Re: [svtoolkit-help] discovery.sh only produce one file

SourceForge Headquarters 225 Broadway Suite 1600 San Diego, CA 92101 +1 (858) 422-6466

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