The current GATK version is 3.7-0
Examples: Monday, today, last week, Mar 26, 3/26/04

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a very small output !

basically, I am using DataProcessingPiepline, and interestingly, given an unaligned bam file which is 6gig, the DataProcessingPipeline sometimes does the all processes of the pipeline but produces a very small output (200K) or most of the times, doesn't produce anything.
The log file is as following,

INFO 11:57:55,892 QScriptManager - Compiling 1 QScript
INFO 11:58:08,656 QScriptManager - Compilation complete
INFO 11:58:09,062 HelpFormatter - ----------------------------------------------------------------------
INFO 11:58:09,062 HelpFormatter - Queue v2.4-3-g2a7af43, Compiled 2013/02/27 12:20:10
INFO 11:58:09,062 HelpFormatter - Copyright (c) 2012 The Broad Institute
INFO 11:58:09,063 HelpFormatter - For support and documentation go to
INFO 11:58:09,063 HelpFormatter - Program Args: -S /medpop/mpg-psrl/Parabase/Tools/Queue-2.3-6-gebbba25/DataProcessingPipeline.scala -bwa /broad/software/free/Linux/redhat_5_x86_64/pkgs/bwa_0.5.9/bwa -i /medpop/mpg-psrl/Parabase/Projects/Seattle/c1094WELa.49487/xc1094WELa.49487._new.bam -R /medpop/mpg-psrl/Parabase/hg19/ucsc.hg19.fasta -D /medpop/mpg-psrl/Parabase/hg19/dbsnp_137.hg19.vcf -p c1094WELa.49487 -outputDir /medpop/mpg-psrl/Parabase/Projects/Seattle/c1094WELa.49487/ -bwape -run
INFO 11:58:09,063 HelpFormatter - Date/Time: 2013/03/04 11:58:09
INFO 11:58:09,063 HelpFormatter - ----------------------------------------------------------------------
INFO 11:58:09,063 HelpFormatter - ----------------------------------------------------------------------
INFO 11:58:09,071 QCommandLine - Scripting DataProcessingPipeline
INFO 11:58:09,314 QCommandLine - Added 13 functions
INFO 11:58:09,314 QGraph - Generating graph.
INFO 11:58:09,342 QGraph - Running jobs.
INFO 11:58:09,358 QGraph - 0 Pend, 0 Run, 0 Fail, 13 Done
INFO 11:58:09,409 QCommandLine - Writing final jobs report...
INFO 11:58:09,410 QJobsReporter - Writing JobLogging GATKReport to file /medpop/mpg-psrl/Parabase/Projects/Seattle/c1094WELa.49487/DataProcessingPipeline.jobreport.txt
INFO 11:58:09,432 QJobsReporter - Plotting JobLogging GATKReport to file /medpop/mpg-psrl/Parabase/Projects/Seattle/c1094WELa.49487/DataProcessingPipeline.jobreport.pdf
WARN 11:58:09,452 RScriptExecutor - Skipping: Rscript (resource)org/broadinstitute/sting/queue/util/queueJobReport.R /medpop/mpg-psrl/Parabase/Projects/Seattle/c1094WELa.49487/DataProcessingPipeline.jobreport.txt /medpop/mpg-psrl/Parabase/Projects/Seattle/c1094WELa.49487/DataProcessingPipeline.jobreport.pdf
INFO 11:58:09,456 QCommandLine - Script completed successfully with 13 total jobs

and the command I am using,

java -Xmx4g -jar /medpop/mpg-psrl/Parabase/Tools/Queue-2.4-3-g2a7af43/Queue.jar -S /medpop/mpg-psrl/Parabase/Tools/Queue-2.3-6-gebbba25/DataProcessingPipeline.scala -bwa /broad/software/free/Linux/redhat_5_x86_64/pkgs/bwa_0.5.9/bwa -i /medpop/mpg-psrl/Parabase/Projects/Seattle/c1094WELa.49487/c1094WELa.49487._new.bam -R /medpop/mpg-psrl/Parabase/hg19/ucsc.hg19.fasta -D /medpop/mpg-psrl/Parabase/hg19/dbsnp_137.hg19.vcf -p c1094WELa.49487 -outputDir /medpop/mpg-psrl/Parabase/Projects/Seattle/c1094WELa.49487/ -bwape -run > /medpop/mpg-psrl/Parabase/Projects/Seattle/c1094WELa.49487/c1094WELa.49487.gatkpipline.log

What could be wrong here, since it doesn't really complain about anything !

Best Answer


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