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What does "Conflicting collector combinations in option list" mean?

wxingwxing Posts: 6Member
edited January 2013 in Ask the GATK team

Hi, folks,

I am trying my queue scala scripts, often get error message:

Conflicting collector combinations in option list; please refer to the release notes for the combinations allowed

However, from the debug information, the command line looks correct (?):

ERROR 12:07:05,460 FunctionEdge - Error: 'java' '-Xmx8192m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/Users/wxing/TPU/run/.queue/tmp' '-cp' '/Users/wxing/TPU/gatk/dist/Queue.jar' 'net.sf.picard.sam.SortSam' 'INPUT=/Users/wxing/TPU/run/SRR064286_1.fastq.aligned.sam' 'TMP_DIR=/Users/wxing/TPU/run/.queue/tmp' 'OUTPUT=/Users/wxing/TPU/run/SRR064286_1.fastq.aligned.bam' 'VALIDATION_STRINGENCY=SILENT' 'SO=coordinate' 'CREATE_INDEX=true'

Anyone had similar issues? any tricks for debugging?

Many thanks, Wei

Post edited by Geraldine_VdAuwera on
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