[15:06:59] Command: --force --outdir /home/yquentin/work/wolbachia/prokka/wObr --addgenes --prefix wObr --locustag wObr --species Wolbachia endosymbiont --strain wObr --compliant --quiet /home/yquentin/work/wolbachia/prokka/wObr.fna
[15:06:59] Looking for 'aragorn' - found /usr/local/bioinfo/bin/aragorn
[15:06:59] Determined aragorn version is 1.2
[15:06:59] Looking for 'barrnap' - found /usr/local/bioinfo/bin/barrnap
[15:06:59] Determined barrnap version is 0.5
[15:06:59] Looking for 'blastp' - found /usr/local/bioinfo/src/NCBI_Blast+/ncbi-blast-2.6.0+/bin/blastp
[15:06:59] Determined blastp version is 2.6
[15:06:59] Looking for 'cmpress' - found /usr/local/bioinfo/src/PROKKA/prokka-1.10/bin/../binaries/linux/cmpress
[15:06:59] Determined cmpress version is 1.1
[15:06:59] Looking for 'cmscan' - found /usr/local/bioinfo/src/PROKKA/prokka-1.10/bin/../binaries/linux/cmscan
[15:06:59] Determined cmscan version is 1.1
[15:06:59] Looking for 'egrep' - found /bin/egrep
[15:06:59] Looking for 'find' - found /bin/find
[15:06:59] Looking for 'grep' - found /bin/grep
[15:06:59] Looking for 'hmmpress' - found /usr/local/bioinfo/bin/hmmpress
[15:06:59] Determined hmmpress version is 3.1
[15:06:59] Looking for 'hmmscan' - found /usr/local/bioinfo/bin/hmmscan
[15:06:59] Determined hmmscan version is 3.1
[15:06:59] Looking for 'less' - found /usr/bin/less
[15:06:59] Looking for 'makeblastdb' - found /usr/local/bioinfo/src/NCBI_Blast+/ncbi-blast-2.6.0+/bin/makeblastdb
[15:06:59] Determined makeblastdb version is 2.6
[15:06:59] Looking for 'minced' - found /usr/local/bioinfo/bin/minced
[15:07:00] Determined minced version is 1.6
[15:07:00] Looking for 'parallel' - found /usr/local/bioinfo/bin/parallel
[15:07:00] Determined parallel version is 20141022
[15:07:00] Looking for 'prodigal' - found /usr/local/bioinfo/bin/prodigal
[15:07:01] Determined prodigal version is 2.6
[15:07:01] Looking for 'rnammer' - found /usr/local/bioinfo/bin/rnammer
[15:07:01] Determined rnammer version is 1.2
[15:07:01] Looking for 'sed' - found /bin/sed
[15:07:01] Looking for 'signalp' - found /usr/local/bioinfo/bin/signalp
[15:07:01] Determined signalp version is 4.1
[15:07:01] Looking for 'tbl2asn' - found /home/yquentin/save/scripts/tbl2asn
[15:07:01] Determined tbl2asn version is 25.3
[15:07:01] Using genetic code table 11.
[15:07:01] Loading and checking input file: /home/yquentin/work/wolbachia/prokka/wObr.fna
[15:07:01] Wrote 120 contigs
[15:07:01] Predicting tRNAs and tmRNAs
[15:07:01] Running: aragorn -gc11  -w \/home\/yquentin\/work\/wolbachia\/prokka\/wObr\/wObr\.fna
[15:07:02] 1 tRNA-Thr c[3387,3460] 34 (tgt)
[15:07:02] 1 tRNA-Arg [1411,1486] 36 (tct)
[15:07:02] 1 tRNA-Trp [1198,1271] 34 (cca)
[15:07:02] 1 tRNA-Val [1705,1778] 34 (gac)
[15:07:02] 1 tRNA-Arg [2641,2718] 36 (acg)
[15:07:02] 2 tRNA-Leu [14144,14230] 35 (taa)
[15:07:02] 1 tRNA-Cys [1942,2014] 34 (gca)
[15:07:02] 1 tRNA-Leu [3842,3925] 34 (caa)
[15:07:02] 1 tRNA-Ile [572,648] 35 (gat)
[15:07:02] 1 tRNA-Gly c[64,137] 34 (gcc)
[15:07:02] 2 tRNA-Met [1354,1430] 35 (cat)
[15:07:02] 1 tRNA-Asn [1232,1304] 33 (gtt)
[15:07:02] 1 tRNA-His c[1025,1100] 34 (gtg)
[15:07:02] 1 tRNA-Gln c[989,1061] 33 (ttg)
[15:07:02] 2 tRNA-Met c[2021,2093] 33 (cat)
[15:07:02] 1 tRNA-Ser c[18511,18598] 35 (gga)
[15:07:02] 1 tRNA-Met c[24168,24244] 35 (cat)
[15:07:02] 1 tRNA-Ser c[7840,6] 35 (gct)
[15:07:02] tRNA c[7840,6] has start(7840) > end (6) - skipping.
[15:07:02] 1 tRNA-Ser c[4010,4098] 35 (tga)
[15:07:02] 2 tRNA-Lys c[10065,10138] 34 (ttt)
[15:07:02] 3 tRNA-Ala [10439,10514] 34 (tgc)
[15:07:02] 1 tRNA-Thr [153,227] 35 (ggt)
[15:07:02] 1 tRNA-Leu [6991,7073] 35 (tag)
[15:07:02] 1 tRNA-Val c[5980,6052] 34 (tac)
[15:07:02] 2 tRNA-Pro c[13112,13187] 36 (tgg)
[15:07:02] 3 tRNA-Glu c[14036,14108] 34 (ttc)
[15:07:02] 1 tRNA-Phe c[2159,2232] 34 (gaa)
[15:07:02] 1 tRNA-Arg c[3903,3977] 35 (cct)
[15:07:02] 1 tRNA-Leu c[7569,7656] 35 (gag)
[15:07:02] 2 tRNA-Asp [17858,17934] 35 (gtc)
[15:07:02] 3 tRNA-Gly c[77867,77938] 33 (tcc)
[15:07:02] 4 tRNA-Tyr c[77942,78025] 36 (gta)
[15:07:02] Found 31 tRNAs
[15:07:02] Predicting Ribosomal RNAs
[15:07:02] Running Barrnap with 8 threads
[15:07:03] 1 gnl|Prokka|wObr_contig000003 23546 16S ribosomal RNA
[15:07:03] 2 gnl|Prokka|wObr_contig000021 8483 23S ribosomal RNA (partial)
[15:07:03] 3 gnl|Prokka|wObr_contig000052 4962 5S ribosomal RNA
[15:07:03] Found 3 rRNAs
[15:07:03] Skipping ncRNA search, enable with --rfam if desired.
[15:07:03] Total of 34 tRNA + rRNA features
[15:07:03] Searching for CRISPR repeats
[15:07:04] Found 0 CRISPRs
[15:07:04] Predicting coding sequences
[15:07:04] Contigs total 1121046 bp, so using single mode
[15:07:04] Running: prodigal -i \/home\/yquentin\/work\/wolbachia\/prokka\/wObr\/wObr\.fna -c -m -g 11 -p single -f sco -q
[15:07:05] Excluding CDS which overlaps existing RNA (rRNA) at gnl|Prokka|wObr_contig000003:24692..24943 on + strand
[15:07:06] Excluding CDS which overlaps existing RNA (tRNA) at gnl|Prokka|wObr_contig000032:1052..1387 on - strand
[15:07:06] Excluding CDS which overlaps existing RNA (tRNA) at gnl|Prokka|wObr_contig000032:1969..2097 on - strand
[15:07:06] Excluding CDS which overlaps existing RNA (tRNA) at gnl|Prokka|wObr_contig000032:2084..3385 on - strand
[15:07:06] Excluding CDS which overlaps existing RNA (tRNA) at gnl|Prokka|wObr_contig000100:124..273 on + strand
[15:07:06] Found 1027 CDS
[15:07:06] Connecting features back to sequences
[15:07:06] Option --gram not specified, will NOT check for signal peptides.
[15:07:06] Not using genus-specific database. Try --usegenus to enable it.
[15:07:06] Annotating CDS, please be patient.
[15:07:06] Will use 8 CPUs for similarity searching.
[15:07:08] There are still 1027 unannotated CDS left (started with 1027)
[15:07:08] Will use blast to search against /usr/local/bioinfo/src/PROKKA/prokka-1.10/bin/../db/kingdom/Bacteria/sprot with 8 CPUs
[15:07:08] Running: cat \/home\/yquentin\/work\/wolbachia\/prokka\/wObr\/proteins\.faa | parallel --gnu -j 8 --block 19139 --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\/wObr\/proteins\.bls 2> /dev/null
[15:07:37] Modify product: Uncharacterized metal-dependent hydrolase YcfH => putative metal-dependent hydrolase YcfH
[15:07:37] Modify product: Actin-binding protein Smlt3054 => Actin-binding protein
[15:07:37] Modify product: Transcription termination/antitermination protein NusG => hypothetical protein
[15:07:37] Modify product: Cytochrome b561 homolog 2 => hypothetical protein
[15:07:37] Modify product: SCO1 protein homolog => hypothetical protein
[15:07:37] Modify product: Transcription termination factor Rho => hypothetical protein
[15:07:37] Modify product: Actin-binding protein Smlt3054 => Actin-binding protein
[15:07:37] Modify product: Uncharacterized zinc protease Rv2782c => putative zinc protease
[15:07:37] Modify product: Uncharacterized zinc protease Rv2782c => putative zinc protease
[15:07:37] Modify product: Actin-binding protein Smlt3054 => Actin-binding protein
[15:07:37] Modify product: Bifunctional protein FolD => Bifunctional protein FolD protein
[15:07:37] Modify product: Uncharacterized zinc protease Rv2782c => putative zinc protease
[15:07:38] Modify product: Probable murein peptide carboxypeptidase => putative murein peptide carboxypeptidase
[15:07:38] Modify product: Actin-binding protein Smlt3054 => Actin-binding protein
[15:07:38] Modify product: Transcription termination/antitermination protein NusA => hypothetical protein
[15:07:38] Modify product: Probable tRNA-dihydrouridine synthase => putative tRNA-dihydrouridine synthase
[15:07:38] Modify product: Probable GTP-binding protein EngB => putative GTP-binding protein EngB
[15:07:38] Modify product: Co-chaperone protein HscB homolog => hypothetical protein
[15:07:38] Modify product: Probable phospholipid ABC transporter-binding protein MlaD => putative phospholipid ABC transporter-binding protein MlaD
[15:07:38] Modify product: Probable protein kinase UbiB => putative protein kinase UbiB
[15:07:38] Modify product: Probable peroxiredoxin => putative peroxiredoxin
[15:07:38] Modify product: Probable ribonucleotide transport ATP-binding protein mkl => putative ribonucleotide transport ATP-binding protein mkl
[15:07:38] Modify product: Probable phospholipid ABC transporter permease protein MlaE => putative phospholipid ABC transporter permease protein MlaE
[15:07:38] Modify product: N utilization substance protein B homolog => hypothetical protein
[15:07:38] Modify product: Uncharacterized oxidoreductase YciK => putative oxidoreductase YciK
[15:07:38] Modify product: Probable chromosome-partitioning protein ParB => putative chromosome-partitioning protein ParB
[15:07:39] Modify product: Stringent starvation protein A homolog => hypothetical protein
[15:07:39] Modify product: Probable acyltransferase YihG => putative acyltransferase YihG
[15:07:39] Modify product: Riboflavin biosynthesis protein VVA0006 => Riboflavin biosynthesis protein
[15:07:39] Modify product: Putative multidrug export ATP-binding/permease protein SAV1866 => Putative multidrug export ATP-binding/permease protein
[15:07:39] Modify product: Probable transcriptional regulatory protein aq_1575 => putative transcriptional regulatory protein
[15:07:39] Modify product: Uncharacterized oxidoreductase Rv0945 => putative oxidoreductase
[15:07:39] Cleaned 32 /product names
[15:07:39] Deleting unwanted file: /home/yquentin/work/wolbachia/prokka/wObr/proteins.faa
[15:07:39] Deleting unwanted file: /home/yquentin/work/wolbachia/prokka/wObr/proteins.bls
[15:07:39] There are still 450 unannotated CDS left (started with 1027)
[15:07:39] Will use hmmer3 to search against /usr/local/bioinfo/src/PROKKA/prokka-1.10/bin/../db/hmm/HAMAP.hmm with 8 CPUs
[15:07:39] Running: cat \/home\/yquentin\/work\/wolbachia\/prokka\/wObr\/proteins\.faa | parallel --gnu -j 8 --block 6406 --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\/wObr\/proteins\.bls 2> /dev/null
[15:07:53] Deleting unwanted file: /home/yquentin/work/wolbachia/prokka/wObr/proteins.faa
[15:07:53] Deleting unwanted file: /home/yquentin/work/wolbachia/prokka/wObr/proteins.bls
[15:07:53] There are still 424 unannotated CDS left (started with 1027)
[15:07:53] Will use hmmer3 to search against /usr/local/bioinfo/src/PROKKA/prokka-1.10/bin/../db/hmm/CLUSTERS.hmm with 8 CPUs
[15:07:53] Running: cat \/home\/yquentin\/work\/wolbachia\/prokka\/wObr\/proteins\.faa | parallel --gnu -j 8 --block 5906 --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\/wObr\/proteins\.bls 2> /dev/null
[15:08:26] Deleting unwanted file: /home/yquentin/work/wolbachia/prokka/wObr/proteins.faa
[15:08:26] Deleting unwanted file: /home/yquentin/work/wolbachia/prokka/wObr/proteins.bls
[15:08:27] There are still 406 unannotated CDS left (started with 1027)
[15:08:27] Will use hmmer3 to search against /usr/local/bioinfo/src/PROKKA/prokka-1.10/bin/../db/hmm/Pfam.hmm with 8 CPUs
[15:08:27] Running: cat \/home\/yquentin\/work\/wolbachia\/prokka\/wObr\/proteins\.faa | parallel --gnu -j 8 --block 5645 --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\/wObr\/proteins\.bls 2> /dev/null
[15:09:01] Modify product: COQ9 => hypothetical protein
[15:09:01] Modify product: Transposase DDE domain => Transposase DDE domain protein
[15:09:01] Modify product: DSBA-like thioredoxin domain => DSBA-like thioredoxin domain protein
[15:09:01] Modify product: Ankyrin repeat => Ankyrin repeat protein
[15:09:01] Modify product: Alpha/beta hydrolase family => Alpha/beta hydrolase family protein
[15:09:01] Modify product: Na+/H+ antiporter family => Na+/H+ antiporter family protein
[15:09:01] Modify product: Alpha/beta hydrolase family => Alpha/beta hydrolase family protein
[15:09:01] Modify product: Piwi/Argonaute/Zwille siRNA-binding domain => Piwi/Argonaute/Zwille siRNA-binding domain protein
[15:09:01] Modify product: Major Facilitator Superfamily => Major Facilitator Superfamily protein
[15:09:01] Modify product: Ankyrin repeat => Ankyrin repeat protein
[15:09:01] Modify product: Sodium:dicarboxylate symporter family => Sodium:dicarboxylate symporter family protein
[15:09:01] Modify product: Na+/H+ antiporter family => Na+/H+ antiporter family protein
[15:09:01] Modify product: RmlD substrate binding domain => RmlD substrate binding domain protein
[15:09:01] Modify product: Transposase IS200 like => Transposase IS200 like protein
[15:09:01] Modify product: TrbC/VIRB2 family => TrbC/VIRB2 family protein
[15:09:01] Modify product: DnaJ domain => DnaJ domain protein
[15:09:01] Modify product: Transposase IS200 like => Transposase IS200 like protein
[15:09:01] Modify product: Transposase DDE domain => Transposase DDE domain protein
[15:09:01] Modify product: PD-(D/E)XK nuclease superfamily => PD-(D/E)XK nuclease superfamily protein
[15:09:01] Modify product: Tim44-like domain => Tim44-like domain protein
[15:09:01] Modify product: RDD family => RDD family protein
[15:09:01] Modify product: YGGT family => YGGT family protein
[15:09:01] Modify product: EVE domain => EVE domain protein
[15:09:01] Modify product: AhpC/TSA family => AhpC/TSA family protein
[15:09:01] Modify product: Ankyrin repeat => Ankyrin repeat protein
[15:09:01] Modify product: Transposase IS66 family => Transposase IS66 family protein
[15:09:01] Modify product: Phage capsid family => Phage capsid family protein
[15:09:01] Modify product: PAS domain => PAS domain protein
[15:09:02] Modify product: Phosphotransferase enzyme family => Phosphotransferase enzyme family protein
[15:09:02] Modify product: KAP family P-loop domain => KAP family P-loop domain protein
[15:09:02] Modify product: Transposase IS200 like => Transposase IS200 like protein
[15:09:02] Modify product: RDD family => RDD family protein
[15:09:02] Modify product: SURF1 family => SURF1 family protein
[15:09:02] Modify product: Terminase-like family => Terminase-like family protein
[15:09:02] Modify product: Uracil DNA glycosylase superfamily => Uracil DNA glycosylase superfamily protein
[15:09:02] Modify product: ETC complex I subunit conserved region => hypothetical protein
[15:09:02] Modify product: Integral membrane protein TerC family => Integral membrane protein TerC family protein
[15:09:02] Modify product: SPFH domain / Band 7 family => SPFH domain / Band 7 family protein
[15:09:02] Modify product: TrbC/VIRB2 family => TrbC/VIRB2 family protein
[15:09:02] Modify product: Alpha/beta hydrolase family => Alpha/beta hydrolase family protein
[15:09:02] Cleaned 40 /product names
[15:09:02] Deleting unwanted file: /home/yquentin/work/wolbachia/prokka/wObr/proteins.faa
[15:09:02] Deleting unwanted file: /home/yquentin/work/wolbachia/prokka/wObr/proteins.bls
[15:09:02] Labelling remaining 297 proteins as 'hypothetical protein'
[15:09:02] Possible /pseudo 'putative zinc protease' at gnl|Prokka|wObr_contig000001 position 33616
[15:09:02] Possible /pseudo 'Amino-acid carrier protein AlsT' at gnl|Prokka|wObr_contig000008 position 6624
[15:09:02] Possible /pseudo 'Aminopyrimidine aminohydrolase' at gnl|Prokka|wObr_contig000021 position 2669
[15:09:02] Possible /pseudo 'TrbL/VirB6 plasmid conjugal transfer protein' at gnl|Prokka|wObr_contig000030 position 4644
[15:09:02] Possible /pseudo 'TrbL/VirB6 plasmid conjugal transfer protein' at gnl|Prokka|wObr_contig000030 position 7541
[15:09:02] Possible /pseudo 'TrbL/VirB6 plasmid conjugal transfer protein' at gnl|Prokka|wObr_contig000030 position 9931
[15:09:02] Possible /pseudo 'Ankyrin repeats (3 copies)' at gnl|Prokka|wObr_contig000040 position 2271
[15:09:02] Possible /pseudo 'Arginine/agmatine antiporter' at gnl|Prokka|wObr_contig000040 position 9503
[15:09:02] Possible /pseudo 'Exopolysaccharide synthesis, ExoD' at gnl|Prokka|wObr_contig000041 position 14933
[15:09:02] Possible /pseudo 'Transposase, Mutator family' at gnl|Prokka|wObr_contig000118 position 3291
[15:09:02] Possible /pseudo 'Glutamine--fructose-6-phosphate aminotransferase [isomerizing]' at gnl|Prokka|wObr_contig000120 position 19520
[15:09:02] Found 525 unique /gene codes.
[15:09:02] Fixed 24 colliding /gene names.
[15:09:02] Adding /locus_tag identifiers
[15:09:02] Assigned 1061 locus_tags to CDS and RNA features.
[15:09:02] Writing outputs to /home/yquentin/work/wolbachia/prokka/wObr/
[15:09:06] Generating annotation statistics file
[15:09:06] Generating Genbank and Sequin files
[15:09:06] 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\/wObr\/wObr\.err -i \/home\/yquentin\/work\/wolbachia\/prokka\/wObr\/wObr\.fsa 2> /dev/null
[15:09:13] Deleting unwanted file: /home/yquentin/work/wolbachia/prokka/wObr/errorsummary.val
[15:09:13] Deleting unwanted file: /home/yquentin/work/wolbachia/prokka/wObr/wObr.dr
[15:09:13] Deleting unwanted file: /home/yquentin/work/wolbachia/prokka/wObr/wObr.fixedproducts
[15:09:13] Deleting unwanted file: /home/yquentin/work/wolbachia/prokka/wObr/wObr.ecn
[15:09:13] Deleting unwanted file: /home/yquentin/work/wolbachia/prokka/wObr/wObr.val
[15:09:13] Output files:
[15:09:13] /home/yquentin/work/wolbachia/prokka/wObr/wObr.fsa
[15:09:13] /home/yquentin/work/wolbachia/prokka/wObr/wObr.log
[15:09:13] /home/yquentin/work/wolbachia/prokka/wObr/wObr.txt
[15:09:13] /home/yquentin/work/wolbachia/prokka/wObr/wObr.gff
[15:09:13] /home/yquentin/work/wolbachia/prokka/wObr/wObr.ffn
[15:09:13] /home/yquentin/work/wolbachia/prokka/wObr/wObr.err
[15:09:13] /home/yquentin/work/wolbachia/prokka/wObr/wObr.gbk
[15:09:13] /home/yquentin/work/wolbachia/prokka/wObr/wObr.sqn
[15:09:13] /home/yquentin/work/wolbachia/prokka/wObr/wObr.tbl
[15:09:13] /home/yquentin/work/wolbachia/prokka/wObr/wObr.fna
[15:09:13] /home/yquentin/work/wolbachia/prokka/wObr/wObr.faa
[15:09:13] Walltime used: 2.23 minutes
[15:09:13] If you use this result please cite the Prokka paper:
[15:09:13] Seemann T (2014) Prokka: rapid prokaryotic genome annotation. Bioinformatics. 30(14):2068-9.
[15:09:13] Type 'prokka --citation' for more details.
[15:09:13] Thank you, come again.