[10:41:07] Command: --force --outdir /home/yquentin/work/wolbachia/prokka/Cameroon --addgenes --prefix Cameroon --locustag Cameroon --species Wolbachia endosymbiont --strain Cameroon --compliant --quiet /home/yquentin/work/wolbachia/prokka/Cameroon.fna
[10:41:07] Looking for 'aragorn' - found /usr/local/bioinfo/bin/aragorn
[10:41:07] Determined aragorn version is 1.2
[10:41:07] Looking for 'barrnap' - found /usr/local/bioinfo/bin/barrnap
[10:41:08] Determined barrnap version is 0.5
[10:41:08] Looking for 'blastp' - found /usr/local/bioinfo/src/NCBI_Blast+/ncbi-blast-2.6.0+/bin/blastp
[10:41:08] Determined blastp version is 2.6
[10:41:08] Looking for 'cmpress' - found /usr/local/bioinfo/src/PROKKA/prokka-1.10/bin/../binaries/linux/cmpress
[10:41:08] Determined cmpress version is 1.1
[10:41:08] Looking for 'cmscan' - found /usr/local/bioinfo/src/PROKKA/prokka-1.10/bin/../binaries/linux/cmscan
[10:41:08] Determined cmscan version is 1.1
[10:41:08] Looking for 'egrep' - found /bin/egrep
[10:41:08] Looking for 'find' - found /bin/find
[10:41:08] Looking for 'grep' - found /bin/grep
[10:41:08] Looking for 'hmmpress' - found /usr/local/bioinfo/bin/hmmpress
[10:41:08] Determined hmmpress version is 3.1
[10:41:08] Looking for 'hmmscan' - found /usr/local/bioinfo/bin/hmmscan
[10:41:08] Determined hmmscan version is 3.1
[10:41:08] Looking for 'less' - found /usr/bin/less
[10:41:08] Looking for 'makeblastdb' - found /usr/local/bioinfo/src/NCBI_Blast+/ncbi-blast-2.6.0+/bin/makeblastdb
[10:41:08] Determined makeblastdb version is 2.6
[10:41:08] Looking for 'minced' - found /usr/local/bioinfo/bin/minced
[10:41:08] Determined minced version is 1.6
[10:41:08] Looking for 'parallel' - found /usr/local/bioinfo/bin/parallel
[10:41:08] Determined parallel version is 20141022
[10:41:08] Looking for 'prodigal' - found /usr/local/bioinfo/bin/prodigal
[10:41:09] Determined prodigal version is 2.6
[10:41:09] Looking for 'rnammer' - found /usr/local/bioinfo/bin/rnammer
[10:41:09] Determined rnammer version is 1.2
[10:41:09] Looking for 'sed' - found /bin/sed
[10:41:09] Looking for 'signalp' - found /usr/local/bioinfo/bin/signalp
[10:41:10] Determined signalp version is 4.1
[10:41:10] Looking for 'tbl2asn' - found /home/yquentin/save/scripts/tbl2asn
[10:41:10] Determined tbl2asn version is 25.3
[10:41:10] Using genetic code table 11.
[10:41:10] Loading and checking input file: /home/yquentin/work/wolbachia/prokka/Cameroon.fna
[10:41:10] Wrote 1 contigs
[10:41:10] Predicting tRNAs and tmRNAs
[10:41:10] Running: aragorn -gc11  -w \/home\/yquentin\/work\/wolbachia\/prokka\/Cameroon\/Cameroon\.fna
[10:41:10] 1 tmRNA* [645,974] 189,239 ANDNFAANSNVVALVA*
[10:41:10] 2 tRNA-Glu [69609,69682] 35 (ttc)
[10:41:10] 3 tRNA-Cys c[72500,72571] 34 (gca)
[10:41:10] 4 tRNA-Arg c[159449,159523] 36 (acg)
[10:41:10] 5 tRNA-Leu c[179923,180006] 34 (caa)
[10:41:10] 6 tRNA-Gln c[195748,195822] 33 (ttg)
[10:41:10] 7 tRNA-Ser c[210610,210695] 35 (cag)
[10:41:10] 8 tRNA-Leu c[271760,271846] 35 (taa)
[10:41:10] 9 tRNA-Leu c[296754,296841] 35 (gag)
[10:41:10] 10 tRNA-Arg c[335424,335499] 36 (tct)
[10:41:10] 11 tRNA-Arg c[395518,395593] 36 (ccg)
[10:41:10] 12 tRNA-Ile c[449788,449864] 35 (gat)
[10:41:10] 13 tRNA-Met c[462734,462807] 34 (cat)
[10:41:10] 14 tRNA-Leu c[494083,494165] 35 (tag)
[10:41:10] 15 tRNA-Phe c[536196,536269] 34 (gaa)
[10:41:10] 16 tRNA-Asp [541923,541997] 35 (gtc)
[10:41:10] 17 tRNA-Gly c[580460,580532] 34 (tcc)
[10:41:10] 18 tRNA-Tyr c[580536,580620] 36 (gta)
[10:41:10] 19 tRNA-Ser c[610788,610880] 36 (gct)
[10:41:10] 20 tRNA-Asn [617251,617325] 34 (gtt)
[10:41:10] 21 tRNA-Thr c[634198,634271] 35 (tgt)
[10:41:10] 22 tRNA-Arg c[653319,653395] 35 (cct)
[10:41:10] 23 tRNA-Ser c[686466,686555] 36 (gga)
[10:41:10] 24 tRNA-Trp [735984,736057] 34 (cca)
[10:41:10] 25 tRNA-His [768366,768439] 34 (gtg)
[10:41:10] 26 tRNA-Met [786230,786304] 35 (cat)
[10:41:10] 27 tRNA-Thr [788698,788771] 34 (ggt)
[10:41:10] 28 tRNA-Pro [812138,812215] 36 (tgg)
[10:41:10] 29 tRNA-Met c[815960,816035] 35 (cat)
[10:41:10] 30 tRNA-Gly [817286,817359] 34 (gcc)
[10:41:10] 31 tRNA-Val c[872868,872940] 34 (tac)
[10:41:10] 32 tRNA-Ser [879341,879430] 36 (tga)
[10:41:10] 33 tRNA-Ala c[914364,914438] 35 (tgc)
[10:41:10] 34 tRNA-Lys [914600,914672] 34 (ttt)
[10:41:10] 35 tRNA-Val c[939579,939652] 34 (gac)
[10:41:10] Found 35 tRNAs
[10:41:10] Predicting Ribosomal RNAs
[10:41:10] Running Barrnap with 8 threads
[10:41:11] 1 gnl|Prokka|Cameroon_contig000001 558583 16S ribosomal RNA
[10:41:11] 2 gnl|Prokka|Cameroon_contig000001 668841 5S ribosomal RNA (partial)
[10:41:11] 3 gnl|Prokka|Cameroon_contig000001 668997 23S ribosomal RNA
[10:41:11] Found 3 rRNAs
[10:41:11] Skipping ncRNA search, enable with --rfam if desired.
[10:41:11] Total of 37 tRNA + rRNA features
[10:41:11] Searching for CRISPR repeats
[10:41:11] Found 0 CRISPRs
[10:41:11] Predicting coding sequences
[10:41:11] Contigs total 960618 bp, so using single mode
[10:41:11] Running: prodigal -i \/home\/yquentin\/work\/wolbachia\/prokka\/Cameroon\/Cameroon\.fna -c -m -g 11 -p single -f sco -q
[10:41:13] Excluding CDS which overlaps existing RNA (tRNA) at gnl|Prokka|Cameroon_contig000001:462770..464101 on - strand
[10:41:13] Excluding CDS which overlaps existing RNA (rRNA) at gnl|Prokka|Cameroon_contig000001:559524..559646 on - strand
[10:41:13] Found 793 CDS
[10:41:13] Connecting features back to sequences
[10:41:13] Option --gram not specified, will NOT check for signal peptides.
[10:41:13] Not using genus-specific database. Try --usegenus to enable it.
[10:41:13] Annotating CDS, please be patient.
[10:41:13] Will use 8 CPUs for similarity searching.
[10:41:14] There are still 793 unannotated CDS left (started with 793)
[10:41:14] Will use blast to search against /usr/local/bioinfo/src/PROKKA/prokka-1.10/bin/../db/kingdom/Bacteria/sprot with 8 CPUs
[10:41:14] Running: cat \/home\/yquentin\/work\/wolbachia\/prokka\/Cameroon\/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\/Cameroon\/proteins\.bls 2> /dev/null
[10:41:22] Modify product: Probable tRNA-dihydrouridine synthase => putative tRNA-dihydrouridine synthase
[10:41:22] Modify product: Uncharacterized zinc protease Rv2782c => putative zinc protease
[10:41:22] Modify product: Uncharacterized zinc protease Rv2782c => putative zinc protease
[10:41:22] Modify product: Probable glycerol-3-phosphate acyltransferase => putative glycerol-3-phosphate acyltransferase
[10:41:22] Modify product: Probable GTP-binding protein EngB => putative GTP-binding protein EngB
[10:41:22] Modify product: Probable protein kinase UbiB => putative protein kinase UbiB
[10:41:22] Modify product: Probable transcriptional regulatory protein aq_1575 => putative transcriptional regulatory protein
[10:41:22] Modify product: N utilization substance protein B homolog => hypothetical protein
[10:41:23] Modify product: GTP-binding protein TypA/BipA homolog => hypothetical protein
[10:41:23] Modify product: Stringent starvation protein A homolog => hypothetical protein
[10:41:23] Modify product: Putative O-methyltransferase MSMEG_5073/MSMEI_4947 => Putative O-methyltransferase/MSMEI_4947
[10:41:23] Modify product: Uncharacterized metal-dependent hydrolase YcfH => putative metal-dependent hydrolase YcfH
[10:41:23] Modify product: Uncharacterized HIT-like protein HP_0404 => putative HIT-like protein
[10:41:23] Modify product: Probable dipeptidase PepE => putative dipeptidase PepE
[10:41:23] Modify product: Transcription termination factor Rho => hypothetical protein
[10:41:23] Modify product: Transcription termination/antitermination protein NusA => hypothetical protein
[10:41:23] Modify product: Uncharacterized ABC transporter ATP-binding protein TM_0288 => putative ABC transporter ATP-binding protein
[10:41:23] Modify product: Uncharacterized oxidoreductase YciK => putative oxidoreductase YciK
[10:41:23] Modify product: Probable peroxiredoxin => putative peroxiredoxin
[10:41:23] Modify product: Uncharacterized zinc protease Rv2782c => putative zinc protease
[10:41:23] Modify product: Cytochrome b561 homolog 2 => hypothetical protein
[10:41:23] Modify product: Putative NAD(P)H nitroreductase SA2311 => Putative NAD(P)H nitroreductase
[10:41:23] Modify product: SCO1 protein homolog => hypothetical protein
[10:41:23] Modify product: Co-chaperone protein HscB homolog => hypothetical protein
[10:41:23] Modify product: Bifunctional protein FolD => Bifunctional protein FolD protein
[10:41:23] Modify product: Transcription termination/antitermination protein NusG => hypothetical protein
[10:41:23] Cleaned 26 /product names
[10:41:23] Deleting unwanted file: /home/yquentin/work/wolbachia/prokka/Cameroon/proteins.faa
[10:41:23] Deleting unwanted file: /home/yquentin/work/wolbachia/prokka/Cameroon/proteins.bls
[10:41:23] There are still 283 unannotated CDS left (started with 793)
[10:41:23] Will use hmmer3 to search against /usr/local/bioinfo/src/PROKKA/prokka-1.10/bin/../db/hmm/HAMAP.hmm with 8 CPUs
[10:41:23] Running: cat \/home\/yquentin\/work\/wolbachia\/prokka\/Cameroon\/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\/Cameroon\/proteins\.bls 2> /dev/null
[10:41:29] Deleting unwanted file: /home/yquentin/work/wolbachia/prokka/Cameroon/proteins.faa
[10:41:29] Deleting unwanted file: /home/yquentin/work/wolbachia/prokka/Cameroon/proteins.bls
[10:41:29] There are still 256 unannotated CDS left (started with 793)
[10:41:29] Will use hmmer3 to search against /usr/local/bioinfo/src/PROKKA/prokka-1.10/bin/../db/hmm/CLUSTERS.hmm with 8 CPUs
[10:41:29] Running: cat \/home\/yquentin\/work\/wolbachia\/prokka\/Cameroon\/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\/Cameroon\/proteins\.bls 2> /dev/null
[10:41:44] Deleting unwanted file: /home/yquentin/work/wolbachia/prokka/Cameroon/proteins.faa
[10:41:44] Deleting unwanted file: /home/yquentin/work/wolbachia/prokka/Cameroon/proteins.bls
[10:41:44] There are still 238 unannotated CDS left (started with 793)
[10:41:44] Will use hmmer3 to search against /usr/local/bioinfo/src/PROKKA/prokka-1.10/bin/../db/hmm/Pfam.hmm with 8 CPUs
[10:41:44] Running: cat \/home\/yquentin\/work\/wolbachia\/prokka\/Cameroon\/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\/Cameroon\/proteins\.bls 2> /dev/null
[10:42:02] Modify product: RDD family => RDD family protein
[10:42:02] Modify product: Acetyltransferase (GNAT) family => Acetyltransferase (GNAT) family protein
[10:42:02] Modify product: RDD family => RDD family protein
[10:42:02] Modify product: SURF1 family => SURF1 family protein
[10:42:02] Modify product: Major Facilitator Superfamily => Major Facilitator Superfamily protein
[10:42:02] Modify product: Integral membrane protein TerC family => Integral membrane protein TerC family protein
[10:42:02] Modify product: PD-(D/E)XK nuclease superfamily => PD-(D/E)XK nuclease superfamily protein
[10:42:02] Modify product: Alpha/beta hydrolase family => Alpha/beta hydrolase family protein
[10:42:02] Modify product: TrbC/VIRB2 family => TrbC/VIRB2 family protein
[10:42:02] Modify product: Uracil DNA glycosylase superfamily => Uracil DNA glycosylase superfamily protein
[10:42:02] Modify product: RmlD substrate binding domain => RmlD substrate binding domain protein
[10:42:02] Modify product: ETC complex I subunit conserved region => hypothetical protein
[10:42:02] Modify product: Tim44-like domain => Tim44-like domain protein
[10:42:02] Modify product: DSBA-like thioredoxin domain => DSBA-like thioredoxin domain protein
[10:42:02] Modify product: HemY protein N-terminus => hypothetical protein
[10:42:02] Modify product: AsmA family => AsmA family protein
[10:42:02] Modify product: YGGT family => YGGT family protein
[10:42:02] Cleaned 17 /product names
[10:42:02] Deleting unwanted file: /home/yquentin/work/wolbachia/prokka/Cameroon/proteins.faa
[10:42:02] Deleting unwanted file: /home/yquentin/work/wolbachia/prokka/Cameroon/proteins.bls
[10:42:02] Labelling remaining 196 proteins as 'hypothetical protein'
[10:42:02] Possible /pseudo 'Phosphoribosylaminoimidazole-succinocarboxamide synthase' at gnl|Prokka|Cameroon_contig000001 position 7797
[10:42:02] Possible /pseudo 'putative zinc protease' at gnl|Prokka|Cameroon_contig000001 position 31373
[10:42:02] Possible /pseudo 'Riboflavin biosynthesis protein RibF' at gnl|Prokka|Cameroon_contig000001 position 33753
[10:42:02] Possible /pseudo 'Response regulator PleD' at gnl|Prokka|Cameroon_contig000001 position 260854
[10:42:02] Possible /pseudo 'Glutathione synthetase' at gnl|Prokka|Cameroon_contig000001 position 495508
[10:42:02] Possible /pseudo 'Dihydrolipoyl dehydrogenase' at gnl|Prokka|Cameroon_contig000001 position 498560
[10:42:02] Possible /pseudo 'Pyridoxine 5'-phosphate synthase' at gnl|Prokka|Cameroon_contig000001 position 600837
[10:42:02] Possible /pseudo 'TrbL/VirB6 plasmid conjugal transfer protein' at gnl|Prokka|Cameroon_contig000001 position 712208
[10:42:02] Possible /pseudo 'TrbL/VirB6 plasmid conjugal transfer protein' at gnl|Prokka|Cameroon_contig000001 position 714646
[10:42:02] Possible /pseudo 'TrbL/VirB6 plasmid conjugal transfer protein' at gnl|Prokka|Cameroon_contig000001 position 717773
[10:42:02] Found 488 unique /gene codes.
[10:42:02] Fixed 18 colliding /gene names.
[10:42:02] Adding /locus_tag identifiers
[10:42:02] Assigned 831 locus_tags to CDS and RNA features.
[10:42:02] Writing outputs to /home/yquentin/work/wolbachia/prokka/Cameroon/
[10:42:03] Generating annotation statistics file
[10:42:03] Generating Genbank and Sequin files
[10:42:03] 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\/Cameroon\/Cameroon\.err -i \/home\/yquentin\/work\/wolbachia\/prokka\/Cameroon\/Cameroon\.fsa 2> /dev/null
[10:42:05] Deleting unwanted file: /home/yquentin/work/wolbachia/prokka/Cameroon/errorsummary.val
[10:42:05] Deleting unwanted file: /home/yquentin/work/wolbachia/prokka/Cameroon/Cameroon.dr
[10:42:05] Deleting unwanted file: /home/yquentin/work/wolbachia/prokka/Cameroon/Cameroon.fixedproducts
[10:42:05] Deleting unwanted file: /home/yquentin/work/wolbachia/prokka/Cameroon/Cameroon.ecn
[10:42:05] Deleting unwanted file: /home/yquentin/work/wolbachia/prokka/Cameroon/Cameroon.val
[10:42:05] Output files:
[10:42:05] /home/yquentin/work/wolbachia/prokka/Cameroon/Cameroon.fna
[10:42:05] /home/yquentin/work/wolbachia/prokka/Cameroon/Cameroon.ffn
[10:42:05] /home/yquentin/work/wolbachia/prokka/Cameroon/Cameroon.txt
[10:42:05] /home/yquentin/work/wolbachia/prokka/Cameroon/Cameroon.err
[10:42:05] /home/yquentin/work/wolbachia/prokka/Cameroon/Cameroon.fsa
[10:42:05] /home/yquentin/work/wolbachia/prokka/Cameroon/Cameroon.log
[10:42:05] /home/yquentin/work/wolbachia/prokka/Cameroon/Cameroon.faa
[10:42:05] /home/yquentin/work/wolbachia/prokka/Cameroon/Cameroon.tbl
[10:42:05] /home/yquentin/work/wolbachia/prokka/Cameroon/Cameroon.gbk
[10:42:05] /home/yquentin/work/wolbachia/prokka/Cameroon/Cameroon.sqn
[10:42:05] /home/yquentin/work/wolbachia/prokka/Cameroon/Cameroon.gff
[10:42:05] Walltime used: 0.97 minutes
[10:42:05] If you use this result please cite the Prokka paper:
[10:42:05] Seemann T (2014) Prokka: rapid prokaryotic genome annotation. Bioinformatics. 30(14):2068-9.
[10:42:05] Type 'prokka --citation' for more details.
[10:42:05] Thank you, come again.