[svtoolkit-help] installtest error

[w y <yw...@we...>]

Hi,
When I ran discovery.sh, I got an error:
Files - and benchmark/test1.discovery.vcf differ
Error: test results do not match benchmark data

Besides, I got another error when I ran genotyping.sh:
INFO  18:09:37,496 ShellJobRunner - Starting: bwa index
test2/altalign/installtest.sites.alt.fasta
INFO  18:09:37,497 ShellJobRunner - Output written to
/home/yaowen/soft/svtoolkit_1.03.619/installtest/test2/logs/Q-11685@node12-4.out
INFO  18:09:37,567 ShellJobRunner - Done: bwa index
test2/altalign/installtest.sites.alt.fasta
INFO  18:09:37,587 ShellJobRunner - Starting: java -Xmx1g
-Djava.io.tmpdir=/home/yaowen/soft/svtoolkit_1.03.619/installtest/tmpdir
-cp
/home/yaowen/soft/svtoolkit_1.03.619/lib/SVToolkit.jar:/home/yaowen/soft/svtoolkit_1.03.619/lib/gatk/GenomeAnalysisTK.jar:/home/yaowen/soft/svtoolkit_1.03.619/lib/gatk/Queue.jar
org.broadinstitute.sting.gatk.CommandLineGATK -T SVAltAligner -R
/home/yaowen/soft/svtoolkit_1.03.619/installtest/data/human_b36_chr1.fasta
-I /home/yaowen/soft/svtoolkit_1.03.619/installtest/data/installtest.bam -O
/home/yaowen/soft/svtoolkit_1.03.619/installtest/test2/altalign/installtest.alt.bam
-md test2/metadata -U ALLOW_UNINDEXED_BAM -altReference
test2/altalign/installtest.sites.alt.fasta -alignUnmappedMates true
INFO  18:09:37,587 ShellJobRunner - Output written to
/home/yaowen/soft/svtoolkit_1.03.619/installtest/test2/logs/Q-11685@node12-5.out
ERROR 18:09:43,369 ShellJobRunner - Error: java -Xmx1g
-Djava.io.tmpdir=/home/yaowen/soft/svtoolkit_1.03.619/installtest/tmpdir
-cp
/home/yaowen/soft/svtoolkit_1.03.619/lib/SVToolkit.jar:/home/yaowen/soft/svtoolkit_1.03.619/lib/gatk/GenomeAnalysisTK.jar:/home/yaowen/soft/svtoolkit_1.03.619/lib/gatk/Queue.jar
org.broadinstitute.sting.gatk.CommandLineGATK -T SVAltAligner -R
/home/yaowen/soft/svtoolkit_1.03.619/installtest/data/human_b36_chr1.fasta
-I /home/yaowen/soft/svtoolkit_1.03.619/installtest/data/installtest.bam -O
/home/yaowen/soft/svtoolkit_1.03.619/installtest/test2/altalign/installtest.alt.bam
-md test2/metadata -U ALLOW_UNINDEXED_BAM -altReference
test2/altalign/installtest.sites.alt.fasta -alignUnmappedMates true
ERROR 18:09:43,370 ShellJobRunner - INFO  18:09:42,208 HelpFormatter -
---------------------------------------------------------------------------
INFO  18:09:42,210 HelpFormatter - The Genome Analysis Toolkit (GATK)
v1.0.5039M, Compiled 2011/01/20 22:58:34
INFO  18:09:42,211 HelpFormatter - Copyright (c) 2010 The Broad Institute
INFO  18:09:42,211 HelpFormatter - Please view our documentation at
http://www.broadinstitute.org/gsa/wiki
INFO  18:09:42,211 HelpFormatter - For support, please view our support
site at http://getsatisfaction.com/gsa
INFO  18:09:42,211 HelpFormatter - Program Args: -T SVAltAligner -R
/home/yaowen/soft/svtoolkit_1.03.619/installtest/data/human_b36_chr1.fasta
-I /home/yaowen/soft/svtoolkit_1.03.619/installtest/data/installtest.bam -O
/home/yaowen/soft/svtoolkit_1.03.619/installtest/test2/altalign/installtest.alt.bam
-md test2/metadata -U ALLOW_UNINDEXED_BAM -altReference
test2/altalign/installtest.sites.alt.fasta -alignUnmappedMates true
INFO  18:09:42,211 HelpFormatter - Date/Time: 2011/12/08 18:09:42
INFO  18:09:42,211 HelpFormatter -
---------------------------------------------------------------------------
INFO  18:09:42,211 HelpFormatter -
---------------------------------------------------------------------------
INFO  18:09:42,215 GenomeAnalysisEngine - Strictness is SILENT
#
# An unexpected error has been detected by Java Runtime Environment:
#
#  SIGFPE (0x8) at pc=0x0000003027607927, pid=11823, tid=1076017504
#
# Java VM: Java HotSpot(TM) 64-Bit Server VM (11.2-b01 mixed mode
linux-amd64)
# Problematic frame:
# C  [ld-linux-x86-64.so.2+0x7927]
#
# An error report file with more information is saved as:
# /home/yaowen/soft/svtoolkit_1.03.619/installtest/hs_err_pid11823.log
#
# If you would like to submit a bug report, please visit:
#   http://java.sun.com/webapps/bugreport/crash.jsp
# The crash happened outside the Java Virtual Machine in native code.
# See problematic frame for where to report the bug.
#
/home/yaowen/soft/svtoolkit_1.03.619/installtest/tmpdir/.exec9048318414659209772:
line 2: 11823 Aborted                 java -Xmx1g
-Djava.io.tmpdir=/home/yaowen/soft/svtoolkit_1.03.619/installtest/tmpdir
-cp
/home/yaowen/soft/svtoolkit_1.03.619/lib/SVToolkit.jar:/home/yaowen/soft/svtoolkit_1.03.619/lib/gatk/GenomeAnalysisTK.jar:/home/yaowen/soft/svtoolkit_1.03.619/lib/gatk/Queue.jar
org.broadinstitute.sting.gatk.CommandLineGATK -T SVAltAligner -R
/home/yaowen/soft/svtoolkit_1.03.619/installtest/data/human_b36_chr1.fasta
-I /home/yaowen/soft/svtoolkit_1.03.619/installtest/data/installtest.bam -O
/home/yaowen/soft/svtoolkit_1.03.619/installtest/test2/altalign/installtest.alt.bam
-md test2/metadata -U ALLOW_UNINDEXED_BAM -altReference
test2/altalign/installtest.sites.alt.fasta -alignUnmappedMates true

INFO  18:09:43,373 QCommandLine - Done with errors
INFO  18:09:43,375 QGraph - -------
INFO  18:09:43,385 QGraph - Failed: java -Xmx1g
-Djava.io.tmpdir=/home/yaowen/soft/svtoolkit_1.03.619/installtest/tmpdir
-cp
/home/yaowen/soft/svtoolkit_1.03.619/lib/SVToolkit.jar:/home/yaowen/soft/svtoolkit_1.03.619/lib/gatk/GenomeAnalysisTK.jar:/home/yaowen/soft/svtoolkit_1.03.619/lib/gatk/Queue.jar
org.broadinstitute.sting.gatk.CommandLineGATK -T SVAltAligner -R
/home/yaowen/soft/svtoolkit_1.03.619/installtest/data/human_b36_chr1.fasta
-I /home/yaowen/soft/svtoolkit_1.03.619/installtest/data/installtest.bam -O
/home/yaowen/soft/svtoolkit_1.03.619/installtest/test2/altalign/installtest.alt.bam
-md test2/metadata -U ALLOW_UNINDEXED_BAM -altReference
test2/altalign/installtest.sites.alt.fasta -alignUnmappedMates true
INFO  18:09:43,386 QGraph - Log:
/home/yaowen/soft/svtoolkit_1.03.619/installtest/test2/logs/Q-11685@node12-5.out

I tried different versions of Genome_STRiP, but I still got the same errors.

If anyone could help, that would be great.

Andrew