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FAQ

Please consult the following resources for additional troubleshooting guides:

VM runs out of memory or disk​

  • Default pipeline settings are tuned for batches of 150 samples. Larger batches or cohorts may require additional VM resources. Most runtime attributes can be modified through the RuntimeAttr inputs. These can be formatted like this in an input json:

    "MyWorkflow.runtime_attr_override": {
      "disk_gb": 100,
      "mem_gb": 16
    },

    Note that a subset of the struct attributes can be specified. See wdl/Structs.wdl for available attributes.

Calculated read length causes error in MELT workflow​

Example error message from GatherSampleEvidence.MELT.GetWgsMetrics:

Exception in thread "main" java.lang.ArrayIndexOutOfBoundsException: The requested index 701766 is out of counter bounds. Possible cause of exception can be wrong READ_LENGTH parameter (much smaller than actual read length)

This error message was observed for a sample with an average read length of 117, but for which half the reads were of length 90 and half were of length 151. As a workaround, override the calculated read length by providing a read_length input of 151 (or the expected read length for the sample in question) to GatherSampleEvidence.