Re: [svtoolkit-help] installtest error
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Re: [svtoolkit-help] installtest error
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From: Bob H. <han...@br...> - 2011-12-08 16:26:52
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With respect to the first error, it would be helpful if you did the diff manually between the expected output and the output produced and sent that. With respect to the second error, this is the java VM crashing, so the information from hs_err_pid*.log might be helpful. Since it is crashing in SVAltAligner, the bwa shared library is a likely suspect. uname -a might also be helpful. You might want to also check whether SV_DIR / LD_LIBRARY_PATH is being set as you expect by the scripts. -Bob On 12/8/11 6:11 AM, w y wrote: > Hi, > When I ran discovery.sh, I got an error: > Files - and benchmark/test1.discovery.vcf differ > Error: test results do not match benchmark data > > Besides, I got another error when I ran genotyping.sh: > INFO 18:09:37,496 ShellJobRunner - Starting: bwa index > test2/altalign/installtest.sites.alt.fasta > INFO 18:09:37,497 ShellJobRunner - Output written to > /home/yaowen/soft/svtoolkit_1.03.619/installtest/test2/logs/Q-11685@node12-4.out > > INFO 18:09:37,567 ShellJobRunner - Done: bwa index > test2/altalign/installtest.sites.alt.fasta > INFO 18:09:37,587 ShellJobRunner - Starting: java -Xmx1g > -Djava.io.tmpdir=/home/yaowen/soft/svtoolkit_1.03.619/installtest/tmpdir > -cp > /home/yaowen/soft/svtoolkit_1.03.619/lib/SVToolkit.jar:/home/yaowen/soft/svtoolkit_1.03.619/lib/gatk/GenomeAnalysisTK.jar:/home/yaowen/soft/svtoolkit_1.03.619/lib/gatk/Queue.jar > org.broadinstitute.sting.gatk.CommandLineGATK -T SVAltAligner -R > /home/yaowen/soft/svtoolkit_1.03.619/installtest/data/human_b36_chr1.fasta > -I > /home/yaowen/soft/svtoolkit_1.03.619/installtest/data/installtest.bam > -O > /home/yaowen/soft/svtoolkit_1.03.619/installtest/test2/altalign/installtest.alt.bam > -md test2/metadata -U ALLOW_UNINDEXED_BAM -altReference > test2/altalign/installtest.sites.alt.fasta -alignUnmappedMates true > INFO 18:09:37,587 ShellJobRunner - Output written to > /home/yaowen/soft/svtoolkit_1.03.619/installtest/test2/logs/Q-11685@node12-5.out > > ERROR 18:09:43,369 ShellJobRunner - Error: java -Xmx1g > -Djava.io.tmpdir=/home/yaowen/soft/svtoolkit_1.03.619/installtest/tmpdir > -cp > /home/yaowen/soft/svtoolkit_1.03.619/lib/SVToolkit.jar:/home/yaowen/soft/svtoolkit_1.03.619/lib/gatk/GenomeAnalysisTK.jar:/home/yaowen/soft/svtoolkit_1.03.619/lib/gatk/Queue.jar > org.broadinstitute.sting.gatk.CommandLineGATK -T SVAltAligner -R > /home/yaowen/soft/svtoolkit_1.03.619/installtest/data/human_b36_chr1.fasta > -I > /home/yaowen/soft/svtoolkit_1.03.619/installtest/data/installtest.bam > -O > /home/yaowen/soft/svtoolkit_1.03.619/installtest/test2/altalign/installtest.alt.bam > -md test2/metadata -U ALLOW_UNINDEXED_BAM -altReference > test2/altalign/installtest.sites.alt.fasta -alignUnmappedMates true > ERROR 18:09:43,370 ShellJobRunner - INFO 18:09:42,208 HelpFormatter - > --------------------------------------------------------------------------- > > INFO 18:09:42,210 HelpFormatter - The Genome Analysis Toolkit (GATK) > v1.0.5039M, Compiled 2011/01/20 22:58:34 > INFO 18:09:42,211 HelpFormatter - Copyright (c) 2010 The Broad Institute > INFO 18:09:42,211 HelpFormatter - Please view our documentation at > http://www.broadinstitute.org/gsa/wiki > INFO 18:09:42,211 HelpFormatter - For support, please view our > support site at http://getsatisfaction.com/gsa > INFO 18:09:42,211 HelpFormatter - Program Args: -T SVAltAligner -R > /home/yaowen/soft/svtoolkit_1.03.619/installtest/data/human_b36_chr1.fasta > -I > /home/yaowen/soft/svtoolkit_1.03.619/installtest/data/installtest.bam > -O > /home/yaowen/soft/svtoolkit_1.03.619/installtest/test2/altalign/installtest.alt.bam > -md test2/metadata -U ALLOW_UNINDEXED_BAM -altReference > test2/altalign/installtest.sites.alt.fasta -alignUnmappedMates true > INFO 18:09:42,211 HelpFormatter - Date/Time: 2011/12/08 18:09:42 > INFO 18:09:42,211 HelpFormatter - > --------------------------------------------------------------------------- > > INFO 18:09:42,211 HelpFormatter - > --------------------------------------------------------------------------- > > INFO 18:09:42,215 GenomeAnalysisEngine - Strictness is SILENT > # > # An unexpected error has been detected by Java Runtime Environment: > # > # SIGFPE (0x8) at pc=0x0000003027607927, pid=11823, tid=1076017504 > # > # Java VM: Java HotSpot(TM) 64-Bit Server VM (11.2-b01 mixed mode > linux-amd64) > # Problematic frame: > # C [ld-linux-x86-64.so.2+0x7927] > # > # An error report file with more information is saved as: > # /home/yaowen/soft/svtoolkit_1.03.619/installtest/hs_err_pid11823.log > # > # If you would like to submit a bug report, please visit: > # http://java.sun.com/webapps/bugreport/crash.jsp > # The crash happened outside the Java Virtual Machine in native code. > # See problematic frame for where to report the bug. > # > /home/yaowen/soft/svtoolkit_1.03.619/installtest/tmpdir/.exec9048318414659209772: > line 2: 11823 Aborted java -Xmx1g > -Djava.io.tmpdir=/home/yaowen/soft/svtoolkit_1.03.619/installtest/tmpdir > -cp > /home/yaowen/soft/svtoolkit_1.03.619/lib/SVToolkit.jar:/home/yaowen/soft/svtoolkit_1.03.619/lib/gatk/GenomeAnalysisTK.jar:/home/yaowen/soft/svtoolkit_1.03.619/lib/gatk/Queue.jar > org.broadinstitute.sting.gatk.CommandLineGATK -T SVAltAligner -R > /home/yaowen/soft/svtoolkit_1.03.619/installtest/data/human_b36_chr1.fasta > -I > /home/yaowen/soft/svtoolkit_1.03.619/installtest/data/installtest.bam > -O > /home/yaowen/soft/svtoolkit_1.03.619/installtest/test2/altalign/installtest.alt.bam > -md test2/metadata -U ALLOW_UNINDEXED_BAM -altReference > test2/altalign/installtest.sites.alt.fasta -alignUnmappedMates true > > INFO 18:09:43,373 QCommandLine - Done with errors > INFO 18:09:43,375 QGraph - ------- > INFO 18:09:43,385 QGraph - Failed: java -Xmx1g > -Djava.io.tmpdir=/home/yaowen/soft/svtoolkit_1.03.619/installtest/tmpdir > -cp > /home/yaowen/soft/svtoolkit_1.03.619/lib/SVToolkit.jar:/home/yaowen/soft/svtoolkit_1.03.619/lib/gatk/GenomeAnalysisTK.jar:/home/yaowen/soft/svtoolkit_1.03.619/lib/gatk/Queue.jar > org.broadinstitute.sting.gatk.CommandLineGATK -T SVAltAligner -R > /home/yaowen/soft/svtoolkit_1.03.619/installtest/data/human_b36_chr1.fasta > -I > /home/yaowen/soft/svtoolkit_1.03.619/installtest/data/installtest.bam > -O > /home/yaowen/soft/svtoolkit_1.03.619/installtest/test2/altalign/installtest.alt.bam > -md test2/metadata -U ALLOW_UNINDEXED_BAM -altReference > test2/altalign/installtest.sites.alt.fasta -alignUnmappedMates true > INFO 18:09:43,386 QGraph - Log: > /home/yaowen/soft/svtoolkit_1.03.619/installtest/test2/logs/Q-11685@node12-5.out > > > I tried different versions of Genome_STRiP, but I still got the same > errors. > > If anyone could help, that would be great. > Andrew > > > > > ------------------------------------------------------------------------------ > Cloud Services Checklist: Pricing and Packaging Optimization > This white paper is intended to serve as a reference, checklist and point of > discussion for anyone considering optimizing the pricing and packaging model > of a cloud services business. Read Now! > http://www.accelacomm.com/jaw/sfnl/114/51491232/ > > > _______________________________________________ > svtoolkit-help mailing list > svt...@li... > https://lists.sourceforge.net/lists/listinfo/svtoolkit-help |
