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Unable to run SVPreprocess. Java cannot find the main class
I'm sure this is obvious but I can't seem to find my bug. I have been trying to execute the commands as listed in the documentation for our data but I am thwarted at every turn.
Here are the steps I have taken.
1) Download and decompress the latest-n-greatest release of genomeStrip (svtoolkit_2.00.1774.tar.gz)
2) Ensure that the java classpath includes the genomeSTRiP directory and the necessary dependencies.
export GS=$HOME/apps/svtoolkit export CLASSPATH=".:$GS/lib:$GS/lib/depend:$GS/lib/gatk:$GS/lib/SVToolkit.jar:$GS/lib/gatk/Queue.jar"
3) Execute the SVPreprocess command
java -Xmx8g -cp $CLASSPATH org.broadinstitute.gatk.queue.QCommandLine \ -S $GS/qscript/SVPreprocess.q \ -S $GS/qscript/SVQScript.q \ -cp $CLASSPATH \ -gatk GenomeAnalysisTK.jar \ -configFile $GS/conf/genstrip_parameters.txt \ -R /data/hs37d5.fa \ -tempDir /tmp \ -md metadata \ -genomeMaskFile $HOME/apps/masks/Homo_sapiens_assembly19.mask.101.fasta \ -genderMapFile $GS/conf/gf48_gender.tab \ -I $HOME/data/align.2017-12-14/bams/SAFID_abc1.recal.bam
I continue to get this error message:
Error: Could not find or load main class org.broadinstitute.gatk.queue.QCommandLine
I'm not sure what I'm doing wrong here.
Can anyone help me out?