[svtoolkit-help] svtoolkit with prefix java

[<mc...@na...>]

Hi Bob,
I'm running svtoolkit on linux server machine where I cannot be a root.
So I need to use a java installed at another path.
The machine has java1.6 already installed, and it seems svtoolkit uses this java instead of what I installed customely by setting java as just java.
Which is not the java path I put in.
INFO  10:37:53,469 QGraph - Failed:   'java'  '-Xmx2048m'  '-XX:+UseParallelOldGC'  '-XX:ParallelGCThreads=4'  '-XX:GCTimeLimit=50'  '-XX:GCHeapFreeLimit=10'  '-Djava.io.tmpdir=/scratch2/x1477hyk/SVanalysis/.queue/tmp'  '-cp' '/scratch2/x1477hyk/svtoolkit/lib/SVToolkit.jar:/scratch2/x1477hyk/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/scratch2/x1477hyk/svtoolkit/lib/gatk/Queue.jar'  '-cp' '/scratch2/x1477hyk/svtoolkit/lib/SVToolkit.jar:/scratch2/x1477hyk/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/scratch2/x1477hyk/svtoolkit/lib/gatk/Queue.jar'  'org.broadinstitute.sv.apps.CreateMetaDataDirectory'  '-md' 'output_metadata_directory'  '-configFile' '/scratch2/x1477hyk/svtoolkit/conf/genstrip_parameters.txt'

so I get 
INFO  10:37:53,470 QCommandLine - Script failed: 6752 Pend, 0 Run, 2 Fail, 0 Done
is there any way to force svtoolkit to use my java? or other solution to fix this problem?
Thanks,Seungmin Kim