[10:41:17] Command: --force --outdir /home/yquentin/work/wolbachia/prokka/wCle --addgenes --prefix wCle --locustag wCle --species Wolbachia endosymbiont --strain wCle --compliant --quiet /home/yquentin/work/wolbachia/prokka/wCle.fna
[10:41:17] Looking for 'aragorn' - found /usr/local/bioinfo/bin/aragorn
[10:41:17] Determined aragorn version is 1.2
[10:41:17] Looking for 'barrnap' - found /usr/local/bioinfo/bin/barrnap
[10:41:17] Determined barrnap version is 0.5
[10:41:17] Looking for 'blastp' - found /usr/local/bioinfo/src/NCBI_Blast+/ncbi-blast-2.6.0+/bin/blastp
[10:41:17] Determined blastp version is 2.6
[10:41:17] Looking for 'cmpress' - found /usr/local/bioinfo/src/PROKKA/prokka-1.10/bin/../binaries/linux/cmpress
[10:41:17] Determined cmpress version is 1.1
[10:41:17] Looking for 'cmscan' - found /usr/local/bioinfo/src/PROKKA/prokka-1.10/bin/../binaries/linux/cmscan
[10:41:17] Determined cmscan version is 1.1
[10:41:17] Looking for 'egrep' - found /bin/egrep
[10:41:17] Looking for 'find' - found /bin/find
[10:41:17] Looking for 'grep' - found /bin/grep
[10:41:17] Looking for 'hmmpress' - found /usr/local/bioinfo/bin/hmmpress
[10:41:17] Determined hmmpress version is 3.1
[10:41:17] Looking for 'hmmscan' - found /usr/local/bioinfo/bin/hmmscan
[10:41:17] Determined hmmscan version is 3.1
[10:41:17] Looking for 'less' - found /usr/bin/less
[10:41:17] Looking for 'makeblastdb' - found /usr/local/bioinfo/src/NCBI_Blast+/ncbi-blast-2.6.0+/bin/makeblastdb
[10:41:17] Determined makeblastdb version is 2.6
[10:41:17] Looking for 'minced' - found /usr/local/bioinfo/bin/minced
[10:41:17] Determined minced version is 1.6
[10:41:17] Looking for 'parallel' - found /usr/local/bioinfo/bin/parallel
[10:41:17] Determined parallel version is 20141022
[10:41:17] Looking for 'prodigal' - found /usr/local/bioinfo/bin/prodigal
[10:41:17] Determined prodigal version is 2.6
[10:41:17] Looking for 'rnammer' - found /usr/local/bioinfo/bin/rnammer
[10:41:17] Determined rnammer version is 1.2
[10:41:17] Looking for 'sed' - found /bin/sed
[10:41:17] Looking for 'signalp' - found /usr/local/bioinfo/bin/signalp
[10:41:18] Determined signalp version is 4.1
[10:41:18] Looking for 'tbl2asn' - found /home/yquentin/save/scripts/tbl2asn
[10:41:18] Determined tbl2asn version is 25.3
[10:41:18] Using genetic code table 11.
[10:41:18] Loading and checking input file: /home/yquentin/work/wolbachia/prokka/wCle.fna
[10:41:18] Wrote 1 contigs
[10:41:18] Predicting tRNAs and tmRNAs
[10:41:18] Running: aragorn -gc11  -w \/home\/yquentin\/work\/wolbachia\/prokka\/wCle\/wCle\.fna
[10:41:18] 1 tRNA-Leu [3992,4079] 35 (gag)
[10:41:18] 2 tRNA-Ser [100201,100285] 35 (cag)
[10:41:18] 3 tRNA-Gln c[149173,149247] 33 (ttg)
[10:41:18] 4 tRNA-Leu [162591,162674] 34 (caa)
[10:41:18] 5 tRNA-Ser c[287026,287114] 36 (gga)
[10:41:18] 6 tRNA-Met c[319267,319342] 34 (cat)
[10:41:18] 7 tRNA-Met [358875,358949] 35 (cat)
[10:41:18] 8 tRNA-Thr c[384462,384535] 34 (ggt)
[10:41:18] 9 tRNA-Arg c[474290,474365] 36 (acg)
[10:41:18] 10 tRNA-Val c[496914,496988] 35 (gac)
[10:41:18] 11 tRNA-Arg c[546685,546758] 35 (cct)
[10:41:18] 12 tRNA-Thr [572520,572593] 34 (tgt)
[10:41:18] 13 tRNA-Ser [620342,620431] 36 (tga)
[10:41:18] 14 tRNA-Ile [626367,626443] 35 (gat)
[10:41:18] 15 tmRNA* c[651079,651413] 194,244 ANDNFAANGNEFRVAA*
[10:41:18] 16 tRNA-Glu [660883,660955] 34 (ttc)
[10:41:18] 17 tRNA-Ala c[665639,665714] 34 (tgc)
[10:41:18] 18 tRNA-Lys c[670458,670531] 34 (ttt)
[10:41:18] 19 tRNA-His c[686941,687016] 34 (gtg)
[10:41:18] 20 tRNA-Leu [709699,709785] 35 (taa)
[10:41:18] 21 tRNA-Pro c[748638,748713] 36 (tgg)
[10:41:18] 22 tRNA-Val [755342,755417] 34 (tac)
[10:41:18] 23 tRNA-Met c[772395,772470] 35 (cat)
[10:41:18] 24 tRNA-Gly [773707,773780] 34 (gcc)
[10:41:18] 25 tRNA-Cys [865648,865720] 34 (gca)
[10:41:18] 26 tRNA-Tyr [900534,900618] 36 (gta)
[10:41:18] 27 tRNA-Gly [900622,900694] 34 (tcc)
[10:41:18] 28 tRNA-Trp [901962,902035] 34 (cca)
[10:41:18] 29 tRNA-Phe c[934877,934950] 34 (gaa)
[10:41:18] 30 tRNA-Asp [940742,940817] 36 (gtc)
[10:41:18] 31 tRNA-Asn [984912,984984] 33 (gtt)
[10:41:18] 32 tRNA-Arg c[1046393,1046468] 36 (ccg)
[10:41:18] 33 tRNA-Ser c[1089686,1089777] 35 (gct)
[10:41:18] 34 tRNA-Arg [1121565,1121641] 35 (tct)
[10:41:18] 35 tRNA-Leu c[1130808,1130890] 35 (tag)
[10:41:18] Found 35 tRNAs
[10:41:18] Predicting Ribosomal RNAs
[10:41:18] Running Barrnap with 8 threads
[10:41:19] 1 gnl|Prokka|wCle_contig000001 364317 16S ribosomal RNA
[10:41:19] 2 gnl|Prokka|wCle_contig000001 597788 5S ribosomal RNA
[10:41:19] 3 gnl|Prokka|wCle_contig000001 597964 23S ribosomal RNA
[10:41:19] Found 3 rRNAs
[10:41:19] Skipping ncRNA search, enable with --rfam if desired.
[10:41:19] Total of 37 tRNA + rRNA features
[10:41:19] Searching for CRISPR repeats
[10:41:19] Found 0 CRISPRs
[10:41:19] Predicting coding sequences
[10:41:19] Contigs total 1250060 bp, so using single mode
[10:41:19] Running: prodigal -i \/home\/yquentin\/work\/wolbachia\/prokka\/wCle\/wCle\.fna -c -m -g 11 -p single -f sco -q
[10:41:21] Excluding CDS which overlaps existing RNA (tRNA) at gnl|Prokka|wCle_contig000001:4035..5192 on + strand
[10:41:21] Excluding CDS which overlaps existing RNA (tRNA) at gnl|Prokka|wCle_contig000001:149238..149573 on - strand
[10:41:21] Excluding CDS which overlaps existing RNA (tRNA) at gnl|Prokka|wCle_contig000001:162605..163303 on + strand
[10:41:21] Excluding CDS which overlaps existing RNA (tRNA) at gnl|Prokka|wCle_contig000001:319342..320031 on - strand
[10:41:21] Excluding CDS which overlaps existing RNA (tRNA) at gnl|Prokka|wCle_contig000001:357349..358911 on - strand
[10:41:22] Excluding CDS which overlaps existing RNA (tRNA) at gnl|Prokka|wCle_contig000001:1130762..1130884 on - strand
[10:41:22] Found 1368 CDS
[10:41:22] Connecting features back to sequences
[10:41:22] Option --gram not specified, will NOT check for signal peptides.
[10:41:22] Not using genus-specific database. Try --usegenus to enable it.
[10:41:22] Annotating CDS, please be patient.
[10:41:22] Will use 8 CPUs for similarity searching.
[10:41:23] There are still 1368 unannotated CDS left (started with 1368)
[10:41:23] Will use blast to search against /usr/local/bioinfo/src/PROKKA/prokka-1.10/bin/../db/kingdom/Bacteria/sprot with 8 CPUs
[10:41:23] Running: cat \/home\/yquentin\/work\/wolbachia\/prokka\/wCle\/proteins\.faa | parallel --gnu -j 8 --block 21897 --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\/wCle\/proteins\.bls 2> /dev/null
[10:41:34] Modify product: Probable ribonucleotide transport ATP-binding protein mkl => putative ribonucleotide transport ATP-binding protein mkl
[10:41:34] Modify product: Probable phospholipid ABC transporter permease protein MlaE => putative phospholipid ABC transporter permease protein MlaE
[10:41:34] Modify product: Uncharacterized oxidoreductase YciK => putative oxidoreductase YciK
[10:41:34] Modify product: Cytochrome b561 homolog 2 => hypothetical protein
[10:41:34] Modify product: Bifunctional protein FolD => Bifunctional protein FolD protein
[10:41:34] Modify product: Probable protein kinase UbiB => putative protein kinase UbiB
[10:41:34] Modify product: Probable glucarate transporter => putative glucarate transporter
[10:41:34] Modify product: Actin-binding protein Smlt3054 => Actin-binding protein
[10:41:34] Modify product: Probable GTP-binding protein EngB => putative GTP-binding protein EngB
[10:41:35] Modify product: Probable glycerol-3-phosphate acyltransferase => putative glycerol-3-phosphate acyltransferase
[10:41:35] Modify product: Uncharacterized ABC transporter ATP-binding protein TM_0288 => putative ABC transporter ATP-binding protein
[10:41:35] Modify product: Putative multidrug export ATP-binding/permease protein SAV1866 => Putative multidrug export ATP-binding/permease protein
[10:41:35] Modify product: Actin-binding protein Smlt3054 => Actin-binding protein
[10:41:35] Modify product: Actin-binding protein Smlt3054 => Actin-binding protein
[10:41:35] Modify product: Probable peroxiredoxin => putative peroxiredoxin
[10:41:35] Modify product: GTP-binding protein TypA/BipA homolog => hypothetical protein
[10:41:35] Modify product: Probable transcriptional regulatory protein aq_1575 => putative transcriptional regulatory protein
[10:41:35] Modify product: SCO1 protein homolog => hypothetical protein
[10:41:35] Modify product: Uncharacterized metal-dependent hydrolase YcfH => putative metal-dependent hydrolase YcfH
[10:41:35] Modify product: Uncharacterized HIT-like protein HP_0404 => putative HIT-like protein
[10:41:35] Modify product: Putative O-methyltransferase MSMEG_5073/MSMEI_4947 => Putative O-methyltransferase/MSMEI_4947
[10:41:35] Modify product: Uncharacterized zinc protease Rv2782c => putative zinc protease
[10:41:35] Modify product: Putative multidrug export ATP-binding/permease protein SAV1866 => Putative multidrug export ATP-binding/permease protein
[10:41:35] Modify product: Probable murein peptide carboxypeptidase => putative murein peptide carboxypeptidase
[10:41:35] Modify product: Actin-binding protein Smlt3054 => Actin-binding protein
[10:41:35] Modify product: Uncharacterized zinc protease Rv2782c => putative zinc protease
[10:41:35] Modify product: Uncharacterized zinc protease Rv2782c => putative zinc protease
[10:41:35] Modify product: Probable tRNA-dihydrouridine synthase => putative tRNA-dihydrouridine synthase
[10:41:35] Modify product: Transcription termination factor Rho => hypothetical protein
[10:41:35] Modify product: Transcription termination/antitermination protein NusA => hypothetical protein
[10:41:35] Modify product: Probable phospholipid ABC transporter-binding protein MlaD => putative phospholipid ABC transporter-binding protein MlaD
[10:41:35] Modify product: Transcription termination/antitermination protein NusG => hypothetical protein
[10:41:35] Modify product: Co-chaperone protein HscB homolog => hypothetical protein
[10:41:35] Modify product: N utilization substance protein B homolog => hypothetical protein
[10:41:35] Cleaned 34 /product names
[10:41:35] Deleting unwanted file: /home/yquentin/work/wolbachia/prokka/wCle/proteins.faa
[10:41:35] Deleting unwanted file: /home/yquentin/work/wolbachia/prokka/wCle/proteins.bls
[10:41:36] There are still 754 unannotated CDS left (started with 1368)
[10:41:36] Will use hmmer3 to search against /usr/local/bioinfo/src/PROKKA/prokka-1.10/bin/../db/hmm/HAMAP.hmm with 8 CPUs
[10:41:36] Running: cat \/home\/yquentin\/work\/wolbachia\/prokka\/wCle\/proteins\.faa | parallel --gnu -j 8 --block 8665 --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\/wCle\/proteins\.bls 2> /dev/null
[10:41:44] Deleting unwanted file: /home/yquentin/work/wolbachia/prokka/wCle/proteins.faa
[10:41:44] Deleting unwanted file: /home/yquentin/work/wolbachia/prokka/wCle/proteins.bls
[10:41:45] There are still 723 unannotated CDS left (started with 1368)
[10:41:45] Will use hmmer3 to search against /usr/local/bioinfo/src/PROKKA/prokka-1.10/bin/../db/hmm/CLUSTERS.hmm with 8 CPUs
[10:41:45] Running: cat \/home\/yquentin\/work\/wolbachia\/prokka\/wCle\/proteins\.faa | parallel --gnu -j 8 --block 8037 --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\/wCle\/proteins\.bls 2> /dev/null
[10:42:09] Deleting unwanted file: /home/yquentin/work/wolbachia/prokka/wCle/proteins.faa
[10:42:09] Deleting unwanted file: /home/yquentin/work/wolbachia/prokka/wCle/proteins.bls
[10:42:09] There are still 695 unannotated CDS left (started with 1368)
[10:42:09] Will use hmmer3 to search against /usr/local/bioinfo/src/PROKKA/prokka-1.10/bin/../db/hmm/Pfam.hmm with 8 CPUs
[10:42:09] Running: cat \/home\/yquentin\/work\/wolbachia\/prokka\/wCle\/proteins\.faa | parallel --gnu -j 8 --block 7666 --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\/wCle\/proteins\.bls 2> /dev/null
[10:42:35] Modify product: Transposase DDE domain => Transposase DDE domain protein
[10:42:35] Modify product: Transposase DDE domain => Transposase DDE domain protein
[10:42:35] Modify product: Transposase DDE domain => Transposase DDE domain protein
[10:42:35] Modify product: Transposase DDE domain => Transposase DDE domain protein
[10:42:35] Modify product: Sodium:dicarboxylate symporter family => Sodium:dicarboxylate symporter family protein
[10:42:35] Modify product: Transposase DDE domain => Transposase DDE domain protein
[10:42:35] Modify product: Transposase DDE domain => Transposase DDE domain protein
[10:42:35] Modify product: Transposase DDE domain => Transposase DDE domain protein
[10:42:35] Modify product: Transposase DDE domain => Transposase DDE domain protein
[10:42:35] Modify product: Piwi/Argonaute/Zwille siRNA-binding domain => Piwi/Argonaute/Zwille siRNA-binding domain protein
[10:42:35] Modify product: TrbC/VIRB2 family => TrbC/VIRB2 family protein
[10:42:35] Modify product: TrbC/VIRB2 family => TrbC/VIRB2 family protein
[10:42:35] Modify product: TrbC/VIRB2 family => TrbC/VIRB2 family protein
[10:42:35] Modify product: SPFH domain / Band 7 family => SPFH domain / Band 7 family protein
[10:42:35] Modify product: Phage capsid family => Phage capsid family protein
[10:42:35] Modify product: Transposase DDE domain => Transposase DDE domain protein
[10:42:35] Modify product: Phage capsid family => Phage capsid family protein
[10:42:35] Modify product: Transposase DDE domain => Transposase DDE domain protein
[10:42:35] Modify product: Transposase DDE domain => Transposase DDE domain protein
[10:42:35] Modify product: Transposase DDE domain => Transposase DDE domain protein
[10:42:35] Modify product: Transposase DDE domain => Transposase DDE domain protein
[10:42:35] Modify product: Tim44-like domain => Tim44-like domain protein
[10:42:35] Modify product: Ankyrin repeat => Ankyrin repeat protein
[10:42:35] Modify product: Transposase DDE domain => Transposase DDE domain protein
[10:42:35] Modify product: Transposase DDE domain => Transposase DDE domain protein
[10:42:35] Modify product: Na+/H+ antiporter family => Na+/H+ antiporter family protein
[10:42:35] Modify product: Transposase DDE domain => Transposase DDE domain protein
[10:42:35] Modify product: Acetyltransferase (GNAT) family => Acetyltransferase (GNAT) family protein
[10:42:35] Modify product: Transposase DDE domain => Transposase DDE domain protein
[10:42:35] Modify product: Transposase DDE domain => Transposase DDE domain protein
[10:42:35] Modify product: EVE domain => EVE domain protein
[10:42:35] Modify product: Transposase DDE domain => Transposase DDE domain protein
[10:42:35] Modify product: TrbC/VIRB2 family => TrbC/VIRB2 family protein
[10:42:35] Modify product: Transposase DDE domain => Transposase DDE domain protein
[10:42:35] Modify product: Transposase DDE domain => Transposase DDE domain protein
[10:42:35] Modify product: Transposase DDE domain => Transposase DDE domain protein
[10:42:35] Modify product: Transposase DDE domain => Transposase DDE domain protein
[10:42:35] Modify product: Transposase DDE domain => Transposase DDE domain protein
[10:42:35] Modify product: PD-(D/E)XK nuclease superfamily => PD-(D/E)XK nuclease superfamily protein
[10:42:35] Modify product: Transposase DDE domain => Transposase DDE domain protein
[10:42:35] Modify product: Transposase DDE domain => Transposase DDE domain protein
[10:42:35] Modify product: Transposase DDE domain => Transposase DDE domain protein
[10:42:35] Modify product: Transposase DDE domain => Transposase DDE domain protein
[10:42:35] Modify product: Transposase IS116/IS110/IS902 family => Transposase IS116/IS110/IS902 family protein
[10:42:35] Modify product: Transposase DDE domain => Transposase DDE domain protein
[10:42:35] Modify product: Transposase DDE domain => Transposase DDE domain protein
[10:42:35] Modify product: Transposase DDE domain => Transposase DDE domain protein
[10:42:35] Modify product: Transposase DDE domain => Transposase DDE domain protein
[10:42:35] Modify product: Transposase DDE domain => Transposase DDE domain protein
[10:42:35] Modify product: Transposase DDE domain => Transposase DDE domain protein
[10:42:35] Modify product: Transposase DDE domain => Transposase DDE domain protein
[10:42:35] Modify product: Uracil DNA glycosylase superfamily => Uracil DNA glycosylase superfamily protein
[10:42:35] Modify product: Transposase DDE domain => Transposase DDE domain protein
[10:42:35] Modify product: Transposase DDE domain => Transposase DDE domain protein
[10:42:35] Modify product: Ankyrin repeat => Ankyrin repeat protein
[10:42:35] Modify product: Transposase DDE domain => Transposase DDE domain protein
[10:42:35] Modify product: Ankyrin repeat => Ankyrin repeat protein
[10:42:35] Modify product: RmlD substrate binding domain => RmlD substrate binding domain protein
[10:42:35] Modify product: Transposase DDE domain => Transposase DDE domain protein
[10:42:35] Modify product: Transposase DDE domain => Transposase DDE domain protein
[10:42:35] Modify product: Transposase DDE domain => Transposase DDE domain protein
[10:42:35] Modify product: Transposase DDE domain => Transposase DDE domain protein
[10:42:35] Modify product: COQ9 => hypothetical protein
[10:42:35] Modify product: Transposase DDE domain => Transposase DDE domain protein
[10:42:35] Modify product: Transposase DDE domain => Transposase DDE domain protein
[10:42:35] Modify product: Transposase DDE domain => Transposase DDE domain protein
[10:42:35] Modify product: Transposase IS116/IS110/IS902 family => Transposase IS116/IS110/IS902 family protein
[10:42:35] Modify product: Transposase DDE domain => Transposase DDE domain protein
[10:42:35] Modify product: Transposase DDE domain => Transposase DDE domain protein
[10:42:35] Modify product: Bacterial SH3 domain => Bacterial SH3 domain protein
[10:42:35] Modify product: Transposase DDE domain => Transposase DDE domain protein
[10:42:35] Modify product: Transposase DDE domain => Transposase DDE domain protein
[10:42:35] Modify product: Transposase DDE domain => Transposase DDE domain protein
[10:42:35] Modify product: Transposase DDE domain => Transposase DDE domain protein
[10:42:35] Modify product: Transposase DDE domain => Transposase DDE domain protein
[10:42:35] Modify product: Transposase DDE domain => Transposase DDE domain protein
[10:42:35] Modify product: Transposase DDE domain => Transposase DDE domain protein
[10:42:35] Modify product: RDD family => RDD family protein
[10:42:35] Modify product: Transposase DDE domain => Transposase DDE domain protein
[10:42:35] Modify product: Transposase DDE domain => Transposase DDE domain protein
[10:42:35] Modify product: Transposase DDE domain => Transposase DDE domain protein
[10:42:35] Modify product: Transposase DDE domain => Transposase DDE domain protein
[10:42:35] Modify product: Ankyrin repeat => Ankyrin repeat protein
[10:42:35] Modify product: AsmA family => AsmA family protein
[10:42:35] Modify product: RDD family => RDD family protein
[10:42:35] Modify product: Transposase DDE domain => Transposase DDE domain protein
[10:42:35] Modify product: Transposase DDE domain => Transposase DDE domain protein
[10:42:35] Modify product: Transposase DDE domain => Transposase DDE domain protein
[10:42:35] Modify product: Transposase DDE domain => Transposase DDE domain protein
[10:42:35] Modify product: Transposase DDE domain => Transposase DDE domain protein
[10:42:35] Modify product: Terminase-like family => Terminase-like family protein
[10:42:35] Modify product: SURF1 family => SURF1 family protein
[10:42:35] Modify product: Transposase DDE domain => Transposase DDE domain protein
[10:42:35] Modify product: Acetyltransferase (GNAT) family => Acetyltransferase (GNAT) family protein
[10:42:35] Modify product: Transposase DDE domain => Transposase DDE domain protein
[10:42:35] Modify product: Transposase DDE domain => Transposase DDE domain protein
[10:42:35] Modify product: Transposase DDE domain => Transposase DDE domain protein
[10:42:35] Modify product: Transposase DDE domain => Transposase DDE domain protein
[10:42:35] Modify product: Transposase DDE domain => Transposase DDE domain protein
[10:42:35] Modify product: Transposase DDE domain => Transposase DDE domain protein
[10:42:35] Modify product: Transposase DDE domain => Transposase DDE domain protein
[10:42:35] Modify product: Transposase DDE domain => Transposase DDE domain protein
[10:42:35] Modify product: Terminase-like family => Terminase-like family protein
[10:42:35] Modify product: Sodium:dicarboxylate symporter family => Sodium:dicarboxylate symporter family protein
[10:42:35] Modify product: Transposase DDE domain => Transposase DDE domain protein
[10:42:35] Modify product: Transposase DDE domain => Transposase DDE domain protein
[10:42:35] Modify product: Transposase DDE domain => Transposase DDE domain protein
[10:42:35] Modify product: Transposase DDE domain => Transposase DDE domain protein
[10:42:35] Modify product: Transposase DDE domain => Transposase DDE domain protein
[10:42:35] Modify product: Transposase DDE domain => Transposase DDE domain protein
[10:42:35] Modify product: Ankyrin repeat => Ankyrin repeat protein
[10:42:35] Modify product: KAP family P-loop domain => KAP family P-loop domain protein
[10:42:35] Modify product: Transposase DDE domain => Transposase DDE domain protein
[10:42:35] Modify product: Transposase DDE domain => Transposase DDE domain protein
[10:42:35] Modify product: Transposase DDE domain => Transposase DDE domain protein
[10:42:35] Modify product: Transposase DDE domain => Transposase DDE domain protein
[10:42:35] Modify product: Transposase DDE domain => Transposase DDE domain protein
[10:42:35] Modify product: Ankyrin repeat => Ankyrin repeat protein
[10:42:35] Modify product: Transposase DDE domain => Transposase DDE domain protein
[10:42:35] Modify product: Transposase DDE domain => Transposase DDE domain protein
[10:42:35] Modify product: Transposase DDE domain => Transposase DDE domain protein
[10:42:35] Modify product: Transposase DDE domain => Transposase DDE domain protein
[10:42:35] Modify product: Transposase DDE domain => Transposase DDE domain protein
[10:42:35] Modify product: Transposase DDE domain => Transposase DDE domain protein
[10:42:35] Modify product: Transposase DDE domain => Transposase DDE domain protein
[10:42:35] Modify product: Transposase DDE domain => Transposase DDE domain protein
[10:42:35] Modify product: Transposase DDE domain => Transposase DDE domain protein
[10:42:35] Modify product: MgtE intracellular N domain => MgtE intracellular N domain protein
[10:42:35] Modify product: Major Facilitator Superfamily => Major Facilitator Superfamily protein
[10:42:35] Modify product: Transposase DDE domain => Transposase DDE domain protein
[10:42:35] Modify product: Transposase DDE domain => Transposase DDE domain protein
[10:42:35] Modify product: Transposase DDE domain => Transposase DDE domain protein
[10:42:35] Modify product: Helix-turn-helix domain => Helix-turn-helix domain protein
[10:42:35] Modify product: Transposase DDE domain => Transposase DDE domain protein
[10:42:35] Modify product: Transposase DDE domain => Transposase DDE domain protein
[10:42:35] Modify product: Transposase DDE domain => Transposase DDE domain protein
[10:42:35] Modify product: Transposase DDE domain => Transposase DDE domain protein
[10:42:35] Modify product: Transposase DDE domain => Transposase DDE domain protein
[10:42:35] Modify product: Ankyrin repeat => Ankyrin repeat protein
[10:42:35] Modify product: Transposase DDE domain => Transposase DDE domain protein
[10:42:35] Modify product: Transposase DDE domain => Transposase DDE domain protein
[10:42:35] Modify product: Transposase DDE domain => Transposase DDE domain protein
[10:42:35] Modify product: ETC complex I subunit conserved region => hypothetical protein
[10:42:35] Modify product: RDD family => RDD family protein
[10:42:35] Modify product: Transposase DDE domain => Transposase DDE domain protein
[10:42:35] Modify product: Transposase DDE domain => Transposase DDE domain protein
[10:42:35] Modify product: Transposase DDE domain => Transposase DDE domain protein
[10:42:35] Modify product: Transposase DDE domain => Transposase DDE domain protein
[10:42:35] Modify product: Terminase-like family => Terminase-like family protein
[10:42:35] Modify product: Integral membrane protein TerC family => Integral membrane protein TerC family protein
[10:42:35] Modify product: Ankyrin repeat => Ankyrin repeat protein
[10:42:35] Modify product: Transposase DDE domain => Transposase DDE domain protein
[10:42:35] Modify product: Transposase DDE domain => Transposase DDE domain protein
[10:42:35] Modify product: Transposase DDE domain => Transposase DDE domain protein
[10:42:35] Modify product: Transposase DDE domain => Transposase DDE domain protein
[10:42:35] Modify product: Transposase DDE domain => Transposase DDE domain protein
[10:42:35] Modify product: Transposase DDE domain => Transposase DDE domain protein
[10:42:35] Modify product: Transposase DDE domain => Transposase DDE domain protein
[10:42:35] Modify product: Transposase DDE domain => Transposase DDE domain protein
[10:42:35] Modify product: Alpha/beta hydrolase family => Alpha/beta hydrolase family protein
[10:42:35] Modify product: Transposase DDE domain => Transposase DDE domain protein
[10:42:35] Cleaned 161 /product names
[10:42:35] Deleting unwanted file: /home/yquentin/work/wolbachia/prokka/wCle/proteins.faa
[10:42:35] Deleting unwanted file: /home/yquentin/work/wolbachia/prokka/wCle/proteins.bls
[10:42:35] Labelling remaining 449 proteins as 'hypothetical protein'
[10:42:35] Possible /pseudo 'Inner membrane transport protein YdhC' at gnl|Prokka|wCle_contig000001 position 69101
[10:42:35] Possible /pseudo 'Transposase DDE domain protein' at gnl|Prokka|wCle_contig000001 position 359926
[10:42:35] Possible /pseudo 'Transposase DDE domain protein' at gnl|Prokka|wCle_contig000001 position 396211
[10:42:35] Possible /pseudo 'Transposase DDE domain protein' at gnl|Prokka|wCle_contig000001 position 446009
[10:42:35] Possible /pseudo 'Transposase DDE domain protein' at gnl|Prokka|wCle_contig000001 position 489797
[10:42:35] Possible /pseudo 'ATP-dependent Clp protease ATP-binding subunit ClpA' at gnl|Prokka|wCle_contig000001 position 490731
[10:42:35] Possible /pseudo 'ATP-dependent Clp protease ATP-binding subunit ClpA' at gnl|Prokka|wCle_contig000001 position 491475
[10:42:35] Possible /pseudo 'PD-(D/E)XK nuclease family transposase' at gnl|Prokka|wCle_contig000001 position 497758
[10:42:35] Possible /pseudo 'PD-(D/E)XK nuclease family transposase' at gnl|Prokka|wCle_contig000001 position 498624
[10:42:35] Possible /pseudo 'Response regulator PleD' at gnl|Prokka|wCle_contig000001 position 512504
[10:42:35] Possible /pseudo 'Transposase DDE domain protein' at gnl|Prokka|wCle_contig000001 position 794710
[10:42:35] Possible /pseudo 'PD-(D/E)XK nuclease family transposase' at gnl|Prokka|wCle_contig000001 position 823895
[10:42:35] Possible /pseudo 'Transposase DDE domain protein' at gnl|Prokka|wCle_contig000001 position 863578
[10:42:35] Possible /pseudo 'Transposase DDE domain protein' at gnl|Prokka|wCle_contig000001 position 893881
[10:42:35] Possible /pseudo 'Queuine tRNA-ribosyltransferase' at gnl|Prokka|wCle_contig000001 position 972598
[10:42:35] Possible /pseudo 'Arginine/agmatine antiporter' at gnl|Prokka|wCle_contig000001 position 981798
[10:42:35] Possible /pseudo 'TrbL/VirB6 plasmid conjugal transfer protein' at gnl|Prokka|wCle_contig000001 position 1004873
[10:42:35] Possible /pseudo 'TrbL/VirB6 plasmid conjugal transfer protein' at gnl|Prokka|wCle_contig000001 position 1007263
[10:42:35] Possible /pseudo 'TrbL/VirB6 plasmid conjugal transfer protein' at gnl|Prokka|wCle_contig000001 position 1010469
[10:42:35] Possible /pseudo 'putative zinc protease' at gnl|Prokka|wCle_contig000001 position 1164269
[10:42:35] Found 558 unique /gene codes.
[10:42:35] Fixed 36 colliding /gene names.
[10:42:35] Adding /locus_tag identifiers
[10:42:35] Assigned 1406 locus_tags to CDS and RNA features.
[10:42:35] Writing outputs to /home/yquentin/work/wolbachia/prokka/wCle/
[10:42:37] Generating annotation statistics file
[10:42:37] Generating Genbank and Sequin files
[10:42:37] 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\/wCle\/wCle\.err -i \/home\/yquentin\/work\/wolbachia\/prokka\/wCle\/wCle\.fsa 2> /dev/null
[10:42:40] Deleting unwanted file: /home/yquentin/work/wolbachia/prokka/wCle/errorsummary.val
[10:42:40] Deleting unwanted file: /home/yquentin/work/wolbachia/prokka/wCle/wCle.dr
[10:42:40] Deleting unwanted file: /home/yquentin/work/wolbachia/prokka/wCle/wCle.fixedproducts
[10:42:40] Deleting unwanted file: /home/yquentin/work/wolbachia/prokka/wCle/wCle.ecn
[10:42:40] Deleting unwanted file: /home/yquentin/work/wolbachia/prokka/wCle/wCle.val
[10:42:40] Output files:
[10:42:40] /home/yquentin/work/wolbachia/prokka/wCle/wCle.sqn
[10:42:40] /home/yquentin/work/wolbachia/prokka/wCle/wCle.err
[10:42:40] /home/yquentin/work/wolbachia/prokka/wCle/wCle.faa
[10:42:40] /home/yquentin/work/wolbachia/prokka/wCle/wCle.fna
[10:42:40] /home/yquentin/work/wolbachia/prokka/wCle/wCle.gff
[10:42:40] /home/yquentin/work/wolbachia/prokka/wCle/wCle.fsa
[10:42:40] /home/yquentin/work/wolbachia/prokka/wCle/wCle.log
[10:42:40] /home/yquentin/work/wolbachia/prokka/wCle/wCle.txt
[10:42:40] /home/yquentin/work/wolbachia/prokka/wCle/wCle.ffn
[10:42:40] /home/yquentin/work/wolbachia/prokka/wCle/wCle.gbk
[10:42:40] /home/yquentin/work/wolbachia/prokka/wCle/wCle.tbl
[10:42:40] Walltime used: 1.38 minutes
[10:42:40] If you use this result please cite the Prokka paper:
[10:42:40] Seemann T (2014) Prokka: rapid prokaryotic genome annotation. Bioinformatics. 30(14):2068-9.
[10:42:40] Type 'prokka --citation' for more details.
[10:42:40] Share and enjoy!