svtoolkit-help Mailing List for Structural Variation Toolkit (Page 3)
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From: Bob H. <han...@br...> - 2015-06-12 20:07:28
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Hi, Markus, If the GTF is reasonably similar to gencode, then it should work. The recognized feature types are gene, transcript, exon, UTR, CDS, start_codon and stop_codon. The gene features must contain a gene_id attribute (and optional gene_name). The transcript features must contain a transcript_id attribute (and optional transcript_name). For efficiency, we require that the input GTF files are sorted in a particular order and obey certain conventions: 1. Every "gene" record must have a unique gene_id and the coordinates in the gene record must contain union of all the coordinates in all records with the same gene_id. 2. Records in the input file grouped by gene_id, and among the records with the same gene_id, the gene record must come first. 3. The sort order of gene records (i.e. between the groups) is based on chromosome, then start, then end coordinate. 4. The sort order of records within each gene record group is that the gene record must come first, followed by all other records ordered by chromosome, then start, then end coordinate. 5. Chromosomes must be in reference sequence order. 6. Genes are not allowed to span chromosomes. The SortGTFFile utility is a rather quick-and-dirty piece of code to convert gencode GTFs into an order compatible with the above. One thing I see that it assumes is that gene_id is the first attribute in each record (although the rest of the code does not depend on this). SortGTFFile does not fully parse the records. Hope this helps. If you have an example file you can't get correctly sorted, let me know. You can always get a little bit of command line help (at least a listing of the arguments) with "java -cp SVToolkit.jar:GenomeAnalysisTK.jar org.broadinstitute.sv.apps.SortGTFFile --help" -Bob On 6/10/15 11:15 AM, Markus Sällman Almén wrote: > Hi, > I have used the deletion pipeline and would now like to use the Gene > Overlap Annotator to classify my deletions. This is a non-human > organism so I need to use my own GTF annotation file, which do not > work as it is even if it is pretty similar to GENCODEs GTF. > The specifications for this file is not clear to me, including the > sort order. Also, the link to the SortGTFFile utility in the > documentation seems dead. > > Could you please provide some clearer specifications of the GTF file > and information about > SortGTFFile? > > Best, > Markus > > > > ------------------------------------------------------------------------------ > > > _______________________________________________ > svtoolkit-help mailing list > svt...@li... > https://lists.sourceforge.net/lists/listinfo/svtoolkit-help |
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From: Markus S. A. <mar...@im...> - 2015-06-10 15:33:24
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Hi, I have used the deletion pipeline and would now like to use the Gene Overlap Annotator to classify my deletions. This is a non-human organism so I need to use my own GTF annotation file, which do not work as it is even if it is pretty similar to GENCODEs GTF. The specifications for this file is not clear to me, including the sort order. Also, the link to the SortGTFFile utility in the documentation seems dead. Could you please provide some clearer specifications of the GTF file and information about SortGTFFile? Best, Markus |
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From: mehar <meh...@he...> - 2015-06-07 09:41:58
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Hi, I am using the GenomeStrip version extracted from "svtoolkit_2.00.1572.tar.gz" . Taking the example from http://www.broadinstitute.org/software/genomestrip/org_broadinstitute_sv_qscript_CNVDiscoveryPipeline.html , executed the following command: |classpath="${SV_DIR}/lib/SVToolkit.jar:${SV_DIR}/lib/gatk/GenomeAnalysisTK.jar:${SV_DIR}/lib/gatk/Queue.jar" java-Xmx4g -cp ${classpath} \ org.broadinstitute.gatk.queue.QCommandLine \ -S ${SV_DIR}/qscript/discovery/cnv/CNVDiscoveryPipeline.q \ -S ${SV_DIR}/qscript/SVQScript.q \ -cp ${classpath} \ -gatk ${SV_DIR}/lib/gatk/GenomeAnalysisTK.jar \ -configFile ${SV_DIR}/conf/genstrip_parameters.txt \ -R canFam3.fa \ -genomeMaskFile mask.canFam3.fa -I BC_Bams.list \ -md meta_directory \ -runDirectory CNV \ -jobLogDir CNV/logs \ -tilingWindowSize1000 \ -tilingWindowOverlap500 \ -maximumReferenceGapLength1000 \ -boundaryPrecision100 \ -minimumRefinedLength500 \ -run| And have the following error: |##### ERROR ------------------------------------------------------------------------------------------ ##### ERROR stack trace org.broadinstitute.gatk.utils.exceptions.UserException$CannotExecuteQScript: Unable to executeQScript: CNVDiscoveryPipeline.script() threw the following exception: java.lang.NullPointerException at org.broadinstitute.gatk.queue.QCommandLine$$anonfun$execute$5.apply(QCommandLine.scala:159) at org.broadinstitute.gatk.queue.QCommandLine$$anonfun$execute$5.apply(QCommandLine.scala:147) at scala.collection.Iterator$class.foreach(Iterator.scala:727) at scala.collection.AbstractIterator.foreach(Iterator.scala:1157) at scala.collection.IterableLike$class.foreach(IterableLike.scala:72) at scala.collection.AbstractIterable.foreach(Iterable.scala:54) at org.broadinstitute.gatk.queue.QCommandLine.execute(QCommandLine.scala:147) at org.broadinstitute.gatk.utils.commandline.CommandLineProgram.start(CommandLineProgram.java:248) at org.broadinstitute.gatk.utils.commandline.CommandLineProgram.start(CommandLineProgram.java:155) at org.broadinstitute.gatk.queue.QCommandLine$.main(QCommandLine.scala:62) at org.broadinstitute.gatk.queue.QCommandLine.main(QCommandLine.scala) Caused by: java.lang.NullPointerException atCNVDiscoveryPipeline.sequenceIntervalMap$lzycompute(CNVDiscoveryPipeline.q:59) atCNVDiscoveryPipeline.sequenceIntervalMap(CNVDiscoveryPipeline.q:55) atCNVDiscoveryPipeline.createStages(CNVDiscoveryPipeline.q:213) atCNVDiscoveryPipeline.script(CNVDiscoveryPipeline.q:97) at org.broadinstitute.gatk.queue.QCommandLine$$anonfun$execute$5.apply(QCommandLine.scala:156) ... 10 more ##### ERROR ------------------------------------------------------------------------------------------ ##### ERROR A GATK RUNTIME ERROR has occurred (version <unknown>): ##### ERROR ##### ERROR This might be a bug. Please check the documentation guide to see if this is a known problem. ##### ERROR If not, please post the error message, with stack trace, to the GATK forum. ##### ERROR Visit our website and forum for extensive documentation and answers to ##### ERROR commonly asked questionshttp://www.broadinstitute.org/gatk ##### ERROR ##### ERROR MESSAGE: Unable to execute QScript: CNVDiscoveryPipeline.script() threw the following exception: java.lang.NullPointerException ##### ERROR ------------------------------------------------------------------------------------------ INFO11:56:34,380 QCommandLine - Shutting down jobs. Please wait... | Could someone help to fix this. Thanks. |
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From: Bob H. <han...@br...> - 2015-04-10 12:18:58
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I'm not positive I understand the question. If you are trying to get the CNV pipeline to run locally, without using LSF or SGE or some other workflow manager, you can try -jobRunner Shell -gatkJobRunner Shell I don't know if this will work. -Bob On 4/10/15 1:21 AM, 周在威 wrote: > Thanks for quickly reply. How to remove -jobRunner and > -gatkJobRunner? in svtools.jar or QScript.q? > > > > > > > ------------------------------------------------------------------------------ > BPM Camp - Free Virtual Workshop May 6th at 10am PDT/1PM EDT > Develop your own process in accordance with the BPMN 2 standard > Learn Process modeling best practices with Bonita BPM through live exercises > http://www.bonitasoft.com/be-part-of-it/events/bpm-camp-virtual- event?utm_ > source=Sourceforge_BPM_Camp_5_6_15&utm_medium=email&utm_campaign=VA_SF > > > _______________________________________________ > svtoolkit-help mailing list > svt...@li... > https://lists.sourceforge.net/lists/listinfo/svtoolkit-help |
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From: 周在威 <zho...@16...> - 2015-04-10 05:21:56
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Thanks for quickly reply. How to remove -jobRunner and -gatkJobRunner? in svtools.jar or QScript.q? |
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From: Bob H. <han...@br...> - 2015-04-08 13:21:17
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I assume you could install LSF (although it is not free, of course) or SGE, although I haven't done this personally. Your achievable parallelism will be limited by the available resources, however, including the 32G of RAM. -Bob On 4/7/15 7:08 PM, 周在威 wrote: > Thanks for quickly reply. My system is centos6.6 with i7 4790k and 32G > memory , can i install LSF or SGE to parallel? > > > > > > ------------------------------------------------------------------------------ > BPM Camp - Free Virtual Workshop May 6th at 10am PDT/1PM EDT > Develop your own process in accordance with the BPMN 2 standard > Learn Process modeling best practices with Bonita BPM through live exercises > http://www.bonitasoft.com/be-part-of-it/events/bpm-camp-virtual- event?utm_ > source=Sourceforge_BPM_Camp_5_6_15&utm_medium=email&utm_campaign=VA_SF > > > _______________________________________________ > svtoolkit-help mailing list > svt...@li... > https://lists.sourceforge.net/lists/listinfo/svtoolkit-help |
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From: 周在威 <zho...@16...> - 2015-04-07 23:08:34
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Thanks for quickly reply. My system is centos6.6 with i7 4790k and 32G memory , can i install LSF or SGE to parallel? |
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From: Bob H. <han...@br...> - 2015-04-06 01:58:58
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The short answer is that if you just remove -jobRunner and -gatkJobRunner, then Queue will run all of the processing jobs synchronously as child processes. However, the longer answer is that you won't be able to do more than toy scenarios in this way. To get good results, you need to process a number of genomes together. It is possible to run with 30-50 genomes, but our experience has been that the results in this case are OK, but not great (false discovery rate around 5-10%). With 100-200 genomes, results are much improved (< 5% FDR) and with 500-1000 genomes the results get noticeably better (we can often get 2-3% FDR). Processing even 30-50 genomes on a personal desktop seems pretty daunting, since it looks like you are processing human data. -Bob On 4/4/15 6:38 PM, 周在威 wrote: > Hi all, > I ran in to errors when run genomestrip2 on my personal desktop not > cloud system, the error as follows: > INFO 18:32:25,780 QScriptManager - Compiling 4 QScripts > INFO 18:32:31,567 QScriptManager - Compilation complete > INFO 18:32:31,611 HelpFormatter - > ---------------------------------------------------------------------- > INFO 18:32:31,611 HelpFormatter - Queue v3.3.GS2-0-g7ad6c61, Compiled > 2015/02/06 10:59:46 > INFO 18:32:31,611 HelpFormatter - Copyright (c) 2012 The Broad Institute > INFO 18:32:31,611 HelpFormatter - For support and documentation go to > http://www.broadinstitute.org/gatk > INFO 18:32:31,611 HelpFormatter - Program Args: -cp > /media/D/genomestrip/svtoolkit/lib/SVToolkit.jar:/media/D/genomestrip/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/media/D/genomestrip/svtoolkit/lib/gatk/Queue.jar > -S > /media/D/genomestrip/svtoolkit/qscript/discovery/cnv/CNVDiscoveryStage1.q > -S > /media/D/genomestrip/svtoolkit/qscript/discovery/cnv/CNVDiscoveryStageBase.q > -S > /media/D/genomestrip/svtoolkit/qscript/discovery/cnv/CNVDiscoveryGenotyper.q > -S /media/D/genomestrip/svtoolkit/qscript/SVQScript.q -gatk > /media/D/genomestrip/svtoolkit/lib/gatk/GenomeAnalysisTK.jar > -jobLogDir run1/cnv_stage1/seq_GL000221.1/logs -memLimit 2.0 > -jobRunner Lsf706 -gatkJobRunner Lsf706 -run -sequenceName GL000221.1 > -runDirectory run1/cnv_stage1/seq_GL000221.1 -sentinelFile > run1/cnv_sentinel_files/stage_1_seq_GL000221.1.sent --disableJobReport > -configFile /media/D/genomestrip/cmt/conf/genstrip_parameters.txt -R > /media/D/genomestrip/Homo_sapiens_assembly19/Homo_sapiens_assembly19.fasta > -ploidyMapFile > /media/D/genomestrip/Homo_sapiens_assembly19/Homo_sapiens_assembly19.ploidymap.txt > -genomeMaskFile > /media/D/genomestrip/Homo_sapiens_assembly19/Homo_sapiens_assembly19.svmask.fasta > -genomeMaskFile > /media/D/genomestrip/Homo_sapiens_assembly19/Homo_sapiens_assembly19.lcmask.fasta > -copyNumberMaskFile > /media/D/genomestrip/Homo_sapiens_assembly19/Homo_sapiens_assembly19.gcmask.fasta > -readDepthMaskFile > /media/D/genomestrip/Homo_sapiens_assembly19/Homo_sapiens_assembly19.rdmask.bed > -genderMaskBedFile > /media/D/genomestrip/Homo_sapiens_assembly19/Homo_sapiens_assembly19.gendermask.bed > -vdjBedFile > /media/D/genomestrip/Homo_sapiens_assembly19/Homo_sapiens_assembly19.vdjregions.bed > -genderMapFile > /media/D/genomestrip/Homo_sapiens_assembly19/cmt_gender.map -md > cmt/metadata -disableGATKTraversal -I > run1/bam_headers/merged_headers.bam -intervalList GL000221.1 > -scannedWindowsVcfFile > run1/cnv_stage1/seq_GL000221.1/seq_GL000221.1.sites.vcf > -tilingWindowSize 1000 -tilingWindowOverlap 500 > -maximumReferenceGapLength 1000 > INFO 18:32:31,611 HelpFormatter - Executing as > wei@localhost.localdomain on Linux 2.6.32-504.el6.x86_64 amd64; > OpenJDK 64-Bit Server VM 1.7.0_65-mockbuild_2014_07_16_06_06-b00. > INFO 18:32:31,612 HelpFormatter - Date/Time: 2015/03/27 18:32:31 > INFO 18:32:31,612 HelpFormatter - > ---------------------------------------------------------------------- > INFO 18:32:31,612 HelpFormatter - > ---------------------------------------------------------------------- > INFO 18:32:31,615 QCommandLine - Scripting CNVDiscoveryStage1 > INFO 18:32:31,688 QCommandLine - Added 2 functions > INFO 18:32:31,688 QGraph - Generating graph. > INFO 18:32:31,694 QGraph - Running jobs. > ERROR 18:32:31,726 QGraph - Uncaught error running jobs. > java.lang.UnsatisfiedLinkError: Unable to load library 'lsf': > liblsf.so: cannot open shared object file: No such file or directory > at com.sun.jna.NativeLibrary.loadLibrary(NativeLibrary.java:163) > at com.sun.jna.NativeLibrary.getInstance(NativeLibrary.java:236) > at com.sun.jna.NativeLibrary.getInstance(NativeLibrary.java:199) > at > org.broadinstitute.gatk.utils.jna.lsf.v7_0_6.LibBat.<clinit>(LibBat.java:91) > at > org.broadinstitute.gatk.queue.engine.lsf.Lsf706JobRunner$.<init>(Lsf706JobRunner.scala:237) > at > org.broadinstitute.gatk.queue.engine.lsf.Lsf706JobRunner$.<clinit>(Lsf706JobRunner.scala) > at > org.broadinstitute.gatk.queue.engine.lsf.Lsf706JobRunner.<init>(Lsf706JobRunner.scala:48) > at > org.broadinstitute.gatk.queue.engine.lsf.Lsf706JobManager.create(Lsf706JobManager.scala:36) > at > org.broadinstitute.gatk.queue.engine.lsf.Lsf706JobManager.create(Lsf706JobManager.scala:34) > at > org.broadinstitute.gatk.queue.engine.QGraph.newRunner(QGraph.scala:684) > at > org.broadinstitute.gatk.queue.engine.QGraph.runJobs(QGraph.scala:433) > at org.broadinstitute.gatk.queue.engine.QGraph.run(QGraph.scala:156) > at > org.broadinstitute.gatk.queue.QCommandLine.execute(QCommandLine.scala:171) > at > org.broadinstitute.gatk.utils.commandline.CommandLineProgram.start(CommandLineProgram.java:248) > at > org.broadinstitute.gatk.utils.commandline.CommandLineProgram.start(CommandLineProgram.java:155) > at > org.broadinstitute.gatk.queue.QCommandLine$.main(QCommandLine.scala:62) > at org.broadinstitute.gatk.queue.QCommandLine.main(QCommandLine.scala) > INFO 18:32:31,727 QCommandLine - Done with errors > Exception in thread "main" java.lang.UnsatisfiedLinkError: Unable to > load library 'lsf': liblsf.so: cannot open shared object file: No such > file or directory > at com.sun.jna.NativeLibrary.loadLibrary(NativeLibrary.java:163) > at com.sun.jna.NativeLibrary.getInstance(NativeLibrary.java:236) > at com.sun.jna.NativeLibrary.getInstance(NativeLibrary.java:199) > at > org.broadinstitute.gatk.utils.jna.lsf.v7_0_6.LibBat.<clinit>(LibBat.java:91) > at > org.broadinstitute.gatk.queue.engine.lsf.Lsf706JobRunner$.<init>(Lsf706JobRunner.scala:237) > at > org.broadinstitute.gatk.queue.engine.lsf.Lsf706JobRunner$.<clinit>(Lsf706JobRunner.scala) > at > org.broadinstitute.gatk.queue.engine.lsf.Lsf706JobRunner.<init>(Lsf706JobRunner.scala:48) > at > org.broadinstitute.gatk.queue.engine.lsf.Lsf706JobManager.create(Lsf706JobManager.scala:36) > at > org.broadinstitute.gatk.queue.engine.lsf.Lsf706JobManager.create(Lsf706JobManager.scala:34) > at > org.broadinstitute.gatk.queue.engine.QGraph.newRunner(QGraph.scala:684) > at > org.broadinstitute.gatk.queue.engine.QGraph.runJobs(QGraph.scala:433) > at org.broadinstitute.gatk.queue.engine.QGraph.run(QGraph.scala:156) > at > org.broadinstitute.gatk.queue.QCommandLine.execute(QCommandLine.scala:171) > at > org.broadinstitute.gatk.utils.commandline.CommandLineProgram.start(CommandLineProgram.java:248) > at > org.broadinstitute.gatk.utils.commandline.CommandLineProgram.start(CommandLineProgram.java:155) > at > org.broadinstitute.gatk.queue.QCommandLine$.main(QCommandLine.scala:62) > at org.broadinstitute.gatk.queue.QCommandLine.main(QCommandLine.scala) > INFO 18:32:31,729 QCommandLine - Shutting down jobs. Please wait... > can i disable LSF in any parameters or just impossible to run > genomestrip2 on personal desktop? > Thanks. > > Zaiwei > > > > > ------------------------------------------------------------------------------ > Dive into the World of Parallel Programming The Go Parallel Website, sponsored > by Intel and developed in partnership with Slashdot Media, is your hub for all > things parallel software development, from weekly thought leadership blogs to > news, videos, case studies, tutorials and more. Take a look and join the > conversation now. http://goparallel.sourceforge.net/ > > > _______________________________________________ > svtoolkit-help mailing list > svt...@li... > https://lists.sourceforge.net/lists/listinfo/svtoolkit-help |
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From: 周在威 <zho...@16...> - 2015-04-04 22:38:28
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Hi all, I ran in to errors when run genomestrip2 on my personal desktop not cloud system, the error as follows: INFO 18:32:25,780 QScriptManager - Compiling 4 QScripts INFO 18:32:31,567 QScriptManager - Compilation complete INFO 18:32:31,611 HelpFormatter - ---------------------------------------------------------------------- INFO 18:32:31,611 HelpFormatter - Queue v3.3.GS2-0-g7ad6c61, Compiled 2015/02/06 10:59:46 INFO 18:32:31,611 HelpFormatter - Copyright (c) 2012 The Broad Institute INFO 18:32:31,611 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk INFO 18:32:31,611 HelpFormatter - Program Args: -cp /media/D/genomestrip/svtoolkit/lib/SVToolkit.jar:/media/D/genomestrip/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/media/D/genomestrip/svtoolkit/lib/gatk/Queue.jar -S /media/D/genomestrip/svtoolkit/qscript/discovery/cnv/CNVDiscoveryStage1.q -S /media/D/genomestrip/svtoolkit/qscript/discovery/cnv/CNVDiscoveryStageBase.q -S /media/D/genomestrip/svtoolkit/qscript/discovery/cnv/CNVDiscoveryGenotyper.q -S /media/D/genomestrip/svtoolkit/qscript/SVQScript.q -gatk /media/D/genomestrip/svtoolkit/lib/gatk/GenomeAnalysisTK.jar -jobLogDir run1/cnv_stage1/seq_GL000221.1/logs -memLimit 2.0 -jobRunner Lsf706 -gatkJobRunner Lsf706 -run -sequenceName GL000221.1 -runDirectory run1/cnv_stage1/seq_GL000221.1 -sentinelFile run1/cnv_sentinel_files/stage_1_seq_GL000221.1.sent --disableJobReport -configFile /media/D/genomestrip/cmt/conf/genstrip_parameters.txt -R /media/D/genomestrip/Homo_sapiens_assembly19/Homo_sapiens_assembly19.fasta -ploidyMapFile /media/D/genomestrip/Homo_sapiens_assembly19/Homo_sapiens_assembly19.ploidymap.txt -genomeMaskFile /media/D/genomestrip/Homo_sapiens_assembly19/Homo_sapiens_assembly19.svmask.fasta -genomeMaskFile /media/D/genomestrip/Homo_sapiens_assembly19/Homo_sapiens_assembly19.lcmask.fasta -copyNumberMaskFile /media/D/genomestrip/Homo_sapiens_assembly19/Homo_sapiens_assembly19.gcmask.fasta -readDepthMaskFile /media/D/genomestrip/Homo_sapiens_assembly19/Homo_sapiens_assembly19.rdmask.bed -genderMaskBedFile /media/D/genomestrip/Homo_sapiens_assembly19/Homo_sapiens_assembly19.gendermask.bed -vdjBedFile /media/D/genomestrip/Homo_sapiens_assembly19/Homo_sapiens_assembly19.vdjregions.bed -genderMapFile /media/D/genomestrip/Homo_sapiens_assembly19/cmt_gender.map -md cmt/metadata -disableGATKTraversal -I run1/bam_headers/merged_headers.bam -intervalList GL000221.1 -scannedWindowsVcfFile run1/cnv_stage1/seq_GL000221.1/seq_GL000221.1.sites.vcf -tilingWindowSize 1000 -tilingWindowOverlap 500 -maximumReferenceGapLength 1000 INFO 18:32:31,611 HelpFormatter - Executing as wei@localhost.localdomain on Linux 2.6.32-504.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_65-mockbuild_2014_07_16_06_06-b00. INFO 18:32:31,612 HelpFormatter - Date/Time: 2015/03/27 18:32:31 INFO 18:32:31,612 HelpFormatter - ---------------------------------------------------------------------- INFO 18:32:31,612 HelpFormatter - ---------------------------------------------------------------------- INFO 18:32:31,615 QCommandLine - Scripting CNVDiscoveryStage1 INFO 18:32:31,688 QCommandLine - Added 2 functions INFO 18:32:31,688 QGraph - Generating graph. INFO 18:32:31,694 QGraph - Running jobs. ERROR 18:32:31,726 QGraph - Uncaught error running jobs. java.lang.UnsatisfiedLinkError: Unable to load library 'lsf': liblsf.so: cannot open shared object file: No such file or directory at com.sun.jna.NativeLibrary.loadLibrary(NativeLibrary.java:163) at com.sun.jna.NativeLibrary.getInstance(NativeLibrary.java:236) at com.sun.jna.NativeLibrary.getInstance(NativeLibrary.java:199) at org.broadinstitute.gatk.utils.jna.lsf.v7_0_6.LibBat.<clinit>(LibBat.java:91) at org.broadinstitute.gatk.queue.engine.lsf.Lsf706JobRunner$.<init>(Lsf706JobRunner.scala:237) at org.broadinstitute.gatk.queue.engine.lsf.Lsf706JobRunner$.<clinit>(Lsf706JobRunner.scala) at org.broadinstitute.gatk.queue.engine.lsf.Lsf706JobRunner.<init>(Lsf706JobRunner.scala:48) at org.broadinstitute.gatk.queue.engine.lsf.Lsf706JobManager.create(Lsf706JobManager.scala:36) at org.broadinstitute.gatk.queue.engine.lsf.Lsf706JobManager.create(Lsf706JobManager.scala:34) at org.broadinstitute.gatk.queue.engine.QGraph.newRunner(QGraph.scala:684) at org.broadinstitute.gatk.queue.engine.QGraph.runJobs(QGraph.scala:433) at org.broadinstitute.gatk.queue.engine.QGraph.run(QGraph.scala:156) at org.broadinstitute.gatk.queue.QCommandLine.execute(QCommandLine.scala:171) at org.broadinstitute.gatk.utils.commandline.CommandLineProgram.start(CommandLineProgram.java:248) at org.broadinstitute.gatk.utils.commandline.CommandLineProgram.start(CommandLineProgram.java:155) at org.broadinstitute.gatk.queue.QCommandLine$.main(QCommandLine.scala:62) at org.broadinstitute.gatk.queue.QCommandLine.main(QCommandLine.scala) INFO 18:32:31,727 QCommandLine - Done with errors Exception in thread "main" java.lang.UnsatisfiedLinkError: Unable to load library 'lsf': liblsf.so: cannot open shared object file: No such file or directory at com.sun.jna.NativeLibrary.loadLibrary(NativeLibrary.java:163) at com.sun.jna.NativeLibrary.getInstance(NativeLibrary.java:236) at com.sun.jna.NativeLibrary.getInstance(NativeLibrary.java:199) at org.broadinstitute.gatk.utils.jna.lsf.v7_0_6.LibBat.<clinit>(LibBat.java:91) at org.broadinstitute.gatk.queue.engine.lsf.Lsf706JobRunner$.<init>(Lsf706JobRunner.scala:237) at org.broadinstitute.gatk.queue.engine.lsf.Lsf706JobRunner$.<clinit>(Lsf706JobRunner.scala) at org.broadinstitute.gatk.queue.engine.lsf.Lsf706JobRunner.<init>(Lsf706JobRunner.scala:48) at org.broadinstitute.gatk.queue.engine.lsf.Lsf706JobManager.create(Lsf706JobManager.scala:36) at org.broadinstitute.gatk.queue.engine.lsf.Lsf706JobManager.create(Lsf706JobManager.scala:34) at org.broadinstitute.gatk.queue.engine.QGraph.newRunner(QGraph.scala:684) at org.broadinstitute.gatk.queue.engine.QGraph.runJobs(QGraph.scala:433) at org.broadinstitute.gatk.queue.engine.QGraph.run(QGraph.scala:156) at org.broadinstitute.gatk.queue.QCommandLine.execute(QCommandLine.scala:171) at org.broadinstitute.gatk.utils.commandline.CommandLineProgram.start(CommandLineProgram.java:248) at org.broadinstitute.gatk.utils.commandline.CommandLineProgram.start(CommandLineProgram.java:155) at org.broadinstitute.gatk.queue.QCommandLine$.main(QCommandLine.scala:62) at org.broadinstitute.gatk.queue.QCommandLine.main(QCommandLine.scala) INFO 18:32:31,729 QCommandLine - Shutting down jobs. Please wait... can i disable LSF in any parameters or just impossible to run genomestrip2 on personal desktop? Thanks. Zaiwei |
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From: Bob H. <han...@br...> - 2015-03-09 12:24:37
|
There is some documentation on how to use SGE here: http://www.broadinstitute.org/software/genomestrip/org_broadinstitute_sv_qscript_QCommandLine.html Also see the job You need to supply "-jobRunner Drmaa" and for the CNV pipeline also "-gatkJobRunner Drmaa". Depending on your SGE configuration, you may also need to make liberal use of -jobNative to pass additional arguments. For example -jobNative "-q myqueue" -jobNative "-l virtual_free=8000m" etc. -Bob On 3/9/15 4:02 AM, shiyujian2 wrote: > Hello, > I'm running into difficulties trying to run CNVDiscovery pipeline with > svtoolkit_2.00.1529 > <http://www.broadinstitute.org/software/genomestrip/download/72/svtoolkit_2.00.1529.tar.gz?redirect=node/2> version. > I copied my command as below > classpath=/xxx/svtoolkit/lib/SVToolkit.jar:/xxx/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/xxx/svtoolkit/lib/gatk/Queue.jar > export > PATH=/xxx/R-3.0.2/bin/:/xxx/svtoolkit/:/xxx/svtoolkit/bwa/:$PATH; > export SV_DIR=/xxx/svtoolkit; > /xxx/bin/software/jre1.7.0_25/bin/java -Xmx10g -XX:+UseParallelOldGC > -XX:ParallelGCThreads=4 -XX:GCTimeLimit=50 -XX:GCHeapFreeLimit=10 > -Djava.io.tmpdir=/xxx/.queue/tmp -cp ${classpath} > org.broadinstitute.gatk.queue.QCommandLine > -S ${SV_DIR}/qscript/discovery/cnv/CNVDiscoveryPipeline.q > -S ${SV_DIR}/qscript/SVQScript.q > -cp ${classpath} > -gatk ${SV_DIR}/lib/gatk/GenomeAnalysisTK.jar > -R /xxx/hg19.fa > -I /xxx/discovery.bams.args.list > -genderMapFile /xxx/gender.map > -md /xxx/metadata > -configFile /xxx/conf/genstrip_parameters.txt > -runDirectory /xxx/cnvdiscovery > -genomeMaskFile /xxx/svtoolkit/database/hg19_mask101.fasta > -intervalList chr1:1-4010001 > -tilingWindowSize 1000 -tilingWindowOverlap 500 > -maximumReferenceGapLength 1000 -boundaryPrecision 100 > -minimumRefinedLength 500 > -jobLogDir /xxx/cnvdiscovery/logs > -run > Error from Shell CNVDiscoveryPipeline run > INFO 14:48:37,214 HelpFormatter - Date/Time: 2015/03/09 14:48:37 > INFO 14:48:37,214 HelpFormatter - > ---------------------------------------------------------------------- > INFO 14:48:37,214 HelpFormatter - > ---------------------------------------------------------------------- > INFO 14:48:37,221 QCommandLine - Scripting CNVDiscoveryStage1 > INFO 14:48:37,394 QCommandLine - Added 2 functions > INFO 14:48:37,395 QGraph - Generating graph. > INFO 14:48:37,406 QGraph - Running jobs. > ERROR 14:48:37,833 QGraph - Uncaught error running jobs. > java.lang.UnsatisfiedLinkError: Unable to load library 'lsf': > liblsf.so: cannot open shared object file: No such file or directory > at com.sun.jna.NativeLibrary.loadLibrary(NativeLibrary.java:163) > at com.sun.jna.NativeLibrary.getInstance(NativeLibrary.java:236) > at com.sun.jna.NativeLibrary.getInstance(NativeLibrary.java:199) > at > org.broadinstitute.gatk.utils.jna.lsf.v7_0_6.LibBat.<clinit>(LibBat.java:91) > at > org.broadinstitute.gatk.queue.engine.lsf.Lsf706JobRunner$.<init>(Lsf706JobRunner.scala:237) > at > org.broadinstitute.gatk.queue.engine.lsf.Lsf706JobRunner$.<clinit>(Lsf706JobRunner.scala) > at > org.broadinstitute.gatk.queue.engine.lsf.Lsf706JobRunner.<init>(Lsf706JobRunner.scala:48) > at > org.broadinstitute.gatk.queue.engine.lsf.Lsf706JobManager.create(Lsf706JobManager.scala:36) > at > org.broadinstitute.gatk.queue.engine.lsf.Lsf706JobManager.create(Lsf706JobManager.scala:34) > at > org.broadinstitute.gatk.queue.engine.QGraph.newRunner(QGraph.scala:684) > at > org.broadinstitute.gatk.queue.engine.QGraph.runJobs(QGraph.scala:433) > at > org.broadinstitute.gatk.queue.engine.QGraph.run(QGraph.scala:156) > at > org.broadinstitute.gatk.queue.QCommandLine.execute(QCommandLine.scala:171) > at > org.broadinstitute.gatk.utils.commandline.CommandLineProgram.start(CommandLineProgram.java:248) > at > org.broadinstitute.gatk.utils.commandline.CommandLineProgram.start(CommandLineProgram.java:155) > at > org.broadinstitute.gatk.queue.QCommandLine$.main(QCommandLine.scala:62) > at > org.broadinstitute.gatk.queue.QCommandLine.main(QCommandLine.scala) > INFO 14:48:37,834 QCommandLine - Done with errors > I am running on SGE cluster system, can I handle this problem through > any parameters? > Thanks, > Yujian > > > ------------------------------------------------------------------------------ > Dive into the World of Parallel Programming The Go Parallel Website, sponsored > by Intel and developed in partnership with Slashdot Media, is your hub for all > things parallel software development, from weekly thought leadership blogs to > news, videos, case studies, tutorials and more. Take a look and join the > conversation now. http://goparallel.sourceforge.net/ > > > _______________________________________________ > svtoolkit-help mailing list > svt...@li... > https://lists.sourceforge.net/lists/listinfo/svtoolkit-help |
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From: shiyujian2 <shi...@ge...> - 2015-03-09 08:15:17
|
Hello,
I'm running into difficulties trying to run CNVDiscovery pipeline with svtoolkit_2.00.1529 version. I copied my command as below
classpath=/xxx/svtoolkit/lib/SVToolkit.jar:/xxx/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/xxx/svtoolkit/lib/gatk/Queue.jar
export PATH=/xxx/R-3.0.2/bin/:/xxx/svtoolkit/:/xxx/svtoolkit/bwa/:$PATH; export SV_DIR=/xxx/svtoolkit;
/xxx/bin/software/jre1.7.0_25/bin/java -Xmx10g -XX:+UseParallelOldGC -XX:ParallelGCThreads=4 -XX:GCTimeLimit=50 -XX:GCHeapFreeLimit=10
-Djava.io.tmpdir=/xxx/.queue/tmp -cp ${classpath} org.broadinstitute.gatk.queue.QCommandLine
-S ${SV_DIR}/qscript/discovery/cnv/CNVDiscoveryPipeline.q
-S ${SV_DIR}/qscript/SVQScript.q
-cp ${classpath}
-gatk ${SV_DIR}/lib/gatk/GenomeAnalysisTK.jar
-R /xxx/hg19.fa
-I /xxx/discovery.bams.args.list
-genderMapFile /xxx/gender.map
-md /xxx/metadata
-configFile /xxx/conf/genstrip_parameters.txt
-runDirectory /xxx/cnvdiscovery
-genomeMaskFile /xxx/svtoolkit/database/hg19_mask101.fasta
-intervalList chr1:1-4010001
-tilingWindowSize 1000 -tilingWindowOverlap 500 -maximumReferenceGapLength 1000 -boundaryPrecision 100 -minimumRefinedLength 500
-jobLogDir /xxx/cnvdiscovery/logs
-run
Error from Shell CNVDiscoveryPipeline run
INFO 14:48:37,214 HelpFormatter - Date/Time: 2015/03/09 14:48:37
INFO 14:48:37,214 HelpFormatter - ----------------------------------------------------------------------
INFO 14:48:37,214 HelpFormatter - ----------------------------------------------------------------------
INFO 14:48:37,221 QCommandLine - Scripting CNVDiscoveryStage1
INFO 14:48:37,394 QCommandLine - Added 2 functions
INFO 14:48:37,395 QGraph - Generating graph.
INFO 14:48:37,406 QGraph - Running jobs.
ERROR 14:48:37,833 QGraph - Uncaught error running jobs.
java.lang.UnsatisfiedLinkError: Unable to load library 'lsf': liblsf.so: cannot open shared object file: No such file or directory
at com.sun.jna.NativeLibrary.loadLibrary(NativeLibrary.java:163)
at com.sun.jna.NativeLibrary.getInstance(NativeLibrary.java:236)
at com.sun.jna.NativeLibrary.getInstance(NativeLibrary.java:199)
at org.broadinstitute.gatk.utils.jna.lsf.v7_0_6.LibBat.<clinit>(LibBat.java:91)
at org.broadinstitute.gatk.queue.engine.lsf.Lsf706JobRunner$.<init>(Lsf706JobRunner.scala:237)
at org.broadinstitute.gatk.queue.engine.lsf.Lsf706JobRunner$.<clinit>(Lsf706JobRunner.scala)
at org.broadinstitute.gatk.queue.engine.lsf.Lsf706JobRunner.<init>(Lsf706JobRunner.scala:48)
at org.broadinstitute.gatk.queue.engine.lsf.Lsf706JobManager.create(Lsf706JobManager.scala:36)
at org.broadinstitute.gatk.queue.engine.lsf.Lsf706JobManager.create(Lsf706JobManager.scala:34)
at org.broadinstitute.gatk.queue.engine.QGraph.newRunner(QGraph.scala:684)
at org.broadinstitute.gatk.queue.engine.QGraph.runJobs(QGraph.scala:433)
at org.broadinstitute.gatk.queue.engine.QGraph.run(QGraph.scala:156)
at org.broadinstitute.gatk.queue.QCommandLine.execute(QCommandLine.scala:171)
at org.broadinstitute.gatk.utils.commandline.CommandLineProgram.start(CommandLineProgram.java:248)
at org.broadinstitute.gatk.utils.commandline.CommandLineProgram.start(CommandLineProgram.java:155)
at org.broadinstitute.gatk.queue.QCommandLine$.main(QCommandLine.scala:62)
at org.broadinstitute.gatk.queue.QCommandLine.main(QCommandLine.scala)
INFO 14:48:37,834 QCommandLine - Done with errors
I am running on SGE cluster system, can I handle this problem through any parameters?
Thanks,
Yujian |
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From: Homann, O. <oh...@am...> - 2015-02-26 22:22:45
|
Hi Bob, Reporting back with the results of a few more tests. 1) Using -disableJobReport did not help. 2) The error seems to be reproducible (i.e. not the occasional LSF problem that you have encountered). 3) When I ran the same script after changing the number of bam files in my .list file from two to one, it completed successfully. The bam file retained for this test was the same one that failed on ReduceInsertSizeHistograms in the two-bam test. Given that it worked as a single input file and that I can successfully run ReduceInsertSizeHistograms as an independent java command, the problem seems to be narrowed down to the behavior of queue for multiple bam files (and perhaps it is specific to Shell mode, since no one else is reporting any problems). 4) Will report back with LSF9+Drmaa details when I am able... having unrelated issues with my cluster at the moment. Thanks for your assistance. Regards, Oliver From: Homann, Oliver Sent: Wednesday, February 25, 2015 1:23 PM To: 'Bob Handsaker'; svt...@li... Subject: RE: [svtoolkit-help] Having trouble with SVPreprocess Hello Bob, Thanks for the response. Queue wrote a *.fail file for the step. I will attempt a rerun with --disableJobReport and report back tomorrow. Any advice you can have on getting queue to work with LSF 9.1 + Drmaa would be much appreciated. I installed the library at https://github.com/PlatformLSF/lsf-drmaa, and while that took me beyond the 'missing libdrmaa.so' error I eventually got stuck on an exception complaining that I haven't set up SGE_ROOT (which struck me as odd, since I was trying to use LSF, not SGE). Regards, Oliver From: Bob Handsaker [mailto:han...@br...] Sent: Wednesday, February 25, 2015 12:56 PM To: svt...@li...<mailto:svt...@li...> Subject: Re: [svtoolkit-help] Having trouble with SVPreprocess Hi, Oliver, First of all, the "mysample/mysample/null" is OK. That is actually sample/library/readgroup (and in this case you are grouping by library, which is the default and usual thing to do). Second, there is a known bug, which we are in the process of fixing, where some of the preprocessing steps do not catch and report I/O errors (they use java PrintWriter but do not check for errors). But since you are checking the output file, that is probably not the issue here. But just fyi. Third, we have seen occasional problem with this happening with LSF (but it is random and occasional and goes away when you rerun). I don't know if shell mode has the same problem, since I never use that. One thing to try is --disableJobReport, if you are not already doing that. Also check to see if Queue wrote a .*.done file for this step. If those things are going wrong, it is a queue problem. Also, we successfully run LSF 9.1 here with Drmaa. We had to have our IT staff install the LSF Drmaa library. But it did take a while to get it working. I think they had to try different versions of the drmaa library. Seva Kashin worked on that and may be able to help if that would be useful. -Bob On 2/25/15, 12:02 PM, Homann, Oliver wrote: Hello, I'm running into difficulties trying to run SVPreprocess, and was hoping you might have some ideas about what has gone wrong. After a while the run fails with a (seemingly uninformative) ReduceInsertSizeHistograms error (see end of e-mail). Oddly, I can run that exact same command at the command line (just changing the output name), and it works without reporting any errors. In both cases an output file of the same size is created, which makes me wonder if this is even the step that is truly failing. A few other observations/comments: * I note that the log appends 'null' to the name of the sample it is processing... is this a clue to something being amiss? * I've had to build my own genome bundle because my alignments include the hs37d5 decoy "chromosome". Perhaps I did something odd there that is contributing to the problem? * I am doing this test using the Shell mode since I can't seem to get Queue to work with LSF 9 and drmaa. Any suggestions would be greatly appreciated. Regards, Oliver Homann ================================================================== Error from Shell SVPreprocess run ================================================================== ERROR 17:34:50,817 FunctionEdge - Error: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/mypath/scripts/.queue/tmp' '-cp' '/myjars/svtoolkit_versions/svtoolkit/lib/SVToolkit.jar:/myjars/svtoolkit_versions/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/myjars/svtoolkit_versions/svtoolkit/lib/gatk/Queue.jar' '-cp' '/myjars/svtoolkit_versions/svtoolkit/lib/SVToolkit.jar:/myjars/svtoolkit_versions/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/myjars/svtoolkit_versions/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.ReduceInsertSizeHistograms' '-I' '/mypath/output/isd/mysample.hist.bin' '-O' '/mypath/output/isd/mysample.dist.bin' ERROR 17:34:50,830 FunctionEdge - Contents of /mypath/output/logs/SVPreprocess-6.out: INFO 16:35:09,560 HelpFormatter - ------------------------------------------------------------------- INFO 16:35:09,562 HelpFormatter - Program Name: org.broadinstitute.sv.apps.ReduceInsertSizeHistograms INFO 16:35:09,566 HelpFormatter - Program Args: -I /mypath/output/isd/mysample.hist.bin -O /mypath/output/isd/mysample.dist.bin INFO 16:35:09,569 HelpFormatter - Executing as me...@my...<mailto:me...@my...> on Linux 2.6.32-358.el6.x86_64 amd64; Java HotSpot(TM) 64-Bit Server VM 1.7.0_25-b15. INFO 16:35:09,570 HelpFormatter - Date/Time: 2015/02/24 16:35:09 INFO 16:35:09,570 HelpFormatter - ------------------------------------------------------------------- INFO 16:35:09,570 HelpFormatter - ------------------------------------------------------------------- Processing mysample/mysample/null ... INFO 16:35:20,573 CommandLineProgram - Program completed. ================================================================== ------------------------------------------------------------------------------ Dive into the World of Parallel Programming The Go Parallel Website, sponsored by Intel and developed in partnership with Slashdot Media, is your hub for all things parallel software development, from weekly thought leadership blogs to news, videos, case studies, tutorials and more. Take a look and join the conversation now. http://goparallel.sourceforge.net/ _______________________________________________ svtoolkit-help mailing list svt...@li...<mailto:svt...@li...> https://lists.sourceforge.net/lists/listinfo/svtoolkit-help |
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From: Homann, O. <oh...@am...> - 2015-02-25 21:23:57
|
Hello Bob, Thanks for the response. Queue wrote a *.fail file for the step. I will attempt a rerun with --disableJobReport and report back tomorrow. Any advice you can have on getting queue to work with LSF 9.1 + Drmaa would be much appreciated. I installed the library at https://github.com/PlatformLSF/lsf-drmaa, and while that took me beyond the 'missing libdrmaa.so' error I eventually got stuck on an exception complaining that I haven't set up SGE_ROOT (which struck me as odd, since I was trying to use LSF, not SGE). Regards, Oliver From: Bob Handsaker [mailto:han...@br...] Sent: Wednesday, February 25, 2015 12:56 PM To: svt...@li... Subject: Re: [svtoolkit-help] Having trouble with SVPreprocess Hi, Oliver, First of all, the "mysample/mysample/null" is OK. That is actually sample/library/readgroup (and in this case you are grouping by library, which is the default and usual thing to do). Second, there is a known bug, which we are in the process of fixing, where some of the preprocessing steps do not catch and report I/O errors (they use java PrintWriter but do not check for errors). But since you are checking the output file, that is probably not the issue here. But just fyi. Third, we have seen occasional problem with this happening with LSF (but it is random and occasional and goes away when you rerun). I don't know if shell mode has the same problem, since I never use that. One thing to try is --disableJobReport, if you are not already doing that. Also check to see if Queue wrote a .*.done file for this step. If those things are going wrong, it is a queue problem. Also, we successfully run LSF 9.1 here with Drmaa. We had to have our IT staff install the LSF Drmaa library. But it did take a while to get it working. I think they had to try different versions of the drmaa library. Seva Kashin worked on that and may be able to help if that would be useful. -Bob On 2/25/15, 12:02 PM, Homann, Oliver wrote: Hello, I'm running into difficulties trying to run SVPreprocess, and was hoping you might have some ideas about what has gone wrong. After a while the run fails with a (seemingly uninformative) ReduceInsertSizeHistograms error (see end of e-mail). Oddly, I can run that exact same command at the command line (just changing the output name), and it works without reporting any errors. In both cases an output file of the same size is created, which makes me wonder if this is even the step that is truly failing. A few other observations/comments: * I note that the log appends 'null' to the name of the sample it is processing... is this a clue to something being amiss? * I've had to build my own genome bundle because my alignments include the hs37d5 decoy "chromosome". Perhaps I did something odd there that is contributing to the problem? * I am doing this test using the Shell mode since I can't seem to get Queue to work with LSF 9 and drmaa. Any suggestions would be greatly appreciated. Regards, Oliver Homann ================================================================== Error from Shell SVPreprocess run ================================================================== ERROR 17:34:50,817 FunctionEdge - Error: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/mypath/scripts/.queue/tmp' '-cp' '/myjars/svtoolkit_versions/svtoolkit/lib/SVToolkit.jar:/myjars/svtoolkit_versions/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/myjars/svtoolkit_versions/svtoolkit/lib/gatk/Queue.jar' '-cp' '/myjars/svtoolkit_versions/svtoolkit/lib/SVToolkit.jar:/myjars/svtoolkit_versions/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/myjars/svtoolkit_versions/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.ReduceInsertSizeHistograms' '-I' '/mypath/output/isd/mysample.hist.bin' '-O' '/mypath/output/isd/mysample.dist.bin' ERROR 17:34:50,830 FunctionEdge - Contents of /mypath/output/logs/SVPreprocess-6.out: INFO 16:35:09,560 HelpFormatter - ------------------------------------------------------------------- INFO 16:35:09,562 HelpFormatter - Program Name: org.broadinstitute.sv.apps.ReduceInsertSizeHistograms INFO 16:35:09,566 HelpFormatter - Program Args: -I /mypath/output/isd/mysample.hist.bin -O /mypath/output/isd/mysample.dist.bin INFO 16:35:09,569 HelpFormatter - Executing as me...@my...<mailto:me...@my...> on Linux 2.6.32-358.el6.x86_64 amd64; Java HotSpot(TM) 64-Bit Server VM 1.7.0_25-b15. INFO 16:35:09,570 HelpFormatter - Date/Time: 2015/02/24 16:35:09 INFO 16:35:09,570 HelpFormatter - ------------------------------------------------------------------- INFO 16:35:09,570 HelpFormatter - ------------------------------------------------------------------- Processing mysample/mysample/null ... INFO 16:35:20,573 CommandLineProgram - Program completed. ================================================================== ------------------------------------------------------------------------------ Dive into the World of Parallel Programming The Go Parallel Website, sponsored by Intel and developed in partnership with Slashdot Media, is your hub for all things parallel software development, from weekly thought leadership blogs to news, videos, case studies, tutorials and more. Take a look and join the conversation now. http://goparallel.sourceforge.net/ _______________________________________________ svtoolkit-help mailing list svt...@li...<mailto:svt...@li...> https://lists.sourceforge.net/lists/listinfo/svtoolkit-help |
|
From: Bob H. <han...@br...> - 2015-02-25 20:55:47
|
Hi, Oliver, First of all, the "mysample/mysample/null" is OK. That is actually sample/library/readgroup (and in this case you are grouping by library, which is the default and usual thing to do). Second, there is a known bug, which we are in the process of fixing, where some of the preprocessing steps do not catch and report I/O errors (they use java PrintWriter but do not check for errors). But since you are checking the output file, that is probably not the issue here. But just fyi. Third, we have seen occasional problem with this happening with LSF (but it is random and occasional and goes away when you rerun). I don't know if shell mode has the same problem, since I never use that. One thing to try is --disableJobReport, if you are not already doing that. Also check to see if Queue wrote a .*.done file for this step. If those things are going wrong, it is a queue problem. Also, we successfully run LSF 9.1 here with Drmaa. We had to have our IT staff install the LSF Drmaa library. But it did take a while to get it working. I think they had to try different versions of the drmaa library. Seva Kashin worked on that and may be able to help if that would be useful. -Bob On 2/25/15, 12:02 PM, Homann, Oliver wrote: > > Hello, > > I'm running into difficulties trying to run SVPreprocess, and was > hoping you might have some ideas about what has gone wrong. After a > while the run fails with a (seemingly uninformative) > ReduceInsertSizeHistograms error (see end of e-mail). Oddly, I can run > that exact same command at the command line (just changing the output > name), and it works without reporting any errors. In both cases an > output file of the same size is created, which makes me wonder if this > is even the step that is truly failing. > > A few other observations/comments: > > ·I note that the log appends 'null' to the name of the sample it is > processing... is this a clue to something being amiss? > > ·I've had to build my own genome bundle because my alignments include > the hs37d5 decoy "chromosome". Perhaps I did something odd there that > is contributing to the problem? > > ·I am doing this test using the Shell mode since I can't seem to get > Queue to work with LSF 9 and drmaa. > > Any suggestions would be greatly appreciated. > > Regards, > > Oliver Homann > > ================================================================== > > Error from Shell SVPreprocess run > > ================================================================== > > ERROR 17:34:50,817 FunctionEdge - Error: 'java' '-Xmx2048m' > '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' > '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' > '-Djava.io.tmpdir=/mypath/scripts/.queue/tmp' '-cp' > '/myjars/svtoolkit_versions/svtoolkit/lib/SVToolkit.jar:/myjars/svtoolkit_versions/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/myjars/svtoolkit_versions/svtoolkit/lib/gatk/Queue.jar' > '-cp' > '/myjars/svtoolkit_versions/svtoolkit/lib/SVToolkit.jar:/myjars/svtoolkit_versions/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/myjars/svtoolkit_versions/svtoolkit/lib/gatk/Queue.jar' > 'org.broadinstitute.sv.apps.ReduceInsertSizeHistograms' '-I' > '/mypath/output/isd/mysample.hist.bin' '-O' > '/mypath/output/isd/mysample.dist.bin' > > ERROR 17:34:50,830 FunctionEdge - Contents of > /mypath/output/logs/SVPreprocess-6.out: > > INFO 16:35:09,560 HelpFormatter - > ------------------------------------------------------------------- > > INFO 16:35:09,562 HelpFormatter - Program Name: > org.broadinstitute.sv.apps.ReduceInsertSizeHistograms > > INFO 16:35:09,566 HelpFormatter - Program Args: -I > /mypath/output/isd/mysample.hist.bin -O > /mypath/output/isd/mysample.dist.bin > > INFO 16:35:09,569 HelpFormatter - Executing as me...@my... on > Linux 2.6.32-358.el6.x86_64 amd64; Java HotSpot(TM) 64-Bit Server VM > 1.7.0_25-b15. > > INFO 16:35:09,570 HelpFormatter - Date/Time: 2015/02/24 16:35:09 > > INFO 16:35:09,570 HelpFormatter - > ------------------------------------------------------------------- > > INFO 16:35:09,570 HelpFormatter - > ------------------------------------------------------------------- > > Processing mysample/mysample/null ... > > INFO 16:35:20,573 CommandLineProgram - Program completed. > > ================================================================== > > > > ------------------------------------------------------------------------------ > Dive into the World of Parallel Programming The Go Parallel Website, sponsored > by Intel and developed in partnership with Slashdot Media, is your hub for all > things parallel software development, from weekly thought leadership blogs to > news, videos, case studies, tutorials and more. Take a look and join the > conversation now. http://goparallel.sourceforge.net/ > > > _______________________________________________ > svtoolkit-help mailing list > svt...@li... > https://lists.sourceforge.net/lists/listinfo/svtoolkit-help |
|
From: Homann, O. <oh...@am...> - 2015-02-25 17:03:08
|
Hello, I'm running into difficulties trying to run SVPreprocess, and was hoping you might have some ideas about what has gone wrong. After a while the run fails with a (seemingly uninformative) ReduceInsertSizeHistograms error (see end of e-mail). Oddly, I can run that exact same command at the command line (just changing the output name), and it works without reporting any errors. In both cases an output file of the same size is created, which makes me wonder if this is even the step that is truly failing. A few other observations/comments: * I note that the log appends 'null' to the name of the sample it is processing... is this a clue to something being amiss? * I've had to build my own genome bundle because my alignments include the hs37d5 decoy "chromosome". Perhaps I did something odd there that is contributing to the problem? * I am doing this test using the Shell mode since I can't seem to get Queue to work with LSF 9 and drmaa. Any suggestions would be greatly appreciated. Regards, Oliver Homann ================================================================== Error from Shell SVPreprocess run ================================================================== ERROR 17:34:50,817 FunctionEdge - Error: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/mypath/scripts/.queue/tmp' '-cp' '/myjars/svtoolkit_versions/svtoolkit/lib/SVToolkit.jar:/myjars/svtoolkit_versions/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/myjars/svtoolkit_versions/svtoolkit/lib/gatk/Queue.jar' '-cp' '/myjars/svtoolkit_versions/svtoolkit/lib/SVToolkit.jar:/myjars/svtoolkit_versions/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/myjars/svtoolkit_versions/svtoolkit/lib/gatk/Queue.jar' 'org.broadinstitute.sv.apps.ReduceInsertSizeHistograms' '-I' '/mypath/output/isd/mysample.hist.bin' '-O' '/mypath/output/isd/mysample.dist.bin' ERROR 17:34:50,830 FunctionEdge - Contents of /mypath/output/logs/SVPreprocess-6.out: INFO 16:35:09,560 HelpFormatter - ------------------------------------------------------------------- INFO 16:35:09,562 HelpFormatter - Program Name: org.broadinstitute.sv.apps.ReduceInsertSizeHistograms INFO 16:35:09,566 HelpFormatter - Program Args: -I /mypath/output/isd/mysample.hist.bin -O /mypath/output/isd/mysample.dist.bin INFO 16:35:09,569 HelpFormatter - Executing as me...@my... on Linux 2.6.32-358.el6.x86_64 amd64; Java HotSpot(TM) 64-Bit Server VM 1.7.0_25-b15. INFO 16:35:09,570 HelpFormatter - Date/Time: 2015/02/24 16:35:09 INFO 16:35:09,570 HelpFormatter - ------------------------------------------------------------------- INFO 16:35:09,570 HelpFormatter - ------------------------------------------------------------------- Processing mysample/mysample/null ... INFO 16:35:20,573 CommandLineProgram - Program completed. ================================================================== |
|
From: Bob H. <han...@br...> - 2015-02-18 02:01:37
|
Hi, Oliver, The relatedness shouldn't cause any problem. Genome STRiP doesn't have any mode that is specific to trios or related individuals, so you can use Mendelian violations as a QC metric. When you do this, you should take into account the quality of each genotype call (e.g. CNQ). CNQ is phred-scaled, so a CNQ of 13, for example, corresponds to 95% confidence and is where we generally set our default filters for calling a variant site. However, at 95% confidence you would still expect occasional mendel errors, but you should see them decrease if you look only at genotypes with higher confidence thresholds. -Bob On 2/17/15, 6:10 PM, Homann, Oliver wrote: > > Hello, > > I'm hoping to use STRiP for CNV detection in support of a sequencing > project. After looking over the documentation, I find myself unsure > of whether it is appropriate for my dataset. Specifically, I have > ~100 samples covering 10 pedigrees, and wonder whether the > inter-relatedness of some of the samples would impact SV modeling and > detection. Any guidance you can offer would be much appreciated. > > Regards, > > Oliver Homann > > > > ------------------------------------------------------------------------------ > Download BIRT iHub F-Type - The Free Enterprise-Grade BIRT Server > from Actuate! Instantly Supercharge Your Business Reports and Dashboards > with Interactivity, Sharing, Native Excel Exports, App Integration & more > Get technology previously reserved for billion-dollar corporations, FREE > http://pubads.g.doubleclick.net/gampad/clk?id=190641631&iu=/4140/ostg.clktrk > > > _______________________________________________ > svtoolkit-help mailing list > svt...@li... > https://lists.sourceforge.net/lists/listinfo/svtoolkit-help |
|
From: Homann, O. <oh...@am...> - 2015-02-18 00:10:12
|
Hello, I'm hoping to use STRiP for CNV detection in support of a sequencing project. After looking over the documentation, I find myself unsure of whether it is appropriate for my dataset. Specifically, I have ~100 samples covering 10 pedigrees, and wonder whether the inter-relatedness of some of the samples would impact SV modeling and detection. Any guidance you can offer would be much appreciated. Regards, Oliver Homann |
|
From: Peng C. <ant...@gm...> - 2015-02-17 22:37:26
|
Hi Bob, I tested the new version r1533. It works perfect. Thank you for your help. Peng On Sat, Feb 7, 2015 at 5:00 AM, < svt...@li...> wrote: > Send svtoolkit-help mailing list submissions to > svt...@li... > > To subscribe or unsubscribe via the World Wide Web, visit > https://lists.sourceforge.net/lists/listinfo/svtoolkit-help > or, via email, send a message with subject or body 'help' to > svt...@li... > > You can reach the person managing the list at > svt...@li... > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of svtoolkit-help digest..." > > > Today's Topics: > > 1. Re: (no subject) (Bob Handsaker) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Fri, 06 Feb 2015 11:19:47 -0500 > From: Bob Handsaker <han...@br...> > Subject: Re: [svtoolkit-help] (no subject) > To: svt...@li... > Cc: Seva Kashin <sk...@br...> > Message-ID: <54D...@br...> > Content-Type: text/plain; charset="iso-8859-1" > > Hi, Peng, > > This was reported by a couple of other people too. > The code was expecting a bed file specifying the locations of V(D)J > recombination regions as part of the metadata bundle (and was failing if > this file was not found). > So this affects people who are not using one of the pre-built reference > metadata bundles. > > We just pushed out a new release (r1533) that fixes this problem (now if > there is no reference.vdjregions.bed file, then VDJ flagging/filtering > will just not be done). > If you need to use the previous release for some reason, there are two > workarounds: Either create a small dummy vdjregions.bed file or edit > the Queue scripts to remove this. > > If you encounter more problems, let us know. > > -Bob > > On 2/5/15, 6:13 PM, Peng Chen wrote: > > I am trying to run the CNV pipeline of genomestrip 2.0. However, I got > > an error message that I can not figure out what is wrong. I would > > appreciate if you could help me out of here. The command I ran and > > part of the log file is in the following. > > > > java -cp ${classpath} ${mx} \ > > org.broadinstitute.gatk.queue.QCommandLine \ > > -S ${SV_DIR}/qscript/discovery/cnv/CNVDiscoveryPipeline.q \ > > -S ${SV_DIR}/qscript/SVQScript.q \ > > -cp ${classpath} \ > > -gatk ${SV_DIR}/lib/gatk/GenomeAnalysisTK.jar \ > > -configFile ${SV_DIR}/conf/genstrip_parameters.txt \ > > -R /home/chenp4/cp/sv/fastqc/cp-qced/fq/gs/gmask/hg38_chr21.fasta \ > > -genomeMaskFile > > /home/chenp4/cp/sv/fastqc/cp-qced/fq/gs/gmask/hg38_mask_100_chr21.fasta \ > > -I ${bam} \ > > -genderMapFile ${SV_DIR}/gender_map \ > > -md > > /home/chenp4/cp/sv/fastqc/cp-qced/fq/svtoolkit/batch2_run/metadata \ > > -runDirectory ${runDir} \ > > -jobLogDir ${runDir}/logs \ > > -ploidyMapFile > > /home/chenp4/cp/sv/fastqc/cp-qced/fq/svtoolkit/chr21_ploidymayfile.txt \ > > -tilingWindowSize 1000 \ > > -tilingWindowOverlap 500 \ > > -maximumReferenceGapLength 1000 \ > > -boundaryPrecision 100 \ > > -minimumRefinedLength 500 \ > > -run > > > > > > > ------------------------------------------------------------------------------------------------------------ > > The error message: > > > > INFO 14:18:05,148 HelpFormatter - Program Args: -cp > > > /home/chenp4/cp/sv/fastqc/cp-qced/fq/svtoolkit/lib/SVToolkit.jar:/home/chenp4/cp/sv/fastqc/cp-qced/fq/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/home/chenp4/cp/sv/fastqc/cp-qced/fq/svtoolkit/lib/gatk/Queue.jar > > -S > > /home/chenp4/cp/sv/fastqc/cp-qced/fq/svtoolkit/qscript/SVGenotyper2.q > > -S /home/chenp4/cp/sv/fastqc/cp-qced/fq/svtoolkit/qscript/SVQScript.q > > -gatk > > > /home/chenp4/cp/sv/fastqc/cp-qced/fq/svtoolkit/lib/gatk/GenomeAnalysisTK.jar > > -jobLogDir > > > /home/chenp4/cp/sv/fastqc/cp-qced/fq/svtoolkit/batch1_run/cnv_stage2/seq_chr21/logs > > -memLimit 2.0 -jobRunner Shell -gatkJobRunner Shell -run > > --disableJobReport -configFile > > > /home/chenp4/cp/sv/fastqc/cp-qced/fq/svtoolkit/conf/genstrip_parameters.txt > > -P depth.readCountCacheIgnoreGenomeMask:true -P > > genotyping.modules:depth -R > > /home/chenp4/cp/sv/fastqc/cp-qced/fq/gs/gmask/hg38_chr21.fasta > > -genomeMaskFile > > /home/chenp4/cp/sv/fastqc/cp-qced/fq/gs/gmask/hg38_mask_100_chr21.fasta > -ploidyMapFile > > /home/chenp4/cp/sv/fastqc/cp-qced/fq/svtoolkit/chr21_ploidymayfile.txt > > -genderMapFile > > /home/chenp4/cp/sv/fastqc/cp-qced/fq/svtoolkit/gender_map -md > > /home/chenp4/cp/sv/fastqc/cp-qced/fq/svtoolkit/batch2_run/metadata > > -disableGATKTraversal -vcf > > > /home/chenp4/cp/sv/fastqc/cp-qced/fq/svtoolkit/batch1_run/cnv_stage1/seq_chr21/seq_chr21.sites.vcf > > -parallelRecords 1000 -I > > > /home/chenp4/cp/sv/fastqc/cp-qced/fq/svtoolkit/batch1_run/bam_headers/merged_headers.bam > > -O > > > /home/chenp4/cp/sv/fastqc/cp-qced/fq/svtoolkit/batch1_run/cnv_stage2/seq_chr21/seq_chr21.genotypes.vcf > > -runDirectory > > > /home/chenp4/cp/sv/fastqc/cp-qced/fq/svtoolkit/batch1_run/cnv_stage2/seq_chr21 > > -duplicateScoreThreshold 0.0 > > INFO 14:18:05,150 HelpFormatter - Executing as p692 on Linux > > 2.6.18-128.el5 amd64; Java HotSpot(TM) 64-Bit Server VM 1.7.0_05-b06. > > INFO 14:18:05,150 HelpFormatter - Date/Time: 2015/02/05 14:18:05 > > INFO 14:18:05,150 HelpFormatter - > > ---------------------------------------------------------------------- > > INFO 14:18:05,150 HelpFormatter - > > ---------------------------------------------------------------------- > > INFO 14:18:05,160 QCommandLine - Scripting SVGenotyper > > INFO 14:18:05,800 QCommandLine - Done with errors > > ##### ERROR > > > ------------------------------------------------------------------------------------------ > > ##### ERROR stack trace > > > org.broadinstitute.gatk.utils.exceptions.UserException$CannotExecuteQScript: > > Unable to execute QScript: SVGenotyper.script() threw the following > > exception: java.lang.NullPointerException > > at > > > org.broadinstitute.gatk.queue.QCommandLine$$anonfun$execute$5.apply(QCommandLine.scala:159) > > at > > > org.broadinstitute.gatk.queue.QCommandLine$$anonfun$execute$5.apply(QCommandLine.scala:147) > > at scala.collection.Iterator$class.foreach(Iterator.scala:727) > > at scala.collection.AbstractIterator.foreach(Iterator.scala:1157) > > at > > scala.collection.IterableLike$class.foreach(IterableLike.scala:72) > > at scala.collection.AbstractIterable.foreach(Iterable.scala:54) > > at > > > org.broadinstitute.gatk.queue.QCommandLine.execute(QCommandLine.scala:147) > > at > > > org.broadinstitute.gatk.utils.commandline.CommandLineProgram.start(CommandLineProgram.java:248) > > at > > > org.broadinstitute.gatk.utils.commandline.CommandLineProgram.start(CommandLineProgram.java:155) > > at > > org.broadinstitute.gatk.queue.QCommandLine$.main(QCommandLine.scala:62) > > at > > org.broadinstitute.gatk.queue.QCommandLine.main(QCommandLine.scala) > > Caused by: java.lang.NullPointerException > > at > > > org.broadinstitute.sv.qscript.SVQScript$GenotyperDefaultFilterAnnotations.<init>(SVQScript.q:1133) > > at SVGenotyper.script(SVGenotyper2.q:37) > > at > > > org.broadinstitute.gatk.queue.QCommandLine$$anonfun$execute$5.apply(QCommandLine.scala:156) > > ... 10 more > > ##### ERROR > > > ------------------------------------------------------------------------------------------ > > ##### ERROR A GATK RUNTIME ERROR has occurred (version <unknown>): > > ##### ERROR > > ##### ERROR This might be a bug. Please check the documentation guide > > to see if this is a known problem. > > ##### ERROR If not, please post the error message, with stack trace, > > to the GATK forum. > > ##### ERROR Visit our website and forum for extensive documentation > > and answers to > > ##### ERROR commonly asked questions http://www.broadinstitute.org/gatk > > ##### ERROR > > ##### ERROR MESSAGE: Unable to execute QScript: SVGenotyper.script() > > threw the following exception: java.lang.NullPointerException > > ##### ERROR > > > ------------------------------------------------------------------------------------------ > > INFO 14:18:05,807 QCommandLine - Shutting down jobs. Please wait... > > INFO 14:18:17,930 QGraph - Writing incremental jobs reports... > > INFO 14:18:17,930 QGraph - 2 Pend, 0 Run, 1 Fail, 0 Done > > INFO 14:18:17,933 QCommandLine - Writing final jobs report... > > INFO 14:18:17,934 QCommandLine - Done with errors > > INFO 14:18:17,936 QGraph - ------- > > > > > > Thank you. > > Peng > > > > > > > ------------------------------------------------------------------------------ > > Dive into the World of Parallel Programming. The Go Parallel Website, > > sponsored by Intel and developed in partnership with Slashdot Media, is > your > > hub for all things parallel software development, from weekly thought > > leadership blogs to news, videos, case studies, tutorials and more. Take > a > > look and join the conversation now. http://goparallel.sourceforge.net/ > > > > > > _______________________________________________ > > svtoolkit-help mailing list > > svt...@li... > > https://lists.sourceforge.net/lists/listinfo/svtoolkit-help > > -------------- next part -------------- > An HTML attachment was scrubbed... > > ------------------------------ > > > ------------------------------------------------------------------------------ > Dive into the World of Parallel Programming. The Go Parallel Website, > sponsored by Intel and developed in partnership with Slashdot Media, is > your > hub for all things parallel software development, from weekly thought > leadership blogs to news, videos, case studies, tutorials and more. Take a > look and join the conversation now. http://goparallel.sourceforge.net/ > > ------------------------------ > > _______________________________________________ > svtoolkit-help mailing list > svt...@li... > https://lists.sourceforge.net/lists/listinfo/svtoolkit-help > > > End of svtoolkit-help Digest, Vol 31, Issue 2 > ********************************************* > |
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From: Bob H. <han...@br...> - 2015-02-06 16:19:57
|
Hi, Peng,
This was reported by a couple of other people too.
The code was expecting a bed file specifying the locations of V(D)J
recombination regions as part of the metadata bundle (and was failing if
this file was not found).
So this affects people who are not using one of the pre-built reference
metadata bundles.
We just pushed out a new release (r1533) that fixes this problem (now if
there is no reference.vdjregions.bed file, then VDJ flagging/filtering
will just not be done).
If you need to use the previous release for some reason, there are two
workarounds: Either create a small dummy vdjregions.bed file or edit
the Queue scripts to remove this.
If you encounter more problems, let us know.
-Bob
On 2/5/15, 6:13 PM, Peng Chen wrote:
> I am trying to run the CNV pipeline of genomestrip 2.0. However, I got
> an error message that I can not figure out what is wrong. I would
> appreciate if you could help me out of here. The command I ran and
> part of the log file is in the following.
>
> java -cp ${classpath} ${mx} \
> org.broadinstitute.gatk.queue.QCommandLine \
> -S ${SV_DIR}/qscript/discovery/cnv/CNVDiscoveryPipeline.q \
> -S ${SV_DIR}/qscript/SVQScript.q \
> -cp ${classpath} \
> -gatk ${SV_DIR}/lib/gatk/GenomeAnalysisTK.jar \
> -configFile ${SV_DIR}/conf/genstrip_parameters.txt \
> -R /home/chenp4/cp/sv/fastqc/cp-qced/fq/gs/gmask/hg38_chr21.fasta \
> -genomeMaskFile
> /home/chenp4/cp/sv/fastqc/cp-qced/fq/gs/gmask/hg38_mask_100_chr21.fasta \
> -I ${bam} \
> -genderMapFile ${SV_DIR}/gender_map \
> -md
> /home/chenp4/cp/sv/fastqc/cp-qced/fq/svtoolkit/batch2_run/metadata \
> -runDirectory ${runDir} \
> -jobLogDir ${runDir}/logs \
> -ploidyMapFile
> /home/chenp4/cp/sv/fastqc/cp-qced/fq/svtoolkit/chr21_ploidymayfile.txt \
> -tilingWindowSize 1000 \
> -tilingWindowOverlap 500 \
> -maximumReferenceGapLength 1000 \
> -boundaryPrecision 100 \
> -minimumRefinedLength 500 \
> -run
>
>
> ------------------------------------------------------------------------------------------------------------
> The error message:
>
> INFO 14:18:05,148 HelpFormatter - Program Args: -cp
> /home/chenp4/cp/sv/fastqc/cp-qced/fq/svtoolkit/lib/SVToolkit.jar:/home/chenp4/cp/sv/fastqc/cp-qced/fq/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/home/chenp4/cp/sv/fastqc/cp-qced/fq/svtoolkit/lib/gatk/Queue.jar
> -S
> /home/chenp4/cp/sv/fastqc/cp-qced/fq/svtoolkit/qscript/SVGenotyper2.q
> -S /home/chenp4/cp/sv/fastqc/cp-qced/fq/svtoolkit/qscript/SVQScript.q
> -gatk
> /home/chenp4/cp/sv/fastqc/cp-qced/fq/svtoolkit/lib/gatk/GenomeAnalysisTK.jar
> -jobLogDir
> /home/chenp4/cp/sv/fastqc/cp-qced/fq/svtoolkit/batch1_run/cnv_stage2/seq_chr21/logs
> -memLimit 2.0 -jobRunner Shell -gatkJobRunner Shell -run
> --disableJobReport -configFile
> /home/chenp4/cp/sv/fastqc/cp-qced/fq/svtoolkit/conf/genstrip_parameters.txt
> -P depth.readCountCacheIgnoreGenomeMask:true -P
> genotyping.modules:depth -R
> /home/chenp4/cp/sv/fastqc/cp-qced/fq/gs/gmask/hg38_chr21.fasta
> -genomeMaskFile
> /home/chenp4/cp/sv/fastqc/cp-qced/fq/gs/gmask/hg38_mask_100_chr21.fasta -ploidyMapFile
> /home/chenp4/cp/sv/fastqc/cp-qced/fq/svtoolkit/chr21_ploidymayfile.txt
> -genderMapFile
> /home/chenp4/cp/sv/fastqc/cp-qced/fq/svtoolkit/gender_map -md
> /home/chenp4/cp/sv/fastqc/cp-qced/fq/svtoolkit/batch2_run/metadata
> -disableGATKTraversal -vcf
> /home/chenp4/cp/sv/fastqc/cp-qced/fq/svtoolkit/batch1_run/cnv_stage1/seq_chr21/seq_chr21.sites.vcf
> -parallelRecords 1000 -I
> /home/chenp4/cp/sv/fastqc/cp-qced/fq/svtoolkit/batch1_run/bam_headers/merged_headers.bam
> -O
> /home/chenp4/cp/sv/fastqc/cp-qced/fq/svtoolkit/batch1_run/cnv_stage2/seq_chr21/seq_chr21.genotypes.vcf
> -runDirectory
> /home/chenp4/cp/sv/fastqc/cp-qced/fq/svtoolkit/batch1_run/cnv_stage2/seq_chr21
> -duplicateScoreThreshold 0.0
> INFO 14:18:05,150 HelpFormatter - Executing as p692 on Linux
> 2.6.18-128.el5 amd64; Java HotSpot(TM) 64-Bit Server VM 1.7.0_05-b06.
> INFO 14:18:05,150 HelpFormatter - Date/Time: 2015/02/05 14:18:05
> INFO 14:18:05,150 HelpFormatter -
> ----------------------------------------------------------------------
> INFO 14:18:05,150 HelpFormatter -
> ----------------------------------------------------------------------
> INFO 14:18:05,160 QCommandLine - Scripting SVGenotyper
> INFO 14:18:05,800 QCommandLine - Done with errors
> ##### ERROR
> ------------------------------------------------------------------------------------------
> ##### ERROR stack trace
> org.broadinstitute.gatk.utils.exceptions.UserException$CannotExecuteQScript:
> Unable to execute QScript: SVGenotyper.script() threw the following
> exception: java.lang.NullPointerException
> at
> org.broadinstitute.gatk.queue.QCommandLine$$anonfun$execute$5.apply(QCommandLine.scala:159)
> at
> org.broadinstitute.gatk.queue.QCommandLine$$anonfun$execute$5.apply(QCommandLine.scala:147)
> at scala.collection.Iterator$class.foreach(Iterator.scala:727)
> at scala.collection.AbstractIterator.foreach(Iterator.scala:1157)
> at
> scala.collection.IterableLike$class.foreach(IterableLike.scala:72)
> at scala.collection.AbstractIterable.foreach(Iterable.scala:54)
> at
> org.broadinstitute.gatk.queue.QCommandLine.execute(QCommandLine.scala:147)
> at
> org.broadinstitute.gatk.utils.commandline.CommandLineProgram.start(CommandLineProgram.java:248)
> at
> org.broadinstitute.gatk.utils.commandline.CommandLineProgram.start(CommandLineProgram.java:155)
> at
> org.broadinstitute.gatk.queue.QCommandLine$.main(QCommandLine.scala:62)
> at
> org.broadinstitute.gatk.queue.QCommandLine.main(QCommandLine.scala)
> Caused by: java.lang.NullPointerException
> at
> org.broadinstitute.sv.qscript.SVQScript$GenotyperDefaultFilterAnnotations.<init>(SVQScript.q:1133)
> at SVGenotyper.script(SVGenotyper2.q:37)
> at
> org.broadinstitute.gatk.queue.QCommandLine$$anonfun$execute$5.apply(QCommandLine.scala:156)
> ... 10 more
> ##### ERROR
> ------------------------------------------------------------------------------------------
> ##### ERROR A GATK RUNTIME ERROR has occurred (version <unknown>):
> ##### ERROR
> ##### ERROR This might be a bug. Please check the documentation guide
> to see if this is a known problem.
> ##### ERROR If not, please post the error message, with stack trace,
> to the GATK forum.
> ##### ERROR Visit our website and forum for extensive documentation
> and answers to
> ##### ERROR commonly asked questions http://www.broadinstitute.org/gatk
> ##### ERROR
> ##### ERROR MESSAGE: Unable to execute QScript: SVGenotyper.script()
> threw the following exception: java.lang.NullPointerException
> ##### ERROR
> ------------------------------------------------------------------------------------------
> INFO 14:18:05,807 QCommandLine - Shutting down jobs. Please wait...
> INFO 14:18:17,930 QGraph - Writing incremental jobs reports...
> INFO 14:18:17,930 QGraph - 2 Pend, 0 Run, 1 Fail, 0 Done
> INFO 14:18:17,933 QCommandLine - Writing final jobs report...
> INFO 14:18:17,934 QCommandLine - Done with errors
> INFO 14:18:17,936 QGraph - -------
>
>
> Thank you.
> Peng
>
>
> ------------------------------------------------------------------------------
> Dive into the World of Parallel Programming. The Go Parallel Website,
> sponsored by Intel and developed in partnership with Slashdot Media, is your
> hub for all things parallel software development, from weekly thought
> leadership blogs to news, videos, case studies, tutorials and more. Take a
> look and join the conversation now. http://goparallel.sourceforge.net/
>
>
> _______________________________________________
> svtoolkit-help mailing list
> svt...@li...
> https://lists.sourceforge.net/lists/listinfo/svtoolkit-help
|
|
From: Peng C. <ant...@gm...> - 2015-02-05 23:13:42
|
I am trying to run the CNV pipeline of genomestrip 2.0. However, I got an
error message that I can not figure out what is wrong. I would appreciate
if you could help me out of here. The command I ran and part of the log
file is in the following.
java -cp ${classpath} ${mx} \
org.broadinstitute.gatk.queue.QCommandLine \
-S ${SV_DIR}/qscript/discovery/cnv/CNVDiscoveryPipeline.q \
-S ${SV_DIR}/qscript/SVQScript.q \
-cp ${classpath} \
-gatk ${SV_DIR}/lib/gatk/GenomeAnalysisTK.jar \
-configFile ${SV_DIR}/conf/genstrip_parameters.txt \
-R /home/chenp4/cp/sv/fastqc/cp-qced/fq/gs/gmask/hg38_chr21.fasta \
-genomeMaskFile
/home/chenp4/cp/sv/fastqc/cp-qced/fq/gs/gmask/hg38_mask_100_chr21.fasta \
-I ${bam} \
-genderMapFile ${SV_DIR}/gender_map \
-md /home/chenp4/cp/sv/fastqc/cp-qced/fq/svtoolkit/batch2_run/metadata \
-runDirectory ${runDir} \
-jobLogDir ${runDir}/logs \
-ploidyMapFile
/home/chenp4/cp/sv/fastqc/cp-qced/fq/svtoolkit/chr21_ploidymayfile.txt \
-tilingWindowSize 1000 \
-tilingWindowOverlap 500 \
-maximumReferenceGapLength 1000 \
-boundaryPrecision 100 \
-minimumRefinedLength 500 \
-run
------------------------------------------------------------------------------------------------------------
The error message:
INFO 14:18:05,148 HelpFormatter - Program Args: -cp
/home/chenp4/cp/sv/fastqc/cp-qced/fq/svtoolkit/lib/SVToolkit.jar:/home/chenp4/cp/sv/fastqc/cp-qced/fq/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/home/chenp4/cp/sv/fastqc/cp-qced/fq/svtoolkit/lib/gatk/Queue.jar
-S /home/chenp4/cp/sv/fastqc/cp-qced/fq/svtoolkit/qscript/SVGenotyper2.q -S
/home/chenp4/cp/sv/fastqc/cp-qced/fq/svtoolkit/qscript/SVQScript.q -gatk
/home/chenp4/cp/sv/fastqc/cp-qced/fq/svtoolkit/lib/gatk/GenomeAnalysisTK.jar
-jobLogDir
/home/chenp4/cp/sv/fastqc/cp-qced/fq/svtoolkit/batch1_run/cnv_stage2/seq_chr21/logs
-memLimit 2.0 -jobRunner Shell -gatkJobRunner Shell -run --disableJobReport
-configFile
/home/chenp4/cp/sv/fastqc/cp-qced/fq/svtoolkit/conf/genstrip_parameters.txt
-P depth.readCountCacheIgnoreGenomeMask:true -P genotyping.modules:depth -R
/home/chenp4/cp/sv/fastqc/cp-qced/fq/gs/gmask/hg38_chr21.fasta
-genomeMaskFile
/home/chenp4/cp/sv/fastqc/cp-qced/fq/gs/gmask/hg38_mask_100_chr21.fasta
-ploidyMapFile
/home/chenp4/cp/sv/fastqc/cp-qced/fq/svtoolkit/chr21_ploidymayfile.txt
-genderMapFile /home/chenp4/cp/sv/fastqc/cp-qced/fq/svtoolkit/gender_map
-md /home/chenp4/cp/sv/fastqc/cp-qced/fq/svtoolkit/batch2_run/metadata
-disableGATKTraversal -vcf
/home/chenp4/cp/sv/fastqc/cp-qced/fq/svtoolkit/batch1_run/cnv_stage1/seq_chr21/seq_chr21.sites.vcf
-parallelRecords 1000 -I
/home/chenp4/cp/sv/fastqc/cp-qced/fq/svtoolkit/batch1_run/bam_headers/merged_headers.bam
-O
/home/chenp4/cp/sv/fastqc/cp-qced/fq/svtoolkit/batch1_run/cnv_stage2/seq_chr21/seq_chr21.genotypes.vcf
-runDirectory
/home/chenp4/cp/sv/fastqc/cp-qced/fq/svtoolkit/batch1_run/cnv_stage2/seq_chr21
-duplicateScoreThreshold 0.0
INFO 14:18:05,150 HelpFormatter - Executing as p692 on Linux
2.6.18-128.el5 amd64; Java HotSpot(TM) 64-Bit Server VM 1.7.0_05-b06.
INFO 14:18:05,150 HelpFormatter - Date/Time: 2015/02/05 14:18:05
INFO 14:18:05,150 HelpFormatter -
----------------------------------------------------------------------
INFO 14:18:05,150 HelpFormatter -
----------------------------------------------------------------------
INFO 14:18:05,160 QCommandLine - Scripting SVGenotyper
INFO 14:18:05,800 QCommandLine - Done with errors
##### ERROR
------------------------------------------------------------------------------------------
##### ERROR stack trace
org.broadinstitute.gatk.utils.exceptions.UserException$CannotExecuteQScript:
Unable to execute QScript: SVGenotyper.script() threw the following
exception: java.lang.NullPointerException
at
org.broadinstitute.gatk.queue.QCommandLine$$anonfun$execute$5.apply(QCommandLine.scala:159)
at
org.broadinstitute.gatk.queue.QCommandLine$$anonfun$execute$5.apply(QCommandLine.scala:147)
at scala.collection.Iterator$class.foreach(Iterator.scala:727)
at scala.collection.AbstractIterator.foreach(Iterator.scala:1157)
at
scala.collection.IterableLike$class.foreach(IterableLike.scala:72)
at scala.collection.AbstractIterable.foreach(Iterable.scala:54)
at
org.broadinstitute.gatk.queue.QCommandLine.execute(QCommandLine.scala:147)
at
org.broadinstitute.gatk.utils.commandline.CommandLineProgram.start(CommandLineProgram.java:248)
at
org.broadinstitute.gatk.utils.commandline.CommandLineProgram.start(CommandLineProgram.java:155)
at
org.broadinstitute.gatk.queue.QCommandLine$.main(QCommandLine.scala:62)
at
org.broadinstitute.gatk.queue.QCommandLine.main(QCommandLine.scala)
Caused by: java.lang.NullPointerException
at
org.broadinstitute.sv.qscript.SVQScript$GenotyperDefaultFilterAnnotations.<init>(SVQScript.q:1133)
at SVGenotyper.script(SVGenotyper2.q:37)
at
org.broadinstitute.gatk.queue.QCommandLine$$anonfun$execute$5.apply(QCommandLine.scala:156)
... 10 more
##### ERROR
------------------------------------------------------------------------------------------
##### ERROR A GATK RUNTIME ERROR has occurred (version <unknown>):
##### ERROR
##### ERROR This might be a bug. Please check the documentation guide to
see if this is a known problem.
##### ERROR If not, please post the error message, with stack trace, to the
GATK forum.
##### ERROR Visit our website and forum for extensive documentation and
answers to
##### ERROR commonly asked questions http://www.broadinstitute.org/gatk
##### ERROR
##### ERROR MESSAGE: Unable to execute QScript: SVGenotyper.script() threw
the following exception: java.lang.NullPointerException
##### ERROR
------------------------------------------------------------------------------------------
INFO 14:18:05,807 QCommandLine - Shutting down jobs. Please wait...
INFO 14:18:17,930 QGraph - Writing incremental jobs reports...
INFO 14:18:17,930 QGraph - 2 Pend, 0 Run, 1 Fail, 0 Done
INFO 14:18:17,933 QCommandLine - Writing final jobs report...
INFO 14:18:17,934 QCommandLine - Done with errors
INFO 14:18:17,936 QGraph - -------
Thank you.
Peng
|
|
From: Bob H. <han...@br...> - 2015-01-28 14:28:46
|
Hi, Amrita, I'll take a stab below.... On 1/27/15, 7:27 PM, Basu, Amrita wrote: > I am a potential user of GenomeStrip and had a few support related questions in order to make sure this tool is compatible with my system to process thousands of genomes. > > > 1. Is it hadoop-friendly? No, the methods are designed around direct bam file access (or cram in the future). > 2. Does it have a parallelization strategy? Yes, based on the Queue workflow engine. See the documentation pages here: http://www.broadinstitute.org/software/genomestrip/documentation > 3. Is the algorithm tractable? Any I/O issues? Well, all NGS algorithms have to swallow a lot of data, so disk bandwidth tends to be an issue at scale. We have focused a lot of our efforts recently on the scalability of our new CNV discovery pipeline. We are routinely calling in batches of 500-1000 deep (30x) whole genomes with this pipeline and we appear to have headroom to scale further. The older deletion discovery pipeline has suffered a bit from lack of recent attention to performance, but we did successfully run it on 1000 Genomes Phase 3 (2500 individuals at 4-8x coverage). The best strategy for scaling up the deletion discovery pipeline is to limit the batch sizes (we ran 1000G phase 3 in 5 batches of 500 samples each). > 4. Scalable? Can be run on multiple nodes? Which parts are not scalable? Yes, see above. Our design target is to write all of the code to run in java on large data sets using a maximum 4G heap. We can't always achieve this, but most of the code meets this criteria. One notable place where the memory depends on the input data is the read pair clustering step in deletion discovery. That part of the code probably has the worst theoretical (and practical) scalability. > 5. How well does it do on the genome in a bottle dataset? As far as I know, genomes in a bottle is only NA12878. Genome STRiP is a set of population-based methods, so we haven't tried to benchmark against genomes-in-a-bottle. In theory, calling more samples together should improve results. In our recent testing, we are finding this to be even more true than I would have expected. For example, we do OK when calling in 100 deep (30x) whole genome samples, but much better when we call in 500 or 1000 together. Hope this helps, -Bob > > Thanks, > Amrita > > > ------------------------------------------------------------------------------ > Dive into the World of Parallel Programming. The Go Parallel Website, > sponsored by Intel and developed in partnership with Slashdot Media, is your > hub for all things parallel software development, from weekly thought > leadership blogs to news, videos, case studies, tutorials and more. Take a > look and join the conversation now. http://goparallel.sourceforge.net/ > _______________________________________________ > svtoolkit-help mailing list > svt...@li... > https://lists.sourceforge.net/lists/listinfo/svtoolkit-help |
|
From: Basu, A. <amr...@lm...> - 2015-01-28 01:33:34
|
I am a potential user of GenomeStrip and had a few support related questions in order to make sure this tool is compatible with my system to process thousands of genomes. 1. Is it hadoop-friendly? 2. Does it have a parallelization strategy? 3. Is the algorithm tractable? Any I/O issues? 4. Scalable? Can be run on multiple nodes? Which parts are not scalable? 5. How well does it do on the genome in a bottle dataset? Thanks, Amrita |
|
From: 马辰宇 <hn...@gm...> - 2014-09-15 14:02:25
|
Hi, I've noticed that in the newest version of GATK(version 3.2.2), some class names altered, which might cause inconvenience when dealing large deletions with Genome Strip. So I wonder whether there is a new version of Genome Strip recently to fix this problem? Thanks a lot! Best wishes, Chenyu Ma Computational & Evolutionary Genomics Group Institute of Zoology, CAS Address: 1 Beichen West Road, Chaoyang District, Beijing 100101, P.R.China Tel: +86-10-64806606 |
|
From: Bob H. <han...@br...> - 2014-04-19 15:38:07
|
No, the problem is with the genome mask - it doesn't contain any of the unplaced contigs (e.g. GL000207.1). If you didn't run ComputeGenomeMask on the same reference, then you will have trouble calling variants accurately where there are paralogs or near paralogs on the unplaced contigs. You need to start with the exact reference your bam files are aligned to (check the bam header with samtools view -H if you are not sure), then use that exact same reference as -R and use that exact same reference with ComputeGenomeMask. -Bob On 4/19/14 6:53 AM, P?nar Kavak wrote: > > Thank you very much Bob, > I think it is the ploidy map, because I built my own genome mask > according to my reference with ComputeGenomeMask. > All map and fai files are attached. > If that is the problem, how can I modify the ploidy map file? > Thanks, > pinar > > 18 Nis 2014 16:24 tarihinde > <svt...@li... > <mailto:svt...@li...>> yazdı: > > Send svtoolkit-help mailing list submissions to >     svt...@li... > <mailto:svt...@li...> > > To subscribe or unsubscribe via the World Wide Web, visit >     https://lists.sourceforge.net/lists/listinfo/svtoolkit-help > or, via email, send a message with subject or body 'help' to >     svt...@li... > <mailto:svt...@li...> > > You can reach the person managing the list at >     svt...@li... > <mailto:svt...@li...> > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of svtoolkit-help digest..." > > > Today's Topics: > >   1. Re: "Invalid sequence position" (Bob Handsaker) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Fri, 18 Apr 2014 09:15:42 -0400 > From: Bob Handsaker <han...@br... > <mailto:han...@br...>> > Subject: Re: [svtoolkit-help] "Invalid sequence position" > To: svt...@li... > <mailto:svt...@li...> > Message-ID: <535...@br... > <mailto:535...@br...>> > Content-Type: text/plain; charset="iso-8859-1" > > It looks from the location of the NullPointerException like this is an > inconsistency between your reference sequence and ploidy map on > the one hand > and your genome mask on the other (i.e. it looks like the genome > mask is > based on a different reference sequence). > If you think this is not the case, can you post the .fai files for (a) > the reference sequence (b) the genome mask and also post your > ploidy map > file. > > I'll put in a check for this in the code so it won't get a > NullPointerException and generate a better error message. > > -Bob > > On 4/18/14 6:17 AM, P?nar Kavak wrote: > > Hi, > > > > Sorry for re-posting the same error subject, but when I run the > > preprocessing step of SVToolkit,? I get the same error and could not > > find out a solution. I use the? SVToolkit version 1.04 (build 1358). > > I'll appreciate any help. Thanks, > > > > Pinar Kavak > > Researcher > > Turkey > > > > Here is command and the output log file is following: > > > > COMMAND > > ----------------------------------------------------------------- > > > > SV_TMPDIR=./tmpdir > > SV_TMPDIR=/tmp > > IN_DIR=/export/storage > > REF_DIR=/export/working/ortak/b37_bundle_2.5 > > > > runDir=/export/working/pinar/genomeStrip > > sites=/export/working/pinar/genomeStrip/sizofreni.discovery.vcf > > genotypes=/export/working/pinar/genomeStrip/sizofreni.genotypes.vcf > > > > export LD_LIBRARY_PATH=${SV_DIR}/bwa:${LD_LIBRARY_PATH} > > > > mx="-Xmx16g" > > > classpath="${SV_DIR}/lib/SVToolkit.jar:${SV_DIR}/lib/gatk/GenomeAnalysisTK.jar:${SV_DIR}/lib/gatk/Queue.jar" > > > > mkdir -p ${runDir}/logs || exit 1 > > mkdir -p ${runDir}/metadata || exit 1 > > > > java -cp ${classpath} ${mx} -jar ${SV_DIR}/lib/SVToolkit.jar > > > > > > java -cp ${classpath} ${mx} \ > > -Djava.io.tmpdir=${SV_TMPDIR} \ > > -Djava.library.path=bwa \ > > org.broadinstitute.sting.queue.QCommandLine \ > > -cp ${classpath} \ > > -S ${SV_DIR}/qscript/SVPreprocess.q \ > > -S ${SV_DIR}/qscript/SVQScript.q \ > > -md ${runDir}/metadata \ > > -configFile installtest/conf/genstrip_installtest_parameters.txt \ > > -tempDir ${SV_TMPDIR} \ > > -gatk ${SV_DIR}/lib/gatk/GenomeAnalysisTK.jar \ > > -R ${REF_DIR}/human_g1k_v37.fasta \ > > -genomeMaskFile ${REF_DIR}/mask/human_g1k_v37.mask.fasta \ > > -ploidyMapFile ${REF_DIR}/mask/humgen_g1k_v37_ploidy.map \ > > -copyNumberMaskFile ${REF_DIR}/mask/cn2_mask_g1k_v37.fasta \ > > -computeGCProfiles \ > > -bamFilesAreDisjoint \ > > -I ${IN_DIR}/Nurten_SIZOFRENI/WGS/bam/2367.realigned.bam \ > > -I ${IN_DIR}/Nurten_SIZOFRENI/WGS/bam/855.realigned.bam \ > > -runDirectory ${runDir} \ > > -jobLogDir ${runDir}/logs \ > > --disableJobReport \ > > -run > > > > > > OUTPUT LOG > > > > ------------------ > > > > SVToolkit version 1.04 (build 1358) > > Build date: 2014/02/13 15:47:19 > > Web site:? http://www.broadinstitute.org/software/genomestrip > > INFO 18:46:59,457 QScriptManager - Compiling 2 QScripts > > INFO 18:47:13,419 QScriptManager - Compilation complete > > INFO 18:47:13,665 HelpFormatter - > > > ---------------------------------------------------------------------- > > INFO 18:47:13,665 HelpFormatter - Queue v2.5-2-g5671483, Compiled > > 2013/08/22 15:09:27 > > INFO 18:47:13,665 HelpFormatter - Copyright (c) 2012 The Broad > Institute > > INFO 18:47:13,666 HelpFormatter - For support and documentation > go to? > > http://www.broadinstitute.org/gatk > > INFO 18:47:13,666 HelpFormatter - Program Args: -cp > > > /export/home/ortak/TOOLS/svtoolkit/lib/SVToolkit.jar:/export/home/ortak/TOOLS/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/export/home/ortak/TOOLS/svtoolkit/lib/gatk/Queue.jar > > -S /export/home/ortak/TOOLS/svtoolkit/qscript/SVPreprocess.q -S > > /export/home/ortak/TOOLS/svtoolkit/qscript/SVQScript.q -md > > /export/working/pinar/genomeStrip/metadata -configFile > > installtest/conf/genstrip_installtest_parameters.txt -tempDir /tmp > > -gatk > /export/home/ortak/TOOLS/svtoolkit/lib/gatk/GenomeAnalysisTK.jar > > -R /export/working/ortak/b37_bundle_2.5/human_g1k_v37.fasta > > -genomeMaskFile > > /export/working/ortak/b37_bundle_2.5/mask/human_g1k_v37.mask.fasta > > -ploidyMapFile > > /export/working/ortak/b37_bundle_2.5/mask/humgen_g1k_v37_ploidy.map > > -copyNumberMaskFile > > /export/working/ortak/b37_bundle_2.5/mask/cn2_mask_g1k_v37.fasta > > -computeGCProfiles -bamFilesAreDisjoint -I > > /export/storage/Nurten_SIZOFRENI/WGS/bam/2367.realigned.bam -I > > /export/storage/Nurten_SIZOFRENI/WGS/bam/855.realigned.bam > > -runDirectory /export/working/pinar/genomeStrip -jobLogDir > > /export/working/pinar/genomeStrip/logs --disableJobReport -run > > INFO 18:47:13,667 HelpFormatter - Date/Time: 2014/04/17 18:47:13 > > INFO 18:47:13,667 HelpFormatter - > > > ---------------------------------------------------------------------- > > INFO 18:47:13,667 HelpFormatter - > > > ---------------------------------------------------------------------- > > INFO 18:47:13,676 QCommandLine - Scripting SVPreprocess > > INFO 18:47:13,887 QCommandLine - Added 12 functions > > INFO 18:47:13,887 QGraph - Generating graph. > > INFO 18:47:13,914 QGraph - Running jobs. > > INFO 18:47:13,969 FunctionEdge - Starting: 'java' '-Xmx4096m' > > '-XX:+UseParallelOldGC' '-XXarallelGCThreads=4' '-XX:GCTimeLimit=50' > > '-XX:GCHeapFreeLimit=10' > > '-Djava.io.tmpdir=/export/home/ortak/TOOLS/svtoolkit/.queue/tmp' > '-cp' > > > '/export/home/ortak/TOOLS/svtoolkit/lib/SVToolkit.jar:/export/home/ortak/TOOLS/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/export/home/ortak/TOOLS/svtoolkit/lib/gatk/Queue.jar' > > '-cp' > > > '/export/home/ortak/TOOLS/svtoolkit/lib/SVToolkit.jar:/export/home/ortak/TOOLS/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/export/home/ortak/TOOLS/svtoolkit/lib/gatk/Queue.jar' > > 'org.broadinstitute.sv.apps.ComputeGCProfiles' '-O' > > > '/export/working/pinar/genomeStrip/metadata/gcprofile/reference.gcprof.zip' > > '-R' '/export/working/ortak/b37_bundle_2.5/human_g1k_v37.fasta' > '-md' > > '/export/working/pinar/genomeStrip/metadata' > '-writeReferenceProfile' > > 'true' '-genomeMaskFile' > > '/export/working/ortak/b37_bundle_2.5/mask/human_g1k_v37.mask.fasta' > > '-copyNumberMaskFile' > > '/export/working/ortak/b37_bundle_2.5/mask/cn2_mask_g1k_v37.fasta' > > '-configFile' 'installtest/conf/genstrip_installtest_parameters.txt' > > INFO 18:47:13,971 FunctionEdge - Output written to > > /export/working/pinar/genomeStrip/logs/SVPreprocess-3.out > > > > INFO 18:58:01,912 QGraph - 6 Pend, 1 Run, 0 Fail, 5 Done > > ERROR 18:58:01,923 FunctionEdge - Error: 'java' '-Xmx4096m' > > '-XX:+UseParallelOldGC' '-XXarallelGCThreads=4' '-XX:GCTimeLimit=50' > > '-XX:GCHeapFreeLimit=10' > > '-Djava.io.tmpdir=/export/home/ortak/TOOLS/svtoolkit/.queue/tmp' > '-cp' > > > '/export/home/ortak/TOOLS/svtoolkit/lib/SVToolkit.jar:/export/home/ortak/TOOLS/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/export/home/ortak/TOOLS/svtoolkit/lib/gatk/Queue.jar' > > '-cp' > > > '/export/home/ortak/TOOLS/svtoolkit/lib/SVToolkit.jar:/export/home/ortak/TOOLS/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/export/home/ortak/TOOLS/svtoolkit/lib/gatk/Queue.jar' > > 'org.broadinstitute.sv.apps.ComputeGCProfiles' '-O' > > > '/export/working/pinar/genomeStrip/metadata/gcprofile/reference.gcprof.zip' > > '-R' '/export/working/ortak/b37_bundle_2.5/human_g1k_v37.fasta' > '-md' > > '/export/working/pinar/genomeStrip/metadata' > '-writeReferenceProfile' > > 'true' '-genomeMaskFile' > > '/export/working/ortak/b37_bundle_2.5/mask/human_g1k_v37.mask.fasta' > > '-copyNumberMaskFile' > > '/export/working/ortak/b37_bundle_2.5/mask/cn2_mask_g1k_v37.fasta' > > '-configFile' 'installtest/conf/genstrip_installtest_parameters.txt' > > ERROR 18:58:01,929 FunctionEdge - Contents of > > /export/working/pinar/genomeStrip/logs/SVPreprocess-3.out: > > INFO 18:47:21,668 HelpFormatter - > > ---------------------------------------------------------- > > INFO 18:47:21,671 HelpFormatter - Program Name: > > org.broadinstitute.sv.apps.ComputeGCProfiles > > INFO 18:47:21,678 HelpFormatter - Program Args: -O > > > /export/working/pinar/genomeStrip/metadata/gcprofile/reference.gcprof.zip > > -R /export/working/ortak/b37_bundle_2.5/human_g1k_v37.fasta -md > > /export/working/pinar/genomeStrip/metadata > -writeReferenceProfile true > > -genomeMaskFile > > /export/working/ortak/b37_bundle_2.5/mask/human_g1k_v37.mask.fasta > > -copyNumberMaskFile > > /export/working/ortak/b37_bundle_2.5/mask/cn2_mask_g1k_v37.fasta > > -configFile installtest/conf/genstrip_installtest_parameters.txt > > INFO 18:47:21,678 HelpFormatter - Date/Time: 2014/04/17 18:47:21 > > INFO 18:47:21,678 HelpFormatter - > > ---------------------------------------------------------- > > INFO 18:47:21,678 HelpFormatter - > > ---------------------------------------------------------- > > INFO 18:47:21,686 MetaData - Opening metadata ... > > INFO 18:47:21,688 MetaData - Adding metadata directory > > /export/working/pinar/genomeStrip/metadata ... > > INFO 18:47:21,690 MetaData - Opened metadata. > > INFO 18:47:21,690 ComputeGCProfiles - Opening reference sequence ... > > INFO 18:47:21,692 ComputeGCProfiles - Opened reference sequence. > > INFO 18:47:21,693 ComputeGCProfiles - Opening genome mask ... > > INFO 18:47:21,694 ComputeGCProfiles - Opened genome mask. > > INFO 18:47:21,694 ComputeGCProfiles - Opening copy number mask ... > > INFO 18:47:21,695 ComputeGCProfiles - Opened copy number mask. > > INFO 18:47:21,695 ComputeGCProfiles - Initializing algorithm ... > > #INFO: ReadCountAlgorithm: detected metadata version 1, forcing > legacy > > behavior > > INFO 18:47:21,701 MetaData - Loading insert size histograms ... > > INFO 18:47:22,451 ComputeGCProfiles - Algorithm initialized. > > INFO 18:47:22,452 ComputeGCProfiles - Computing reference GC > profile ... > > #DBG: Thu Apr 17 18:47:22 EEST 2014 computing reference profile for > > the interval 1:1-249250621 > > #DBG: Thu Apr 17 18:48:14 EEST 2014 computing reference profile for > > the interval 2:1-243199373 > > #DBG: Thu Apr 17 18:49:07 EEST 2014 computing reference profile for > > the interval 3:1-198022430 > > > > #DBG: Thu Apr 17 18:49:49 EEST 2014 computing reference profile for > > the interval 4:1-191154276 > > #DBG: Thu Apr 17 18:50:30 EEST 2014 computing reference profile for > > the interval 5:1-180915260 > > #DBG: Thu Apr 17 18:51:08 EEST 2014 computing reference profile for > > the interval 6:1-171115067 > > #DBG: Thu Apr 17 18:51:45 EEST 2014 computing reference profile for > > the interval 7:1-159138663 > > #DBG: Thu Apr 17 18:52:18 EEST 2014 computing reference profile for > > the interval 8:1-146364022 > > #DBG: Thu Apr 17 18:52:49 EEST 2014 computing reference profile for > > the interval 9:1-141213431 > > #DBG: Thu Apr 17 18:53:17 EEST 2014 computing reference profile for > > the interval 10:1-135534747 > > #DBG: Thu Apr 17 18:53:45 EEST 2014 computing reference profile for > > the interval 11:1-135006516 > > #DBG: Thu Apr 17 18:54:14 EEST 2014 computing reference profile for > > the interval 12:1-133851895 > > #DBG: Thu Apr 17 18:54:42 EEST 2014 computing reference profile for > > the interval 13:1-115169878 > > #DBG: Thu Apr 17 18:55:05 EEST 2014 computing reference profile for > > the interval 14:1-107349540 > > #DBG: Thu Apr 17 18:55:26 EEST 2014 computing reference profile for > > the interval 15:1-102531392 > > #DBG: Thu Apr 17 18:55:46 EEST 2014 computing reference profile for > > the interval 16:1-90354753 > > #DBG: Thu Apr 17 18:56:04 EEST 2014 computing reference profile for > > the interval 17:1-81195210 > > #DBG: Thu Apr 17 18:56:21 EEST 2014 computing reference profile for > > the interval 18:1-78077248 > > #DBG: Thu Apr 17 18:56:37 EEST 2014 computing reference profile for > > the interval 19:1-59128983 > > #DBG: Thu Apr 17 18:56:49 EEST 2014 computing reference profile for > > the interval 20:1-63025520 > > #DBG: Thu Apr 17 18:57:02 EEST 2014 computing reference profile for > > the interval 21:1-48129895 > > #DBG: Thu Apr 17 18:57:12 EEST 2014 computing reference profile for > > the interval 22:1-51304566 > > #DBG: Thu Apr 17 18:57:21 EEST 2014 computing reference profile for > > the interval X:1-155270560 > > #DBG: Thu Apr 17 18:57:52 EEST 2014 computing reference profile for > > the interval Y:1-59373566 > > #DBG: Thu Apr 17 18:58:01 EEST 2014 computing reference profile for > > the interval MT:1-16569 > > #DBG: Thu Apr 17 18:58:01 EEST 2014 computing reference profile for > > the interval GL000207.1:1-4262 > > Exception in thread "main" java.lang.RuntimeException: Invalid > > sequence position: GL000207.1:201 > > at > > > org.broadinstitute.sv.commandline.CommandLineProgram.execute(CommandLineProgram.java:50) > > at > > > org.broadinstitute.sting.commandline.CommandLineProgram.start(CommandLineProgram.java:245) > > at > > > org.broadinstitute.sting.commandline.CommandLineProgram.start(CommandLineProgram.java:152) > > at > > > org.broadinstitute.sv.commandline.CommandLineProgram.run(CommandLineProgram.java:25) > > at > > > org.broadinstitute.sv.apps.ComputeGCProfiles.main(ComputeGCProfiles.java:125) > > Caused by: java.lang.IllegalArgumentException: Invalid sequence > > position: GL000207.1:201 > > at > > > org.broadinstitute.sv.mask.GenomeMaskFastaFile.getMaskBit(GenomeMaskFastaFile.java:80) > > at > > > org.broadinstitute.sv.metadata.gc.GCProfileAlgorithm.computeIntervalProfile(GCProfileAlgorithm.java:332) > > at > > > org.broadinstitute.sv.metadata.gc.GCProfileAlgorithm.computeReferenceProfileMap(GCProfileAlgorithm.java:243) > > at > > > org.broadinstitute.sv.metadata.gc.GCProfileAlgorithm.computeReferenceProfile(GCProfileAlgorithm.java:191) > > at > > > org.broadinstitute.sv.apps.ComputeGCProfiles.run(ComputeGCProfiles.java:172) > > at > > > org.broadinstitute.sv.commandline.CommandLineProgram.execute(CommandLineProgram.java:39) > > ... 4 more > > INFO 18:58:01,930 QGraph - Writing incremental jobs reports... > > INFO 18:58:01,933 FunctionEdge - Starting: 'java' '-Xmx4096m' > > '-XX:+UseParallelOldGC' '-XXarallelGCThreads=4' '-XX:GCTimeLimit=50' > > '-XX:GCHeapFreeLimit=10' > > '-Djava.io.tmpdir=/export/home/ortak/TOOLS/svtoolkit/.queue/tmp' > '-cp' > > > '/export/home/ortak/TOOLS/svtoolkit/lib/SVToolkit.jar:/export/home/ortak/TOOLS/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/export/home/ortak/TOOLS/svtoolkit/lib/gatk/Queue.jar' > > '-cp' > > > '/export/home/ortak/TOOLS/svtoolkit/lib/SVToolkit.jar:/export/home/ortak/TOOLS/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/export/home/ortak/TOOLS/svtoolkit/lib/gatk/Queue.jar' > > 'org.broadinstitute.sv.apps.ComputeGenomeSizes' '-O' > > '/export/working/pinar/genomeStrip/metadata/genome_sizes.txt' '-R' > > '/export/working/ortak/b37_bundle_2.5/human_g1k_v37.fasta' > > '-ploidyMapFile' > > > '/export/working/ortak/b37_bundle_2.5/mask/humgen_g1k_v37_ploidy.map' > > '-genomeMaskFile' > > '/export/working/ortak/b37_bundle_2.5/mask/human_g1k_v37.mask.fasta' > > INFO 18:58:01,933 FunctionEdge - Output written to > > /export/working/pinar/genomeStrip/logs/SVPreprocess-2.out > > INFO 19:01:54,542 QGraph - 5 Pend, 1 Run, 1 Fail, 5 Done > > ERROR 19:01:54,549 FunctionEdge - Error: 'java' '-Xmx4096m' > > '-XX:+UseParallelOldGC' '-XXarallelGCThreads=4' '-XX:GCTimeLimit=50' > > '-XX:GCHeapFreeLimit=10' > > '-Djava.io.tmpdir=/export/home/ortak/TOOLS/svtoolkit/.queue/tmp' > '-cp' > > > '/export/home/ortak/TOOLS/svtoolkit/lib/SVToolkit.jar:/export/home/ortak/TOOLS/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/export/home/ortak/TOOLS/svtoolkit/lib/gatk/Queue.jar' > > '-cp' > > > '/export/home/ortak/TOOLS/svtoolkit/lib/SVToolkit.jar:/export/home/ortak/TOOLS/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/export/home/ortak/TOOLS/svtoolkit/lib/gatk/Queue.jar' > > 'org.broadinstitute.sv.apps.ComputeGenomeSizes' '-O' > > '/export/working/pinar/genomeStrip/metadata/genome_sizes.txt' '-R' > > '/export/working/ortak/b37_bundle_2.5/human_g1k_v37.fasta' > > '-ploidyMapFile' > > > '/export/working/ortak/b37_bundle_2.5/mask/humgen_g1k_v37_ploidy.map' > > '-genomeMaskFile' > > '/export/working/ortak/b37_bundle_2.5/mask/human_g1k_v37.mask.fasta' > > ERROR 19:01:54,551 FunctionEdge - Contents of > > /export/working/pinar/genomeStrip/logs/SVPreprocess-2.out: > > INFO 18:58:09,523 HelpFormatter - > > ----------------------------------------------------------- > > INFO 18:58:09,526 HelpFormatter - Program Name: > > org.broadinstitute.sv.apps.ComputeGenomeSizes > > INFO 18:58:09,533 HelpFormatter - Program Args: -O > > /export/working/pinar/genomeStrip/metadata/genome_sizes.txt -R > > /export/working/ortak/b37_bundle_2.5/human_g1k_v37.fasta > > -ploidyMapFile > > /export/working/ortak/b37_bundle_2.5/mask/humgen_g1k_v37_ploidy.map > > -genomeMaskFile > > /export/working/ortak/b37_bundle_2.5/mask/human_g1k_v37.mask.fasta > > INFO 18:58:09,534 HelpFormatter - Date/Time: 2014/04/17 18:58:09 > > INFO 18:58:09,534 HelpFormatter - > > ----------------------------------------------------------- > > INFO 18:58:09,534 HelpFormatter - > > ----------------------------------------------------------- > > INFO 18:58:09,549 ComputeGenomeSizes - Processing interval > > 1:1-249250621 ... > > > > INFO 18:58:28,244 ComputeGenomeSizes - Processing interval > > 2:1-243199373 ... > > INFO 18:58:46,064 ComputeGenomeSizes - Processing interval > > 3:1-198022430 ... > > INFO 18:59:00,273 ComputeGenomeSizes - Processing interval > > 4:1-191154276 ... > > INFO 18:59:14,199 ComputeGenomeSizes - Processing interval > > 5:1-180915260 ... > > INFO 18:59:27,249 ComputeGenomeSizes - Processing interval > > 6:1-171115067 ... > > INFO 18:59:39,596 ComputeGenomeSizes - Processing interval > > 7:1-159138663 ... > > INFO 18:59:51,039 ComputeGenomeSizes - Processing interval > > 8:1-146364022 ... > > INFO 19:00:01,565 ComputeGenomeSizes - Processing interval > > 9:1-141213431 ... > > INFO 19:00:12,362 ComputeGenomeSizes - Processing interval > > 10:1-135534747 ... > > INFO 19:00:22,179 ComputeGenomeSizes - Processing interval > > 11:1-135006516 ... > > INFO 19:00:31,886 ComputeGenomeSizes - Processing interval > > 12:1-133851895 ... > > INFO 19:00:41,484 ComputeGenomeSizes - Processing interval > > 13:1-115169878 ... > > INFO 19:00:49,752 ComputeGenomeSizes - Processing interval > > 14:1-107349540 ... > > INFO 19:00:57,475 ComputeGenomeSizes - Processing interval > > 15:1-102531392 ... > > INFO 19:01:04,955 ComputeGenomeSizes - Processing interval > > 16:1-90354753 ... > > INFO 19:01:11,456 ComputeGenomeSizes - Processing interval > > 17:1-81195210 ... > > INFO 19:01:17,264 ComputeGenomeSizes - Processing interval > > 18:1-78077248 ... > > INFO 19:01:23,082 ComputeGenomeSizes - Processing interval > > 19:1-59128983 ... > > INFO 19:01:27,400 ComputeGenomeSizes - Processing interval > > 20:1-63025520 ... > > INFO 19:01:31,924 ComputeGenomeSizes - Processing interval > > 21:1-48129895 ... > > INFO 19:01:35,388 ComputeGenomeSizes - Processing interval > > 22:1-51304566 ... > > INFO 19:01:39,081 ComputeGenomeSizes - Processing interval > > X:1-155270560 ... > > INFO 19:01:50,250 ComputeGenomeSizes - Processing interval > > Y:1-59373566 ... > > INFO 19:01:54,512 ComputeGenomeSizes - Processing interval > MT:1-16569 ... > > INFO 19:01:54,514 ComputeGenomeSizes - Processing interval > > GL000207.1:1-4262 ... > > Exception in thread "main" java.lang.RuntimeException > > at > > > org.broadinstitute.sv.commandline.CommandLineProgram.execute(CommandLineProgram.java:50) > > at > > > org.broadinstitute.sting.commandline.CommandLineProgram.start(CommandLineProgram.java:245) > > at > > > org.broadinstitute.sting.commandline.CommandLineProgram.start(CommandLineProgram.java:152) > > at > > > org.broadinstitute.sv.commandline.CommandLineProgram.run(CommandLineProgram.java:25) > > at > > > org.broadinstitute.sv.apps.ComputeGenomeSizes.main(ComputeGenomeSizes.java:56) > > Caused by: java.lang.NullPointerException > > at > > > org.broadinstitute.sv.apps.ComputeGenomeSizes.run(ComputeGenomeSizes.java:74) > > at > > > org.broadinstitute.sv.commandline.CommandLineProgram.execute(CommandLineProgram.java:39) > > ... 4 more > > INFO 19:01:54,551 QGraph - Writing incremental jobs reports... > > INFO 19:01:54,552 QGraph - 5 Pend, 0 Run, 2 Fail, 5 Done > > INFO 19:01:54,555 QCommandLine - Writing final jobs report... > > INFO 19:01:54,556 QCommandLine - Done with errors > > INFO 19:01:54,558 QGraph - ------- > > INFO 19:01:54,560 QGraph - Failed: 'java' '-Xmx4096m' > > '-XX:+UseParallelOldGC' '-XXarallelGCThreads=4' '-XX:GCTimeLimit=50' > > '-XX:GCHeapFreeLimit=10' > > '-Djava.io.tmpdir=/export/home/ortak/TOOLS/svtoolkit/.queue/tmp' > '-cp' > > > '/export/home/ortak/TOOLS/svtoolkit/lib/SVToolkit.jar:/export/home/ortak/TOOLS/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/export/home/ortak/TOOLS/svtoolkit/lib/gatk/Queue.jar' > > '-cp' > > > '/export/home/ortak/TOOLS/svtoolkit/lib/SVToolkit.jar:/export/home/ortak/TOOLS/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/export/home/ortak/TOOLS/svtoolkit/lib/gatk/Queue.jar' > > 'org.broadinstitute.sv.apps.ComputeGCProfiles' '-O' > > > '/export/working/pinar/genomeStrip/metadata/gcprofile/reference.gcprof.zip' > > '-R' '/export/working/ortak/b37_bundle_2.5/human_g1k_v37.fasta' > '-md' > > '/export/working/pinar/genomeStrip/metadata' > '-writeReferenceProfile' > > 'true' '-genomeMaskFile' > > '/export/working/ortak/b37_bundle_2.5/mask/human_g1k_v37.mask.fasta' > > '-copyNumberMaskFile' > > '/export/working/ortak/b37_bundle_2.5/mask/cn2_mask_g1k_v37.fasta' > > '-configFile' 'installtest/conf/genstrip_installtest_parameters.txt' > > INFO 19:01:54,560 QGraph - Log: > > /export/working/pinar/genomeStrip/logs/SVPreprocess-3.out > > INFO 19:01:54,561 QGraph - ------- > > INFO 19:01:54,562 QGraph - Failed: 'java' '-Xmx4096m' > > '-XX:+UseParallelOldGC' '-XXarallelGCThreads=4' '-XX:GCTimeLimit=50' > > '-XX:GCHeapFreeLimit=10' > > '-Djava.io.tmpdir=/export/home/ortak/TOOLS/svtoolkit/.queue/tmp' > '-cp' > > > '/export/home/ortak/TOOLS/svtoolkit/lib/SVToolkit.jar:/export/home/ortak/TOOLS/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/export/home/ortak/TOOLS/svtoolkit/lib/gatk/Queue.jar' > > '-cp' > > > '/export/home/ortak/TOOLS/svtoolkit/lib/SVToolkit.jar:/export/home/ortak/TOOLS/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/export/home/ortak/TOOLS/svtoolkit/lib/gatk/Queue.jar' > > 'org.broadinstitute.sv.apps.ComputeGenomeSizes' '-O' > > '/export/working/pinar/genomeStrip/metadata/genome_sizes.txt' '-R' > > '/export/working/ortak/b37_bundle_2.5/human_g1k_v37.fasta' > > '-ploidyMapFile' > > > '/export/working/ortak/b37_bundle_2.5/mask/humgen_g1k_v37_ploidy.map' > > '-genomeMaskFile' > > '/export/working/ortak/b37_bundle_2.5/mask/human_g1k_v37.mask.fasta' > > INFO 19:01:54,563 QGraph - Log: > > /export/working/pinar/genomeStrip/logs/SVPreprocess-2.out > > INFO 19:01:54,563 QCommandLine - Script failed with 12 total jobs > > > > > > > > > > > ------------------------------------------------------------------------------ > > Learn Graph Databases - Download FREE O'Reilly Book > > "Graph Databases" is the definitive new guide to graph databases > and their > > applications. Written by three acclaimed leaders in the field, > > this first edition is now available. Download your free book today! > > http://p.sf.net/sfu/NeoTech > > > > > > _______________________________________________ > > svtoolkit-help mailing list > > svt...@li... > <mailto:svt...@li...> > > https://lists.sourceforge.net/lists/listinfo/svtoolkit-help > > -------------- next part -------------- > An HTML attachment was scrubbed... > > ------------------------------ > > ------------------------------------------------------------------------------ > Learn Graph Databases - Download FREE O'Reilly Book > "Graph Databases" is the definitive new guide to graph databases > and their > applications. Written by three acclaimed leaders in the field, > this first edition is now available. Download your free book today! > http://p.sf.net/sfu/NeoTech > > ------------------------------ > > _______________________________________________ > svtoolkit-help mailing list > svt...@li... > <mailto:svt...@li...> > https://lists.sourceforge.net/lists/listinfo/svtoolkit-help > > > End of svtoolkit-help Digest, Vol 28, Issue 3 > ********************************************* > > > > ------------------------------------------------------------------------------ > Learn Graph Databases - Download FREE O'Reilly Book > "Graph Databases" is the definitive new guide to graph databases and their > applications. Written by three acclaimed leaders in the field, > this first edition is now available. Download your free book today! > http://p.sf.net/sfu/NeoTech > > > _______________________________________________ > svtoolkit-help mailing list > svt...@li... > https://lists.sourceforge.net/lists/listinfo/svtoolkit-help |
|
From: Bob H. <han...@br...> - 2014-04-18 13:15:55
|
It looks from the location of the NullPointerException like this is an
inconsistency between your reference sequence and ploidy map on the one hand
and your genome mask on the other (i.e. it looks like the genome mask is
based on a different reference sequence).
If you think this is not the case, can you post the .fai files for (a)
the reference sequence (b) the genome mask and also post your ploidy map
file.
I'll put in a check for this in the code so it won't get a
NullPointerException and generate a better error message.
-Bob
On 4/18/14 6:17 AM, P?nar Kavak wrote:
> Hi,
>
> Sorry for re-posting the same error subject, but when I run the
> preprocessing step of SVToolkit, I get the same error and could not
> find out a solution. I use the SVToolkit version 1.04 (build 1358).
> I'll appreciate any help. Thanks,
>
> Pinar Kavak
> Researcher
> Turkey
>
> Here is command and the output log file is following:
>
> COMMAND
> -----------------------------------------------------------------
>
> SV_TMPDIR=./tmpdir
> SV_TMPDIR=/tmp
> IN_DIR=/export/storage
> REF_DIR=/export/working/ortak/b37_bundle_2.5
>
> runDir=/export/working/pinar/genomeStrip
> sites=/export/working/pinar/genomeStrip/sizofreni.discovery.vcf
> genotypes=/export/working/pinar/genomeStrip/sizofreni.genotypes.vcf
>
> export LD_LIBRARY_PATH=${SV_DIR}/bwa:${LD_LIBRARY_PATH}
>
> mx="-Xmx16g"
> classpath="${SV_DIR}/lib/SVToolkit.jar:${SV_DIR}/lib/gatk/GenomeAnalysisTK.jar:${SV_DIR}/lib/gatk/Queue.jar"
>
> mkdir -p ${runDir}/logs || exit 1
> mkdir -p ${runDir}/metadata || exit 1
>
> java -cp ${classpath} ${mx} -jar ${SV_DIR}/lib/SVToolkit.jar
>
>
> java -cp ${classpath} ${mx} \
> -Djava.io.tmpdir=${SV_TMPDIR} \
> -Djava.library.path=bwa \
> org.broadinstitute.sting.queue.QCommandLine \
> -cp ${classpath} \
> -S ${SV_DIR}/qscript/SVPreprocess.q \
> -S ${SV_DIR}/qscript/SVQScript.q \
> -md ${runDir}/metadata \
> -configFile installtest/conf/genstrip_installtest_parameters.txt \
> -tempDir ${SV_TMPDIR} \
> -gatk ${SV_DIR}/lib/gatk/GenomeAnalysisTK.jar \
> -R ${REF_DIR}/human_g1k_v37.fasta \
> -genomeMaskFile ${REF_DIR}/mask/human_g1k_v37.mask.fasta \
> -ploidyMapFile ${REF_DIR}/mask/humgen_g1k_v37_ploidy.map \
> -copyNumberMaskFile ${REF_DIR}/mask/cn2_mask_g1k_v37.fasta \
> -computeGCProfiles \
> -bamFilesAreDisjoint \
> -I ${IN_DIR}/Nurten_SIZOFRENI/WGS/bam/2367.realigned.bam \
> -I ${IN_DIR}/Nurten_SIZOFRENI/WGS/bam/855.realigned.bam \
> -runDirectory ${runDir} \
> -jobLogDir ${runDir}/logs \
> --disableJobReport \
> -run
>
>
> OUTPUT LOG
>
> ------------------
>
> SVToolkit version 1.04 (build 1358)
> Build date: 2014/02/13 15:47:19
> Web site:Â http://www.broadinstitute.org/software/genomestrip
> INFO 18:46:59,457 QScriptManager - Compiling 2 QScripts
> INFO 18:47:13,419 QScriptManager - Compilation complete
> INFO 18:47:13,665 HelpFormatter -
> ----------------------------------------------------------------------
> INFO 18:47:13,665 HelpFormatter - Queue v2.5-2-g5671483, Compiled
> 2013/08/22 15:09:27
> INFO 18:47:13,665 HelpFormatter - Copyright (c) 2012 The Broad Institute
> INFO 18:47:13,666 HelpFormatter - For support and documentation go toÂ
> http://www.broadinstitute.org/gatk
> INFO 18:47:13,666 HelpFormatter - Program Args: -cp
> /export/home/ortak/TOOLS/svtoolkit/lib/SVToolkit.jar:/export/home/ortak/TOOLS/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/export/home/ortak/TOOLS/svtoolkit/lib/gatk/Queue.jar
> -S /export/home/ortak/TOOLS/svtoolkit/qscript/SVPreprocess.q -S
> /export/home/ortak/TOOLS/svtoolkit/qscript/SVQScript.q -md
> /export/working/pinar/genomeStrip/metadata -configFile
> installtest/conf/genstrip_installtest_parameters.txt -tempDir /tmp
> -gatk /export/home/ortak/TOOLS/svtoolkit/lib/gatk/GenomeAnalysisTK.jar
> -R /export/working/ortak/b37_bundle_2.5/human_g1k_v37.fasta
> -genomeMaskFile
> /export/working/ortak/b37_bundle_2.5/mask/human_g1k_v37.mask.fasta
> -ploidyMapFile
> /export/working/ortak/b37_bundle_2.5/mask/humgen_g1k_v37_ploidy.map
> -copyNumberMaskFile
> /export/working/ortak/b37_bundle_2.5/mask/cn2_mask_g1k_v37.fasta
> -computeGCProfiles -bamFilesAreDisjoint -I
> /export/storage/Nurten_SIZOFRENI/WGS/bam/2367.realigned.bam -I
> /export/storage/Nurten_SIZOFRENI/WGS/bam/855.realigned.bam
> -runDirectory /export/working/pinar/genomeStrip -jobLogDir
> /export/working/pinar/genomeStrip/logs --disableJobReport -run
> INFO 18:47:13,667 HelpFormatter - Date/Time: 2014/04/17 18:47:13
> INFO 18:47:13,667 HelpFormatter -
> ----------------------------------------------------------------------
> INFO 18:47:13,667 HelpFormatter -
> ----------------------------------------------------------------------
> INFO 18:47:13,676 QCommandLine - Scripting SVPreprocess
> INFO 18:47:13,887 QCommandLine - Added 12 functions
> INFO 18:47:13,887 QGraph - Generating graph.
> INFO 18:47:13,914 QGraph - Running jobs.
> INFO 18:47:13,969 FunctionEdge - Starting: 'java' '-Xmx4096m'
> '-XX:+UseParallelOldGC' '-XXarallelGCThreads=4' '-XX:GCTimeLimit=50'
> '-XX:GCHeapFreeLimit=10'
> '-Djava.io.tmpdir=/export/home/ortak/TOOLS/svtoolkit/.queue/tmp' '-cp'
> '/export/home/ortak/TOOLS/svtoolkit/lib/SVToolkit.jar:/export/home/ortak/TOOLS/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/export/home/ortak/TOOLS/svtoolkit/lib/gatk/Queue.jar'
> '-cp'
> '/export/home/ortak/TOOLS/svtoolkit/lib/SVToolkit.jar:/export/home/ortak/TOOLS/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/export/home/ortak/TOOLS/svtoolkit/lib/gatk/Queue.jar'
> 'org.broadinstitute.sv.apps.ComputeGCProfiles' '-O'
> '/export/working/pinar/genomeStrip/metadata/gcprofile/reference.gcprof.zip'
> '-R' '/export/working/ortak/b37_bundle_2.5/human_g1k_v37.fasta' '-md'
> '/export/working/pinar/genomeStrip/metadata' '-writeReferenceProfile'
> 'true' '-genomeMaskFile'
> '/export/working/ortak/b37_bundle_2.5/mask/human_g1k_v37.mask.fasta'
> '-copyNumberMaskFile'
> '/export/working/ortak/b37_bundle_2.5/mask/cn2_mask_g1k_v37.fasta'
> '-configFile' 'installtest/conf/genstrip_installtest_parameters.txt'
> INFO 18:47:13,971 FunctionEdge - Output written to
> /export/working/pinar/genomeStrip/logs/SVPreprocess-3.out
>
> INFO 18:58:01,912 QGraph - 6 Pend, 1 Run, 0 Fail, 5 Done
> ERROR 18:58:01,923 FunctionEdge - Error: 'java' '-Xmx4096m'
> '-XX:+UseParallelOldGC' '-XXarallelGCThreads=4' '-XX:GCTimeLimit=50'
> '-XX:GCHeapFreeLimit=10'
> '-Djava.io.tmpdir=/export/home/ortak/TOOLS/svtoolkit/.queue/tmp' '-cp'
> '/export/home/ortak/TOOLS/svtoolkit/lib/SVToolkit.jar:/export/home/ortak/TOOLS/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/export/home/ortak/TOOLS/svtoolkit/lib/gatk/Queue.jar'
> '-cp'
> '/export/home/ortak/TOOLS/svtoolkit/lib/SVToolkit.jar:/export/home/ortak/TOOLS/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/export/home/ortak/TOOLS/svtoolkit/lib/gatk/Queue.jar'
> 'org.broadinstitute.sv.apps.ComputeGCProfiles' '-O'
> '/export/working/pinar/genomeStrip/metadata/gcprofile/reference.gcprof.zip'
> '-R' '/export/working/ortak/b37_bundle_2.5/human_g1k_v37.fasta' '-md'
> '/export/working/pinar/genomeStrip/metadata' '-writeReferenceProfile'
> 'true' '-genomeMaskFile'
> '/export/working/ortak/b37_bundle_2.5/mask/human_g1k_v37.mask.fasta'
> '-copyNumberMaskFile'
> '/export/working/ortak/b37_bundle_2.5/mask/cn2_mask_g1k_v37.fasta'
> '-configFile' 'installtest/conf/genstrip_installtest_parameters.txt'
> ERROR 18:58:01,929 FunctionEdge - Contents of
> /export/working/pinar/genomeStrip/logs/SVPreprocess-3.out:
> INFO 18:47:21,668 HelpFormatter -
> ----------------------------------------------------------
> INFO 18:47:21,671 HelpFormatter - Program Name:
> org.broadinstitute.sv.apps.ComputeGCProfiles
> INFO 18:47:21,678 HelpFormatter - Program Args: -O
> /export/working/pinar/genomeStrip/metadata/gcprofile/reference.gcprof.zip
> -R /export/working/ortak/b37_bundle_2.5/human_g1k_v37.fasta -md
> /export/working/pinar/genomeStrip/metadata -writeReferenceProfile true
> -genomeMaskFile
> /export/working/ortak/b37_bundle_2.5/mask/human_g1k_v37.mask.fasta
> -copyNumberMaskFile
> /export/working/ortak/b37_bundle_2.5/mask/cn2_mask_g1k_v37.fasta
> -configFile installtest/conf/genstrip_installtest_parameters.txt
> INFO 18:47:21,678 HelpFormatter - Date/Time: 2014/04/17 18:47:21
> INFO 18:47:21,678 HelpFormatter -
> ----------------------------------------------------------
> INFO 18:47:21,678 HelpFormatter -
> ----------------------------------------------------------
> INFO 18:47:21,686 MetaData - Opening metadata ...
> INFO 18:47:21,688 MetaData - Adding metadata directory
> /export/working/pinar/genomeStrip/metadata ...
> INFO 18:47:21,690 MetaData - Opened metadata.
> INFO 18:47:21,690 ComputeGCProfiles - Opening reference sequence ...
> INFO 18:47:21,692 ComputeGCProfiles - Opened reference sequence.
> INFO 18:47:21,693 ComputeGCProfiles - Opening genome mask ...
> INFO 18:47:21,694 ComputeGCProfiles - Opened genome mask.
> INFO 18:47:21,694 ComputeGCProfiles - Opening copy number mask ...
> INFO 18:47:21,695 ComputeGCProfiles - Opened copy number mask.
> INFO 18:47:21,695 ComputeGCProfiles - Initializing algorithm ...
> #INFO: ReadCountAlgorithm: detected metadata version 1, forcing legacy
> behavior
> INFO 18:47:21,701 MetaData - Loading insert size histograms ...
> INFO 18:47:22,451 ComputeGCProfiles - Algorithm initialized.
> INFO 18:47:22,452 ComputeGCProfiles - Computing reference GC profile ...
> #DBG: Thu Apr 17 18:47:22 EEST 2014 computing reference profile for
> the interval 1:1-249250621
> #DBG: Thu Apr 17 18:48:14 EEST 2014 computing reference profile for
> the interval 2:1-243199373
> #DBG: Thu Apr 17 18:49:07 EEST 2014 computing reference profile for
> the interval 3:1-198022430
>
> #DBG: Thu Apr 17 18:49:49 EEST 2014 computing reference profile for
> the interval 4:1-191154276
> #DBG: Thu Apr 17 18:50:30 EEST 2014 computing reference profile for
> the interval 5:1-180915260
> #DBG: Thu Apr 17 18:51:08 EEST 2014 computing reference profile for
> the interval 6:1-171115067
> #DBG: Thu Apr 17 18:51:45 EEST 2014 computing reference profile for
> the interval 7:1-159138663
> #DBG: Thu Apr 17 18:52:18 EEST 2014 computing reference profile for
> the interval 8:1-146364022
> #DBG: Thu Apr 17 18:52:49 EEST 2014 computing reference profile for
> the interval 9:1-141213431
> #DBG: Thu Apr 17 18:53:17 EEST 2014 computing reference profile for
> the interval 10:1-135534747
> #DBG: Thu Apr 17 18:53:45 EEST 2014 computing reference profile for
> the interval 11:1-135006516
> #DBG: Thu Apr 17 18:54:14 EEST 2014 computing reference profile for
> the interval 12:1-133851895
> #DBG: Thu Apr 17 18:54:42 EEST 2014 computing reference profile for
> the interval 13:1-115169878
> #DBG: Thu Apr 17 18:55:05 EEST 2014 computing reference profile for
> the interval 14:1-107349540
> #DBG: Thu Apr 17 18:55:26 EEST 2014 computing reference profile for
> the interval 15:1-102531392
> #DBG: Thu Apr 17 18:55:46 EEST 2014 computing reference profile for
> the interval 16:1-90354753
> #DBG: Thu Apr 17 18:56:04 EEST 2014 computing reference profile for
> the interval 17:1-81195210
> #DBG: Thu Apr 17 18:56:21 EEST 2014 computing reference profile for
> the interval 18:1-78077248
> #DBG: Thu Apr 17 18:56:37 EEST 2014 computing reference profile for
> the interval 19:1-59128983
> #DBG: Thu Apr 17 18:56:49 EEST 2014 computing reference profile for
> the interval 20:1-63025520
> #DBG: Thu Apr 17 18:57:02 EEST 2014 computing reference profile for
> the interval 21:1-48129895
> #DBG: Thu Apr 17 18:57:12 EEST 2014 computing reference profile for
> the interval 22:1-51304566
> #DBG: Thu Apr 17 18:57:21 EEST 2014 computing reference profile for
> the interval X:1-155270560
> #DBG: Thu Apr 17 18:57:52 EEST 2014 computing reference profile for
> the interval Y:1-59373566
> #DBG: Thu Apr 17 18:58:01 EEST 2014 computing reference profile for
> the interval MT:1-16569
> #DBG: Thu Apr 17 18:58:01 EEST 2014 computing reference profile for
> the interval GL000207.1:1-4262
> Exception in thread "main" java.lang.RuntimeException: Invalid
> sequence position: GL000207.1:201
> at
> org.broadinstitute.sv.commandline.CommandLineProgram.execute(CommandLineProgram.java:50)
> at
> org.broadinstitute.sting.commandline.CommandLineProgram.start(CommandLineProgram.java:245)
> at
> org.broadinstitute.sting.commandline.CommandLineProgram.start(CommandLineProgram.java:152)
> at
> org.broadinstitute.sv.commandline.CommandLineProgram.run(CommandLineProgram.java:25)
> at
> org.broadinstitute.sv.apps.ComputeGCProfiles.main(ComputeGCProfiles.java:125)
> Caused by: java.lang.IllegalArgumentException: Invalid sequence
> position: GL000207.1:201
> at
> org.broadinstitute.sv.mask.GenomeMaskFastaFile.getMaskBit(GenomeMaskFastaFile.java:80)
> at
> org.broadinstitute.sv.metadata.gc.GCProfileAlgorithm.computeIntervalProfile(GCProfileAlgorithm.java:332)
> at
> org.broadinstitute.sv.metadata.gc.GCProfileAlgorithm.computeReferenceProfileMap(GCProfileAlgorithm.java:243)
> at
> org.broadinstitute.sv.metadata.gc.GCProfileAlgorithm.computeReferenceProfile(GCProfileAlgorithm.java:191)
> at
> org.broadinstitute.sv.apps.ComputeGCProfiles.run(ComputeGCProfiles.java:172)
> at
> org.broadinstitute.sv.commandline.CommandLineProgram.execute(CommandLineProgram.java:39)
> ... 4 more
> INFO 18:58:01,930 QGraph - Writing incremental jobs reports...
> INFO 18:58:01,933 FunctionEdge - Starting: 'java' '-Xmx4096m'
> '-XX:+UseParallelOldGC' '-XXarallelGCThreads=4' '-XX:GCTimeLimit=50'
> '-XX:GCHeapFreeLimit=10'
> '-Djava.io.tmpdir=/export/home/ortak/TOOLS/svtoolkit/.queue/tmp' '-cp'
> '/export/home/ortak/TOOLS/svtoolkit/lib/SVToolkit.jar:/export/home/ortak/TOOLS/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/export/home/ortak/TOOLS/svtoolkit/lib/gatk/Queue.jar'
> '-cp'
> '/export/home/ortak/TOOLS/svtoolkit/lib/SVToolkit.jar:/export/home/ortak/TOOLS/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/export/home/ortak/TOOLS/svtoolkit/lib/gatk/Queue.jar'
> 'org.broadinstitute.sv.apps.ComputeGenomeSizes' '-O'
> '/export/working/pinar/genomeStrip/metadata/genome_sizes.txt' '-R'
> '/export/working/ortak/b37_bundle_2.5/human_g1k_v37.fasta'
> '-ploidyMapFile'
> '/export/working/ortak/b37_bundle_2.5/mask/humgen_g1k_v37_ploidy.map'
> '-genomeMaskFile'
> '/export/working/ortak/b37_bundle_2.5/mask/human_g1k_v37.mask.fasta'
> INFO 18:58:01,933 FunctionEdge - Output written to
> /export/working/pinar/genomeStrip/logs/SVPreprocess-2.out
> INFO 19:01:54,542 QGraph - 5 Pend, 1 Run, 1 Fail, 5 Done
> ERROR 19:01:54,549 FunctionEdge - Error: 'java' '-Xmx4096m'
> '-XX:+UseParallelOldGC' '-XXarallelGCThreads=4' '-XX:GCTimeLimit=50'
> '-XX:GCHeapFreeLimit=10'
> '-Djava.io.tmpdir=/export/home/ortak/TOOLS/svtoolkit/.queue/tmp' '-cp'
> '/export/home/ortak/TOOLS/svtoolkit/lib/SVToolkit.jar:/export/home/ortak/TOOLS/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/export/home/ortak/TOOLS/svtoolkit/lib/gatk/Queue.jar'
> '-cp'
> '/export/home/ortak/TOOLS/svtoolkit/lib/SVToolkit.jar:/export/home/ortak/TOOLS/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/export/home/ortak/TOOLS/svtoolkit/lib/gatk/Queue.jar'
> 'org.broadinstitute.sv.apps.ComputeGenomeSizes' '-O'
> '/export/working/pinar/genomeStrip/metadata/genome_sizes.txt' '-R'
> '/export/working/ortak/b37_bundle_2.5/human_g1k_v37.fasta'
> '-ploidyMapFile'
> '/export/working/ortak/b37_bundle_2.5/mask/humgen_g1k_v37_ploidy.map'
> '-genomeMaskFile'
> '/export/working/ortak/b37_bundle_2.5/mask/human_g1k_v37.mask.fasta'
> ERROR 19:01:54,551 FunctionEdge - Contents of
> /export/working/pinar/genomeStrip/logs/SVPreprocess-2.out:
> INFO 18:58:09,523 HelpFormatter -
> -----------------------------------------------------------
> INFO 18:58:09,526 HelpFormatter - Program Name:
> org.broadinstitute.sv.apps.ComputeGenomeSizes
> INFO 18:58:09,533 HelpFormatter - Program Args: -O
> /export/working/pinar/genomeStrip/metadata/genome_sizes.txt -R
> /export/working/ortak/b37_bundle_2.5/human_g1k_v37.fasta
> -ploidyMapFile
> /export/working/ortak/b37_bundle_2.5/mask/humgen_g1k_v37_ploidy.map
> -genomeMaskFile
> /export/working/ortak/b37_bundle_2.5/mask/human_g1k_v37.mask.fasta
> INFO 18:58:09,534 HelpFormatter - Date/Time: 2014/04/17 18:58:09
> INFO 18:58:09,534 HelpFormatter -
> -----------------------------------------------------------
> INFO 18:58:09,534 HelpFormatter -
> -----------------------------------------------------------
> INFO 18:58:09,549 ComputeGenomeSizes - Processing interval
> 1:1-249250621 ...
>
> INFO 18:58:28,244 ComputeGenomeSizes - Processing interval
> 2:1-243199373 ...
> INFO 18:58:46,064 ComputeGenomeSizes - Processing interval
> 3:1-198022430 ...
> INFO 18:59:00,273 ComputeGenomeSizes - Processing interval
> 4:1-191154276 ...
> INFO 18:59:14,199 ComputeGenomeSizes - Processing interval
> 5:1-180915260 ...
> INFO 18:59:27,249 ComputeGenomeSizes - Processing interval
> 6:1-171115067 ...
> INFO 18:59:39,596 ComputeGenomeSizes - Processing interval
> 7:1-159138663 ...
> INFO 18:59:51,039 ComputeGenomeSizes - Processing interval
> 8:1-146364022 ...
> INFO 19:00:01,565 ComputeGenomeSizes - Processing interval
> 9:1-141213431 ...
> INFO 19:00:12,362 ComputeGenomeSizes - Processing interval
> 10:1-135534747 ...
> INFO 19:00:22,179 ComputeGenomeSizes - Processing interval
> 11:1-135006516 ...
> INFO 19:00:31,886 ComputeGenomeSizes - Processing interval
> 12:1-133851895 ...
> INFO 19:00:41,484 ComputeGenomeSizes - Processing interval
> 13:1-115169878 ...
> INFO 19:00:49,752 ComputeGenomeSizes - Processing interval
> 14:1-107349540 ...
> INFO 19:00:57,475 ComputeGenomeSizes - Processing interval
> 15:1-102531392 ...
> INFO 19:01:04,955 ComputeGenomeSizes - Processing interval
> 16:1-90354753 ...
> INFO 19:01:11,456 ComputeGenomeSizes - Processing interval
> 17:1-81195210 ...
> INFO 19:01:17,264 ComputeGenomeSizes - Processing interval
> 18:1-78077248 ...
> INFO 19:01:23,082 ComputeGenomeSizes - Processing interval
> 19:1-59128983 ...
> INFO 19:01:27,400 ComputeGenomeSizes - Processing interval
> 20:1-63025520 ...
> INFO 19:01:31,924 ComputeGenomeSizes - Processing interval
> 21:1-48129895 ...
> INFO 19:01:35,388 ComputeGenomeSizes - Processing interval
> 22:1-51304566 ...
> INFO 19:01:39,081 ComputeGenomeSizes - Processing interval
> X:1-155270560 ...
> INFO 19:01:50,250 ComputeGenomeSizes - Processing interval
> Y:1-59373566 ...
> INFO 19:01:54,512 ComputeGenomeSizes - Processing interval MT:1-16569 ...
> INFO 19:01:54,514 ComputeGenomeSizes - Processing interval
> GL000207.1:1-4262 ...
> Exception in thread "main" java.lang.RuntimeException
> at
> org.broadinstitute.sv.commandline.CommandLineProgram.execute(CommandLineProgram.java:50)
> at
> org.broadinstitute.sting.commandline.CommandLineProgram.start(CommandLineProgram.java:245)
> at
> org.broadinstitute.sting.commandline.CommandLineProgram.start(CommandLineProgram.java:152)
> at
> org.broadinstitute.sv.commandline.CommandLineProgram.run(CommandLineProgram.java:25)
> at
> org.broadinstitute.sv.apps.ComputeGenomeSizes.main(ComputeGenomeSizes.java:56)
> Caused by: java.lang.NullPointerException
> at
> org.broadinstitute.sv.apps.ComputeGenomeSizes.run(ComputeGenomeSizes.java:74)
> at
> org.broadinstitute.sv.commandline.CommandLineProgram.execute(CommandLineProgram.java:39)
> ... 4 more
> INFO 19:01:54,551 QGraph - Writing incremental jobs reports...
> INFO 19:01:54,552 QGraph - 5 Pend, 0 Run, 2 Fail, 5 Done
> INFO 19:01:54,555 QCommandLine - Writing final jobs report...
> INFO 19:01:54,556 QCommandLine - Done with errors
> INFO 19:01:54,558 QGraph - -------
> INFO 19:01:54,560 QGraph - Failed: 'java' '-Xmx4096m'
> '-XX:+UseParallelOldGC' '-XXarallelGCThreads=4' '-XX:GCTimeLimit=50'
> '-XX:GCHeapFreeLimit=10'
> '-Djava.io.tmpdir=/export/home/ortak/TOOLS/svtoolkit/.queue/tmp' '-cp'
> '/export/home/ortak/TOOLS/svtoolkit/lib/SVToolkit.jar:/export/home/ortak/TOOLS/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/export/home/ortak/TOOLS/svtoolkit/lib/gatk/Queue.jar'
> '-cp'
> '/export/home/ortak/TOOLS/svtoolkit/lib/SVToolkit.jar:/export/home/ortak/TOOLS/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/export/home/ortak/TOOLS/svtoolkit/lib/gatk/Queue.jar'
> 'org.broadinstitute.sv.apps.ComputeGCProfiles' '-O'
> '/export/working/pinar/genomeStrip/metadata/gcprofile/reference.gcprof.zip'
> '-R' '/export/working/ortak/b37_bundle_2.5/human_g1k_v37.fasta' '-md'
> '/export/working/pinar/genomeStrip/metadata' '-writeReferenceProfile'
> 'true' '-genomeMaskFile'
> '/export/working/ortak/b37_bundle_2.5/mask/human_g1k_v37.mask.fasta'
> '-copyNumberMaskFile'
> '/export/working/ortak/b37_bundle_2.5/mask/cn2_mask_g1k_v37.fasta'
> '-configFile' 'installtest/conf/genstrip_installtest_parameters.txt'
> INFO 19:01:54,560 QGraph - Log:
> /export/working/pinar/genomeStrip/logs/SVPreprocess-3.out
> INFO 19:01:54,561 QGraph - -------
> INFO 19:01:54,562 QGraph - Failed: 'java' '-Xmx4096m'
> '-XX:+UseParallelOldGC' '-XXarallelGCThreads=4' '-XX:GCTimeLimit=50'
> '-XX:GCHeapFreeLimit=10'
> '-Djava.io.tmpdir=/export/home/ortak/TOOLS/svtoolkit/.queue/tmp' '-cp'
> '/export/home/ortak/TOOLS/svtoolkit/lib/SVToolkit.jar:/export/home/ortak/TOOLS/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/export/home/ortak/TOOLS/svtoolkit/lib/gatk/Queue.jar'
> '-cp'
> '/export/home/ortak/TOOLS/svtoolkit/lib/SVToolkit.jar:/export/home/ortak/TOOLS/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/export/home/ortak/TOOLS/svtoolkit/lib/gatk/Queue.jar'
> 'org.broadinstitute.sv.apps.ComputeGenomeSizes' '-O'
> '/export/working/pinar/genomeStrip/metadata/genome_sizes.txt' '-R'
> '/export/working/ortak/b37_bundle_2.5/human_g1k_v37.fasta'
> '-ploidyMapFile'
> '/export/working/ortak/b37_bundle_2.5/mask/humgen_g1k_v37_ploidy.map'
> '-genomeMaskFile'
> '/export/working/ortak/b37_bundle_2.5/mask/human_g1k_v37.mask.fasta'
> INFO 19:01:54,563 QGraph - Log:
> /export/working/pinar/genomeStrip/logs/SVPreprocess-2.out
> INFO 19:01:54,563 QCommandLine - Script failed with 12 total jobs
>
>
>
>
> ------------------------------------------------------------------------------
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> applications. Written by three acclaimed leaders in the field,
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> http://p.sf.net/sfu/NeoTech
>
>
> _______________________________________________
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|
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