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

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

As of now, I do not have any concrete plans to handle Interpro5 yet just
because of time constraints, but I would love to. The newest SVN source
code however will let you skip interproscan with the "--skip INTERPRO"
option.  I realize that everyone does not want every kind of annotation
every time, and so I introduced some controls in run_annotation: --skip,
--just, and --goto (skip and just can be invoked multiple times in a single
command).

I would love a volunteer for the new Interpro script!  Volunteers: please
contact me directly.  I have so many other distinct ideas for modules, but
I don't have any time.  The good news is that the ideas are very modular
and so it is possible for volunteers to be semi-independent.


On Wed, Jun 26, 2013 at 8:11 AM, Lee Katz <ls...@gm...> wrote:

> 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.
>



-- 
Lee Katz, Ph.D.