broadinstitute / gatk

Official code repository for GATK versions 4 and up
https://software.broadinstitute.org/gatk
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[EchoCallset] Retry with more memory VCF extract [VS-1351] #8814

Closed mcovarr closed 3 weeks ago

mcovarr commented 3 weeks ago

Intentionally failing test run here where I sabotaged the code to simulate an out of memory condition. You can see on the first attempt memory usage looks like

echo 'MEM_SIZE: 40.0, MEM_UNIT: GB, memory_mb: 37000, memory_gib: 40'

after three retry-with-more-memory retries, things look like:

echo 'MEM_SIZE: 69.12, MEM_UNIT: GB, memory_mb: 66120, memory_gib: 40'