FAQ
VM runs out of memory or disk
-
Default pipeline settings are tuned for batches of 100 samples. Larger batches or cohorts may require additional VM resources. Most runtime attributes can be modified through the RuntimeAttr inputs. These are formatted like this in the 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
.