[maker-devel] maker-2.23 with tophat / cufflinks input

[Carson Holt]

You should be fine then.  It may never even happen again (semi-random),
but if it does, you can try reinstalling the Proc::ProcessTable module
from CPAN.  You can also change line 89 from 'require Proc::ProcessTable'
to 'use Proc::ProcessTable', which would load at the start rather than at
runtime (safe to do on your system because Proc::ProcessTable is already
there).

Thanks,
Carson



On 12-02-23 12:41 PM, "Olaf Mueller" <olaf.mueller at duke.edu> wrote:

>Thanks Carson,
>
>That's good to know. I'm running maker on a single machine (dual Xeon
>quad cores) under linux x64 (ubuntu 11.04), and maker was compiled on
>this computer without MPICH2 hooked in.
>
>Best
>Olaf
>
>On 02/23/2012 12:31 PM, Carson Holt wrote:
>> The error is caused by a perl module that is loaded at runtime to access
>> the system's Process Table.  This is an error that sometimes happens in
>> cluster environments like SGE.  It's not related to the GFF3.  It's more
>> related to the specific system running MAKER at the time and can be
>> semi-random.  MAKER has auto-retry on contigs, so it would have done
>>it's
>> best to recover from any failure.  If the master_index_datastore.log
>>file
>> shows all input contigs as being of status FINISHED, you are fine.
>>
>> If you are on a cluster and you continually get the error you may need
>>to
>> install the Proc::ProcessTable locally on that specific node and not
>>just
>> globally for the cluster.  Errors with fold_constants happen when you
>> compile on one system and then run on another.  The issue can sometimes
>>be
>> related to floating points being slightly different between the two
>> systems.  So clusters that have non-identical architectures within the
>> same cluster can have these types of errors more often.
>>
>> Thanks,
>> Carson
>>
>>
>>
>> On 12-02-23 12:16 PM, "Olaf Mueller"<olaf.mueller at duke.edu>  wrote:
>>
>>> Hi,
>>>
>>> I've done a preliminary run on an alga genome with maker 2.23beta,
>>>using
>>> only mRNA-seq tophat/cufflinks input and no additional evidence source.
>>>
>>> As prerequisite a cufflinks transcripts.gtf (merged from different read
>>> sample mappings) has been converted with maker cufflinks2gff3
>>> (strandless transcripts/exons removed). I provided the resulting gff3
>>> via pred_gff and model_gff to maker, and also didn't call est2genome or
>>> other predictors.
>>>
>>> During maker run for some scaffolds, I receive this error message for
>>> some chunks, while gathering GFF3 input into hits:
>>>
>>> Gathering GFF3 input into hits - chunk:0
>>> panic: fold_constants JMPENV_PUSH returned 2 at
>>> /home/muol/Documents/Software/maker/lib/File/..//Proc/Signal.pm line 89
>>> Gathering GFF3 input into hits - chunk:2
>>> ...
>>>
>>> The index log nevertheless reports these scaffolds as finished and
>>> annotations are generated. Do I have to be concerned about this message
>>> because it is related to my cufflinks input?
>>>
>>> Thanks
>>> Olaf
>>>
>>>
>>> _______________________________________________
>>> maker-devel mailing list
>>> maker-devel at box290.bluehost.com
>>> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>>
>
>-- 
>Olaf Mueller, PhD
>Duke University
>Department of Biology, PO Box 90338
>369 Biological Sciences Bldg.
>Science Drive
>Durham, NC 27708, USA
>
>phone: (919) 660-7402
>email: olaf.mueller at duke.edu
>