java being run with -D64 instead of -d64
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jrandall commented
https://github.com/wtsi-hgi/arvados-pipelines/blob/master/cwl/tools/gatk-4.0/HaplotypeCaller.cwl#L5
-d64
is an option that tells Java to make sure to use 64 bit mode (although almost certainly it is the default anyway). -D64
might not mean anything, or perhaps it sets a system property named 64
to no value? It is not clear, but it is not the same as -d64
:
$ docker run -it mercury/gatk-4.0.0.0:v1 java -h | grep '\-d64'
-d64 use a 64-bit data model if available
$ docker run -it mercury/gatk-4.0.0.0:v1 java -h | grep -A 1 '\-D'
-D<name>=<value>
set a system property