[15:37:38] Command: --force --outdir /home/yquentin/work/wolbachia/prokka/wLsi --addgenes --prefix wLsi --locustag wLsi --species Wolbachia endosymbiont --strain wLsi --compliant /home/formation/public_html/M2_Phylogenomique/data/Wolbachia/Additional/Litomosoides_sigmodontis_wolbachia_2.0.fna
[15:37:38] Looking for 'aragorn' - found /usr/local/bioinfo/bin/aragorn
[15:37:38] Determined aragorn version is 1.2
[15:37:38] Looking for 'barrnap' - found /usr/local/bioinfo/bin/barrnap
[15:37:38] Determined barrnap version is 0.5
[15:37:38] Looking for 'blastp' - found /usr/local/bioinfo/src/NCBI_Blast+/ncbi-blast-2.6.0+/bin/blastp
[15:37:38] Determined blastp version is 2.6
[15:37:38] Looking for 'cmpress' - found /usr/local/bioinfo/src/PROKKA/prokka-1.10/bin/../binaries/linux/cmpress
[15:37:38] Determined cmpress version is 1.1
[15:37:38] Looking for 'cmscan' - found /usr/local/bioinfo/src/PROKKA/prokka-1.10/bin/../binaries/linux/cmscan
[15:37:38] Determined cmscan version is 1.1
[15:37:38] Looking for 'egrep' - found /bin/egrep
[15:37:38] Looking for 'find' - found /bin/find
[15:37:38] Looking for 'grep' - found /bin/grep
[15:37:38] Looking for 'hmmpress' - found /usr/local/bioinfo/bin/hmmpress
[15:37:38] Determined hmmpress version is 3.1
[15:37:38] Looking for 'hmmscan' - found /usr/local/bioinfo/bin/hmmscan
[15:37:38] Determined hmmscan version is 3.1
[15:37:38] Looking for 'less' - found /usr/bin/less
[15:37:38] Looking for 'makeblastdb' - found /usr/local/bioinfo/src/NCBI_Blast+/ncbi-blast-2.6.0+/bin/makeblastdb
[15:37:38] Determined makeblastdb version is 2.6
[15:37:38] Looking for 'minced' - found /usr/local/bioinfo/bin/minced
[15:37:38] Determined minced version is 1.6
[15:37:38] Looking for 'parallel' - found /usr/local/bioinfo/bin/parallel
[15:37:38] Determined parallel version is 20141022
[15:37:38] Looking for 'prodigal' - found /usr/local/bioinfo/bin/prodigal
[15:37:38] Determined prodigal version is 2.6
[15:37:38] Looking for 'rnammer' - found /usr/local/bioinfo/bin/rnammer
[15:37:38] Determined rnammer version is 1.2
[15:37:38] Looking for 'sed' - found /bin/sed
[15:37:38] Looking for 'signalp' - found /usr/local/bioinfo/bin/signalp
[15:37:38] Determined signalp version is 4.1
[15:37:38] Looking for 'tbl2asn' - found /home/yquentin/save/scripts/tbl2asn
[15:37:38] Determined tbl2asn version is 25.3
[15:37:38] Using genetic code table 11.
[15:37:38] Loading and checking input file: /home/formation/public_html/M2_Phylogenomique/data/Wolbachia/Additional/Litomosoides_sigmodontis_wolbachia_2.0.fna
[15:37:39] Wrote 10 contigs
[15:37:39] Predicting tRNAs and tmRNAs
[15:37:39] Running: aragorn -gc11  -w \/home\/yquentin\/work\/wolbachia\/prokka\/wLsi\/wLsi\.fna
[15:37:39] 1 tRNA-Ile [12815,12889] 35 (gat)
[15:37:39] 2 tRNA-Arg c[40168,40244] 36 (cct)
[15:37:39] 3 tRNA-Glu c[49883,49956] 35 (ttc)
[15:37:39] 4 tRNA-Leu [63875,63962] 35 (gag)
[15:37:39] 5 tRNA-Phe c[140023,140097] 35 (gaa)
[15:37:39] 6 tRNA-Asp [145565,145639] 35 (gtc)
[15:37:39] 7 tRNA-Leu c[146732,146819] 35 (taa)
[15:37:39] 8 tRNA-Met [201741,201816] 34 (cat)
[15:37:39] 9 tRNA-Arg c[219945,220020] 36 (acg)
[15:37:39] 10 tRNA-Gln c[245244,245318] 33 (ttg)
[15:37:39] 11 tRNA-Cys c[317150,317222] 34 (gca)
[15:37:39] 12 tRNA-Ser c[326800,326888] 36 (gga)
[15:37:39] 13 tmRNA* c[348076,348411] 198,245 ANDNFAAENDVAVAA*
[15:37:39] 14 tRNA-Trp c[361054,361127] 34 (cca)
[15:37:39] 15 tRNA-Gly c[362401,362473] 34 (tcc)
[15:37:39] 16 tRNA-Tyr c[362477,362560] 36 (gta)
[15:37:39] 17 tRNA-Ser c[384212,384300] 35 (tga)
[15:37:39] 18 tRNA-Met c[415942,416017] 35 (cat)
[15:37:39] 19 tRNA-His [422796,422871] 34 (gtg)
[15:37:39] 20 tRNA-Gly c[502590,502663] 34 (gcc)
[15:37:39] 21 tRNA-Arg [538382,538456] 35 (ccg)
[15:37:39] 22 tRNA-Lys c[577422,577495] 34 (ttt)
[15:37:39] 1 tRNA-Ser [48439,48524] 35 (cag)
[15:37:39] 2 tRNA-Pro c[58308,58383] 36 (tgg)
[15:37:39] 3 tRNA-Val [98888,98960] 34 (tac)
[15:37:39] 4 tRNA-Arg [137740,137814] 35 (tct)
[15:37:39] 5 tRNA-Met [236616,236690] 35 (cat)
[15:37:39] 1 tRNA-Leu [5224,5307] 34 (caa)
[15:37:39] 2 tRNA-Leu [79501,79583] 35 (tag)
[15:37:39] 3 tRNA-Ser c[109906,109997] 35 (gct)
[15:37:39] 4 tRNA-Thr c[115858,115931] 34 (ggt)
[15:37:39] 5 tRNA-Val [128347,128420] 34 (gac)
[15:37:39] 6 tRNA-Asn c[131454,131526] 33 (gtt)
[15:37:39] 7 tRNA-Thr c[133391,133463] 34 (tgt)
[15:37:39] 1 tRNA-Ala [21593,21666] 34 (tgc)
[15:37:39] Found 35 tRNAs
[15:37:39] Predicting Ribosomal RNAs
[15:37:39] Running Barrnap with 8 threads
[15:37:39] 1 gnl|Prokka|wLsi_contig000001 22292 23S ribosomal RNA
[15:37:39] 2 gnl|Prokka|wLsi_contig000001 25150 5S ribosomal RNA (partial)
[15:37:39] 3 gnl|Prokka|wLsi_contig000001 107779 16S ribosomal RNA
[15:37:39] Found 3 rRNAs
[15:37:39] Skipping ncRNA search, enable with --rfam if desired.
[15:37:39] Total of 37 tRNA + rRNA features
[15:37:39] Searching for CRISPR repeats
[15:37:40] Found 0 CRISPRs
[15:37:40] Predicting coding sequences
[15:37:40] Contigs total 1048936 bp, so using single mode
[15:37:40] Running: prodigal -i \/home\/yquentin\/work\/wolbachia\/prokka\/wLsi\/wLsi\.fna -c -m -g 11 -p single -f sco -q
[15:37:41] Excluding CDS which overlaps existing RNA (rRNA) at gnl|Prokka|wLsi_contig000001:23150..23278 on + strand
[15:37:41] Excluding CDS which overlaps existing RNA (rRNA) at gnl|Prokka|wLsi_contig000001:108925..109176 on + strand
[15:37:41] Excluding CDS which overlaps existing RNA (tRNA) at gnl|Prokka|wLsi_contig000001:145385..145630 on - strand
[15:37:41] Excluding CDS which overlaps existing RNA (tRNA) at gnl|Prokka|wLsi_contig000001:200446..201741 on + strand
[15:37:41] Excluding CDS which overlaps existing RNA (tRNA) at gnl|Prokka|wLsi_contig000001:245309..245644 on - strand
[15:37:41] Excluding CDS which overlaps existing RNA (tRNA) at gnl|Prokka|wLsi_contig000003:79486..79644 on + strand
[15:37:41] Excluding CDS which overlaps existing RNA (tRNA) at gnl|Prokka|wLsi_contig000003:115821..115940 on - strand
[15:37:41] Excluding CDS which overlaps existing RNA (tRNA) at gnl|Prokka|wLsi_contig000003:128383..129342 on + strand
[15:37:41] Found 880 CDS
[15:37:41] Connecting features back to sequences
[15:37:41] Option --gram not specified, will NOT check for signal peptides.
[15:37:41] Not using genus-specific database. Try --usegenus to enable it.
[15:37:41] Annotating CDS, please be patient.
[15:37:41] Will use 8 CPUs for similarity searching.
[15:37:42] There are still 880 unannotated CDS left (started with 880)
[15:37:42] Will use blast to search against /usr/local/bioinfo/src/PROKKA/prokka-1.10/bin/../db/kingdom/Bacteria/sprot with 8 CPUs
[15:37:42] Running: cat \/home\/yquentin\/work\/wolbachia\/prokka\/wLsi\/proteins\.faa | parallel --gnu -j 8 --block 15090 --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\/wLsi\/proteins\.bls 2> /dev/null
[15:37:49] Modify product: Uncharacterized zinc protease Rv2782c => putative zinc protease
[15:37:50] Modify product: GTP-binding protein TypA/BipA homolog => hypothetical protein
[15:37:50] Modify product: SCO1 protein homolog => hypothetical protein
[15:37:50] Modify product: Transcription termination/antitermination protein NusG => hypothetical protein
[15:37:50] Modify product: Uncharacterized zinc protease Rv2782c => putative zinc protease
[15:37:50] Modify product: Probable dipeptidase PepE => putative dipeptidase PepE
[15:37:50] Modify product: N utilization substance protein B homolog => hypothetical protein
[15:37:50] Modify product: Uncharacterized ABC transporter ATP-binding protein TM_0288 => putative ABC transporter ATP-binding protein
[15:37:50] Modify product: Uncharacterized oxidoreductase YciK => putative oxidoreductase YciK
[15:37:50] Modify product: Probable transcriptional regulatory protein aq_1575 => putative transcriptional regulatory protein
[15:37:50] Modify product: Probable tRNA-dihydrouridine synthase => putative tRNA-dihydrouridine synthase
[15:37:50] Modify product: Transcription termination/antitermination protein NusA => hypothetical protein
[15:37:50] Modify product: Probable murein peptide carboxypeptidase => putative murein peptide carboxypeptidase
[15:37:50] Modify product: Cytochrome b561 homolog 2 => hypothetical protein
[15:37:51] Modify product: Transcription termination factor Rho => hypothetical protein
[15:37:51] Modify product: Bifunctional protein FolD => Bifunctional protein FolD protein
[15:37:51] Modify product: Probable UbiX-like flavin prenyltransferase => putative UbiX-like flavin prenyltransferase
[15:37:51] Modify product: Stringent starvation protein A homolog => hypothetical protein
[15:37:51] Modify product: Putative O-methyltransferase MSMEG_5073/MSMEI_4947 => Putative O-methyltransferase/MSMEI_4947
[15:37:51] Modify product: Probable GTP-binding protein EngB => putative GTP-binding protein EngB
[15:37:51] Modify product: Probable peroxiredoxin => putative peroxiredoxin
[15:37:51] Modify product: Probable protein kinase UbiB => putative protein kinase UbiB
[15:37:51] Modify product: Co-chaperone protein HscB homolog => hypothetical protein
[15:37:51] Modify product: Uncharacterized HIT-like protein HP_0404 => putative HIT-like protein
[15:37:51] Cleaned 24 /product names
[15:37:51] Deleting unwanted file: /home/yquentin/work/wolbachia/prokka/wLsi/proteins.faa
[15:37:51] Deleting unwanted file: /home/yquentin/work/wolbachia/prokka/wLsi/proteins.bls
[15:37:51] There are still 365 unannotated CDS left (started with 880)
[15:37:51] Will use hmmer3 to search against /usr/local/bioinfo/src/PROKKA/prokka-1.10/bin/../db/hmm/HAMAP.hmm with 8 CPUs
[15:37:51] Running: cat \/home\/yquentin\/work\/wolbachia\/prokka\/wLsi\/proteins\.faa | parallel --gnu -j 8 --block 3592 --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\/wLsi\/proteins\.bls 2> /dev/null
[15:37:55] Deleting unwanted file: /home/yquentin/work/wolbachia/prokka/wLsi/proteins.faa
[15:37:55] Deleting unwanted file: /home/yquentin/work/wolbachia/prokka/wLsi/proteins.bls
[15:37:55] There are still 340 unannotated CDS left (started with 880)
[15:37:55] Will use hmmer3 to search against /usr/local/bioinfo/src/PROKKA/prokka-1.10/bin/../db/hmm/CLUSTERS.hmm with 8 CPUs
[15:37:55] Running: cat \/home\/yquentin\/work\/wolbachia\/prokka\/wLsi\/proteins\.faa | parallel --gnu -j 8 --block 3211 --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\/wLsi\/proteins\.bls 2> /dev/null
[15:38:06] Deleting unwanted file: /home/yquentin/work/wolbachia/prokka/wLsi/proteins.faa
[15:38:06] Deleting unwanted file: /home/yquentin/work/wolbachia/prokka/wLsi/proteins.bls
[15:38:06] There are still 321 unannotated CDS left (started with 880)
[15:38:06] Will use hmmer3 to search against /usr/local/bioinfo/src/PROKKA/prokka-1.10/bin/../db/hmm/Pfam.hmm with 8 CPUs
[15:38:06] Running: cat \/home\/yquentin\/work\/wolbachia\/prokka\/wLsi\/proteins\.faa | parallel --gnu -j 8 --block 2915 --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\/wLsi\/proteins\.bls 2> /dev/null
[15:38:18] Modify product: ETC complex I subunit conserved region => hypothetical protein
[15:38:18] Modify product: Tim44-like domain => Tim44-like domain protein
[15:38:18] Modify product: Peptidase M16 inactive domain => Peptidase M16 inactive domain protein
[15:38:18] Modify product: SPFH domain / Band 7 family => SPFH domain / Band 7 family protein
[15:38:18] Modify product: Zinc-finger domain => Zinc-finger domain protein
[15:38:18] Modify product: PD-(D/E)XK nuclease superfamily => PD-(D/E)XK nuclease superfamily protein
[15:38:18] Modify product: YGGT family => YGGT family protein
[15:38:18] Modify product: PAS domain => PAS domain protein
[15:38:18] Modify product: Uracil DNA glycosylase superfamily => Uracil DNA glycosylase superfamily protein
[15:38:18] Modify product: BioY family => BioY family protein
[15:38:18] Modify product: COQ9 => hypothetical protein
[15:38:18] Modify product: AhpC/TSA family => AhpC/TSA family protein
[15:38:18] Modify product: SURF1 family => SURF1 family protein
[15:38:18] Modify product: RDD family => RDD family protein
[15:38:18] Modify product: Integral membrane protein TerC family => Integral membrane protein TerC family protein
[15:38:18] Modify product: Sodium:alanine symporter family => Sodium:alanine symporter family protein
[15:38:18] Modify product: EVE domain => EVE domain protein
[15:38:18] Modify product: Alpha/beta hydrolase family => Alpha/beta hydrolase family protein
[15:38:18] Modify product: RDD family => RDD family protein
[15:38:18] Modify product: TrbC/VIRB2 family => TrbC/VIRB2 family protein
[15:38:18] Cleaned 20 /product names
[15:38:18] Deleting unwanted file: /home/yquentin/work/wolbachia/prokka/wLsi/proteins.faa
[15:38:18] Deleting unwanted file: /home/yquentin/work/wolbachia/prokka/wLsi/proteins.bls
[15:38:18] Labelling remaining 278 proteins as 'hypothetical protein'
[15:38:18] Possible /pseudo 'tRNA pseudouridine synthase B' at gnl|Prokka|wLsi_contig000001 position 324988
[15:38:18] Possible /pseudo 'ATP-dependent DNA helicase RecG' at gnl|Prokka|wLsi_contig000001 position 335592
[15:38:18] Possible /pseudo 'ATP-dependent DNA helicase RecG' at gnl|Prokka|wLsi_contig000001 position 335916
[15:38:18] Possible /pseudo 'TrbL/VirB6 plasmid conjugal transfer protein' at gnl|Prokka|wLsi_contig000001 position 444592
[15:38:18] Possible /pseudo 'TrbL/VirB6 plasmid conjugal transfer protein' at gnl|Prokka|wLsi_contig000001 position 447681
[15:38:18] Possible /pseudo 'TrbL/VirB6 plasmid conjugal transfer protein' at gnl|Prokka|wLsi_contig000001 position 450152
[15:38:18] Possible /pseudo 'Enolase' at gnl|Prokka|wLsi_contig000001 position 461494
[15:38:18] Possible /pseudo 'Enolase' at gnl|Prokka|wLsi_contig000001 position 461850
[15:38:18] Possible /pseudo 'GTPase Obg' at gnl|Prokka|wLsi_contig000001 position 462808
[15:38:18] Possible /pseudo 'ATP synthase subunit b' at gnl|Prokka|wLsi_contig000001 position 515291
[15:38:18] Possible /pseudo 'Arginine/agmatine antiporter' at gnl|Prokka|wLsi_contig000002 position 154093
[15:38:18] Possible /pseudo 'Elongation factor Tu' at gnl|Prokka|wLsi_contig000003 position 38721
[15:38:18] Possible /pseudo 'Chaperone protein HscA' at gnl|Prokka|wLsi_contig000007 position 943
[15:38:18] Found 487 unique /gene codes.
[15:38:18] Fixed 19 colliding /gene names.
[15:38:18] Adding /locus_tag identifiers
[15:38:18] Assigned 918 locus_tags to CDS and RNA features.
[15:38:18] Writing outputs to /home/yquentin/work/wolbachia/prokka/wLsi/
[15:38:19] Generating annotation statistics file
[15:38:19] Generating Genbank and Sequin files
[15:38:19] 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\/wLsi\/wLsi\.err -i \/home\/yquentin\/work\/wolbachia\/prokka\/wLsi\/wLsi\.fsa 2> /dev/null
[15:38:21] Deleting unwanted file: /home/yquentin/work/wolbachia/prokka/wLsi/errorsummary.val
[15:38:21] Deleting unwanted file: /home/yquentin/work/wolbachia/prokka/wLsi/wLsi.dr
[15:38:21] Deleting unwanted file: /home/yquentin/work/wolbachia/prokka/wLsi/wLsi.fixedproducts
[15:38:21] Deleting unwanted file: /home/yquentin/work/wolbachia/prokka/wLsi/wLsi.ecn
[15:38:21] Deleting unwanted file: /home/yquentin/work/wolbachia/prokka/wLsi/wLsi.val
[15:38:21] Output files:
[15:38:21] /home/yquentin/work/wolbachia/prokka/wLsi/wLsi.sqn
[15:38:21] /home/yquentin/work/wolbachia/prokka/wLsi/wLsi.gbk
[15:38:21] /home/yquentin/work/wolbachia/prokka/wLsi/wLsi.fna
[15:38:21] /home/yquentin/work/wolbachia/prokka/wLsi/wLsi.tbl
[15:38:21] /home/yquentin/work/wolbachia/prokka/wLsi/wLsi.gff
[15:38:21] /home/yquentin/work/wolbachia/prokka/wLsi/wLsi.faa
[15:38:21] /home/yquentin/work/wolbachia/prokka/wLsi/wLsi.ffn
[15:38:21] /home/yquentin/work/wolbachia/prokka/wLsi/wLsi.log
[15:38:21] /home/yquentin/work/wolbachia/prokka/wLsi/wLsi.fsa
[15:38:21] /home/yquentin/work/wolbachia/prokka/wLsi/wLsi.txt
[15:38:21] /home/yquentin/work/wolbachia/prokka/wLsi/wLsi.err
[15:38:21] Walltime used: 0.72 minutes
[15:38:21] If you use this result please cite the Prokka paper:
[15:38:21] Seemann T (2014) Prokka: rapid prokaryotic genome annotation. Bioinformatics. 30(14):2068-9.
[15:38:21] Type 'prokka --citation' for more details.
[15:38:21] Share and enjoy!