[ensembl-dev] Gene build pipeline - 2 issues
Marc Hoeppner
mphoeppner at gmail.com
Mon Aug 26 10:59:24 BST 2013
Hi EnsEMBL team,
been playing with the pipeline again, but am having problems (again).
Please see below for details - am happy about any suggestions.
Cheers,
Marc
########
1) Pmatch
########
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:
TARGET 0.064u 0.008s 0+0k 0pf 0sw
BUILD 0.116u 0.040s 0+0k 0pf 0sw
SEARCH 22.949u 0.172s 0+0k 0pf 0sw
WARN: For multiple species use species attribute in DBAdaptor->new()
WRITING: Lost the will to live Error
Job 1198 failed: [
-------------------- EXCEPTION --------------------
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.
]
STACK Bio::EnsEMBL::Pipeline::Job::run_module
/opt/bioinformatics/ensembl-70/ensembl-pipeline/modules/Bio/EnsEMBL/Pipeline/Job.pm:720
STACK (eval)
/opt/bioinformatics/ensembl-70/ensembl-pipeline/modules/Bio/EnsEMBL/Pipeline/runner.pl:219
STACK main::run_jobs_with_lsfcopy
/opt/bioinformatics/ensembl-70/ensembl-pipeline/modules/Bio/EnsEMBL/Pipeline/runner.pl:218
STACK toplevel
/opt/bioinformatics/ensembl-70/ensembl-pipeline/modules/Bio/EnsEMBL/Pipeline/runner.pl:128
Date (localtime) = Fri Aug 23 14:53:27 2013
Ensembl API version = 70
##########
2) Unigene
##########
This one really bothers me 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?).
Running job 1791
Module is BlastGenscanDNA
Input id is contig:vchicken_test:10_68:1:50000:1
Analysis is unigene
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$
-------------------- WARNING ----------------------
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$
FILE: Analysis/Runnable/Blast.pm LINE: 380
CALLED BY: EnsEMBL/Analysis/Runnable.pm LINE: 729
Date (localtime) = Fri Aug 23 14:54:47 2013
Ensembl API version = 70
And here the config for the unigene search:
[unigene]
db=unigene
db_file=/data2/projects/annotation/EnsEMBL/chicken/refseqs/unigene.fa
program=blastall
program_file=blastall
parameters=-cpus => 1, -hitdist => 40
module=BlastGenscanDNA
input_id_type=CONTIG
(Blast.pm is configured to use 'ncbi' as default type, so unigene should
inherit that, no?)
--
Marc P. Hoeppner, PhD
Department of Medical Biochemistry and Microbiology
Uppsala University, Sweden
marc.hoeppner at imbim.uu.se
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