[10:41:32] Command: --force --outdir /home/yquentin/work/wolbachia/prokka/wPip_Mol --addgenes --prefix wPip_Mol --locustag wPip_Mol --species Wolbachia endosymbiont --strain wPip_Mol --compliant --quiet /home/yquentin/work/wolbachia/prokka/wPip_Mol.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
[10:41:32] Determined makeblastdb version is 2.6
[10:41:32] Looking for 'minced' - found /usr/local/bioinfo/bin/minced
[10:41:32] Determined minced version is 1.6
[10:41:32] Looking for 'parallel' - found /usr/local/bioinfo/bin/parallel
[10:41:32] Determined parallel version is 20141022
[10:41:32] Looking for 'prodigal' - found /usr/local/bioinfo/bin/prodigal
[10:41:32] Determined prodigal version is 2.6
[10:41:32] Looking for 'rnammer' - found /usr/local/bioinfo/bin/rnammer
[10:41:32] Determined rnammer version is 1.2
[10:41:32] Looking for 'sed' - found /bin/sed
[10:41:32] 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/wPip_Mol.fna
[10:41:33] Wrote 103 contigs
[10:41:33] Predicting tRNAs and tmRNAs
[10:41:33] Running: aragorn -gc11  -w \/home\/yquentin\/work\/wolbachia\/prokka\/wPip_Mol\/wPip_Mol\.fna
[10:41:33] 1 tRNA-Ala c[24148,24223] 34 (tgc)
[10:41:33] 2 tRNA-Lys [24524,24597] 34 (ttt)
[10:41:33] 3 tRNA-Ser [30563,30648] 35 (tga)
[10:41:33] 4 tRNA-Cys [106179,106251] 34 (gca)
[10:41:33] 5 tRNA-Val c[145222,145295] 34 (gac)
[10:41:33] 6 tRNA-Ile [176382,176458] 35 (gat)
[10:41:33] 7 tRNA-Asp c[264342,264418] 35 (gtc)
[10:41:33] 8 tRNA-Leu [275617,275704] 35 (gag)
[10:41:33] 9 tRNA-Leu c[316735,316821] 35 (taa)
[10:41:33] 10 tRNA-Arg c[328012,328089] 36 (acg)
[10:41:33] 11 tmRNA* [347370,347702] 195,242 ANDNFAAEDNVALAA*
[10:41:33] 12 tRNA-Leu [419802,419885] 34 (caa)
[10:41:33] 13 tRNA-Phe c[468785,468858] 34 (gaa)
[10:41:33] 14 tRNA-Arg c[484850,484924] 35 (cct)
[10:41:33] 1 tRNA-Thr [74690,74763] 34 (tgt)
[10:41:33] 2 tRNA-Gln c[80481,80553] 33 (ttg)
[10:41:33] 3 tRNA-Trp c[107244,107317] 34 (cca)
[10:41:33] 4 tRNA-Leu [113850,113932] 35 (tag)
[10:41:33] 5 tRNA-His c[206884,206959] 34 (gtg)
[10:41:33] 6 tRNA-Met c[217734,217806] 33 (cat)
[10:41:33] 7 tRNA-Asn [233539,233611] 33 (gtt)
[10:41:33] 8 tRNA-Met c[268513,268589] 35 (cat)
[10:41:33] 9 tRNA-Gly [269815,269888] 34 (gcc)
[10:41:33] 10 tRNA-Ser [277150,277237] 35 (gga)
[10:41:33] 11 tRNA-Ser [381282,381374] 36 (gct)
[10:41:33] 12 tRNA-Arg [392056,392131] 36 (ccg)
[10:41:33] 13 tRNA-Arg [421374,421449] 36 (tct)
[10:41:33] 14 tRNA-Thr [448039,448113] 35 (ggt)
[10:41:33] 15 tRNA-Met c[470406,470482] 35 (cat)
[10:41:33] 16 tRNA-Ser c[512325,512410] 35 (cag)
[10:41:33] 17 tRNA-Pro c[526261,526336] 36 (tgg)
[10:41:33] 18 tRNA-Glu c[527185,527257] 34 (ttc)
[10:41:33] 1 tRNA-Val c[2353,2424] 34 (tac)
[10:41:33] 2 tRNA-Gln c[4003,4071] 31 (ttg)
[10:41:33] 1 tRNA-Val c[54,126] 34 (tac)
[10:41:33] 1 tRNA-Tyr [262,345] 36 (gta)
[10:41:33] 2 tRNA-Gly [349,420] 33 (tcc)
[10:41:33] Found 37 tRNAs
[10:41:33] Predicting Ribosomal RNAs
[10:41:33] Running Barrnap with 8 threads
[10:41:34] 1 gnl|Prokka|wPip_Mol_contig000001 89162 16S ribosomal RNA
[10:41:34] 2 gnl|Prokka|wPip_Mol_contig000001 186782 23S ribosomal RNA
[10:41:34] 3 gnl|Prokka|wPip_Mol_contig000001 189613 5S ribosomal RNA
[10:41:34] Found 3 rRNAs
[10:41:34] Skipping ncRNA search, enable with --rfam if desired.
[10:41:34] Total of 39 tRNA + rRNA features
[10:41:34] Searching for CRISPR repeats
[10:41:35] Found 0 CRISPRs
[10:41:35] Predicting coding sequences
[10:41:35] Contigs total 1435676 bp, so using single mode
[10:41:35] Running: prodigal -i \/home\/yquentin\/work\/wolbachia\/prokka\/wPip_Mol\/wPip_Mol\.fna -c -m -g 11 -p single -f sco -q
[10:41:36] Excluding CDS which overlaps existing RNA (rRNA) at gnl|Prokka|wPip_Mol_contig000001:90308..90559 on + strand
[10:41:36] Excluding CDS which overlaps existing RNA (tRNA) at gnl|Prokka|wPip_Mol_contig000002:80544..80879 on - strand
[10:41:36] Excluding CDS which overlaps existing RNA (tRNA) at gnl|Prokka|wPip_Mol_contig000002:217682..217810 on - strand
[10:41:36] Excluding CDS which overlaps existing RNA (tRNA) at gnl|Prokka|wPip_Mol_contig000002:217797..219098 on - strand
[10:41:37] Excluding CDS which overlaps existing RNA (tRNA) at gnl|Prokka|wPip_Mol_contig000002:448010..448159 on + strand
[10:41:37] Found 1234 CDS
[10:41:37] Connecting features back to sequences
[10:41:37] Option --gram not specified, will NOT check for signal peptides.
[10:41:37] Not using genus-specific database. Try --usegenus to enable it.
[10:41:37] Annotating CDS, please be patient.
[10:41:37] Will use 8 CPUs for similarity searching.
[10:41:37] There are still 1234 unannotated CDS left (started with 1234)
[10:41:37] Will use blast to search against /usr/local/bioinfo/src/PROKKA/prokka-1.10/bin/../db/kingdom/Bacteria/sprot with 8 CPUs
[10:41:37] Running: cat \/home\/yquentin\/work\/wolbachia\/prokka\/wPip_Mol\/proteins\.faa | parallel --gnu -j 8 --block 23322 --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\/wPip_Mol\/proteins\.bls 2> /dev/null
[10:41:52] Modify product: SCO1 protein homolog => hypothetical protein
[10:41:52] Modify product: Probable GTP-binding protein EngB => putative GTP-binding protein EngB
[10:41:52] Modify product: N utilization substance protein B homolog => hypothetical protein
[10:41:52] Modify product: Transcription termination/antitermination protein NusA => hypothetical protein
[10:41:52] Modify product: Uncharacterized zinc protease Rv2782c => putative zinc protease
[10:41:52] Modify product: Uncharacterized zinc protease Rv2782c => putative zinc protease
[10:41:52] Modify product: Actin-binding protein Smlt3054 => Actin-binding protein
[10:41:52] Modify product: Transcription termination factor Rho => hypothetical protein
[10:41:52] Modify product: Probable tRNA-dihydrouridine synthase => putative tRNA-dihydrouridine synthase
[10:41:52] Modify product: Transcription termination/antitermination protein NusG => hypothetical protein
[10:41:53] Modify product: Riboflavin biosynthesis protein VVA0006 => Riboflavin biosynthesis protein
[10:41:53] Modify product: Co-chaperone protein HscB homolog => hypothetical protein
[10:41:53] Modify product: Uncharacterized oxidoreductase Rv0945 => putative oxidoreductase
[10:41:53] Modify product: Probable transcriptional regulatory protein aq_1575 => putative transcriptional regulatory 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: Probable acyltransferase YihG => putative acyltransferase YihG
[10:41:53] Modify product: Probable phospholipid ABC transporter-binding protein MlaD => putative phospholipid ABC transporter-binding protein MlaD
[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 peroxiredoxin => putative peroxiredoxin
[10:41:53] Modify product: Probable protein kinase UbiB => putative protein kinase UbiB
[10:41:53] Modify product: Uncharacterized zinc protease Rv2782c => putative zinc protease
[10:41:53] Modify product: Cytochrome b561 homolog 2 => hypothetical protein
[10:41:53] Modify product: Uncharacterized metal-dependent hydrolase YcfH => putative metal-dependent hydrolase YcfH
[10:41:53] Modify product: Actin-binding protein Smlt3054 => Actin-binding protein
[10:41:53] Modify product: Uncharacterized oxidoreductase YciK => putative oxidoreductase YciK
[10:41:53] Modify product: Stringent starvation protein A homolog => hypothetical protein
[10:41:53] Modify product: Putative O-methyltransferase MSMEG_5073/MSMEI_4947 => Putative O-methyltransferase/MSMEI_4947
[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 murein peptide carboxypeptidase => putative murein peptide carboxypeptidase
[10:41:54] Modify product: Actin-binding protein Smlt3054 => Actin-binding protein
[10:41:54] Modify product: Bifunctional protein FolD => Bifunctional protein FolD protein
[10:41:54] Cleaned 33 /product names
[10:41:54] Deleting unwanted file: /home/yquentin/work/wolbachia/prokka/wPip_Mol/proteins.faa
[10:41:54] Deleting unwanted file: /home/yquentin/work/wolbachia/prokka/wPip_Mol/proteins.bls
[10:41:54] There are still 621 unannotated CDS left (started with 1234)
[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\/wPip_Mol\/proteins\.faa | parallel --gnu -j 8 --block 9445 --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\/wPip_Mol\/proteins\.bls 2> /dev/null
[10:42:07] Deleting unwanted file: /home/yquentin/work/wolbachia/prokka/wPip_Mol/proteins.faa
[10:42:07] Deleting unwanted file: /home/yquentin/work/wolbachia/prokka/wPip_Mol/proteins.bls
[10:42:08] There are still 587 unannotated CDS left (started with 1234)
[10:42:08] Will use hmmer3 to search against /usr/local/bioinfo/src/PROKKA/prokka-1.10/bin/../db/hmm/CLUSTERS.hmm with 8 CPUs
[10:42:08] Running: cat \/home\/yquentin\/work\/wolbachia\/prokka\/wPip_Mol\/proteins\.faa | parallel --gnu -j 8 --block 8713 --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\/wPip_Mol\/proteins\.bls 2> /dev/null
[10:42:37] Deleting unwanted file: /home/yquentin/work/wolbachia/prokka/wPip_Mol/proteins.faa
[10:42:37] Deleting unwanted file: /home/yquentin/work/wolbachia/prokka/wPip_Mol/proteins.bls
[10:42:37] There are still 548 unannotated CDS left (started with 1234)
[10:42:37] Will use hmmer3 to search against /usr/local/bioinfo/src/PROKKA/prokka-1.10/bin/../db/hmm/Pfam.hmm with 8 CPUs
[10:42:37] Running: cat \/home\/yquentin\/work\/wolbachia\/prokka\/wPip_Mol\/proteins\.faa | parallel --gnu -j 8 --block 8091 --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\/wPip_Mol\/proteins\.bls 2> /dev/null
[10:42:59] Modify product: COQ9 => hypothetical protein
[10:42:59] Modify product: DnaJ domain => DnaJ domain protein
[10:42:59] Modify product: EVE domain => EVE domain protein
[10:42:59] Modify product: Ankyrin repeat => Ankyrin repeat protein
[10:42:59] Modify product: RmlD substrate binding domain => RmlD substrate binding domain protein
[10:42:59] Modify product: Ankyrin repeat => Ankyrin repeat protein
[10:42:59] Modify product: SPFH domain / Band 7 family => SPFH domain / Band 7 family protein
[10:42:59] Modify product: TrbC/VIRB2 family => TrbC/VIRB2 family protein
[10:42:59] Modify product: Ankyrin repeat => Ankyrin repeat protein
[10:42:59] Modify product: Tim44-like domain => Tim44-like domain protein
[10:42:59] Modify product: TrbC/VIRB2 family => TrbC/VIRB2 family protein
[10:42:59] Modify product: Phage capsid family => Phage capsid family protein
[10:42:59] Modify product: Ankyrin repeat => Ankyrin repeat protein
[10:42:59] Modify product: Integral membrane protein TerC family => Integral membrane protein TerC family protein
[10:42:59] Modify product: DSBA-like thioredoxin domain => DSBA-like thioredoxin domain protein
[10:42:59] Modify product: MgtE intracellular N domain => MgtE intracellular N domain protein
[10:42:59] Modify product: Terminase-like family => Terminase-like family protein
[10:42:59] Modify product: Terminase-like family => Terminase-like family protein
[10:42:59] Modify product: PD-(D/E)XK nuclease superfamily => PD-(D/E)XK nuclease superfamily protein
[10:42:59] Modify product: RDD family => RDD family protein
[10:42:59] Modify product: SURF1 family => SURF1 family protein
[10:42:59] Modify product: YGGT family => YGGT family protein
[10:42:59] Modify product: Sodium:dicarboxylate symporter family => Sodium:dicarboxylate symporter family protein
[10:42:59] Modify product: Na+/H+ antiporter family => Na+/H+ antiporter family protein
[10:42:59] Modify product: Transposase DDE domain => Transposase DDE domain protein
[10:42:59] Modify product: Piwi/Argonaute/Zwille siRNA-binding domain => Piwi/Argonaute/Zwille siRNA-binding domain protein
[10:42:59] Modify product: RDD family => RDD family protein
[10:42:59] Modify product: Ankyrin repeat => Ankyrin repeat protein
[10:42:59] Modify product: KAP family P-loop domain => KAP family P-loop domain protein
[10:42:59] Modify product: PAAR motif => PAAR motif protein
[10:42:59] Modify product: Alpha/beta hydrolase family => Alpha/beta hydrolase family protein
[10:42:59] Modify product: Major Facilitator Superfamily => Major Facilitator Superfamily protein
[10:42:59] Modify product: Transposase DDE domain => Transposase DDE domain protein
[10:42:59] Modify product: RDD family => RDD family protein
[10:42:59] Modify product: Terminase-like family => Terminase-like family protein
[10:42:59] Modify product: CobQ/CobB/MinD/ParA nucleotide binding domain => CobQ/CobB/MinD/ParA nucleotide binding domain protein
[10:42:59] Modify product: Transposase IS116/IS110/IS902 family => Transposase IS116/IS110/IS902 family protein
[10:42:59] Modify product: Uracil DNA glycosylase superfamily => Uracil DNA glycosylase superfamily protein
[10:42:59] Modify product: ETC complex I subunit conserved region => hypothetical protein
[10:42:59] Modify product: Alpha/beta hydrolase family => Alpha/beta hydrolase family protein
[10:42:59] Modify product: Integrase core domain => Integrase core domain protein
[10:42:59] Modify product: Alpha/beta hydrolase family => Alpha/beta hydrolase family protein
[10:42:59] Modify product: Piwi/Argonaute/Zwille siRNA-binding domain => Piwi/Argonaute/Zwille siRNA-binding domain protein
[10:42:59] Modify product: Phosphotransferase enzyme family => Phosphotransferase enzyme family protein
[10:42:59] Modify product: AhpC/TSA family => AhpC/TSA family protein
[10:42:59] Modify product: TrbC/VIRB2 family => TrbC/VIRB2 family protein
[10:42:59] Modify product: Helix-turn-helix domain => Helix-turn-helix domain protein
[10:42:59] Modify product: PAAR motif => PAAR motif protein
[10:42:59] Modify product: PAAR motif => PAAR motif protein
[10:42:59] Modify product: PAAR motif => PAAR motif protein
[10:42:59] Modify product: Ankyrin repeat => Ankyrin repeat protein
[10:42:59] Modify product: Helix-turn-helix domain => Helix-turn-helix domain protein
[10:42:59] Modify product: Ankyrin repeat => Ankyrin repeat protein
[10:42:59] Modify product: Glyoxalase-like domain => Glyoxalase-like domain protein
[10:42:59] Modify product: Tetratricopeptide repeat => Tetratricopeptide repeat protein
[10:43:00] Modify product: Ankyrin repeat => Ankyrin repeat protein
[10:43:00] Cleaned 56 /product names
[10:43:00] Deleting unwanted file: /home/yquentin/work/wolbachia/prokka/wPip_Mol/proteins.faa
[10:43:00] Deleting unwanted file: /home/yquentin/work/wolbachia/prokka/wPip_Mol/proteins.bls
[10:43:00] Labelling remaining 389 proteins as 'hypothetical protein'
[10:43:00] Possible /pseudo 'Threonine--tRNA ligase' at gnl|Prokka|wPip_Mol_contig000001 position 27956
[10:43:00] Possible /pseudo 'Collagen triple helix repeat (20 copies)' at gnl|Prokka|wPip_Mol_contig000001 position 73119
[10:43:00] Possible /pseudo 'Amino-acid carrier protein AlsT' at gnl|Prokka|wPip_Mol_contig000001 position 139171
[10:43:00] Possible /pseudo 'Aminopyrimidine aminohydrolase' at gnl|Prokka|wPip_Mol_contig000001 position 178479
[10:43:00] Possible /pseudo 'Protein translocase subunit SecY' at gnl|Prokka|wPip_Mol_contig000001 position 214280
[10:43:00] Possible /pseudo 'Ankyrin repeats (3 copies)' at gnl|Prokka|wPip_Mol_contig000001 position 335780
[10:43:00] Possible /pseudo 'Exopolysaccharide synthesis, ExoD' at gnl|Prokka|wPip_Mol_contig000001 position 487016
[10:43:00] Possible /pseudo 'Chromosome partition protein Smc' at gnl|Prokka|wPip_Mol_contig000001 position 519253
[10:43:00] Possible /pseudo '1-deoxy-D-xylulose 5-phosphate reductoisomerase' at gnl|Prokka|wPip_Mol_contig000001 position 532857
[10:43:00] Possible /pseudo 'Phosphocholine transferase AnkX' at gnl|Prokka|wPip_Mol_contig000001 position 560612
[10:43:00] Possible /pseudo 'DNA ligase' at gnl|Prokka|wPip_Mol_contig000002 position 7736
[10:43:00] Possible /pseudo 'putative zinc protease' at gnl|Prokka|wPip_Mol_contig000002 position 43658
[10:43:00] Possible /pseudo 'TrbL/VirB6 plasmid conjugal transfer protein' at gnl|Prokka|wPip_Mol_contig000002 position 146749
[10:43:00] Possible /pseudo 'TrbL/VirB6 plasmid conjugal transfer protein' at gnl|Prokka|wPip_Mol_contig000002 position 149646
[10:43:00] Possible /pseudo 'Type IV secretion system protein virB4' at gnl|Prokka|wPip_Mol_contig000002 position 195060
[10:43:00] Possible /pseudo 'Dihydropteroate synthase' at gnl|Prokka|wPip_Mol_contig000002 position 264501
[10:43:00] Possible /pseudo 'Arginine/agmatine antiporter' at gnl|Prokka|wPip_Mol_contig000002 position 286400
[10:43:00] Possible /pseudo 'Ankyrin repeats (3 copies)' at gnl|Prokka|wPip_Mol_contig000002 position 293755
[10:43:00] Possible /pseudo 'Ankyrin repeats (3 copies)' at gnl|Prokka|wPip_Mol_contig000002 position 295068
[10:43:00] Possible /pseudo 'Ankyrin repeats (3 copies)' at gnl|Prokka|wPip_Mol_contig000002 position 297435
[10:43:00] Possible /pseudo 'tRNA pseudouridine synthase B' at gnl|Prokka|wPip_Mol_contig000002 position 404403
[10:43:00] Possible /pseudo 'anaerobic benzoate catabolism transcriptional regulator' at gnl|Prokka|wPip_Mol_contig000008 position 9703
[10:43:00] Found 548 unique /gene codes.
[10:43:00] Fixed 33 colliding /gene names.
[10:43:00] Adding /locus_tag identifiers
[10:43:00] Assigned 1274 locus_tags to CDS and RNA features.
[10:43:00] Writing outputs to /home/yquentin/work/wolbachia/prokka/wPip_Mol/
[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\/wPip_Mol\/wPip_Mol\.err -i \/home\/yquentin\/work\/wolbachia\/prokka\/wPip_Mol\/wPip_Mol\.fsa 2> /dev/null
[10:43:07] Deleting unwanted file: /home/yquentin/work/wolbachia/prokka/wPip_Mol/errorsummary.val
[10:43:07] Deleting unwanted file: /home/yquentin/work/wolbachia/prokka/wPip_Mol/wPip_Mol.dr
[10:43:07] Deleting unwanted file: /home/yquentin/work/wolbachia/prokka/wPip_Mol/wPip_Mol.fixedproducts
[10:43:07] Deleting unwanted file: /home/yquentin/work/wolbachia/prokka/wPip_Mol/wPip_Mol.ecn
[10:43:07] Deleting unwanted file: /home/yquentin/work/wolbachia/prokka/wPip_Mol/wPip_Mol.val
[10:43:07] Output files:
[10:43:07] /home/yquentin/work/wolbachia/prokka/wPip_Mol/wPip_Mol.txt
[10:43:07] /home/yquentin/work/wolbachia/prokka/wPip_Mol/wPip_Mol.log
[10:43:07] /home/yquentin/work/wolbachia/prokka/wPip_Mol/wPip_Mol.fsa
[10:43:07] /home/yquentin/work/wolbachia/prokka/wPip_Mol/wPip_Mol.tbl
[10:43:07] /home/yquentin/work/wolbachia/prokka/wPip_Mol/wPip_Mol.gbk
[10:43:07] /home/yquentin/work/wolbachia/prokka/wPip_Mol/wPip_Mol.err
[10:43:07] /home/yquentin/work/wolbachia/prokka/wPip_Mol/wPip_Mol.fna
[10:43:07] /home/yquentin/work/wolbachia/prokka/wPip_Mol/wPip_Mol.ffn
[10:43:07] /home/yquentin/work/wolbachia/prokka/wPip_Mol/wPip_Mol.sqn
[10:43:07] /home/yquentin/work/wolbachia/prokka/wPip_Mol/wPip_Mol.gff
[10:43:07] /home/yquentin/work/wolbachia/prokka/wPip_Mol/wPip_Mol.faa
[10:43:07] Walltime used: 1.58 minutes
[10:43:07] If you use this result please cite the Prokka paper:
[10:43:07] Seemann T (2014) Prokka: rapid prokaryotic genome annotation. Bioinformatics. 30(14):2068-9.
[10:43:07] Type 'prokka --citation' for more details.
[10:43:07] Share and enjoy!