Can you please provide
a) GATK version used: 188.8.131.52
b) Exact GATK commands used
c) The entire error log if applicable.
I am running Mutect2_PON to generate a panel of normals. Everything seems to be working okay and I am not getting any errors, but there are currently 37 shards running (one fore each sample in the panel), and within those shards, I will see something like the following:
Where most of the secondary shards ran and completed relatively quickly, but still 5 hours later 1 or 2 of the shards look like they have not even started. Is this expected behavior? Or do these shards need to be restarted somehow?
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