Solved!<br><br>The problem is that subroutine CreateAlignmentNetsJobs cannot handle DnaFragChunkSet class.<div><br>However, it is easy to solve: just use method 'get_all_DnaFragChunks' (below).</div><div><br></div>
<div>-------------------------------</div><div>Replace:</div><div><br></div><div> my $query_dna_list = $self->{'collection'}->get_all_dna_objects;</div><div><div> </div><div>To:</div><div><br></div><div> my $query_dna_list_raw = $self->{'collection'}->get_all_dna_objects;</div>
<div><br></div><div> my $query_dna_list;</div><div><br></div><div> for my $obj (@{$query_dna_list_raw}) {</div><div> if ($obj->isa("Bio::EnsEMBL::Compara::Production::DnaFragChunkSet")) {</div><div> push @{$query_dna_list}, @{$obj->get_all_DnaFragChunks};</div>
<div> } else {</div><div> push @{$query_dna_list}, $obj;</div><div> }</div><div> }</div><div><br></div><br><div class="gmail_quote">On Fri, Dec 2, 2011 at 9:24 AM, Zhang Di <span dir="ltr"><<a href="mailto:aureliano.jz@gmail.com">aureliano.jz@gmail.com</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;"><div>Thank you, Javier</div><div><br></div>Sorry for not checking the subsequent output!<div><br></div><div>The last line is Bio::EnsEMBL::Compara::Production::DnaFragChunkSet=HASH(0x1e16ed0)<br>
<br>Seems that it works well with Bio::EnsEMBL::Compara::Production::DnaFragChunk, without any problem finding the method 'dnafrag' for it.<br>
<br>I guess that the program died immediately after it met the first DnaFragChunkSet qy_dna_object.<br><br>I'm using the version 64 API. checked out 2 mouth ago at a same time.<div><div class="h5"><br><br><br><div class="gmail_quote">
On Fri, Dec 2, 2011 at 2:05 AM, Javier Herrero <span dir="ltr"><<a href="mailto:jherrero@ebi.ac.uk" target="_blank">jherrero@ebi.ac.uk</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div 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 $qy_dna_object is always a
Bio::EnsEMBL::Compara::Production::DnaFragChunk object? I am
guessing that in subsequent iterations, the variable is set to
something different.<br>
<br>
Could also please tell us what version of the API you are using?<br>
<br>
Thanks<br>
<br>
Javier<div><div><br>
<br>
On 01/12/11 08:14, Zhang Di wrote:
</div></div><blockquote type="cite"><div><div>
<div>Hi,</div>
<div>
<div><br>
</div>
<div><br>
</div>
</div>
<div> I'm running the compara pipeline for 2x alignment (first
run PairAligner then Chain Net).</div>
<div> The raw and chain steps works fine.</div>
<div> the pipeline failed at the CreateAlignmentNetsJobs step
complaining that: </div>
<div><br>
</div>
<blockquote style="margin:0 0 0 40px;border:none;padding:0px">
<div>Job with id=8380 died in status 'RUN' for the following
reason: Can't locate object method "dnafrag" via package
"Bio::EnsEMBL::Compara::Production::DnaFragChunkSet" at
/data/ensembl/ensembl-compara/modules/Bio/EnsEMBL/Compara/Production/GenomicAlignBlock/CreateAlignmentNetsJobs.pm
line 200.</div>
</blockquote>
<div><br>
</div>
<div> After some debug effort (just print "$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></fieldset>
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</font></span></pre><span><font color="#888888">
</font></span></blockquote><span><font color="#888888">
<br>
<pre cols="72">--
Javier Herrero, PhD
Ensembl Compara Project Leader
European Bioinformatics Institute (EMBL-EBI)
Wellcome Trust Genome Campus, Hinxton
Cambridge - CB10 1SD - UK</pre>
</font></span></div>
</blockquote></div><br><br clear="all"><div><br></div></div></div><span class="HOEnZb"><font color="#888888">-- <br>Zhang Di<br>
</font></span></div>
</blockquote></div><br><br clear="all"><div><br></div>-- <br>Zhang Di<br>
</div>