[svtoolkit-help] SGE Queue

[Ankit M. <ank...@gm...>]

Hi,

I was trying to use this version on our SGE grid setup. The queue.jar which is provided with this tool does not have the patch for SGE grid and if I try to use new version of Queue.jar while keeping everything same it gives error for 4 functions:

ERROR 12:46:57,784 QGraph - Missing 2 values for function:  'java'  '-Xmx4096m'  '-Djava.io.tmpdir=/local/projects-isi/ECENT/Merge_25_AshKenazi/genome_strip/temp_dir'  '-cp' 'SVToolkit.jar:GenomeAnalysisTK.jar' org.broadinstitute.sv.apps.MergeInsertSizeHistograms '-I' '/local/projects-isi/ECENT/Merge_25_AshKenazi/genome_strip/null/isd/Merge_25_samtools_sorted.reheader.hist.bin'  '-O' '/local/projects-isi/ECENT/Merge_25_AshKenazi/genome_strip/isd.hist.bin'  
ERROR 12:46:57,784 QGraph -   @Argument: jarFile - jar 
ERROR 12:46:57,784 QGraph -   @Argument: javaMainClass - Main class to run from javaClasspath 
ERROR 12:46:57,785 QGraph - Missing 2 values for function:  'java'  '-Xmx4096m'  '-Djava.io.tmpdir=/local/projects-isi/ECENT/Merge_25_AshKenazi/genome_strip/temp_dir'  '-cp' 'SVToolkit.jar:GenomeAnalysisTK.jar' org.broadinstitute.sv.apps.ComputeInsertStatistics '-I' '/local/projects-isi/ECENT/Merge_25_AshKenazi/genome_strip/isd.hist.bin'  '-O' '/local/projects-isi/ECENT/Merge_25_AshKenazi/genome_strip/isd.stats.dat'  
ERROR 12:46:57,785 QGraph -   @Argument: jarFile - jar 
ERROR 12:46:57,785 QGraph -   @Argument: javaMainClass - Main class to run from javaClasspath 
ERROR 12:46:57,787 QGraph - Missing 2 values for function:  'java'  '-Xmx4096m'  '-Djava.io.tmpdir=/local/projects-isi/ECENT/Merge_25_AshKenazi/genome_strip/temp_dir'  '-cp' 'SVToolkit.jar:GenomeAnalysisTK.jar' org.broadinstitute.sv.apps.MergeReadDepthCoverage '-I' '/local/projects-isi/ECENT/Merge_25_AshKenazi/genome_strip/null/depth/Merge_25_samtools_sorted.reheader.depth.txt'  '-O' '/local/projects-isi/ECENT/Merge_25_AshKenazi/genome_strip/depth.dat'  
ERROR 12:46:57,787 QGraph -   @Argument: jarFile - jar 
ERROR 12:46:57,787 QGraph -   @Argument: javaMainClass - Main class to run from javaClasspath 
ERROR 12:46:57,788 QGraph - Missing 2 values for function:  'java'  '-Xmx4096m'  '-Djava.io.tmpdir=/local/projects-isi/ECENT/Merge_25_AshKenazi/genome_strip/temp_dir'  '-cp' 'SVToolkit.jar:GenomeAnalysisTK.jar' org.broadinstitute.sv.apps.MergeReadSpanCoverage '-I' '/local/projects-isi/ECENT/Merge_25_AshKenazi/genome_strip/null/spans/Merge_25_samtools_sorted.reheader.spans.txt'  '-O' '/local/projects-isi/ECENT/Merge_25_AshKenazi/genome_strip/spans.dat'  
ERROR 12:46:57,788 QGraph -   @Argument: jarFile - jar 
ERROR 12:46:57,788 QGraph -   @Argument: javaMainClass - Main class to run from javaClasspath 
INFO  12:46:57,812 QGraph - ------- 
INFO  12:46:57,813 QGraph - Pending:  'java'  '-Xmx4096m'  '-Djava.io.tmpdir=/local/projects-isi/ECENT/Merge_25_AshKenazi/genome_strip/temp_dir'  '-cp' 'SVToolkit.jar:GenomeAnalysisTK.jar' org.broadinstitute.sting.gatk.CommandLineGATK '-T' 'ComputeInsertSizeDistributions'  '-R' '/local/sequence-isi/reference/GATK/resources/human_g1k_v37.fasta'  '-I' '/local/projects-isi/ECENT/Merge_25_AshKenazi/genome_strip/Merge_25_samtools_sorted.reheader.bam'  '-O' '/local/projects-isi/ECENT/Merge_25_AshKenazi/genome_strip/null/isd/Merge_25_samtools_sorted.reheader.hist.bin'  -createEmpty



The dry run completes without error with previous version of Queue, but the above error comes with new version. Would it be possible for you to look into this and test the program with new version?

Thank you very much

Ankit Maroo
Bioinformatics Analyst 
Institute for Genome Sciences 
University of Maryland.