Hi there, I'm having trouble getting picard's CollectOxoGMetrics to produce output. Specifically, commands like:
java -Xmx2g -jar ~/tools/picard-tools-1.140/picard.jar CollectOxoGMetrics I=test.bam O=test.oxog.csv R=~/resources/GRCh38.p2.fa
produces a "test.oxog.csv" file with some header information including the command line arguments, etc., but no other content besides a few blank lines. No warning or error information is emitted, and other metrics commands seem to work just fine. I've tried a couple of different bams now (one in-house generated, one from Illumina) and got the same results for each one.
Am I missing something obvious?