Re: [svtoolkit-help] SGE Queue

[Bob H. <han...@br...>]

I am looking into updating to a more recent release of the GATK (not 
just Queue), but this may not be quick.
Just going by the error messages below, it seems possible this could be 
fixed by changes to the queue scripts.
If you make any progress in figuring this out, let me know.
-Bob

On 3/1/12 12:51 PM, Maroo, Ankit wrote:
> 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.
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