[svtoolkit-help] cannot submit sample batches for processing

[Sergiu N. <ser...@sc...>]

SV_preprocess requires a full node in order to run the processing of a 
single sample. However it doesn't accept a list of files as input, or am 
I doing something wrong with the -I parameter?

I tried using the file paths separated by space and a file with the same 
paths separated by newlines. The docs are rather vague about it.

The bellow command works, but it requires a full node rather than a 
core. I can't afford it.

java -Xmx4g -cp 
$/proj/sens2016011/nobackup/genomestrip/lib/svtoolkit/lib/SVToolkit.jar:/proj/sens2016011/nobackup/genomestrip/lib/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/proj/sens2016011/nobackup/genomestrip/lib/svtoolkit/lib/gatk/Queue.jar 
             org.broadinstitute.gatk.queue.QCommandLine             -S 
$/proj/sens2016011/nobackup/genomestrip/lib/svtoolkit/qscript/SVPreprocess.q 
             -S 
$/proj/sens2016011/nobackup/genomestrip/lib/svtoolkit/qscript/SVQScript.q 
             -gatk 
$/proj/sens2016011/nobackup/genomestrip/lib/svtoolkit/lib/gatk/GenomeAnalysisTK.jar 
             -configFile 
$/proj/sens2016011/nobackup/genomestrip/lib/svtoolkit/conf/genstrip_parameters.txt 
             -R /sw/data/uppnex/GATK/2.8/b37/human_g1k_v37.fasta 
     -I 
/proj/sens2016011/nobackup/melt/data/bam_links/00028285.sorted.bam 
       -md meta             -bamFilesAreDisjoint true 
-jobLogDir /proj/sens2016011/nobackup/genomestrip/tests/logs 
-run -jobRunner Drmaa -gatkJobRunner Drmaa -jobNative '-t 4:0:0' 
-jobNative '-p node' -jobNative '-A sens2016011-bianca'


Thanks!
-- 
---
Sergiu Netotea, PhD
Researcher at NBIS
(National Bioinformatics Infrastructure Sweden)
Department of Biology and Biological Engineering
Chalmers University of Technology
Kemivägen 10, SE-412 96 Göteborg
ser...@sc...
skype: sergiunetotea
+46 (0)70 28 36 306