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

[Lee K. <ls...@gm...>]

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...>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 --organism=cgtest
> --prediction=/mnt/data2/home1/lquintri/cgtest/prediction.gb
> --inputdir=/mnt/data2/home1/lquintri/cgtest/annotation
> --gb=/mnt/data2/home1/lquintri/cgtest/annotation.gb 2>&1 |tee --append
> cgtest/log/genbank.txt
> run_annotation_genbank.pl: main::main: Putting all annotations in
> /mnt/data2/home1/lquintri/cgtest/annotation into memory
> run_annotation_genbank.pl: main::main: Transforming the prediction
> genbank into a set of features
> 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.pmline
> 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
> 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.