svtoolkit-help Mailing List for Structural Variation Toolkit (Page 7)
Status: Beta
Brought to you by:
bhandsaker
Menu
▾
▴
svtoolkit-help — bug reports and trouble shooting
You can subscribe to this list here.
| 2011 |
Jan
|
Feb
(2) |
Mar
(7) |
Apr
(3) |
May
|
Jun
(9) |
Jul
(2) |
Aug
(2) |
Sep
(15) |
Oct
(13) |
Nov
(11) |
Dec
(8) |
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 2012 |
Jan
(14) |
Feb
(5) |
Mar
(4) |
Apr
(8) |
May
(2) |
Jun
(8) |
Jul
(6) |
Aug
(4) |
Sep
(8) |
Oct
(5) |
Nov
(2) |
Dec
(4) |
| 2013 |
Jan
(4) |
Feb
|
Mar
(4) |
Apr
|
May
(8) |
Jun
(3) |
Jul
|
Aug
(1) |
Sep
|
Oct
(4) |
Nov
|
Dec
(3) |
| 2014 |
Jan
|
Feb
|
Mar
(3) |
Apr
(5) |
May
|
Jun
|
Jul
|
Aug
|
Sep
(1) |
Oct
|
Nov
|
Dec
|
| 2015 |
Jan
(2) |
Feb
(9) |
Mar
(2) |
Apr
(6) |
May
|
Jun
(7) |
Jul
|
Aug
(2) |
Sep
(4) |
Oct
(4) |
Nov
(1) |
Dec
(1) |
| 2016 |
Jan
|
Feb
|
Mar
|
Apr
|
May
|
Jun
|
Jul
(2) |
Aug
(3) |
Sep
(3) |
Oct
(1) |
Nov
|
Dec
|
| 2017 |
Jan
|
Feb
(2) |
Mar
|
Apr
|
May
|
Jun
|
Jul
|
Aug
|
Sep
(3) |
Oct
(3) |
Nov
(1) |
Dec
|
| 2018 |
Jan
(2) |
Feb
|
Mar
|
Apr
|
May
(3) |
Jun
(6) |
Jul
|
Aug
(4) |
Sep
|
Oct
(1) |
Nov
|
Dec
|
|
From: Ashish K. <as...@we...> - 2012-04-04 21:19:56
|
Hi Bob, While trying to run discovery pipeline over the whole-genome, there are certain regions that are high depth region (and presumably very low complexity). For eg. on a chr10's 2Mb region, the discovery is able to complete only about 20% of the region in 3 days of computation. Shall I parallelise this region further into smaller discovery regions or there are other ways that GenomeSTRiP can cope up with in such a situation? Thanks, Ashish |
|
From: Bob H. <han...@br...> - 2012-04-04 15:12:36
|
Thanks for reporting this. It has been reported by others as well. If you (or someone else) has a patch to the Q scripts to allow it to work with newer versions of queue.jar, please let me know. Otherwise, this will probably get rolled into support for a newer version of the gatk, which may not happen right away. -Bob On 4/4/12 8:36 AM, Ankit Maroo wrote: > Hi, > > I was trying to use this version on our SGE grid setup. The queue.jar which is provided with this tool does not have the patch for SGE grid and if I try to use new version of Queue.jar while keeping everything same it gives error for 4 functions: > > ERROR 12:46:57,784 QGraph - Missing 2 values for function: 'java' '-Xmx4096m' '-Djava.io.tmpdir=/local/projects-isi/ECENT/Merge_25_AshKenazi/genome_strip/temp_dir' '-cp' 'SVToolkit.jar:GenomeAnalysisTK.jar' org.broadinstitute.sv.apps.MergeInsertSizeHistograms '-I' '/local/projects-isi/ECENT/Merge_25_AshKenazi/genome_strip/null/isd/Merge_25_samtools_sorted.reheader.hist.bin' '-O' '/local/projects-isi/ECENT/Merge_25_AshKenazi/genome_strip/isd.hist.bin' > ERROR 12:46:57,784 QGraph - @Argument: jarFile - jar > ERROR 12:46:57,784 QGraph - @Argument: javaMainClass - Main class to run from javaClasspath > ERROR 12:46:57,785 QGraph - Missing 2 values for function: 'java' '-Xmx4096m' '-Djava.io.tmpdir=/local/projects-isi/ECENT/Merge_25_AshKenazi/genome_strip/temp_dir' '-cp' 'SVToolkit.jar:GenomeAnalysisTK.jar' org.broadinstitute.sv.apps.ComputeInsertStatistics '-I' '/local/projects-isi/ECENT/Merge_25_AshKenazi/genome_strip/isd.hist.bin' '-O' '/local/projects-isi/ECENT/Merge_25_AshKenazi/genome_strip/isd.stats.dat' > ERROR 12:46:57,785 QGraph - @Argument: jarFile - jar > ERROR 12:46:57,785 QGraph - @Argument: javaMainClass - Main class to run from javaClasspath > ERROR 12:46:57,787 QGraph - Missing 2 values for function: 'java' '-Xmx4096m' '-Djava.io.tmpdir=/local/projects-isi/ECENT/Merge_25_AshKenazi/genome_strip/temp_dir' '-cp' 'SVToolkit.jar:GenomeAnalysisTK.jar' org.broadinstitute.sv.apps.MergeReadDepthCoverage '-I' '/local/projects-isi/ECENT/Merge_25_AshKenazi/genome_strip/null/depth/Merge_25_samtools_sorted.reheader.depth.txt' '-O' '/local/projects-isi/ECENT/Merge_25_AshKenazi/genome_strip/depth.dat' > ERROR 12:46:57,787 QGraph - @Argument: jarFile - jar > ERROR 12:46:57,787 QGraph - @Argument: javaMainClass - Main class to run from javaClasspath > ERROR 12:46:57,788 QGraph - Missing 2 values for function: 'java' '-Xmx4096m' '-Djava.io.tmpdir=/local/projects-isi/ECENT/Merge_25_AshKenazi/genome_strip/temp_dir' '-cp' 'SVToolkit.jar:GenomeAnalysisTK.jar' org.broadinstitute.sv.apps.MergeReadSpanCoverage '-I' '/local/projects-isi/ECENT/Merge_25_AshKenazi/genome_strip/null/spans/Merge_25_samtools_sorted.reheader.spans.txt' '-O' '/local/projects-isi/ECENT/Merge_25_AshKenazi/genome_strip/spans.dat' > ERROR 12:46:57,788 QGraph - @Argument: jarFile - jar > ERROR 12:46:57,788 QGraph - @Argument: javaMainClass - Main class to run from javaClasspath > INFO 12:46:57,812 QGraph - ------- > INFO 12:46:57,813 QGraph - Pending: 'java' '-Xmx4096m' '-Djava.io.tmpdir=/local/projects-isi/ECENT/Merge_25_AshKenazi/genome_strip/temp_dir' '-cp' 'SVToolkit.jar:GenomeAnalysisTK.jar' org.broadinstitute.sting.gatk.CommandLineGATK '-T' 'ComputeInsertSizeDistributions' '-R' '/local/sequence-isi/reference/GATK/resources/human_g1k_v37.fasta' '-I' '/local/projects-isi/ECENT/Merge_25_AshKenazi/genome_strip/Merge_25_samtools_sorted.reheader.bam' '-O' '/local/projects-isi/ECENT/Merge_25_AshKenazi/genome_strip/null/isd/Merge_25_samtools_sorted.reheader.hist.bin' -createEmpty > > > > The dry run completes without error with previous version of Queue, but the above error comes with new version. Would it be possible for you to look into this and test the program with new version? > > Thank you very much > > Ankit Maroo > Bioinformatics Analyst > Institute for Genome Sciences > University of Maryland. > ------------------------------------------------------------------------------ > Better than sec? Nothing is better than sec when it comes to > monitoring Big Data applications. Try Boundary one-second > resolution app monitoring today. Free. > http://p.sf.net/sfu/Boundary-dev2dev > _______________________________________________ > svtoolkit-help mailing list > svt...@li... > https://lists.sourceforge.net/lists/listinfo/svtoolkit-help |
|
From: Ankit M. <ank...@gm...> - 2012-04-04 12:36:37
|
Hi, I was trying to use this version on our SGE grid setup. The queue.jar which is provided with this tool does not have the patch for SGE grid and if I try to use new version of Queue.jar while keeping everything same it gives error for 4 functions: ERROR 12:46:57,784 QGraph - Missing 2 values for function: 'java' '-Xmx4096m' '-Djava.io.tmpdir=/local/projects-isi/ECENT/Merge_25_AshKenazi/genome_strip/temp_dir' '-cp' 'SVToolkit.jar:GenomeAnalysisTK.jar' org.broadinstitute.sv.apps.MergeInsertSizeHistograms '-I' '/local/projects-isi/ECENT/Merge_25_AshKenazi/genome_strip/null/isd/Merge_25_samtools_sorted.reheader.hist.bin' '-O' '/local/projects-isi/ECENT/Merge_25_AshKenazi/genome_strip/isd.hist.bin' ERROR 12:46:57,784 QGraph - @Argument: jarFile - jar ERROR 12:46:57,784 QGraph - @Argument: javaMainClass - Main class to run from javaClasspath ERROR 12:46:57,785 QGraph - Missing 2 values for function: 'java' '-Xmx4096m' '-Djava.io.tmpdir=/local/projects-isi/ECENT/Merge_25_AshKenazi/genome_strip/temp_dir' '-cp' 'SVToolkit.jar:GenomeAnalysisTK.jar' org.broadinstitute.sv.apps.ComputeInsertStatistics '-I' '/local/projects-isi/ECENT/Merge_25_AshKenazi/genome_strip/isd.hist.bin' '-O' '/local/projects-isi/ECENT/Merge_25_AshKenazi/genome_strip/isd.stats.dat' ERROR 12:46:57,785 QGraph - @Argument: jarFile - jar ERROR 12:46:57,785 QGraph - @Argument: javaMainClass - Main class to run from javaClasspath ERROR 12:46:57,787 QGraph - Missing 2 values for function: 'java' '-Xmx4096m' '-Djava.io.tmpdir=/local/projects-isi/ECENT/Merge_25_AshKenazi/genome_strip/temp_dir' '-cp' 'SVToolkit.jar:GenomeAnalysisTK.jar' org.broadinstitute.sv.apps.MergeReadDepthCoverage '-I' '/local/projects-isi/ECENT/Merge_25_AshKenazi/genome_strip/null/depth/Merge_25_samtools_sorted.reheader.depth.txt' '-O' '/local/projects-isi/ECENT/Merge_25_AshKenazi/genome_strip/depth.dat' ERROR 12:46:57,787 QGraph - @Argument: jarFile - jar ERROR 12:46:57,787 QGraph - @Argument: javaMainClass - Main class to run from javaClasspath ERROR 12:46:57,788 QGraph - Missing 2 values for function: 'java' '-Xmx4096m' '-Djava.io.tmpdir=/local/projects-isi/ECENT/Merge_25_AshKenazi/genome_strip/temp_dir' '-cp' 'SVToolkit.jar:GenomeAnalysisTK.jar' org.broadinstitute.sv.apps.MergeReadSpanCoverage '-I' '/local/projects-isi/ECENT/Merge_25_AshKenazi/genome_strip/null/spans/Merge_25_samtools_sorted.reheader.spans.txt' '-O' '/local/projects-isi/ECENT/Merge_25_AshKenazi/genome_strip/spans.dat' ERROR 12:46:57,788 QGraph - @Argument: jarFile - jar ERROR 12:46:57,788 QGraph - @Argument: javaMainClass - Main class to run from javaClasspath INFO 12:46:57,812 QGraph - ------- INFO 12:46:57,813 QGraph - Pending: 'java' '-Xmx4096m' '-Djava.io.tmpdir=/local/projects-isi/ECENT/Merge_25_AshKenazi/genome_strip/temp_dir' '-cp' 'SVToolkit.jar:GenomeAnalysisTK.jar' org.broadinstitute.sting.gatk.CommandLineGATK '-T' 'ComputeInsertSizeDistributions' '-R' '/local/sequence-isi/reference/GATK/resources/human_g1k_v37.fasta' '-I' '/local/projects-isi/ECENT/Merge_25_AshKenazi/genome_strip/Merge_25_samtools_sorted.reheader.bam' '-O' '/local/projects-isi/ECENT/Merge_25_AshKenazi/genome_strip/null/isd/Merge_25_samtools_sorted.reheader.hist.bin' -createEmpty The dry run completes without error with previous version of Queue, but the above error comes with new version. Would it be possible for you to look into this and test the program with new version? Thank you very much Ankit Maroo Bioinformatics Analyst Institute for Genome Sciences University of Maryland. |
|
From: Bob H. <han...@br...> - 2012-03-29 17:24:08
|
Hi, Jaemin, It seems like something is wrong - human chr1 (243Mb) runs for me in about 3 hours, mostly cpu bound. Human chr2 actually takes slightly longer than chr1, so it is possible that there is some run time dependency on repetitiveness. Is horse chr31 very repetitive? If so, then another thing to check for is memory usage (i.e. is your process swapping excessively). The java bindings for bwa will use a big chunk of non-heap virtual memory in addition to the java heap. You can run with a fairly small java heap (I think I use 1Gb), but it will take additional memory approximately the size of the reference genome. To answer your question directly, there is an unadvertised -L argument that takes an interval (e.g. chr1:100-200) that would do what I think you are asking for. You would probably have to concatenate the resulting fasta files together yourself, however. But I would look first to see why your performance seems so slow. -Bob On 3/29/12 4:12 AM, Jaemin Kim wrote: > Hi, > > I'm Jaemin Kim, a graduate student in Seoul National University in Korea. > > I'm trying to extract the CNV of horse genomes and I started with > running Mask Files. > I guess the computation is very heavy; it takes about 2 days to > compute 25Mb chromosome 31. > I see that it is allowed to compute chromosome by chromosome and then > merge later. > > What if I even partition the chromosome region (for instance, by 10Mb) > and then merge later? I know this would change the result of output > Mask files, but do you think this would be significantly different? > > I need to make the computation as fast as possible, and so I need your > advice. > > > Thank you so much for your consideration! > I will be waiting for your reply. > > > Sincerely, > > Jaemin Kim > > > ------------------------------------------------------------------------------ > This SF email is sponsosred by: > Try Windows Azure free for 90 days Click Here > http://p.sf.net/sfu/sfd2d-msazure > > > _______________________________________________ > svtoolkit-help mailing list > svt...@li... > https://lists.sourceforge.net/lists/listinfo/svtoolkit-help |
|
From: Jaemin K. <jm...@sn...> - 2012-03-29 08:13:01
|
.Bold { font-weight: bold; }
.Title { font-weight: bold; font-size: 18px; color: #cc3300; }
.Code { border: #8b4513 1px solid; padding-right: 5px; padding-left: 5px;color: #000066; font-family: 'Courier New' , Monospace;background-color: #ff9933; }
.Bold { font-weight: bold; }
.Title { font-weight: bold; font-size: 18px; color: #cc3300; }
.Code { border: #8b4513 1px solid; padding-right: 5px; padding-left: 5px;color: #000066; font-family: 'Courier New' , Monospace;background-color: #ff9933; }Hi,
I'm Jaemin Kim, a graduate student in Seoul National University in Korea.
I'm trying to extract the CNV of horse genomes and I started with running Mask Files.
I guess the computation is very heavy; it takes about 2 days to compute 25Mb chromosome 31.
I see that it is allowed to compute chromosome by chromosome and then merge later.
What if I even partition the chromosome region (for instance, by 10Mb) and then merge later? I know this would change the result of output Mask files, but do you think this would be significantly different?
I need to make the computation as fast as possible, and so I need your advice.
Thank you so much for your consideration!
I will be waiting for your reply.
Sincerely,
Jaemin Kim |
|
From: Bob H. <han...@br...> - 2012-03-02 19:14:32
|
I am looking into updating to a more recent release of the GATK (not just Queue), but this may not be quick. Just going by the error messages below, it seems possible this could be fixed by changes to the queue scripts. If you make any progress in figuring this out, let me know. -Bob On 3/1/12 12:51 PM, Maroo, Ankit wrote: > Hi, > > I was trying to use this version on our SGE grid setup. The queue.jar which is provided with this tool does not have the patch for SGE grid and if I try to use new version of Queue.jar while keeping everything same it gives error for 4 functions: > > ERROR 12:46:57,784 QGraph - Missing 2 values for function: 'java' '-Xmx4096m' '-Djava.io.tmpdir=/local/projects-isi/ECENT/Merge_25_AshKenazi/genome_strip/temp_dir' '-cp' 'SVToolkit.jar:GenomeAnalysisTK.jar' org.broadinstitute.sv.apps.MergeInsertSizeHistograms '-I' '/local/projects-isi/ECENT/Merge_25_AshKenazi/genome_strip/null/isd/Merge_25_samtools_sorted.reheader.hist.bin' '-O' '/local/projects-isi/ECENT/Merge_25_AshKenazi/genome_strip/isd.hist.bin' > ERROR 12:46:57,784 QGraph - @Argument: jarFile - jar > ERROR 12:46:57,784 QGraph - @Argument: javaMainClass - Main class to run from javaClasspath > ERROR 12:46:57,785 QGraph - Missing 2 values for function: 'java' '-Xmx4096m' '-Djava.io.tmpdir=/local/projects-isi/ECENT/Merge_25_AshKenazi/genome_strip/temp_dir' '-cp' 'SVToolkit.jar:GenomeAnalysisTK.jar' org.broadinstitute.sv.apps.ComputeInsertStatistics '-I' '/local/projects-isi/ECENT/Merge_25_AshKenazi/genome_strip/isd.hist.bin' '-O' '/local/projects-isi/ECENT/Merge_25_AshKenazi/genome_strip/isd.stats.dat' > ERROR 12:46:57,785 QGraph - @Argument: jarFile - jar > ERROR 12:46:57,785 QGraph - @Argument: javaMainClass - Main class to run from javaClasspath > ERROR 12:46:57,787 QGraph - Missing 2 values for function: 'java' '-Xmx4096m' '-Djava.io.tmpdir=/local/projects-isi/ECENT/Merge_25_AshKenazi/genome_strip/temp_dir' '-cp' 'SVToolkit.jar:GenomeAnalysisTK.jar' org.broadinstitute.sv.apps.MergeReadDepthCoverage '-I' '/local/projects-isi/ECENT/Merge_25_AshKenazi/genome_strip/null/depth/Merge_25_samtools_sorted.reheader.depth.txt' '-O' '/local/projects-isi/ECENT/Merge_25_AshKenazi/genome_strip/depth.dat' > ERROR 12:46:57,787 QGraph - @Argument: jarFile - jar > ERROR 12:46:57,787 QGraph - @Argument: javaMainClass - Main class to run from javaClasspath > ERROR 12:46:57,788 QGraph - Missing 2 values for function: 'java' '-Xmx4096m' '-Djava.io.tmpdir=/local/projects-isi/ECENT/Merge_25_AshKenazi/genome_strip/temp_dir' '-cp' 'SVToolkit.jar:GenomeAnalysisTK.jar' org.broadinstitute.sv.apps.MergeReadSpanCoverage '-I' '/local/projects-isi/ECENT/Merge_25_AshKenazi/genome_strip/null/spans/Merge_25_samtools_sorted.reheader.spans.txt' '-O' '/local/projects-isi/ECENT/Merge_25_AshKenazi/genome_strip/spans.dat' > ERROR 12:46:57,788 QGraph - @Argument: jarFile - jar > ERROR 12:46:57,788 QGraph - @Argument: javaMainClass - Main class to run from javaClasspath > INFO 12:46:57,812 QGraph - ------- > INFO 12:46:57,813 QGraph - Pending: 'java' '-Xmx4096m' '-Djava.io.tmpdir=/local/projects-isi/ECENT/Merge_25_AshKenazi/genome_strip/temp_dir' '-cp' 'SVToolkit.jar:GenomeAnalysisTK.jar' org.broadinstitute.sting.gatk.CommandLineGATK '-T' 'ComputeInsertSizeDistributions' '-R' '/local/sequence-isi/reference/GATK/resources/human_g1k_v37.fasta' '-I' '/local/projects-isi/ECENT/Merge_25_AshKenazi/genome_strip/Merge_25_samtools_sorted.reheader.bam' '-O' '/local/projects-isi/ECENT/Merge_25_AshKenazi/genome_strip/null/isd/Merge_25_samtools_sorted.reheader.hist.bin' -createEmpty > > > > The dry run completes without error with previous version of Queue, but the above error comes with new version. Would it be possible for you to look into this and test the program with new version? > > Thank you very much > > Ankit Maroo > Bioinformatics Analyst > Institute for Genome Sciences > University of Maryland. > ------------------------------------------------------------------------------ > Virtualization& Cloud Management Using Capacity Planning > Cloud computing makes use of virtualization - but cloud computing > also focuses on allowing computing to be delivered as a service. > http://www.accelacomm.com/jaw/sfnl/114/51521223/ > _______________________________________________ > svtoolkit-help mailing list > svt...@li... > https://lists.sourceforge.net/lists/listinfo/svtoolkit-help |
|
From: Maroo, A. <AM...@so...> - 2012-03-01 17:51:45
|
Hi, I was trying to use this version on our SGE grid setup. The queue.jar which is provided with this tool does not have the patch for SGE grid and if I try to use new version of Queue.jar while keeping everything same it gives error for 4 functions: ERROR 12:46:57,784 QGraph - Missing 2 values for function: 'java' '-Xmx4096m' '-Djava.io.tmpdir=/local/projects-isi/ECENT/Merge_25_AshKenazi/genome_strip/temp_dir' '-cp' 'SVToolkit.jar:GenomeAnalysisTK.jar' org.broadinstitute.sv.apps.MergeInsertSizeHistograms '-I' '/local/projects-isi/ECENT/Merge_25_AshKenazi/genome_strip/null/isd/Merge_25_samtools_sorted.reheader.hist.bin' '-O' '/local/projects-isi/ECENT/Merge_25_AshKenazi/genome_strip/isd.hist.bin' ERROR 12:46:57,784 QGraph - @Argument: jarFile - jar ERROR 12:46:57,784 QGraph - @Argument: javaMainClass - Main class to run from javaClasspath ERROR 12:46:57,785 QGraph - Missing 2 values for function: 'java' '-Xmx4096m' '-Djava.io.tmpdir=/local/projects-isi/ECENT/Merge_25_AshKenazi/genome_strip/temp_dir' '-cp' 'SVToolkit.jar:GenomeAnalysisTK.jar' org.broadinstitute.sv.apps.ComputeInsertStatistics '-I' '/local/projects-isi/ECENT/Merge_25_AshKenazi/genome_strip/isd.hist.bin' '-O' '/local/projects-isi/ECENT/Merge_25_AshKenazi/genome_strip/isd.stats.dat' ERROR 12:46:57,785 QGraph - @Argument: jarFile - jar ERROR 12:46:57,785 QGraph - @Argument: javaMainClass - Main class to run from javaClasspath ERROR 12:46:57,787 QGraph - Missing 2 values for function: 'java' '-Xmx4096m' '-Djava.io.tmpdir=/local/projects-isi/ECENT/Merge_25_AshKenazi/genome_strip/temp_dir' '-cp' 'SVToolkit.jar:GenomeAnalysisTK.jar' org.broadinstitute.sv.apps.MergeReadDepthCoverage '-I' '/local/projects-isi/ECENT/Merge_25_AshKenazi/genome_strip/null/depth/Merge_25_samtools_sorted.reheader.depth.txt' '-O' '/local/projects-isi/ECENT/Merge_25_AshKenazi/genome_strip/depth.dat' ERROR 12:46:57,787 QGraph - @Argument: jarFile - jar ERROR 12:46:57,787 QGraph - @Argument: javaMainClass - Main class to run from javaClasspath ERROR 12:46:57,788 QGraph - Missing 2 values for function: 'java' '-Xmx4096m' '-Djava.io.tmpdir=/local/projects-isi/ECENT/Merge_25_AshKenazi/genome_strip/temp_dir' '-cp' 'SVToolkit.jar:GenomeAnalysisTK.jar' org.broadinstitute.sv.apps.MergeReadSpanCoverage '-I' '/local/projects-isi/ECENT/Merge_25_AshKenazi/genome_strip/null/spans/Merge_25_samtools_sorted.reheader.spans.txt' '-O' '/local/projects-isi/ECENT/Merge_25_AshKenazi/genome_strip/spans.dat' ERROR 12:46:57,788 QGraph - @Argument: jarFile - jar ERROR 12:46:57,788 QGraph - @Argument: javaMainClass - Main class to run from javaClasspath INFO 12:46:57,812 QGraph - ------- INFO 12:46:57,813 QGraph - Pending: 'java' '-Xmx4096m' '-Djava.io.tmpdir=/local/projects-isi/ECENT/Merge_25_AshKenazi/genome_strip/temp_dir' '-cp' 'SVToolkit.jar:GenomeAnalysisTK.jar' org.broadinstitute.sting.gatk.CommandLineGATK '-T' 'ComputeInsertSizeDistributions' '-R' '/local/sequence-isi/reference/GATK/resources/human_g1k_v37.fasta' '-I' '/local/projects-isi/ECENT/Merge_25_AshKenazi/genome_strip/Merge_25_samtools_sorted.reheader.bam' '-O' '/local/projects-isi/ECENT/Merge_25_AshKenazi/genome_strip/null/isd/Merge_25_samtools_sorted.reheader.hist.bin' -createEmpty The dry run completes without error with previous version of Queue, but the above error comes with new version. Would it be possible for you to look into this and test the program with new version? Thank you very much Ankit Maroo Bioinformatics Analyst Institute for Genome Sciences University of Maryland. |
|
From: Ashish K. <as...@we...> - 2012-02-14 15:45:34
|
Refers to a R package at this location: http://cran.r-project.org/web/packages/coin/index.html You just need to get this package installed in R. Cheers Ashish -----Original Message----- From: Sophia Derdak [mailto:sd...@pc...] Sent: 14 February 2012 14:39 To: svt...@li... Subject: [svtoolkit-help] discovery ERROR: there is no package called 'coin' Dear colleagues, when running the discovery.sh script (adjusted to my folder structure, see attached) from installtest, I get the following output; basically the problem seems to be that there is a package called coin missing. What is this package and where should it be? I am also attaching the log output from this run. SVToolkit version 1.03 (build 619) Build date: 2011/02/12 17:23:22 Web site: http://www.broadinstitute.org/gsa/wiki/index.php/Genome_STRiP INFO 13:52:12,832 QScriptManager - Compiling 2 QScripts INFO 13:52:17,314 QScriptManager - Compilation complete INFO 13:52:19,653 HelpFormatter - --------------------------------------------------------- INFO 13:52:19,653 HelpFormatter - Program Name: org.broadinstitute.sting.queue.QCommandLine INFO 13:52:19,653 HelpFormatter - Program Args: -S /apps/SVTOOLKIT/qscript/SVPreprocess.q -S /apps/SVTOOLKIT/qscript/SVQScript.q -gatk /apps/SVTOOLKIT/lib/gatk/GenomeAnalysisTK.jar -cp /apps/SVTOOLKIT/lib/SVToolkit.jar:/apps/SVTOOLKIT/lib/gatk/GenomeAnalysisTK.jar:/apps/SVTOOLKIT/lib/gatk/Queue.jar -configFile /apps/SVTOOLKIT/installtest/conf/genstrip_installtest_parameters.txt -tempDir /home/production/sderdak/temp -R /apps/SVTOOLKIT/installtest/data/human_b36_chr1.fasta -genomeMaskFile /apps/SVTOOLKIT/installtest/data/human_b36_chr1.mask.fasta -genderMapFile /apps/SVTOOLKIT/installtest/data/installtest_gender.map -runDirectory /home/production/sderdak/svtoolkit_test -md /home/production/sderdak/svtoolkit_test/metadata -jobLogDir /home/production/sderdak/svtoolkit_test/logs -I /apps/SVTOOLKIT/installtest/data/installtest.bam -run INFO 13:52:19,653 HelpFormatter - Date/Time: 2012/02/14 13:52:19 INFO 13:52:19,653 HelpFormatter - --------------------------------------------------------- INFO 13:52:19,654 HelpFormatter - --------------------------------------------------------- INFO 13:52:19,655 QCommandLine - Scripting SVPreprocess INFO 13:52:19,723 QCommandLine - Added 7 functions INFO 13:52:19,723 QGraph - Generating graph. INFO 13:52:19,743 QGraph - Running jobs. INFO 13:52:19,749 QGraph - Deleting intermediate files. INFO 13:52:19,750 QCommandLine - Done INFO 13:52:21,688 QScriptManager - Compiling 2 QScripts INFO 13:52:26,150 QScriptManager - Compilation complete INFO 13:52:28,466 HelpFormatter - --------------------------------------------------------- INFO 13:52:28,466 HelpFormatter - Program Name: org.broadinstitute.sting.queue.QCommandLine INFO 13:52:28,466 HelpFormatter - Program Args: -S /apps/SVTOOLKIT/qscript/SVDiscovery.q -S /apps/SVTOOLKIT/qscript/SVQScript.q -gatk /apps/SVTOOLKIT/lib/gatk/GenomeAnalysisTK.jar -cp /apps/SVTOOLKIT/lib/SVToolkit.jar:/apps/SVTOOLKIT/lib/gatk/GenomeAnalysisTK.jar:/apps/SVTOOLKIT/lib/gatk/Queue.jar -configFile /apps/SVTOOLKIT/installtest/conf/genstrip_installtest_parameters.txt -tempDir /home/production/sderdak/temp -R /apps/SVTOOLKIT/installtest/data/human_b36_chr1.fasta -genomeMaskFile /apps/SVTOOLKIT/installtest/data/human_b36_chr1.mask.fasta -genderMapFile /apps/SVTOOLKIT/installtest/data/installtest_gender.map -runDirectory /home/production/sderdak/svtoolkit_test -md /home/production/sderdak/svtoolkit_test/metadata -jobLogDir /home/production/sderdak/svtoolkit_test/logs -L 1 -minimumSize 100 -maximumSize 1000000 -I /apps/SVTOOLKIT/installtest/data/installtest.bam -O /apps/SVTOOLKIT/installtest/benchmark/test1.discovery.vcf -run INFO 13:52:28,466 HelpFormatter - Date/Time: 2012/02/14 13:52:28 INFO 13:52:28,466 HelpFormatter - --------------------------------------------------------- INFO 13:52:28,466 HelpFormatter - --------------------------------------------------------- INFO 13:52:28,468 QCommandLine - Scripting SVDiscovery INFO 13:52:28,534 QCommandLine - Added 2 functions INFO 13:52:28,534 QGraph - Generating graph. INFO 13:52:28,544 QGraph - Running jobs. WARN 13:52:28,554 IOUtils - Unable to delete /apps/SVTOOLKIT/installtest/benchmark/test1.discovery.vcf INFO 13:52:28,572 ShellJobRunner - Starting: java -Xmx4g -Djava.io.tmpdir=/home/production/sderdak/temp -cp /apps/SVTOOLKIT/lib/SVToolkit.jar:/apps/SVTOOLKIT/lib/gatk/GenomeAnalysisTK.jar:/apps/SVTOOLKIT/lib/gatk/Queue.jar -verbose:gc org.broadinstitute.sv.main.SVDiscovery -T SVDiscovery -R /apps/SVTOOLKIT/installtest/data/human_b36_chr1.fasta -I /apps/SVTOOLKIT/installtest/data/installtest.bam -O /home/production/sderdak/svtoolkit_test/test1.discovery.unfiltered.vcf -md /home/production/sderdak/svtoolkit_test/metadata -disableGATKTraversal -configFile /apps/SVTOOLKIT/installtest/conf/genstrip_installtest_parameters.txt -runDirectory /home/production/sderdak/svtoolkit_test -genderMapFile /apps/SVTOOLKIT/installtest/data/installtest_gender.map -genomeMaskFile /apps/SVTOOLKIT/installtest/data/human_b36_chr1.mask.fasta -L 1 -filePrefix test1 -searchLocus 1 -searchWindow 1 -searchMinimumSize 100 -searchMaximumSize 1000000 INFO 13:52:28,572 ShellJobRunner - Output written to /home/production/sderdak/svtoolkit_test/logs/Q-4407@n8-1.out ERROR 13:52:42,426 ShellJobRunner - Error: java -Xmx4g -Djava.io.tmpdir=/home/production/sderdak/temp -cp /apps/SVTOOLKIT/lib/SVToolkit.jar:/apps/SVTOOLKIT/lib/gatk/GenomeAnalysisTK.jar:/apps/SVTOOLKIT/lib/gatk/Queue.jar -verbose:gc org.broadinstitute.sv.main.SVDiscovery -T SVDiscovery -R /apps/SVTOOLKIT/installtest/data/human_b36_chr1.fasta -I /apps/SVTOOLKIT/installtest/data/installtest.bam -O /home/production/sderdak/svtoolkit_test/test1.discovery.unfiltered.vcf -md /home/production/sderdak/svtoolkit_test/metadata -disableGATKTraversal -configFile /apps/SVTOOLKIT/installtest/conf/genstrip_installtest_parameters.txt -runDirectory /home/production/sderdak/svtoolkit_test -genderMapFile /apps/SVTOOLKIT/installtest/data/installtest_gender.map -genomeMaskFile /apps/SVTOOLKIT/installtest/data/human_b36_chr1.mask.fasta -L 1 -filePrefix test1 -searchLocus 1 -searchWindow 1 -searchMinimumSize 100 -searchMaximumSize 1000000 ERROR 13:52:42,426 ShellJobRunner - [GC 3072K->480K(8896K), 0.0017910 secs] [GC 3552K->827K(11968K), 0.0011520 secs] [GC 6971K->4376K(11968K), 0.0247150 secs] [Full GC 4376K->4374K(18816K), 0.0166730 secs] [GC 10518K->6887K(22784K), 0.0032890 secs] [GC 16999K->12435K(24960K), 0.0076720 secs] [Full GC 12435K->12428K(37440K), 0.0285140 secs] [GC 24447K->12639K(48320K), 0.0205120 secs] [GC 29791K->12895K(48320K), 0.0026380 secs] [GC 30047K->13216K(52736K), 0.0015270 secs] [GC 36448K->13151K(53888K), 0.0012050 secs] [GC 36383K->13391K(56192K), 0.0014730 secs] [GC 40271K->13599K(57024K), 0.0013080 secs] [GC 40479K->13823K(58944K), 0.0018550 secs] [GC 43903K->13999K(59648K), 0.0045090 secs] [GC 44079K->14271K(62144K), 0.0022270 secs] [GC 47743K->14575K(62592K), 0.0047930 secs] [GC 48047K->14720K(66112K), 0.0030170 secs] [GC 51968K->15280K(66304K), 0.0025500 secs] [GC 52528K->15620K(68864K), 0.0027080 secs] [GC 55236K->15712K(69120K), 0.0036740 secs] [GC 55328K->16144K(71808K), 0.0031310 secs] [GC 58192K->16556K(72128K), 0.0031330 secs] [GC 58604K->16888K(75008K), 0.0034090 secs] [GC 61560K->17360K(75264K), 0.0034490 secs] [GC 62032K->17744K(78400K), 0.0033960 secs] [GC 65296K->18164K(78656K), 0.0030270 secs] [GC 65716K->18411K(81152K), 0.0034330 secs] [GC 68203K->18827K(81344K), 0.0028290 secs] [GC 68619K->19341K(83776K), 0.0036700 secs] [GC 71309K->19430K(84032K), 0.0116790 secs] [GC 71398K->19867K(87616K), 0.0073410 secs] INFO 13:52:31,530 HelpFormatter - --------------------------------------------------------------------------- INFO 13:52:31,532 HelpFormatter - The Genome Analysis Toolkit (GATK) v1.0.5039M, Compiled 2011/01/20 22:58:34 INFO 13:52:31,532 HelpFormatter - Copyright (c) 2010 The Broad Institute INFO 13:52:31,532 HelpFormatter - Please view our documentation at http://www.broadinstitute.org/gsa/wiki INFO 13:52:31,532 HelpFormatter - For support, please view our support site at http://getsatisfaction.com/gsa INFO 13:52:31,532 HelpFormatter - Program Args: -T SVDiscovery -R /apps/SVTOOLKIT/installtest/data/human_b36_chr1.fasta -O /home/production/sderdak/svtoolkit_test/test1.discovery.unfiltered.vcf -md /home/production/sderdak/svtoolkit_test/metadata -disableGATKTraversal -configFile /apps/SVTOOLKIT/installtest/conf/genstrip_installtest_parameters.txt -runDirectory /home/production/sderdak/svtoolkit_test -genderMapFile /apps/SVTOOLKIT/installtest/data/installtest_gender.map -genomeMaskFile /apps/SVTOOLKIT/installtest/data/human_b36_chr1.mask.fasta -L 1 -filePrefix test1 -searchLocus 1 -searchWindow 1 -searchMinimumSize 100 -searchMaximumSize 1000000 INFO 13:52:31,532 HelpFormatter - Date/Time: 2012/02/14 13:52:31 INFO 13:52:31,533 HelpFormatter - --------------------------------------------------------------------------- INFO 13:52:31,533 HelpFormatter - --------------------------------------------------------------------------- INFO 13:52:31,549 GenomeAnalysisEngine - Strictness is SILENT INFO 13:52:31,627 SVDiscovery - Initializing SVDiscovery ... INFO 13:52:31,631 SVDiscovery - Opening reference sequence ... INFO 13:52:31,631 SVDiscovery - Opened reference sequence. INFO 13:52:31,631 SVDiscovery - Opening genome mask ... INFO 13:52:31,631 SVDiscovery - Opened genome mask. INFO 13:52:31,631 SVDiscovery - Initializing input data set ... [GC 75291K->23286K(87744K), 0.0053900 secs] INFO 13:52:31,779 SVDiscovery - Initialized data set: 1 file, 900 read groups, 45 samples. INFO 13:52:31,779 SVDiscovery - Opening metadata from /home/production/sderdak/svtoolkit_test/metadata ... INFO 13:52:31,782 SVDiscovery - Opened metadata. INFO 13:52:31,783 SVDiscovery - Initializing discovery algorithm ... INFO 13:52:31,784 SVDiscovery - Loading insert size histograms ... INFO 13:52:31,832 SVDiscovery - Loaded 47 histograms. INFO 13:52:31,927 SVDiscovery - Processing locus: 1:0-0:100-1000000 INFO 13:52:31,927 SVDiscovery - Locus search window: 1:0-0 INFO 13:52:31,927 SVDiscovery - Selecting read pairs ... INFO 13:52:31,928 SVDiscovery - Reading input file /apps/SVTOOLKIT/installtest/data/installtest.bam ... [GC 78710K->30853K(88960K), 0.0225700 secs] [Full GC 30853K->18529K(96064K), 0.0494600 secs] [GC 73825K->18689K(99584K), 0.0120350 secs] [GC 73985K->18849K(103424K), 0.0115620 secs] [GC 77793K->19009K(103488K), 0.0145240 secs] [GC 77953K->19009K(108928K), 0.0152100 secs] [GC 83521K->19105K(108672K), 0.0009450 secs] [GC 83617K->19169K(111296K), 0.0008710 secs] [GC 88225K->19329K(112512K), 0.0007470 secs] [GC 88385K->19361K(113792K), 0.0010330 secs] [GC 91745K->19713K(114944K), 0.0010300 secs] [GC 92097K->19777K(115200K), 0.0012700 secs] [GC 92444K->23278K(116096K), 0.0024210 secs] INFO 13:52:34,179 SVDiscovery - Processing clusters ... [GC 97902K->20577K(116672K), 0.0022160 secs] INFO 13:52:34,276 SVDiscovery - Clustering: Generating clusters for 6 read pairs. INFO 13:52:34,276 SVDiscovery - Clustering: Generating clusters for 2 read pairs. INFO 13:52:34,276 SVDiscovery - Processing cluster 1:61722491-61722556 1:61723000-61723144 LR 6 [GC 97121K->60120K(137472K), 6.3453430 secs] [Full GC 60120K->49911K(161216K), 0.0665450 secs] [GC 126455K->52056K(185216K), 0.0193480 secs] [GC 140376K->52024K(185856K), 0.0169610 secs] [GC 140344K->52056K(194624K), 0.0167830 secs] #DBG: RC Cache fill 1:61712557-61812556 100000 45 7.307225 sec [GC 152600K->51960K(196224K), 0.0151720 secs] Error: Exception processing cluster: Error running script /apps/SVTOOLKIT/R/discovery/compute_ranksum_pvalue.R: Error in compute.ranksum.pvalue.coin(dataFile) : could not find function "wilcox_test" Calls: main -> compute.ranksum.pvalue.coin In addition: Warning message: In library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE, : there is no package called 'coin' Execution halted Cluster: 1:61722491-61722556 1:61723000-61723144 LR 6 INFO 13:52:42,238 GATKRunReport - Aggregating data for run report [GC 58947K->52088K(205888K), 0.0118240 secs] [Full GC 52088K->13053K(205888K), 0.0492310 secs] ##### ERROR ------------------------------------------------------------------------------------------ ##### ERROR stack trace java.lang.RuntimeException: Error running script /apps/SVTOOLKIT/R/discovery/compute_ranksum_pvalue.R: Error in compute.ranksum.pvalue.coin(dataFile) : could not find function "wilcox_test" Calls: main -> compute.ranksum.pvalue.coin In addition: Warning message: In library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE, : there is no package called 'coin' Execution halted at org.broadinstitute.sv.discovery.ClusterDepthModule.computeRankSumPValue(ClusterDepthModule.java:284) at org.broadinstitute.sv.discovery.ClusterDepthModule.computeDepth(ClusterDepthModule.java:195) at org.broadinstitute.sv.discovery.DeletionDiscoveryAlgorithm.processCluster(DeletionDiscoveryAlgorithm.java:395) 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: Error running script /apps/SVTOOLKIT/R/discovery/compute_ranksum_pvalue.R: Error in compute.ranksum.pvalue.coin(dataFile) : ##### ERROR could not find function "wilcox_test" ##### ERROR Calls: main -> compute.ranksum.pvalue.coin ##### ERROR In addition: Warning message: ##### ERROR In library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE, : ##### ERROR there is no package called 'coin' ##### ERROR Execution halted ##### ERROR ------------------------------------------------------------------------------------------ INFO 13:52:42,427 QCommandLine - Done with errors INFO 13:52:42,429 QGraph - ------- INFO 13:52:42,433 QGraph - Failed: java -Xmx4g -Djava.io.tmpdir=/home/production/sderdak/temp -cp /apps/SVTOOLKIT/lib/SVToolkit.jar:/apps/SVTOOLKIT/lib/gatk/GenomeAnalysisTK.jar:/apps/SVTOOLKIT/lib/gatk/Queue.jar -verbose:gc org.broadinstitute.sv.main.SVDiscovery -T SVDiscovery -R /apps/SVTOOLKIT/installtest/data/human_b36_chr1.fasta -I /apps/SVTOOLKIT/installtest/data/installtest.bam -O /home/production/sderdak/svtoolkit_test/test1.discovery.unfiltered.vcf -md /home/production/sderdak/svtoolkit_test/metadata -disableGATKTraversal -configFile /apps/SVTOOLKIT/installtest/conf/genstrip_installtest_parameters.txt -runDirectory /home/production/sderdak/svtoolkit_test -genderMapFile /apps/SVTOOLKIT/installtest/data/installtest_gender.map -genomeMaskFile /apps/SVTOOLKIT/installtest/data/human_b36_chr1.mask.fasta -L 1 -filePrefix test1 -searchLocus 1 -searchWindow 1 -searchMinimumSize 100 -searchMaximumSize 1000000 INFO 13:52:42,433 QGraph - Log: /home/production/sderdak/svtoolkit_test/logs/Q-4407@n8-1.out thanks for any suggestions, cheers, Sophia -- Sophia Derdak, PhD Data Analysis Group National Center for Genomic Analysis (CNAG) Parc Cientific de Barcelona Torre I, 2a planta Baldiri Reixac, 4 08028 Barcelona, SPAIN http://www.cnag.cat Tel: +34 9340 20846 Email: sd...@pc... |
|
From: Sophia D. <sd...@pc...> - 2012-02-14 15:14:57
|
Dear colleagues, when running the discovery.sh script (adjusted to my folder structure, see attached) from installtest, I get the following output; basically the problem seems to be that there is a package called coin missing. What is this package and where should it be? I am also attaching the log output from this run. SVToolkit version 1.03 (build 619) Build date: 2011/02/12 17:23:22 Web site: http://www.broadinstitute.org/gsa/wiki/index.php/Genome_STRiP INFO 13:52:12,832 QScriptManager - Compiling 2 QScripts INFO 13:52:17,314 QScriptManager - Compilation complete INFO 13:52:19,653 HelpFormatter - --------------------------------------------------------- INFO 13:52:19,653 HelpFormatter - Program Name: org.broadinstitute.sting.queue.QCommandLine INFO 13:52:19,653 HelpFormatter - Program Args: -S /apps/SVTOOLKIT/qscript/SVPreprocess.q -S /apps/SVTOOLKIT/qscript/SVQScript.q -gatk /apps/SVTOOLKIT/lib/gatk/GenomeAnalysisTK.jar -cp /apps/SVTOOLKIT/lib/SVToolkit.jar:/apps/SVTOOLKIT/lib/gatk/GenomeAnalysisTK.jar:/apps/SVTOOLKIT/lib/gatk/Queue.jar -configFile /apps/SVTOOLKIT/installtest/conf/genstrip_installtest_parameters.txt -tempDir /home/production/sderdak/temp -R /apps/SVTOOLKIT/installtest/data/human_b36_chr1.fasta -genomeMaskFile /apps/SVTOOLKIT/installtest/data/human_b36_chr1.mask.fasta -genderMapFile /apps/SVTOOLKIT/installtest/data/installtest_gender.map -runDirectory /home/production/sderdak/svtoolkit_test -md /home/production/sderdak/svtoolkit_test/metadata -jobLogDir /home/production/sderdak/svtoolkit_test/logs -I /apps/SVTOOLKIT/installtest/data/installtest.bam -run INFO 13:52:19,653 HelpFormatter - Date/Time: 2012/02/14 13:52:19 INFO 13:52:19,653 HelpFormatter - --------------------------------------------------------- INFO 13:52:19,654 HelpFormatter - --------------------------------------------------------- INFO 13:52:19,655 QCommandLine - Scripting SVPreprocess INFO 13:52:19,723 QCommandLine - Added 7 functions INFO 13:52:19,723 QGraph - Generating graph. INFO 13:52:19,743 QGraph - Running jobs. INFO 13:52:19,749 QGraph - Deleting intermediate files. INFO 13:52:19,750 QCommandLine - Done INFO 13:52:21,688 QScriptManager - Compiling 2 QScripts INFO 13:52:26,150 QScriptManager - Compilation complete INFO 13:52:28,466 HelpFormatter - --------------------------------------------------------- INFO 13:52:28,466 HelpFormatter - Program Name: org.broadinstitute.sting.queue.QCommandLine INFO 13:52:28,466 HelpFormatter - Program Args: -S /apps/SVTOOLKIT/qscript/SVDiscovery.q -S /apps/SVTOOLKIT/qscript/SVQScript.q -gatk /apps/SVTOOLKIT/lib/gatk/GenomeAnalysisTK.jar -cp /apps/SVTOOLKIT/lib/SVToolkit.jar:/apps/SVTOOLKIT/lib/gatk/GenomeAnalysisTK.jar:/apps/SVTOOLKIT/lib/gatk/Queue.jar -configFile /apps/SVTOOLKIT/installtest/conf/genstrip_installtest_parameters.txt -tempDir /home/production/sderdak/temp -R /apps/SVTOOLKIT/installtest/data/human_b36_chr1.fasta -genomeMaskFile /apps/SVTOOLKIT/installtest/data/human_b36_chr1.mask.fasta -genderMapFile /apps/SVTOOLKIT/installtest/data/installtest_gender.map -runDirectory /home/production/sderdak/svtoolkit_test -md /home/production/sderdak/svtoolkit_test/metadata -jobLogDir /home/production/sderdak/svtoolkit_test/logs -L 1 -minimumSize 100 -maximumSize 1000000 -I /apps/SVTOOLKIT/installtest/data/installtest.bam -O /apps/SVTOOLKIT/installtest/benchmark/test1.discovery.vcf -run INFO 13:52:28,466 HelpFormatter - Date/Time: 2012/02/14 13:52:28 INFO 13:52:28,466 HelpFormatter - --------------------------------------------------------- INFO 13:52:28,466 HelpFormatter - --------------------------------------------------------- INFO 13:52:28,468 QCommandLine - Scripting SVDiscovery INFO 13:52:28,534 QCommandLine - Added 2 functions INFO 13:52:28,534 QGraph - Generating graph. INFO 13:52:28,544 QGraph - Running jobs. WARN 13:52:28,554 IOUtils - Unable to delete /apps/SVTOOLKIT/installtest/benchmark/test1.discovery.vcf INFO 13:52:28,572 ShellJobRunner - Starting: java -Xmx4g -Djava.io.tmpdir=/home/production/sderdak/temp -cp /apps/SVTOOLKIT/lib/SVToolkit.jar:/apps/SVTOOLKIT/lib/gatk/GenomeAnalysisTK.jar:/apps/SVTOOLKIT/lib/gatk/Queue.jar -verbose:gc org.broadinstitute.sv.main.SVDiscovery -T SVDiscovery -R /apps/SVTOOLKIT/installtest/data/human_b36_chr1.fasta -I /apps/SVTOOLKIT/installtest/data/installtest.bam -O /home/production/sderdak/svtoolkit_test/test1.discovery.unfiltered.vcf -md /home/production/sderdak/svtoolkit_test/metadata -disableGATKTraversal -configFile /apps/SVTOOLKIT/installtest/conf/genstrip_installtest_parameters.txt -runDirectory /home/production/sderdak/svtoolkit_test -genderMapFile /apps/SVTOOLKIT/installtest/data/installtest_gender.map -genomeMaskFile /apps/SVTOOLKIT/installtest/data/human_b36_chr1.mask.fasta -L 1 -filePrefix test1 -searchLocus 1 -searchWindow 1 -searchMinimumSize 100 -searchMaximumSize 1000000 INFO 13:52:28,572 ShellJobRunner - Output written to /home/production/sderdak/svtoolkit_test/logs/Q-4407@n8-1.out ERROR 13:52:42,426 ShellJobRunner - Error: java -Xmx4g -Djava.io.tmpdir=/home/production/sderdak/temp -cp /apps/SVTOOLKIT/lib/SVToolkit.jar:/apps/SVTOOLKIT/lib/gatk/GenomeAnalysisTK.jar:/apps/SVTOOLKIT/lib/gatk/Queue.jar -verbose:gc org.broadinstitute.sv.main.SVDiscovery -T SVDiscovery -R /apps/SVTOOLKIT/installtest/data/human_b36_chr1.fasta -I /apps/SVTOOLKIT/installtest/data/installtest.bam -O /home/production/sderdak/svtoolkit_test/test1.discovery.unfiltered.vcf -md /home/production/sderdak/svtoolkit_test/metadata -disableGATKTraversal -configFile /apps/SVTOOLKIT/installtest/conf/genstrip_installtest_parameters.txt -runDirectory /home/production/sderdak/svtoolkit_test -genderMapFile /apps/SVTOOLKIT/installtest/data/installtest_gender.map -genomeMaskFile /apps/SVTOOLKIT/installtest/data/human_b36_chr1.mask.fasta -L 1 -filePrefix test1 -searchLocus 1 -searchWindow 1 -searchMinimumSize 100 -searchMaximumSize 1000000 ERROR 13:52:42,426 ShellJobRunner - [GC 3072K->480K(8896K), 0.0017910 secs] [GC 3552K->827K(11968K), 0.0011520 secs] [GC 6971K->4376K(11968K), 0.0247150 secs] [Full GC 4376K->4374K(18816K), 0.0166730 secs] [GC 10518K->6887K(22784K), 0.0032890 secs] [GC 16999K->12435K(24960K), 0.0076720 secs] [Full GC 12435K->12428K(37440K), 0.0285140 secs] [GC 24447K->12639K(48320K), 0.0205120 secs] [GC 29791K->12895K(48320K), 0.0026380 secs] [GC 30047K->13216K(52736K), 0.0015270 secs] [GC 36448K->13151K(53888K), 0.0012050 secs] [GC 36383K->13391K(56192K), 0.0014730 secs] [GC 40271K->13599K(57024K), 0.0013080 secs] [GC 40479K->13823K(58944K), 0.0018550 secs] [GC 43903K->13999K(59648K), 0.0045090 secs] [GC 44079K->14271K(62144K), 0.0022270 secs] [GC 47743K->14575K(62592K), 0.0047930 secs] [GC 48047K->14720K(66112K), 0.0030170 secs] [GC 51968K->15280K(66304K), 0.0025500 secs] [GC 52528K->15620K(68864K), 0.0027080 secs] [GC 55236K->15712K(69120K), 0.0036740 secs] [GC 55328K->16144K(71808K), 0.0031310 secs] [GC 58192K->16556K(72128K), 0.0031330 secs] [GC 58604K->16888K(75008K), 0.0034090 secs] [GC 61560K->17360K(75264K), 0.0034490 secs] [GC 62032K->17744K(78400K), 0.0033960 secs] [GC 65296K->18164K(78656K), 0.0030270 secs] [GC 65716K->18411K(81152K), 0.0034330 secs] [GC 68203K->18827K(81344K), 0.0028290 secs] [GC 68619K->19341K(83776K), 0.0036700 secs] [GC 71309K->19430K(84032K), 0.0116790 secs] [GC 71398K->19867K(87616K), 0.0073410 secs] INFO 13:52:31,530 HelpFormatter - --------------------------------------------------------------------------- INFO 13:52:31,532 HelpFormatter - The Genome Analysis Toolkit (GATK) v1.0.5039M, Compiled 2011/01/20 22:58:34 INFO 13:52:31,532 HelpFormatter - Copyright (c) 2010 The Broad Institute INFO 13:52:31,532 HelpFormatter - Please view our documentation at http://www.broadinstitute.org/gsa/wiki INFO 13:52:31,532 HelpFormatter - For support, please view our support site at http://getsatisfaction.com/gsa INFO 13:52:31,532 HelpFormatter - Program Args: -T SVDiscovery -R /apps/SVTOOLKIT/installtest/data/human_b36_chr1.fasta -O /home/production/sderdak/svtoolkit_test/test1.discovery.unfiltered.vcf -md /home/production/sderdak/svtoolkit_test/metadata -disableGATKTraversal -configFile /apps/SVTOOLKIT/installtest/conf/genstrip_installtest_parameters.txt -runDirectory /home/production/sderdak/svtoolkit_test -genderMapFile /apps/SVTOOLKIT/installtest/data/installtest_gender.map -genomeMaskFile /apps/SVTOOLKIT/installtest/data/human_b36_chr1.mask.fasta -L 1 -filePrefix test1 -searchLocus 1 -searchWindow 1 -searchMinimumSize 100 -searchMaximumSize 1000000 INFO 13:52:31,532 HelpFormatter - Date/Time: 2012/02/14 13:52:31 INFO 13:52:31,533 HelpFormatter - --------------------------------------------------------------------------- INFO 13:52:31,533 HelpFormatter - --------------------------------------------------------------------------- INFO 13:52:31,549 GenomeAnalysisEngine - Strictness is SILENT INFO 13:52:31,627 SVDiscovery - Initializing SVDiscovery ... INFO 13:52:31,631 SVDiscovery - Opening reference sequence ... INFO 13:52:31,631 SVDiscovery - Opened reference sequence. INFO 13:52:31,631 SVDiscovery - Opening genome mask ... INFO 13:52:31,631 SVDiscovery - Opened genome mask. INFO 13:52:31,631 SVDiscovery - Initializing input data set ... [GC 75291K->23286K(87744K), 0.0053900 secs] INFO 13:52:31,779 SVDiscovery - Initialized data set: 1 file, 900 read groups, 45 samples. INFO 13:52:31,779 SVDiscovery - Opening metadata from /home/production/sderdak/svtoolkit_test/metadata ... INFO 13:52:31,782 SVDiscovery - Opened metadata. INFO 13:52:31,783 SVDiscovery - Initializing discovery algorithm ... INFO 13:52:31,784 SVDiscovery - Loading insert size histograms ... INFO 13:52:31,832 SVDiscovery - Loaded 47 histograms. INFO 13:52:31,927 SVDiscovery - Processing locus: 1:0-0:100-1000000 INFO 13:52:31,927 SVDiscovery - Locus search window: 1:0-0 INFO 13:52:31,927 SVDiscovery - Selecting read pairs ... INFO 13:52:31,928 SVDiscovery - Reading input file /apps/SVTOOLKIT/installtest/data/installtest.bam ... [GC 78710K->30853K(88960K), 0.0225700 secs] [Full GC 30853K->18529K(96064K), 0.0494600 secs] [GC 73825K->18689K(99584K), 0.0120350 secs] [GC 73985K->18849K(103424K), 0.0115620 secs] [GC 77793K->19009K(103488K), 0.0145240 secs] [GC 77953K->19009K(108928K), 0.0152100 secs] [GC 83521K->19105K(108672K), 0.0009450 secs] [GC 83617K->19169K(111296K), 0.0008710 secs] [GC 88225K->19329K(112512K), 0.0007470 secs] [GC 88385K->19361K(113792K), 0.0010330 secs] [GC 91745K->19713K(114944K), 0.0010300 secs] [GC 92097K->19777K(115200K), 0.0012700 secs] [GC 92444K->23278K(116096K), 0.0024210 secs] INFO 13:52:34,179 SVDiscovery - Processing clusters ... [GC 97902K->20577K(116672K), 0.0022160 secs] INFO 13:52:34,276 SVDiscovery - Clustering: Generating clusters for 6 read pairs. INFO 13:52:34,276 SVDiscovery - Clustering: Generating clusters for 2 read pairs. INFO 13:52:34,276 SVDiscovery - Processing cluster 1:61722491-61722556 1:61723000-61723144 LR 6 [GC 97121K->60120K(137472K), 6.3453430 secs] [Full GC 60120K->49911K(161216K), 0.0665450 secs] [GC 126455K->52056K(185216K), 0.0193480 secs] [GC 140376K->52024K(185856K), 0.0169610 secs] [GC 140344K->52056K(194624K), 0.0167830 secs] #DBG: RC Cache fill 1:61712557-61812556 100000 45 7.307225 sec [GC 152600K->51960K(196224K), 0.0151720 secs] Error: Exception processing cluster: Error running script /apps/SVTOOLKIT/R/discovery/compute_ranksum_pvalue.R: Error in compute.ranksum.pvalue.coin(dataFile) : could not find function "wilcox_test" Calls: main -> compute.ranksum.pvalue.coin In addition: Warning message: In library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE, : there is no package called 'coin' Execution halted Cluster: 1:61722491-61722556 1:61723000-61723144 LR 6 INFO 13:52:42,238 GATKRunReport - Aggregating data for run report [GC 58947K->52088K(205888K), 0.0118240 secs] [Full GC 52088K->13053K(205888K), 0.0492310 secs] ##### ERROR ------------------------------------------------------------------------------------------ ##### ERROR stack trace java.lang.RuntimeException: Error running script /apps/SVTOOLKIT/R/discovery/compute_ranksum_pvalue.R: Error in compute.ranksum.pvalue.coin(dataFile) : could not find function "wilcox_test" Calls: main -> compute.ranksum.pvalue.coin In addition: Warning message: In library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE, : there is no package called 'coin' Execution halted at org.broadinstitute.sv.discovery.ClusterDepthModule.computeRankSumPValue(ClusterDepthModule.java:284) at org.broadinstitute.sv.discovery.ClusterDepthModule.computeDepth(ClusterDepthModule.java:195) at org.broadinstitute.sv.discovery.DeletionDiscoveryAlgorithm.processCluster(DeletionDiscoveryAlgorithm.java:395) 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: Error running script /apps/SVTOOLKIT/R/discovery/compute_ranksum_pvalue.R: Error in compute.ranksum.pvalue.coin(dataFile) : ##### ERROR could not find function "wilcox_test" ##### ERROR Calls: main -> compute.ranksum.pvalue.coin ##### ERROR In addition: Warning message: ##### ERROR In library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE, : ##### ERROR there is no package called 'coin' ##### ERROR Execution halted ##### ERROR ------------------------------------------------------------------------------------------ INFO 13:52:42,427 QCommandLine - Done with errors INFO 13:52:42,429 QGraph - ------- INFO 13:52:42,433 QGraph - Failed: java -Xmx4g -Djava.io.tmpdir=/home/production/sderdak/temp -cp /apps/SVTOOLKIT/lib/SVToolkit.jar:/apps/SVTOOLKIT/lib/gatk/GenomeAnalysisTK.jar:/apps/SVTOOLKIT/lib/gatk/Queue.jar -verbose:gc org.broadinstitute.sv.main.SVDiscovery -T SVDiscovery -R /apps/SVTOOLKIT/installtest/data/human_b36_chr1.fasta -I /apps/SVTOOLKIT/installtest/data/installtest.bam -O /home/production/sderdak/svtoolkit_test/test1.discovery.unfiltered.vcf -md /home/production/sderdak/svtoolkit_test/metadata -disableGATKTraversal -configFile /apps/SVTOOLKIT/installtest/conf/genstrip_installtest_parameters.txt -runDirectory /home/production/sderdak/svtoolkit_test -genderMapFile /apps/SVTOOLKIT/installtest/data/installtest_gender.map -genomeMaskFile /apps/SVTOOLKIT/installtest/data/human_b36_chr1.mask.fasta -L 1 -filePrefix test1 -searchLocus 1 -searchWindow 1 -searchMinimumSize 100 -searchMaximumSize 1000000 INFO 13:52:42,433 QGraph - Log: /home/production/sderdak/svtoolkit_test/logs/Q-4407@n8-1.out thanks for any suggestions, cheers, Sophia -- Sophia Derdak, PhD Data Analysis Group National Center for Genomic Analysis (CNAG) Parc Cientific de Barcelona Torre I, 2a planta Baldiri Reixac, 4 08028 Barcelona, SPAIN http://www.cnag.cat Tel: +34 9340 20846 Email: sd...@pc... |
|
From: Ashish K. <as...@we...> - 2012-02-13 13:48:39
|
Hi Bob, That's great. And if memory becomes an issue, I could always increase the max heap size. Thanks, Ashish. -----Original Message----- From: Bob Handsaker [mailto:han...@br...] Sent: 12 February 2012 21:54 To: svt...@li... Subject: Re: [svtoolkit-help] SVtoolkit Error: Exception processing cluster: Permitted to write any record upstream of position... Hi, Ashish, As a workaround, you can use the -vcfCachingDistance argument to SVDiscovery. The default (since build 683) is 10000, but you can try increasing this to 20000. The minimum amount you need to increase by is the difference between the two positions in the error message. Larger values will increase the memory footprint by holding more data in memory before writing to the VCF file. -Bob On 2/12/12 6:56 AM, Ashish Kumar wrote: > Hi Bob, > > I've got a similar error on the latest release version: > SVToolkit version 1.04 (build 840) > Build date: 2012/01/20 13:17:44 > > Following is the error stack: > > ##### ERROR > ---------------------------------------------------------------------- > -------------------- > ##### ERROR stack trace > java.lang.IllegalArgumentException: Permitted to write any record upstream of position 10804760, but a record at 21:10803683 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$VCFWriterAdapter.add(VCFWriterFactory.java:76) > at org.broadinstitute.sv.discovery.DeletionDiscoveryAlgorithm.writeVCFRecord(DeletionDiscoveryAlgorithm.java:646) > at org.broadinstitute.sv.discovery.DeletionDiscoveryAlgorithm.processCluster(DeletionDiscoveryAlgorithm.java:444) > at org.broadinstitute.sv.discovery.DeletionDiscoveryAlgorithm.processClusters(DeletionDiscoveryAlgorithm.java:342) > at org.broadinstitute.sv.discovery.DeletionDiscoveryAlgorithm.runDiscovery(DeletionDiscoveryAlgorithm.java:191) > at org.broadinstitute.sv.discovery.SVDiscoveryWalker.onTraversalDone(SVDiscoveryWalker.java:168) > at org.broadinstitute.sv.discovery.SVDiscoveryWalker.onTraversalDone(SVDiscoveryWalker.java:45) > at org.broadinstitute.sting.gatk.executive.Accumulator$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 10804760, but a record at 21:10803683 was just added. > ##### ERROR > ---------------------------------------------------------------------- > -------------------- > > Let me know if you would need any additional information. > > Thanks, > Ashish > > > -----Original Message----- > From: Bob Handsaker [mailto:han...@br...] > Sent: 21 November 2011 17:25 > To: svt...@li... > Subject: Re: [svtoolkit-help] SVtoolkit Error: Exception processing cluster: Permitted to write any record upstream of position... > > 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 > > ---------------------------------------------------------------------- > -------- 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 > > ---------------------------------------------------------------------- > -------- Virtualization& Cloud Management Using Capacity Planning > Cloud computing makes use of virtualization - but cloud computing also > focuses on allowing computing to be delivered as a service. > http://www.accelacomm.com/jaw/sfnl/114/51521223/ > _______________________________________________ > svtoolkit-help mailing list > svt...@li... > https://lists.sourceforge.net/lists/listinfo/svtoolkit-help ------------------------------------------------------------------------------ Virtualization & Cloud Management Using Capacity Planning Cloud computing makes use of virtualization - but cloud computing also focuses on allowing computing to be delivered as a service. http://www.accelacomm.com/jaw/sfnl/114/51521223/ _______________________________________________ svtoolkit-help mailing list svt...@li... https://lists.sourceforge.net/lists/listinfo/svtoolkit-help |
|
From: Bob H. <han...@br...> - 2012-02-12 21:54:05
|
Hi, Ashish, As a workaround, you can use the -vcfCachingDistance argument to SVDiscovery. The default (since build 683) is 10000, but you can try increasing this to 20000. The minimum amount you need to increase by is the difference between the two positions in the error message. Larger values will increase the memory footprint by holding more data in memory before writing to the VCF file. -Bob On 2/12/12 6:56 AM, Ashish Kumar wrote: > Hi Bob, > > I've got a similar error on the latest release version: > SVToolkit version 1.04 (build 840) > Build date: 2012/01/20 13:17:44 > > Following is the error stack: > > ##### ERROR ------------------------------------------------------------------------------------------ > ##### ERROR stack trace > java.lang.IllegalArgumentException: Permitted to write any record upstream of position 10804760, but a record at 21:10803683 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:646) > at org.broadinstitute.sv.discovery.DeletionDiscoveryAlgorithm.processCluster(DeletionDiscoveryAlgorithm.java:444) > at org.broadinstitute.sv.discovery.DeletionDiscoveryAlgorithm.processClusters(DeletionDiscoveryAlgorithm.java:342) > at org.broadinstitute.sv.discovery.DeletionDiscoveryAlgorithm.runDiscovery(DeletionDiscoveryAlgorithm.java:191) > at org.broadinstitute.sv.discovery.SVDiscoveryWalker.onTraversalDone(SVDiscoveryWalker.java:168) > 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 10804760, but a record at 21:10803683 was just added. > ##### ERROR ------------------------------------------------------------------------------------------ > > Let me know if you would need any additional information. > > Thanks, > Ashish > > > -----Original Message----- > From: Bob Handsaker [mailto:han...@br...] > Sent: 21 November 2011 17:25 > To: svt...@li... > Subject: Re: [svtoolkit-help] SVtoolkit Error: Exception processing cluster: Permitted to write any record upstream of position... > > 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 > > ------------------------------------------------------------------------------ > 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 > > ------------------------------------------------------------------------------ > Virtualization& Cloud Management Using Capacity Planning > Cloud computing makes use of virtualization - but cloud computing > also focuses on allowing computing to be delivered as a service. > http://www.accelacomm.com/jaw/sfnl/114/51521223/ > _______________________________________________ > svtoolkit-help mailing list > svt...@li... > https://lists.sourceforge.net/lists/listinfo/svtoolkit-help |
|
From: Ashish K. <as...@we...> - 2012-02-12 11:56:39
|
Hi Bob, I've got a similar error on the latest release version: SVToolkit version 1.04 (build 840) Build date: 2012/01/20 13:17:44 Following is the error stack: ##### ERROR ------------------------------------------------------------------------------------------ ##### ERROR stack trace java.lang.IllegalArgumentException: Permitted to write any record upstream of position 10804760, but a record at 21:10803683 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$VCFWriterAdapter.add(VCFWriterFactory.java:76) at org.broadinstitute.sv.discovery.DeletionDiscoveryAlgorithm.writeVCFRecord(DeletionDiscoveryAlgorithm.java:646) at org.broadinstitute.sv.discovery.DeletionDiscoveryAlgorithm.processCluster(DeletionDiscoveryAlgorithm.java:444) at org.broadinstitute.sv.discovery.DeletionDiscoveryAlgorithm.processClusters(DeletionDiscoveryAlgorithm.java:342) at org.broadinstitute.sv.discovery.DeletionDiscoveryAlgorithm.runDiscovery(DeletionDiscoveryAlgorithm.java:191) at org.broadinstitute.sv.discovery.SVDiscoveryWalker.onTraversalDone(SVDiscoveryWalker.java:168) at org.broadinstitute.sv.discovery.SVDiscoveryWalker.onTraversalDone(SVDiscoveryWalker.java:45) at org.broadinstitute.sting.gatk.executive.Accumulator$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 10804760, but a record at 21:10803683 was just added. ##### ERROR ------------------------------------------------------------------------------------------ Let me know if you would need any additional information. Thanks, Ashish -----Original Message----- From: Bob Handsaker [mailto:han...@br...] Sent: 21 November 2011 17:25 To: svt...@li... Subject: Re: [svtoolkit-help] SVtoolkit Error: Exception processing cluster: Permitted to write any record upstream of position... 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 ------------------------------------------------------------------------------ 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: Bob H. <han...@br...> - 2012-01-31 16:38:19
|
It's unlikely that there's some internal processing error in Genome STRiP that will cause it to terminate without some error messages (like a java exception report). I would suspect that either (a) the error output is getting lost somewhere or (b) the job has been killed externally, if you are running in lsf this might be due to exceeding a resource or runtime limit. When I see jobs killed due to resource limits on our cluster, I often end up with a core file and hs_err_*.log file and lsf reports the reason for termination, which may be in a separate log file. Hope this helps, -Bob On 1/31/12 11:05 AM, Verena Tischler wrote: > Hi, > > running GenomeSTRiP, I run into the problem, that the SVDiscovery step > does not work for one chromosome without giving a particularly helpful > error message. > The error is independant from using the released GenomeSTRiP version > or the interim version. > > Here is what I get: > <lots of similar lines here> > #DBG: RC Cache miss chr7.fa:103685075-104038844 353770 5 > 31.443630 sec > INFO 03:53:01,710 SVDiscovery - Clustering: Generating clusters for > 285 read pairs. > INFO 03:53:01,727 SVDiscovery - Clustering: LR split size 285 / 285 > maximal clique size 228 clique count 1 > INFO 03:53:01,728 SVDiscovery - Clustering: LR split size 57 / 285 > maximal clique size 22 clique count 1 > INFO 03:53:01,728 SVDiscovery - Clustering: LR split size 35 / 285 > maximal clique size 17 clique count 1 > INFO 03:53:01,728 SVDiscovery - Clustering: LR split size 18 / 285 > maximal clique size 9 clique count 1 > INFO 03:53:01,728 SVDiscovery - Clustering: LR split size 9 / 285 > maximal clique size 6 clique count 1 > INFO 03:53:01,728 SVDiscovery - Clustering: LR split size 3 / 285 > maximal clique size 2 clique count 1 > INFO 03:53:01,728 SVDiscovery - Processing cluster > chr7.fa:103684956-103685204 chr7.fa:104017134-104017254 LR 2 > [GC 1468359K->72359K(1776128K), 0 > > <truncated> > INFO 13:54:06,102 QCommandLine - Done with errors > INFO 13:54:06,113 QGraph - ------- > INFO 13:54:06,126 QGraph - Failed: > > The chromosome is far longer than the point where GS breaks and there > are also no obvious genomic annotations that might cause trouble > > Any ideas what the problem might be? > > Thanks a lot in advance for your help > Verena > > > > ------------------------------------------------------------------------------ > Keep Your Developer Skills Current with LearnDevNow! > The most comprehensive online learning library for Microsoft developers > is just $99.99! Visual Studio, SharePoint, SQL - plus HTML5, CSS3, MVC3, > Metro Style Apps, more. Free future releases when you subscribe now! > http://p.sf.net/sfu/learndevnow-d2d > > > _______________________________________________ > svtoolkit-help mailing list > svt...@li... > https://lists.sourceforge.net/lists/listinfo/svtoolkit-help |
|
From: Verena T. <tis...@go...> - 2012-01-31 16:05:50
|
Hi, running GenomeSTRiP, I run into the problem, that the SVDiscovery step does not work for one chromosome without giving a particularly helpful error message. The error is independant from using the released GenomeSTRiP version or the interim version. Here is what I get: <lots of similar lines here> #DBG: RC Cache miss chr7.fa:103685075-104038844 353770 5 31.443630 sec INFO 03:53:01,710 SVDiscovery - Clustering: Generating clusters for 285 read pairs. INFO 03:53:01,727 SVDiscovery - Clustering: LR split size 285 / 285 maximal clique size 228 clique count 1 INFO 03:53:01,728 SVDiscovery - Clustering: LR split size 57 / 285 maximal clique size 22 clique count 1 INFO 03:53:01,728 SVDiscovery - Clustering: LR split size 35 / 285 maximal clique size 17 clique count 1 INFO 03:53:01,728 SVDiscovery - Clustering: LR split size 18 / 285 maximal clique size 9 clique count 1 INFO 03:53:01,728 SVDiscovery - Clustering: LR split size 9 / 285 maximal clique size 6 clique count 1 INFO 03:53:01,728 SVDiscovery - Clustering: LR split size 3 / 285 maximal clique size 2 clique count 1 INFO 03:53:01,728 SVDiscovery - Processing cluster chr7.fa:103684956-103685204 chr7.fa:104017134-104017254 LR 2 [GC 1468359K->72359K(1776128K), 0 <truncated> INFO 13:54:06,102 QCommandLine - Done with errors INFO 13:54:06,113 QGraph - ------- INFO 13:54:06,126 QGraph - Failed: The chromosome is far longer than the point where GS breaks and there are also no obvious genomic annotations that might cause trouble Any ideas what the problem might be? Thanks a lot in advance for your help Verena |
|
From: Boel B. <bry...@gm...> - 2012-01-31 14:24:08
|
This question has already been answered using my other registered email. Thanks. Den 30 januari 2012 12:05 skrev Boel Brynedal <bry...@br...>: > Hi, > > Very glad to find out that your program is out and ready to be used, exactly what I was looking for. > > When running the discovery.sh test I get the message that: "Error: test results do not match benchmark data". > I quick look revealed that only one result file was produced (test1.discovery.vcf) while the other one (test1.genotypes.vcf) is missing. Did something go wrong, or should only one file be produced? > > Output fr discovery.sh: > $ ./discovery.sh > SVToolkit version 1.03 (build 619) > Build date: 2011/02/12 17:23:22 > Web site: http://www.broadinstitute.org/gsa/wiki/index.php/Genome_STRiP > INFO 11:37:59,050 QScriptManager - Compiling 2 QScripts > INFO 11:38:05,021 QScriptManager - Compilation complete > INFO 11:38:10,911 HelpFormatter - --------------------------------------------------------- > INFO 11:38:10,911 HelpFormatter - Program Name: org.broadinstitute.sting.queue.QCommandLine > INFO 11:38:10,912 HelpFormatter - Program Args: -S /scratch/bb447/svtoolkit/qscript/SVPreprocess.q -S /scratch/bb447/svtoolkit/qscript/SVQScript.q -gatk /scratch/bb447/svtoolkit/lib/gatk/GenomeAnalysisTK.jar -cp /scratch/bb447/svtoolkit/lib/SVToolkit.jar:/scratch/bb447/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/scratch/bb447/svtoolkit/lib/gatk/Queue.jar -configFile conf/genstrip_installtest_parameters.txt -tempDir ./tmpdir -R data/human_b36_chr1.fasta -genomeMaskFile data/human_b36_chr1.mask.fasta -genderMapFile data/installtest_gender.map -runDirectory test1 -md test1/metadata -jobLogDir test1/logs -I data/installtest.bam -run > INFO 11:38:10,912 HelpFormatter - Date/Time: 2012/01/30 11:38:10 > INFO 11:38:10,912 HelpFormatter - --------------------------------------------------------- > INFO 11:38:10,912 HelpFormatter - --------------------------------------------------------- > INFO 11:38:10,913 QCommandLine - Scripting SVPreprocess > INFO 11:38:11,049 QCommandLine - Added 7 functions > INFO 11:38:11,049 QGraph - Generating graph. > INFO 11:38:11,073 QGraph - Running jobs. > INFO 11:38:11,080 QGraph - Deleting intermediate files. > INFO 11:38:11,081 QCommandLine - Done > INFO 11:38:13,403 QScriptManager - Compiling 2 QScripts > INFO 11:38:18,509 QScriptManager - Compilation complete > INFO 11:38:21,037 HelpFormatter - --------------------------------------------------------- > INFO 11:38:21,037 HelpFormatter - Program Name: org.broadinstitute.sting.queue.QCommandLine > INFO 11:38:21,037 HelpFormatter - Program Args: -S /scratch/bb447/svtoolkit/qscript/SVDiscovery.q -S /scratch/bb447/svtoolkit/qscript/SVQScript.q -gatk /scratch/bb447/svtoolkit/lib/gatk/GenomeAnalysisTK.jar -cp /scratch/bb447/svtoolkit/lib/SVToolkit.jar:/scratch/bb447/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/scratch/bb447/svtoolkit/lib/gatk/Queue.jar -configFile conf/genstrip_installtest_parameters.txt -tempDir ./tmpdir -R data/human_b36_chr1.fasta -genomeMaskFile data/human_b36_chr1.mask.fasta -genderMapFile data/installtest_gender.map -runDirectory test1 -md test1/metadata -jobLogDir test1/logs -L 1 -minimumSize 100 -maximumSize 1000000 -I data/installtest.bam -O test1.discovery.vcf -run > INFO 11:38:21,038 HelpFormatter - Date/Time: 2012/01/30 11:38:21 > INFO 11:38:21,038 HelpFormatter - --------------------------------------------------------- > INFO 11:38:21,038 HelpFormatter - --------------------------------------------------------- > INFO 11:38:21,039 QCommandLine - Scripting SVDiscovery > INFO 11:38:21,183 QCommandLine - Added 2 functions > INFO 11:38:21,184 QGraph - Generating graph. > INFO 11:38:21,196 QGraph - Running jobs. > INFO 11:38:21,250 ShellJobRunner - Starting: java -Xmx4g -Djava.io.tmpdir=/net/scratch/bb447/svtoolkit/installtest/tmpdir -cp /scratch/bb447/svtoolkit/lib/SVToolkit.jar:/scratch/bb447/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/scratch/bb447/svtoolkit/lib/gatk/Queue.jar -verbose:gc org.broadinstitute.sv.main.SVDiscovery -T SVDiscovery -R /net/scratch/bb447/svtoolkit/installtest/data/human_b36_chr1.fasta -I /net/scratch/bb447/svtoolkit/installtest/data/installtest.bam -O /net/scratch/bb447/svtoolkit/installtest/test1/test1.discovery.unfiltered.vcf -md test1/metadata -disableGATKTraversal -configFile conf/genstrip_installtest_parameters.txt -runDirectory test1 -genderMapFile data/installtest_gender.map -genomeMaskFile data/human_b36_chr1.mask.fasta -L 1 -filePrefix test1 -searchLocus 1 -searchWindow 1 -searchMinimumSize 100 -searchMaximumSize 1000000 > INFO 11:38:21,250 ShellJobRunner - Output written to /net/scratch/bb447/svtoolkit/installtest/test1/logs/Q-2973@compute-26-8-1.out > INFO 11:38:48,558 ShellJobRunner - Done: java -Xmx4g -Djava.io.tmpdir=/net/scratch/bb447/svtoolkit/installtest/tmpdir -cp /scratch/bb447/svtoolkit/lib/SVToolkit.jar:/scratch/bb447/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/scratch/bb447/svtoolkit/lib/gatk/Queue.jar -verbose:gc org.broadinstitute.sv.main.SVDiscovery -T SVDiscovery -R /net/scratch/bb447/svtoolkit/installtest/data/human_b36_chr1.fasta -I /net/scratch/bb447/svtoolkit/installtest/data/installtest.bam -O /net/scratch/bb447/svtoolkit/installtest/test1/test1.discovery.unfiltered.vcf -md test1/metadata -disableGATKTraversal -configFile conf/genstrip_installtest_parameters.txt -runDirectory test1 -genderMapFile data/installtest_gender.map -genomeMaskFile data/human_b36_chr1.mask.fasta -L 1 -filePrefix test1 -searchLocus 1 -searchWindow 1 -searchMinimumSize 100 -searchMaximumSize 1000000 > INFO 11:38:48,562 ShellJobRunner - Starting: java -Xmx4g -Djava.io.tmpdir=/net/scratch/bb447/svtoolkit/installtest/tmpdir -jar /scratch/bb447/svtoolkit/lib/gatk/GenomeAnalysisTK.jar -T VariantFiltration -B:variant,VCF test1/test1.discovery.unfiltered.vcf -o test1.discovery.vcf -R data/human_b36_chr1.fasta -filterName COVERAGE -filter "GSDEPTHCALLTHRESHOLD == \"NA\" || GSDEPTHCALLTHRESHOLD >= 1.0" -filterName COHERENCE -filter "GSCOHPVALUE == \"NA\" || GSCOHPVALUE <= 0.01" -filterName DEPTHPVAL -filter "GSDEPTHPVALUE == \"NA\" || GSDEPTHPVALUE >= 0.01" -filterName DEPTH -filter "GSDEPTHRATIO == \"NA\" || GSDEPTHRATIO > 0.8 || (GSDEPTHRATIO > 0.63 && (GSMEMBPVALUE == \"NA\" || GSMEMBPVALUE >= 0.01))" > INFO 11:38:48,562 ShellJobRunner - Output written to /net/scratch/bb447/svtoolkit/installtest/test1/logs/Q-2973@compute-26-8-2.out > INFO 11:38:54,842 ShellJobRunner - Done: java -Xmx4g -Djava.io.tmpdir=/net/scratch/bb447/svtoolkit/installtest/tmpdir -jar /scratch/bb447/svtoolkit/lib/gatk/GenomeAnalysisTK.jar -T VariantFiltration -B:variant,VCF test1/test1.discovery.unfiltered.vcf -o test1.discovery.vcf -R data/human_b36_chr1.fasta -filterName COVERAGE -filter "GSDEPTHCALLTHRESHOLD == \"NA\" || GSDEPTHCALLTHRESHOLD >= 1.0" -filterName COHERENCE -filter "GSCOHPVALUE == \"NA\" || GSCOHPVALUE <= 0.01" -filterName DEPTHPVAL -filter "GSDEPTHPVALUE == \"NA\" || GSDEPTHPVALUE >= 0.01" -filterName DEPTH -filter "GSDEPTHRATIO == \"NA\" || GSDEPTHRATIO > 0.8 || (GSDEPTHRATIO > 0.63 && (GSMEMBPVALUE == \"NA\" || GSMEMBPVALUE >= 0.01))" > INFO 11:38:54,843 QGraph - Deleting intermediate files. > INFO 11:38:54,844 QCommandLine - Done > Files - and benchmark/test1.discovery.vcf differ > Error: test results do not match benchmark data > > Please let me know if there is any more information that might be helpful. > Thanks, > Boel > > --~*~**~***~*~***~**~*~-- > Boel Brynedal, PhD. > Post Doctoral Associate > Department of Neurology & Department of Genetics, > Yale Medical School, New Haven, CT. > Medical and Population Genetics, The Broad Institute, Cambridge, MA. > > > > ------------------------------------------------------------------------------ > Keep Your Developer Skills Current with LearnDevNow! > The most comprehensive online learning library for Microsoft developers > is just $99.99! Visual Studio, SharePoint, SQL - plus HTML5, CSS3, MVC3, > Metro Style Apps, more. Free future releases when you subscribe now! > http://p.sf.net/sfu/learndevnow-d2d > _______________________________________________ > svtoolkit-help mailing list > svt...@li... > https://lists.sourceforge.net/lists/listinfo/svtoolkit-help |
|
From: Bob H. <han...@br...> - 2012-01-30 19:33:33
|
Hi, Boel, This is a problem that I think was reported once before (or I ran into it). Ideally, I should be rounding off these values and then the comparisons should pass. You can safely comment out the line in the script that does the diff and carry on. -Bob On 1/30/12 1:43 PM, Boel Brynedal wrote: > Hi, > > Updated to the latest interim version, but get the same error message. > Turns out the only difference is the GSCOHERENCE value > (-3.162711280554605 vs -3.1627112805546047) and the GSCOHFN value > (-0.5271185467591009 vs -0.5271185467591007), see the two rows below. > Might this be an issue? > The file "test1.genotypes.vcf" is not created at all, if it was suppose to. > > Thanks! > Boel > > 1 61722559 DEL_1 T <DEL> . DEPTH;DEPTHPVAL CIEND=-8,8;CIPOS=-8,8;END=61722981;GSCOHERENCE=-3.162711280554605;GSCOHFN=-0.5271185467591009;GSCOHPVALUE=0.901;GSCOORDS=61722491,61722556,61723000,61723144;GSDEPTHCALLTHRESHOLD=0.9600579875024452;GSDEPTHNOBSSAMPLES=5;GSDEPTHNTOTALSAMPLES=5;GSDEPTHOBSSAMPLES=NA07051,NA11830,NA11920,NA12003,NA12249;GSDEPTHPVALUE=0.035631;GSDEPTHPVALUECOUNTS=74,35512,511,321039;GSDEPTHRANKSUMPVALUE=0.9802336;GSDEPTHRATIO=1.3091622731975827;GSDMAX=543;GSDMIN=1;GSDOPT=420;GSDSPAN=443;GSMEMBNPAIRS=6;GSMEMBNSAMPLES=5;GSMEMBOBSSAMPLES=NA07051,NA12249,NA11920,NA12003,NA11830;GSMEMBPVALUE=0.4945;GSMEMBSTATISTIC=40.43627779276575;GSNDEPTHCALLS=39;GSNPAIRS=6;GSNSAMPLES=5;GSOUTLEFT=0;GSOUTLIERS=0;GSOUTRIGHT=0;GSREADGROUPS=ERR000550,ERR000567,SRR003115,SRR003135,SRR006095,SRR006165;GSREADNAMES=EAS139_44:6:82:100:15931,EAS139_47:7:5:530:8011,SRR003115.6626735,SRR003135.5278653,SRR006095.2235470,SRR006165.7774794;GSSAMPLES=NA07051,NA12249,NA11920,NA12003,NA11830,NA07051;IMPRECISE;SVLEN=-420;SVTYPE=DEL > > 1 61722559 DEL_1 T <DEL> . DEPTH;DEPTHPVAL CIEND=-8,8;CIPOS=-8,8;END=61722981;GSCOHERENCE=-3.1627112805546047;GSCOHFN=-0.5271185467591007;GSCOHPVALUE=0.901;GSCOORDS=61722491,61722556,61723000,61723144;GSDEPTHCALLTHRESHOLD=0.9600579875024452;GSDEPTHNOBSSAMPLES=5;GSDEPTHNTOTALSAMPLES=5;GSDEPTHOBSSAMPLES=NA07051,NA11830,NA11920,NA12003,NA12249;GSDEPTHPVALUE=0.035631;GSDEPTHPVALUECOUNTS=74,35512,511,321039;GSDEPTHRANKSUMPVALUE=0.9802336;GSDEPTHRATIO=1.3091622731975827;GSDMAX=543;GSDMIN=1;GSDOPT=420;GSDSPAN=443;GSMEMBNPAIRS=6;GSMEMBNSAMPLES=5;GSMEMBOBSSAMPLES=NA07051,NA12249,NA11920,NA12003,NA11830;GSMEMBPVALUE=0.4945;GSMEMBSTATISTIC=40.43627779276575;GSNDEPTHCALLS=39;GSNPAIRS=6;GSNSAMPLES=5;GSOUTLEFT=0;GSOUTLIERS=0;GSOUTRIGHT=0;GSREADGROUPS=ERR000550,ERR000567,SRR003115,SRR003135,SRR006095,SRR006165;GSREADNAMES=EAS139_44:6:82:100:15931,EAS139_47:7:5:530:8011,SRR003115.6626735,SRR003135.5278653,SRR006095.2235470,SRR006165.7774794;GSSAMPLES=NA07051,NA12249,NA11920,NA12003,NA11830,NA07051;IMPRECISE;SVLEN=-420;SVTYPE=DEL > > > Den 30 januari 2012 12:18 skrev Bob Handsaker<han...@br...>: >> Hi, Boel, >> I would encourage you to try using the latest interim release. >> These are updates that are missing documentation for some new features >> and occasional incompatibilities, but people have generally been able to >> use them successfully. >> The interim releases are available at >> ftp://ftp.broadinstitute.org/pub/svtoolkit/releases/interim/. >> What would be helpful to diagnose the problem is a manual diff of >> test1.discovery.vcf and benchmark/test1.discovery.vcf. >> There are a couple of lines (like ##fileDate) that are not expected to >> match, but other mismatches are likely indicating a problem. >> -Bob >> >> On 1/30/12 12:08 PM, Boel Brynedal wrote: >>> Hi, >>> >>> Very glad to find out that your program is out and ready to be used, >>> exactly what I was looking for. >>> >>> When running the discovery.sh test I get the message that: "Error: >>> test results do not match benchmark data". >>> I quick look revealed that only one result file was produced >>> (test1.discovery.vcf) while the other one (test1.genotypes.vcf) is >>> missing. Did something go wrong, or should only one file be produced? >>> >>> Output fr discovery.sh: >>> $ ./discovery.sh >>> SVToolkit version 1.03 (build 619) >>> Build date: 2011/02/12 17:23:22 >>> Web site: http://www.broadinstitute.org/gsa/wiki/index.php/Genome_STRiP >>> INFO 11:37:59,050 QScriptManager - Compiling 2 QScripts >>> INFO 11:38:05,021 QScriptManager - Compilation complete >>> INFO 11:38:10,911 HelpFormatter - >>> --------------------------------------------------------- >>> INFO 11:38:10,911 HelpFormatter - Program Name: >>> org.broadinstitute.sting.queue.QCommandLine >>> INFO 11:38:10,912 HelpFormatter - Program Args: -S >>> /scratch/bb447/svtoolkit/qscript/SVPreprocess.q -S >>> /scratch/bb447/svtoolkit/qscript/SVQScript.q -gatk >>> /scratch/bb447/svtoolkit/lib/gatk/GenomeAnalysisTK.jar -cp >>> /scratch/bb447/svtoolkit/lib/SVToolkit.jar:/scratch/bb447/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/scratch/bb447/svtoolkit/lib/gatk/Queue.jar >>> -configFile conf/genstrip_installtest_parameters.txt -tempDir ./tmpdir >>> -R data/human_b36_chr1.fasta -genomeMaskFile >>> data/human_b36_chr1.mask.fasta -genderMapFile >>> data/installtest_gender.map -runDirectory test1 -md test1/metadata >>> -jobLogDir test1/logs -I data/installtest.bam -run >>> INFO 11:38:10,912 HelpFormatter - Date/Time: 2012/01/30 11:38:10 >>> INFO 11:38:10,912 HelpFormatter - >>> --------------------------------------------------------- >>> INFO 11:38:10,912 HelpFormatter - >>> --------------------------------------------------------- >>> INFO 11:38:10,913 QCommandLine - Scripting SVPreprocess >>> INFO 11:38:11,049 QCommandLine - Added 7 functions >>> INFO 11:38:11,049 QGraph - Generating graph. >>> INFO 11:38:11,073 QGraph - Running jobs. >>> INFO 11:38:11,080 QGraph - Deleting intermediate files. >>> INFO 11:38:11,081 QCommandLine - Done >>> INFO 11:38:13,403 QScriptManager - Compiling 2 QScripts >>> INFO 11:38:18,509 QScriptManager - Compilation complete >>> INFO 11:38:21,037 HelpFormatter - >>> --------------------------------------------------------- >>> INFO 11:38:21,037 HelpFormatter - Program Name: >>> org.broadinstitute.sting.queue.QCommandLine >>> INFO 11:38:21,037 HelpFormatter - Program Args: -S >>> /scratch/bb447/svtoolkit/qscript/SVDiscovery.q -S >>> /scratch/bb447/svtoolkit/qscript/SVQScript.q -gatk >>> /scratch/bb447/svtoolkit/lib/gatk/GenomeAnalysisTK.jar -cp >>> /scratch/bb447/svtoolkit/lib/SVToolkit.jar:/scratch/bb447/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/scratch/bb447/svtoolkit/lib/gatk/Queue.jar >>> -configFile conf/genstrip_installtest_parameters.txt -tempDir ./tmpdir >>> -R data/human_b36_chr1.fasta -genomeMaskFile >>> data/human_b36_chr1.mask.fasta -genderMapFile >>> data/installtest_gender.map -runDirectory test1 -md test1/metadata >>> -jobLogDir test1/logs -L 1 -minimumSize 100 -maximumSize 1000000 -I >>> data/installtest.bam -O test1.discovery.vcf -run >>> INFO 11:38:21,038 HelpFormatter - Date/Time: 2012/01/30 11:38:21 >>> INFO 11:38:21,038 HelpFormatter - >>> --------------------------------------------------------- >>> INFO 11:38:21,038 HelpFormatter - >>> --------------------------------------------------------- >>> INFO 11:38:21,039 QCommandLine - Scripting SVDiscovery >>> INFO 11:38:21,183 QCommandLine - Added 2 functions >>> INFO 11:38:21,184 QGraph - Generating graph. >>> INFO 11:38:21,196 QGraph - Running jobs. >>> INFO 11:38:21,250 ShellJobRunner - Starting: java -Xmx4g >>> -Djava.io.tmpdir=/net/scratch/bb447/svtoolkit/installtest/tmpdir -cp >>> /scratch/bb447/svtoolkit/lib/SVToolkit.jar:/scratch/bb447/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/scratch/bb447/svtoolkit/lib/gatk/Queue.jar >>> -verbose:gc org.broadinstitute.sv.main.SVDiscovery -T SVDiscovery -R >>> /net/scratch/bb447/svtoolkit/installtest/data/human_b36_chr1.fasta -I >>> /net/scratch/bb447/svtoolkit/installtest/data/installtest.bam -O >>> /net/scratch/bb447/svtoolkit/installtest/test1/test1.discovery.unfiltered.vcf >>> -md test1/metadata -disableGATKTraversal -configFile >>> conf/genstrip_installtest_parameters.txt -runDirectory test1 >>> -genderMapFile data/installtest_gender.map -genomeMaskFile >>> data/human_b36_chr1.mask.fasta -L 1 -filePrefix test1 -searchLocus 1 >>> -searchWindow 1 -searchMinimumSize 100 -searchMaximumSize 1000000 >>> INFO 11:38:21,250 ShellJobRunner - Output written to >>> /net/scratch/bb447/svtoolkit/installtest/test1/logs/Q-2973@compute-26-8-1.out >>> INFO 11:38:48,558 ShellJobRunner - Done: java -Xmx4g >>> -Djava.io.tmpdir=/net/scratch/bb447/svtoolkit/installtest/tmpdir -cp >>> /scratch/bb447/svtoolkit/lib/SVToolkit.jar:/scratch/bb447/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/scratch/bb447/svtoolkit/lib/gatk/Queue.jar >>> -verbose:gc org.broadinstitute.sv.main.SVDiscovery -T SVDiscovery -R >>> /net/scratch/bb447/svtoolkit/installtest/data/human_b36_chr1.fasta -I >>> /net/scratch/bb447/svtoolkit/installtest/data/installtest.bam -O >>> /net/scratch/bb447/svtoolkit/installtest/test1/test1.discovery.unfiltered.vcf >>> -md test1/metadata -disableGATKTraversal -configFile >>> conf/genstrip_installtest_parameters.txt -runDirectory test1 >>> -genderMapFile data/installtest_gender.map -genomeMaskFile >>> data/human_b36_chr1.mask.fasta -L 1 -filePrefix test1 -searchLocus 1 >>> -searchWindow 1 -searchMinimumSize 100 -searchMaximumSize 1000000 >>> INFO 11:38:48,562 ShellJobRunner - Starting: java -Xmx4g >>> -Djava.io.tmpdir=/net/scratch/bb447/svtoolkit/installtest/tmpdir -jar >>> /scratch/bb447/svtoolkit/lib/gatk/GenomeAnalysisTK.jar -T >>> VariantFiltration -B:variant,VCF test1/test1.discovery.unfiltered.vcf >>> -o test1.discovery.vcf -R data/human_b36_chr1.fasta -filterName >>> COVERAGE -filter "GSDEPTHCALLTHRESHOLD == \"NA\" || >>> GSDEPTHCALLTHRESHOLD>= 1.0" -filterName COHERENCE -filter >>> "GSCOHPVALUE == \"NA\" || GSCOHPVALUE<= 0.01" -filterName DEPTHPVAL >>> -filter "GSDEPTHPVALUE == \"NA\" || GSDEPTHPVALUE>= 0.01" -filterName >>> DEPTH -filter "GSDEPTHRATIO == \"NA\" || GSDEPTHRATIO> 0.8 || >>> (GSDEPTHRATIO> 0.63&& (GSMEMBPVALUE == \"NA\" || GSMEMBPVALUE>= >>> 0.01))" >>> INFO 11:38:48,562 ShellJobRunner - Output written to >>> /net/scratch/bb447/svtoolkit/installtest/test1/logs/Q-2973@compute-26-8-2.out >>> INFO 11:38:54,842 ShellJobRunner - Done: java -Xmx4g >>> -Djava.io.tmpdir=/net/scratch/bb447/svtoolkit/installtest/tmpdir -jar >>> /scratch/bb447/svtoolkit/lib/gatk/GenomeAnalysisTK.jar -T >>> VariantFiltration -B:variant,VCF test1/test1.discovery.unfiltered.vcf >>> -o test1.discovery.vcf -R data/human_b36_chr1.fasta -filterName >>> COVERAGE -filter "GSDEPTHCALLTHRESHOLD == \"NA\" || >>> GSDEPTHCALLTHRESHOLD>= 1.0" -filterName COHERENCE -filter >>> "GSCOHPVALUE == \"NA\" || GSCOHPVALUE<= 0.01" -filterName DEPTHPVAL >>> -filter "GSDEPTHPVALUE == \"NA\" || GSDEPTHPVALUE>= 0.01" -filterName >>> DEPTH -filter "GSDEPTHRATIO == \"NA\" || GSDEPTHRATIO> 0.8 || >>> (GSDEPTHRATIO> 0.63&& (GSMEMBPVALUE == \"NA\" || GSMEMBPVALUE>= >>> 0.01))" >>> INFO 11:38:54,843 QGraph - Deleting intermediate files. >>> INFO 11:38:54,844 QCommandLine - Done >>> Files - and benchmark/test1.discovery.vcf differ >>> Error: test results do not match benchmark data >>> >>> Please let me know if there is any more information that might be helpful. >>> Thanks, >>> Boel >>> >>> --~*~**~***~*~***~**~*~-- >>> Boel Brynedal, PhD. >>> Post Doctoral Associate >>> Department of Neurology& Department of Genetics, >>> Yale Medical School, New Haven, CT. >>> Medical and Population Genetics, The Broad Institute, Cambridge, MA. >>> >>> ------------------------------------------------------------------------------ >>> Try before you buy = See our experts in action! >>> The most comprehensive online learning library for Microsoft developers >>> is just $99.99! Visual Studio, SharePoint, SQL - plus HTML5, CSS3, MVC3, >>> Metro Style Apps, more. Free future releases when you subscribe now! >>> http://p.sf.net/sfu/learndevnow-dev2 >>> _______________________________________________ >>> svtoolkit-help mailing list >>> svt...@li... >>> https://lists.sourceforge.net/lists/listinfo/svtoolkit-help >> >> ------------------------------------------------------------------------------ >> Try before you buy = See our experts in action! >> The most comprehensive online learning library for Microsoft developers >> is just $99.99! Visual Studio, SharePoint, SQL - plus HTML5, CSS3, MVC3, >> Metro Style Apps, more. Free future releases when you subscribe now! >> http://p.sf.net/sfu/learndevnow-dev2 >> _______________________________________________ >> svtoolkit-help mailing list >> svt...@li... >> https://lists.sourceforge.net/lists/listinfo/svtoolkit-help |
|
From: Boel B. <bry...@gm...> - 2012-01-30 18:44:08
|
Hi, Updated to the latest interim version, but get the same error message. Turns out the only difference is the GSCOHERENCE value (-3.162711280554605 vs -3.1627112805546047) and the GSCOHFN value (-0.5271185467591009 vs -0.5271185467591007), see the two rows below. Might this be an issue? The file "test1.genotypes.vcf" is not created at all, if it was suppose to. Thanks! Boel 1 61722559 DEL_1 T <DEL> . DEPTH;DEPTHPVAL CIEND=-8,8;CIPOS=-8,8;END=61722981;GSCOHERENCE=-3.162711280554605;GSCOHFN=-0.5271185467591009;GSCOHPVALUE=0.901;GSCOORDS=61722491,61722556,61723000,61723144;GSDEPTHCALLTHRESHOLD=0.9600579875024452;GSDEPTHNOBSSAMPLES=5;GSDEPTHNTOTALSAMPLES=5;GSDEPTHOBSSAMPLES=NA07051,NA11830,NA11920,NA12003,NA12249;GSDEPTHPVALUE=0.035631;GSDEPTHPVALUECOUNTS=74,35512,511,321039;GSDEPTHRANKSUMPVALUE=0.9802336;GSDEPTHRATIO=1.3091622731975827;GSDMAX=543;GSDMIN=1;GSDOPT=420;GSDSPAN=443;GSMEMBNPAIRS=6;GSMEMBNSAMPLES=5;GSMEMBOBSSAMPLES=NA07051,NA12249,NA11920,NA12003,NA11830;GSMEMBPVALUE=0.4945;GSMEMBSTATISTIC=40.43627779276575;GSNDEPTHCALLS=39;GSNPAIRS=6;GSNSAMPLES=5;GSOUTLEFT=0;GSOUTLIERS=0;GSOUTRIGHT=0;GSREADGROUPS=ERR000550,ERR000567,SRR003115,SRR003135,SRR006095,SRR006165;GSREADNAMES=EAS139_44:6:82:100:15931,EAS139_47:7:5:530:8011,SRR003115.6626735,SRR003135.5278653,SRR006095.2235470,SRR006165.7774794;GSSAMPLES=NA07051,NA12249,NA11920,NA12003,NA11830,NA07051;IMPRECISE;SVLEN=-420;SVTYPE=DEL 1 61722559 DEL_1 T <DEL> . DEPTH;DEPTHPVAL CIEND=-8,8;CIPOS=-8,8;END=61722981;GSCOHERENCE=-3.1627112805546047;GSCOHFN=-0.5271185467591007;GSCOHPVALUE=0.901;GSCOORDS=61722491,61722556,61723000,61723144;GSDEPTHCALLTHRESHOLD=0.9600579875024452;GSDEPTHNOBSSAMPLES=5;GSDEPTHNTOTALSAMPLES=5;GSDEPTHOBSSAMPLES=NA07051,NA11830,NA11920,NA12003,NA12249;GSDEPTHPVALUE=0.035631;GSDEPTHPVALUECOUNTS=74,35512,511,321039;GSDEPTHRANKSUMPVALUE=0.9802336;GSDEPTHRATIO=1.3091622731975827;GSDMAX=543;GSDMIN=1;GSDOPT=420;GSDSPAN=443;GSMEMBNPAIRS=6;GSMEMBNSAMPLES=5;GSMEMBOBSSAMPLES=NA07051,NA12249,NA11920,NA12003,NA11830;GSMEMBPVALUE=0.4945;GSMEMBSTATISTIC=40.43627779276575;GSNDEPTHCALLS=39;GSNPAIRS=6;GSNSAMPLES=5;GSOUTLEFT=0;GSOUTLIERS=0;GSOUTRIGHT=0;GSREADGROUPS=ERR000550,ERR000567,SRR003115,SRR003135,SRR006095,SRR006165;GSREADNAMES=EAS139_44:6:82:100:15931,EAS139_47:7:5:530:8011,SRR003115.6626735,SRR003135.5278653,SRR006095.2235470,SRR006165.7774794;GSSAMPLES=NA07051,NA12249,NA11920,NA12003,NA11830,NA07051;IMPRECISE;SVLEN=-420;SVTYPE=DEL Den 30 januari 2012 12:18 skrev Bob Handsaker <han...@br...>: > Hi, Boel, > I would encourage you to try using the latest interim release. > These are updates that are missing documentation for some new features > and occasional incompatibilities, but people have generally been able to > use them successfully. > The interim releases are available at > ftp://ftp.broadinstitute.org/pub/svtoolkit/releases/interim/. > What would be helpful to diagnose the problem is a manual diff of > test1.discovery.vcf and benchmark/test1.discovery.vcf. > There are a couple of lines (like ##fileDate) that are not expected to > match, but other mismatches are likely indicating a problem. > -Bob > > On 1/30/12 12:08 PM, Boel Brynedal wrote: >> Hi, >> >> Very glad to find out that your program is out and ready to be used, >> exactly what I was looking for. >> >> When running the discovery.sh test I get the message that: "Error: >> test results do not match benchmark data". >> I quick look revealed that only one result file was produced >> (test1.discovery.vcf) while the other one (test1.genotypes.vcf) is >> missing. Did something go wrong, or should only one file be produced? >> >> Output fr discovery.sh: >> $ ./discovery.sh >> SVToolkit version 1.03 (build 619) >> Build date: 2011/02/12 17:23:22 >> Web site: http://www.broadinstitute.org/gsa/wiki/index.php/Genome_STRiP >> INFO 11:37:59,050 QScriptManager - Compiling 2 QScripts >> INFO 11:38:05,021 QScriptManager - Compilation complete >> INFO 11:38:10,911 HelpFormatter - >> --------------------------------------------------------- >> INFO 11:38:10,911 HelpFormatter - Program Name: >> org.broadinstitute.sting.queue.QCommandLine >> INFO 11:38:10,912 HelpFormatter - Program Args: -S >> /scratch/bb447/svtoolkit/qscript/SVPreprocess.q -S >> /scratch/bb447/svtoolkit/qscript/SVQScript.q -gatk >> /scratch/bb447/svtoolkit/lib/gatk/GenomeAnalysisTK.jar -cp >> /scratch/bb447/svtoolkit/lib/SVToolkit.jar:/scratch/bb447/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/scratch/bb447/svtoolkit/lib/gatk/Queue.jar >> -configFile conf/genstrip_installtest_parameters.txt -tempDir ./tmpdir >> -R data/human_b36_chr1.fasta -genomeMaskFile >> data/human_b36_chr1.mask.fasta -genderMapFile >> data/installtest_gender.map -runDirectory test1 -md test1/metadata >> -jobLogDir test1/logs -I data/installtest.bam -run >> INFO 11:38:10,912 HelpFormatter - Date/Time: 2012/01/30 11:38:10 >> INFO 11:38:10,912 HelpFormatter - >> --------------------------------------------------------- >> INFO 11:38:10,912 HelpFormatter - >> --------------------------------------------------------- >> INFO 11:38:10,913 QCommandLine - Scripting SVPreprocess >> INFO 11:38:11,049 QCommandLine - Added 7 functions >> INFO 11:38:11,049 QGraph - Generating graph. >> INFO 11:38:11,073 QGraph - Running jobs. >> INFO 11:38:11,080 QGraph - Deleting intermediate files. >> INFO 11:38:11,081 QCommandLine - Done >> INFO 11:38:13,403 QScriptManager - Compiling 2 QScripts >> INFO 11:38:18,509 QScriptManager - Compilation complete >> INFO 11:38:21,037 HelpFormatter - >> --------------------------------------------------------- >> INFO 11:38:21,037 HelpFormatter - Program Name: >> org.broadinstitute.sting.queue.QCommandLine >> INFO 11:38:21,037 HelpFormatter - Program Args: -S >> /scratch/bb447/svtoolkit/qscript/SVDiscovery.q -S >> /scratch/bb447/svtoolkit/qscript/SVQScript.q -gatk >> /scratch/bb447/svtoolkit/lib/gatk/GenomeAnalysisTK.jar -cp >> /scratch/bb447/svtoolkit/lib/SVToolkit.jar:/scratch/bb447/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/scratch/bb447/svtoolkit/lib/gatk/Queue.jar >> -configFile conf/genstrip_installtest_parameters.txt -tempDir ./tmpdir >> -R data/human_b36_chr1.fasta -genomeMaskFile >> data/human_b36_chr1.mask.fasta -genderMapFile >> data/installtest_gender.map -runDirectory test1 -md test1/metadata >> -jobLogDir test1/logs -L 1 -minimumSize 100 -maximumSize 1000000 -I >> data/installtest.bam -O test1.discovery.vcf -run >> INFO 11:38:21,038 HelpFormatter - Date/Time: 2012/01/30 11:38:21 >> INFO 11:38:21,038 HelpFormatter - >> --------------------------------------------------------- >> INFO 11:38:21,038 HelpFormatter - >> --------------------------------------------------------- >> INFO 11:38:21,039 QCommandLine - Scripting SVDiscovery >> INFO 11:38:21,183 QCommandLine - Added 2 functions >> INFO 11:38:21,184 QGraph - Generating graph. >> INFO 11:38:21,196 QGraph - Running jobs. >> INFO 11:38:21,250 ShellJobRunner - Starting: java -Xmx4g >> -Djava.io.tmpdir=/net/scratch/bb447/svtoolkit/installtest/tmpdir -cp >> /scratch/bb447/svtoolkit/lib/SVToolkit.jar:/scratch/bb447/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/scratch/bb447/svtoolkit/lib/gatk/Queue.jar >> -verbose:gc org.broadinstitute.sv.main.SVDiscovery -T SVDiscovery -R >> /net/scratch/bb447/svtoolkit/installtest/data/human_b36_chr1.fasta -I >> /net/scratch/bb447/svtoolkit/installtest/data/installtest.bam -O >> /net/scratch/bb447/svtoolkit/installtest/test1/test1.discovery.unfiltered.vcf >> -md test1/metadata -disableGATKTraversal -configFile >> conf/genstrip_installtest_parameters.txt -runDirectory test1 >> -genderMapFile data/installtest_gender.map -genomeMaskFile >> data/human_b36_chr1.mask.fasta -L 1 -filePrefix test1 -searchLocus 1 >> -searchWindow 1 -searchMinimumSize 100 -searchMaximumSize 1000000 >> INFO 11:38:21,250 ShellJobRunner - Output written to >> /net/scratch/bb447/svtoolkit/installtest/test1/logs/Q-2973@compute-26-8-1.out >> INFO 11:38:48,558 ShellJobRunner - Done: java -Xmx4g >> -Djava.io.tmpdir=/net/scratch/bb447/svtoolkit/installtest/tmpdir -cp >> /scratch/bb447/svtoolkit/lib/SVToolkit.jar:/scratch/bb447/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/scratch/bb447/svtoolkit/lib/gatk/Queue.jar >> -verbose:gc org.broadinstitute.sv.main.SVDiscovery -T SVDiscovery -R >> /net/scratch/bb447/svtoolkit/installtest/data/human_b36_chr1.fasta -I >> /net/scratch/bb447/svtoolkit/installtest/data/installtest.bam -O >> /net/scratch/bb447/svtoolkit/installtest/test1/test1.discovery.unfiltered.vcf >> -md test1/metadata -disableGATKTraversal -configFile >> conf/genstrip_installtest_parameters.txt -runDirectory test1 >> -genderMapFile data/installtest_gender.map -genomeMaskFile >> data/human_b36_chr1.mask.fasta -L 1 -filePrefix test1 -searchLocus 1 >> -searchWindow 1 -searchMinimumSize 100 -searchMaximumSize 1000000 >> INFO 11:38:48,562 ShellJobRunner - Starting: java -Xmx4g >> -Djava.io.tmpdir=/net/scratch/bb447/svtoolkit/installtest/tmpdir -jar >> /scratch/bb447/svtoolkit/lib/gatk/GenomeAnalysisTK.jar -T >> VariantFiltration -B:variant,VCF test1/test1.discovery.unfiltered.vcf >> -o test1.discovery.vcf -R data/human_b36_chr1.fasta -filterName >> COVERAGE -filter "GSDEPTHCALLTHRESHOLD == \"NA\" || >> GSDEPTHCALLTHRESHOLD>= 1.0" -filterName COHERENCE -filter >> "GSCOHPVALUE == \"NA\" || GSCOHPVALUE<= 0.01" -filterName DEPTHPVAL >> -filter "GSDEPTHPVALUE == \"NA\" || GSDEPTHPVALUE>= 0.01" -filterName >> DEPTH -filter "GSDEPTHRATIO == \"NA\" || GSDEPTHRATIO> 0.8 || >> (GSDEPTHRATIO> 0.63&& (GSMEMBPVALUE == \"NA\" || GSMEMBPVALUE>= >> 0.01))" >> INFO 11:38:48,562 ShellJobRunner - Output written to >> /net/scratch/bb447/svtoolkit/installtest/test1/logs/Q-2973@compute-26-8-2.out >> INFO 11:38:54,842 ShellJobRunner - Done: java -Xmx4g >> -Djava.io.tmpdir=/net/scratch/bb447/svtoolkit/installtest/tmpdir -jar >> /scratch/bb447/svtoolkit/lib/gatk/GenomeAnalysisTK.jar -T >> VariantFiltration -B:variant,VCF test1/test1.discovery.unfiltered.vcf >> -o test1.discovery.vcf -R data/human_b36_chr1.fasta -filterName >> COVERAGE -filter "GSDEPTHCALLTHRESHOLD == \"NA\" || >> GSDEPTHCALLTHRESHOLD>= 1.0" -filterName COHERENCE -filter >> "GSCOHPVALUE == \"NA\" || GSCOHPVALUE<= 0.01" -filterName DEPTHPVAL >> -filter "GSDEPTHPVALUE == \"NA\" || GSDEPTHPVALUE>= 0.01" -filterName >> DEPTH -filter "GSDEPTHRATIO == \"NA\" || GSDEPTHRATIO> 0.8 || >> (GSDEPTHRATIO> 0.63&& (GSMEMBPVALUE == \"NA\" || GSMEMBPVALUE>= >> 0.01))" >> INFO 11:38:54,843 QGraph - Deleting intermediate files. >> INFO 11:38:54,844 QCommandLine - Done >> Files - and benchmark/test1.discovery.vcf differ >> Error: test results do not match benchmark data >> >> Please let me know if there is any more information that might be helpful. >> Thanks, >> Boel >> >> --~*~**~***~*~***~**~*~-- >> Boel Brynedal, PhD. >> Post Doctoral Associate >> Department of Neurology& Department of Genetics, >> Yale Medical School, New Haven, CT. >> Medical and Population Genetics, The Broad Institute, Cambridge, MA. >> >> ------------------------------------------------------------------------------ >> Try before you buy = See our experts in action! >> The most comprehensive online learning library for Microsoft developers >> is just $99.99! Visual Studio, SharePoint, SQL - plus HTML5, CSS3, MVC3, >> Metro Style Apps, more. Free future releases when you subscribe now! >> http://p.sf.net/sfu/learndevnow-dev2 >> _______________________________________________ >> svtoolkit-help mailing list >> svt...@li... >> https://lists.sourceforge.net/lists/listinfo/svtoolkit-help > > > ------------------------------------------------------------------------------ > Try before you buy = See our experts in action! > The most comprehensive online learning library for Microsoft developers > is just $99.99! Visual Studio, SharePoint, SQL - plus HTML5, CSS3, MVC3, > Metro Style Apps, more. Free future releases when you subscribe now! > http://p.sf.net/sfu/learndevnow-dev2 > _______________________________________________ > svtoolkit-help mailing list > svt...@li... > https://lists.sourceforge.net/lists/listinfo/svtoolkit-help |
|
From: Bob H. <han...@br...> - 2012-01-30 17:18:41
|
Hi, Boel, I would encourage you to try using the latest interim release. These are updates that are missing documentation for some new features and occasional incompatibilities, but people have generally been able to use them successfully. The interim releases are available at ftp://ftp.broadinstitute.org/pub/svtoolkit/releases/interim/. What would be helpful to diagnose the problem is a manual diff of test1.discovery.vcf and benchmark/test1.discovery.vcf. There are a couple of lines (like ##fileDate) that are not expected to match, but other mismatches are likely indicating a problem. -Bob On 1/30/12 12:08 PM, Boel Brynedal wrote: > Hi, > > Very glad to find out that your program is out and ready to be used, > exactly what I was looking for. > > When running the discovery.sh test I get the message that: "Error: > test results do not match benchmark data". > I quick look revealed that only one result file was produced > (test1.discovery.vcf) while the other one (test1.genotypes.vcf) is > missing. Did something go wrong, or should only one file be produced? > > Output fr discovery.sh: > $ ./discovery.sh > SVToolkit version 1.03 (build 619) > Build date: 2011/02/12 17:23:22 > Web site: http://www.broadinstitute.org/gsa/wiki/index.php/Genome_STRiP > INFO 11:37:59,050 QScriptManager - Compiling 2 QScripts > INFO 11:38:05,021 QScriptManager - Compilation complete > INFO 11:38:10,911 HelpFormatter - > --------------------------------------------------------- > INFO 11:38:10,911 HelpFormatter - Program Name: > org.broadinstitute.sting.queue.QCommandLine > INFO 11:38:10,912 HelpFormatter - Program Args: -S > /scratch/bb447/svtoolkit/qscript/SVPreprocess.q -S > /scratch/bb447/svtoolkit/qscript/SVQScript.q -gatk > /scratch/bb447/svtoolkit/lib/gatk/GenomeAnalysisTK.jar -cp > /scratch/bb447/svtoolkit/lib/SVToolkit.jar:/scratch/bb447/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/scratch/bb447/svtoolkit/lib/gatk/Queue.jar > -configFile conf/genstrip_installtest_parameters.txt -tempDir ./tmpdir > -R data/human_b36_chr1.fasta -genomeMaskFile > data/human_b36_chr1.mask.fasta -genderMapFile > data/installtest_gender.map -runDirectory test1 -md test1/metadata > -jobLogDir test1/logs -I data/installtest.bam -run > INFO 11:38:10,912 HelpFormatter - Date/Time: 2012/01/30 11:38:10 > INFO 11:38:10,912 HelpFormatter - > --------------------------------------------------------- > INFO 11:38:10,912 HelpFormatter - > --------------------------------------------------------- > INFO 11:38:10,913 QCommandLine - Scripting SVPreprocess > INFO 11:38:11,049 QCommandLine - Added 7 functions > INFO 11:38:11,049 QGraph - Generating graph. > INFO 11:38:11,073 QGraph - Running jobs. > INFO 11:38:11,080 QGraph - Deleting intermediate files. > INFO 11:38:11,081 QCommandLine - Done > INFO 11:38:13,403 QScriptManager - Compiling 2 QScripts > INFO 11:38:18,509 QScriptManager - Compilation complete > INFO 11:38:21,037 HelpFormatter - > --------------------------------------------------------- > INFO 11:38:21,037 HelpFormatter - Program Name: > org.broadinstitute.sting.queue.QCommandLine > INFO 11:38:21,037 HelpFormatter - Program Args: -S > /scratch/bb447/svtoolkit/qscript/SVDiscovery.q -S > /scratch/bb447/svtoolkit/qscript/SVQScript.q -gatk > /scratch/bb447/svtoolkit/lib/gatk/GenomeAnalysisTK.jar -cp > /scratch/bb447/svtoolkit/lib/SVToolkit.jar:/scratch/bb447/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/scratch/bb447/svtoolkit/lib/gatk/Queue.jar > -configFile conf/genstrip_installtest_parameters.txt -tempDir ./tmpdir > -R data/human_b36_chr1.fasta -genomeMaskFile > data/human_b36_chr1.mask.fasta -genderMapFile > data/installtest_gender.map -runDirectory test1 -md test1/metadata > -jobLogDir test1/logs -L 1 -minimumSize 100 -maximumSize 1000000 -I > data/installtest.bam -O test1.discovery.vcf -run > INFO 11:38:21,038 HelpFormatter - Date/Time: 2012/01/30 11:38:21 > INFO 11:38:21,038 HelpFormatter - > --------------------------------------------------------- > INFO 11:38:21,038 HelpFormatter - > --------------------------------------------------------- > INFO 11:38:21,039 QCommandLine - Scripting SVDiscovery > INFO 11:38:21,183 QCommandLine - Added 2 functions > INFO 11:38:21,184 QGraph - Generating graph. > INFO 11:38:21,196 QGraph - Running jobs. > INFO 11:38:21,250 ShellJobRunner - Starting: java -Xmx4g > -Djava.io.tmpdir=/net/scratch/bb447/svtoolkit/installtest/tmpdir -cp > /scratch/bb447/svtoolkit/lib/SVToolkit.jar:/scratch/bb447/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/scratch/bb447/svtoolkit/lib/gatk/Queue.jar > -verbose:gc org.broadinstitute.sv.main.SVDiscovery -T SVDiscovery -R > /net/scratch/bb447/svtoolkit/installtest/data/human_b36_chr1.fasta -I > /net/scratch/bb447/svtoolkit/installtest/data/installtest.bam -O > /net/scratch/bb447/svtoolkit/installtest/test1/test1.discovery.unfiltered.vcf > -md test1/metadata -disableGATKTraversal -configFile > conf/genstrip_installtest_parameters.txt -runDirectory test1 > -genderMapFile data/installtest_gender.map -genomeMaskFile > data/human_b36_chr1.mask.fasta -L 1 -filePrefix test1 -searchLocus 1 > -searchWindow 1 -searchMinimumSize 100 -searchMaximumSize 1000000 > INFO 11:38:21,250 ShellJobRunner - Output written to > /net/scratch/bb447/svtoolkit/installtest/test1/logs/Q-2973@compute-26-8-1.out > INFO 11:38:48,558 ShellJobRunner - Done: java -Xmx4g > -Djava.io.tmpdir=/net/scratch/bb447/svtoolkit/installtest/tmpdir -cp > /scratch/bb447/svtoolkit/lib/SVToolkit.jar:/scratch/bb447/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/scratch/bb447/svtoolkit/lib/gatk/Queue.jar > -verbose:gc org.broadinstitute.sv.main.SVDiscovery -T SVDiscovery -R > /net/scratch/bb447/svtoolkit/installtest/data/human_b36_chr1.fasta -I > /net/scratch/bb447/svtoolkit/installtest/data/installtest.bam -O > /net/scratch/bb447/svtoolkit/installtest/test1/test1.discovery.unfiltered.vcf > -md test1/metadata -disableGATKTraversal -configFile > conf/genstrip_installtest_parameters.txt -runDirectory test1 > -genderMapFile data/installtest_gender.map -genomeMaskFile > data/human_b36_chr1.mask.fasta -L 1 -filePrefix test1 -searchLocus 1 > -searchWindow 1 -searchMinimumSize 100 -searchMaximumSize 1000000 > INFO 11:38:48,562 ShellJobRunner - Starting: java -Xmx4g > -Djava.io.tmpdir=/net/scratch/bb447/svtoolkit/installtest/tmpdir -jar > /scratch/bb447/svtoolkit/lib/gatk/GenomeAnalysisTK.jar -T > VariantFiltration -B:variant,VCF test1/test1.discovery.unfiltered.vcf > -o test1.discovery.vcf -R data/human_b36_chr1.fasta -filterName > COVERAGE -filter "GSDEPTHCALLTHRESHOLD == \"NA\" || > GSDEPTHCALLTHRESHOLD>= 1.0" -filterName COHERENCE -filter > "GSCOHPVALUE == \"NA\" || GSCOHPVALUE<= 0.01" -filterName DEPTHPVAL > -filter "GSDEPTHPVALUE == \"NA\" || GSDEPTHPVALUE>= 0.01" -filterName > DEPTH -filter "GSDEPTHRATIO == \"NA\" || GSDEPTHRATIO> 0.8 || > (GSDEPTHRATIO> 0.63&& (GSMEMBPVALUE == \"NA\" || GSMEMBPVALUE>= > 0.01))" > INFO 11:38:48,562 ShellJobRunner - Output written to > /net/scratch/bb447/svtoolkit/installtest/test1/logs/Q-2973@compute-26-8-2.out > INFO 11:38:54,842 ShellJobRunner - Done: java -Xmx4g > -Djava.io.tmpdir=/net/scratch/bb447/svtoolkit/installtest/tmpdir -jar > /scratch/bb447/svtoolkit/lib/gatk/GenomeAnalysisTK.jar -T > VariantFiltration -B:variant,VCF test1/test1.discovery.unfiltered.vcf > -o test1.discovery.vcf -R data/human_b36_chr1.fasta -filterName > COVERAGE -filter "GSDEPTHCALLTHRESHOLD == \"NA\" || > GSDEPTHCALLTHRESHOLD>= 1.0" -filterName COHERENCE -filter > "GSCOHPVALUE == \"NA\" || GSCOHPVALUE<= 0.01" -filterName DEPTHPVAL > -filter "GSDEPTHPVALUE == \"NA\" || GSDEPTHPVALUE>= 0.01" -filterName > DEPTH -filter "GSDEPTHRATIO == \"NA\" || GSDEPTHRATIO> 0.8 || > (GSDEPTHRATIO> 0.63&& (GSMEMBPVALUE == \"NA\" || GSMEMBPVALUE>= > 0.01))" > INFO 11:38:54,843 QGraph - Deleting intermediate files. > INFO 11:38:54,844 QCommandLine - Done > Files - and benchmark/test1.discovery.vcf differ > Error: test results do not match benchmark data > > Please let me know if there is any more information that might be helpful. > Thanks, > Boel > > --~*~**~***~*~***~**~*~-- > Boel Brynedal, PhD. > Post Doctoral Associate > Department of Neurology& Department of Genetics, > Yale Medical School, New Haven, CT. > Medical and Population Genetics, The Broad Institute, Cambridge, MA. > > ------------------------------------------------------------------------------ > Try before you buy = See our experts in action! > The most comprehensive online learning library for Microsoft developers > is just $99.99! Visual Studio, SharePoint, SQL - plus HTML5, CSS3, MVC3, > Metro Style Apps, more. Free future releases when you subscribe now! > http://p.sf.net/sfu/learndevnow-dev2 > _______________________________________________ > svtoolkit-help mailing list > svt...@li... > https://lists.sourceforge.net/lists/listinfo/svtoolkit-help |
|
From: Boel B. <bry...@gm...> - 2012-01-30 17:08:17
|
Hi, Very glad to find out that your program is out and ready to be used, exactly what I was looking for. When running the discovery.sh test I get the message that: "Error: test results do not match benchmark data". I quick look revealed that only one result file was produced (test1.discovery.vcf) while the other one (test1.genotypes.vcf) is missing. Did something go wrong, or should only one file be produced? Output fr discovery.sh: $ ./discovery.sh SVToolkit version 1.03 (build 619) Build date: 2011/02/12 17:23:22 Web site: http://www.broadinstitute.org/gsa/wiki/index.php/Genome_STRiP INFO 11:37:59,050 QScriptManager - Compiling 2 QScripts INFO 11:38:05,021 QScriptManager - Compilation complete INFO 11:38:10,911 HelpFormatter - --------------------------------------------------------- INFO 11:38:10,911 HelpFormatter - Program Name: org.broadinstitute.sting.queue.QCommandLine INFO 11:38:10,912 HelpFormatter - Program Args: -S /scratch/bb447/svtoolkit/qscript/SVPreprocess.q -S /scratch/bb447/svtoolkit/qscript/SVQScript.q -gatk /scratch/bb447/svtoolkit/lib/gatk/GenomeAnalysisTK.jar -cp /scratch/bb447/svtoolkit/lib/SVToolkit.jar:/scratch/bb447/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/scratch/bb447/svtoolkit/lib/gatk/Queue.jar -configFile conf/genstrip_installtest_parameters.txt -tempDir ./tmpdir -R data/human_b36_chr1.fasta -genomeMaskFile data/human_b36_chr1.mask.fasta -genderMapFile data/installtest_gender.map -runDirectory test1 -md test1/metadata -jobLogDir test1/logs -I data/installtest.bam -run INFO 11:38:10,912 HelpFormatter - Date/Time: 2012/01/30 11:38:10 INFO 11:38:10,912 HelpFormatter - --------------------------------------------------------- INFO 11:38:10,912 HelpFormatter - --------------------------------------------------------- INFO 11:38:10,913 QCommandLine - Scripting SVPreprocess INFO 11:38:11,049 QCommandLine - Added 7 functions INFO 11:38:11,049 QGraph - Generating graph. INFO 11:38:11,073 QGraph - Running jobs. INFO 11:38:11,080 QGraph - Deleting intermediate files. INFO 11:38:11,081 QCommandLine - Done INFO 11:38:13,403 QScriptManager - Compiling 2 QScripts INFO 11:38:18,509 QScriptManager - Compilation complete INFO 11:38:21,037 HelpFormatter - --------------------------------------------------------- INFO 11:38:21,037 HelpFormatter - Program Name: org.broadinstitute.sting.queue.QCommandLine INFO 11:38:21,037 HelpFormatter - Program Args: -S /scratch/bb447/svtoolkit/qscript/SVDiscovery.q -S /scratch/bb447/svtoolkit/qscript/SVQScript.q -gatk /scratch/bb447/svtoolkit/lib/gatk/GenomeAnalysisTK.jar -cp /scratch/bb447/svtoolkit/lib/SVToolkit.jar:/scratch/bb447/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/scratch/bb447/svtoolkit/lib/gatk/Queue.jar -configFile conf/genstrip_installtest_parameters.txt -tempDir ./tmpdir -R data/human_b36_chr1.fasta -genomeMaskFile data/human_b36_chr1.mask.fasta -genderMapFile data/installtest_gender.map -runDirectory test1 -md test1/metadata -jobLogDir test1/logs -L 1 -minimumSize 100 -maximumSize 1000000 -I data/installtest.bam -O test1.discovery.vcf -run INFO 11:38:21,038 HelpFormatter - Date/Time: 2012/01/30 11:38:21 INFO 11:38:21,038 HelpFormatter - --------------------------------------------------------- INFO 11:38:21,038 HelpFormatter - --------------------------------------------------------- INFO 11:38:21,039 QCommandLine - Scripting SVDiscovery INFO 11:38:21,183 QCommandLine - Added 2 functions INFO 11:38:21,184 QGraph - Generating graph. INFO 11:38:21,196 QGraph - Running jobs. INFO 11:38:21,250 ShellJobRunner - Starting: java -Xmx4g -Djava.io.tmpdir=/net/scratch/bb447/svtoolkit/installtest/tmpdir -cp /scratch/bb447/svtoolkit/lib/SVToolkit.jar:/scratch/bb447/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/scratch/bb447/svtoolkit/lib/gatk/Queue.jar -verbose:gc org.broadinstitute.sv.main.SVDiscovery -T SVDiscovery -R /net/scratch/bb447/svtoolkit/installtest/data/human_b36_chr1.fasta -I /net/scratch/bb447/svtoolkit/installtest/data/installtest.bam -O /net/scratch/bb447/svtoolkit/installtest/test1/test1.discovery.unfiltered.vcf -md test1/metadata -disableGATKTraversal -configFile conf/genstrip_installtest_parameters.txt -runDirectory test1 -genderMapFile data/installtest_gender.map -genomeMaskFile data/human_b36_chr1.mask.fasta -L 1 -filePrefix test1 -searchLocus 1 -searchWindow 1 -searchMinimumSize 100 -searchMaximumSize 1000000 INFO 11:38:21,250 ShellJobRunner - Output written to /net/scratch/bb447/svtoolkit/installtest/test1/logs/Q-2973@compute-26-8-1.out INFO 11:38:48,558 ShellJobRunner - Done: java -Xmx4g -Djava.io.tmpdir=/net/scratch/bb447/svtoolkit/installtest/tmpdir -cp /scratch/bb447/svtoolkit/lib/SVToolkit.jar:/scratch/bb447/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/scratch/bb447/svtoolkit/lib/gatk/Queue.jar -verbose:gc org.broadinstitute.sv.main.SVDiscovery -T SVDiscovery -R /net/scratch/bb447/svtoolkit/installtest/data/human_b36_chr1.fasta -I /net/scratch/bb447/svtoolkit/installtest/data/installtest.bam -O /net/scratch/bb447/svtoolkit/installtest/test1/test1.discovery.unfiltered.vcf -md test1/metadata -disableGATKTraversal -configFile conf/genstrip_installtest_parameters.txt -runDirectory test1 -genderMapFile data/installtest_gender.map -genomeMaskFile data/human_b36_chr1.mask.fasta -L 1 -filePrefix test1 -searchLocus 1 -searchWindow 1 -searchMinimumSize 100 -searchMaximumSize 1000000 INFO 11:38:48,562 ShellJobRunner - Starting: java -Xmx4g -Djava.io.tmpdir=/net/scratch/bb447/svtoolkit/installtest/tmpdir -jar /scratch/bb447/svtoolkit/lib/gatk/GenomeAnalysisTK.jar -T VariantFiltration -B:variant,VCF test1/test1.discovery.unfiltered.vcf -o test1.discovery.vcf -R data/human_b36_chr1.fasta -filterName COVERAGE -filter "GSDEPTHCALLTHRESHOLD == \"NA\" || GSDEPTHCALLTHRESHOLD >= 1.0" -filterName COHERENCE -filter "GSCOHPVALUE == \"NA\" || GSCOHPVALUE <= 0.01" -filterName DEPTHPVAL -filter "GSDEPTHPVALUE == \"NA\" || GSDEPTHPVALUE >= 0.01" -filterName DEPTH -filter "GSDEPTHRATIO == \"NA\" || GSDEPTHRATIO > 0.8 || (GSDEPTHRATIO > 0.63 && (GSMEMBPVALUE == \"NA\" || GSMEMBPVALUE >= 0.01))" INFO 11:38:48,562 ShellJobRunner - Output written to /net/scratch/bb447/svtoolkit/installtest/test1/logs/Q-2973@compute-26-8-2.out INFO 11:38:54,842 ShellJobRunner - Done: java -Xmx4g -Djava.io.tmpdir=/net/scratch/bb447/svtoolkit/installtest/tmpdir -jar /scratch/bb447/svtoolkit/lib/gatk/GenomeAnalysisTK.jar -T VariantFiltration -B:variant,VCF test1/test1.discovery.unfiltered.vcf -o test1.discovery.vcf -R data/human_b36_chr1.fasta -filterName COVERAGE -filter "GSDEPTHCALLTHRESHOLD == \"NA\" || GSDEPTHCALLTHRESHOLD >= 1.0" -filterName COHERENCE -filter "GSCOHPVALUE == \"NA\" || GSCOHPVALUE <= 0.01" -filterName DEPTHPVAL -filter "GSDEPTHPVALUE == \"NA\" || GSDEPTHPVALUE >= 0.01" -filterName DEPTH -filter "GSDEPTHRATIO == \"NA\" || GSDEPTHRATIO > 0.8 || (GSDEPTHRATIO > 0.63 && (GSMEMBPVALUE == \"NA\" || GSMEMBPVALUE >= 0.01))" INFO 11:38:54,843 QGraph - Deleting intermediate files. INFO 11:38:54,844 QCommandLine - Done Files - and benchmark/test1.discovery.vcf differ Error: test results do not match benchmark data Please let me know if there is any more information that might be helpful. Thanks, Boel --~*~**~***~*~***~**~*~-- Boel Brynedal, PhD. Post Doctoral Associate Department of Neurology & Department of Genetics, Yale Medical School, New Haven, CT. Medical and Population Genetics, The Broad Institute, Cambridge, MA. |
|
From: Boel B. <bry...@br...> - 2012-01-30 17:00:31
|
Hi, Very glad to find out that your program is out and ready to be used, exactly what I was looking for. When running the discovery.sh test I get the message that: "Error: test results do not match benchmark data". I quick look revealed that only one result file was produced (test1.discovery.vcf) while the other one (test1.genotypes.vcf) is missing. Did something go wrong, or should only one file be produced? Output fr discovery.sh: $ ./discovery.sh SVToolkit version 1.03 (build 619) Build date: 2011/02/12 17:23:22 Web site: http://www.broadinstitute.org/gsa/wiki/index.php/Genome_STRiP INFO 11:37:59,050 QScriptManager - Compiling 2 QScripts INFO 11:38:05,021 QScriptManager - Compilation complete INFO 11:38:10,911 HelpFormatter - --------------------------------------------------------- INFO 11:38:10,911 HelpFormatter - Program Name: org.broadinstitute.sting.queue.QCommandLine INFO 11:38:10,912 HelpFormatter - Program Args: -S /scratch/bb447/svtoolkit/qscript/SVPreprocess.q -S /scratch/bb447/svtoolkit/qscript/SVQScript.q -gatk /scratch/bb447/svtoolkit/lib/gatk/GenomeAnalysisTK.jar -cp /scratch/bb447/svtoolkit/lib/SVToolkit.jar:/scratch/bb447/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/scratch/bb447/svtoolkit/lib/gatk/Queue.jar -configFile conf/genstrip_installtest_parameters.txt -tempDir ./tmpdir -R data/human_b36_chr1.fasta -genomeMaskFile data/human_b36_chr1.mask.fasta -genderMapFile data/installtest_gender.map -runDirectory test1 -md test1/metadata -jobLogDir test1/logs -I data/installtest.bam -run INFO 11:38:10,912 HelpFormatter - Date/Time: 2012/01/30 11:38:10 INFO 11:38:10,912 HelpFormatter - --------------------------------------------------------- INFO 11:38:10,912 HelpFormatter - --------------------------------------------------------- INFO 11:38:10,913 QCommandLine - Scripting SVPreprocess INFO 11:38:11,049 QCommandLine - Added 7 functions INFO 11:38:11,049 QGraph - Generating graph. INFO 11:38:11,073 QGraph - Running jobs. INFO 11:38:11,080 QGraph - Deleting intermediate files. INFO 11:38:11,081 QCommandLine - Done INFO 11:38:13,403 QScriptManager - Compiling 2 QScripts INFO 11:38:18,509 QScriptManager - Compilation complete INFO 11:38:21,037 HelpFormatter - --------------------------------------------------------- INFO 11:38:21,037 HelpFormatter - Program Name: org.broadinstitute.sting.queue.QCommandLine INFO 11:38:21,037 HelpFormatter - Program Args: -S /scratch/bb447/svtoolkit/qscript/SVDiscovery.q -S /scratch/bb447/svtoolkit/qscript/SVQScript.q -gatk /scratch/bb447/svtoolkit/lib/gatk/GenomeAnalysisTK.jar -cp /scratch/bb447/svtoolkit/lib/SVToolkit.jar:/scratch/bb447/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/scratch/bb447/svtoolkit/lib/gatk/Queue.jar -configFile conf/genstrip_installtest_parameters.txt -tempDir ./tmpdir -R data/human_b36_chr1.fasta -genomeMaskFile data/human_b36_chr1.mask.fasta -genderMapFile data/installtest_gender.map -runDirectory test1 -md test1/metadata -jobLogDir test1/logs -L 1 -minimumSize 100 -maximumSize 1000000 -I data/installtest.bam -O test1.discovery.vcf -run INFO 11:38:21,038 HelpFormatter - Date/Time: 2012/01/30 11:38:21 INFO 11:38:21,038 HelpFormatter - --------------------------------------------------------- INFO 11:38:21,038 HelpFormatter - --------------------------------------------------------- INFO 11:38:21,039 QCommandLine - Scripting SVDiscovery INFO 11:38:21,183 QCommandLine - Added 2 functions INFO 11:38:21,184 QGraph - Generating graph. INFO 11:38:21,196 QGraph - Running jobs. INFO 11:38:21,250 ShellJobRunner - Starting: java -Xmx4g -Djava.io.tmpdir=/net/scratch/bb447/svtoolkit/installtest/tmpdir -cp /scratch/bb447/svtoolkit/lib/SVToolkit.jar:/scratch/bb447/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/scratch/bb447/svtoolkit/lib/gatk/Queue.jar -verbose:gc org.broadinstitute.sv.main.SVDiscovery -T SVDiscovery -R /net/scratch/bb447/svtoolkit/installtest/data/human_b36_chr1.fasta -I /net/scratch/bb447/svtoolkit/installtest/data/installtest.bam -O /net/scratch/bb447/svtoolkit/installtest/test1/test1.discovery.unfiltered.vcf -md test1/metadata -disableGATKTraversal -configFile conf/genstrip_installtest_parameters.txt -runDirectory test1 -genderMapFile data/installtest_gender.map -genomeMaskFile data/human_b36_chr1.mask.fasta -L 1 -filePrefix test1 -searchLocus 1 -searchWindow 1 -searchMinimumSize 100 -searchMaximumSize 1000000 INFO 11:38:21,250 ShellJobRunner - Output written to /net/scratch/bb447/svtoolkit/installtest/test1/logs/Q-2973@compute-26-8-1.out INFO 11:38:48,558 ShellJobRunner - Done: java -Xmx4g -Djava.io.tmpdir=/net/scratch/bb447/svtoolkit/installtest/tmpdir -cp /scratch/bb447/svtoolkit/lib/SVToolkit.jar:/scratch/bb447/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/scratch/bb447/svtoolkit/lib/gatk/Queue.jar -verbose:gc org.broadinstitute.sv.main.SVDiscovery -T SVDiscovery -R /net/scratch/bb447/svtoolkit/installtest/data/human_b36_chr1.fasta -I /net/scratch/bb447/svtoolkit/installtest/data/installtest.bam -O /net/scratch/bb447/svtoolkit/installtest/test1/test1.discovery.unfiltered.vcf -md test1/metadata -disableGATKTraversal -configFile conf/genstrip_installtest_parameters.txt -runDirectory test1 -genderMapFile data/installtest_gender.map -genomeMaskFile data/human_b36_chr1.mask.fasta -L 1 -filePrefix test1 -searchLocus 1 -searchWindow 1 -searchMinimumSize 100 -searchMaximumSize 1000000 INFO 11:38:48,562 ShellJobRunner - Starting: java -Xmx4g -Djava.io.tmpdir=/net/scratch/bb447/svtoolkit/installtest/tmpdir -jar /scratch/bb447/svtoolkit/lib/gatk/GenomeAnalysisTK.jar -T VariantFiltration -B:variant,VCF test1/test1.discovery.unfiltered.vcf -o test1.discovery.vcf -R data/human_b36_chr1.fasta -filterName COVERAGE -filter "GSDEPTHCALLTHRESHOLD == \"NA\" || GSDEPTHCALLTHRESHOLD >= 1.0" -filterName COHERENCE -filter "GSCOHPVALUE == \"NA\" || GSCOHPVALUE <= 0.01" -filterName DEPTHPVAL -filter "GSDEPTHPVALUE == \"NA\" || GSDEPTHPVALUE >= 0.01" -filterName DEPTH -filter "GSDEPTHRATIO == \"NA\" || GSDEPTHRATIO > 0.8 || (GSDEPTHRATIO > 0.63 && (GSMEMBPVALUE == \"NA\" || GSMEMBPVALUE >= 0.01))" INFO 11:38:48,562 ShellJobRunner - Output written to /net/scratch/bb447/svtoolkit/installtest/test1/logs/Q-2973@compute-26-8-2.out INFO 11:38:54,842 ShellJobRunner - Done: java -Xmx4g -Djava.io.tmpdir=/net/scratch/bb447/svtoolkit/installtest/tmpdir -jar /scratch/bb447/svtoolkit/lib/gatk/GenomeAnalysisTK.jar -T VariantFiltration -B:variant,VCF test1/test1.discovery.unfiltered.vcf -o test1.discovery.vcf -R data/human_b36_chr1.fasta -filterName COVERAGE -filter "GSDEPTHCALLTHRESHOLD == \"NA\" || GSDEPTHCALLTHRESHOLD >= 1.0" -filterName COHERENCE -filter "GSCOHPVALUE == \"NA\" || GSCOHPVALUE <= 0.01" -filterName DEPTHPVAL -filter "GSDEPTHPVALUE == \"NA\" || GSDEPTHPVALUE >= 0.01" -filterName DEPTH -filter "GSDEPTHRATIO == \"NA\" || GSDEPTHRATIO > 0.8 || (GSDEPTHRATIO > 0.63 && (GSMEMBPVALUE == \"NA\" || GSMEMBPVALUE >= 0.01))" INFO 11:38:54,843 QGraph - Deleting intermediate files. INFO 11:38:54,844 QCommandLine - Done Files - and benchmark/test1.discovery.vcf differ Error: test results do not match benchmark data Please let me know if there is any more information that might be helpful. Thanks, Boel --~*~**~***~*~***~**~*~-- Boel Brynedal, PhD. Post Doctoral Associate Department of Neurology & Department of Genetics, Yale Medical School, New Haven, CT. Medical and Population Genetics, The Broad Institute, Cambridge, MA. |
|
From: Bob H. <han...@br...> - 2012-01-29 22:08:03
|
That individual step shouldn't require -runDirectory (the input and output files are passed explicitly). It sounds like some transient problem in your cluster environment, but it's hard to tell what it might be. -Bob On 1/29/12 3:41 PM, Thomas Zichner wrote: > Dear Bob, > > thank you very much for your reply! > I now ran it on my local machine instead of the cluster and it works. I > don't know what the actual problem might have been. > > The only thing I noticed is that the calling of the filtering step > doesn't contain the "-runDirectory" parameter. Could this cause problems? > > Kind regards > Thomas > > > > > On 20.01.2012 16:21, Bob Handsaker wrote: >> No idea offhand. Have you looked in the log file produced by queue? >> What I would try is to take the log file from queue, which lists the >> java command that was run, and run this command directly. >> If the behavior persists, then maybe truncate the unfiltered.vcf down to >> just the first record and if the problem still persists, then post the >> short vcf file. >> -Bob >> >> On 1/20/12 3:01 AM, Thomas Zichner wrote: >>> 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 >>> > ------------------------------------------------------------------------------ > Try before you buy = See our experts in action! > The most comprehensive online learning library for Microsoft developers > is just $99.99! Visual Studio, SharePoint, SQL - plus HTML5, CSS3, MVC3, > Metro Style Apps, more. Free future releases when you subscribe now! > http://p.sf.net/sfu/learndevnow-dev2 > _______________________________________________ > svtoolkit-help mailing list > svt...@li... > https://lists.sourceforge.net/lists/listinfo/svtoolkit-help |
|
From: Thomas Z. <tho...@em...> - 2012-01-29 20:42:04
|
Dear Bob, thank you very much for your reply! I now ran it on my local machine instead of the cluster and it works. I don't know what the actual problem might have been. The only thing I noticed is that the calling of the filtering step doesn't contain the "-runDirectory" parameter. Could this cause problems? Kind regards Thomas On 20.01.2012 16:21, Bob Handsaker wrote: > No idea offhand. Have you looked in the log file produced by queue? > What I would try is to take the log file from queue, which lists the > java command that was run, and run this command directly. > If the behavior persists, then maybe truncate the unfiltered.vcf down to > just the first record and if the problem still persists, then post the > short vcf file. > -Bob > > On 1/20/12 3:01 AM, Thomas Zichner wrote: >> 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...> - 2012-01-25 19:25:12
|
It should be there in that release. Perhaps your classpath is wrong? The main class org.broadinstitute.sv.apps.ComputeGenomeMask is in SVToolkit.jar. -Bob On 1/25/12 12:24 PM, Periklis Makrythanasis wrote: > > Hi, > > I have downloaded the svtoolkit_1.03.619.tar.gz package and according > to the instructions I found at the wiki, I tried to invoke > ComputeGenomeMask in order to create the mask. > > I got the following error: > > Exception in thread "main" java.lang.NoClassDefFoundError: > org/broadinstitute/sv/apps/ComputeGenomeMask > > Caused by: java.lang.ClassNotFoundException: > org.broadinstitute.sv.apps.ComputeGenomeMask > > at java.net.URLClassLoader$1.run(Unknown Source) > > at java.security.AccessController.doPrivileged(Native Method) > > at java.net.URLClassLoader.findClass(Unknown Source) > > at java.lang.ClassLoader.loadClass(Unknown Source) > > at sun.misc.Launcher$AppClassLoader.loadClass(Unknown Source) > > at java.lang.ClassLoader.loadClass(Unknown Source) > > Could not find the main class: > org.broadinstitute.sv.apps.ComputeGenomeMask. Program will exit. > > I looked at the files included in the tar.gz file and wasn't able to > locate the ComputeGenomeMask. Can you please help? > > All the best > > Periklis > > ---------------------------------------------------------- > > Periklis Makrythanasis, MD, PhD > > Department of Genetic Medicine and Development > > University of Geneva Medical School, > > 1 rue Michel-Servet > > 1211 Geneva, Switzerland > > tel: +41-22-379-5112 and +41-22-379-5707 > > fax:+41-22-379-5706 > > email: Per...@un... > > ---------------------------------------------------------- > > > > ------------------------------------------------------------------------------ > Keep Your Developer Skills Current with LearnDevNow! > The most comprehensive online learning library for Microsoft developers > is just $99.99! Visual Studio, SharePoint, SQL - plus HTML5, CSS3, MVC3, > Metro Style Apps, more. Free future releases when you subscribe now! > http://p.sf.net/sfu/learndevnow-d2d > > > _______________________________________________ > svtoolkit-help mailing list > svt...@li... > https://lists.sourceforge.net/lists/listinfo/svtoolkit-help |
|
From: Periklis M. <Per...@un...> - 2012-01-25 18:08:28
|
Hi,
I have downloaded the svtoolkit_1.03.619.tar.gz package and according to the
instructions I found at the wiki, I tried to invoke ComputeGenomeMask in
order to create the mask.
I got the following error:
Exception in thread "main" java.lang.NoClassDefFoundError:
org/broadinstitute/sv/apps/ComputeGenomeMask
Caused by: java.lang.ClassNotFoundException:
org.broadinstitute.sv.apps.ComputeGenomeMask
at java.net.URLClassLoader$1.run(Unknown Source)
at java.security.AccessController.doPrivileged(Native Method)
at java.net.URLClassLoader.findClass(Unknown Source)
at java.lang.ClassLoader.loadClass(Unknown Source)
at sun.misc.Launcher$AppClassLoader.loadClass(Unknown Source)
at java.lang.ClassLoader.loadClass(Unknown Source)
Could not find the main class: org.broadinstitute.sv.apps.ComputeGenomeMask.
Program will exit.
I looked at the files included in the tar.gz file and wasn't able to locate
the ComputeGenomeMask. Can you please help?
All the best
Periklis
----------------------------------------------------------
Periklis Makrythanasis, MD, PhD
Department of Genetic Medicine and Development
University of Geneva Medical School,
1 rue Michel-Servet
1211 Geneva, Switzerland
tel: +41-22-379-5112 and +41-22-379-5707
fax:+41-22-379-5706
email: Per...@un...
----------------------------------------------------------
|
|
From: Bob H. <han...@br...> - 2012-01-20 15:22:18
|
No idea offhand. Have you looked in the log file produced by queue? What I would try is to take the log file from queue, which lists the java command that was run, and run this command directly. If the behavior persists, then maybe truncate the unfiltered.vcf down to just the first record and if the problem still persists, then post the short vcf file. -Bob On 1/20/12 3:01 AM, Thomas Zichner wrote: > 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 > > ------------------------------------------------------------------------------ > Keep Your Developer Skills Current with LearnDevNow! > The most comprehensive online learning library for Microsoft developers > is just $99.99! Visual Studio, SharePoint, SQL - plus HTML5, CSS3, MVC3, > Metro Style Apps, more. Free future releases when you subscribe now! > http://p.sf.net/sfu/learndevnow-d2d > _______________________________________________ > svtoolkit-help mailing list > svt...@li... > https://lists.sourceforge.net/lists/listinfo/svtoolkit-help |
3 messages has been excluded from this view by a project administrator.
