Stalled Shards

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L. A. Liggett

• March 09, 2020 19:22

Can you please provide
a) GATK version used: 4.1.5.0

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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  Bhanu Gandham

  • March 10, 2020 20:28

  Hi L. A. Liggett

   

  This is more of Terra question. I have let the team know, someone from the Terra team will reach out to you with a recommendation shortly.

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