Hi, I'm trying to run genomestrip on a UGE cluster. I would like to export my current environment using -jobNative "-V", but I get this error:
##### ERROR ------------------------------------------------------------------------------------------
##### ERROR A GATK RUNTIME ERROR has occurred (version ):
##### ERROR
##### ERROR This might be a bug. Please check the documentation guide to see if this is a known problem.
##### ERROR If not, please post the error message, with stack trace, to the GATK forum.
##### ERROR Visit our website and forum for extensive documentation and answers to
##### ERROR commonly asked questions http://www.broadinstitute.org/gatk
##### ERROR
##### ERROR MESSAGE: Value for argument with name '--job_native_arg' (-jobNative) is missing.
##### ERROR ------------------------------------------------------------------------------------------
This is the full command:
java -Xmx4g -cp ${classpath} \
org.broadinstitute.gatk.queue.QCommandLine \
-S ${SV_DIR}/qscript/SVQScript.q \
-S ${SV_DIR}/qscript/SVPreprocess.q \
-cp ${classpath} \
-gatk ${SV_DIR}/lib/gatk/GenomeAnalysisTK.jar \
-configFile ${CONFIG_FILE} \
-R ${REF_FASTA} \
-I ${INPUT_BAM_FILES}\
-jobQueue ${JOB_QUEUE} \
-jobLogDir ${JOB_LOG_DIR} \
-jobRunner ${JOB_RUNNER} \
-gatkJobRunner ${JOB_RUNNER} \
-jobNative "-v PATH " \
-jobNative "-v SV_DIR" \
-jobNative "-l mfree=8G" \
-jobNative "-q all.q" \
-jobNative "-V " \
-qsub \
-md ${METADATA_DIR} \
-bamFilesAreDisjoint false
The command works if I remove the
-jobNative "-V " \
line, and also fails if I use "-cwd" instead of "-V".