<html>
<head>
<meta content="text/html; charset=ISO-8859-1"
http-equiv="Content-Type">
</head>
<body bgcolor="#FFFFFF" text="#000000">
Dear Zhang<br>
<br>
As you mention, if the object is a
Bio::EnsEMBL::Compara::Production::DnaFragChunk, Perl should be
looking for the 'dnafrag' method in that module (or one of its
parents).<br>
<br>
I have noticed that this call is made in a loop. Could you please
check that the $qy_dna_object is always a
Bio::EnsEMBL::Compara::Production::DnaFragChunk object? I am
guessing that in subsequent iterations, the variable is set to
something different.<br>
<br>
Could also please tell us what version of the API you are using?<br>
<br>
Thanks<br>
<br>
Javier<br>
<br>
On 01/12/11 08:14, Zhang Di wrote:
<blockquote
cite="mid:CAMHeD-dPYaBz7veR42MxoTrVKsTHt9MDMVacv-E+XQtBsPCmBg@mail.gmail.com"
type="cite">
<div>Hi,</div>
<div>
<div><br>
</div>
<div><br>
</div>
</div>
<div> I'm running the compara pipeline for 2x alignment (first
run PairAligner then Chain Net).</div>
<div> The raw and chain steps works fine.</div>
<div> the pipeline failed at the CreateAlignmentNetsJobs step
complaining that: </div>
<div><br>
</div>
<blockquote style="margin: 0 0 0 40px; border: none; padding:
0px;">
<div>Job with id=8380 died in status 'RUN' for the following
reason: Can't locate object method "dnafrag" via package
"Bio::EnsEMBL::Compara::Production::DnaFragChunkSet" at
/data/ensembl/ensembl-compara/modules/Bio/EnsEMBL/Compara/Production/GenomicAlignBlock/CreateAlignmentNetsJobs.pm
line 200.</div>
</blockquote>
<div><br>
</div>
<div> After some debug effort (just print "$qy_dna_object";), I
found that $qy_dna_object is an instance of
Bio::EnsEMBL::Compara::Production::DnaFragChunk, and this class
has the method 'dnafrag'.</div>
<div>
<div><br>
</div>
<div> I'm not very familiar with perl object-oriented
system. why did it try to find method 'dnafrag' via
package Bio::EnsEMBL::Compara::Production::DnaFragChunkSet
while the data is an instance of DnaFragChunk?</div>
</div>
<div><br>
</div>
-- <br>
Zhang Di<br>
<br>
<fieldset class="mimeAttachmentHeader"></fieldset>
<br>
<pre wrap="">_______________________________________________
Dev mailing list <a class="moz-txt-link-abbreviated" href="mailto:Dev@ensembl.org">Dev@ensembl.org</a>
List admin (including subscribe/unsubscribe): <a class="moz-txt-link-freetext" href="http://lists.ensembl.org/mailman/listinfo/dev">http://lists.ensembl.org/mailman/listinfo/dev</a>
Ensembl Blog: <a class="moz-txt-link-freetext" href="http://www.ensembl.info/">http://www.ensembl.info/</a>
</pre>
</blockquote>
<br>
<pre class="moz-signature" cols="72">--
Javier Herrero, PhD
Ensembl Compara Project Leader
European Bioinformatics Institute (EMBL-EBI)
Wellcome Trust Genome Campus, Hinxton
Cambridge - CB10 1SD - UK</pre>
</body>
</html>