[svtoolkit-help] cannot submit sample batches for processing
Status: Beta
Brought to you by:
bhandsaker
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From: Sergiu N. <ser...@sc...> - 2018-08-21 13:26:42
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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
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