Zinc-finger domain => Zinc-finger domain protein
[15:09:05] Modify product: Transposase DDE domain => Transposase DDE domain protein
[15:09:05] Modify product: Transposase DDE domain => Transposase DDE domain protein
[15:09:05] Modify product: Integrase core domain => Integrase core domain protein
[15:09:05] Modify product: Integrase core domain => Integrase core domain protein
[15:09:05] Modify product: Transposase IS116/IS110/IS902 family => Transposase IS116/IS110/IS902 family protein
[15:09:05] Modify product: Transposase DDE domain => Transposase DDE domain protein
[15:09:05] Modify product: Transposase DDE domain => Transposase DDE domain protein
[15:09:05] Modify product: Transposase IS116/IS110/IS902 family => Transposase IS116/IS110/IS902 family protein
[15:09:05] Modify product: Transposase IS116/IS110/IS902 family => Transposase IS116/IS110/IS902 family protein
[15:09:05] Modify product: Tim44-like domain => Tim44-like domain protein
[15:09:05] Modify product: Integral membrane protein TerC family => Integral membrane protein TerC family protein
[15:09:05] Modify product: Transposase IS116/IS110/IS902 family => Transposase IS116/IS110/IS902 family protein
[15:09:05] Modify product: Transposase IS116/IS110/IS902 family => Transposase IS116/IS110/IS902 family protein
[15:09:05] Modify product: Sodium:dicarboxylate symporter family => Sodium:dicarboxylate symporter family protein
[15:09:05] Modify product: Transposase DDE domain => Transposase DDE domain protein
[15:09:05] Modify product: Transposase IS116/IS110/IS902 family => Transposase IS116/IS110/IS902 family protein
[15:09:05] Modify product: EVE domain => EVE domain protein
[15:09:05] Modify product: Transposase DDE domain => Transposase DDE domain protein
[15:09:05] Modify product: Ankyrin repeat => Ankyrin repeat protein
[15:09:05] Modify product: PAS domain => PAS domain protein
[15:09:05] Modify product: Transposase IS66 family => Transposase IS66 family protein
[15:09:05] Modify product: Transposase DDE domain => Transposase DDE domain protein
[15:09:05] Modify product: Transposase DDE domain => Transposase DDE domain protein
[15:09:05] Modify product: Transposase DDE domain => Transposase DDE domain protein
[15:09:05] Modify product: PD-(D/E)XK nuclease superfamily => PD-(D/E)XK nuclease superfamily protein
[15:09:05] Modify product: Integrase core domain => Integrase core domain protein
[15:09:05] Modify product: Transposase IS116/IS110/IS902 family => Transposase IS116/IS110/IS902 family protein
[15:09:05] Modify product: Transposase IS116/IS110/IS902 family => Transposase IS116/IS110/IS902 family protein
[15:09:05] Modify product: Transposase DDE domain => Transposase DDE domain protein
[15:09:05] Modify product: Transposase IS116/IS110/IS902 family => Transposase IS116/IS110/IS902 family protein
[15:09:05] Modify product: Transposase DDE domain => Transposase DDE domain protein
[15:09:05] Modify product: Transposase IS66 family => Transposase IS66 family protein
[15:09:05] Modify product: Transposase DDE domain => Transposase DDE domain protein
[15:09:05] Modify product: Transposase DDE domain => Transposase DDE domain protein
[15:09:05] Modify product: COQ9 => hypothetical protein
[15:09:05] Modify product: Transposase IS66 family => Transposase IS66 family protein
[15:09:05] Modify product: Transposase IS66 family => Transposase IS66 family protein
[15:09:05] Modify product: Terminase-like family => Terminase-like family protein
[15:09:05] Modify product: Transposase IS116/IS110/IS902 family => Transposase IS116/IS110/IS902 family protein
[15:09:05] Modify product: Major Facilitator Superfamily => Major Facilitator Superfamily protein
[15:09:05] Modify product: Transposase IS116/IS110/IS902 family => Transposase IS116/IS110/IS902 family protein
[15:09:05] Modify product: Transposase IS116/IS110/IS902 family => Transposase IS116/IS110/IS902 family protein
[15:09:05] Modify product: Transposase DDE domain => Transposase DDE domain protein
[15:09:05] Modify product: Transposase DDE domain => Transposase DDE domain protein
[15:09:05] Modify product: Bacterial SH3 domain => Bacterial SH3 domain protein
[15:09:05] Modify product: KAP family P-loop domain => KAP family P-loop domain protein
[15:09:05] Modify product: Transposase IS116/IS110/IS902 family => Transposase IS116/IS110/IS902 family protein
[15:09:05] Modify product: Transposase DDE domain => Transposase DDE domain protein
[15:09:05] Modify product: RDD family => RDD family protein
[15:09:05] Modify product: SURF1 family => SURF1 family protein
[15:09:05] Modify product: AhpC/TSA family => AhpC/TSA family protein
[15:09:05] Modify product: Integrase core domain => Integrase core domain protein
[15:09:05] Modify product: Transposase DDE domain => Transposase DDE domain protein
[15:09:05] Modify product: MgtE intracellular N domain => MgtE intracellular N domain protein
[15:09:05] Modify product: Transposase IS66 family => Transposase IS66 family protein
[15:09:05] Modify product: Transposase DDE domain => Transposase DDE domain protein
[15:09:05] Modify product: Terminase-like family => Terminase-like family protein
[15:09:05] Modify product: Transposase IS116/IS110/IS902 family => Transposase IS116/IS110/IS902 family protein
[15:09:05] Modify product: Transposase DDE domain => Transposase DDE domain protein
[15:09:05] Modify product: Transposase IS116/IS110/IS902 family => Transposase IS116/IS110/IS902 family protein
[15:09:05] Modify product: TrbC/VIRB2 family => TrbC/VIRB2 family protein
[15:09:05] Modify product: TrbC/VIRB2 family => TrbC/VIRB2 family protein
[15:09:05] Modify product: TrbC/VIRB2 family => TrbC/VIRB2 family protein
[15:09:05] Modify product: Transposase IS116/IS110/IS902 family => Transposase IS116/IS110/IS902 family protein
[15:09:05] Cleaned 109 /product names
[15:09:05] Deleting unwanted file: /home/yquentin/work/wolbachia/prokka/wRi/proteins.faa
[15:09:05] Deleting unwanted file: /home/yquentin/work/wolbachia/prokka/wRi/proteins.bls
[15:09:05] Labelling remaining 413 proteins as 'hypothetical protein'
[15:09:05] Possible /pseudo 'Exopolysaccharide synthesis, ExoD' at gnl|Prokka|wRi_contig000001 position 102597
[15:09:05] Possible /pseudo 'Aminopyrimidine aminohydrolase' at gnl|Prokka|wRi_contig000001 position 116667
[15:09:05] Possible /pseudo 'Quaternary ammonium compound-resistance protein SugE' at gnl|Prokka|wRi_contig000001 position 153480
[15:09:05] Possible /pseudo 'Transposase IS116/IS110/IS902 family protein' at gnl|Prokka|wRi_contig000001 position 197304
[15:09:05] Possible /pseudo 'Transposase IS116/IS110/IS902 family protein' at gnl|Prokka|wRi_contig000001 position 492670
[15:09:05] Possible /pseudo 'L-allo-threonine aldolase' at gnl|Prokka|wRi_contig000001 position 623406
[15:09:05] Possible /pseudo 'anaerobic benzoate catabolism transcriptional regulator' at gnl|Prokka|wRi_contig000001 position 629456
[15:09:05] Possible /pseudo 'Phosphomannomutase/phosphoglucomutase' at gnl|Prokka|wRi_contig000001 position 640782
[15:09:05] Possible /pseudo 'putative zinc protease' at gnl|Prokka|wRi_contig000001 position 650846
[15:09:05] Possible /pseudo 'RDD family protein' at gnl|Prokka|wRi_contig000001 position 685251
[15:09:05] Possible /pseudo 'anaerobic benzoate catabolism transcriptional regulator' at gnl|Prokka|wRi_contig000001 position 716265
[15:09:05] Possible /pseudo 'Phosphocholine transferase AnkX' at gnl|Prokka|wRi_contig000001 position 741777
[15:09:05] Possible /pseudo 'Transposase IS66 family protein' at gnl|Prokka|wRi_contig000001 position 878027
[15:09:05] Possible /pseudo 'TrbL/VirB6 plasmid conjugal transfer protein' at gnl|Prokka|wRi_contig000001 position 884124
[15:09:05] Possible /pseudo 'TrbL/VirB6 plasmid conjugal transfer protein' at gnl|Prokka|wRi_contig000001 position 887066
[15:09:05] Possible /pseudo 'TrbL/VirB6 plasmid conjugal transfer protein' at gnl|Prokka|wRi_contig000001 position 889463
[15:09:05] Possible /pseudo 'Transposase IS116/IS110/IS902 family protein' at gnl|Prokka|wRi_contig000001 position 972137
[15:09:05] Possible /pseudo 'L-allo-threonine aldolase' at gnl|Prokka|wRi_contig000001 position 1129865
[15:09:05] Possible /pseudo 'anaerobic benzoate catabolism transcriptional regulator' at gnl|Prokka|wRi_contig000001 position 1135915
[15:09:05] Possible /pseudo 'Amino-acid carrier protein AlsT' at gnl|Prokka|wRi_contig000001 position 1173231
[15:09:05] Possible /pseudo 'TrbC/VIRB2 family protein' at gnl|Prokka|wRi_contig000001 position 1403579
[15:09:05] Possible /pseudo 'TrbC/VIRB2 family protein' at gnl|Prokka|wRi_contig000001 position 1403953
[15:09:05] Possible /pseudo 'Initiation-control protein YabA' at gnl|Prokka|wRi_contig000001 position 1432784
[15:09:05] Possible /pseudo 'Initiation-control protein YabA' at gnl|Prokka|wRi_contig000001 position 1434125
[15:09:05] Found 565 unique /gene codes.
[15:09:05] Fixed 40 colliding /gene names.
[15:09:05] Adding /locus_tag identifiers
[15:09:05] Assigned 1434 locus_tags to CDS and RNA features.
[15:09:05] Writing outputs to /home/yquentin/work/wolbachia/prokka/wRi/
[15:09:07] Generating annotation statistics file
[15:09:07] Generating Genbank and Sequin files
[15:09:07] 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
[15:09:11] Deleting unwanted file: /home/yquentin/work/wolbachia/prokka/wRi/errorsummary.val
[15:09:11] Deleting unwanted file: /home/yquentin/work/wolbachia/prokka/wRi/wRi.dr
[15:09:11] Deleting unwanted file: /home/yquentin/work/wolbachia/prokka/wRi/wRi.fixedproducts
[15:09:11] Deleting unwanted file: /home/yquentin/work/wolbachia/prokka/wRi/wRi.ecn
[15:09:11] Deleting unwanted file: /home/yquentin/work/wolbachia/prokka/wRi/wRi.val
[15:09:11] Output files:
[15:09:11] /home/yquentin/work/wolbachia/prokka/wRi/wRi.gff
[15:09:11] /home/yquentin/work/wolbachia/prokka/wRi/wRi.tbl
[15:09:11] /home/yquentin/work/wolbachia/prokka/wRi/wRi.sqn
[15:09:11] /home/yquentin/work/wolbachia/prokka/wRi/wRi.txt
[15:09:11] /home/yquentin/work/wolbachia/prokka/wRi/wRi.ffn
[15:09:11] /home/yquentin/work/wolbachia/prokka/wRi/wRi.gbk
[15:09:11] /home/yquentin/work/wolbachia/prokka/wRi/wRi.err
[15:09:11] /home/yquentin/work/wolbachia/prokka/wRi/wRi.log
[15:09:11] /home/yquentin/work/wolbachia/prokka/wRi/wRi.faa
[15:09:11] /home/yquentin/work/wolbachia/prokka/wRi/wRi.fsa
[15:09:11] /home/yquentin/work/wolbachia/prokka/wRi/wRi.fna
[15:09:11] Walltime used: 2.07 minutes
[15:09:11] If you use this result please cite the Prokka paper:
[15:09:11] Seemann T (2014) Prokka: rapid prokaryotic genome annotation. Bioinformatics. 30(14):2068-9.
[15:09:11] Type 'prokka --citation' for more details.
[15:09:11] Thank you, come again.