Re: [Cg-pipeline-users] run_annotation_genbank.pl and compatibility with interproscan5

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I'm not really sure what to make out of this yet, except the error is
complaining about a source tag.  Is there a line in the CARD output file
with the stop site as 25250?  If so, could you send it to me?  I will bet
that it just needs to be removed from the file, but I'm not completely
sure.  You could back up the sql file and then remove the aforementioned
line from it and try again.

On Wed, Jun 26, 2013 at 8:41 AM, Laure QUINTRIC
<Lau...@if...>wrote:

> 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:Laure.Quintric@**ifremer.fr<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<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<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<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<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>
>>     <http://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
>>
>>     ------------------------------**------------------------------**
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>>
>>
>>
>>
>> --
>> Lee Katz, Ph.D.
>>
>

-- 
Lee Katz, Ph.D.

Re: [Cg-pipeline-users] run_annotation_genbank.pl and compatibility with interproscan5

A computational genomics pipeline for prokaryotic sequencing projects

Re: [Cg-pipeline-users] run_annotation_genbank.pl and compatibility with interproscan5