Re: [svtoolkit-help] SGE Queue

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

Thanks for reporting this.
It has been reported by others as well.
If you (or someone else) has a patch to the Q scripts to allow it to 
work with newer versions of queue.jar, please let me know.
Otherwise, this will probably get rolled into support for a newer 
version of the gatk, which may not happen right away.
-Bob

On 4/4/12 8:36 AM, Ankit Maroo 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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