[15:06:44] Command: --force --outdir /home/yquentin/work/wolbachia/prokka/wGmo --addgenes --prefix wGmo --locustag wGmo --species Wolbachia endosymbiont --strain wGmo --compliant --quiet /home/yquentin/work/wolbachia/prokka/wGmo.fna
[15:06:44] Looking for 'aragorn' - found /usr/local/bioinfo/bin/aragorn
[15:06:44] Determined aragorn version is 1.2
[15:06:44] Looking for 'barrnap' - found /usr/local/bioinfo/bin/barrnap
[15:06:44] Determined barrnap version is 0.5
[15:06:44] Looking for 'blastp' - found /usr/local/bioinfo/src/NCBI_Blast+/ncbi-blast-2.6.0+/bin/blastp
[15:06:44] Determined blastp version is 2.6
[15:06:44] Looking for 'cmpress' - found /usr/local/bioinfo/src/PROKKA/prokka-1.10/bin/../binaries/linux/cmpress
[15:06:44] Determined cmpress version is 1.1
[15:06:44] Looking for 'cmscan' - found /usr/local/bioinfo/src/PROKKA/prokka-1.10/bin/../binaries/linux/cmscan
[15:06:44] Determined cmscan version is 1.1
[15:06:44] Looking for 'egrep' - found /bin/egrep
[15:06:44] Looking for 'find' - found /bin/find
[15:06:44] Looking for 'grep' - found /bin/grep
[15:06:45] Looking for 'hmmpress' - found /usr/local/bioinfo/bin/hmmpress
[15:06:45] Determined hmmpress version is 3.1
[15:06:45] Looking for 'hmmscan' - found /usr/local/bioinfo/bin/hmmscan
[15:06:45] Determined hmmscan version is 3.1
[15:06:45] Looking for 'less' - found /usr/bin/less
[15:06:45] Looking for 'makeblastdb' - found /usr/local/bioinfo/src/NCBI_Blast+/ncbi-blast-2.6.0+/bin/makeblastdb
[15:06:45] Determined makeblastdb version is 2.6
[15:06:45] Looking for 'minced' - found /usr/local/bioinfo/bin/minced
[15:06:45] Determined minced version is 1.6
[15:06:45] Looking for 'parallel' - found /usr/local/bioinfo/bin/parallel
[15:06:45] Determined parallel version is 20141022
[15:06:45] Looking for 'prodigal' - found /usr/local/bioinfo/bin/prodigal
[15:06:45] Determined prodigal version is 2.6
[15:06:46] Looking for 'rnammer' - found /usr/local/bioinfo/bin/rnammer
[15:06:46] Determined rnammer version is 1.2
[15:06:46] Looking for 'sed' - found /bin/sed
[15:06:46] Looking for 'signalp' - found /usr/local/bioinfo/bin/signalp
[15:06:46] Determined signalp version is 4.1
[15:06:46] Looking for 'tbl2asn' - found /home/yquentin/save/scripts/tbl2asn
[15:06:46] Determined tbl2asn version is 25.3
[15:06:46] Using genetic code table 11.
[15:06:46] Loading and checking input file: /home/yquentin/work/wolbachia/prokka/wGmo.fna
[15:06:46] Wrote 201 contigs
[15:06:46] Predicting tRNAs and tmRNAs
[15:06:46] Running: aragorn -gc11  -w \/home\/yquentin\/work\/wolbachia\/prokka\/wGmo\/wGmo\.fna
[15:06:47] 1 tRNA-Asp [4779,4855] 35 (gtc)
[15:06:47] 1 tRNA-Cys [1008,1096] 36 (gca)
[15:06:47] 1 tRNA-Thr [3413,3486] 34 (tgt)
[15:06:47] 1 tRNA-Arg [3007,3083] 35 (cct)
[15:06:47] 1 tRNA-Leu [1842,1929] 35 (gag)
[15:06:47] 1 tmRNA* c[8833,9168] 195,245 ANDNFAAGSNECCVAA*
[15:06:47] 1 tRNA-Leu [8597,8680] 34 (caa)
[15:06:47] 1 tRNA-Ser c[6212,6297] 35 (cag)
[15:06:47] 1 tRNA-Met [1613,1689] 35 (cat)
[15:06:47] 1 tRNA-Ala c[9476,9551] 34 (tgc)
[15:06:47] 2 tRNA-Lys [9893,9966] 34 (ttt)
[15:06:47] 3 tRNA-Ser [16016,16104] 35 (tga)
[15:06:47] 1 tRNA-Leu c[11427,11509] 35 (tag)
[15:06:47] 1 tRNA-Thr [2912,2985] 34 (ggt)
[15:06:47] 1 tRNA-Gly c[2312,2383] 33 (tcc)
[15:06:47] 2 tRNA-Tyr c[2388,2470] 35 (gta)
[15:06:47] 1 tRNA-Thr c[11916,11989] 34 (ggt)
[15:06:47] 2 tRNA-Met c[13546,13622] 35 (cat)
[15:06:47] 1 tRNA-Pro c[5298,5373] 36 (tgg)
[15:06:47] 2 tRNA-Glu c[6304,6376] 34 (ttc)
[15:06:47] 1 tRNA-Leu [3234,3320] 35 (taa)
[15:06:47] 1 tRNA-Val c[2896,2968] 34 (tac)
[15:06:47] Found 22 tRNAs
[15:06:47] Predicting Ribosomal RNAs
[15:06:47] Running Barrnap with 8 threads
[15:06:48] 1 gnl|Prokka|wGmo_contig000025 8720 23S ribosomal RNA
[15:06:48] 2 gnl|Prokka|wGmo_contig000025 11552 5S ribosomal RNA (partial)
[15:06:48] 3 gnl|Prokka|wGmo_contig000049 1138 16S ribosomal RNA
[15:06:48] Found 3 rRNAs
[15:06:48] Skipping ncRNA search, enable with --rfam if desired.
[15:06:48] Total of 24 tRNA + rRNA features
[15:06:48] Searching for CRISPR repeats
[15:06:49] Found 0 CRISPRs
[15:06:49] Predicting coding sequences
[15:06:49] Contigs total 1019510 bp, so using single mode
[15:06:49] Running: prodigal -i \/home\/yquentin\/work\/wolbachia\/prokka\/wGmo\/wGmo\.fna -c -m -g 11 -p single -f sco -q
[15:06:50] Excluding CDS which overlaps existing RNA (rRNA) at gnl|Prokka|wGmo_contig000049:1574..1696 on + strand
[15:06:50] Excluding CDS which overlaps existing RNA (tRNA) at gnl|Prokka|wGmo_contig000063:997..1209 on + strand
[15:06:50] Excluding CDS which overlaps existing RNA (tRNA) at gnl|Prokka|wGmo_contig000085:3072..3188 on - strand
[15:06:51] Excluding CDS which overlaps existing RNA (tRNA) at gnl|Prokka|wGmo_contig000125:9934..11238 on + strand
[15:06:51] Excluding CDS which overlaps existing RNA (tRNA) at gnl|Prokka|wGmo_contig000125:15938..16135 on + strand
[15:06:51] Excluding CDS which overlaps existing RNA (tRNA) at gnl|Prokka|wGmo_contig000129:11345..11503 on - strand
[15:06:51] Excluding CDS which overlaps existing RNA (tRNA) at gnl|Prokka|wGmo_contig000142:2882..3019 on + strand
[15:06:51] Excluding CDS which overlaps existing RNA (tRNA) at gnl|Prokka|wGmo_contig000148:11882..12019 on - strand
[15:06:51] Found 1110 CDS
[15:06:51] Connecting features back to sequences
[15:06:51] Option --gram not specified, will NOT check for signal peptides.
[15:06:51] Not using genus-specific database. Try --usegenus to enable it.
[15:06:51] Annotating CDS, please be patient.
[15:06:51] Will use 8 CPUs for similarity searching.
[15:06:52] There are still 1110 unannotated CDS left (started with 1110)
[15:06:52] Will use blast to search against /usr/local/bioinfo/src/PROKKA/prokka-1.10/bin/../db/kingdom/Bacteria/sprot with 8 CPUs
[15:06:52] Running: cat \/home\/yquentin\/work\/wolbachia\/prokka\/wGmo\/proteins\.faa | parallel --gnu -j 8 --block 16762 --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\/wGmo\/proteins\.bls 2> /dev/null
[15:07:08] Modify product: Probable peroxiredoxin => putative peroxiredoxin
[15:07:08] Modify product: Cytochrome b561 homolog 2 => hypothetical protein
[15:07:09] Modify product: Uncharacterized ABC transporter ATP-binding protein TM_0288 => putative ABC transporter ATP-binding protein
[15:07:09] Modify product: Probable transcriptional regulatory protein aq_1575 => putative transcriptional regulatory protein
[15:07:09] Modify product: Uncharacterized zinc protease Rv2782c => putative zinc protease
[15:07:09] Modify product: Uncharacterized zinc protease Rv2782c => putative zinc protease
[15:07:09] Modify product: Co-chaperone protein HscB homolog => hypothetical protein
[15:07:09] Modify product: Transcription termination factor Rho => hypothetical protein
[15:07:09] Modify product: Probable protein kinase UbiB => putative protein kinase UbiB
[15:07:09] Modify product: Probable tRNA-dihydrouridine synthase => putative tRNA-dihydrouridine synthase
[15:07:09] Modify product: Probable acyltransferase YihG => putative acyltransferase YihG
[15:07:09] Modify product: Transcription termination/antitermination protein NusA => hypothetical protein
[15:07:09] Modify product: Probable GTP-binding protein EngB => putative GTP-binding protein EngB
[15:07:09] Modify product: Probable phospholipid ABC transporter-binding protein MlaD => putative phospholipid ABC transporter-binding protein MlaD
[15:07:10] Modify product: Bifunctional protein FolD => Bifunctional protein FolD protein
[15:07:10] Modify product: Probable phospholipid ABC transporter permease protein MlaE => putative phospholipid ABC transporter permease protein MlaE
[15:07:10] Modify product: Uncharacterized metal-dependent hydrolase YcfH => putative metal-dependent hydrolase YcfH
[15:07:10] Modify product: Uncharacterized HIT-like protein HP_0404 => putative HIT-like protein
[15:07:10] Modify product: Transcription termination/antitermination protein NusG => hypothetical protein
[15:07:10] Modify product: Probable tRNA-dihydrouridine synthase => putative tRNA-dihydrouridine synthase
[15:07:10] Modify product: SCO1 protein homolog => hypothetical protein
[15:07:10] Modify product: Transcription termination/antitermination protein NusG => hypothetical protein
[15:07:10] Modify product: Putative O-methyltransferase Rv1220c => Putative O-methyltransferase
[15:07:11] Cleaned 23 /product names
[15:07:11] Deleting unwanted file: /home/yquentin/work/wolbachia/prokka/wGmo/proteins.faa
[15:07:11] Deleting unwanted file: /home/yquentin/work/wolbachia/prokka/wGmo/proteins.bls
[15:07:11] There are still 515 unannotated CDS left (started with 1110)
[15:07:11] Will use hmmer3 to search against /usr/local/bioinfo/src/PROKKA/prokka-1.10/bin/../db/hmm/HAMAP.hmm with 8 CPUs
[15:07:11] Running: cat \/home\/yquentin\/work\/wolbachia\/prokka\/wGmo\/proteins\.faa | parallel --gnu -j 8 --block 5275 --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\/wGmo\/proteins\.bls 2> /dev/null
[15:07:22] Modify product: Transcription termination/antitermination protein NusG => hypothetical protein
[15:07:22] Cleaned 1 /product names
[15:07:22] Deleting unwanted file: /home/yquentin/work/wolbachia/prokka/wGmo/proteins.faa
[15:07:22] Deleting unwanted file: /home/yquentin/work/wolbachia/prokka/wGmo/proteins.bls
[15:07:22] There are still 479 unannotated CDS left (started with 1110)
[15:07:22] Will use hmmer3 to search against /usr/local/bioinfo/src/PROKKA/prokka-1.10/bin/../db/hmm/CLUSTERS.hmm with 8 CPUs
[15:07:22] Running: cat \/home\/yquentin\/work\/wolbachia\/prokka\/wGmo\/proteins\.faa | parallel --gnu -j 8 --block 4748 --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\/wGmo\/proteins\.bls 2> /dev/null
[15:07:49] Deleting unwanted file: /home/yquentin/work/wolbachia/prokka/wGmo/proteins.faa
[15:07:49] Deleting unwanted file: /home/yquentin/work/wolbachia/prokka/wGmo/proteins.bls
[15:07:49] There are still 459 unannotated CDS left (started with 1110)
[15:07:49] Will use hmmer3 to search against /usr/local/bioinfo/src/PROKKA/prokka-1.10/bin/../db/hmm/Pfam.hmm with 8 CPUs
[15:07:49] Running: cat \/home\/yquentin\/work\/wolbachia\/prokka\/wGmo\/proteins\.faa | parallel --gnu -j 8 --block 4521 --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\/wGmo\/proteins\.bls 2> /dev/null
[15:08:18] Modify product: Peptidase M16 inactive domain => Peptidase M16 inactive domain protein
[15:08:18] Modify product: Transposase IS116/IS110/IS902 family => Transposase IS116/IS110/IS902 family protein
[15:08:18] Modify product: EVE domain => EVE domain protein
[15:08:18] Modify product: Transposase IS116/IS110/IS902 family => Transposase IS116/IS110/IS902 family protein
[15:08:18] Modify product: Alpha/beta hydrolase family => Alpha/beta hydrolase family protein
[15:08:18] Modify product: Transposase IS66 family => Transposase IS66 family protein
[15:08:18] Modify product: Transposase DDE domain => Transposase DDE domain protein
[15:08:18] Modify product: Major Facilitator Superfamily => Major Facilitator Superfamily protein
[15:08:18] Modify product: Transposase DDE domain => Transposase DDE domain protein
[15:08:18] Modify product: Transposase DDE domain => Transposase DDE domain protein
[15:08:18] Modify product: TrbC/VIRB2 family => TrbC/VIRB2 family protein
[15:08:18] Modify product: RDD family => RDD family protein
[15:08:18] Modify product: Bacterial SH3 domain => Bacterial SH3 domain protein
[15:08:18] Modify product: SNF2 family N-terminal domain => hypothetical protein
[15:08:18] Modify product: AhpC/TSA family => AhpC/TSA family protein
[15:08:18] Modify product: SURF1 family => SURF1 family protein
[15:08:18] Modify product: RDD family => RDD family protein
[15:08:18] Modify product: Sodium:dicarboxylate symporter family => Sodium:dicarboxylate symporter family protein
[15:08:18] Modify product: Transposase IS116/IS110/IS902 family => Transposase IS116/IS110/IS902 family protein
[15:08:18] Modify product: Integral membrane protein TerC family => Integral membrane protein TerC family protein
[15:08:18] Modify product: Tetratricopeptide repeat => Tetratricopeptide repeat protein
[15:08:18] Modify product: Zinc-finger domain => Zinc-finger domain protein
[15:08:18] Modify product: AcrB/AcrD/AcrF family => AcrB/AcrD/AcrF family protein
[15:08:18] Modify product: TrbC/VIRB2 family => TrbC/VIRB2 family protein
[15:08:18] Modify product: COQ9 => hypothetical protein
[15:08:18] Modify product: PAS domain => PAS domain protein
[15:08:18] Modify product: MgtE intracellular N domain => MgtE intracellular N domain protein
[15:08:18] Modify product: Transposase IS116/IS110/IS902 family => Transposase IS116/IS110/IS902 family protein
[15:08:18] Modify product: Piwi/Argonaute/Zwille siRNA-binding domain => Piwi/Argonaute/Zwille siRNA-binding domain protein
[15:08:18] Modify product: Piwi/Argonaute/Zwille siRNA-binding domain => Piwi/Argonaute/Zwille siRNA-binding domain protein
[15:08:18] Modify product: Acetyltransferase (GNAT) family => Acetyltransferase (GNAT) family protein
[15:08:18] Modify product: HemY protein N-terminus => hypothetical protein
[15:08:18] Modify product: Transposase DDE domain => Transposase DDE domain protein
[15:08:18] Modify product: Transposase DDE domain => Transposase DDE domain protein
[15:08:18] Modify product: Tim44-like domain => Tim44-like domain protein
[15:08:18] Modify product: Uracil DNA glycosylase superfamily => Uracil DNA glycosylase superfamily protein
[15:08:18] Modify product: Phage capsid family => Phage capsid family protein
[15:08:18] Modify product: RDD family => RDD family protein
[15:08:18] Modify product: RDD family => RDD family protein
[15:08:18] Modify product: Resolvase, N terminal domain => hypothetical protein
[15:08:18] Modify product: Ankyrin repeat => Ankyrin repeat protein
[15:08:18] Modify product: PAAR motif => PAAR motif protein
[15:08:18] Cleaned 42 /product names
[15:08:18] Deleting unwanted file: /home/yquentin/work/wolbachia/prokka/wGmo/proteins.faa
[15:08:18] Deleting unwanted file: /home/yquentin/work/wolbachia/prokka/wGmo/proteins.bls
[15:08:18] Labelling remaining 351 proteins as 'hypothetical protein'
[15:08:18] Possible /pseudo 'Cell cycle response regulator CtrA' at gnl|Prokka|wGmo_contig000007 position 9423
[15:08:18] Possible /pseudo 'Superoxide dismutase [Fe]' at gnl|Prokka|wGmo_contig000007 position 16621
[15:08:18] Possible /pseudo 'Glycine--tRNA ligase beta subunit' at gnl|Prokka|wGmo_contig000018 position 2580
[15:08:18] Possible /pseudo 'ATP synthase subunit beta' at gnl|Prokka|wGmo_contig000025 position 14726
[15:08:18] Possible /pseudo 'DNA repair protein RadA' at gnl|Prokka|wGmo_contig000027 position 973
[15:08:18] Possible /pseudo 'Tyrosine recombinase XerC' at gnl|Prokka|wGmo_contig000029 position 3353
[15:08:18] Possible /pseudo 'Protein TolB' at gnl|Prokka|wGmo_contig000038 position 3726
[15:08:18] Possible /pseudo 'Septum formation initiator' at gnl|Prokka|wGmo_contig000039 position 1887
[15:08:18] Possible /pseudo 'Phage terminase large subunit (GpA)' at gnl|Prokka|wGmo_contig000050 position 477
[15:08:18] Possible /pseudo 'Aminopyrimidine aminohydrolase' at gnl|Prokka|wGmo_contig000062 position 3017
[15:08:18] Possible /pseudo 'Isoleucine--tRNA ligase' at gnl|Prokka|wGmo_contig000066 position 4334
[15:08:18] Possible /pseudo 'Isoleucine--tRNA ligase' at gnl|Prokka|wGmo_contig000066 position 5402
[15:08:18] Possible /pseudo 'Exopolysaccharide synthesis, ExoD' at gnl|Prokka|wGmo_contig000085 position 963
[15:08:18] Possible /pseudo 'Peptide chain release factor 2' at gnl|Prokka|wGmo_contig000087 position 340
[15:08:18] Possible /pseudo 'Ribonuclease D' at gnl|Prokka|wGmo_contig000093 position 827
[15:08:18] Possible /pseudo 'Tyrosine recombinase XerD' at gnl|Prokka|wGmo_contig000094 position 3047
[15:08:18] Possible /pseudo 'Transposase DDE domain protein' at gnl|Prokka|wGmo_contig000097 position 1602
[15:08:18] Possible /pseudo 'DNA translocase FtsK' at gnl|Prokka|wGmo_contig000097 position 5195
[15:08:18] Possible /pseudo 'Carbamoyl-phosphate synthase large chain' at gnl|Prokka|wGmo_contig000107 position 365
[15:08:18] Possible /pseudo 'TrbL/VirB6 plasmid conjugal transfer protein' at gnl|Prokka|wGmo_contig000112 position 8016
[15:08:18] Possible /pseudo 'TrbL/VirB6 plasmid conjugal transfer protein' at gnl|Prokka|wGmo_contig000112 position 9989
[15:08:18] Possible /pseudo 'TrbL/VirB6 plasmid conjugal transfer protein' at gnl|Prokka|wGmo_contig000112 position 12093
[15:08:18] Possible /pseudo 'TrbL/VirB6 plasmid conjugal transfer protein' at gnl|Prokka|wGmo_contig000112 position 13773
[15:08:18] Possible /pseudo 'Protein translocase subunit SecA' at gnl|Prokka|wGmo_contig000115 position 272
[15:08:18] Possible /pseudo 'Amidophosphoribosyltransferase' at gnl|Prokka|wGmo_contig000119 position 1616
[15:08:18] Possible /pseudo 'Na(+)/H(+) antiporter subunit D' at gnl|Prokka|wGmo_contig000119 position 4690
[15:08:18] Possible /pseudo 'Bifunctional ligase/repressor BirA' at gnl|Prokka|wGmo_contig000125 position 6183
[15:08:18] Possible /pseudo 'Ferredoxin--NADP reductase' at gnl|Prokka|wGmo_contig000125 position 16803
[15:08:18] Possible /pseudo 'Piwi/Argonaute/Zwille siRNA-binding domain protein' at gnl|Prokka|wGmo_contig000131 position 1166
[15:08:18] Possible /pseudo 'PD-(D/E)XK nuclease family transposase' at gnl|Prokka|wGmo_contig000136 position 5940
[15:08:18] Possible /pseudo 'Aconitate hydratase A' at gnl|Prokka|wGmo_contig000142 position 9939
[15:08:18] Possible /pseudo 'Quaternary ammonium compound-resistance protein SugE' at gnl|Prokka|wGmo_contig000148 position 3640
[15:08:18] Possible /pseudo '30S ribosomal protein S1' at gnl|Prokka|wGmo_contig000150 position 2499
[15:08:18] Possible /pseudo '30S ribosomal protein S1' at gnl|Prokka|wGmo_contig000150 position 3350
[15:08:18] Possible /pseudo 'Dihydroorotase' at gnl|Prokka|wGmo_contig000163 position 5987
[15:08:18] Possible /pseudo 'NAD-specific glutamate dehydrogenase' at gnl|Prokka|wGmo_contig000168 position 1253
[15:08:18] Possible /pseudo 'Ubiquinone/menaquinone biosynthesis C-methyltransferase UbiE' at gnl|Prokka|wGmo_contig000170 position 5752
[15:08:18] Possible /pseudo 'Holliday junction ATP-dependent DNA helicase RuvA' at gnl|Prokka|wGmo_contig000172 position 10252
[15:08:18] Possible /pseudo 'DNA replication and repair protein RecF' at gnl|Prokka|wGmo_contig000176 position 5668
[15:08:18] Possible /pseudo 'Amino-acid carrier protein AlsT' at gnl|Prokka|wGmo_contig000177 position 11423
[15:08:18] Possible /pseudo 'Elongation factor 4' at gnl|Prokka|wGmo_contig000178 position 1087
[15:08:18] Possible /pseudo 'ATP synthase subunit a' at gnl|Prokka|wGmo_contig000179 position 338
[15:08:18] Possible /pseudo '4-hydroxy-tetrahydrodipicolinate reductase' at gnl|Prokka|wGmo_contig000181 position 482
[15:08:18] Possible /pseudo '5'-nucleotidase SurE' at gnl|Prokka|wGmo_contig000183 position 6689
[15:08:18] Possible /pseudo 'Ribosomal large subunit pseudouridine synthase D' at gnl|Prokka|wGmo_contig000190 position 1414
[15:08:18] Possible /pseudo 'NADH-quinone oxidoreductase chain 3' at gnl|Prokka|wGmo_contig000190 position 4960
[15:08:18] Possible /pseudo 'Protein translocase subunit SecD' at gnl|Prokka|wGmo_contig000191 position 10891
[15:08:18] Possible /pseudo 'Protein translocase subunit SecD' at gnl|Prokka|wGmo_contig000191 position 11051
[15:08:18] Possible /pseudo 'RDD family protein' at gnl|Prokka|wGmo_contig000193 position 4185
[15:08:18] Found 519 unique /gene codes.
[15:08:18] Fixed 63 colliding /gene names.
[15:08:18] Adding /locus_tag identifiers
[15:08:18] Assigned 1135 locus_tags to CDS and RNA features.
[15:08:18] Writing outputs to /home/yquentin/work/wolbachia/prokka/wGmo/
[15:08:20] Generating annotation statistics file
[15:08:20] Generating Genbank and Sequin files
[15:08:20] 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\/wGmo\/wGmo\.err -i \/home\/yquentin\/work\/wolbachia\/prokka\/wGmo\/wGmo\.fsa 2> /dev/null
[15:08:25] Deleting unwanted file: /home/yquentin/work/wolbachia/prokka/wGmo/errorsummary.val
[15:08:25] Deleting unwanted file: /home/yquentin/work/wolbachia/prokka/wGmo/wGmo.dr
[15:08:25] Deleting unwanted file: /home/yquentin/work/wolbachia/prokka/wGmo/wGmo.fixedproducts
[15:08:25] Deleting unwanted file: /home/yquentin/work/wolbachia/prokka/wGmo/wGmo.ecn
[15:08:25] Deleting unwanted file: /home/yquentin/work/wolbachia/prokka/wGmo/wGmo.val
[15:08:25] Output files:
[15:08:25] /home/yquentin/work/wolbachia/prokka/wGmo/wGmo.gff
[15:08:25] /home/yquentin/work/wolbachia/prokka/wGmo/wGmo.ffn
[15:08:25] /home/yquentin/work/wolbachia/prokka/wGmo/wGmo.fsa
[15:08:25] /home/yquentin/work/wolbachia/prokka/wGmo/wGmo.sqn
[15:08:25] /home/yquentin/work/wolbachia/prokka/wGmo/wGmo.txt
[15:08:25] /home/yquentin/work/wolbachia/prokka/wGmo/wGmo.err
[15:08:25] /home/yquentin/work/wolbachia/prokka/wGmo/wGmo.log
[15:08:25] /home/yquentin/work/wolbachia/prokka/wGmo/wGmo.gbk
[15:08:25] /home/yquentin/work/wolbachia/prokka/wGmo/wGmo.faa
[15:08:25] /home/yquentin/work/wolbachia/prokka/wGmo/wGmo.tbl
[15:08:25] /home/yquentin/work/wolbachia/prokka/wGmo/wGmo.fna
[15:08:25] Walltime used: 1.68 minutes
[15:08:25] If you use this result please cite the Prokka paper:
[15:08:25] Seemann T (2014) Prokka: rapid prokaryotic genome annotation. Bioinformatics. 30(14):2068-9.
[15:08:25] Type 'prokka --citation' for more details.
[15:08:25] Share and enjoy!