[svtoolkit-help] ArgumentMatchStringValue error for MergeInsertSizeHistograms during running installtest

[Yige Wu <yi...@wu...>]

Hi All,

I was running the discovery.sh under the directory 
/svtoolkit/installtest and got the following error during SVPreprocess. 
I think it says the input file "installtest.hist.bin" has the 
inappropriate data type, although there's no error or warning for the 
previous step that generated this file (also pasted below). I'm clueless 
where should I begin to check for this error. (tried the latest 2 
versions of svtoolkit, got the same error; java version "1.8.0_45"; 
samtools version 1.6)

Error for MergeInsertSizeHistograms:

ERROR 19:54:21,182 FunctionEdge - Error:  'java'  '-Xmx2048m' 
'-XX:+UseParallelOldGC'  '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50'  
'-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/home/yigewu2012/tmpdir'  
'-cp' 
'/home/yigewu2012/svtoolkit/lib/SVToolkit.jar:/home/yigewu2012/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/home/yigewu2012/svtoolkit/lib/gatk/Queue.jar' 
'-cp' 
'/home/yigewu2012/svtoolkit/lib/SVToolkit.jar:/home/yigewu2012/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/home/yigewu2012/svtoolkit/lib/gatk/Queue.jar' 
'org.broadinstitute.sv.apps.MergeInsertSizeHistograms'  '-I' 
'/home/yigewu2012/test1/metadata/isd/installtest.hist.bin'  '-O' 
'/home/yigewu2012/test1/metadata/isd.hist.bin'
ERROR 19:54:21,184 FunctionEdge - Contents of 
/home/yigewu2012/test1/logs/SVPreprocess-8.out:
Exception in thread "main" 
org.broadinstitute.gatk.utils.exceptions.UserException$CommandLineException: 
Invalid command line: Failed to parse value 
org.broadinstitute.gatk.utils.commandline.ArgumentMatchStringValue@60615d72 
for argument mInputFiles.  This is most commonly caused by providing an 
incorrect data type (e.g. a double when an int is required)
         at 
org.broadinstitute.gatk.utils.commandline.SimpleArgumentTypeDescriptor.parse(ArgumentTypeDescriptor.java:756)
         at 
org.broadinstitute.gatk.utils.commandline.CompoundArgumentTypeDescriptor.parse(ArgumentTypeDescriptor.java:834)
         at 
org.broadinstitute.gatk.utils.commandline.ArgumentTypeDescriptor.parse(ArgumentTypeDescriptor.java:137)
         at 
org.broadinstitute.gatk.utils.commandline.ArgumentSource.parse(ArgumentSource.java:119)
         at 
org.broadinstitute.gatk.utils.commandline.ParsingEngine.loadValueIntoObject(ParsingEngine.java:509)
         at 
org.broadinstitute.gatk.utils.commandline.ParsingEngine.loadArgumentsIntoObject(ParsingEngine.java:429)
         at 
org.broadinstitute.gatk.utils.commandline.ParsingEngine.loadArgumentsIntoObject(ParsingEngine.java:403)
         at 
org.broadinstitute.gatk.utils.commandline.CommandLineProgram.start(CommandLineProgram.java:235)
         at 
org.broadinstitute.gatk.utils.commandline.CommandLineProgram.start(CommandLineProgram.java:158)
         at 
org.broadinstitute.sv.commandline.CommandLineProgram.runAndReturnResult(CommandLineProgram.java:29)
         at 
org.broadinstitute.sv.commandline.CommandLineProgram.run(CommandLineProgram.java:25)
         at 
org.broadinstitute.sv.apps.MergeInsertSizeHistograms.main(MergeInsertSizeHistograms.java:40) 


The log for generating "installtest.hist.bin":

INFO  19:53:51,177 FunctionEdge - Done:  'java'  '-Xmx2048m' 
'-XX:+UseParallelOldGC'  '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50'  
'-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/home/yigewu2012/tmpdir'  
'-cp' 
'/home/yigewu2012/svtoolkit/lib/SVToolkit.jar:/home/yigewu2012/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/home/yigewu2012/svtoolkit/lib/gatk/Queue.jar' 
org.broadinstitute.sv.main.SVCommandLine '-T' 
'ComputeInsertSizeHistogramsWalker'  '-R' 
'/home/yigewu2012/svtoolkit/installtest/data/human_b36_chr1.fasta' '-I' 
'/home/yigewu2012/svtoolkit/installtest/data/installtest.bam' '-O' 
'/home/yigewu2012/test1/metadata/isd/installtest.hist.bin' 
'-disableGATKTraversal' 'true'  '-md' 'test1/metadata' '-genomeInterval' 
'1:61700000-61900000'  '-configFile' 
'/home/yigewu2012/svtoolkit/installtest/conf/genstrip_installtest_parameters.txt' 
'-chimerismFile' 'test1/metadata/isd/installtest.chimer.dat' 
'-createHistogramFile' 'true'  -createEmpty

/svtoolkit/installtest.

/svtoolkit/installtest