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Re: [Cg-pipeline-users] run_annotation_genbank.pl and compatibility with interproscan5
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From: Laure Q. <Lau...@if...> - 2013-06-26 12:41:59
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Here are the first lines of the file /mnt/data2/home1/lquintri/cgtest/annotation/aa.fasta.card_hits.sql cgtest_0001|NC_011595.7058613.p01|1.6|12.16|/home12/caparmor/bioinfo/softs/sources/cgp/data/CARD.faa|43.59|445|MacA. [M] COG0845 Membrane-fusion protein. Encoded by gene ABBFA_003018. Homology: Secretion protein HlyD (HMMPfam: PF00529, score: 9.1e-08). ARO:1000001 process or component of antibiotic biology or chemistry. ARO:3000533 macA. [Acinetobacter baumannii AB307-0294]|1|55|25.8|56.4102564102564|NC_011595.7058613.p01|NC_011595.7058613.p01 cgtest_0001|NC_010410.6003290.p01|10.0|22.97|/home12/caparmor/bioinfo/softs/sources/cgp/data/CARD.faa|20.55|483|putative Outer membrane efflux protein. Evidence 3 : Function proposed based on presence of conserved amino acid motif, structural feature or limited homology; Product type pm : putative membrane component. Encoded by gene ABAYE1172. Homology: Outer membrane efflux protein (HMMPfam: PF02321, score: 7.6e-26). ARO:1000001 process or component of antibiotic biology or chemistry. ARO:3000779 adeH. [Acinetobacter baumannii AYE]|2|49|23.5|45.2054794520548|NC_010410.6003290.p01|NC_010410.6003290.p01 cgtest_0002|AJ250203.gene.p01|0.62|25.97|/home12/caparmor/bioinfo/softs/sources/cgp/data/CARD.faa|31.34|410|tet31 protein. Encoded by gene tet31. ARO:3000476 tet31. ARO:1000001 process or component of antibiotic biology or chemistry. [Aeromonas salmonicida]|1|57|26.6|43.2835820895522|AJ250203.gene.p01|AJ250203.gene.p01 cgtest_0003|NC_005054.2598278.p01|7.6|9.73|/home12/caparmor/bioinfo/softs/sources/cgp/data/CARD.faa|61.11|384|sensor histidine kinase VanS. Homology: Signal transduction histidine kinase-related protein, C-terminal (FPrintScan: PR00344, score: 7.5e-10). similar to PIR:B41838, and PIR:B41838; identified by sequence similarity; putative. Homology: ATPase-like, ATP-binding domain (HMMPfam: PF02518, score: 5.5e-22) (Gene3D: G3DSA:3.30.565.10, score: 5.7e-28). Homology: Signal transduction histidine kinase, subgroup 1, dimerisation/phosphoacceptor domain (HMMPfam: PF00512, score: 7.7e-12). Encoded by gene vanS. ARO:1000001 process or component of antibiotic biology or chemistry. ARO:3000071 vanS. [Staphylococcus aureus]|1|48|23.1|72.2222222222222|NC_005054.2598278.p01|NC_005054.2598278.p01 cgtest_0003|NC_014475.1.orf1.gene.p01|7.9|9.73|/home12/caparmor/bioinfo/softs/sources/cgp/data/CARD.faa|61.11|364|VanS. Encoded by gene vanS. ARO:1000001 process or component of antibiotic biology or chemistry. ARO:3000071 vanS. [Enterococcus faecalis]|2|47|22.7|72.2222222222222|NC_014475.1.orf1.gene.p01|NC_014475.1.orf1.gene.p01 cgtest_0005|NC_002758.1119966.p01|0.55|11.01|/home12/caparmor/bioinfo/softs/sources/cgp/data/CARD.faa|41.03|889|DNA gyrase subunit A. Encoded by gene gyrA. Homology: DNA topoisomerase, type IIA, subunit A/ C-terminal, alpha-beta (Gene3D: G3DSA:3.90.199.10, score: 8.6e-114). Homology: DNA gyrase/topoisomerase IV, subunit A, C-terminal beta-pinwheel (HMMPfam: PF03989, score: 1.6e-11). Homology: DNA topoisomerase, type IIA, subunit A, alpha-helical (Gene3D: G3DSA:1.10.268.10, score: 2.1e-31). Homology: DNA topoisomerase, type IIA, subunit A/C-terminal (HMMPfam: PF00521, score: 2.1e-157). ARO:1000001 process or component of antibiotic biology or chemistry. ARO:3000618 fluoroquinolone resistant gyrA. [Staphylococcus aureus subsp. aureus Mu50]|5|60|27.7|51.2820512820513|NC_002758.1119966.p01|NC_002758.1119966.p01 cgtest_0005|NC_002951.3236187.p01|0.55|11.01|/home12/caparmor/bioinfo/softs/sources/cgp/data/CARD.faa|41.03|887|DNA gyrase, A subunit. Encoded by gene gyrA. Homology: DNA topoisomerase, type IIA, subunit A/ C-terminal, alpha-beta (Gene3D: G3DSA:3.90.199.10, score: 4.2e-114). Homology: DNA topoisomerase, type IIA, subunit A/C-terminal (HMMPfam: PF00521, score: 8.3e-158). Homology: DNA topoisomerase, type IIA, subunit A, alpha-helical (Gene3D: G3DSA:1.10.268.10, score: 1.5e-31). identified by similarity to SP:P20831; match to protein family HMM PF00521; match to protein family HMM PF03989; match to protein family HMM TIGR01063. Homology: DNA gyrase/topoisomerase IV, subunit A, C-terminal beta-pinwheel (HMMPfam: PF03989, score: 1.6e-11). ARO:1000001 process or component of antibiotic biology or chemistry. ARO:3000618 fluoroquinolone resistant gyrA. [Staphylococcus aureus subsp. aureus COL]|2|60|27.7|51.2820512820513|NC_002951.3236187.p01|NC_002951.3236187.p01 Le 26/06/2013 14:11, Lee Katz a écrit : > This might be a bug that I introduced if you are using the SVN version. > Could you show me the first few lines of this file? > > /mnt/data2/home1/lquintri/cgtest/annotation/aa.fasta.card_hits.sql > > > On Wed, Jun 26, 2013 at 5:09 AM, Laure QUINTRIC > <Lau...@if... <mailto:Lau...@if...>> wrote: > > Hello, > > do you plan to update cg-pipeline in order to handle interproscan5 xml > output, which is different from interproscan4 ? > > I also have the error below, do you have an idea of the problem ? > ANNOTATION GENBANK FILE CREATION START on cgtest Tue Jun 25 19:20:04 > (CG-Pipeline v0.4.0.0) > COMMAND > run_annotation_genbank.pl <http://run_annotation_genbank.pl> > --organism=cgtest > --prediction=/mnt/data2/home1/lquintri/cgtest/prediction.gb > <http://prediction.gb> > --inputdir=/mnt/data2/home1/lquintri/cgtest/annotation > --gb=/mnt/data2/home1/lquintri/cgtest/annotation.gb > <http://annotation.gb> 2>&1 |tee --append > cgtest/log/genbank.txt > run_annotation_genbank.pl <http://run_annotation_genbank.pl>: > main::main: Putting all annotations in > /mnt/data2/home1/lquintri/cgtest/annotation into memory > run_annotation_genbank.pl <http://run_annotation_genbank.pl>: > main::main: Transforming the prediction > genbank into a set of features > run_annotation_genbank.pl <http://run_annotation_genbank.pl>: > main::readSqlFile: TID3 > /mnt/data2/home1/lquintri/cgtest/annotation/aa.fasta.card_hits.sql > > --------------------- WARNING --------------------- > MSG: exception while parsing location line [1..25250] in reading > EMBL/GenBank/SwissProt, ignoring feature source > (seqid=NODE_100_length_25148_cov_343.557709): Eval-group not allowed at > runtime, use re 'eval' in regex m/(.*?)\(((?x-ism: > (?> > [^()]+ > | > \( > (??{.../ at > /home12/caparmor/bioinfo/softs/perlmodules/lib/perl5/Bio/Factory/FTLocationFactory.pm > line 160, <GEN0> line 14. > > --------------------------------------------------- > Thread 2 terminated abnormally: Can't call method "primary_tag" on an > undefined value at > /home12/caparmor/bioinfo/softs/perlmodules/lib/perl5/Bio/SeqIO/genbank.pm > <http://genbank.pm> line > 687, <GEN0> line 14. > Can't use an undefined value as an ARRAY reference at > /mnt/data/home12/bioinfo/softs/sources/cgp/scripts/run_annotation_genbank.pl > <http://run_annotation_genbank.pl> > line 43. > Perl exited with active threads: > 2 running and unjoined > -1 finished and unjoined > 0 running and detached > ANNOTATION GENBANK END on cgtest Tue Jun 25 19:20:04 (CG-Pipeline > v0.4.0.0) > > Thank you, > Regards, > Laure > > ------------------------------------------------------------------------------ > This SF.net email is sponsored by Windows: > > Build for Windows Store. > > http://p.sf.net/sfu/windows-dev2dev > _______________________________________________ > Cg-pipeline-users mailing list > Cg-...@li... > <mailto:Cg-...@li...> > https://lists.sourceforge.net/lists/listinfo/cg-pipeline-users > > > > > -- > Lee Katz, Ph.D. |
