The Frontline Support team will be slow to respond December 17-18 due to an institute-wide retreat and offline December 22- January 1, while the institute is closed. Thank you for your patience during these next few weeks. Happy Holidays!
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?