[maker-devel] Maker issues

[Daniel Standage]

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.



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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
>>>
>>>
>>
>
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