Re: [svtoolkit-help] genotyping.sh crashing

[Bob H. <han...@br...>]

The problem is that the previous job (bwa index 
test2/altalign/installtest.sites.alt.fasta) failed.
And I am guessing it didn't return a non-zero exit status or it didn't 
create the bwt index files.

There is a similar report here 
http://gatkforums.broadinstitute.org/discussion/1338/genome-strip-test-installation-error
where they say they had an newer version of bwa installed, so this may 
be similar.

-Bob

On 9/23/12 9:12 AM, yw wrote:
> Hi,
>    I am trying to configure GenomeSTRiP. Till now, I have run 
> discovery.sh without error. When I came to genotyping.sh. It went 
> wrong. All the output information is shown below:
>
> SVToolkit version 1.04 (build 982)
> Build date: 2012/08/10 18:30:21
> Web site: http://www.broadinstitute.org/gsa/wiki/index.php/Genome_STRiP
> INFO  15:58:10,295 QScriptManager - Compiling 2 QScripts
> INFO  15:58:20,855 QScriptManager - Compilation complete
> INFO  15:58:20,987 HelpFormatter - 
> ---------------------------------------------------------
> INFO  15:58:20,987 HelpFormatter - Program Name: 
> org.broadinstitute.sting.queue.QCommandLine
> INFO  15:58:20,988 HelpFormatter - Program Args: -S 
> /home/wbxie/software/svtoolkit/qscript/SVPreprocess.q -S 
> /home/wbxie/software/svtoolkit/qscript/SVQScript.q -gatk 
> /home/wbxie/software/svtoolkit/lib/gatk/GenomeAnalysisTK.jar -cp 
> /home/wbxie/software/svtoolkit/lib/SVToolkit.jar:/home/wbxie/software/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/home/wbxie/software/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 -copyNumberMaskFile 
> data/cn2_mask_g1k_b36_chr1.fasta -runDirectory test2 -md 
> test2/metadata -computeGCProfiles -jobLogDir test2/logs -I 
> data/installtest.bam -run
> INFO  15:58:20,988 HelpFormatter - Date/Time: 2012/09/23 15:58:20
> INFO  15:58:20,989 HelpFormatter - 
> ---------------------------------------------------------
> INFO  15:58:20,989 HelpFormatter - 
> ---------------------------------------------------------
> INFO  15:58:20,995 QCommandLine - Scripting SVPreprocess
> INFO  15:58:21,326 QCommandLine - Added 10 functions
> INFO  15:58:21,326 QGraph - Generating graph.
> INFO  15:58:21,371 QGraph - Generating scatter gather jobs.
> INFO  15:58:21,373 QGraph - Removing original jobs.
> INFO  15:58:21,375 QGraph - Adding scatter gather jobs.
> INFO  15:58:21,376 QGraph - Regenerating graph.
> INFO  15:58:21,388 QGraph - Running jobs.
> INFO  15:58:21,479 FunctionEdge - Starting: java -Xmx4g 
> -Djava.io.tmpdir=/home/wbxie/software/svtoolkit/installtest/tmpdir -cp 
> /home/wbxie/software/svtoolkit/lib/SVToolkit.jar:/home/wbxie/software/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/home/wbxie/software/svtoolkit/lib/gatk/Queue.jar 
> org.broadinstitute.sting.gatk.CommandLineGATK -T 
> ComputeInsertSizeHistograms -R 
> /home/wbxie/software/svtoolkit/installtest/data/human_b36_chr1.fasta 
> -I /home/wbxie/software/svtoolkit/installtest/data/installtest.bam -O 
> /home/wbxie/software/svtoolkit/installtest/test2/metadata/isd/installtest.hist.bin 
> -md test2/metadata -createEmpty
> INFO  15:58:21,480 FunctionEdge - Output written to 
> /home/wbxie/software/svtoolkit/installtest/test2/logs/Q-16019@r910-1.out
> INFO  15:59:14,762 QGraph - 9 Pend, 1 Run, 0 Fail, 0 Done
> INFO  15:59:14,773 FunctionEdge - Done: java -Xmx4g 
> -Djava.io.tmpdir=/home/wbxie/software/svtoolkit/installtest/tmpdir -cp 
> /home/wbxie/software/svtoolkit/lib/SVToolkit.jar:/home/wbxie/software/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/home/wbxie/software/svtoolkit/lib/gatk/Queue.jar 
> org.broadinstitute.sting.gatk.CommandLineGATK -T 
> ComputeInsertSizeHistograms -R 
> /home/wbxie/software/svtoolkit/installtest/data/human_b36_chr1.fasta 
> -I /home/wbxie/software/svtoolkit/installtest/data/installtest.bam -O 
> /home/wbxie/software/svtoolkit/installtest/test2/metadata/isd/installtest.hist.bin 
> -md test2/metadata -createEmpty
> INFO  15:59:14,778 FunctionEdge - Starting: java -Xmx4g 
> -Djava.io.tmpdir=/home/wbxie/software/svtoolkit/installtest/tmpdir -cp 
> /home/wbxie/software/svtoolkit/lib/SVToolkit.jar:/home/wbxie/software/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/home/wbxie/software/svtoolkit/lib/gatk/Queue.jar 
> -cp 
> "/home/wbxie/software/svtoolkit/lib/SVToolkit.jar:/home/wbxie/software/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/home/wbxie/software/svtoolkit/lib/gatk/Queue.jar" 
> org.broadinstitute.sv.apps.MergeInsertSizeHistograms -I 
> /home/wbxie/software/svtoolkit/installtest/test2/metadata/isd/installtest.hist.bin 
> -O /home/wbxie/software/svtoolkit/installtest/test2/metadata/isd.hist.bin
> INFO  15:59:14,778 FunctionEdge - Output written to 
> /home/wbxie/software/svtoolkit/installtest/test2/logs/Q-16019@r910-2.out
> INFO  15:59:15,234 FunctionEdge - Starting: java -Xmx4g 
> -Djava.io.tmpdir=/home/wbxie/software/svtoolkit/installtest/tmpdir -cp 
> /home/wbxie/software/svtoolkit/lib/SVToolkit.jar:/home/wbxie/software/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/home/wbxie/software/svtoolkit/lib/gatk/Queue.jar 
> org.broadinstitute.sting.gatk.CommandLineGATK -T 
> ComputeReadDepthCoverage -R 
> /home/wbxie/software/svtoolkit/installtest/data/human_b36_chr1.fasta 
> -I /home/wbxie/software/svtoolkit/installtest/data/installtest.bam -O 
> /home/wbxie/software/svtoolkit/installtest/test2/metadata/depth/installtest.depth.txt 
> -md test2/metadata -genomeMaskFile data/human_b36_chr1.mask.fasta 
> -minMapQ 10
> INFO  15:59:15,235 FunctionEdge - Output written to 
> /home/wbxie/software/svtoolkit/installtest/test2/logs/Q-16019@r910-4.out
> INFO  16:00:08,246 QGraph - 7 Pend, 2 Run, 0 Fail, 1 Done
> INFO  16:00:08,249 FunctionEdge - Done: java -Xmx4g 
> -Djava.io.tmpdir=/home/wbxie/software/svtoolkit/installtest/tmpdir -cp 
> /home/wbxie/software/svtoolkit/lib/SVToolkit.jar:/home/wbxie/software/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/home/wbxie/software/svtoolkit/lib/gatk/Queue.jar 
> -cp 
> "/home/wbxie/software/svtoolkit/lib/SVToolkit.jar:/home/wbxie/software/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/home/wbxie/software/svtoolkit/lib/gatk/Queue.jar" 
> org.broadinstitute.sv.apps.MergeInsertSizeHistograms -I 
> /home/wbxie/software/svtoolkit/installtest/test2/metadata/isd/installtest.hist.bin 
> -O /home/wbxie/software/svtoolkit/installtest/test2/metadata/isd.hist.bin
> INFO  16:00:08,252 FunctionEdge - Done: java -Xmx4g 
> -Djava.io.tmpdir=/home/wbxie/software/svtoolkit/installtest/tmpdir -cp 
> /home/wbxie/software/svtoolkit/lib/SVToolkit.jar:/home/wbxie/software/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/home/wbxie/software/svtoolkit/lib/gatk/Queue.jar 
> org.broadinstitute.sting.gatk.CommandLineGATK -T 
> ComputeReadDepthCoverage -R 
> /home/wbxie/software/svtoolkit/installtest/data/human_b36_chr1.fasta 
> -I /home/wbxie/software/svtoolkit/installtest/data/installtest.bam -O 
> /home/wbxie/software/svtoolkit/installtest/test2/metadata/depth/installtest.depth.txt 
> -md test2/metadata -genomeMaskFile data/human_b36_chr1.mask.fasta 
> -minMapQ 10
> INFO  16:00:08,255 FunctionEdge - Starting: java -Xmx4g 
> -Djava.io.tmpdir=/home/wbxie/software/svtoolkit/installtest/tmpdir -cp 
> /home/wbxie/software/svtoolkit/lib/SVToolkit.jar:/home/wbxie/software/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/home/wbxie/software/svtoolkit/lib/gatk/Queue.jar 
> -cp 
> "/home/wbxie/software/svtoolkit/lib/SVToolkit.jar:/home/wbxie/software/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/home/wbxie/software/svtoolkit/lib/gatk/Queue.jar" 
> org.broadinstitute.sv.apps.ComputeInsertStatistics -I 
> /home/wbxie/software/svtoolkit/installtest/test2/metadata/isd.hist.bin 
> -O /home/wbxie/software/svtoolkit/installtest/test2/metadata/isd.stats.dat
> INFO  16:00:08,255 FunctionEdge - Output written to 
> /home/wbxie/software/svtoolkit/installtest/test2/logs/Q-16019@r910-3.out
> INFO  16:00:09,077 FunctionEdge - Starting: java -Xmx4g 
> -Djava.io.tmpdir=/home/wbxie/software/svtoolkit/installtest/tmpdir -cp 
> /home/wbxie/software/svtoolkit/lib/SVToolkit.jar:/home/wbxie/software/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/home/wbxie/software/svtoolkit/lib/gatk/Queue.jar 
> org.broadinstitute.sting.gatk.CommandLineGATK -T 
> ComputeReadSpanCoverage -R 
> /home/wbxie/software/svtoolkit/installtest/data/human_b36_chr1.fasta 
> -I /home/wbxie/software/svtoolkit/installtest/data/installtest.bam -O 
> /home/wbxie/software/svtoolkit/installtest/test2/metadata/spans/installtest.spans.txt 
> -md test2/metadata -maxInsertSizeStandardDeviations 3
> INFO  16:00:09,077 FunctionEdge - Output written to 
> /home/wbxie/software/svtoolkit/installtest/test2/logs/Q-16019@r910-6.out
> INFO  16:01:02,106 QGraph - 5 Pend, 2 Run, 0 Fail, 3 Done
> INFO  16:01:02,110 FunctionEdge - Done: java -Xmx4g 
> -Djava.io.tmpdir=/home/wbxie/software/svtoolkit/installtest/tmpdir -cp 
> /home/wbxie/software/svtoolkit/lib/SVToolkit.jar:/home/wbxie/software/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/home/wbxie/software/svtoolkit/lib/gatk/Queue.jar 
> -cp 
> "/home/wbxie/software/svtoolkit/lib/SVToolkit.jar:/home/wbxie/software/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/home/wbxie/software/svtoolkit/lib/gatk/Queue.jar" 
> org.broadinstitute.sv.apps.ComputeInsertStatistics -I 
> /home/wbxie/software/svtoolkit/installtest/test2/metadata/isd.hist.bin 
> -O /home/wbxie/software/svtoolkit/installtest/test2/metadata/isd.stats.dat
> INFO  16:01:02,113 FunctionEdge - Done: java -Xmx4g 
> -Djava.io.tmpdir=/home/wbxie/software/svtoolkit/installtest/tmpdir -cp 
> /home/wbxie/software/svtoolkit/lib/SVToolkit.jar:/home/wbxie/software/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/home/wbxie/software/svtoolkit/lib/gatk/Queue.jar 
> org.broadinstitute.sting.gatk.CommandLineGATK -T 
> ComputeReadSpanCoverage -R 
> /home/wbxie/software/svtoolkit/installtest/data/human_b36_chr1.fasta 
> -I /home/wbxie/software/svtoolkit/installtest/data/installtest.bam -O 
> /home/wbxie/software/svtoolkit/installtest/test2/metadata/spans/installtest.spans.txt 
> -md test2/metadata -maxInsertSizeStandardDeviations 3
> INFO  16:01:02,116 FunctionEdge - Starting: java -Xmx4g 
> -Djava.io.tmpdir=/home/wbxie/software/svtoolkit/installtest/tmpdir -cp 
> /home/wbxie/software/svtoolkit/lib/SVToolkit.jar:/home/wbxie/software/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/home/wbxie/software/svtoolkit/lib/gatk/Queue.jar 
> -cp 
> "/home/wbxie/software/svtoolkit/lib/SVToolkit.jar:/home/wbxie/software/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/home/wbxie/software/svtoolkit/lib/gatk/Queue.jar" 
> org.broadinstitute.sv.apps.MergeReadSpanCoverage -I 
> /home/wbxie/software/svtoolkit/installtest/test2/metadata/spans/installtest.spans.txt 
> -O /home/wbxie/software/svtoolkit/installtest/test2/metadata/spans.dat
> INFO  16:01:02,116 FunctionEdge - Output written to 
> /home/wbxie/software/svtoolkit/installtest/test2/logs/Q-16019@r910-7.out
> INFO  16:01:02,840 FunctionEdge - Starting: java -Xmx4g 
> -Djava.io.tmpdir=/home/wbxie/software/svtoolkit/installtest/tmpdir -cp 
> /home/wbxie/software/svtoolkit/lib/SVToolkit.jar:/home/wbxie/software/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/home/wbxie/software/svtoolkit/lib/gatk/Queue.jar 
> -cp 
> "/home/wbxie/software/svtoolkit/lib/SVToolkit.jar:/home/wbxie/software/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/home/wbxie/software/svtoolkit/lib/gatk/Queue.jar" 
> org.broadinstitute.sv.apps.MergeReadDepthCoverage -I 
> /home/wbxie/software/svtoolkit/installtest/test2/metadata/depth/installtest.depth.txt 
> -O /home/wbxie/software/svtoolkit/installtest/test2/metadata/depth.dat
> INFO  16:01:02,840 FunctionEdge - Output written to 
> /home/wbxie/software/svtoolkit/installtest/test2/logs/Q-16019@r910-5.out
> INFO  16:01:03,514 FunctionEdge - Starting: java -Xmx4g 
> -Djava.io.tmpdir=/home/wbxie/software/svtoolkit/installtest/tmpdir -cp 
> /home/wbxie/software/svtoolkit/lib/SVToolkit.jar:/home/wbxie/software/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/home/wbxie/software/svtoolkit/lib/gatk/Queue.jar 
> -cp 
> "/home/wbxie/software/svtoolkit/lib/SVToolkit.jar:/home/wbxie/software/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/home/wbxie/software/svtoolkit/lib/gatk/Queue.jar" 
> org.broadinstitute.sv.apps.ComputeGCProfiles -O 
> /home/wbxie/software/svtoolkit/installtest/test2/metadata/gcprofile/reference.gcprof.zip 
> -R data/human_b36_chr1.fasta -md test2/metadata -writeReferenceProfile 
> true -genomeMaskFile data/human_b36_chr1.mask.fasta 
> -copyNumberMaskFile data/cn2_mask_g1k_b36_chr1.fasta
> INFO  16:01:03,515 FunctionEdge - Output written to 
> /home/wbxie/software/svtoolkit/installtest/test2/logs/Q-16019@r910-8.out
> INFO  16:01:52,913 QGraph - 2 Pend, 3 Run, 0 Fail, 5 Done
> INFO  16:01:52,921 FunctionEdge - Done: java -Xmx4g 
> -Djava.io.tmpdir=/home/wbxie/software/svtoolkit/installtest/tmpdir -cp 
> /home/wbxie/software/svtoolkit/lib/SVToolkit.jar:/home/wbxie/software/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/home/wbxie/software/svtoolkit/lib/gatk/Queue.jar 
> -cp 
> "/home/wbxie/software/svtoolkit/lib/SVToolkit.jar:/home/wbxie/software/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/home/wbxie/software/svtoolkit/lib/gatk/Queue.jar" 
> org.broadinstitute.sv.apps.MergeReadSpanCoverage -I 
> /home/wbxie/software/svtoolkit/installtest/test2/metadata/spans/installtest.spans.txt 
> -O /home/wbxie/software/svtoolkit/installtest/test2/metadata/spans.dat
> INFO  16:01:52,923 FunctionEdge - Done: java -Xmx4g 
> -Djava.io.tmpdir=/home/wbxie/software/svtoolkit/installtest/tmpdir -cp 
> /home/wbxie/software/svtoolkit/lib/SVToolkit.jar:/home/wbxie/software/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/home/wbxie/software/svtoolkit/lib/gatk/Queue.jar 
> -cp 
> "/home/wbxie/software/svtoolkit/lib/SVToolkit.jar:/home/wbxie/software/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/home/wbxie/software/svtoolkit/lib/gatk/Queue.jar" 
> org.broadinstitute.sv.apps.MergeReadDepthCoverage -I 
> /home/wbxie/software/svtoolkit/installtest/test2/metadata/depth/installtest.depth.txt 
> -O /home/wbxie/software/svtoolkit/installtest/test2/metadata/depth.dat
> INFO  16:01:52,925 FunctionEdge - Done: java -Xmx4g 
> -Djava.io.tmpdir=/home/wbxie/software/svtoolkit/installtest/tmpdir -cp 
> /home/wbxie/software/svtoolkit/lib/SVToolkit.jar:/home/wbxie/software/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/home/wbxie/software/svtoolkit/lib/gatk/Queue.jar 
> -cp 
> "/home/wbxie/software/svtoolkit/lib/SVToolkit.jar:/home/wbxie/software/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/home/wbxie/software/svtoolkit/lib/gatk/Queue.jar" 
> org.broadinstitute.sv.apps.ComputeGCProfiles -O 
> /home/wbxie/software/svtoolkit/installtest/test2/metadata/gcprofile/reference.gcprof.zip 
> -R data/human_b36_chr1.fasta -md test2/metadata -writeReferenceProfile 
> true -genomeMaskFile data/human_b36_chr1.mask.fasta 
> -copyNumberMaskFile data/cn2_mask_g1k_b36_chr1.fasta
> INFO  16:01:52,927 FunctionEdge - Starting: java -Xmx4g 
> -Djava.io.tmpdir=/home/wbxie/software/svtoolkit/installtest/tmpdir -cp 
> /home/wbxie/software/svtoolkit/lib/SVToolkit.jar:/home/wbxie/software/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/home/wbxie/software/svtoolkit/lib/gatk/Queue.jar 
> -cp 
> "/home/wbxie/software/svtoolkit/lib/SVToolkit.jar:/home/wbxie/software/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/home/wbxie/software/svtoolkit/lib/gatk/Queue.jar" 
> org.broadinstitute.sv.apps.ComputeGCProfiles -I 
> /home/wbxie/software/svtoolkit/installtest/data/installtest.bam -O 
> /home/wbxie/software/svtoolkit/installtest/test2/metadata/gcprofile/installtest.bam.gcprof.zip 
> -R data/human_b36_chr1.fasta -md test2/metadata -referenceProfile 
> test2/metadata/gcprofile/reference.gcprof.zip -genomeMaskFile 
> data/human_b36_chr1.mask.fasta -copyNumberMaskFile 
> data/cn2_mask_g1k_b36_chr1.fasta
> INFO  16:01:52,928 FunctionEdge - Output written to 
> /home/wbxie/software/svtoolkit/installtest/test2/logs/Q-16019@r910-9.out
> INFO  16:02:00,425 QGraph - 1 Pend, 1 Run, 0 Fail, 8 Done
> INFO  16:02:22,924 FunctionEdge - Done: java -Xmx4g 
> -Djava.io.tmpdir=/home/wbxie/software/svtoolkit/installtest/tmpdir -cp 
> /home/wbxie/software/svtoolkit/lib/SVToolkit.jar:/home/wbxie/software/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/home/wbxie/software/svtoolkit/lib/gatk/Queue.jar 
> -cp 
> "/home/wbxie/software/svtoolkit/lib/SVToolkit.jar:/home/wbxie/software/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/home/wbxie/software/svtoolkit/lib/gatk/Queue.jar" 
> org.broadinstitute.sv.apps.ComputeGCProfiles -I 
> /home/wbxie/software/svtoolkit/installtest/data/installtest.bam -O 
> /home/wbxie/software/svtoolkit/installtest/test2/metadata/gcprofile/installtest.bam.gcprof.zip 
> -R data/human_b36_chr1.fasta -md test2/metadata -referenceProfile 
> test2/metadata/gcprofile/reference.gcprof.zip -genomeMaskFile 
> data/human_b36_chr1.mask.fasta -copyNumberMaskFile 
> data/cn2_mask_g1k_b36_chr1.fasta
> INFO  16:02:22,926 FunctionEdge - Starting: java -Xmx4g 
> -Djava.io.tmpdir=/home/wbxie/software/svtoolkit/installtest/tmpdir -cp 
> /home/wbxie/software/svtoolkit/lib/SVToolkit.jar:/home/wbxie/software/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/home/wbxie/software/svtoolkit/lib/gatk/Queue.jar 
> -cp 
> "/home/wbxie/software/svtoolkit/lib/SVToolkit.jar:/home/wbxie/software/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/home/wbxie/software/svtoolkit/lib/gatk/Queue.jar" 
> org.broadinstitute.sv.apps.MergeGCProfiles -I 
> /home/wbxie/software/svtoolkit/installtest/test2/metadata/gcprofile/installtest.bam.gcprof.zip 
> -O 
> /home/wbxie/software/svtoolkit/installtest/test2/metadata/gcprofiles.zip
> INFO  16:02:22,927 FunctionEdge - Output written to 
> /home/wbxie/software/svtoolkit/installtest/test2/logs/Q-16019@r910-10.out
> INFO  16:02:23,629 QGraph - 0 Pend, 1 Run, 0 Fail, 9 Done
> INFO  16:02:52,932 FunctionEdge - Done: java -Xmx4g 
> -Djava.io.tmpdir=/home/wbxie/software/svtoolkit/installtest/tmpdir -cp 
> /home/wbxie/software/svtoolkit/lib/SVToolkit.jar:/home/wbxie/software/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/home/wbxie/software/svtoolkit/lib/gatk/Queue.jar 
> -cp 
> "/home/wbxie/software/svtoolkit/lib/SVToolkit.jar:/home/wbxie/software/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/home/wbxie/software/svtoolkit/lib/gatk/Queue.jar" 
> org.broadinstitute.sv.apps.MergeGCProfiles -I 
> /home/wbxie/software/svtoolkit/installtest/test2/metadata/gcprofile/installtest.bam.gcprof.zip 
> -O 
> /home/wbxie/software/svtoolkit/installtest/test2/metadata/gcprofiles.zip
> INFO  16:02:52,933 QGraph - 0 Pend, 0 Run, 0 Fail, 10 Done
> INFO  16:02:52,935 QCommandLine - Done
> INFO  16:03:01,726 QScriptManager - Compiling 2 QScripts
> INFO  16:03:12,978 QScriptManager - Compilation complete
> INFO  16:03:13,101 HelpFormatter - 
> ---------------------------------------------------------
> INFO  16:03:13,102 HelpFormatter - Program Name: 
> org.broadinstitute.sting.queue.QCommandLine
> INFO  16:03:13,103 HelpFormatter - Program Args: -S 
> /home/wbxie/software/svtoolkit/qscript/SVAltAlign.q -S 
> /home/wbxie/software/svtoolkit/qscript/SVQScript.q -gatk 
> /home/wbxie/software/svtoolkit/lib/gatk/GenomeAnalysisTK.jar -cp 
> /home/wbxie/software/svtoolkit/lib/SVToolkit.jar:/home/wbxie/software/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/home/wbxie/software/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 -runDirectory test2 -md test2/metadata 
> -jobLogDir test2/logs -vcf data/installtest.sites.vcf -I 
> data/installtest.bam -O test2/installtest.alt.bam -run
> INFO  16:03:13,103 HelpFormatter - Date/Time: 2012/09/23 16:03:13
> INFO  16:03:13,104 HelpFormatter - 
> ---------------------------------------------------------
> INFO  16:03:13,104 HelpFormatter - 
> ---------------------------------------------------------
> INFO  16:03:13,110 QCommandLine - Scripting SVAltAlign
> INFO  16:03:13,365 QCommandLine - Added 7 functions
> INFO  16:03:13,366 QGraph - Generating graph.
> INFO  16:03:13,407 QGraph - Generating scatter gather jobs.
> INFO  16:03:13,409 QGraph - Removing original jobs.
> INFO  16:03:13,411 QGraph - Adding scatter gather jobs.
> INFO  16:03:13,412 QGraph - Regenerating graph.
> INFO  16:03:13,419 QGraph - Running jobs.
> INFO  16:03:13,484 FunctionEdge - Starting: java -Xmx4g 
> -Djava.io.tmpdir=/home/wbxie/software/svtoolkit/installtest/tmpdir -cp 
> /home/wbxie/software/svtoolkit/lib/SVToolkit.jar:/home/wbxie/software/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/home/wbxie/software/svtoolkit/lib/gatk/Queue.jar 
> -cp 
> "/home/wbxie/software/svtoolkit/lib/SVToolkit.jar:/home/wbxie/software/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/home/wbxie/software/svtoolkit/lib/gatk/Queue.jar" 
> org.broadinstitute.sv.apps.GenerateAltAlleleFasta -I 
> /home/wbxie/software/svtoolkit/installtest/data/installtest.sites.vcf 
> -O 
> /home/wbxie/software/svtoolkit/installtest/test2/altalign/installtest.sites.alt.fasta 
> -R data/human_b36_chr1.fasta
> INFO  16:03:13,484 FunctionEdge - Output written to 
> /home/wbxie/software/svtoolkit/installtest/test2/logs/Q-16882@r910-1.out
> INFO  16:03:14,183 QGraph - 6 Pend, 1 Run, 0 Fail, 0 Done
> INFO  16:03:43,481 FunctionEdge - Done: java -Xmx4g 
> -Djava.io.tmpdir=/home/wbxie/software/svtoolkit/installtest/tmpdir -cp 
> /home/wbxie/software/svtoolkit/lib/SVToolkit.jar:/home/wbxie/software/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/home/wbxie/software/svtoolkit/lib/gatk/Queue.jar 
> -cp 
> "/home/wbxie/software/svtoolkit/lib/SVToolkit.jar:/home/wbxie/software/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/home/wbxie/software/svtoolkit/lib/gatk/Queue.jar" 
> org.broadinstitute.sv.apps.GenerateAltAlleleFasta -I 
> /home/wbxie/software/svtoolkit/installtest/data/installtest.sites.vcf 
> -O 
> /home/wbxie/software/svtoolkit/installtest/test2/altalign/installtest.sites.alt.fasta 
> -R data/human_b36_chr1.fasta
> INFO  16:03:43,484 FunctionEdge - Starting: java -Xmx4g 
> -Djava.io.tmpdir=/home/wbxie/software/svtoolkit/installtest/tmpdir -cp 
> /home/wbxie/software/svtoolkit/lib/SVToolkit.jar:/home/wbxie/software/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/home/wbxie/software/svtoolkit/lib/gatk/Queue.jar 
> -cp 
> "/home/wbxie/software/svtoolkit/lib/SVToolkit.jar:/home/wbxie/software/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/home/wbxie/software/svtoolkit/lib/gatk/Queue.jar" 
> net.sf.picard.sam.CreateSequenceDictionary 
> O=/home/wbxie/software/svtoolkit/installtest/test2/altalign/installtest.sites.alt.dict 
> R=test2/altalign/installtest.sites.alt.fasta 
> TRUNCATE_NAMES_AT_WHITESPACE=TRUE
> INFO  16:03:43,485 FunctionEdge - Output written to 
> /home/wbxie/software/svtoolkit/installtest/test2/logs/Q-16882@r910-2.out
> INFO  16:03:43,986 FunctionEdge - Starting: java -Xmx4g 
> -Djava.io.tmpdir=/home/wbxie/software/svtoolkit/installtest/tmpdir -cp 
> /home/wbxie/software/svtoolkit/lib/SVToolkit.jar:/home/wbxie/software/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/home/wbxie/software/svtoolkit/lib/gatk/Queue.jar 
> -cp 
> "/home/wbxie/software/svtoolkit/lib/SVToolkit.jar:/home/wbxie/software/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/home/wbxie/software/svtoolkit/lib/gatk/Queue.jar" 
> org.broadinstitute.sv.apps.IndexFastaFile -I 
> /home/wbxie/software/svtoolkit/installtest/test2/altalign/installtest.sites.alt.fasta 
> -O 
> /home/wbxie/software/svtoolkit/installtest/test2/altalign/installtest.sites.alt.fasta.fai
> INFO  16:03:43,987 FunctionEdge - Output written to 
> /home/wbxie/software/svtoolkit/installtest/test2/logs/Q-16882@r910-3.out
> INFO  16:03:44,572 FunctionEdge - Starting: bwa index 
> test2/altalign/installtest.sites.alt.fasta
> INFO  16:03:44,572 FunctionEdge - Output written to 
> /home/wbxie/software/svtoolkit/installtest/test2/logs/Q-16882@r910-4.out
> INFO  16:03:44,680 QGraph - 3 Pend, 3 Run, 0 Fail, 1 Done
> INFO  16:04:13,485 FunctionEdge - Done: java -Xmx4g 
> -Djava.io.tmpdir=/home/wbxie/software/svtoolkit/installtest/tmpdir -cp 
> /home/wbxie/software/svtoolkit/lib/SVToolkit.jar:/home/wbxie/software/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/home/wbxie/software/svtoolkit/lib/gatk/Queue.jar 
> -cp 
> "/home/wbxie/software/svtoolkit/lib/SVToolkit.jar:/home/wbxie/software/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/home/wbxie/software/svtoolkit/lib/gatk/Queue.jar" 
> net.sf.picard.sam.CreateSequenceDictionary 
> O=/home/wbxie/software/svtoolkit/installtest/test2/altalign/installtest.sites.alt.dict 
> R=test2/altalign/installtest.sites.alt.fasta 
> TRUNCATE_NAMES_AT_WHITESPACE=TRUE
> INFO  16:04:13,487 FunctionEdge - Done: java -Xmx4g 
> -Djava.io.tmpdir=/home/wbxie/software/svtoolkit/installtest/tmpdir -cp 
> /home/wbxie/software/svtoolkit/lib/SVToolkit.jar:/home/wbxie/software/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/home/wbxie/software/svtoolkit/lib/gatk/Queue.jar 
> -cp 
> "/home/wbxie/software/svtoolkit/lib/SVToolkit.jar:/home/wbxie/software/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/home/wbxie/software/svtoolkit/lib/gatk/Queue.jar" 
> org.broadinstitute.sv.apps.IndexFastaFile -I 
> /home/wbxie/software/svtoolkit/installtest/test2/altalign/installtest.sites.alt.fasta 
> -O 
> /home/wbxie/software/svtoolkit/installtest/test2/altalign/installtest.sites.alt.fasta.fai
> INFO  16:04:13,489 FunctionEdge - Done: bwa index 
> test2/altalign/installtest.sites.alt.fasta
> INFO  16:04:13,514 FunctionEdge - Starting: java -Xmx1g 
> -Djava.io.tmpdir=/home/wbxie/software/svtoolkit/installtest/tmpdir -cp 
> /home/wbxie/software/svtoolkit/lib/SVToolkit.jar:/home/wbxie/software/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/home/wbxie/software/svtoolkit/lib/gatk/Queue.jar 
> org.broadinstitute.sting.gatk.CommandLineGATK -T SVAltAligner -R 
> /home/wbxie/software/svtoolkit/installtest/data/human_b36_chr1.fasta 
> -I /home/wbxie/software/svtoolkit/installtest/data/installtest.bam -O 
> /home/wbxie/software/svtoolkit/installtest/test2/altalign/installtest.alt.bam 
> -md test2/metadata -U ALLOW_UNINDEXED_BAM -altReference 
> test2/altalign/installtest.sites.alt.fasta -alignUnmappedMates true
> INFO  16:04:13,514 FunctionEdge - Output written to 
> /home/wbxie/software/svtoolkit/installtest/test2/logs/Q-16882@r910-5.out
> ERROR 16:05:01,564 FunctionEdge - Error: java -Xmx1g 
> -Djava.io.tmpdir=/home/wbxie/software/svtoolkit/installtest/tmpdir -cp 
> /home/wbxie/software/svtoolkit/lib/SVToolkit.jar:/home/wbxie/software/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/home/wbxie/software/svtoolkit/lib/gatk/Queue.jar 
> org.broadinstitute.sting.gatk.CommandLineGATK -T SVAltAligner -R 
> /home/wbxie/software/svtoolkit/installtest/data/human_b36_chr1.fasta 
> -I /home/wbxie/software/svtoolkit/installtest/data/installtest.bam -O 
> /home/wbxie/software/svtoolkit/installtest/test2/altalign/installtest.alt.bam 
> -md test2/metadata -U ALLOW_UNINDEXED_BAM -altReference 
> test2/altalign/installtest.sites.alt.fasta -alignUnmappedMates true
> org.broadinstitute.sting.queue.util.JobExitException: Failed to run job.
> Command line:
> sh 
> /home/wbxie/software/svtoolkit/installtest/tmpdir/.exec5518112783651967939
> Exit code: 1
> Standard error contained:
> INFO  16:04:19,251 HelpFormatter - 
> -----------------------------------------------------------------------------------
> INFO  16:04:19,256 HelpFormatter - The Genome Analysis Toolkit (GATK) 
> v1.0-6121-g40e3165, Compiled 2011/09/04 20:57:29
> INFO  16:04:19,256 HelpFormatter - Copyright (c) 2010 The Broad Institute
> INFO  16:04:19,257 HelpFormatter - Please view our documentation at 
> http://www.broadinstitute.org/gsa/wiki
> INFO  16:04:19,257 HelpFormatter - For support, please view our 
> support site at http://getsatisfaction.com/gsa
> INFO  16:04:19,258 HelpFormatter - Program Args: -T SVAltAligner -R 
> /home/wbxie/software/svtoolkit/installtest/data/human_b36_chr1.fasta 
> -I /home/wbxie/software/svtoolkit/installtest/data/installtest.bam -O 
> /home/wbxie/software/svtoolkit/installtest/test2/altalign/installtest.alt.bam 
> -md test2/metadata -U ALLOW_UNINDEXED_BAM -altReference 
> test2/altalign/installtest.sites.alt.fasta -alignUnmappedMates true
> INFO  16:04:19,258 HelpFormatter - Date/Time: 2012/09/23 16:04:19
> INFO  16:04:19,259 HelpFormatter - 
> -----------------------------------------------------------------------------------
> INFO  16:04:19,259 HelpFormatter - 
> -----------------------------------------------------------------------------------
> INFO  16:04:19,271 GenomeAnalysisEngine - Strictness is SILENT
> ##### ERROR 
> ------------------------------------------------------------------------------------------
> ##### ERROR stack trace
> org.broadinstitute.sting.utils.exceptions.ReviewedStingException: 
> Reverse BWT file is missing; please rerun 'bwa aln' to regenerate it.
>     at 
> org.broadinstitute.sting.alignment.bwa.c.BWACAligner.<init>(BWACAligner.java:39)
>     at 
> org.broadinstitute.sv.breakpoint.BreakpointAligner.initialize(BreakpointAligner.java:46)
>     at 
> org.broadinstitute.sv.breakpoint.SVAltAlignerWalker.initialize(SVAltAlignerWalker.java:86)
>     at 
> org.broadinstitute.sting.gatk.executive.LinearMicroScheduler.execute(LinearMicroScheduler.java:49)
>     at 
> org.broadinstitute.sting.gatk.GenomeAnalysisEngine.execute(GenomeAnalysisEngine.java:234)
>     at 
> org.broadinstitute.sting.gatk.CommandLineExecutable.execute(CommandLineExecutable.java:113)
>     at 
> org.broadinstitute.sting.commandline.CommandLineProgram.start(CommandLineProgram.java:221)
>     at 
> org.broadinstitute.sting.gatk.CommandLineGATK.main(CommandLineGATK.java:87)
> ##### 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: Reverse BWT file is missing; please rerun 'bwa 
> aln' to regenerate it.
> ##### 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  16:05:01,566 QGraph - 2 Pend, 1 Run, 0 Fail, 4 Done
> INFO  16:05:01,567 QGraph - 2 Pend, 0 Run, 1 Fail, 4 Done
> INFO  16:05:01,567 QCommandLine - Done with errors
> INFO  16:05:01,569 QGraph - -------
> INFO  16:05:01,575 QGraph - Failed: java -Xmx1g 
> -Djava.io.tmpdir=/home/wbxie/software/svtoolkit/installtest/tmpdir -cp 
> /home/wbxie/software/svtoolkit/lib/SVToolkit.jar:/home/wbxie/software/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/home/wbxie/software/svtoolkit/lib/gatk/Queue.jar 
> org.broadinstitute.sting.gatk.CommandLineGATK -T SVAltAligner -R 
> /home/wbxie/software/svtoolkit/installtest/data/human_b36_chr1.fasta 
> -I /home/wbxie/software/svtoolkit/installtest/data/installtest.bam -O 
> /home/wbxie/software/svtoolkit/installtest/test2/altalign/installtest.alt.bam 
> -md test2/metadata -U ALLOW_UNINDEXED_BAM -altReference 
> test2/altalign/installtest.sites.alt.fasta -alignUnmappedMates true
> INFO  16:05:01,576 QGraph - Log: 
> /home/wbxie/software/svtoolkit/installtest/test2/logs/Q-16882@r910-5.out
>
> Any advices? Thank you in advance.
>
> Andrew
>
>
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