[10:41:28] Command: --force --outdir /home/yquentin/work/wolbachia/prokka/wMuni --addgenes --prefix wMuni --locustag wMuni --species Wolbachia endosymbiont --strain wMuni --compliant --quiet /home/yquentin/work/wolbachia/prokka/wMuni.fna
[10:41:28] Looking for 'aragorn' - found /usr/local/bioinfo/bin/aragorn
[10:41:28] Determined aragorn version is 1.2
[10:41:28] Looking for 'barrnap' - found /usr/local/bioinfo/bin/barrnap
[10:41:28] Determined barrnap version is 0.5
[10:41:28] Looking for 'blastp' - found /usr/local/bioinfo/src/NCBI_Blast+/ncbi-blast-2.6.0+/bin/blastp
[10:41:28] Determined blastp version is 2.6
[10:41:28] Looking for 'cmpress' - found /usr/local/bioinfo/src/PROKKA/prokka-1.10/bin/../binaries/linux/cmpress
[10:41:28] Determined cmpress version is 1.1
[10:41:28] Looking for 'cmscan' - found /usr/local/bioinfo/src/PROKKA/prokka-1.10/bin/../binaries/linux/cmscan
[10:41:28] Determined cmscan version is 1.1
[10:41:28] Looking for 'egrep' - found /bin/egrep
[10:41:28] Looking for 'find' - found /bin/find
[10:41:28] Looking for 'grep' - found /bin/grep
[10:41:28] Looking for 'hmmpress' - found /usr/local/bioinfo/bin/hmmpress
[10:41:28] Determined hmmpress version is 3.1
[10:41:28] Looking for 'hmmscan' - found /usr/local/bioinfo/bin/hmmscan
[10:41:28] Determined hmmscan version is 3.1
[10:41:28] Looking for 'less' - found /usr/bin/less
[10:41:28] Looking for 'makeblastdb' - found /usr/local/bioinfo/src/NCBI_Blast+/ncbi-blast-2.6.0+/bin/makeblastdb
[10:41:29] Determined makeblastdb version is 2.6
[10:41:29] Looking for 'minced' - found /usr/local/bioinfo/bin/minced
[10:41:29] Determined minced version is 1.6
[10:41:29] Looking for 'parallel' - found /usr/local/bioinfo/bin/parallel
[10:41:29] Determined parallel version is 20141022
[10:41:29] Looking for 'prodigal' - found /usr/local/bioinfo/bin/prodigal
[10:41:29] Determined prodigal version is 2.6
[10:41:29] Looking for 'rnammer' - found /usr/local/bioinfo/bin/rnammer
[10:41:29] Determined rnammer version is 1.2
[10:41:29] Looking for 'sed' - found /bin/sed
[10:41:29] Looking for 'signalp' - found /usr/local/bioinfo/bin/signalp
[10:41:29] Determined signalp version is 4.1
[10:41:29] Looking for 'tbl2asn' - found /home/yquentin/save/scripts/tbl2asn
[10:41:29] Determined tbl2asn version is 25.3
[10:41:29] Using genetic code table 11.
[10:41:29] Loading and checking input file: /home/yquentin/work/wolbachia/prokka/wMuni.fna
[10:41:29] Wrote 256 contigs
[10:41:29] Predicting tRNAs and tmRNAs
[10:41:29] Running: aragorn -gc11  -w \/home\/yquentin\/work\/wolbachia\/prokka\/wMuni\/wMuni\.fna
[10:41:30] 1 tRNA-Asp c[5832,5908] 35 (gtc)
[10:41:30] 1 tRNA-Leu [7097,7180] 34 (caa)
[10:41:30] 1 tRNA-Cys c[4383,4455] 34 (gca)
[10:41:30] 1 tRNA-Glu [8676,8748] 34 (ttc)
[10:41:30] 2 tRNA-Pro [9680,9755] 36 (tgg)
[10:41:30] 3 tRNA-Val [16471,16543] 34 (tac)
[10:41:30] 1 tRNA-Met [2733,2806] 34 (cat)
[10:41:30] 1 tRNA-Leu [13019,13106] 35 (gag)
[10:41:30] 1 tRNA-Thr [5855,5928] 34 (tgt)
[10:41:30] 1 tRNA-Lys c[2725,2798] 34 (ttt)
[10:41:30] 2 tRNA-Ala [3140,3215] 34 (tgc)
[10:41:30] 1 tRNA-Ile c[2730,2806] 35 (gat)
[10:41:30] 1 tRNA-Trp c[8154,8227] 34 (cca)
[10:41:30] 1 tRNA-Ser [2802,2887] 35 (cag)
[10:41:30] 1 tRNA-Thr [599,672] 34 (ggt)
[10:41:30] 1 tRNA-Gln c[768,842] 33 (ttg)
[10:41:30] Found 16 tRNAs
[10:41:30] Predicting Ribosomal RNAs
[10:41:30] Running Barrnap with 8 threads
[10:41:30] Found 0 rRNAs
[10:41:30] Skipping ncRNA search, enable with --rfam if desired.
[10:41:30] Total of 16 tRNA + rRNA features
[10:41:30] Searching for CRISPR repeats
[10:41:31] Found 0 CRISPRs
[10:41:31] Predicting coding sequences
[10:41:31] Contigs total 867873 bp, so using single mode
[10:41:31] Running: prodigal -i \/home\/yquentin\/work\/wolbachia\/prokka\/wMuni\/wMuni\.fna -c -m -g 11 -p single -f sco -q
[10:41:31] Excluding CDS which overlaps existing RNA (tRNA) at gnl|Prokka|wMuni_contig000034:1441..2733 on + strand
[10:41:31] Excluding CDS which overlaps existing RNA (tRNA) at gnl|Prokka|wMuni_contig000053:1453..2757 on - strand
[10:41:32] Excluding CDS which overlaps existing RNA (tRNA) at gnl|Prokka|wMuni_contig000186:125..706 on + strand
[10:41:32] Excluding CDS which overlaps existing RNA (tRNA) at gnl|Prokka|wMuni_contig000202:833..1168 on - strand
[10:41:32] Found 840 CDS
[10:41:32] Connecting features back to sequences
[10:41:32] Option --gram not specified, will NOT check for signal peptides.
[10:41:32] Not using genus-specific database. Try --usegenus to enable it.
[10:41:32] Annotating CDS, please be patient.
[10:41:32] Will use 8 CPUs for similarity searching.
[10:41:32] There are still 840 unannotated CDS left (started with 840)
[10:41:32] Will use blast to search against /usr/local/bioinfo/src/PROKKA/prokka-1.10/bin/../db/kingdom/Bacteria/sprot with 8 CPUs
[10:41:32] Running: cat \/home\/yquentin\/work\/wolbachia\/prokka\/wMuni\/proteins\.faa | parallel --gnu -j 8 --block 12919 --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\/wMuni\/proteins\.bls 2> /dev/null
[10:41:39] Modify product: Probable phospholipid ABC transporter-binding protein MlaD => putative phospholipid ABC transporter-binding protein MlaD
[10:41:39] Modify product: Bifunctional protein FolD => Bifunctional protein FolD protein
[10:41:39] Modify product: Actin-binding protein Smlt3054 => Actin-binding protein
[10:41:39] Modify product: Probable transcriptional regulatory protein aq_1575 => putative transcriptional regulatory protein
[10:41:40] Modify product: Co-chaperone protein HscB homolog => hypothetical protein
[10:41:40] Modify product: Transcription termination factor Rho => hypothetical protein
[10:41:40] Modify product: Transcription termination/antitermination protein NusA => hypothetical protein
[10:41:40] Modify product: SCO1 protein homolog => hypothetical protein
[10:41:40] Modify product: Probable phospholipid ABC transporter permease protein MlaE => putative phospholipid ABC transporter permease protein MlaE
[10:41:40] Modify product: Probable ribonucleotide transport ATP-binding protein mkl => putative ribonucleotide transport ATP-binding protein mkl
[10:41:40] Modify product: Probable chromosome-partitioning protein ParB => putative chromosome-partitioning protein ParB
[10:41:40] Modify product: Uncharacterized oxidoreductase YciK => putative oxidoreductase YciK
[10:41:40] Modify product: Probable peroxiredoxin => putative peroxiredoxin
[10:41:40] Modify product: Uncharacterized metal-dependent hydrolase YcfH => putative metal-dependent hydrolase YcfH
[10:41:40] Modify product: Uncharacterized HIT-like protein HP_0404 => putative HIT-like protein
[10:41:40] Modify product: Transcription termination/antitermination protein NusG => hypothetical protein
[10:41:40] Modify product: Probable acyltransferase YihG => putative acyltransferase YihG
[10:41:40] Modify product: Probable protein kinase UbiB => putative protein kinase UbiB
[10:41:40] Modify product: Probable GTP-binding protein EngB => putative GTP-binding protein EngB
[10:41:40] Modify product: Putative multidrug export ATP-binding/permease protein SAV1866 => Putative multidrug export ATP-binding/permease protein
[10:41:40] Modify product: GTP-binding protein TypA/BipA homolog => hypothetical protein
[10:41:40] Modify product: Actin-binding protein Smlt3054 => Actin-binding protein
[10:41:40] Modify product: Probable tRNA-dihydrouridine synthase => putative tRNA-dihydrouridine synthase
[10:41:40] Cleaned 23 /product names
[10:41:40] Deleting unwanted file: /home/yquentin/work/wolbachia/prokka/wMuni/proteins.faa
[10:41:40] Deleting unwanted file: /home/yquentin/work/wolbachia/prokka/wMuni/proteins.bls
[10:41:41] There are still 408 unannotated CDS left (started with 840)
[10:41:41] Will use hmmer3 to search against /usr/local/bioinfo/src/PROKKA/prokka-1.10/bin/../db/hmm/HAMAP.hmm with 8 CPUs
[10:41:41] Running: cat \/home\/yquentin\/work\/wolbachia\/prokka\/wMuni\/proteins\.faa | parallel --gnu -j 8 --block 4473 --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\/wMuni\/proteins\.bls 2> /dev/null
[10:41:48] Deleting unwanted file: /home/yquentin/work/wolbachia/prokka/wMuni/proteins.faa
[10:41:48] Deleting unwanted file: /home/yquentin/work/wolbachia/prokka/wMuni/proteins.bls
[10:41:48] There are still 378 unannotated CDS left (started with 840)
[10:41:48] Will use hmmer3 to search against /usr/local/bioinfo/src/PROKKA/prokka-1.10/bin/../db/hmm/CLUSTERS.hmm with 8 CPUs
[10:41:48] Running: cat \/home\/yquentin\/work\/wolbachia\/prokka\/wMuni\/proteins\.faa | parallel --gnu -j 8 --block 3908 --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\/wMuni\/proteins\.bls 2> /dev/null
[10:42:10] Deleting unwanted file: /home/yquentin/work/wolbachia/prokka/wMuni/proteins.faa
[10:42:10] Deleting unwanted file: /home/yquentin/work/wolbachia/prokka/wMuni/proteins.bls
[10:42:10] There are still 364 unannotated CDS left (started with 840)
[10:42:10] Will use hmmer3 to search against /usr/local/bioinfo/src/PROKKA/prokka-1.10/bin/../db/hmm/Pfam.hmm with 8 CPUs
[10:42:10] Running: cat \/home\/yquentin\/work\/wolbachia\/prokka\/wMuni\/proteins\.faa | parallel --gnu -j 8 --block 3724 --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\/wMuni\/proteins\.bls 2> /dev/null
[10:42:35] Modify product: Bacterial SH3 domain => Bacterial SH3 domain protein
[10:42:35] Modify product: KAP family P-loop domain => KAP family P-loop domain protein
[10:42:35] Modify product: Tetratricopeptide repeat => Tetratricopeptide repeat protein
[10:42:35] Modify product: Piwi/Argonaute/Zwille siRNA-binding domain => Piwi/Argonaute/Zwille siRNA-binding domain protein
[10:42:35] Modify product: TrbC/VIRB2 family => TrbC/VIRB2 family protein
[10:42:35] Modify product: Transposase DDE domain => Transposase DDE domain protein
[10:42:35] Modify product: SPFH domain / Band 7 family => SPFH domain / Band 7 family protein
[10:42:35] Modify product: Transposase IS200 like => Transposase IS200 like protein
[10:42:35] Modify product: Transposase IS200 like => Transposase IS200 like protein
[10:42:35] Modify product: Transposase IS200 like => Transposase IS200 like protein
[10:42:35] Modify product: Sodium:dicarboxylate symporter family => Sodium:dicarboxylate symporter family protein
[10:42:35] Modify product: Transposase IS200 like => Transposase IS200 like protein
[10:42:35] Modify product: Transposase IS200 like => Transposase IS200 like protein
[10:42:35] Modify product: Transposase IS200 like => Transposase IS200 like protein
[10:42:35] Modify product: Ankyrin repeat => Ankyrin repeat protein
[10:42:35] Modify product: Transposase DDE domain => Transposase DDE domain protein
[10:42:35] Modify product: Transposase DDE domain => Transposase DDE domain protein
[10:42:35] Modify product: Transposase DDE domain => Transposase DDE domain protein
[10:42:35] Modify product: Transposase IS200 like => Transposase IS200 like protein
[10:42:35] Modify product: Transposase DDE domain => Transposase DDE domain protein
[10:42:35] Modify product: Transposase DDE domain => Transposase DDE domain protein
[10:42:35] Modify product: Transposase IS116/IS110/IS902 family => Transposase IS116/IS110/IS902 family protein
[10:42:35] Modify product: Transposase DDE domain => Transposase DDE domain protein
[10:42:35] Modify product: Transposase DDE domain => Transposase DDE domain protein
[10:42:35] Modify product: Transposase IS200 like => Transposase IS200 like protein
[10:42:35] Modify product: TrbC/VIRB2 family => TrbC/VIRB2 family protein
[10:42:35] Modify product: Transposase IS200 like => Transposase IS200 like protein
[10:42:35] Modify product: Transposase IS200 like => Transposase IS200 like protein
[10:42:35] Modify product: Transposase IS200 like => Transposase IS200 like protein
[10:42:35] Modify product: Transposase IS200 like => Transposase IS200 like protein
[10:42:35] Modify product: Transposase DDE domain => Transposase DDE domain protein
[10:42:35] Modify product: RDD family => RDD family protein
[10:42:35] Modify product: RDD family => RDD family protein
[10:42:35] Modify product: RDD family => RDD family protein
[10:42:35] Modify product: Transposase DDE domain => Transposase DDE domain protein
[10:42:35] Modify product: Tim44-like domain => Tim44-like domain protein
[10:42:35] Modify product: Uracil DNA glycosylase superfamily => Uracil DNA glycosylase superfamily protein
[10:42:35] Modify product: ETC complex I subunit conserved region => hypothetical protein
[10:42:35] Modify product: Integrase core domain => Integrase core domain protein
[10:42:35] Modify product: Transposase DDE domain => Transposase DDE domain protein
[10:42:35] Modify product: TrbC/VIRB2 family => TrbC/VIRB2 family protein
[10:42:35] Modify product: Transposase DDE domain => Transposase DDE domain protein
[10:42:35] Modify product: Acetyltransferase (GNAT) family => Acetyltransferase (GNAT) family protein
[10:42:35] Modify product: Transposase IS200 like => Transposase IS200 like protein
[10:42:35] Modify product: MgtE intracellular N domain => MgtE intracellular N domain protein
[10:42:35] Modify product: Transposase DDE domain => Transposase DDE domain protein
[10:42:35] Modify product: Transposase IS200 like => Transposase IS200 like protein
[10:42:35] Modify product: Transposase IS200 like => Transposase IS200 like protein
[10:42:35] Modify product: Transposase IS200 like => Transposase IS200 like protein
[10:42:35] Modify product: Integral membrane protein TerC family => Integral membrane protein TerC family protein
[10:42:35] Modify product: YGGT family => YGGT family protein
[10:42:35] Modify product: Transposase IS116/IS110/IS902 family => Transposase IS116/IS110/IS902 family protein
[10:42:35] Modify product: Transposase DDE domain => Transposase DDE domain protein
[10:42:35] Modify product: Transposase IS116/IS110/IS902 family => Transposase IS116/IS110/IS902 family protein
[10:42:35] Modify product: Transposase IS200 like => Transposase IS200 like protein
[10:42:35] Modify product: Alpha/beta hydrolase family => Alpha/beta hydrolase family protein
[10:42:35] Modify product: TENA/THI-4/PQQC family => TENA/THI-4/PQQC family protein
[10:42:35] Modify product: PAS domain => PAS domain protein
[10:42:35] Modify product: Zinc-finger domain => Zinc-finger domain protein
[10:42:35] Modify product: COQ9 => hypothetical protein
[10:42:35] Cleaned 60 /product names
[10:42:35] Deleting unwanted file: /home/yquentin/work/wolbachia/prokka/wMuni/proteins.faa
[10:42:35] Deleting unwanted file: /home/yquentin/work/wolbachia/prokka/wMuni/proteins.bls
[10:42:35] Labelling remaining 255 proteins as 'hypothetical protein'
[10:42:35] Possible /pseudo 'Multidrug resistance protein MdtL' at gnl|Prokka|wMuni_contig000003 position 5869
[10:42:35] Possible /pseudo 'PD-(D/E)XK nuclease family transposase' at gnl|Prokka|wMuni_contig000006 position 2708
[10:42:35] Possible /pseudo 'Transposase IS200 like protein' at gnl|Prokka|wMuni_contig000007 position 4774
[10:42:35] Possible /pseudo 'Arginine--tRNA ligase' at gnl|Prokka|wMuni_contig000031 position 39654
[10:42:35] Possible /pseudo 'Arginine--tRNA ligase' at gnl|Prokka|wMuni_contig000031 position 40110
[10:42:35] Possible /pseudo 'RDD family protein' at gnl|Prokka|wMuni_contig000034 position 8411
[10:42:35] Possible /pseudo 'Quaternary ammonium compound-resistance protein SugE' at gnl|Prokka|wMuni_contig000037 position 13569
[10:42:35] Possible /pseudo 'Dephospho-CoA kinase' at gnl|Prokka|wMuni_contig000044 position 1944
[10:42:35] Possible /pseudo 'Membrane protein insertase YidC' at gnl|Prokka|wMuni_contig000047 position 1044
[10:42:35] Possible /pseudo 'Threonine--tRNA ligase' at gnl|Prokka|wMuni_contig000053 position 684
[10:42:35] Possible /pseudo 'Transposase IS200 like protein' at gnl|Prokka|wMuni_contig000055 position 5439
[10:42:35] Found 412 unique /gene codes.
[10:42:35] Fixed 18 colliding /gene names.
[10:42:35] Adding /locus_tag identifiers
[10:42:35] Assigned 856 locus_tags to CDS and RNA features.
[10:42:35] Writing outputs to /home/yquentin/work/wolbachia/prokka/wMuni/
[10:42:36] Generating annotation statistics file
[10:42:36] Generating Genbank and Sequin files
[10:42:36] 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\/wMuni\/wMuni\.err -i \/home\/yquentin\/work\/wolbachia\/prokka\/wMuni\/wMuni\.fsa 2> /dev/null
[10:42:39] Deleting unwanted file: /home/yquentin/work/wolbachia/prokka/wMuni/errorsummary.val
[10:42:39] Deleting unwanted file: /home/yquentin/work/wolbachia/prokka/wMuni/wMuni.dr
[10:42:39] Deleting unwanted file: /home/yquentin/work/wolbachia/prokka/wMuni/wMuni.fixedproducts
[10:42:39] Deleting unwanted file: /home/yquentin/work/wolbachia/prokka/wMuni/wMuni.ecn
[10:42:39] Deleting unwanted file: /home/yquentin/work/wolbachia/prokka/wMuni/wMuni.val
[10:42:39] Output files:
[10:42:39] /home/yquentin/work/wolbachia/prokka/wMuni/wMuni.sqn
[10:42:39] /home/yquentin/work/wolbachia/prokka/wMuni/wMuni.fsa
[10:42:39] /home/yquentin/work/wolbachia/prokka/wMuni/wMuni.fna
[10:42:39] /home/yquentin/work/wolbachia/prokka/wMuni/wMuni.gbk
[10:42:39] /home/yquentin/work/wolbachia/prokka/wMuni/wMuni.tbl
[10:42:39] /home/yquentin/work/wolbachia/prokka/wMuni/wMuni.err
[10:42:39] /home/yquentin/work/wolbachia/prokka/wMuni/wMuni.txt
[10:42:39] /home/yquentin/work/wolbachia/prokka/wMuni/wMuni.log
[10:42:39] /home/yquentin/work/wolbachia/prokka/wMuni/wMuni.ffn
[10:42:39] /home/yquentin/work/wolbachia/prokka/wMuni/wMuni.faa
[10:42:39] /home/yquentin/work/wolbachia/prokka/wMuni/wMuni.gff
[10:42:39] Walltime used: 1.18 minutes
[10:42:39] If you use this result please cite the Prokka paper:
[10:42:39] Seemann T (2014) Prokka: rapid prokaryotic genome annotation. Bioinformatics. 30(14):2068-9.
[10:42:39] Type 'prokka --citation' for more details.
[10:42:39] Share and enjoy!