[ensembl-dev] Problem running gene build pipeline
Marc Hoeppner
mphoeppner at gmail.com
Tue May 14 11:26:32 BST 2013
Hi!
I have been trying to complete a successful run with the gene build
pipeline and am still stuck on the raw computes. I have tried running it
in 'Local' mode as well as LSF (more on that below). In both cases, the
rulemanager throws a bunch of errors I can't pin down. The pipeline is
currently set up on a 48-core AMD machine, and I am using the latest
checkout of branch 71. The local files for the pipeline configuration
live in the sub-folder configs/pipeline-congigs/modules. All relevant
folders are in my PERL5LIB. I made what I think to be the relevant
modifications to BatchQueue.pm, Databases.pm and so on.
-> I have tested the individual modules I want to run using the
test_RunnableDB script and all of them worked.
If I run the rulemanager on the full thing tho - or even on the subset
of one module, it acts up. Here is my syntax:
perl /opt/bioinformatics/ensembl/ensembl-pipeline/scripts/rulemanager.pl
-dbhost localhost -dbuser username -dbpass password -analysis
RepeatMasker -submission_limit 10 -submission_number 10 -once -unlock
This throws a bunch of errors right up front, starting with
1)
'Use of uninitialized value $max_retry in numeric le (<=) at
/data2/ensembl-test/test2/configs/pipeline-configs/modules/Bio/EnsEMBL/Pipeline/Job.pm
line 1029.'
And that comes for every job (i.e thousands for a full genome).
Apparently it doesn't like me limiting the run to a smaller subset? Is
that normal..?
2) Every submission (locally as well as LSF) then comes with this the
following errors:
---------------------------------------------------
Use of uninitialized value in string eq at
/data2/ensembl-test/test2/configs/pipeline-configs/modules/Bio/EnsEMBL/Pipeline/Job.pm
line 1047.
Use of uninitialized value in string eq at
/data2/ensembl-test/test2/configs/pipeline-configs/modules/Bio/EnsEMBL/Pipeline/Job.pm
line 1047.
Job: Null submission ID for the following, but continuing: 878
Use of uninitialized value in numeric ge (>=) at
/data2/ensembl-test/test2/configs/pipeline-configs/modules/Bio/EnsEMBL/Pipeline/Job.pm
line 541.
Use of uninitialized value $this_runner in -x at
/data2/ensembl-test/test2/configs/pipeline-configs/modules/Bio/EnsEMBL/Pipeline/Job.pm
line 335.
3) The individual error messages for each RepeatMasker run then are:
-------------------- EXCEPTION --------------------
MSG: Problems creating runnable RepeatMasker for
contig:vcelegans_test:chrIV_124:1:50000:1 [Can't locate RepeatMasker.pm
in @INC (@INC contains: /opt/bioinformatics/ensembl/ensembl/modules
/opt/bioinformatics/ensembl/ensembl-compara/modules
/opt/bioinformatics/ensembl/ensembl-variation/modules
/opt/bioinformatics/ensembl/ensembl-functgenomics/modules
/opt/bioinformatics/ensembl/ensembl-analysis/modules
/opt/bioinformatics/ensembl/ensembl-pipeline/scripts
/opt/bioinformatics/ensembl/ensembl-killllist/modules
/data2/ensembl-test/test2/configs/pipeline-configs/modules
/usr/bin/tRNAscan_SE /usr/bin/tRNAscan-SE/ /etc/perl
/usr/local/lib/perl/5.14.2 /usr/local/share/perl/5.14.2 /usr/lib/perl5
/usr/share/perl5 /usr/lib/perl/5.14 /usr/share/perl/5.14
/usr/local/lib/site_perl .) at
/data2/ensembl-test/test2/configs/pipeline-configs/modules/Bio/EnsEMBL/Pipeline/Job.pm
line 641.
]
This latest part is what bugs me the most, since the RepeatMasker.pm
definitely is in
/opt/bioinformatics/ensembl-71/ensembl-analysis/modules/Bio/EnsEMBL/Analysis/RunnableDB/RepeatMasker.pm
So I am pretty much at a loss here.
Any sort of helpful advice would be greatly appreciated!
Cheers,
Marc
P.S.: Regarding LSF - although probably unrelated to my issues - I
should say that I am using openlava instead, which is an open source
fork of the original Platform LSF and should feature the same sort of
functionality and binaries/commands. Haven't tried the grid engine yet tho.
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