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

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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.
>
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