about MUTECT2

BogdanBogdan Palo Alto, CAMember ✭✭

Dear all,

we are running MUTECT2 on the computer cluster, and on specific WGA BAM files (that have been post-processed with GATK), we do get the following errors :) Please could you advise if there is any way to circumvent these errors .. Many many thanks !

ERROR ------------------------------------------------------------------------------------------
ERROR A GATK RUNTIME ERROR has occurred (version 3.5-0-g36282e4):
ERROR
ERROR This might be a bug. Please check the documentation guide to see if this is a known problem.
ERROR If not, please post the error message, with stack trace, to the GATK forum.
ERROR Visit our website and forum for extensive documentation and answers to
ERROR commonly asked questions http://www.broadinstitute.org/gatk
ERROR
ERROR MESSAGE: Somehow the requested coordinate is not covered by the read. Alignment 150975810 | 44S107M
ERROR ------------------------------------------------------------------------------------------
ERROR
ERROR This might be a bug. Please check the documentation guide to see if this is a known problem.
ERROR If not, please post the error message, with stack trace, to the GATK forum.
ERROR Visit our website and forum for extensive documentation and answers to
ERROR commonly asked questions http://www.broadinstitute.org/gatk
ERROR
ERROR MESSAGE: Somehow the requested coordinate is not covered by the read. Too many deletions?
ERROR ------------------------------------------------------------------------------------------

slurmstepd: error: Exceeded step memory limit at some point.
slurmstepd: error: Exceeded job memory limit at some point.

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