[15:06:39] Command: --force --outdir /home/yquentin/work/wolbachia/prokka/wCam --addgenes --prefix wCam --locustag wCam --species Wolbachia endosymbiont --strain wCam --compliant --quiet /home/yquentin/work/wolbachia/prokka/wCam.fna
[15:06:39] Looking for 'aragorn' - found /usr/local/bioinfo/bin/aragorn
[15:06:39] Determined aragorn version is 1.2
[15:06:39] Looking for 'barrnap' - found /usr/local/bioinfo/bin/barrnap
[15:06:39] Determined barrnap version is 0.5
[15:06:39] Looking for 'blastp' - found /usr/local/bioinfo/src/NCBI_Blast+/ncbi-blast-2.6.0+/bin/blastp
[15:06:40] Determined blastp version is 2.6
[15:06:40] Looking for 'cmpress' - found /usr/local/bioinfo/src/PROKKA/prokka-1.10/bin/../binaries/linux/cmpress
[15:06:40] Determined cmpress version is 1.1
[15:06:40] Looking for 'cmscan' - found /usr/local/bioinfo/src/PROKKA/prokka-1.10/bin/../binaries/linux/cmscan
[15:06:40] Determined cmscan version is 1.1
[15:06:40] Looking for 'egrep' - found /bin/egrep
[15:06:40] Looking for 'find' - found /bin/find
[15:06:40] Looking for 'grep' - found /bin/grep
[15:06:40] Looking for 'hmmpress' - found /usr/local/bioinfo/bin/hmmpress
[15:06:40] Determined hmmpress version is 3.1
[15:06:40] Looking for 'hmmscan' - found /usr/local/bioinfo/bin/hmmscan
[15:06:40] Determined hmmscan version is 3.1
[15:06:40] Looking for 'less' - found /usr/bin/less
[15:06:40] Looking for 'makeblastdb' - found /usr/local/bioinfo/src/NCBI_Blast+/ncbi-blast-2.6.0+/bin/makeblastdb
[15:06:40] Determined makeblastdb version is 2.6
[15:06:40] Looking for 'minced' - found /usr/local/bioinfo/bin/minced
[15:06:40] Determined minced version is 1.6
[15:06:40] Looking for 'parallel' - found /usr/local/bioinfo/bin/parallel
[15:06:41] Determined parallel version is 20141022
[15:06:41] Looking for 'prodigal' - found /usr/local/bioinfo/bin/prodigal
[15:06:41] Determined prodigal version is 2.6
[15:06:41] Looking for 'rnammer' - found /usr/local/bioinfo/bin/rnammer
[15:06:41] Determined rnammer version is 1.2
[15:06:41] Looking for 'sed' - found /bin/sed
[15:06:41] Looking for 'signalp' - found /usr/local/bioinfo/bin/signalp
[15:06:41] Determined signalp version is 4.1
[15:06:41] Looking for 'tbl2asn' - found /home/yquentin/save/scripts/tbl2asn
[15:06:41] Determined tbl2asn version is 25.3
[15:06:41] Using genetic code table 11.
[15:06:41] Loading and checking input file: /home/yquentin/work/wolbachia/prokka/wCam.fna
[15:06:42] Wrote 1 contigs
[15:06:42] Predicting tRNAs and tmRNAs
[15:06:42] Running: aragorn -gc11  -w \/home\/yquentin\/work\/wolbachia\/prokka\/wCam\/wCam\.fna
[15:06:42] 1 tmRNA* [645,974] 189,239 ANDNFAANSNVVALVA*
[15:06:42] 2 tRNA-Glu [69609,69682] 35 (ttc)
[15:06:42] 3 tRNA-Cys c[72500,72571] 34 (gca)
[15:06:42] 4 tRNA-Arg c[159449,159523] 36 (acg)
[15:06:42] 5 tRNA-Leu c[179923,180006] 34 (caa)
[15:06:42] 6 tRNA-Gln c[195748,195822] 33 (ttg)
[15:06:42] 7 tRNA-Ser c[210610,210695] 35 (cag)
[15:06:42] 8 tRNA-Leu c[271760,271846] 35 (taa)
[15:06:42] 9 tRNA-Leu c[296754,296841] 35 (gag)
[15:06:42] 10 tRNA-Arg c[335424,335499] 36 (tct)
[15:06:42] 11 tRNA-Arg c[395518,395593] 36 (ccg)
[15:06:42] 12 tRNA-Ile c[449788,449864] 35 (gat)
[15:06:42] 13 tRNA-Met c[462734,462807] 34 (cat)
[15:06:42] 14 tRNA-Leu c[494083,494165] 35 (tag)
[15:06:42] 15 tRNA-Phe c[536196,536269] 34 (gaa)
[15:06:42] 16 tRNA-Asp [541923,541997] 35 (gtc)
[15:06:42] 17 tRNA-Gly c[580460,580532] 34 (tcc)
[15:06:42] 18 tRNA-Tyr c[580536,580620] 36 (gta)
[15:06:42] 19 tRNA-Ser c[610788,610880] 36 (gct)
[15:06:42] 20 tRNA-Asn [617251,617325] 34 (gtt)
[15:06:42] 21 tRNA-Thr c[634198,634271] 35 (tgt)
[15:06:42] 22 tRNA-Arg c[653319,653395] 35 (cct)
[15:06:42] 23 tRNA-Ser c[686466,686555] 36 (gga)
[15:06:42] 24 tRNA-Trp [735984,736057] 34 (cca)
[15:06:42] 25 tRNA-His [768366,768439] 34 (gtg)
[15:06:42] 26 tRNA-Met [786230,786304] 35 (cat)
[15:06:42] 27 tRNA-Thr [788698,788771] 34 (ggt)
[15:06:42] 28 tRNA-Pro [812138,812215] 36 (tgg)
[15:06:42] 29 tRNA-Met c[815960,816035] 35 (cat)
[15:06:42] 30 tRNA-Gly [817286,817359] 34 (gcc)
[15:06:42] 31 tRNA-Val c[872868,872940] 34 (tac)
[15:06:42] 32 tRNA-Ser [879341,879430] 36 (tga)
[15:06:42] 33 tRNA-Ala c[914364,914438] 35 (tgc)
[15:06:42] 34 tRNA-Lys [914600,914672] 34 (ttt)
[15:06:42] 35 tRNA-Val c[939579,939652] 34 (gac)
[15:06:42] Found 35 tRNAs
[15:06:42] Predicting Ribosomal RNAs
[15:06:42] Running Barrnap with 8 threads
[15:06:43] 1 gnl|Prokka|wCam_contig000001 558583 16S ribosomal RNA
[15:06:43] 2 gnl|Prokka|wCam_contig000001 668841 5S ribosomal RNA (partial)
[15:06:43] 3 gnl|Prokka|wCam_contig000001 668997 23S ribosomal RNA
[15:06:43] Found 3 rRNAs
[15:06:43] Skipping ncRNA search, enable with --rfam if desired.
[15:06:43] Total of 37 tRNA + rRNA features
[15:06:43] Searching for CRISPR repeats
[15:06:44] Found 0 CRISPRs
[15:06:44] Predicting coding sequences
[15:06:44] Contigs total 960618 bp, so using single mode
[15:06:44] Running: prodigal -i \/home\/yquentin\/work\/wolbachia\/prokka\/wCam\/wCam\.fna -c -m -g 11 -p single -f sco -q
[15:06:46] Excluding CDS which overlaps existing RNA (tRNA) at gnl|Prokka|wCam_contig000001:462770..464101 on - strand
[15:06:47] Excluding CDS which overlaps existing RNA (rRNA) at gnl|Prokka|wCam_contig000001:559524..559646 on - strand
[15:06:47] Found 793 CDS
[15:06:47] Connecting features back to sequences
[15:06:47] Option --gram not specified, will NOT check for signal peptides.
[15:06:47] Not using genus-specific database. Try --usegenus to enable it.
[15:06:47] Annotating CDS, please be patient.
[15:06:47] Will use 8 CPUs for similarity searching.
[15:06:48] There are still 793 unannotated CDS left (started with 793)
[15:06:48] Will use blast to search against /usr/local/bioinfo/src/PROKKA/prokka-1.10/bin/../db/kingdom/Bacteria/sprot with 8 CPUs
[15:06:48] Running: cat \/home\/yquentin\/work\/wolbachia\/prokka\/wCam\/proteins\.faa | parallel --gnu -j 8 --block 14144 --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\/wCam\/proteins\.bls 2> /dev/null
[15:06:59] Modify product: Probable GTP-binding protein EngB => putative GTP-binding protein EngB
[15:06:59] Modify product: Probable dipeptidase PepE => putative dipeptidase PepE
[15:06:59] Modify product: Transcription termination factor Rho => hypothetical protein
[15:06:59] Modify product: Transcription termination/antitermination protein NusA => hypothetical protein
[15:06:59] Modify product: Probable tRNA-dihydrouridine synthase => putative tRNA-dihydrouridine synthase
[15:06:59] Modify product: Uncharacterized zinc protease Rv2782c => putative zinc protease
[15:06:59] Modify product: Uncharacterized zinc protease Rv2782c => putative zinc protease
[15:06:59] Modify product: Probable glycerol-3-phosphate acyltransferase => putative glycerol-3-phosphate acyltransferase
[15:06:59] Modify product: GTP-binding protein TypA/BipA homolog => hypothetical protein
[15:06:59] Modify product: Stringent starvation protein A homolog => hypothetical protein
[15:06:59] Modify product: Putative O-methyltransferase MSMEG_5073/MSMEI_4947 => Putative O-methyltransferase/MSMEI_4947
[15:06:59] Modify product: Uncharacterized metal-dependent hydrolase YcfH => putative metal-dependent hydrolase YcfH
[15:06:59] Modify product: Uncharacterized HIT-like protein HP_0404 => putative HIT-like protein
[15:06:59] Modify product: Probable protein kinase UbiB => putative protein kinase UbiB
[15:06:59] Modify product: Probable transcriptional regulatory protein aq_1575 => putative transcriptional regulatory protein
[15:07:00] Modify product: Uncharacterized ABC transporter ATP-binding protein TM_0288 => putative ABC transporter ATP-binding protein
[15:07:00] Modify product: N utilization substance protein B homolog => hypothetical protein
[15:07:00] Modify product: Uncharacterized oxidoreductase YciK => putative oxidoreductase YciK
[15:07:00] Modify product: Putative NAD(P)H nitroreductase SA2311 => Putative NAD(P)H nitroreductase
[15:07:00] Modify product: SCO1 protein homolog => hypothetical protein
[15:07:00] Modify product: Probable peroxiredoxin => putative peroxiredoxin
[15:07:00] Modify product: Co-chaperone protein HscB homolog => hypothetical protein
[15:07:00] Modify product: Bifunctional protein FolD => Bifunctional protein FolD protein
[15:07:00] Modify product: Uncharacterized zinc protease Rv2782c => putative zinc protease
[15:07:00] Modify product: Cytochrome b561 homolog 2 => hypothetical protein
[15:07:00] Modify product: Transcription termination/antitermination protein NusG => hypothetical protein
[15:07:00] Cleaned 26 /product names
[15:07:00] Deleting unwanted file: /home/yquentin/work/wolbachia/prokka/wCam/proteins.faa
[15:07:00] Deleting unwanted file: /home/yquentin/work/wolbachia/prokka/wCam/proteins.bls
[15:07:01] There are still 283 unannotated CDS left (started with 793)
[15:07:01] Will use hmmer3 to search against /usr/local/bioinfo/src/PROKKA/prokka-1.10/bin/../db/hmm/HAMAP.hmm with 8 CPUs
[15:07:01] Running: cat \/home\/yquentin\/work\/wolbachia\/prokka\/wCam\/proteins\.faa | parallel --gnu -j 8 --block 2933 --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\/wCam\/proteins\.bls 2> /dev/null
[15:07:07] Deleting unwanted file: /home/yquentin/work/wolbachia/prokka/wCam/proteins.faa
[15:07:07] Deleting unwanted file: /home/yquentin/work/wolbachia/prokka/wCam/proteins.bls
[15:07:07] There are still 256 unannotated CDS left (started with 793)
[15:07:07] Will use hmmer3 to search against /usr/local/bioinfo/src/PROKKA/prokka-1.10/bin/../db/hmm/CLUSTERS.hmm with 8 CPUs
[15:07:07] Running: cat \/home\/yquentin\/work\/wolbachia\/prokka\/wCam\/proteins\.faa | parallel --gnu -j 8 --block 2545 --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\/wCam\/proteins\.bls 2> /dev/null
[15:07:25] Deleting unwanted file: /home/yquentin/work/wolbachia/prokka/wCam/proteins.faa
[15:07:25] Deleting unwanted file: /home/yquentin/work/wolbachia/prokka/wCam/proteins.bls
[15:07:25] There are still 238 unannotated CDS left (started with 793)
[15:07:25] Will use hmmer3 to search against /usr/local/bioinfo/src/PROKKA/prokka-1.10/bin/../db/hmm/Pfam.hmm with 8 CPUs
[15:07:25] Running: cat \/home\/yquentin\/work\/wolbachia\/prokka\/wCam\/proteins\.faa | parallel --gnu -j 8 --block 2344 --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\/wCam\/proteins\.bls 2> /dev/null
[15:07:43] Modify product: RDD family => RDD family protein
[15:07:43] Modify product: Acetyltransferase (GNAT) family => Acetyltransferase (GNAT) family protein
[15:07:43] Modify product: RDD family => RDD family protein
[15:07:43] Modify product: SURF1 family => SURF1 family protein
[15:07:43] Modify product: Major Facilitator Superfamily => Major Facilitator Superfamily protein
[15:07:43] Modify product: Integral membrane protein TerC family => Integral membrane protein TerC family protein
[15:07:43] Modify product: PD-(D/E)XK nuclease superfamily => PD-(D/E)XK nuclease superfamily protein
[15:07:43] Modify product: Alpha/beta hydrolase family => Alpha/beta hydrolase family protein
[15:07:43] Modify product: TrbC/VIRB2 family => TrbC/VIRB2 family protein
[15:07:43] Modify product: RmlD substrate binding domain => RmlD substrate binding domain protein
[15:07:43] Modify product: ETC complex I subunit conserved region => hypothetical protein
[15:07:43] Modify product: Tim44-like domain => Tim44-like domain protein
[15:07:43] Modify product: DSBA-like thioredoxin domain => DSBA-like thioredoxin domain protein
[15:07:43] Modify product: HemY protein N-terminus => hypothetical protein
[15:07:43] Modify product: Uracil DNA glycosylase superfamily => Uracil DNA glycosylase superfamily protein
[15:07:43] Modify product: AsmA family => AsmA family protein
[15:07:43] Modify product: YGGT family => YGGT family protein
[15:07:43] Cleaned 17 /product names
[15:07:43] Deleting unwanted file: /home/yquentin/work/wolbachia/prokka/wCam/proteins.faa
[15:07:43] Deleting unwanted file: /home/yquentin/work/wolbachia/prokka/wCam/proteins.bls
[15:07:43] Labelling remaining 196 proteins as 'hypothetical protein'
[15:07:43] Possible /pseudo 'Phosphoribosylaminoimidazole-succinocarboxamide synthase' at gnl|Prokka|wCam_contig000001 position 7797
[15:07:43] Possible /pseudo 'putative zinc protease' at gnl|Prokka|wCam_contig000001 position 31373
[15:07:43] Possible /pseudo 'Riboflavin biosynthesis protein RibF' at gnl|Prokka|wCam_contig000001 position 33753
[15:07:43] Possible /pseudo 'Response regulator PleD' at gnl|Prokka|wCam_contig000001 position 260854
[15:07:43] Possible /pseudo 'Glutathione synthetase' at gnl|Prokka|wCam_contig000001 position 495508
[15:07:43] Possible /pseudo 'Dihydrolipoyl dehydrogenase' at gnl|Prokka|wCam_contig000001 position 498560
[15:07:43] Possible /pseudo 'Pyridoxine 5'-phosphate synthase' at gnl|Prokka|wCam_contig000001 position 600837
[15:07:43] Possible /pseudo 'TrbL/VirB6 plasmid conjugal transfer protein' at gnl|Prokka|wCam_contig000001 position 712208
[15:07:43] Possible /pseudo 'TrbL/VirB6 plasmid conjugal transfer protein' at gnl|Prokka|wCam_contig000001 position 714646
[15:07:43] Possible /pseudo 'TrbL/VirB6 plasmid conjugal transfer protein' at gnl|Prokka|wCam_contig000001 position 717773
[15:07:43] Found 488 unique /gene codes.
[15:07:43] Fixed 18 colliding /gene names.
[15:07:43] Adding /locus_tag identifiers
[15:07:44] Assigned 831 locus_tags to CDS and RNA features.
[15:07:44] Writing outputs to /home/yquentin/work/wolbachia/prokka/wCam/
[15:07:45] Generating annotation statistics file
[15:07:45] Generating Genbank and Sequin files
[15:07:45] 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\/wCam\/wCam\.err -i \/home\/yquentin\/work\/wolbachia\/prokka\/wCam\/wCam\.fsa 2> /dev/null
[15:07:48] Deleting unwanted file: /home/yquentin/work/wolbachia/prokka/wCam/errorsummary.val
[15:07:48] Deleting unwanted file: /home/yquentin/work/wolbachia/prokka/wCam/wCam.dr
[15:07:48] Deleting unwanted file: /home/yquentin/work/wolbachia/prokka/wCam/wCam.fixedproducts
[15:07:48] Deleting unwanted file: /home/yquentin/work/wolbachia/prokka/wCam/wCam.ecn
[15:07:48] Deleting unwanted file: /home/yquentin/work/wolbachia/prokka/wCam/wCam.val
[15:07:48] Output files:
[15:07:48] /home/yquentin/work/wolbachia/prokka/wCam/wCam.err
[15:07:48] /home/yquentin/work/wolbachia/prokka/wCam/wCam.faa
[15:07:48] /home/yquentin/work/wolbachia/prokka/wCam/wCam.log
[15:07:48] /home/yquentin/work/wolbachia/prokka/wCam/wCam.gff
[15:07:48] /home/yquentin/work/wolbachia/prokka/wCam/wCam.tbl
[15:07:48] /home/yquentin/work/wolbachia/prokka/wCam/wCam.ffn
[15:07:48] /home/yquentin/work/wolbachia/prokka/wCam/wCam.sqn
[15:07:48] /home/yquentin/work/wolbachia/prokka/wCam/wCam.gbk
[15:07:48] /home/yquentin/work/wolbachia/prokka/wCam/wCam.fna
[15:07:48] /home/yquentin/work/wolbachia/prokka/wCam/wCam.fsa
[15:07:48] /home/yquentin/work/wolbachia/prokka/wCam/wCam.txt
[15:07:48] Walltime used: 1.15 minutes
[15:07:48] If you use this result please cite the Prokka paper:
[15:07:48] Seemann T (2014) Prokka: rapid prokaryotic genome annotation. Bioinformatics. 30(14):2068-9.
[15:07:48] Type 'prokka --citation' for more details.
[15:07:48] Share and enjoy!