[10:41:22] Command: --force --outdir /home/yquentin/work/wolbachia/prokka/wMel --addgenes --prefix wMel --locustag wMel --species Wolbachia endosymbiont --strain wMel --compliant --quiet /home/yquentin/work/wolbachia/prokka/wMel.fna
[10:41:22] Looking for 'aragorn' - found /usr/local/bioinfo/bin/aragorn
[10:41:22] Determined aragorn version is 1.2
[10:41:22] Looking for 'barrnap' - found /usr/local/bioinfo/bin/barrnap
[10:41:22] Determined barrnap version is 0.5
[10:41:22] Looking for 'blastp' - found /usr/local/bioinfo/src/NCBI_Blast+/ncbi-blast-2.6.0+/bin/blastp
[10:41:22] Determined blastp version is 2.6
[10:41:22] Looking for 'cmpress' - found /usr/local/bioinfo/src/PROKKA/prokka-1.10/bin/../binaries/linux/cmpress
[10:41:22] Determined cmpress version is 1.1
[10:41:22] Looking for 'cmscan' - found /usr/local/bioinfo/src/PROKKA/prokka-1.10/bin/../binaries/linux/cmscan
[10:41:22] Determined cmscan version is 1.1
[10:41:22] Looking for 'egrep' - found /bin/egrep
[10:41:22] Looking for 'find' - found /bin/find
[10:41:22] Looking for 'grep' - found /bin/grep
[10:41:23] Looking for 'hmmpress' - found /usr/local/bioinfo/bin/hmmpress
[10:41:23] Determined hmmpress version is 3.1
[10:41:23] Looking for 'hmmscan' - found /usr/local/bioinfo/bin/hmmscan
[10:41:23] Determined hmmscan version is 3.1
[10:41:23] Looking for 'less' - found /usr/bin/less
[10:41:23] Looking for 'makeblastdb' - found /usr/local/bioinfo/src/NCBI_Blast+/ncbi-blast-2.6.0+/bin/makeblastdb
[10:41:23] Determined makeblastdb version is 2.6
[10:41:23] Looking for 'minced' - found /usr/local/bioinfo/bin/minced
[10:41:23] Determined minced version is 1.6
[10:41:23] Looking for 'parallel' - found /usr/local/bioinfo/bin/parallel
[10:41:23] Determined parallel version is 20141022
[10:41:23] Looking for 'prodigal' - found /usr/local/bioinfo/bin/prodigal
[10:41:23] Determined prodigal version is 2.6
[10:41:23] Looking for 'rnammer' - found /usr/local/bioinfo/bin/rnammer
[10:41:23] Determined rnammer version is 1.2
[10:41:23] Looking for 'sed' - found /bin/sed
[10:41:23] Looking for 'signalp' - found /usr/local/bioinfo/bin/signalp
[10:41:23] Determined signalp version is 4.1
[10:41:23] Looking for 'tbl2asn' - found /home/yquentin/save/scripts/tbl2asn
[10:41:24] Determined tbl2asn version is 25.3
[10:41:24] Using genetic code table 11.
[10:41:24] Loading and checking input file: /home/yquentin/work/wolbachia/prokka/wMel.fna
[10:41:24] Wrote 1 contigs
[10:41:24] Predicting tRNAs and tmRNAs
[10:41:24] Running: aragorn -gc11  -w \/home\/yquentin\/work\/wolbachia\/prokka\/wMel\/wMel\.fna
[10:41:24] 1 tRNA-Leu [3028,3115] 35 (gag)
[10:41:24] 2 tRNA-Trp [17456,17529] 34 (cca)
[10:41:24] 3 tRNA-Arg c[44465,44542] 36 (acg)
[10:41:24] 4 tRNA-Thr [83879,83952] 34 (tgt)
[10:41:24] 5 tmRNA* c[117016,117351] 195,245 ANDNFAAEDNVDAIAA*
[10:41:24] 6 tRNA-Ile [124755,124831] 35 (gat)
[10:41:24] 7 tRNA-Arg [140709,140785] 35 (cct)
[10:41:24] 8 tRNA-Leu c[302589,302671] 35 (tag)
[10:41:24] 9 tRNA-Leu [338408,338491] 34 (caa)
[10:41:24] 10 tRNA-Leu [372019,372105] 35 (taa)
[10:41:24] 11 tRNA-Phe c[513733,513807] 34 (gaa)
[10:41:24] 12 tRNA-Asp [519457,519533] 35 (gtc)
[10:41:24] 13 tRNA-Gly c[659238,659309] 33 (tcc)
[10:41:24] 14 tRNA-Tyr c[659314,659396] 35 (gta)
[10:41:24] 15 tRNA-Ser [722498,722586] 36 (gga)
[10:41:24] 16 tRNA-Arg [747473,747547] 35 (ccg)
[10:41:24] 17 tRNA-Met [759967,760040] 34 (cat)
[10:41:24] 18 tRNA-Gln c[793554,793628] 33 (ttg)
[10:41:24] 19 tRNA-Asn [840438,840510] 33 (gtt)
[10:41:24] 20 tRNA-Gly c[849138,849211] 34 (gcc)
[10:41:24] 21 tRNA-Met [850506,850582] 35 (cat)
[10:41:24] 22 tRNA-Ala c[934910,934985] 34 (tgc)
[10:41:24] 23 tRNA-Lys [935327,935400] 34 (ttt)
[10:41:24] 24 tRNA-Ser [941717,941805] 35 (tga)
[10:41:24] 25 tRNA-Ser [956999,957084] 35 (cag)
[10:41:24] 26 tRNA-His c[970678,970753] 34 (gtg)
[10:41:24] 27 tRNA-Val [1004086,1004159] 34 (gac)
[10:41:24] 28 tRNA-Arg c[1080265,1080339] 35 (tct)
[10:41:24] 29 tRNA-Thr c[1105558,1105631] 34 (ggt)
[10:41:24] 30 tRNA-Met c[1107308,1107384] 35 (cat)
[10:41:24] 31 tRNA-Val c[1152148,1152220] 34 (tac)
[10:41:24] 32 tRNA-Pro c[1158601,1158676] 36 (tgg)
[10:41:24] 33 tRNA-Glu c[1159608,1159680] 34 (ttc)
[10:41:24] 34 tRNA-Cys [1186296,1186368] 34 (gca)
[10:41:24] 35 tRNA-Ser [1208802,1208894] 36 (gct)
[10:41:24] Found 35 tRNAs
[10:41:24] Predicting Ribosomal RNAs
[10:41:24] Running Barrnap with 8 threads
[10:41:25] 1 gnl|Prokka|wMel_contig000001 182432 23S ribosomal RNA
[10:41:25] 2 gnl|Prokka|wMel_contig000001 185262 5S ribosomal RNA
[10:41:25] 3 gnl|Prokka|wMel_contig000001 1167939 16S ribosomal RNA
[10:41:25] Found 3 rRNAs
[10:41:25] Skipping ncRNA search, enable with --rfam if desired.
[10:41:25] Total of 37 tRNA + rRNA features
[10:41:25] Searching for CRISPR repeats
[10:41:25] Found 0 CRISPRs
[10:41:25] Predicting coding sequences
[10:41:25] Contigs total 1267782 bp, so using single mode
[10:41:25] Running: prodigal -i \/home\/yquentin\/work\/wolbachia\/prokka\/wMel\/wMel\.fna -c -m -g 11 -p single -f sco -q
[10:41:27] Excluding CDS which overlaps existing RNA (tRNA) at gnl|Prokka|wMel_contig000001:302507..302665 on - strand
[10:41:28] Excluding CDS which overlaps existing RNA (tRNA) at gnl|Prokka|wMel_contig000001:758675..759967 on + strand
[10:41:28] Excluding CDS which overlaps existing RNA (tRNA) at gnl|Prokka|wMel_contig000001:793619..793954 on - strand
[10:41:28] Excluding CDS which overlaps existing RNA (tRNA) at gnl|Prokka|wMel_contig000001:1004122..1005081 on + strand
[10:41:28] Excluding CDS which overlaps existing RNA (tRNA) at gnl|Prokka|wMel_contig000001:1080274..1080684 on + strand
[10:41:28] Excluding CDS which overlaps existing RNA (tRNA) at gnl|Prokka|wMel_contig000001:1107348..1109609 on + strand
[10:41:28] Found 1271 CDS
[10:41:28] Connecting features back to sequences
[10:41:28] Option --gram not specified, will NOT check for signal peptides.
[10:41:28] Not using genus-specific database. Try --usegenus to enable it.
[10:41:28] Annotating CDS, please be patient.
[10:41:28] Will use 8 CPUs for similarity searching.
[10:41:29] There are still 1271 unannotated CDS left (started with 1271)
[10:41:29] Will use blast to search against /usr/local/bioinfo/src/PROKKA/prokka-1.10/bin/../db/kingdom/Bacteria/sprot with 8 CPUs
[10:41:29] Running: cat \/home\/yquentin\/work\/wolbachia\/prokka\/wMel\/proteins\.faa | parallel --gnu -j 8 --block 22676 --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\/wMel\/proteins\.bls 2> /dev/null
[10:41:40] Modify product: SCO1 protein homolog => hypothetical protein
[10:41:41] Modify product: Actin-binding protein Smlt3054 => Actin-binding protein
[10:41:41] Modify product: Bifunctional protein FolD => Bifunctional protein FolD protein
[10:41:41] Modify product: Uncharacterized ABC transporter ATP-binding protein TM_0288 => putative ABC transporter ATP-binding protein
[10:41:41] Modify product: Putative multidrug export ATP-binding/permease protein SAV1866 => Putative multidrug export ATP-binding/permease protein
[10:41:41] Modify product: Probable deoxyribonuclease RhsA => putative deoxyribonuclease RhsA
[10:41:41] Modify product: N utilization substance protein B homolog => hypothetical protein
[10:41:41] Modify product: Probable GTP-binding protein EngB => putative GTP-binding protein EngB
[10:41:41] Modify product: Transcription termination/antitermination protein NusG => hypothetical protein
[10:41:41] Modify product: Probable tRNA-dihydrouridine synthase => putative tRNA-dihydrouridine synthase
[10:41:41] Modify product: Probable transcriptional regulatory protein aq_1575 => putative transcriptional regulatory protein
[10:41:41] Modify product: Uncharacterized zinc protease Rv2782c => putative zinc protease
[10:41:41] Modify product: Probable peroxiredoxin => putative peroxiredoxin
[10:41:41] Modify product: Uncharacterized zinc protease Rv2782c => putative zinc protease
[10:41:41] Modify product: Uncharacterized zinc protease Rv2782c => putative zinc protease
[10:41:41] Modify product: Transcription termination factor Rho => hypothetical protein
[10:41:41] Modify product: Co-chaperone protein HscB homolog => hypothetical protein
[10:41:41] Modify product: Probable murein peptide carboxypeptidase => putative murein peptide carboxypeptidase
[10:41:41] Modify product: Probable glycerol-3-phosphate acyltransferase => putative glycerol-3-phosphate acyltransferase
[10:41:41] Modify product: Putative O-methyltransferase MSMEG_5073/MSMEI_4947 => Putative O-methyltransferase/MSMEI_4947
[10:41:41] Modify product: Stringent starvation protein A homolog => hypothetical protein
[10:41:41] Modify product: Uncharacterized metal-dependent hydrolase YcfH => putative metal-dependent hydrolase YcfH
[10:41:41] Modify product: Uncharacterized HIT-like protein HP_0404 => putative HIT-like protein
[10:41:41] Modify product: Probable acyltransferase YihG => putative acyltransferase YihG
[10:41:41] Modify product: Actin-binding protein Smlt3054 => Actin-binding protein
[10:41:41] Modify product: Probable protein kinase UbiB => putative protein kinase UbiB
[10:41:42] Modify product: Probable phospholipid ABC transporter permease protein MlaE => putative phospholipid ABC transporter permease protein MlaE
[10:41:42] Modify product: Probable ribonucleotide transport ATP-binding protein mkl => putative ribonucleotide transport ATP-binding protein mkl
[10:41:42] Modify product: Cytochrome b561 homolog 2 => hypothetical protein
[10:41:42] Modify product: Probable chromosome-partitioning protein ParB => putative chromosome-partitioning protein ParB
[10:41:42] Modify product: Uncharacterized oxidoreductase YciK => putative oxidoreductase YciK
[10:41:42] Modify product: Transcription termination/antitermination protein NusA => hypothetical protein
[10:41:42] Cleaned 32 /product names
[10:41:42] Deleting unwanted file: /home/yquentin/work/wolbachia/prokka/wMel/proteins.faa
[10:41:42] Deleting unwanted file: /home/yquentin/work/wolbachia/prokka/wMel/proteins.bls
[10:41:42] There are still 641 unannotated CDS left (started with 1271)
[10:41:42] Will use hmmer3 to search against /usr/local/bioinfo/src/PROKKA/prokka-1.10/bin/../db/hmm/HAMAP.hmm with 8 CPUs
[10:41:42] Running: cat \/home\/yquentin\/work\/wolbachia\/prokka\/wMel\/proteins\.faa | parallel --gnu -j 8 --block 8518 --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\/wMel\/proteins\.bls 2> /dev/null
[10:41:50] Deleting unwanted file: /home/yquentin/work/wolbachia/prokka/wMel/proteins.faa
[10:41:50] Deleting unwanted file: /home/yquentin/work/wolbachia/prokka/wMel/proteins.bls
[10:41:50] There are still 607 unannotated CDS left (started with 1271)
[10:41:50] Will use hmmer3 to search against /usr/local/bioinfo/src/PROKKA/prokka-1.10/bin/../db/hmm/CLUSTERS.hmm with 8 CPUs
[10:41:50] Running: cat \/home\/yquentin\/work\/wolbachia\/prokka\/wMel\/proteins\.faa | parallel --gnu -j 8 --block 7790 --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\/wMel\/proteins\.bls 2> /dev/null
[10:42:13] Deleting unwanted file: /home/yquentin/work/wolbachia/prokka/wMel/proteins.faa
[10:42:13] Deleting unwanted file: /home/yquentin/work/wolbachia/prokka/wMel/proteins.bls
[10:42:13] There are still 577 unannotated CDS left (started with 1271)
[10:42:13] Will use hmmer3 to search against /usr/local/bioinfo/src/PROKKA/prokka-1.10/bin/../db/hmm/Pfam.hmm with 8 CPUs
[10:42:13] Running: cat \/home\/yquentin\/work\/wolbachia\/prokka\/wMel\/proteins\.faa | parallel --gnu -j 8 --block 7328 --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\/wMel\/proteins\.bls 2> /dev/null
[10:42:38] Modify product: Transposase IS116/IS110/IS902 family => Transposase IS116/IS110/IS902 family protein
[10:42:38] Modify product: PAAR motif => PAAR motif protein
[10:42:38] Modify product: Piwi/Argonaute/Zwille siRNA-binding domain => Piwi/Argonaute/Zwille siRNA-binding domain protein
[10:42:38] Modify product: Transposase IS116/IS110/IS902 family => Transposase IS116/IS110/IS902 family protein
[10:42:38] Modify product: Transposase DDE domain => Transposase DDE domain protein
[10:42:38] Modify product: Transposase DDE domain => Transposase DDE domain protein
[10:42:38] Modify product: Transposase DDE domain => Transposase DDE domain protein
[10:42:38] Modify product: Integrase core domain => Integrase core domain protein
[10:42:38] Modify product: TrbC/VIRB2 family => TrbC/VIRB2 family protein
[10:42:38] Modify product: RDD family => RDD family protein
[10:42:38] Modify product: Na+/H+ antiporter family => Na+/H+ antiporter family protein
[10:42:38] Modify product: Transposase DDE domain => Transposase DDE domain protein
[10:42:38] Modify product: Phage capsid family => Phage capsid family protein
[10:42:38] Modify product: TrbC/VIRB2 family => TrbC/VIRB2 family protein
[10:42:38] Modify product: SPFH domain / Band 7 family => SPFH domain / Band 7 family protein
[10:42:38] Modify product: Transposase DDE domain => Transposase DDE domain protein
[10:42:38] Modify product: Transposase DDE domain => Transposase DDE domain protein
[10:42:38] Modify product: Transposase IS116/IS110/IS902 family => Transposase IS116/IS110/IS902 family protein
[10:42:38] Modify product: Transposase DDE domain => Transposase DDE domain protein
[10:42:38] Modify product: Zinc-finger domain => Zinc-finger domain protein
[10:42:38] Modify product: Transposase DDE domain => Transposase DDE domain protein
[10:42:38] Modify product: Transposase DDE domain => Transposase DDE domain protein
[10:42:38] Modify product: Transposase DDE domain => Transposase DDE domain protein
[10:42:38] Modify product: YGGT family => YGGT family protein
[10:42:38] Modify product: Transposase DDE domain => Transposase DDE domain protein
[10:42:38] Modify product: Uracil DNA glycosylase superfamily => Uracil DNA glycosylase superfamily protein
[10:42:38] Modify product: ETC complex I subunit conserved region => hypothetical protein
[10:42:38] Modify product: Integrase core domain => Integrase core domain protein
[10:42:38] Modify product: Integral membrane protein TerC family => Integral membrane protein TerC family protein
[10:42:38] Modify product: Sodium:dicarboxylate symporter family => Sodium:dicarboxylate symporter family protein
[10:42:38] Modify product: Transposase DDE domain => Transposase DDE domain protein
[10:42:38] Modify product: Ulp1 protease family, C-terminal catalytic domain => hypothetical protein
[10:42:38] Modify product: Piwi/Argonaute/Zwille siRNA-binding domain => Piwi/Argonaute/Zwille siRNA-binding domain protein
[10:42:38] Modify product: Piwi/Argonaute/Zwille siRNA-binding domain => Piwi/Argonaute/Zwille siRNA-binding domain protein
[10:42:38] Modify product: Transposase DDE domain => Transposase DDE domain protein
[10:42:38] Modify product: Tim44-like domain => Tim44-like domain protein
[10:42:38] Modify product: Ankyrin repeat => Ankyrin repeat protein
[10:42:38] Modify product: Transposase DDE domain => Transposase DDE domain protein
[10:42:38] Modify product: TrbC/VIRB2 family => TrbC/VIRB2 family protein
[10:42:38] Modify product: COQ9 => hypothetical protein
[10:42:38] Modify product: PAS domain => PAS domain protein
[10:42:38] Modify product: Transposase IS116/IS110/IS902 family => Transposase IS116/IS110/IS902 family protein
[10:42:38] Modify product: Transposase DDE domain => Transposase DDE domain protein
[10:42:38] Modify product: Transposase DDE domain => Transposase DDE domain protein
[10:42:38] Modify product: RDD family => RDD family protein
[10:42:38] Modify product: RDD family => RDD family protein
[10:42:38] Modify product: Transposase DDE domain => Transposase DDE domain protein
[10:42:38] Modify product: Transposase IS116/IS110/IS902 family => Transposase IS116/IS110/IS902 family protein
[10:42:38] Modify product: Alpha/beta hydrolase family => Alpha/beta hydrolase family protein
[10:42:38] Modify product: Transposase IS66 family => Transposase IS66 family protein
[10:42:38] Modify product: Terminase-like family => Terminase-like family protein
[10:42:38] Modify product: EVE domain => EVE domain protein
[10:42:38] Modify product: Acetyltransferase (GNAT) family => Acetyltransferase (GNAT) family protein
[10:42:38] Modify product: Terminase-like family => Terminase-like family protein
[10:42:38] Modify product: Major Facilitator Superfamily => Major Facilitator Superfamily protein
[10:42:38] Modify product: Transposase DDE domain => Transposase DDE domain protein
[10:42:38] Modify product: Terminase-like family => Terminase-like family protein
[10:42:38] Modify product: Bacterial SH3 domain => Bacterial SH3 domain protein
[10:42:38] Modify product: KAP family P-loop domain => KAP family P-loop domain protein
[10:42:38] Modify product: Transposase DDE domain => Transposase DDE domain protein
[10:42:38] Modify product: Transposase DDE domain => Transposase DDE domain protein
[10:42:38] Modify product: Transposase IS116/IS110/IS902 family => Transposase IS116/IS110/IS902 family protein
[10:42:38] Modify product: Transposase DDE domain => Transposase DDE domain protein
[10:42:38] Modify product: Transposase IS116/IS110/IS902 family => Transposase IS116/IS110/IS902 family protein
[10:42:38] Modify product: MgtE intracellular N domain => MgtE intracellular N domain protein
[10:42:38] Modify product: Transposase DDE domain => Transposase DDE domain protein
[10:42:38] Modify product: HemY protein N-terminus => hypothetical protein
[10:42:38] Modify product: RDD family => RDD family protein
[10:42:38] Modify product: SURF1 family => SURF1 family protein
[10:42:38] Modify product: AhpC/TSA family => AhpC/TSA family protein
[10:42:38] Modify product: TrbC/VIRB2 family => TrbC/VIRB2 family protein
[10:42:38] Modify product: TrbC/VIRB2 family => TrbC/VIRB2 family protein
[10:42:38] Modify product: TrbC/VIRB2 family => TrbC/VIRB2 family protein
[10:42:38] Cleaned 73 /product names
[10:42:38] Deleting unwanted file: /home/yquentin/work/wolbachia/prokka/wMel/proteins.faa
[10:42:38] Deleting unwanted file: /home/yquentin/work/wolbachia/prokka/wMel/proteins.bls
[10:42:38] Labelling remaining 391 proteins as 'hypothetical protein'
[10:42:38] Possible /pseudo 'Piwi/Argonaute/Zwille siRNA-binding domain protein' at gnl|Prokka|wMel_contig000001 position 36604
[10:42:38] Possible /pseudo 'Quaternary ammonium compound-resistance protein SugE' at gnl|Prokka|wMel_contig000001 position 92251
[10:42:38] Possible /pseudo 'Aminopyrimidine aminohydrolase' at gnl|Prokka|wMel_contig000001 position 127835
[10:42:38] Possible /pseudo 'Exopolysaccharide synthesis, ExoD' at gnl|Prokka|wMel_contig000001 position 138669
[10:42:38] Possible /pseudo 'Phage portal protein, lambda family' at gnl|Prokka|wMel_contig000001 position 254223
[10:42:38] Possible /pseudo 'Phage-related baseplate assembly protein' at gnl|Prokka|wMel_contig000001 position 262366
[10:42:38] Possible /pseudo 'Ankyrin repeats (3 copies)' at gnl|Prokka|wMel_contig000001 position 266255
[10:42:38] Possible /pseudo 'Ankyrin repeats (3 copies)' at gnl|Prokka|wMel_contig000001 position 271150
[10:42:38] Possible /pseudo 'Putative prophage major tail sheath protein' at gnl|Prokka|wMel_contig000001 position 557764
[10:42:38] Possible /pseudo 'L-allo-threonine aldolase' at gnl|Prokka|wMel_contig000001 position 602278
[10:42:38] Possible /pseudo 'anaerobic benzoate catabolism transcriptional regulator' at gnl|Prokka|wMel_contig000001 position 608328
[10:42:38] Possible /pseudo 'putative zinc protease' at gnl|Prokka|wMel_contig000001 position 735747
[10:42:38] Possible /pseudo 'RDD family protein' at gnl|Prokka|wMel_contig000001 position 766986
[10:42:38] Possible /pseudo 'TrbL/VirB6 plasmid conjugal transfer protein' at gnl|Prokka|wMel_contig000001 position 819977
[10:42:38] Possible /pseudo 'TrbL/VirB6 plasmid conjugal transfer protein' at gnl|Prokka|wMel_contig000001 position 822952
[10:42:38] Possible /pseudo 'TrbL/VirB6 plasmid conjugal transfer protein' at gnl|Prokka|wMel_contig000001 position 825349
[10:42:38] Possible /pseudo 'Amino-acid carrier protein AlsT' at gnl|Prokka|wMel_contig000001 position 1009060
[10:42:38] Possible /pseudo 'TrbC/VIRB2 family protein' at gnl|Prokka|wMel_contig000001 position 1231380
[10:42:38] Possible /pseudo 'TrbC/VIRB2 family protein' at gnl|Prokka|wMel_contig000001 position 1231751
[10:42:38] Found 566 unique /gene codes.
[10:42:38] Fixed 38 colliding /gene names.
[10:42:38] Adding /locus_tag identifiers
[10:42:38] Assigned 1309 locus_tags to CDS and RNA features.
[10:42:38] Writing outputs to /home/yquentin/work/wolbachia/prokka/wMel/
[10:42:39] Generating annotation statistics file
[10:42:39] Generating Genbank and Sequin files
[10:42:39] 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\/wMel\/wMel\.err -i \/home\/yquentin\/work\/wolbachia\/prokka\/wMel\/wMel\.fsa 2> /dev/null
[10:42:42] Deleting unwanted file: /home/yquentin/work/wolbachia/prokka/wMel/errorsummary.val
[10:42:42] Deleting unwanted file: /home/yquentin/work/wolbachia/prokka/wMel/wMel.dr
[10:42:42] Deleting unwanted file: /home/yquentin/work/wolbachia/prokka/wMel/wMel.fixedproducts
[10:42:42] Deleting unwanted file: /home/yquentin/work/wolbachia/prokka/wMel/wMel.ecn
[10:42:42] Deleting unwanted file: /home/yquentin/work/wolbachia/prokka/wMel/wMel.val
[10:42:42] Output files:
[10:42:42] /home/yquentin/work/wolbachia/prokka/wMel/wMel.err
[10:42:42] /home/yquentin/work/wolbachia/prokka/wMel/wMel.ffn
[10:42:42] /home/yquentin/work/wolbachia/prokka/wMel/wMel.fsa
[10:42:42] /home/yquentin/work/wolbachia/prokka/wMel/wMel.gbk
[10:42:42] /home/yquentin/work/wolbachia/prokka/wMel/wMel.gff
[10:42:42] /home/yquentin/work/wolbachia/prokka/wMel/wMel.log
[10:42:42] /home/yquentin/work/wolbachia/prokka/wMel/wMel.fna
[10:42:42] /home/yquentin/work/wolbachia/prokka/wMel/wMel.faa
[10:42:42] /home/yquentin/work/wolbachia/prokka/wMel/wMel.tbl
[10:42:42] /home/yquentin/work/wolbachia/prokka/wMel/wMel.txt
[10:42:42] /home/yquentin/work/wolbachia/prokka/wMel/wMel.sqn
[10:42:42] Walltime used: 1.33 minutes
[10:42:42] If you use this result please cite the Prokka paper:
[10:42:42] Seemann T (2014) Prokka: rapid prokaryotic genome annotation. Bioinformatics. 30(14):2068-9.
[10:42:42] Type 'prokka --citation' for more details.
[10:42:42] Thank you, come again.