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From: Thomas Z. <tho...@em...> - 2012-01-20 08:01:58
|
Hi, I am running GenomeSTRiP on individual chromosomes which seems to work very well. In most cases, I get the file discovery.vcf as expected. However, in a few cases I only get discovery.unfiltered.vcf (as well as .discovery.unfiltered.vcf.done). When I rerun GenomeSTRiP, the variant filtration is executed again, however, there is still no output, but also no error message. And as far I can see, also the log file doesn't contain any error message. Any idea what the problem might be? Thank you very much! Kind regards Thomas Zichner |
|
From: Bob H. <han...@br...> - 2011-12-15 15:50:00
|
If it still happens in the latest interim release, let me know. -Bob On 12/15/11 9:23 AM, Verena Tischler wrote: > Hi, > > sorry I just saw that someone encountered the same problem as I > describe below. > > So let me please rephrase my question: Did you already find a solution > to that or did using the interim version solve the problem? > > Thanks a lot > Verena > > 2011/12/15 Verena Tischler <tis...@go... > <mailto:tis...@go...>> > > Hi, > > I am running GenomeSTRiP on eland mapped files and the > preprocessing of bams works fine. > However in the SVDiscovery step I end up with the following error > > ##### ERROR > ------------------------------------------------------------------------------------------ > ##### ERROR stack trace > java.lang.RuntimeException: Invalid cnp coordinates: > DEL_P0009_3706 91702292 91702291 > at > org.broadinstitute.sv.common.VCFFormatter.createVariantContext(VCFFormatter.java:198) > at > org.broadinstitute.sv.common.VCFFormatter.createVariantContext(VCFFormatter.java:166) > at > org.broadinstitute.sv.discovery.DeletionDiscoveryAlgorithm.writeVCFRecord(DeletionDiscoveryAlgorithm.java:599) > at > org.broadinstitute.sv.discovery.DeletionDiscoveryAlgorithm.processCluster(DeletionDiscoveryAlgorithm.java:405) > at > org.broadinstitute.sv.discovery.DeletionDiscoveryAlgorithm.processClusters(DeletionDiscoveryAlgorithm.java:303) > at > org.broadinstitute.sv.discovery.DeletionDiscoveryAlgorithm.runDiscovery(DeletionDiscoveryAlgorithm.java:163) > at > org.broadinstitute.sv.discovery.SVDiscoveryWalker.onTraversalDone(SVDiscoveryWalker.java:150) > at > org.broadinstitute.sv.discovery.SVDiscoveryWalker.onTraversalDone(SVDiscoveryWalker.java:43) > at > org.broadinstitute.sting.gatk.executive.Accumulator$StandardAccumulator.finishTraversal(Accumulator.java:129) > at > org.broadinstitute.sting.gatk.executive.LinearMicroScheduler.execute(LinearMicroScheduler.java:75) > at > org.broadinstitute.sting.gatk.GenomeAnalysisEngine.execute(GenomeAnalysisEngine.java:217) > at > org.broadinstitute.sting.gatk.CommandLineExecutable.execute(CommandLineExecutable.java:111) > at > org.broadinstitute.sv.main.SVCommandLine.execute(SVCommandLine.java:110) > at > org.broadinstitute.sting.commandline.CommandLineProgram.start(CommandLineProgram.java:239) > at > org.broadinstitute.sv.main.SVCommandLine.main(SVCommandLine.java:72) > at > org.broadinstitute.sv.main.SVDiscovery.main(SVDiscovery.java:21) > ##### ERROR > ------------------------------------------------------------------------------------------ > ##### ERROR A GATK RUNTIME ERROR has occurred (version 1.0.5039M): > ##### ERROR > ##### ERROR Please visit to wiki to see if this is a known problem > ##### ERROR If not, please post the error, with stack trace, to > the GATK forum > ##### ERROR Visit our wiki for extensive documentation > http://www.broadinstitute.org/gsa/wiki > ##### ERROR Visit our forum to view answers to commonly asked > questions http://getsatisfaction.com/gsa > ##### ERROR > ##### ERROR MESSAGE: Invalid cnp coordinates: DEL_P0009_3706 > 91702292 91702291 > ##### ERROR > ------------------------------------------------------------------------------------------ > > > This error occurs only for one chromosome, all other chromosomes > run fine > > Thanks a lot for your help > Verena > > > > > ------------------------------------------------------------------------------ > 10 Tips for Better Server Consolidation > Server virtualization is being driven by many needs. > But none more important than the need to reduce IT complexity > while improving strategic productivity. Learn More! > http://www.accelacomm.com/jaw/sdnl/114/51507609/ > > > _______________________________________________ > svtoolkit-help mailing list > svt...@li... > https://lists.sourceforge.net/lists/listinfo/svtoolkit-help |
|
From: Ashish K. <as...@we...> - 2011-12-15 14:59:55
|
Hi,
The interim release that Bob pointed me to, solved the problem for me.
Best,
Ashish.
From: Verena Tischler [mailto:tis...@go...]
Sent: 15 December 2011 15:23
To: svt...@li...
Subject: Re: [svtoolkit-help] error in discovery step: invalid cnp coordinates
Hi,
sorry I just saw that someone encountered the same problem as I describe below.
So let me please rephrase my question: Did you already find a solution to that or did using the interim version solve the problem?
Thanks a lot
Verena
2011/12/15 Verena Tischler <tis...@go...<mailto:tis...@go...>>
Hi,
I am running GenomeSTRiP on eland mapped files and the preprocessing of bams works fine.
However in the SVDiscovery step I end up with the following error
##### ERROR ------------------------------------------------------------------------------------------
##### ERROR stack trace
java.lang.RuntimeException: Invalid cnp coordinates: DEL_P0009_3706 91702292 91702291
at org.broadinstitute.sv.common.VCFFormatter.createVariantContext(VCFFormatter.java:198)
at org.broadinstitute.sv.common.VCFFormatter.createVariantContext(VCFFormatter.java:166)
at org.broadinstitute.sv.discovery.DeletionDiscoveryAlgorithm.writeVCFRecord(DeletionDiscoveryAlgorithm.java:599)
at org.broadinstitute.sv.discovery.DeletionDiscoveryAlgorithm.processCluster(DeletionDiscoveryAlgorithm.java:405)
at org.broadinstitute.sv.discovery.DeletionDiscoveryAlgorithm.processClusters(DeletionDiscoveryAlgorithm.java:303)
at org.broadinstitute.sv.discovery.DeletionDiscoveryAlgorithm.runDiscovery(DeletionDiscoveryAlgorithm.java:163)
at org.broadinstitute.sv.discovery.SVDiscoveryWalker.onTraversalDone(SVDiscoveryWalker.java:150)
at org.broadinstitute.sv.discovery.SVDiscoveryWalker.onTraversalDone(SVDiscoveryWalker.java:43)
at org.broadinstitute.sting.gatk.executive.Accumulator$StandardAccumulator.finishTraversal(Accumulator.java:129)
at org.broadinstitute.sting.gatk.executive.LinearMicroScheduler.execute(LinearMicroScheduler.java:75)
at org.broadinstitute.sting.gatk.GenomeAnalysisEngine.execute(GenomeAnalysisEngine.java:217)
at org.broadinstitute.sting.gatk.CommandLineExecutable.execute(CommandLineExecutable.java:111)
at org.broadinstitute.sv.main.SVCommandLine.execute(SVCommandLine.java:110)
at org.broadinstitute.sting.commandline.CommandLineProgram.start(CommandLineProgram.java:239)
at org.broadinstitute.sv.main.SVCommandLine.main(SVCommandLine.java:72)
at org.broadinstitute.sv.main.SVDiscovery.main(SVDiscovery.java:21)
##### ERROR ------------------------------------------------------------------------------------------
##### ERROR A GATK RUNTIME ERROR has occurred (version 1.0.5039M):
##### ERROR
##### ERROR Please visit to wiki to see if this is a known problem
##### ERROR If not, please post the error, with stack trace, to the GATK forum
##### ERROR Visit our wiki for extensive documentation http://www.broadinstitute.org/gsa/wiki
##### ERROR Visit our forum to view answers to commonly asked questions http://getsatisfaction.com/gsa
##### ERROR
##### ERROR MESSAGE: Invalid cnp coordinates: DEL_P0009_3706 91702292 91702291
##### ERROR ------------------------------------------------------------------------------------------
This error occurs only for one chromosome, all other chromosomes run fine
Thanks a lot for your help
Verena
|
|
From: Verena T. <tis...@go...> - 2011-12-15 14:23:25
|
Hi, sorry I just saw that someone encountered the same problem as I describe below. So let me please rephrase my question: Did you already find a solution to that or did using the interim version solve the problem? Thanks a lot Verena 2011/12/15 Verena Tischler <tis...@go...> > Hi, > > I am running GenomeSTRiP on eland mapped files and the preprocessing of > bams works fine. > However in the SVDiscovery step I end up with the following error > > ##### ERROR > ------------------------------------------------------------------------------------------ > ##### ERROR stack trace > java.lang.RuntimeException: Invalid cnp coordinates: DEL_P0009_3706 > 91702292 91702291 > at > org.broadinstitute.sv.common.VCFFormatter.createVariantContext(VCFFormatter.java:198) > at > org.broadinstitute.sv.common.VCFFormatter.createVariantContext(VCFFormatter.java:166) > at > org.broadinstitute.sv.discovery.DeletionDiscoveryAlgorithm.writeVCFRecord(DeletionDiscoveryAlgorithm.java:599) > at > org.broadinstitute.sv.discovery.DeletionDiscoveryAlgorithm.processCluster(DeletionDiscoveryAlgorithm.java:405) > at > org.broadinstitute.sv.discovery.DeletionDiscoveryAlgorithm.processClusters(DeletionDiscoveryAlgorithm.java:303) > at > org.broadinstitute.sv.discovery.DeletionDiscoveryAlgorithm.runDiscovery(DeletionDiscoveryAlgorithm.java:163) > at > org.broadinstitute.sv.discovery.SVDiscoveryWalker.onTraversalDone(SVDiscoveryWalker.java:150) > at > org.broadinstitute.sv.discovery.SVDiscoveryWalker.onTraversalDone(SVDiscoveryWalker.java:43) > at > org.broadinstitute.sting.gatk.executive.Accumulator$StandardAccumulator.finishTraversal(Accumulator.java:129) > at > org.broadinstitute.sting.gatk.executive.LinearMicroScheduler.execute(LinearMicroScheduler.java:75) > at > org.broadinstitute.sting.gatk.GenomeAnalysisEngine.execute(GenomeAnalysisEngine.java:217) > at > org.broadinstitute.sting.gatk.CommandLineExecutable.execute(CommandLineExecutable.java:111) > at > org.broadinstitute.sv.main.SVCommandLine.execute(SVCommandLine.java:110) > at > org.broadinstitute.sting.commandline.CommandLineProgram.start(CommandLineProgram.java:239) > at org.broadinstitute.sv.main.SVCommandLine.main(SVCommandLine.java:72) > at org.broadinstitute.sv.main.SVDiscovery.main(SVDiscovery.java:21) > ##### ERROR > ------------------------------------------------------------------------------------------ > ##### ERROR A GATK RUNTIME ERROR has occurred (version 1.0.5039M): > ##### ERROR > ##### ERROR Please visit to wiki to see if this is a known problem > ##### ERROR If not, please post the error, with stack trace, to the GATK > forum > ##### ERROR Visit our wiki for extensive documentation > http://www.broadinstitute.org/gsa/wiki > ##### ERROR Visit our forum to view answers to commonly asked questions > http://getsatisfaction.com/gsa > ##### ERROR > ##### ERROR MESSAGE: Invalid cnp coordinates: DEL_P0009_3706 91702292 > 91702291 > ##### ERROR > ------------------------------------------------------------------------------------------ > > > This error occurs only for one chromosome, all other chromosomes run fine > > Thanks a lot for your help > Verena > |
|
From: Verena T. <tis...@go...> - 2011-12-15 14:19:58
|
Hi,
I am running GenomeSTRiP on eland mapped files and the preprocessing of
bams works fine.
However in the SVDiscovery step I end up with the following error
##### ERROR
------------------------------------------------------------------------------------------
##### ERROR stack trace
java.lang.RuntimeException: Invalid cnp coordinates: DEL_P0009_3706
91702292 91702291
at
org.broadinstitute.sv.common.VCFFormatter.createVariantContext(VCFFormatter.java:198)
at
org.broadinstitute.sv.common.VCFFormatter.createVariantContext(VCFFormatter.java:166)
at
org.broadinstitute.sv.discovery.DeletionDiscoveryAlgorithm.writeVCFRecord(DeletionDiscoveryAlgorithm.java:599)
at
org.broadinstitute.sv.discovery.DeletionDiscoveryAlgorithm.processCluster(DeletionDiscoveryAlgorithm.java:405)
at
org.broadinstitute.sv.discovery.DeletionDiscoveryAlgorithm.processClusters(DeletionDiscoveryAlgorithm.java:303)
at
org.broadinstitute.sv.discovery.DeletionDiscoveryAlgorithm.runDiscovery(DeletionDiscoveryAlgorithm.java:163)
at
org.broadinstitute.sv.discovery.SVDiscoveryWalker.onTraversalDone(SVDiscoveryWalker.java:150)
at
org.broadinstitute.sv.discovery.SVDiscoveryWalker.onTraversalDone(SVDiscoveryWalker.java:43)
at
org.broadinstitute.sting.gatk.executive.Accumulator$StandardAccumulator.finishTraversal(Accumulator.java:129)
at
org.broadinstitute.sting.gatk.executive.LinearMicroScheduler.execute(LinearMicroScheduler.java:75)
at
org.broadinstitute.sting.gatk.GenomeAnalysisEngine.execute(GenomeAnalysisEngine.java:217)
at
org.broadinstitute.sting.gatk.CommandLineExecutable.execute(CommandLineExecutable.java:111)
at
org.broadinstitute.sv.main.SVCommandLine.execute(SVCommandLine.java:110)
at
org.broadinstitute.sting.commandline.CommandLineProgram.start(CommandLineProgram.java:239)
at org.broadinstitute.sv.main.SVCommandLine.main(SVCommandLine.java:72)
at org.broadinstitute.sv.main.SVDiscovery.main(SVDiscovery.java:21)
##### ERROR
------------------------------------------------------------------------------------------
##### ERROR A GATK RUNTIME ERROR has occurred (version 1.0.5039M):
##### ERROR
##### ERROR Please visit to wiki to see if this is a known problem
##### ERROR If not, please post the error, with stack trace, to the GATK
forum
##### ERROR Visit our wiki for extensive documentation
http://www.broadinstitute.org/gsa/wiki
##### ERROR Visit our forum to view answers to commonly asked questions
http://getsatisfaction.com/gsa
##### ERROR
##### ERROR MESSAGE: Invalid cnp coordinates: DEL_P0009_3706 91702292
91702291
##### ERROR
------------------------------------------------------------------------------------------
This error occurs only for one chromosome, all other chromosomes run fine
Thanks a lot for your help
Verena
|
|
From: Bob H. <han...@br...> - 2011-12-13 18:32:36
|
Hi, Thomas, The problem is that Genome STRiP internally uses the ZN tag to mean something else, and there's a safety check to make sure this tag has not been set by some other application (or isn't being incorrectly set twice by Genome STRiP). Changing the mapping quality threshold won't help, as the ZN attribute is applied before the mapping quality is checked. Unfortunately, there are no good short term workarounds that I can think of. The choices are: a) remove the ZN tags b) disable the use of read pairs in genotyping (change genotyping.modules in the config file to remove "pairs") -Bob On 12/13/11 11:59 AM, Thomas Zichner wrote: > Hi, > > I have about 50 bam files which were generated using Novoalign. Running > the SV discovery on them works without any problems. However, if I try > to run the SV genotyping, I get the following error message: > > > Error: Exception processing cnp: Tag ZN already set on read > USI-EAS034_PE_FC30HJPAAXX:2:75:1436:50 > CNP: del_664 chr2:359968-365840 > INFO 17:25:39,596 GATKRunReport - Aggregating data for run report > ##### ERROR > ------------------------------------------------------------------------------------------ > ##### ERROR stack trace > java.lang.RuntimeException: Tag ZN already set on read > USI-EAS034_PE_FC30HJPAAXX:2:75:1436:50 > at > org.broadinstitute.sv.genotyping.ReadPairMapper.setRecordAttribute(ReadPairMapper.java:460) > at > org.broadinstitute.sv.genotyping.ReadPairMapper.processReadPair(ReadPairMapper.java:399) > at > org.broadinstitute.sv.genotyping.ReadPairMapper.processReadPairs(ReadPairMapper.java:327) > at > org.broadinstitute.sv.genotyping.ReadPairMapper.getReadPairs(ReadPairMapper.java:176) > at > org.broadinstitute.sv.genotyping.ReadPairMapper.getReadPairs(ReadPairMapper.java:100) > at > org.broadinstitute.sv.genotyping.GenotypingReadPairModule.getReadPairs(GenotypingReadPairModule.java:204) > at > org.broadinstitute.sv.genotyping.GenotypingReadPairModule.genotypeSample(GenotypingReadPairModule.java:78) > at > org.broadinstitute.sv.genotyping.GenotypingReadPairModule.genotypeCnp(GenotypingReadPairModule.java:63) > at > org.broadinstitute.sv.genotyping.GenotypingAlgorithm.genotypeCnpInternal(GenotypingAlgorithm.java:122) > at > org.broadinstitute.sv.genotyping.GenotypingAlgorithm.genotypeCnp(GenotypingAlgorithm.java:94) > at > org.broadinstitute.sv.genotyping.SVGenotyperWalker.map(SVGenotyperWalker.java:183) > at > org.broadinstitute.sv.genotyping.SVGenotyperWalker.map(SVGenotyperWalker.java:53) > at > org.broadinstitute.sting.gatk.traversals.TraverseLoci.traverse(TraverseLoci.java:78) > at > org.broadinstitute.sting.gatk.traversals.TraverseLoci.traverse(TraverseLoci.java:19) > at > org.broadinstitute.sting.gatk.executive.LinearMicroScheduler.execute(LinearMicroScheduler.java:61) > at > org.broadinstitute.sting.gatk.GenomeAnalysisEngine.execute(GenomeAnalysisEngine.java:217) > at > org.broadinstitute.sting.gatk.CommandLineExecutable.execute(CommandLineExecutable.java:111) > at > org.broadinstitute.sv.main.SVCommandLine.execute(SVCommandLine.java:110) > at > org.broadinstitute.sting.commandline.CommandLineProgram.start(CommandLineProgram.java:239) > at org.broadinstitute.sv.main.SVCommandLine.main(SVCommandLine.java:72) > at org.broadinstitute.sv.main.SVGenotyper.main(SVGenotyper.java:21) > > > For my Novoalign files, the ZN tag is set for all reads which have > multiple mapping locations. In case of multiple mapping locations, the > read is place randomly and the number of possible mapping locations is > indicated in the ZN tag. > > All of these reads have a very low mapping quality (usually 0), so I > thought they should be anyway not considered by GenomeSTRiP. > > Any help is very much appreciated. > Best regards > Thomas Zichner > > ------------------------------------------------------------------------------ > Systems Optimization Self Assessment > Improve efficiency and utilization of IT resources. Drive out cost and > improve service delivery. Take 5 minutes to use this Systems Optimization > Self Assessment. http://www.accelacomm.com/jaw/sdnl/114/51450054/ > _______________________________________________ > svtoolkit-help mailing list > svt...@li... > https://lists.sourceforge.net/lists/listinfo/svtoolkit-help |
|
From: Thomas Z. <tho...@em...> - 2011-12-13 17:33:51
|
Hi,
I have about 50 bam files which were generated using Novoalign. Running
the SV discovery on them works without any problems. However, if I try
to run the SV genotyping, I get the following error message:
Error: Exception processing cnp: Tag ZN already set on read
USI-EAS034_PE_FC30HJPAAXX:2:75:1436:50
CNP: del_664 chr2:359968-365840
INFO 17:25:39,596 GATKRunReport - Aggregating data for run report
##### ERROR
------------------------------------------------------------------------------------------
##### ERROR stack trace
java.lang.RuntimeException: Tag ZN already set on read
USI-EAS034_PE_FC30HJPAAXX:2:75:1436:50
at
org.broadinstitute.sv.genotyping.ReadPairMapper.setRecordAttribute(ReadPairMapper.java:460)
at
org.broadinstitute.sv.genotyping.ReadPairMapper.processReadPair(ReadPairMapper.java:399)
at
org.broadinstitute.sv.genotyping.ReadPairMapper.processReadPairs(ReadPairMapper.java:327)
at
org.broadinstitute.sv.genotyping.ReadPairMapper.getReadPairs(ReadPairMapper.java:176)
at
org.broadinstitute.sv.genotyping.ReadPairMapper.getReadPairs(ReadPairMapper.java:100)
at
org.broadinstitute.sv.genotyping.GenotypingReadPairModule.getReadPairs(GenotypingReadPairModule.java:204)
at
org.broadinstitute.sv.genotyping.GenotypingReadPairModule.genotypeSample(GenotypingReadPairModule.java:78)
at
org.broadinstitute.sv.genotyping.GenotypingReadPairModule.genotypeCnp(GenotypingReadPairModule.java:63)
at
org.broadinstitute.sv.genotyping.GenotypingAlgorithm.genotypeCnpInternal(GenotypingAlgorithm.java:122)
at
org.broadinstitute.sv.genotyping.GenotypingAlgorithm.genotypeCnp(GenotypingAlgorithm.java:94)
at
org.broadinstitute.sv.genotyping.SVGenotyperWalker.map(SVGenotyperWalker.java:183)
at
org.broadinstitute.sv.genotyping.SVGenotyperWalker.map(SVGenotyperWalker.java:53)
at
org.broadinstitute.sting.gatk.traversals.TraverseLoci.traverse(TraverseLoci.java:78)
at
org.broadinstitute.sting.gatk.traversals.TraverseLoci.traverse(TraverseLoci.java:19)
at
org.broadinstitute.sting.gatk.executive.LinearMicroScheduler.execute(LinearMicroScheduler.java:61)
at
org.broadinstitute.sting.gatk.GenomeAnalysisEngine.execute(GenomeAnalysisEngine.java:217)
at
org.broadinstitute.sting.gatk.CommandLineExecutable.execute(CommandLineExecutable.java:111)
at
org.broadinstitute.sv.main.SVCommandLine.execute(SVCommandLine.java:110)
at
org.broadinstitute.sting.commandline.CommandLineProgram.start(CommandLineProgram.java:239)
at org.broadinstitute.sv.main.SVCommandLine.main(SVCommandLine.java:72)
at org.broadinstitute.sv.main.SVGenotyper.main(SVGenotyper.java:21)
For my Novoalign files, the ZN tag is set for all reads which have
multiple mapping locations. In case of multiple mapping locations, the
read is place randomly and the number of possible mapping locations is
indicated in the ZN tag.
All of these reads have a very low mapping quality (usually 0), so I
thought they should be anyway not considered by GenomeSTRiP.
Any help is very much appreciated.
Best regards
Thomas Zichner
|
|
From: Bob H. <han...@br...> - 2011-12-08 16:26:52
|
With respect to the first error, it would be helpful if you did the diff manually between the expected output and the output produced and sent that. With respect to the second error, this is the java VM crashing, so the information from hs_err_pid*.log might be helpful. Since it is crashing in SVAltAligner, the bwa shared library is a likely suspect. uname -a might also be helpful. You might want to also check whether SV_DIR / LD_LIBRARY_PATH is being set as you expect by the scripts. -Bob On 12/8/11 6:11 AM, w y wrote: > Hi, > When I ran discovery.sh, I got an error: > Files - and benchmark/test1.discovery.vcf differ > Error: test results do not match benchmark data > > Besides, I got another error when I ran genotyping.sh: > INFO 18:09:37,496 ShellJobRunner - Starting: bwa index > test2/altalign/installtest.sites.alt.fasta > INFO 18:09:37,497 ShellJobRunner - Output written to > /home/yaowen/soft/svtoolkit_1.03.619/installtest/test2/logs/Q-11685@node12-4.out > > INFO 18:09:37,567 ShellJobRunner - Done: bwa index > test2/altalign/installtest.sites.alt.fasta > INFO 18:09:37,587 ShellJobRunner - Starting: java -Xmx1g > -Djava.io.tmpdir=/home/yaowen/soft/svtoolkit_1.03.619/installtest/tmpdir > -cp > /home/yaowen/soft/svtoolkit_1.03.619/lib/SVToolkit.jar:/home/yaowen/soft/svtoolkit_1.03.619/lib/gatk/GenomeAnalysisTK.jar:/home/yaowen/soft/svtoolkit_1.03.619/lib/gatk/Queue.jar > org.broadinstitute.sting.gatk.CommandLineGATK -T SVAltAligner -R > /home/yaowen/soft/svtoolkit_1.03.619/installtest/data/human_b36_chr1.fasta > -I > /home/yaowen/soft/svtoolkit_1.03.619/installtest/data/installtest.bam > -O > /home/yaowen/soft/svtoolkit_1.03.619/installtest/test2/altalign/installtest.alt.bam > -md test2/metadata -U ALLOW_UNINDEXED_BAM -altReference > test2/altalign/installtest.sites.alt.fasta -alignUnmappedMates true > INFO 18:09:37,587 ShellJobRunner - Output written to > /home/yaowen/soft/svtoolkit_1.03.619/installtest/test2/logs/Q-11685@node12-5.out > > ERROR 18:09:43,369 ShellJobRunner - Error: java -Xmx1g > -Djava.io.tmpdir=/home/yaowen/soft/svtoolkit_1.03.619/installtest/tmpdir > -cp > /home/yaowen/soft/svtoolkit_1.03.619/lib/SVToolkit.jar:/home/yaowen/soft/svtoolkit_1.03.619/lib/gatk/GenomeAnalysisTK.jar:/home/yaowen/soft/svtoolkit_1.03.619/lib/gatk/Queue.jar > org.broadinstitute.sting.gatk.CommandLineGATK -T SVAltAligner -R > /home/yaowen/soft/svtoolkit_1.03.619/installtest/data/human_b36_chr1.fasta > -I > /home/yaowen/soft/svtoolkit_1.03.619/installtest/data/installtest.bam > -O > /home/yaowen/soft/svtoolkit_1.03.619/installtest/test2/altalign/installtest.alt.bam > -md test2/metadata -U ALLOW_UNINDEXED_BAM -altReference > test2/altalign/installtest.sites.alt.fasta -alignUnmappedMates true > ERROR 18:09:43,370 ShellJobRunner - INFO 18:09:42,208 HelpFormatter - > --------------------------------------------------------------------------- > > INFO 18:09:42,210 HelpFormatter - The Genome Analysis Toolkit (GATK) > v1.0.5039M, Compiled 2011/01/20 22:58:34 > INFO 18:09:42,211 HelpFormatter - Copyright (c) 2010 The Broad Institute > INFO 18:09:42,211 HelpFormatter - Please view our documentation at > http://www.broadinstitute.org/gsa/wiki > INFO 18:09:42,211 HelpFormatter - For support, please view our > support site at http://getsatisfaction.com/gsa > INFO 18:09:42,211 HelpFormatter - Program Args: -T SVAltAligner -R > /home/yaowen/soft/svtoolkit_1.03.619/installtest/data/human_b36_chr1.fasta > -I > /home/yaowen/soft/svtoolkit_1.03.619/installtest/data/installtest.bam > -O > /home/yaowen/soft/svtoolkit_1.03.619/installtest/test2/altalign/installtest.alt.bam > -md test2/metadata -U ALLOW_UNINDEXED_BAM -altReference > test2/altalign/installtest.sites.alt.fasta -alignUnmappedMates true > INFO 18:09:42,211 HelpFormatter - Date/Time: 2011/12/08 18:09:42 > INFO 18:09:42,211 HelpFormatter - > --------------------------------------------------------------------------- > > INFO 18:09:42,211 HelpFormatter - > --------------------------------------------------------------------------- > > INFO 18:09:42,215 GenomeAnalysisEngine - Strictness is SILENT > # > # An unexpected error has been detected by Java Runtime Environment: > # > # SIGFPE (0x8) at pc=0x0000003027607927, pid=11823, tid=1076017504 > # > # Java VM: Java HotSpot(TM) 64-Bit Server VM (11.2-b01 mixed mode > linux-amd64) > # Problematic frame: > # C [ld-linux-x86-64.so.2+0x7927] > # > # An error report file with more information is saved as: > # /home/yaowen/soft/svtoolkit_1.03.619/installtest/hs_err_pid11823.log > # > # If you would like to submit a bug report, please visit: > # http://java.sun.com/webapps/bugreport/crash.jsp > # The crash happened outside the Java Virtual Machine in native code. > # See problematic frame for where to report the bug. > # > /home/yaowen/soft/svtoolkit_1.03.619/installtest/tmpdir/.exec9048318414659209772: > line 2: 11823 Aborted java -Xmx1g > -Djava.io.tmpdir=/home/yaowen/soft/svtoolkit_1.03.619/installtest/tmpdir > -cp > /home/yaowen/soft/svtoolkit_1.03.619/lib/SVToolkit.jar:/home/yaowen/soft/svtoolkit_1.03.619/lib/gatk/GenomeAnalysisTK.jar:/home/yaowen/soft/svtoolkit_1.03.619/lib/gatk/Queue.jar > org.broadinstitute.sting.gatk.CommandLineGATK -T SVAltAligner -R > /home/yaowen/soft/svtoolkit_1.03.619/installtest/data/human_b36_chr1.fasta > -I > /home/yaowen/soft/svtoolkit_1.03.619/installtest/data/installtest.bam > -O > /home/yaowen/soft/svtoolkit_1.03.619/installtest/test2/altalign/installtest.alt.bam > -md test2/metadata -U ALLOW_UNINDEXED_BAM -altReference > test2/altalign/installtest.sites.alt.fasta -alignUnmappedMates true > > INFO 18:09:43,373 QCommandLine - Done with errors > INFO 18:09:43,375 QGraph - ------- > INFO 18:09:43,385 QGraph - Failed: java -Xmx1g > -Djava.io.tmpdir=/home/yaowen/soft/svtoolkit_1.03.619/installtest/tmpdir > -cp > /home/yaowen/soft/svtoolkit_1.03.619/lib/SVToolkit.jar:/home/yaowen/soft/svtoolkit_1.03.619/lib/gatk/GenomeAnalysisTK.jar:/home/yaowen/soft/svtoolkit_1.03.619/lib/gatk/Queue.jar > org.broadinstitute.sting.gatk.CommandLineGATK -T SVAltAligner -R > /home/yaowen/soft/svtoolkit_1.03.619/installtest/data/human_b36_chr1.fasta > -I > /home/yaowen/soft/svtoolkit_1.03.619/installtest/data/installtest.bam > -O > /home/yaowen/soft/svtoolkit_1.03.619/installtest/test2/altalign/installtest.alt.bam > -md test2/metadata -U ALLOW_UNINDEXED_BAM -altReference > test2/altalign/installtest.sites.alt.fasta -alignUnmappedMates true > INFO 18:09:43,386 QGraph - Log: > /home/yaowen/soft/svtoolkit_1.03.619/installtest/test2/logs/Q-11685@node12-5.out > > > I tried different versions of Genome_STRiP, but I still got the same > errors. > > If anyone could help, that would be great. > Andrew > > > > > ------------------------------------------------------------------------------ > Cloud Services Checklist: Pricing and Packaging Optimization > This white paper is intended to serve as a reference, checklist and point of > discussion for anyone considering optimizing the pricing and packaging model > of a cloud services business. Read Now! > http://www.accelacomm.com/jaw/sfnl/114/51491232/ > > > _______________________________________________ > svtoolkit-help mailing list > svt...@li... > https://lists.sourceforge.net/lists/listinfo/svtoolkit-help |
|
From: w y <yw...@we...> - 2011-12-08 11:12:19
|
Hi, When I ran discovery.sh, I got an error: Files - and benchmark/test1.discovery.vcf differ Error: test results do not match benchmark data Besides, I got another error when I ran genotyping.sh: INFO 18:09:37,496 ShellJobRunner - Starting: bwa index test2/altalign/installtest.sites.alt.fasta INFO 18:09:37,497 ShellJobRunner - Output written to /home/yaowen/soft/svtoolkit_1.03.619/installtest/test2/logs/Q-11685@node12-4.out INFO 18:09:37,567 ShellJobRunner - Done: bwa index test2/altalign/installtest.sites.alt.fasta INFO 18:09:37,587 ShellJobRunner - Starting: java -Xmx1g -Djava.io.tmpdir=/home/yaowen/soft/svtoolkit_1.03.619/installtest/tmpdir -cp /home/yaowen/soft/svtoolkit_1.03.619/lib/SVToolkit.jar:/home/yaowen/soft/svtoolkit_1.03.619/lib/gatk/GenomeAnalysisTK.jar:/home/yaowen/soft/svtoolkit_1.03.619/lib/gatk/Queue.jar org.broadinstitute.sting.gatk.CommandLineGATK -T SVAltAligner -R /home/yaowen/soft/svtoolkit_1.03.619/installtest/data/human_b36_chr1.fasta -I /home/yaowen/soft/svtoolkit_1.03.619/installtest/data/installtest.bam -O /home/yaowen/soft/svtoolkit_1.03.619/installtest/test2/altalign/installtest.alt.bam -md test2/metadata -U ALLOW_UNINDEXED_BAM -altReference test2/altalign/installtest.sites.alt.fasta -alignUnmappedMates true INFO 18:09:37,587 ShellJobRunner - Output written to /home/yaowen/soft/svtoolkit_1.03.619/installtest/test2/logs/Q-11685@node12-5.out ERROR 18:09:43,369 ShellJobRunner - Error: java -Xmx1g -Djava.io.tmpdir=/home/yaowen/soft/svtoolkit_1.03.619/installtest/tmpdir -cp /home/yaowen/soft/svtoolkit_1.03.619/lib/SVToolkit.jar:/home/yaowen/soft/svtoolkit_1.03.619/lib/gatk/GenomeAnalysisTK.jar:/home/yaowen/soft/svtoolkit_1.03.619/lib/gatk/Queue.jar org.broadinstitute.sting.gatk.CommandLineGATK -T SVAltAligner -R /home/yaowen/soft/svtoolkit_1.03.619/installtest/data/human_b36_chr1.fasta -I /home/yaowen/soft/svtoolkit_1.03.619/installtest/data/installtest.bam -O /home/yaowen/soft/svtoolkit_1.03.619/installtest/test2/altalign/installtest.alt.bam -md test2/metadata -U ALLOW_UNINDEXED_BAM -altReference test2/altalign/installtest.sites.alt.fasta -alignUnmappedMates true ERROR 18:09:43,370 ShellJobRunner - INFO 18:09:42,208 HelpFormatter - --------------------------------------------------------------------------- INFO 18:09:42,210 HelpFormatter - The Genome Analysis Toolkit (GATK) v1.0.5039M, Compiled 2011/01/20 22:58:34 INFO 18:09:42,211 HelpFormatter - Copyright (c) 2010 The Broad Institute INFO 18:09:42,211 HelpFormatter - Please view our documentation at http://www.broadinstitute.org/gsa/wiki INFO 18:09:42,211 HelpFormatter - For support, please view our support site at http://getsatisfaction.com/gsa INFO 18:09:42,211 HelpFormatter - Program Args: -T SVAltAligner -R /home/yaowen/soft/svtoolkit_1.03.619/installtest/data/human_b36_chr1.fasta -I /home/yaowen/soft/svtoolkit_1.03.619/installtest/data/installtest.bam -O /home/yaowen/soft/svtoolkit_1.03.619/installtest/test2/altalign/installtest.alt.bam -md test2/metadata -U ALLOW_UNINDEXED_BAM -altReference test2/altalign/installtest.sites.alt.fasta -alignUnmappedMates true INFO 18:09:42,211 HelpFormatter - Date/Time: 2011/12/08 18:09:42 INFO 18:09:42,211 HelpFormatter - --------------------------------------------------------------------------- INFO 18:09:42,211 HelpFormatter - --------------------------------------------------------------------------- INFO 18:09:42,215 GenomeAnalysisEngine - Strictness is SILENT # # An unexpected error has been detected by Java Runtime Environment: # # SIGFPE (0x8) at pc=0x0000003027607927, pid=11823, tid=1076017504 # # Java VM: Java HotSpot(TM) 64-Bit Server VM (11.2-b01 mixed mode linux-amd64) # Problematic frame: # C [ld-linux-x86-64.so.2+0x7927] # # An error report file with more information is saved as: # /home/yaowen/soft/svtoolkit_1.03.619/installtest/hs_err_pid11823.log # # If you would like to submit a bug report, please visit: # http://java.sun.com/webapps/bugreport/crash.jsp # The crash happened outside the Java Virtual Machine in native code. # See problematic frame for where to report the bug. # /home/yaowen/soft/svtoolkit_1.03.619/installtest/tmpdir/.exec9048318414659209772: line 2: 11823 Aborted java -Xmx1g -Djava.io.tmpdir=/home/yaowen/soft/svtoolkit_1.03.619/installtest/tmpdir -cp /home/yaowen/soft/svtoolkit_1.03.619/lib/SVToolkit.jar:/home/yaowen/soft/svtoolkit_1.03.619/lib/gatk/GenomeAnalysisTK.jar:/home/yaowen/soft/svtoolkit_1.03.619/lib/gatk/Queue.jar org.broadinstitute.sting.gatk.CommandLineGATK -T SVAltAligner -R /home/yaowen/soft/svtoolkit_1.03.619/installtest/data/human_b36_chr1.fasta -I /home/yaowen/soft/svtoolkit_1.03.619/installtest/data/installtest.bam -O /home/yaowen/soft/svtoolkit_1.03.619/installtest/test2/altalign/installtest.alt.bam -md test2/metadata -U ALLOW_UNINDEXED_BAM -altReference test2/altalign/installtest.sites.alt.fasta -alignUnmappedMates true INFO 18:09:43,373 QCommandLine - Done with errors INFO 18:09:43,375 QGraph - ------- INFO 18:09:43,385 QGraph - Failed: java -Xmx1g -Djava.io.tmpdir=/home/yaowen/soft/svtoolkit_1.03.619/installtest/tmpdir -cp /home/yaowen/soft/svtoolkit_1.03.619/lib/SVToolkit.jar:/home/yaowen/soft/svtoolkit_1.03.619/lib/gatk/GenomeAnalysisTK.jar:/home/yaowen/soft/svtoolkit_1.03.619/lib/gatk/Queue.jar org.broadinstitute.sting.gatk.CommandLineGATK -T SVAltAligner -R /home/yaowen/soft/svtoolkit_1.03.619/installtest/data/human_b36_chr1.fasta -I /home/yaowen/soft/svtoolkit_1.03.619/installtest/data/installtest.bam -O /home/yaowen/soft/svtoolkit_1.03.619/installtest/test2/altalign/installtest.alt.bam -md test2/metadata -U ALLOW_UNINDEXED_BAM -altReference test2/altalign/installtest.sites.alt.fasta -alignUnmappedMates true INFO 18:09:43,386 QGraph - Log: /home/yaowen/soft/svtoolkit_1.03.619/installtest/test2/logs/Q-11685@node12-5.out I tried different versions of Genome_STRiP, but I still got the same errors. If anyone could help, that would be great. Andrew |
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From: Bob H. <han...@br...> - 2011-11-28 02:40:15
|
I don't have a good theory offhand. One thing to do is to try to eliminate Queue from the equation. Rather than running the java process through Queue, try copying the command line from the Queue output and running it directly. -Bob On 11/25/11 8:15 AM, John Broxholme wrote: > This happened during SVdiscovery. I've seen 'truncated' twice in two attempts with these > data (153 samples from 1000Genomes, selected for chr14). The first time had no "-L" > argument and happened while "Processing cluster 14:82555551-82555838 14:82556031-82556335 > LR 2" > The second has the same input data but I'd specified "-L 14" and the error was thrown > while "Processing cluster 14:85768136-85768422" > > Try 1: > ... > #DBG: RC Cache fill 14:85750104-85860103 110000 153 8.480425 sec > INFO 03:39:35,613 SVDiscovery - Clustering: Generating clusters for 2 read pairs. > INFO 03:39:35,613 SVDiscovery - Processing cluster 14:85762691-85762973 > 14:85763261-85763496 LR 2 > INFO 03:39:36,280 SVDiscovery - Clustering: Generating clusters for 2 read pairs. > INFO 03:39:36,280 SVDiscovery - Processing cluster 14:85768136-85768422 > 14:85768594-85768960 LR 2 > INFO 03:39:36,974 SVDiscovery - Clustering: Generating clusters for 3 read pairs. > INFO 03:39:36,974 SVDiscovery - Clustering: LR split size 3 / 3 maximal clique size 2 c > > <truncated> > at org.broadinstitute.sting.queue.util.ShellJob.run(ShellJob.scala:24) > at > org.broadinstitute.sting.queue.engine.shell.ShellJobRunner.start(ShellJobRunner.scala:54) > at org.broadinstitute.sting.queue.engine.FunctionEdge.start(FunctionEdge.scala:56) > at org.broadinstitute.sting.queue.engine.QGraph.runJobs(QGraph.scala:383) > at org.broadinstitute.sting.queue.engine.QGraph.run(QGraph.scala:123) > at org.broadinstitute.sting.queue.QCommandLine.execute(QCommandLine.scala:111) > at > org.broadinstitute.sting.commandline.CommandLineProgram.start(CommandLineProgram.java:221) > at org.broadinstitute.sting.queue.QCommandLine$.main(QCommandLine.scala:57) > at org.broadinstitute.sting.queue.QCommandLine.main(QCommandLine.scala) > INFO 04:47:49,290 QGraph - 1 Pend, 1 Run, 0 Fail, 0 Done > INFO 04:47:49,294 QGraph - 1 Pend, 0 Run, 1 Fail, 0 Done > INFO 04:47:49,294 QCommandLine - Done with errors > INFO 04:47:49,295 QGraph - ------- > INFO 04:47:49,317 QGraph - Failed: > ... > > Try 2: > ... > INFO 18:19:17,401 SVDiscovery - Clustering: Generating clusters for 2 read pairs. > INFO 18:19:17,403 SVDiscovery - Clustering: Generating clusters for 2 read pairs. > INFO 18:19:17,403 SVDiscovery - Processing cluster 14:82555551-82555838 > 14:82556031-82556335 LR 2 > [GC 369154K->321806K(386752K), 0.0043100 secs] > [GC 368014K->322288K(386048K), 0.0028780 secs] > [GC 368112K->322455K(386048K), 0.0023780 secs] > [GC 367895K->322378K(385280K), 0.0087230 secs] > [GC 367498K->322576K(385344K), 0.0021090 secs] > [GC 367376K->322712K(384832K), 0.0030720 secs] > [GC 367192K->322559K(384576K), 0.0019880 secs] > [GC 366719K->322632K(384000K), 0.0029070 secs] > [GC 366472K->322642K(383936K), 0.0039400 secs] > [GC 366162K->321695K(382272K), 0.0027450 se > > <truncated> > > Any suggestions as to what's 'truncated', what might have caused it and how to fix it? I > have definitely not run out of disk space. > > Thanks > John > |
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From: John B. <jo...@we...> - 2011-11-25 13:15:18
|
This happened during SVdiscovery. I've seen 'truncated' twice in two attempts with these
data (153 samples from 1000Genomes, selected for chr14). The first time had no "-L"
argument and happened while "Processing cluster 14:82555551-82555838 14:82556031-82556335
LR 2"
The second has the same input data but I'd specified "-L 14" and the error was thrown
while "Processing cluster 14:85768136-85768422"
Try 1:
...
#DBG: RC Cache fill 14:85750104-85860103 110000 153 8.480425 sec
INFO 03:39:35,613 SVDiscovery - Clustering: Generating clusters for 2 read pairs.
INFO 03:39:35,613 SVDiscovery - Processing cluster 14:85762691-85762973
14:85763261-85763496 LR 2
INFO 03:39:36,280 SVDiscovery - Clustering: Generating clusters for 2 read pairs.
INFO 03:39:36,280 SVDiscovery - Processing cluster 14:85768136-85768422
14:85768594-85768960 LR 2
INFO 03:39:36,974 SVDiscovery - Clustering: Generating clusters for 3 read pairs.
INFO 03:39:36,974 SVDiscovery - Clustering: LR split size 3 / 3 maximal clique size 2 c
<truncated>
at org.broadinstitute.sting.queue.util.ShellJob.run(ShellJob.scala:24)
at
org.broadinstitute.sting.queue.engine.shell.ShellJobRunner.start(ShellJobRunner.scala:54)
at org.broadinstitute.sting.queue.engine.FunctionEdge.start(FunctionEdge.scala:56)
at org.broadinstitute.sting.queue.engine.QGraph.runJobs(QGraph.scala:383)
at org.broadinstitute.sting.queue.engine.QGraph.run(QGraph.scala:123)
at org.broadinstitute.sting.queue.QCommandLine.execute(QCommandLine.scala:111)
at
org.broadinstitute.sting.commandline.CommandLineProgram.start(CommandLineProgram.java:221)
at org.broadinstitute.sting.queue.QCommandLine$.main(QCommandLine.scala:57)
at org.broadinstitute.sting.queue.QCommandLine.main(QCommandLine.scala)
INFO 04:47:49,290 QGraph - 1 Pend, 1 Run, 0 Fail, 0 Done
INFO 04:47:49,294 QGraph - 1 Pend, 0 Run, 1 Fail, 0 Done
INFO 04:47:49,294 QCommandLine - Done with errors
INFO 04:47:49,295 QGraph - -------
INFO 04:47:49,317 QGraph - Failed:
...
Try 2:
...
INFO 18:19:17,401 SVDiscovery - Clustering: Generating clusters for 2 read pairs.
INFO 18:19:17,403 SVDiscovery - Clustering: Generating clusters for 2 read pairs.
INFO 18:19:17,403 SVDiscovery - Processing cluster 14:82555551-82555838
14:82556031-82556335 LR 2
[GC 369154K->321806K(386752K), 0.0043100 secs]
[GC 368014K->322288K(386048K), 0.0028780 secs]
[GC 368112K->322455K(386048K), 0.0023780 secs]
[GC 367895K->322378K(385280K), 0.0087230 secs]
[GC 367498K->322576K(385344K), 0.0021090 secs]
[GC 367376K->322712K(384832K), 0.0030720 secs]
[GC 367192K->322559K(384576K), 0.0019880 secs]
[GC 366719K->322632K(384000K), 0.0029070 secs]
[GC 366472K->322642K(383936K), 0.0039400 secs]
[GC 366162K->321695K(382272K), 0.0027450 se
<truncated>
Any suggestions as to what's 'truncated', what might have caused it and how to fix it? I
have definitely not run out of disk space.
Thanks
John
--
John Broxholme
Wellcome Trust Centre for Human Genetics
Oxford
|
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From: Bob H. <han...@br...> - 2011-11-23 14:53:44
|
I think it's a fair question! I currently don't support running any of the genome strip functions that require bwa (e.g. genome masking or alt allele alignments) on non-linux platforms. You could try to build libbwa for macos and see if that works for you, but the binary in the distribution is a linux binary. -Bob On 11/22/11 12:01 PM, Mira Han wrote: > > Hi, > I just asked this question at the GSA support website, > but maybe it would be more appropriate for you. > thanks in advance for your help. > I'm trying to test my installation of svtoolkit using the test scripts > provided, but it fails and complains that it cannot find the bwa library. > I am using Mac OS X Lion. > I have the libbwa.so copied into /usr/lib/java/ as well as > /Library/Java/Extensions/. > I have tried booting into both 64bit and 32bit mode and both failed. > Would you have any clue why it's not finding the library? > I know this question is not exactly about your software, but I'm > hoping maybe someone will have knowledge about this problem. > thank you > > Miras-air:installtest mirahan$ java -Xmx1g > -Djava.io.tmpdir=/usr/local/src/svtoolkit/svtoolkit/installtest/tmpdir > -Djava.library.path=/usr/lib/java/ -cp > /usr/local/src/svtoolkit/svtoolkit/lib/SVToolkit.jar:/usr/local/src/svtoolkit/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/usr/local/src/svtoolkit/svtoolkit/lib/gatk/Queue.jar > org.broadinstitute.sting.gatk.CommandLineGATK -T SVAltAligner -R > /usr/local/src/svtoolkit/svtoolkit/installtest/data/human_b36_chr1.fasta > -I /usr/local/src/svtoolkit/svtoolkit/installtest/data/installtest.bam > -O > /usr/local/src/svtoolkit/svtoolkit/installtest/test2/altalign/installtest.alt.bam > -md test2/metadata -U ALLOW_UNINDEXED_BAM -altReference > test2/altalign/installtest.sites.alt.fasta -alignUnmappedMates true > INFO 11:36:26,878 HelpFormatter - > --------------------------------------------------------------------------- > > INFO 11:36:26,880 HelpFormatter - The Genome Analysis Toolkit (GATK) > v1.0.5039M, Compiled 2011/01/20 22:58:34 > INFO 11:36:26,880 HelpFormatter - Copyright (c) 2010 The Broad Institute > INFO 11:36:26,880 HelpFormatter - Please view our documentation > athttp://www.broadinstitute.org/gsa/wiki > INFO 11:36:26,881 HelpFormatter - For support, please view our support > site athttp://getsatisfaction.com/gsa > INFO 11:36:26,881 HelpFormatter - Program Args: -T SVAltAligner -R > /usr/local/src/svtoolkit/svtoolkit/installtest/data/human_b36_chr1.fasta > -I /usr/local/src/svtoolkit/svtoolkit/installtest/data/installtest.bam > -O > /usr/local/src/svtoolkit/svtoolkit/installtest/test2/altalign/installtest.alt.bam > -md test2/metadata -U ALLOW_UNINDEXED_BAM -altReference > test2/altalign/installtest.sites.alt.fasta -alignUnmappedMates true > INFO 11:36:26,881 HelpFormatter - Date/Time: 2011/11/22 11:36:26 > INFO 11:36:26,881 HelpFormatter - > --------------------------------------------------------------------------- > > INFO 11:36:26,881 HelpFormatter - > --------------------------------------------------------------------------- > > INFO 11:36:26,885 GenomeAnalysisEngine - Strictness is SILENT > Exception in thread "main" java.lang.UnsatisfiedLinkError: no bwa in > java.library.path > at java.lang.ClassLoader.loadLibrary(ClassLoader.java:1758) > at java.lang.Runtime.loadLibrary0(Runtime.java:823) > at java.lang.System.loadLibrary(System.java:1045) > at > org.broadinstitute.sting.alignment.bwa.c.BWACAligner.(BWACAligner.java:21) > > at > org.broadinstitute.sv.breakpoint.BreakpointAligner.initialize(BreakpointAligner.java:46) > > at > org.broadinstitute.sv.breakpoint.SVAltAlignerWalker.initialize(SVAltAlignerWalker.java:86) > > at > org.broadinstitute.sting.gatk.executive.LinearMicroScheduler.execute(LinearMicroScheduler.java:49) > > at > org.broadinstitute.sting.gatk.GenomeAnalysisEngine.execute(GenomeAnalysisEngine.java:217) > > at > org.broadinstitute.sting.gatk.CommandLineExecutable.execute(CommandLineExecutable.java:111) > > at > org.broadinstitute.sting.commandline.CommandLineProgram.start(CommandLineProgram.java:239) > > at > org.broadinstitute.sting.gatk.CommandLineGATK.main(CommandLineGATK.java:87) > > Miras-air:installtest mirahan$ ls /usr/lib/java/ > libbwa.so libjdns_sd.jnilib > Miras-air:installtest mirahan$ ls /Library/Java/Extensions/ > libbwa.so > > > ------------------------------------------------------------------------------ > All the data continuously generated in your IT infrastructure > contains a definitive record of customers, application performance, > security threats, fraudulent activity, and more. Splunk takes this > data and makes sense of it. IT sense. And common sense. > http://p.sf.net/sfu/splunk-novd2d > > > _______________________________________________ > svtoolkit-help mailing list > svt...@li... > https://lists.sourceforge.net/lists/listinfo/svtoolkit-help |
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From: Mira H. <mir...@du...> - 2011-11-22 17:02:04
|
Hi, I just asked this question at the GSA support website, but maybe it would be more appropriate for you. thanks in advance for your help. I'm trying to test my installation of svtoolkit using the test scripts provided, but it fails and complains that it cannot find the bwa library. I am using Mac OS X Lion. I have the libbwa.so copied into /usr/lib/java/ as well as /Library/Java/Extensions/. I have tried booting into both 64bit and 32bit mode and both failed. Would you have any clue why it's not finding the library? I know this question is not exactly about your software, but I'm hoping maybe someone will have knowledge about this problem. thank you Miras-air:installtest mirahan$ java -Xmx1g -Djava.io.tmpdir=/usr/local/src/svtoolkit/svtoolkit/installtest/tmpdir -Djava.library.path=/usr/lib/java/ -cp /usr/local/src/svtoolkit/svtoolkit/lib/SVToolkit.jar:/usr/local/src/svtoolkit/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/usr/local/src/svtoolkit/svtoolkit/lib/gatk/Queue.jar org.broadinstitute.sting.gatk.CommandLineGATK -T SVAltAligner -R /usr/local/src/svtoolkit/svtoolkit/installtest/data/human_b36_chr1.fasta -I /usr/local/src/svtoolkit/svtoolkit/installtest/data/installtest.bam -O /usr/local/src/svtoolkit/svtoolkit/installtest/test2/altalign/installtest.alt.bam -md test2/metadata -U ALLOW_UNINDEXED_BAM -altReference test2/altalign/installtest.sites.alt.fasta -alignUnmappedMates true INFO 11:36:26,878 HelpFormatter - --------------------------------------------------------------------------- INFO 11:36:26,880 HelpFormatter - The Genome Analysis Toolkit (GATK) v1.0.5039M, Compiled 2011/01/20 22:58:34 INFO 11:36:26,880 HelpFormatter - Copyright (c) 2010 The Broad Institute INFO 11:36:26,880 HelpFormatter - Please view our documentation athttp://www.broadinstitute.org/gsa/wiki INFO 11:36:26,881 HelpFormatter - For support, please view our support site athttp://getsatisfaction.com/gsa INFO 11:36:26,881 HelpFormatter - Program Args: -T SVAltAligner -R /usr/local/src/svtoolkit/svtoolkit/installtest/data/human_b36_chr1.fasta -I /usr/local/src/svtoolkit/svtoolkit/installtest/data/installtest.bam -O /usr/local/src/svtoolkit/svtoolkit/installtest/test2/altalign/installtest.alt.bam -md test2/metadata -U ALLOW_UNINDEXED_BAM -altReference test2/altalign/installtest.sites.alt.fasta -alignUnmappedMates true INFO 11:36:26,881 HelpFormatter - Date/Time: 2011/11/22 11:36:26 INFO 11:36:26,881 HelpFormatter - --------------------------------------------------------------------------- INFO 11:36:26,881 HelpFormatter - --------------------------------------------------------------------------- INFO 11:36:26,885 GenomeAnalysisEngine - Strictness is SILENT Exception in thread "main" java.lang.UnsatisfiedLinkError: no bwa in java.library.path at java.lang.ClassLoader.loadLibrary(ClassLoader.java:1758) at java.lang.Runtime.loadLibrary0(Runtime.java:823) at java.lang.System.loadLibrary(System.java:1045) at org.broadinstitute.sting.alignment.bwa.c.BWACAligner.(BWACAligner.java:21) at org.broadinstitute.sv.breakpoint.BreakpointAligner.initialize(BreakpointAligner.java:46) at org.broadinstitute.sv.breakpoint.SVAltAlignerWalker.initialize(SVAltAlignerWalker.java:86) at org.broadinstitute.sting.gatk.executive.LinearMicroScheduler.execute(LinearMicroScheduler.java:49) at org.broadinstitute.sting.gatk.GenomeAnalysisEngine.execute(GenomeAnalysisEngine.java:217) at org.broadinstitute.sting.gatk.CommandLineExecutable.execute(CommandLineExecutable.java:111) at org.broadinstitute.sting.commandline.CommandLineProgram.start(CommandLineProgram.java:239) at org.broadinstitute.sting.gatk.CommandLineGATK.main(CommandLineGATK.java:87) Miras-air:installtest mirahan$ ls /usr/lib/java/ libbwa.so libjdns_sd.jnilib Miras-air:installtest mirahan$ ls /Library/Java/Extensions/ libbwa.so |
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From: John B. <jo...@we...> - 2011-11-21 17:54:20
|
[I'm not sure how to reply in a thread, so I'll just send this] I have version 1.04.797 from the interim folder already. Regards, John -- John Broxholme Wellcome Trust Centre for Human Genetics Roosevelt Drive, Oxford, OX3 7BN, UK Tel: (+44 1865) 287611 FAX: 287697 |
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From: Bob H. <han...@br...> - 2011-11-21 17:24:44
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The problem doesn't have anything to do with input data size (at least not directly). It has to do with the requirement that the output records need to be coordinate sorted. The code attempts to buffer to keep the output records in order, but the buffering in this case in insufficient. What version are you using? I have fixed some problems in this area, so you could try with the latest interim release from ftp://ftp.broadinstitute.org/pub/svtoolkit/releases/interim/ and see if this helps. The interim releases don't have updated documentation. They are also not necessarily 100% compatible, but I think people have adapted to them without too much trouble. If it still happens with the latest interim release, let me know. -Bob On 11/21/11 10:48 AM, John Broxholme wrote: > Hi there, > > We're trying to use svtoolkit for SV detection on some deep-sequencing data. This > particular project comprises data from many (up to 800) BAMs. I've reduced the number to > 80 and I still see this kind of error. Where might it come from and how might I fix it? > > I'm not sure which part of the log is most useful, but I've appended what looks to be most > informative. > > Thanks, > John Broxholme > WTCHG, > Oxford, UK > > ... > INFO 00:19:23,590 SVDiscovery - Clustering: LR split size 14 / 95 maximal clique size 2 > clique count 3 > INFO 00:19:23,590 SVDiscovery - Clustering: LR split size 12 / 95 maximal clique size 1 > clique count 18 > INFO 00:19:23,590 SVDiscovery - Processing cluster 14:24437577-24437715 > 14:24519740-24520124 LR 10 > INFO 00:19:24,712 SVDiscovery - Processing cluster 14:24425879-24426190 > 14:24461366-24461735 LR 6 > Error: Exception processing cluster: Permitted to write any record upstream of position > 24427689, but a record at 14:24426202 was just added. > Cluster: 14:24425879-24426190 14:24461366-24461735 LR 6 > [GC 2440851K->2036038K(2645952K), 0.0058190 secs] > [Full GC 2036038K->34379K(2645952K), 0.7118760 secs] > ##### ERROR > ------------------------------------------------------------------------------------------ > ##### ERROR stack trace > java.lang.IllegalArgumentException: Permitted to write any record upstream of position > 24427689, but a record at 14:24426202 was just added. > at > org.broadinstitute.sting.utils.codecs.vcf.SortingVCFWriterBase.noteCurrentRecord(SortingVCFWriterBase.java:101) > at > org.broadinstitute.sting.utils.codecs.vcf.SortingVCFWriter.noteCurrentRecord(SortingVCFWriter.java:55) > at > org.broadinstitute.sting.utils.codecs.vcf.SortingVCFWriterBase.add(SortingVCFWriterBase.java:123) > at > org.broadinstitute.sv.util.vcf.VCFWriterFactory$VCFWriterAdapter.add(VCFWriterFactory.java:76) > at > org.broadinstitute.sv.discovery.DeletionDiscoveryAlgorithm.writeVCFRecord(DeletionDiscoveryAlgorithm.java:641) > at > org.broadinstitute.sv.discovery.DeletionDiscoveryAlgorithm.processCluster(DeletionDiscoveryAlgorithm.java:439) > at > org.broadinstitute.sv.discovery.DeletionDiscoveryAlgorithm.processClusters(DeletionDiscoveryAlgorithm.java:337) > at > org.broadinstitute.sv.discovery.DeletionDiscoveryAlgorithm.runDiscovery(DeletionDiscoveryAlgorithm.java:186) > at > org.broadinstitute.sv.discovery.SVDiscoveryWalker.onTraversalDone(SVDiscoveryWalker.java:166) > at > org.broadinstitute.sv.discovery.SVDiscoveryWalker.onTraversalDone(SVDiscoveryWalker.java:45) > at > org.broadinstitute.sting.gatk.executive.Accumulator$StandardAccumulator.finishTraversal(Accumulator.java:129) > at > org.broadinstitute.sting.gatk.executive.LinearMicroScheduler.execute(LinearMicroScheduler.java:76) > at > org.broadinstitute.sting.gatk.GenomeAnalysisEngine.execute(GenomeAnalysisEngine.java:234) > at > org.broadinstitute.sting.gatk.CommandLineExecutable.execute(CommandLineExecutable.java:113) > at org.broadinstitute.sv.main.SVCommandLine.execute(SVCommandLine.java:105) > at > org.broadinstitute.sting.commandline.CommandLineProgram.start(CommandLineProgram.java:221) > at org.broadinstitute.sv.main.SVCommandLine.main(SVCommandLine.java:67) > at org.broadinstitute.sv.main.SVDiscovery.main(SVDiscovery.java:21) > ##### ERROR > ------------------------------------------------------------------------------------------ > ##### ERROR A GATK RUNTIME ERROR has occurred (version 1.0-6121-g40e3165): > ##### ERROR > ##### ERROR Please visit the wiki to see if this is a known problem > ##### ERROR If not, please post the error, with stack trace, to the GATK forum > ##### ERROR Visit our wiki for extensive documentation http://www.broadinstitute.org/gsa/wiki > ##### ERROR Visit our forum to view answers to commonly asked questions > http://getsatisfaction.com/gsa > ##### ERROR > ##### ERROR MESSAGE: Permitted to write any record upstream of position 24427689, but a > record at 14:24426202 was just added. > ##### ERROR > ------------------------------------------------------------------------------------------ > at org.broadinstitute.sting.queue.util.ShellJob.run(ShellJob.scala:24) > at > org.broadinstitute.sting.queue.engine.shell.ShellJobRunner.start(ShellJobRunner.scala:54) > at org.broadinstitute.sting.queue.engine.FunctionEdge.start(FunctionEdge.scala:56) > at org.broadinstitute.sting.queue.engine.QGraph.runJobs(QGraph.scala:383) > at org.broadinstitute.sting.queue.engine.QGraph.run(QGraph.scala:123) > at org.broadinstitute.sting.queue.QCommandLine.execute(QCommandLine.scala:111) > at > org.broadinstitute.sting.commandline.CommandLineProgram.start(CommandLineProgram.java:221) > at org.broadinstitute.sting.queue.QCommandLine$.main(QCommandLine.scala:57) > at org.broadinstitute.sting.queue.QCommandLine.main(QCommandLine.scala) > INFO 00:19:40,719 QGraph - 74 Pend, 2 Run, 0 Fail, 12 Done > ... > > > ------------------------------------------------------------------------------ > All the data continuously generated in your IT infrastructure > contains a definitive record of customers, application performance, > security threats, fraudulent activity, and more. Splunk takes this > data and makes sense of it. IT sense. And common sense. > http://p.sf.net/sfu/splunk-novd2d > _______________________________________________ > svtoolkit-help mailing list > svt...@li... > https://lists.sourceforge.net/lists/listinfo/svtoolkit-help |
|
From: John B. <jo...@we...> - 2011-11-21 15:49:09
|
Hi there,
We're trying to use svtoolkit for SV detection on some deep-sequencing data. This
particular project comprises data from many (up to 800) BAMs. I've reduced the number to
80 and I still see this kind of error. Where might it come from and how might I fix it?
I'm not sure which part of the log is most useful, but I've appended what looks to be most
informative.
Thanks,
John Broxholme
WTCHG,
Oxford, UK
...
INFO 00:19:23,590 SVDiscovery - Clustering: LR split size 14 / 95 maximal clique size 2
clique count 3
INFO 00:19:23,590 SVDiscovery - Clustering: LR split size 12 / 95 maximal clique size 1
clique count 18
INFO 00:19:23,590 SVDiscovery - Processing cluster 14:24437577-24437715
14:24519740-24520124 LR 10
INFO 00:19:24,712 SVDiscovery - Processing cluster 14:24425879-24426190
14:24461366-24461735 LR 6
Error: Exception processing cluster: Permitted to write any record upstream of position
24427689, but a record at 14:24426202 was just added.
Cluster: 14:24425879-24426190 14:24461366-24461735 LR 6
[GC 2440851K->2036038K(2645952K), 0.0058190 secs]
[Full GC 2036038K->34379K(2645952K), 0.7118760 secs]
##### ERROR
------------------------------------------------------------------------------------------
##### ERROR stack trace
java.lang.IllegalArgumentException: Permitted to write any record upstream of position
24427689, but a record at 14:24426202 was just added.
at
org.broadinstitute.sting.utils.codecs.vcf.SortingVCFWriterBase.noteCurrentRecord(SortingVCFWriterBase.java:101)
at
org.broadinstitute.sting.utils.codecs.vcf.SortingVCFWriter.noteCurrentRecord(SortingVCFWriter.java:55)
at
org.broadinstitute.sting.utils.codecs.vcf.SortingVCFWriterBase.add(SortingVCFWriterBase.java:123)
at
org.broadinstitute.sv.util.vcf.VCFWriterFactory$VCFWriterAdapter.add(VCFWriterFactory.java:76)
at
org.broadinstitute.sv.discovery.DeletionDiscoveryAlgorithm.writeVCFRecord(DeletionDiscoveryAlgorithm.java:641)
at
org.broadinstitute.sv.discovery.DeletionDiscoveryAlgorithm.processCluster(DeletionDiscoveryAlgorithm.java:439)
at
org.broadinstitute.sv.discovery.DeletionDiscoveryAlgorithm.processClusters(DeletionDiscoveryAlgorithm.java:337)
at
org.broadinstitute.sv.discovery.DeletionDiscoveryAlgorithm.runDiscovery(DeletionDiscoveryAlgorithm.java:186)
at
org.broadinstitute.sv.discovery.SVDiscoveryWalker.onTraversalDone(SVDiscoveryWalker.java:166)
at
org.broadinstitute.sv.discovery.SVDiscoveryWalker.onTraversalDone(SVDiscoveryWalker.java:45)
at
org.broadinstitute.sting.gatk.executive.Accumulator$StandardAccumulator.finishTraversal(Accumulator.java:129)
at
org.broadinstitute.sting.gatk.executive.LinearMicroScheduler.execute(LinearMicroScheduler.java:76)
at
org.broadinstitute.sting.gatk.GenomeAnalysisEngine.execute(GenomeAnalysisEngine.java:234)
at
org.broadinstitute.sting.gatk.CommandLineExecutable.execute(CommandLineExecutable.java:113)
at org.broadinstitute.sv.main.SVCommandLine.execute(SVCommandLine.java:105)
at
org.broadinstitute.sting.commandline.CommandLineProgram.start(CommandLineProgram.java:221)
at org.broadinstitute.sv.main.SVCommandLine.main(SVCommandLine.java:67)
at org.broadinstitute.sv.main.SVDiscovery.main(SVDiscovery.java:21)
##### ERROR
------------------------------------------------------------------------------------------
##### ERROR A GATK RUNTIME ERROR has occurred (version 1.0-6121-g40e3165):
##### ERROR
##### ERROR Please visit the wiki to see if this is a known problem
##### ERROR If not, please post the error, with stack trace, to the GATK forum
##### ERROR Visit our wiki for extensive documentation http://www.broadinstitute.org/gsa/wiki
##### ERROR Visit our forum to view answers to commonly asked questions
http://getsatisfaction.com/gsa
##### ERROR
##### ERROR MESSAGE: Permitted to write any record upstream of position 24427689, but a
record at 14:24426202 was just added.
##### ERROR
------------------------------------------------------------------------------------------
at org.broadinstitute.sting.queue.util.ShellJob.run(ShellJob.scala:24)
at
org.broadinstitute.sting.queue.engine.shell.ShellJobRunner.start(ShellJobRunner.scala:54)
at org.broadinstitute.sting.queue.engine.FunctionEdge.start(FunctionEdge.scala:56)
at org.broadinstitute.sting.queue.engine.QGraph.runJobs(QGraph.scala:383)
at org.broadinstitute.sting.queue.engine.QGraph.run(QGraph.scala:123)
at org.broadinstitute.sting.queue.QCommandLine.execute(QCommandLine.scala:111)
at
org.broadinstitute.sting.commandline.CommandLineProgram.start(CommandLineProgram.java:221)
at org.broadinstitute.sting.queue.QCommandLine$.main(QCommandLine.scala:57)
at org.broadinstitute.sting.queue.QCommandLine.main(QCommandLine.scala)
INFO 00:19:40,719 QGraph - 74 Pend, 2 Run, 0 Fail, 12 Done
...
|
|
From: Bob H. <han...@br...> - 2011-11-17 19:57:33
|
It's a bug. What version are you using? You could try the latest interim release at ftp://ftp.broadinstitute.org/pub/svtoolkit/releases/interim/ and see if it helps. Also, if you could look in, e.g. for the first one, the P0011.discovery.clusters.dat file in the run directory and send me the tail of this file (anything after the event DEL_P0011_116) that would be helpful. Or the whole file if it is not too big. I can't promise when I will get time to look at it, though. -Bob On 11/17/11 2:26 PM, Ashish Kumar wrote: > > Hi Bob, > > Following are two errors that I encounter while running the > SVDiscovery process. > > Could you please assist what is being referred as invalid cnp > coordinates? Is that some alignment issue? > > Thanks, > > Ashish. > > 1.Stack trace > > Error: Exception processing cluster: Invalid cnp coordinates: > DEL_P0011_116 107088044 107088043 > > Cluster: 1:107087601-107087956 1:107088131-107088520 LR 2 > > INFO 00:04:16,357 GATKRunReport - Aggregating data for run report > > [GC 987003K->47999K(1502336K), 0.0129670 secs] > > [Full GC 47999K->31291K(1502336K), 0.1004900 secs] > > ##### ERROR > ------------------------------------------------------------------------------------------ > > ##### ERROR stack trace > > java.lang.RuntimeException: Invalid cnp coordinates: DEL_P0011_116 > 107088044 107088043 > > at > org.broadinstitute.sv.common.VCFFormatter.createVariantContext(VCFFormatter.java:198) > > at > org.broadinstitute.sv.common.VCFFormatter.createVariantContext(VCFFormatter.java:166) > > at > org.broadinstitute.sv.discovery.DeletionDiscoveryAlgorithm.writeVCFRecord(DeletionDiscoveryAlgorithm.java:599) > > at > org.broadinstitute.sv.discovery.DeletionDiscoveryAlgorithm.processCluster(DeletionDiscoveryAlgorithm.java:405) > > at > org.broadinstitute.sv.discovery.DeletionDiscoveryAlgorithm.processClusters(DeletionDiscoveryAlgorithm.java:303) > > at > org.broadinstitute.sv.discovery.DeletionDiscoveryAlgorithm.runDiscovery(DeletionDiscoveryAlgorithm.java:163) > > at > org.broadinstitute.sv.discovery.SVDiscoveryWalker.onTraversalDone(SVDiscoveryWalker.java:150) > > at > org.broadinstitute.sv.discovery.SVDiscoveryWalker.onTraversalDone(SVDiscoveryWalker.java:43) > > at > org.broadinstitute.sting.gatk.executive.Accumulator$StandardAccumulator.finishTraversal(Accumulator.java:129) > > at > org.broadinstitute.sting.gatk.executive.LinearMicroScheduler.execute(LinearMicroScheduler.java:75) > > at > org.broadinstitute.sting.gatk.GenomeAnalysisEngine.execute(GenomeAnalysisEngine.java:217) > > at > org.broadinstitute.sting.gatk.CommandLineExecutable.execute(CommandLineExecutable.java:111) > > at > org.broadinstitute.sv.main.SVCommandLine.execute(SVCommandLine.java:110) > > at > org.broadinstitute.sting.commandline.CommandLineProgram.start(CommandLineProgram.java:239) > > at > org.broadinstitute.sv.main.SVCommandLine.main(SVCommandLine.java:72) > > at > org.broadinstitute.sv.main.SVDiscovery.main(SVDiscovery.java:21) > > ##### ERROR > ------------------------------------------------------------------------------------------ > > ##### ERROR A GATK RUNTIME ERROR has occurred (version 1.0.5039M): > > ##### ERROR > > ##### ERROR Please visit to wiki to see if this is a known problem > > ##### ERROR If not, please post the error, with stack trace, to the > GATK forum > > ##### ERROR Visit our wiki for extensive documentation > http://www.broadinstitute.org/gsa/wiki > > ##### ERROR Visit our forum to view answers to commonly asked > questions http://getsatisfaction.com/gsa > > ##### ERROR > > ##### ERROR MESSAGE: Invalid cnp coordinates: DEL_P0011_116 107088044 > 107088043 > > ##### ERROR > ------------------------------------------------------------------------------------------ > > 2.Stack trace > > Error: Exception processing cluster: Invalid cnp coordinates: > DEL_P0019_113 187483130 187483129 > > Cluster: 1:187482695-187483064 1:187483195-187483568 LR 2 > > INFO 01:10:09,053 GATKRunReport - Aggregating data for run report > > [GC 1125151K->46166K(1486208K), 0.0125410 secs] > > [Full GC 46166K->24635K(1486208K), 0.1061040 secs] > > ##### ERROR > ------------------------------------------------------------------------------------------ > > ##### ERROR stack trace > > java.lang.RuntimeException: Invalid cnp coordinates: DEL_P0019_113 > 187483130 187483129 > > at > org.broadinstitute.sv.common.VCFFormatter.createVariantContext(VCFFormatter.java:198) > > at > org.broadinstitute.sv.common.VCFFormatter.createVariantContext(VCFFormatter.java:166) > > at > org.broadinstitute.sv.discovery.DeletionDiscoveryAlgorithm.writeVCFRecord(DeletionDiscoveryAlgorithm.java:599) > > at > org.broadinstitute.sv.discovery.DeletionDiscoveryAlgorithm.processCluster(DeletionDiscoveryAlgorithm.java:405) > > at > org.broadinstitute.sv.discovery.DeletionDiscoveryAlgorithm.processClusters(DeletionDiscoveryAlgorithm.java:303) > > at > org.broadinstitute.sv.discovery.DeletionDiscoveryAlgorithm.runDiscovery(DeletionDiscoveryAlgorithm.java:163) > > at > org.broadinstitute.sv.discovery.SVDiscoveryWalker.onTraversalDone(SVDiscoveryWalker.java:150) > > at > org.broadinstitute.sv.discovery.SVDiscoveryWalker.onTraversalDone(SVDiscoveryWalker.java:43) > > at > org.broadinstitute.sting.gatk.executive.Accumulator$StandardAccumulator.finishTraversal(Accumulator.java:129) > > at > org.broadinstitute.sting.gatk.executive.LinearMicroScheduler.execute(LinearMicroScheduler.java:75) > > at > org.broadinstitute.sting.gatk.GenomeAnalysisEngine.execute(GenomeAnalysisEngine.java:217) > > at > org.broadinstitute.sting.gatk.CommandLineExecutable.execute(CommandLineExecutable.java:111) > > at > org.broadinstitute.sv.main.SVCommandLine.execute(SVCommandLine.java:110) > > at > org.broadinstitute.sting.commandline.CommandLineProgram.start(CommandLineProgram.java:239) > > at > org.broadinstitute.sv.main.SVCommandLine.main(SVCommandLine.java:72) > > at > org.broadinstitute.sv.main.SVDiscovery.main(SVDiscovery.java:21) > > ##### ERROR > ------------------------------------------------------------------------------------------ > > ##### ERROR A GATK RUNTIME ERROR has occurred (version 1.0.5039M): > > ##### ERROR > > ##### ERROR Please visit to wiki to see if this is a known problem > > ##### ERROR If not, please post the error, with stack trace, to the > GATK forum > > ##### ERROR Visit our wiki for extensive documentation > http://www.broadinstitute.org/gsa/wiki > > ##### ERROR Visit our forum to view answers to commonly asked > questions http://getsatisfaction.com/gsa > > ##### ERROR > > ##### ERROR MESSAGE: Invalid cnp coordinates: DEL_P0019_113 187483130 > 187483129 > > ##### ERROR > ------------------------------------------------------------------------------------------ > > > > ------------------------------------------------------------------------------ > All the data continuously generated in your IT infrastructure > contains a definitive record of customers, application performance, > security threats, fraudulent activity, and more. Splunk takes this > data and makes sense of it. IT sense. And common sense. > http://p.sf.net/sfu/splunk-novd2d > > > _______________________________________________ > svtoolkit-help mailing list > svt...@li... > https://lists.sourceforge.net/lists/listinfo/svtoolkit-help |
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From: Ashish K. <as...@we...> - 2011-11-17 19:27:34
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Hi Bob,
Following are two errors that I encounter while running the SVDiscovery process.
Could you please assist what is being referred as invalid cnp coordinates? Is that some alignment issue?
Thanks,
Ashish.
1. Stack trace
Error: Exception processing cluster: Invalid cnp coordinates: DEL_P0011_116 107088044 107088043
Cluster: 1:107087601-107087956 1:107088131-107088520 LR 2
INFO 00:04:16,357 GATKRunReport - Aggregating data for run report
[GC 987003K->47999K(1502336K), 0.0129670 secs]
[Full GC 47999K->31291K(1502336K), 0.1004900 secs]
##### ERROR ------------------------------------------------------------------------------------------
##### ERROR stack trace
java.lang.RuntimeException: Invalid cnp coordinates: DEL_P0011_116 107088044 107088043
at org.broadinstitute.sv.common.VCFFormatter.createVariantContext(VCFFormatter.java:198)
at org.broadinstitute.sv.common.VCFFormatter.createVariantContext(VCFFormatter.java:166)
at org.broadinstitute.sv.discovery.DeletionDiscoveryAlgorithm.writeVCFRecord(DeletionDiscoveryAlgorithm.java:599)
at org.broadinstitute.sv.discovery.DeletionDiscoveryAlgorithm.processCluster(DeletionDiscoveryAlgorithm.java:405)
at org.broadinstitute.sv.discovery.DeletionDiscoveryAlgorithm.processClusters(DeletionDiscoveryAlgorithm.java:303)
at org.broadinstitute.sv.discovery.DeletionDiscoveryAlgorithm.runDiscovery(DeletionDiscoveryAlgorithm.java:163)
at org.broadinstitute.sv.discovery.SVDiscoveryWalker.onTraversalDone(SVDiscoveryWalker.java:150)
at org.broadinstitute.sv.discovery.SVDiscoveryWalker.onTraversalDone(SVDiscoveryWalker.java:43)
at org.broadinstitute.sting.gatk.executive.Accumulator$StandardAccumulator.finishTraversal(Accumulator.java:129)
at org.broadinstitute.sting.gatk.executive.LinearMicroScheduler.execute(LinearMicroScheduler.java:75)
at org.broadinstitute.sting.gatk.GenomeAnalysisEngine.execute(GenomeAnalysisEngine.java:217)
at org.broadinstitute.sting.gatk.CommandLineExecutable.execute(CommandLineExecutable.java:111)
at org.broadinstitute.sv.main.SVCommandLine.execute(SVCommandLine.java:110)
at org.broadinstitute.sting.commandline.CommandLineProgram.start(CommandLineProgram.java:239)
at org.broadinstitute.sv.main.SVCommandLine.main(SVCommandLine.java:72)
at org.broadinstitute.sv.main.SVDiscovery.main(SVDiscovery.java:21)
##### ERROR ------------------------------------------------------------------------------------------
##### ERROR A GATK RUNTIME ERROR has occurred (version 1.0.5039M):
##### ERROR
##### ERROR Please visit to wiki to see if this is a known problem
##### ERROR If not, please post the error, with stack trace, to the GATK forum
##### ERROR Visit our wiki for extensive documentation http://www.broadinstitute.org/gsa/wiki
##### ERROR Visit our forum to view answers to commonly asked questions http://getsatisfaction.com/gsa
##### ERROR
##### ERROR MESSAGE: Invalid cnp coordinates: DEL_P0011_116 107088044 107088043
##### ERROR ------------------------------------------------------------------------------------------
2. Stack trace
Error: Exception processing cluster: Invalid cnp coordinates: DEL_P0019_113 187483130 187483129
Cluster: 1:187482695-187483064 1:187483195-187483568 LR 2
INFO 01:10:09,053 GATKRunReport - Aggregating data for run report
[GC 1125151K->46166K(1486208K), 0.0125410 secs]
[Full GC 46166K->24635K(1486208K), 0.1061040 secs]
##### ERROR ------------------------------------------------------------------------------------------
##### ERROR stack trace
java.lang.RuntimeException: Invalid cnp coordinates: DEL_P0019_113 187483130 187483129
at org.broadinstitute.sv.common.VCFFormatter.createVariantContext(VCFFormatter.java:198)
at org.broadinstitute.sv.common.VCFFormatter.createVariantContext(VCFFormatter.java:166)
at org.broadinstitute.sv.discovery.DeletionDiscoveryAlgorithm.writeVCFRecord(DeletionDiscoveryAlgorithm.java:599)
at org.broadinstitute.sv.discovery.DeletionDiscoveryAlgorithm.processCluster(DeletionDiscoveryAlgorithm.java:405)
at org.broadinstitute.sv.discovery.DeletionDiscoveryAlgorithm.processClusters(DeletionDiscoveryAlgorithm.java:303)
at org.broadinstitute.sv.discovery.DeletionDiscoveryAlgorithm.runDiscovery(DeletionDiscoveryAlgorithm.java:163)
at org.broadinstitute.sv.discovery.SVDiscoveryWalker.onTraversalDone(SVDiscoveryWalker.java:150)
at org.broadinstitute.sv.discovery.SVDiscoveryWalker.onTraversalDone(SVDiscoveryWalker.java:43)
at org.broadinstitute.sting.gatk.executive.Accumulator$StandardAccumulator.finishTraversal(Accumulator.java:129)
at org.broadinstitute.sting.gatk.executive.LinearMicroScheduler.execute(LinearMicroScheduler.java:75)
at org.broadinstitute.sting.gatk.GenomeAnalysisEngine.execute(GenomeAnalysisEngine.java:217)
at org.broadinstitute.sting.gatk.CommandLineExecutable.execute(CommandLineExecutable.java:111)
at org.broadinstitute.sv.main.SVCommandLine.execute(SVCommandLine.java:110)
at org.broadinstitute.sting.commandline.CommandLineProgram.start(CommandLineProgram.java:239)
at org.broadinstitute.sv.main.SVCommandLine.main(SVCommandLine.java:72)
at org.broadinstitute.sv.main.SVDiscovery.main(SVDiscovery.java:21)
##### ERROR ------------------------------------------------------------------------------------------
##### ERROR A GATK RUNTIME ERROR has occurred (version 1.0.5039M):
##### ERROR
##### ERROR Please visit to wiki to see if this is a known problem
##### ERROR If not, please post the error, with stack trace, to the GATK forum
##### ERROR Visit our wiki for extensive documentation http://www.broadinstitute.org/gsa/wiki
##### ERROR Visit our forum to view answers to commonly asked questions http://getsatisfaction.com/gsa
##### ERROR
##### ERROR MESSAGE: Invalid cnp coordinates: DEL_P0019_113 187483130 187483129
##### ERROR ------------------------------------------------------------------------------------------
|
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From: Bob H. <han...@br...> - 2011-11-10 18:39:31
|
I'm unable to reproduce that error here with these bam files (although I can't run completely through discovery because I don't have your reference sequence). If you are running a recent interim release, there should be debugging information on stdout (in addition to the stack trace). Can you send me that output for the pair that fails? Thanks, -Bob On 11/10/11 10:45 AM, Philine Feulner wrote: > Dear Bob, > > I am referring to your reply from the 2011-07-15. I am very sorry that it took me so long to come back to you! > > I run Picard ValidateSam on the bam files and they are fine. > > I also extracted 2 pairs of reads (from different chromosomes and libraries) which failed to run through svtoolkit (error: Left read of read pair fails left read test): > > NG-5241_BS25_4kb_7_68_16539_10233 65 scaffold_1073 245 37 36M = 755 510 CTATCTATCCACGCCGCGCAGACATCTCAAAATCTC 355767676676476474777877867679997675 X0:i:1 X1:i:0 MD:Z:16A19 RG:Z:BS25_4kb_read_run1t_matepair XG:i:0 AM:i:37 NM:i:1 SM:i:37 XM:i:1 XO:i:0 MQ:i:37 OQ:Z:IIGHIIIIHIIIHIIIIIIIIIIIIIIIIIIIHIII XT:A:U > NG-5241_BS25_4kb_7_68_16539_10233 129 scaffold_1073 755 37 36M = 245 -510 TCACTTTCAAACCTTCATATTATGTGTGTCTATATA 345677767886677677677677878786767685 X0:i:1 X1:i:0 MD:Z:36 RG:Z:BS25_4kb_read_run1t_matepair XG:i:0 AM:i:37 NM:i:0 SM:i:37 XM:i:0 XO:i:0 MQ:i:37 OQ:Z:IGFHIEIIIIIIIIIIIHIIIIIIIIIIIIHIIIII XT:A:U > > HWI-ST225_0141:4:1:18064:55456#0 97 groupIV 12453454 37 50M = 12453809 404 CTTATATGACTCCACCAAATGCTCATCTTAACCGTCAATCCGCGAGAGTT 78767677867667667887777677677686638678766374878787 X0:i:1 X1:i:0 MD:Z:7C36C5 RG:Z:BS25_read_run2t_paired_50bp XG:i:0 AM:i:37 NM:i:2 SM:i:37 XM:i:2 XO:i:0 MQ:i:37 OQ:Z:IIIGGHIIIIIIIHIIIIIIIIGIIIIIIIIIIIIIHIIIIIIEIIIIHH XT:A:U > HWI-ST225_0141:4:1:18064:55456#0 145 groupIV 12453809 37 50M = 12453454 -404 TGAGTATTTAGGGAAGAACTTATGTTAAAATGTTTGTTGACCTCAGGACT 76766788676667767878677686777776887687687787766887 X0:i:1 X1:i:0 MD:Z:12A37 RG:Z:BS25_read_run2t_paired_50bp XG:i:0 AM:i:37 NM:i:1 SM:i:37 XM:i:1 XO:i:0 MQ:i:37 OQ:Z:IIIIGIIIIIIIGHIIIIBIIIIIIGGIHIHIIIIIIIIIIHIIIIIIII XT:A:U > > > If I run svtoolkit on these read pairs (bam files attached) only, one pair (from the paired end library) now runs through while the other one (from the mate pair library) still fails. > > Thanks for your help, > Philine > > > > > ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ > Dr Philine Feulner > Westfälische Wilhelms University > Institute for Evolution and Biodiversity > Evolutionary Bioinformatics Group > Hüfferstrasse 1 > 48149 Münster > Germany > Tel: +49 (0) 251 83 21636 > Fax: +49 (0) 251 83 24668 > Email: p.f...@un... > ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ > > > > ------------------------------------------------------------------------------ > RSA(R) Conference 2012 > Save $700 by Nov 18 > Register now > http://p.sf.net/sfu/rsa-sfdev2dev1 > > > _______________________________________________ > svtoolkit-help mailing list > svt...@li... > https://lists.sourceforge.net/lists/listinfo/svtoolkit-help |
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From: Philine F. <p.f...@un...> - 2011-11-10 16:06:51
|
Dear Bob, I am referring to your reply from the 2011-07-15. I am very sorry that it took me so long to come back to you! I run Picard ValidateSam on the bam files and they are fine. I also extracted 2 pairs of reads (from different chromosomes and libraries) which failed to run through svtoolkit (error: Left read of read pair fails left read test): NG-5241_BS25_4kb_7_68_16539_10233 65 scaffold_1073 245 37 36M = 755 510 CTATCTATCCACGCCGCGCAGACATCTCAAAATCTC 355767676676476474777877867679997675 X0:i:1 X1:i:0 MD:Z:16A19 RG:Z:BS25_4kb_read_run1t_matepair XG:i:0 AM:i:37 NM:i:1 SM:i:37 XM:i:1 XO:i:0 MQ:i:37 OQ:Z:IIGHIIIIHIIIHIIIIIIIIIIIIIIIIIIIHIII XT:A:U NG-5241_BS25_4kb_7_68_16539_10233 129 scaffold_1073 755 37 36M = 245 -510 TCACTTTCAAACCTTCATATTATGTGTGTCTATATA 345677767886677677677677878786767685 X0:i:1 X1:i:0 MD:Z:36 RG:Z:BS25_4kb_read_run1t_matepair XG:i:0 AM:i:37 NM:i:0 SM:i:37 XM:i:0 XO:i:0 MQ:i:37 OQ:Z:IGFHIEIIIIIIIIIIIHIIIIIIIIIIIIHIIIII XT:A:U HWI-ST225_0141:4:1:18064:55456#0 97 groupIV 12453454 37 50M = 12453809 404 CTTATATGACTCCACCAAATGCTCATCTTAACCGTCAATCCGCGAGAGTT 78767677867667667887777677677686638678766374878787 X0:i:1 X1:i:0 MD:Z:7C36C5 RG:Z:BS25_read_run2t_paired_50bp XG:i:0 AM:i:37 NM:i:2 SM:i:37 XM:i:2 XO:i:0 MQ:i:37 OQ:Z:IIIGGHIIIIIIIHIIIIIIIIGIIIIIIIIIIIIIHIIIIIIEIIIIHH XT:A:U HWI-ST225_0141:4:1:18064:55456#0 145 groupIV 12453809 37 50M = 12453454 -404 TGAGTATTTAGGGAAGAACTTATGTTAAAATGTTTGTTGACCTCAGGACT 76766788676667767878677686777776887687687787766887 X0:i:1 X1:i:0 MD:Z:12A37 RG:Z:BS25_read_run2t_paired_50bp XG:i:0 AM:i:37 NM:i:1 SM:i:37 XM:i:1 XO:i:0 MQ:i:37 OQ:Z:IIIIGIIIIIIIGHIIIIBIIIIIIGGIHIHIIIIIIIIIIHIIIIIIII XT:A:U If I run svtoolkit on these read pairs (bam files attached) only, one pair (from the paired end library) now runs through while the other one (from the mate pair library) still fails. Thanks for your help, Philine |
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From: Jingerbread <ae4...@gm...> - 2011-10-29 13:30:53
|
Dear Bob, I have located the syntax error. Thanks a lot for your guidance. best, -Jin On Fri, Oct 28, 2011 at 3:50 PM, Jingerbread <ae4...@gm...> wrote: > Hi Bob, > > As you suggested, I have run the interim release; however the same > error persisted (below). I also attach the entire error message > (jindiscovery.sh.o11699) in case you need to see. Can you please offer > some guidance in order to trouble-shoot or get around this problem? > > Many thanks, > > Jin > > > ##### ERROR ------------------------------------------------------------------------------------------ > ##### ERROR stack trace > java.lang.RuntimeException: Cannot parse configuration file: > /share/apps/svtoolkit/el5/x86_64/svtoolkit-1.04.797/svtoolkit/conf/genstrip_parameters.txt > at org.broadinstitute.sv.discovery.SVDiscoveryWalker.initialize(SVDiscoveryWalker.java:135) > at org.broadinstitute.sting.gatk.executive.LinearMicroScheduler.execute(LinearMicroScheduler.java:49) > at org.broadinstitute.sting.gatk.GenomeAnalysisEngine.execute(GenomeAnalysisEngine.java:234) > at org.broadinstitute.sting.gatk.CommandLineExecutable.execute(CommandLineExecutable.java:113) > at org.broadinstitute.sv.main.SVCommandLine.execute(SVCommandLine.java:105) > at org.broadinstitute.sting.commandline.CommandLineProgram.start(CommandLineProgram.java:221) > at org.broadinstitute.sv.main.SVCommandLine.main(SVCommandLine.java:67) > at org.broadinstitute.sv.main.SVDiscovery.main(SVDiscovery.java:21) > Caused by: java.io.FileNotFoundException: > /share/apps/svtoolkit/el5/x86_64/svtoolkit-1.04.797/svtoolkit/conf/genstrip_parameters.txt > (No such file or directory) > at java.io.FileInputStream.open(Native Method) > at java.io.FileInputStream.<init>(FileInputStream.java:120) > at java.io.FileReader.<init>(FileReader.java:55) > at org.broadinstitute.sv.util.ParameterParser.parseParameterFile(ParameterParser.java:30) > at org.broadinstitute.sv.discovery.SVDiscoveryWalker.initialize(SVDiscoveryWalker.java:133) > ... 7 more > ##### ERROR ------------------------------------------------------------------------------------------ > ##### ERROR A GATK RUNTIME ERROR has occurred (version 1.0-6121-g40e3165): > ##### ERROR > ##### ERROR Please visit the wiki to see if this is a known problem > ##### ERROR If not, please post the error, with stack trace, to the GATK forum > ##### ERROR Visit our wiki for extensive documentation > http://www.broadinstitute.org/gsa/wiki > ##### ERROR Visit our forum to view answers to commonly asked > questions http://getsatisfaction.com/gsa > ##### ERROR > ##### ERROR MESSAGE: Cannot parse configuration file: > /share/apps/svtoolkit/el5/x86_64/svtoolkit-1.04.797/svtoolkit/conf/genstrip_parameters.txt > ##### ERROR ------------------------------------------------------------------------------------------ > > > >> If you run the interim release from >> ftp://ftp.broadinstitute.org/pub/svtoolkit/releases/interim/svtoolkit_1.04.797.tar.gz >> then you should hopefully get a more explanatory message / stack trace. >> You can decide whether to run the interim release for your processing or >> just to debug this problem - there is no documentation of any new features >> or potential incompatibilities in the interim releases. > |
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From: Jingerbread <ae4...@gm...> - 2011-10-28 19:50:44
|
Hi Bob, As you suggested, I have run the interim release; however the same error persisted (below). I also attach the entire error message (jindiscovery.sh.o11699) in case you need to see. Can you please offer some guidance in order to trouble-shoot or get around this problem? Many thanks, Jin ##### ERROR ------------------------------------------------------------------------------------------ ##### ERROR stack trace java.lang.RuntimeException: Cannot parse configuration file: /share/apps/svtoolkit/el5/x86_64/svtoolkit-1.04.797/svtoolkit/conf/genstrip_parameters.txt at org.broadinstitute.sv.discovery.SVDiscoveryWalker.initialize(SVDiscoveryWalker.java:135) at org.broadinstitute.sting.gatk.executive.LinearMicroScheduler.execute(LinearMicroScheduler.java:49) at org.broadinstitute.sting.gatk.GenomeAnalysisEngine.execute(GenomeAnalysisEngine.java:234) at org.broadinstitute.sting.gatk.CommandLineExecutable.execute(CommandLineExecutable.java:113) at org.broadinstitute.sv.main.SVCommandLine.execute(SVCommandLine.java:105) at org.broadinstitute.sting.commandline.CommandLineProgram.start(CommandLineProgram.java:221) at org.broadinstitute.sv.main.SVCommandLine.main(SVCommandLine.java:67) at org.broadinstitute.sv.main.SVDiscovery.main(SVDiscovery.java:21) Caused by: java.io.FileNotFoundException: /share/apps/svtoolkit/el5/x86_64/svtoolkit-1.04.797/svtoolkit/conf/genstrip_parameters.txt (No such file or directory) at java.io.FileInputStream.open(Native Method) at java.io.FileInputStream.<init>(FileInputStream.java:120) at java.io.FileReader.<init>(FileReader.java:55) at org.broadinstitute.sv.util.ParameterParser.parseParameterFile(ParameterParser.java:30) at org.broadinstitute.sv.discovery.SVDiscoveryWalker.initialize(SVDiscoveryWalker.java:133) ... 7 more ##### ERROR ------------------------------------------------------------------------------------------ ##### ERROR A GATK RUNTIME ERROR has occurred (version 1.0-6121-g40e3165): ##### ERROR ##### ERROR Please visit the wiki to see if this is a known problem ##### ERROR If not, please post the error, with stack trace, to the GATK forum ##### ERROR Visit our wiki for extensive documentation http://www.broadinstitute.org/gsa/wiki ##### ERROR Visit our forum to view answers to commonly asked questions http://getsatisfaction.com/gsa ##### ERROR ##### ERROR MESSAGE: Cannot parse configuration file: /share/apps/svtoolkit/el5/x86_64/svtoolkit-1.04.797/svtoolkit/conf/genstrip_parameters.txt ##### ERROR ------------------------------------------------------------------------------------------ > If you run the interim release from > ftp://ftp.broadinstitute.org/pub/svtoolkit/releases/interim/svtoolkit_1.04.797.tar.gz > then you should hopefully get a more explanatory message / stack trace. > You can decide whether to run the interim release for your processing or > just to debug this problem - there is no documentation of any new features > or potential incompatibilities in the interim releases. |
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From: Bob H. <han...@br...> - 2011-10-28 15:18:09
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On 10/28/11 10:06 AM, Jingerbread wrote: > Dear Bob, > > Thanks a lot for your rapid response. I have removed the -L 1 argument > as you suggested and now the problem is gone. > > However, I have 2 other issues: > > 1. Pre-processing output empty > > I did not get any summary statistics from the pre-processing step even > thought it was error free. For example, the depth.dat is empty with a > header only. "SAMPLE LIBRARY READGROUP COUNT" If you post the SAM header from one of your input files, perhaps that will help. I suspect some problem with the @RG header (and make sure your bam records have RG tags). > > 2. cannot parse configuration file > I used the downloaded > /svtoolkit/el5/x86_64/svtoolkit-1.03.619/svtoolkit/conf/genstrip_parameters.txt > However I received the following error. Can you please suggest a way > to fix it? Many thanks for your help!!! Hmm. Unfortunately the code is swallowing the error message. It is quite possibly a syntax error on one line in the file. If you run the interim release from ftp://ftp.broadinstitute.org/pub/svtoolkit/releases/interim/svtoolkit_1.04.797.tar.gz then you should hopefully get a more explanatory message / stack trace. You can decide whether to run the interim release for your processing or just to debug this problem - there is no documentation of any new features or potential incompatibilities in the interim releases. -Bob > > ##### ERROR ------------------------------------------------------------------------------------------ > ##### ERROR stack trace > java.lang.RuntimeException: Cannot parse configuration file: > /share/apps/svtoolkit/el5/x86_64/svtoolkit-1.03.619/svtoolkit/conf/genstrip_parameters > .txt > at org.broadinstitute.sv.discovery.SVDiscoveryWalker.initialize(SVDiscoveryWalker.java:122) > at org.broadinstitute.sting.gatk.executive.LinearMicroScheduler.execute(LinearMicroScheduler.java:49) > at org.broadinstitute.sting.gatk.GenomeAnalysisEngine.execute(GenomeAnalysisEngine.java:217) > at org.broadinstitute.sting.gatk.CommandLineExecutable.execute(CommandLineExecutable.java:111) > at org.broadinstitute.sv.main.SVCommandLine.execute(SVCommandLine.java:110) > at org.broadinstitute.sting.commandline.CommandLineProgram.start(CommandLineProgram.java:239) > at org.broadinstitute.sv.main.SVCommandLine.main(SVCommandLine.java:72) > at org.broadinstitute.sv.main.SVDiscovery.main(SVDiscovery.java:21) > ##### ERROR ------------------------------------------------------------------------------------------ > ##### ERROR A GATK RUNTIME ERROR has occurred (version 1.0.5039M): > ##### ERROR > ##### ERROR Please visit to wiki to see if this is a known problem > ##### ERROR If not, please post the error, with stack trace, to the GATK forum > ##### ERROR Visit our wiki for extensive documentation > http://www.broadinstitute.org/gsa/wiki > ##### ERROR Visit our forum to view answers to commonly asked > questions http://getsatisfaction.com/gsa > ##### ERROR > ##### ERROR MESSAGE: Cannot parse configuration file: > /share/apps/svtoolkit/el5/x86_64/svtoolkit-1.03.619/svtoolkit/conf/genstrip_parameters.txt > ##### ERROR ------------------------------------------------------------------------------------------ > > > > On Fri, Oct 28, 2011 at 9:17 AM, Bob Handsaker > <han...@br...> wrote: >> This is usually because you have copied the installation test, which uses >> the argument "-L 1", but your reference genome has not chromosome named "1". >> The -L argument specifies a specific locus to process. This option is used >> in the installation test just to make it run slightly faster. >> -Bob |
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From: Jingerbread <ae4...@gm...> - 2011-10-28 14:06:58
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Dear Bob, Thanks a lot for your rapid response. I have removed the -L 1 argument as you suggested and now the problem is gone. However, I have 2 other issues: 1. Pre-processing output empty I did not get any summary statistics from the pre-processing step even thought it was error free. For example, the depth.dat is empty with a header only. "SAMPLE LIBRARY READGROUP COUNT" 2. cannot parse configuration file I used the downloaded /svtoolkit/el5/x86_64/svtoolkit-1.03.619/svtoolkit/conf/genstrip_parameters.txt However I received the following error. Can you please suggest a way to fix it? Many thanks for your help!!! ##### ERROR ------------------------------------------------------------------------------------------ ##### ERROR stack trace java.lang.RuntimeException: Cannot parse configuration file: /share/apps/svtoolkit/el5/x86_64/svtoolkit-1.03.619/svtoolkit/conf/genstrip_parameters .txt at org.broadinstitute.sv.discovery.SVDiscoveryWalker.initialize(SVDiscoveryWalker.java:122) at org.broadinstitute.sting.gatk.executive.LinearMicroScheduler.execute(LinearMicroScheduler.java:49) at org.broadinstitute.sting.gatk.GenomeAnalysisEngine.execute(GenomeAnalysisEngine.java:217) at org.broadinstitute.sting.gatk.CommandLineExecutable.execute(CommandLineExecutable.java:111) at org.broadinstitute.sv.main.SVCommandLine.execute(SVCommandLine.java:110) at org.broadinstitute.sting.commandline.CommandLineProgram.start(CommandLineProgram.java:239) at org.broadinstitute.sv.main.SVCommandLine.main(SVCommandLine.java:72) at org.broadinstitute.sv.main.SVDiscovery.main(SVDiscovery.java:21) ##### ERROR ------------------------------------------------------------------------------------------ ##### ERROR A GATK RUNTIME ERROR has occurred (version 1.0.5039M): ##### ERROR ##### ERROR Please visit to wiki to see if this is a known problem ##### ERROR If not, please post the error, with stack trace, to the GATK forum ##### ERROR Visit our wiki for extensive documentation http://www.broadinstitute.org/gsa/wiki ##### ERROR Visit our forum to view answers to commonly asked questions http://getsatisfaction.com/gsa ##### ERROR ##### ERROR MESSAGE: Cannot parse configuration file: /share/apps/svtoolkit/el5/x86_64/svtoolkit-1.03.619/svtoolkit/conf/genstrip_parameters.txt ##### ERROR ------------------------------------------------------------------------------------------ On Fri, Oct 28, 2011 at 9:17 AM, Bob Handsaker <han...@br...> wrote: > This is usually because you have copied the installation test, which uses > the argument "-L 1", but your reference genome has not chromosome named "1". > The -L argument specifies a specific locus to process. This option is used > in the installation test just to make it run slightly faster. > -Bob |
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From: Bob H. <han...@br...> - 2011-10-28 13:50:06
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Queue is a very nice job management library written in scala by Khalid Shakir, part of the GATK. It's kind of like "make" in that you define a tree of jobs with dependencies and then queue will run these as parallel jobs when possible, based on the dependency graph. Queue supports LSF and I believe also SGE (although I haven't used this myself) and can also just run jobs synchronously in subshells. If you use -bsub and LSF, for example, then the jobs will be run in parallel when possible. This is all process-level parallelism, not thread-level. Genome STRiP is written in java and is single threaded, so the number of OS threads will depend on the JVM configuration. It's designed to exploit process-level parallelism. -Bob On 10/24/11 7:14 PM, Ashish Kumar wrote: > > Thanks Bob. > > On the parallelisation issue, could you please clarify more. > > 1.When this --windowSize is for e.g. 3 Mb, then does each window run > in parallel or that's only for chunking, and we could optionally make > them run separately and join the outputs later? Is it same for the > SVGenotyper's -parallelJobs option? > > 2.On various runs, I've noticed that the no. of optimal cores required > by the program on a multi-core architecture is 2 cores. Is this > correct or the program can use more cores on a 8-core node in some > different settings? > > Best, > > Ashish. > > *From:*Bob Handsaker [mailto:han...@br...] > *Sent:* 21 October 2011 16:49 > *To:* Ashish Kumar > *Cc:* svt...@li... > *Subject:* Re: [svtoolkit-help] Genome strip - Unrecognized sequence: > 1:0-0 > > Yes, you can use -L to process just a specific interval (or can pass a > file with a list of intervals - the file extension must be .list). > Note that the SVDiscovery queue script also does parallelization > internally, based on the -windowSize parameter. > For example, here are typical parameters to process the genome (or > just the intervals selected with -L) in 3Mb windows for events between > 100bp and 100Kb: > > -windowSize 3000000 > -windowPadding 100000 > -minimumSize 100 > -maximumSize 100000 > > You can invoke the queue script without '-run' to preview the chunking. > > -Bob > > On 10/21/11 11:30 AM, Ashish Kumar wrote: > > Hi Bob, > > On the same issue, if we want to use the --L option, would it be safe > to presume that we can chunk up the chromosomes. > > So, say something like "-L 20:1250000-2500000" would be a valid > option, assuming that this sequence exists in my reference genome? > > Thanks, > > Ashish > > *From:*Bob Handsaker [mailto:han...@br...] > *Sent:* 06 October 2011 14:40 > *To:* svt...@li... > <mailto:svt...@li...> > *Subject:* Re: [svtoolkit-help] Genome strip - Unrecognized sequence: > 1:0-0 > > This is because the example script uses "-L 1" (only process > chromosome 1) to make it faster, > but you likely don't have a sequence named "1" in your reference genome. > To process the whole genome, simply remove the -L argument. > -Bob > > On 10/5/11 2:50 PM, Axel Ericsson wrote: > > Hi > > I have get the following error message when I run the Genome strip: I > forwarded the modified shell script, hope you could point me in the > right direction. > > Best regards Axel > > INFO 14:37:52,013 QScriptManager - Compiling 2 QScripts > > INFO 14:37:59,172 QScriptManager - Compilation complete > > INFO 14:38:02,654 HelpFormatter - > --------------------------------------------------------- > > INFO 14:38:02,655 HelpFormatter - Program Name: > org.broadinstitute.sting.queue.QCommandLine > > INFO 14:38:02,655 HelpFormatter - Program Args: -S > /seq/vsag/axel/tools/Genome_strip/svtoolkit/qscript/SVDiscovery.q -S > /seq/vsag/axel/tools/Genome_strip/svtoolkit/qscript/SVQScript.q -gatk > /seq/vsag/axel/tools/Genome_strip/svtoolkit/lib/gatk/GenomeAnalysisTK.jar > -cp > /seq/vsag/axel/tools/Genome_strip/svtoolkit/lib/SVToolkit.jar:/seq/vsag/axel/tools/Genome_strip/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/seq/vsag/axel/tools/Genome_strip/svtoolkit/lib/gatk/Queue.jar > -configFile conf/genstrip_HCSMA_parameters.txt -tempDir ./tmpdir -R > /seq/references/Canis_lupus_familiaris_assembly2/v0/Canis_lupus_familiaris_assembly2.fasta > -genomeMaskFile > /seq/vsag/hyunji/CCD/capture/genomestrip/canFam2_1_index/work/Canis_lupus_familiaris_assembly2.mask.fasta > -genderMapFile data/HCSMA_gender.map -runDirectory HCSMA -md > HCSMA/metadata -jobLogDir HCSMA/logs -L 1 -minimumSize 100 > -maximumSize 1000000 -I > /seq/vsag/axel/bamfiles/HCSMCRealignment.HCSMA_B90_Homo_1.clean.dedup.recal.bam > -O HCSMA.discovery.vcf -run > > INFO 14:38:02,656 HelpFormatter - Date/Time: 2011/10/05 14:38:02 > > INFO 14:38:02,656 HelpFormatter - > --------------------------------------------------------- > > INFO 14:38:02,657 HelpFormatter - > --------------------------------------------------------- > > INFO 14:38:02,661 QCommandLine - Scripting SVDiscovery > > ##### ERROR > ------------------------------------------------------------------------------------------ > > ##### ERROR stack trace > > java.lang.IllegalArgumentException:*Unrecognized sequence: 1:0-0* > > at > org.broadinstitute.sv.queue.ComputeDiscoveryPartitions.computePartitions(ComputeDiscoveryPartitions.java:96) > > at > org.broadinstitute.sv.qscript.SVQScript.computeDiscoveryPartitions(SVQScript.q:132) > > at SVDiscovery.script(SVDiscovery.q:19) > > at > org.broadinstitute.sting.queue.QCommandLine$$anonfun$execute$1.apply(QCommandLine.scala:46) > > at > org.broadinstitute.sting.queue.QCommandLine$$anonfun$execute$1.apply(QCommandLine.scala:43) > > at scala.collection.Iterator$class.foreach(Iterator.scala:631) > > at > scala.collection.JavaConversions$JIteratorWrapper.foreach(JavaConversions.scala:549) > > at scala.collection.IterableLike$class.foreach(IterableLike.scala:79) > > at > scala.collection.JavaConversions$JListWrapper.foreach(JavaConversions.scala:596) > > at > org.broadinstitute.sting.queue.QCommandLine.execute(QCommandLine.scala:43) > > at > org.broadinstitute.sting.commandline.CommandLineProgram.start(CommandLineProgram.java:239) > > at > org.broadinstitute.sting.queue.QCommandLine$.main(QCommandLine.scala:117) > > at org.broadinstitute.sting.queue.QCommandLine.main(QCommandLine.scala) > > ##### ERROR > ------------------------------------------------------------------------------------------ > > ##### ERROR A GATK RUNTIME ERROR has occurred (version 1.0.5039M): > > ##### ERROR > > ##### ERROR Please visit to wiki to see if this is a known problem > > ##### ERROR If not, please post the error, with stack trace, to the > GATK forum > > ##### ERROR Visit our wiki for extensive documentation > http://www.broadinstitute.org/gsa/wiki > > ##### ERROR Visit our forum to view answers to commonly asked > questions http://getsatisfaction.com/gsa > > ##### ERROR > > ##### ERROR MESSAGE: Unrecognized sequence: 1:0-0 > > ##### ERROR > ------------------------------------------------------------------------------------------ > > > > > > ------------------------------------------------------------------------------ > All the data continuously generated in your IT infrastructure contains a > definitive record of customers, application performance, security > threats, fraudulent activity and more. Splunk takes this data and makes > sense of it. Business sense. IT sense. Common sense. > http://p.sf.net/sfu/splunk-d2dcopy1 > > > > > > _______________________________________________ > svtoolkit-help mailing list > svt...@li... <mailto:svt...@li...> > https://lists.sourceforge.net/lists/listinfo/svtoolkit-help > |
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