[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.



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 
line 218.
STACK Bio::EnsEMBL::Pipeline::Job::run_module 
STACK (eval) 
STACK main::run_jobs_with_lsfcopy 
STACK toplevel 
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 

-------------------- 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:

parameters=-cpus => 1, -hitdist => 40

(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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