Vs 1561 Merging in new monitoring script #9089
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I needed to create a new new version of the cromwell monitoring script to grab specific heap data for identifying where our memory is being used during a previously problematic shard during our AoU extract. It has been uploaded to gs://gvs_quickstart_storage/cromwell_monitoring_script_with_heap.sh
If you want to generate these high-level gatk histograms for extract, just replace the definition of
File monitoring_scriptin the ExtractTask within GvsExtractCallset.wdl to point to the new one.Here's a successful AoU extract using the new monitoring script:
https://app.terra.bio/#workspaces/allofus-drc-wgs-dev/GVS%20AoU%20WGS%20Echo%20Callset%20v2/job_history/aa5bb1e4-b860-48f3-9c8c-53dd5e6ec206