[maker-devel] Maker issues

[Carson Holt]

Thanks.  Typo now fixed on my end too ;-)

Thanks,
Carson


From:  Daniel Standage <daniel.standage at gmail.com>
Date:  Wednesday, 7 November, 2012 11:43 AM
To:  Carson Holt <carsonhh at gmail.com>
Cc:  Maker Mailing List <maker-devel at yandell-lab.org>
Subject:  Re: Maker issues

Looked good for a while, but came across this error.

> total clusters:20 now processing 0
> flattening EST clusters
> doing tblastx of alt-ESTs
> Undefined subroutine &GI::loalize_file called at
> /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/GI.pm line 2648.
> --> rank=NA, hostname=c4
> ERROR: Failed while doing tblastx of alt-ESTs
> ERROR: Chunk failed at level:4, tier_type:2
> FAILED CONTIG:scaffold_58
> 
> ERROR: Chunk failed at level:5, tier_type:0
> FAILED CONTIG:scaffold_58
> 
> examining contents of the fasta file and run log
> Calling Datastore::MD5::mkdir at
> /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm line
> 433.
> Calling uri_escape at
> /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm line
> 433.
> Calling File::Path::mkpath at
> /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm line
> 433.
> 
> 
> 
> --Next Contig--

It seems pretty clear that there is a typo in GI.pm. I changed loalize to
localize and relaunched.


--
Daniel S. Standage
Ph.D. Candidate
Bioinformatics and Computational Biology Program
Department of Genetics, Development, and Cell Biology
Iowa State University



On Wed, Nov 7, 2012 at 9:30 AM, Daniel Standage <daniel.standage at gmail.com>
wrote:
> Done.
> 
> Test job has successfully cleared the preliminary Fasta indexing steps and is
> repeat masking. I'll let you know if there are any problems. Thanks!
> 
> 
> --
> Daniel S. Standage
> Ph.D. Candidate
> Bioinformatics and Computational Biology Program
> Department of Genetics, Development, and Cell Biology
> Iowa State University
> 
> 
> 
> On Wed, Nov 7, 2012 at 9:00 AM, Carson Holt <carsonhh at gmail.com> wrote:
>> 1.006902        Bio::Root::Version
>> /N/u/dstandag/Mason/local/src/PerlLibs/bioperl-live/Bio/Root/Version.pm
>> 
>> One thing I noticed, in the debug output is that you are using Bioperl live
>> (here -->  /N/u/dstandag/Mason/local/src/PerlLibs/bioperl-live).  It's fasta
>> indexer is broken.  I have an open bug I am trying to resolve with the
>> Bioperl developers, but for now use the CPAN version of Bioperl.
>> 
>> Thanks,
>> Carson
>> 
>> 
>> 
>> 
>> From:  Daniel Standage <daniel.standage at gmail.com>
>> Date:  Monday, 5 November, 2012 10:14 AM
>> To:  Carson Holt <carsonhh at gmail.com>
>> Cc:  Maker Mailing List <maker-devel at yandell-lab.org>
>> Subject:  Re: Maker issues
>> 
>> Debug output attached (bzip2 compressed).
>> 
>> 
>> --
>> Daniel S. Standage
>> Ph.D. Candidate
>> Bioinformatics and Computational Biology Program
>> Department of Genetics, Development, and Cell Biology
>> Iowa State University
>> 
>> 
>> 
>> On Mon, Nov 5, 2012 at 10:08 AM, Carson Holt <carsonhh at gmail.com> wrote:
>>> Thanks. Could you also run with the --debug flag set on the command line for
>>> a few minutes and send me that.
>>> 
>>> --Carson
>>> 
>>> 
>>> From:  Daniel Standage <daniel.standage at gmail.com>
>>> Date:  Monday, 5 November, 2012 10:05 AM
>>> To:  Carson Holt <carsonhh at gmail.com>, Maker Mailing List
>>> <maker-devel at yandell-lab.org>
>>> Subject:  Maker issues
>>> 
>>> Carson,
>>> 
>>> I updated to the latest development version, made sure the TMP directory is
>>> on native disk space, and relaunched. I have attached the output of the job
>>> that failed in <5 minutes. It looks pretty similar to the errors I got the
>>> last time I used the dev version.
>>> 
>>> --
>>> Daniel S. Standage
>>> Ph.D. Candidate
>>> Bioinformatics and Computational Biology Program
>>> Department of Genetics, Development, and Cell Biology
>>> Iowa State University
>>> 
>> 
> 



-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://yandell-lab.org/pipermail/maker-devel_yandell-lab.org/attachments/20121107/408eb35e/attachment-0003.html>