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

[Olaf Mueller]

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
>>
>>
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>

-- 
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