When running the GenomeSTRiP test scripts, I get the following error:
hovelson@fantasia:/net/amd/hovelson/bin/svtoolkit/installtest$ ./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 11:28:59,836 QScriptManager - Compiling 2 QScripts
INFO 11:29:05,070 QScriptManager - Compilation complete
INFO 11:29:07,186 HelpFormatter - ---------------------------------------------------------
INFO 11:29:07,186 HelpFormatter - Program Name: org.broadinstitute.sting.queue.QCommandLine
INFO 11:29:07,187 HelpFormatter - Program Args: -S /net/amd/hovelson/bin/svtoolkit/qscript/SVPreprocess.q -S /net/amd/hovelson/bin/svtoolkit/qscript/SVQScript.q -gatk /net/amd/hovelson/bin/svtoolkit/lib/gatk/GenomeAnalysisTK.jar -cp /net/amd/hovelson/bin/svtoolkit/lib/SVToolkit.jar:/net/amd/hovelson/bin/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/net/amd/hovelson/bin/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 11:29:07,187 HelpFormatter - Date/Time: 2013/01/02 11:29:07
INFO 11:29:07,187 HelpFormatter - ---------------------------------------------------------
INFO 11:29:07,187 HelpFormatter - ---------------------------------------------------------
INFO 11:29:07,189 QCommandLine - Scripting SVPreprocess
INFO 11:29:07,274 QCommandLine - Added 7 functions
INFO 11:29:07,275 QGraph - Generating graph.
INFO 11:29:07,295 QGraph - Running jobs.
INFO 11:29:07,301 QGraph - Deleting intermediate files.
INFO 11:29:07,302 QCommandLine - Done
INFO 11:29:09,298 QScriptManager - Compiling 2 QScripts
INFO 11:29:14,170 QScriptManager - Compilation complete
INFO 11:29:16,335 HelpFormatter - ---------------------------------------------------------
INFO 11:29:16,335 HelpFormatter - Program Name: org.broadinstitute.sting.queue.QCommandLine
INFO 11:29:16,335 HelpFormatter - Program Args: -S /net/amd/hovelson/bin/svtoolkit/qscript/SVDiscovery.q -S /net/amd/hovelson/bin/svtoolkit/qscript/SVQScript.q -gatk /net/amd/hovelson/bin/svtoolkit/lib/gatk/GenomeAnalysisTK.jar -cp /net/amd/hovelson/bin/svtoolkit/lib/SVToolkit.jar:/net/amd/hovelson/bin/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/net/amd/hovelson/bin/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 11:29:16,335 HelpFormatter - Date/Time: 2013/01/02 11:29:16
INFO 11:29:16,335 HelpFormatter - ---------------------------------------------------------
INFO 11:29:16,336 HelpFormatter - ---------------------------------------------------------
INFO 11:29:16,337 QCommandLine - Scripting SVDiscovery
INFO 11:29:16,406 QCommandLine - Added 2 functions
INFO 11:29:16,406 QGraph - Generating graph.
INFO 11:29:16,417 QGraph - Running jobs.
INFO 11:29:16,422 QGraph - Deleting intermediate files.
INFO 11:29:16,423 QCommandLine - Done
Files - and benchmark/test1.discovery.vcf differ
Error: test results do not match benchmark data
When I run diff on the test1.discovery.vcf file and benchmark/test1.discovery.vcf files, I see the only difference (aside from header lines in the new test1.discovery.vcf) is that for the variant at chr1:61892810 in the new test1.discovery.vcf file, the GSDEPTHRANKSUMPVALUE=0.008935781, while in the benchmark test1.discovery.vcf, GSDEPTHRANKSUMPVALUE=0.00893578.
hovelson@fantasia:/net/amd/hovelson/bin/svtoolkit/installtest$ diff test1.discovery.vcf benchmark/test1.discovery.vcf
64,65d63
< ##fileDate=20130102
< ##source=GenomeSTRiP_v1.03
71c69
< 1 61892810 DEL_5 C <DEL> . PASS CIEND=-48,49;CIPOS=-48,49;END=61893084;GSCOHERENCE=-1.9466175377489223;GSCOHFN=-0.9733087688744612;GSCOHPVALUE=0.424;GSCOORDS=61892760,61892812,61893082,61893133;GSDEPTHCALLTHRESHOLD=0.044234556389327793;GSDEPTHNOBSSAMPLES=2;GSDEPTHNTOTALSAMPLES=2;GSDEPTHOBSSAMPLES=NA11919,NA12155;GSDEPTHPVALUE=1.15E-4;GSDEPTHRANKSUMPVALUE=0.008935781;GSDEPTHRATIO=0.056153717139996895;GSDMAX=369;GSDMIN=1;GSDOPT=166;GSDSPAN=269;GSMEMBNPAIRS=2;GSMEMBNSAMPLES=2;GSMEMBOBSSAMPLES=NA12155,NA11919;GSMEMBPVALUE=0.1092;GSMEMBSTATISTIC=62.062109599506876;GSNDEPTHCALLS=2;GSNPAIRS=2;GSNSAMPLES=2;GSOBSINREADS=1;GSOBSOUTREADS=12458;GSOUTLEFT=0;GSOUTLIERS=0;GSOUTRIGHT=0;GSREADGROUPS=SRR003123,SRR006158;GSREADNAMES=SRR003123.2623325,SRR006158.13888082;GSSAMPLES=NA12155,NA11919;GSUNOBSINREADS=492;GSUNOBSOUTREADS=344185;IMPRECISE;SVLEN=-166;SVTYPE=DEL
---
> 1 61892810 DEL_5 C <DEL> . PASS CIEND=-48,49;CIPOS=-48,49;END=61893084;GSCOHERENCE=-1.9466175377489223;GSCOHFN=-0.9733087688744612;GSCOHPVALUE=0.424;GSCOORDS=61892760,61892812,61893082,61893133;GSDEPTHCALLTHRESHOLD=0.044234556389327793;GSDEPTHNOBSSAMPLES=2;GSDEPTHNTOTALSAMPLES=2;GSDEPTHOBSSAMPLES=NA11919,NA12155;GSDEPTHPVALUE=1.15E-4;GSDEPTHRANKSUMPVALUE=0.00893578;GSDEPTHRATIO=0.056153717139996895;GSDMAX=369;GSDMIN=1;GSDOPT=166;GSDSPAN=269;GSMEMBNPAIRS=2;GSMEMBNSAMPLES=2;GSMEMBOBSSAMPLES=NA12155,NA11919;GSMEMBPVALUE=0.1092;GSMEMBSTATISTIC=62.062109599506876;GSNDEPTHCALLS=2;GSNPAIRS=2;GSNSAMPLES=2;GSOBSINREADS=1;GSOBSOUTREADS=12458;GSOUTLEFT=0;GSOUTLIERS=0;GSOUTRIGHT=0;GSREADGROUPS=SRR003123,SRR006158;GSREADNAMES=SRR003123.2623325,SRR006158.13888082;GSSAMPLES=NA12155,NA11919;GSUNOBSINREADS=492;GSUNOBSOUTREADS=344185;IMPRECISE;SVLEN=-166;SVTYPE=DEL
Any thoughts on why I'm seeing this difference?