[maker-devel] Maker issues

[Daniel Standage]

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
>>
>>
>
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