<html><head><meta http-equiv="Content-Type" content="text/html charset=iso-8859-1"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">Hi Marc,<div><br><div><div>On 26 Aug 2013, at 10:59, Marc Hoeppner <<a href="mailto:mphoeppner@gmail.com">mphoeppner@gmail.com</a>> wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite">
<meta http-equiv="content-type" content="text/html; charset=ISO-8859-1">
<div bgcolor="#FFFFFF" text="#000000">
<div class="moz-text-flowed" style="font-family: -moz-fixed;
font-size: 12px;" lang="x-western">Hi EnsEMBL team,
<br>
<br>
been playing with the pipeline again, but am having problems
(again). Please see below for details - am happy about any
suggestions.
<br>
<br>
Cheers,
<br>
<br>
Marc
<br>
<br>
########
<br>
1) Pmatch
<br>
########
<br>
<br>
I set up a pmatch analysis as by the documentation and it runs
fine on my test dataset (small chicken chromosome) when I try it
with test_RunnableDB. However, when I run the pipeline, I get
this:
<br>
<br>
TARGET 0.064u 0.008s 0+0k 0pf 0sw
<br>
BUILD 0.116u 0.040s 0+0k 0pf 0sw
<br>
SEARCH 22.949u 0.172s 0+0k 0pf 0sw
<br>
WARN: For multiple species use species attribute in
DBAdaptor->new()
<br>
WRITING: Lost the will to live Error
<br>
Job 1198 failed: [
<br>
-------------------- EXCEPTION --------------------
<br>
MSG: Problems for Pmatch writing output for
chromosome:vchicken_test:10:1:19911089:1 [Can't call method
"version" on an undefined value at
/opt/bioinformatics/ensembl-70/ensembl/modules/Bio/EnsEMBL/DBSQL/MetaContainer.pm
line 218.
<br>
]
<br>
STACK Bio::EnsEMBL::Pipeline::Job::run_module
/opt/bioinformatics/ensembl-70/ensembl-pipeline/modules/Bio/EnsEMBL/Pipeline/Job.pm:720<br>
STACK (eval)
/opt/bioinformatics/ensembl-70/ensembl-pipeline/modules/Bio/EnsEMBL/Pipeline/runner.pl:219<br>
STACK main::run_jobs_with_lsfcopy
/opt/bioinformatics/ensembl-70/ensembl-pipeline/modules/Bio/EnsEMBL/Pipeline/runner.pl:218<br>
STACK toplevel
/opt/bioinformatics/ensembl-70/ensembl-pipeline/modules/Bio/EnsEMBL/Pipeline/runner.pl:128<br>
Date (localtime) = Fri Aug 23 14:53:27 2013
<br>
Ensembl API version = 70
<br>
<br></div></div></blockquote>We would need to see how your coord_system and meta tables are populated.</div><div>The API complains that it can't find the version of your assembly. Your coord_system table should look like this one:</div><div><div>+-----------------------+----------------+------------------+------------+-------+--------------------------------+</div><div>| coord_system_id | species_id | name | version | rank | attrib |</div><div>+-----------------------+----------------+------------------+------------+-------+--------------------------------+</div><div>| 1 | 1 | contig | NULL | 3 | default_version,sequence_level |</div><div>| 2 | 1 | scaffold | oryCun2 | 2 | default_version |</div><div>| 3 | 1 | chromosome | oryCun2 | 1 | default_version |</div><blockquote type="cite"><div bgcolor="#FFFFFF" text="#000000"><div class="moz-text-flowed" style="font-family: -moz-fixed;
font-size: 12px;" lang="x-western">
<br>
##########
<br>
2) Unigene
<br>
##########
<br>
<br>
This one really bothers me <span class="moz-smiley-s3" title=";)"></span>
I think everything is set up correctly (downloaded the unigene
file, header seems to comply with the reference formatting in
Blast.pm etc), bit I cannot for the life of me get it to work.
Specifically, I am trying to use ncbi blast and the command just
looks off - seems like it tries to do a mix of Wublast and Ncbi
blast (works fine with Uniprot though - so perhaps something with
the BlastGenscanDna module?).
<br>
<br>
Running job 1791
<br>
Module is BlastGenscanDNA
<br>
Input id is contig:vchicken_test:10_68:1:50000:1
<br>
Analysis is unigene
<br>
Files are
/data2/projects/annotation/EnsEMBL/chicken/output//unigene/0/contig:vchicken_test:10_114:1:50000:1.unigene.55.retry2.out
/data2/projects/annotation/EnsEMBL/chicken/output//unigene/0/contig:vchicken_test:10_114:1:50000:1.unige$
<br>
<br>
-------------------- WARNING ----------------------
<br>
MSG: Error running Blast cmd </usr/bin/blastall -d
/data2/projects/annotation/EnsEMBL/chicken/refseqs/unigene.fa -i
/tmp/seq.22305.24863.fa -cpus=1 2>&1 >
/tmp/unigene.fa.22305.5651.blast.out>. Returned error 256 BLAST
EXIT: '1', SIGNA$
<br>
FILE: Analysis/Runnable/Blast.pm LINE: 380
<br>
CALLED BY: EnsEMBL/Analysis/Runnable.pm LINE: 729
<br>
Date (localtime) = Fri Aug 23 14:54:47 2013
<br>
Ensembl API version = 70
<br></div></div></blockquote>Have you tried to run the command by itself to see if it works? The error message you have seems to be from the ncbi blast program.</div><div>As the module dies the temporary file containing your chicken sequence should still exists. If not, you will need to comment a line in the run method of ensembl-analysis/modules/Bio/EnsEMBL/Analysis/Runnable.pm:</div><div><br></div><div> #$self->delete_files;</div><div><br></div><div>You probably need to change your parameters in the analysis table of your reference database. We use WU blast at the moment.</div><div><br></div><div>Also, the parameters for blast should be "-cpus 1 -hitdist 40" instead of "<span style="font-family: -moz-fixed; font-size: 12px; ">-cpus => 1, -hitdist => 40"</span></div><div><br></div><div>Regards</div><div>Thibaut</div><div><br><blockquote type="cite"><div bgcolor="#FFFFFF" text="#000000"><div class="moz-text-flowed" style="font-family: -moz-fixed;
font-size: 12px;" lang="x-western">
<br>
And here the config for the unigene search:
<br>
<br>
[unigene]
<br>
db=unigene
<br>
db_file=/data2/projects/annotation/EnsEMBL/chicken/refseqs/unigene.fa
<br>
program=blastall
<br>
program_file=blastall
<br>
parameters=-cpus => 1, -hitdist => 40
<br>
module=BlastGenscanDNA
<br>
input_id_type=CONTIG
<br>
<br>
(Blast.pm is configured to use 'ncbi' as default type, so unigene
should inherit that, no?)<br><br></div></div></blockquote><blockquote type="cite"><div bgcolor="#FFFFFF" text="#000000"><div class="moz-text-flowed" style="font-family: -moz-fixed;
font-size: 12px;" lang="x-western">
<br>
<div class="moz-txt-sig"><span class="moz-txt-tag">-- <br>
</span>Marc P. Hoeppner, PhD
<br>
Department of Medical Biochemistry and Microbiology
<br>
Uppsala University, Sweden
<br>
<a class="moz-txt-link-abbreviated" href="mailto:marc.hoeppner@imbim.uu.se">marc.hoeppner@imbim.uu.se</a>
<br>
<br>
</div>
</div>
</div>
_______________________________________________<br>Dev mailing list <a href="mailto:Dev@ensembl.org">Dev@ensembl.org</a><br>Posting guidelines and subscribe/unsubscribe info: <a href="http://lists.ensembl.org/mailman/listinfo/dev">http://lists.ensembl.org/mailman/listinfo/dev</a><br>Ensembl Blog: <a href="http://www.ensembl.info/">http://www.ensembl.info/</a><br></blockquote></div><br></div></body></html>