REQUIRED for all errors and issues:
a) GATK version used:
b) Exact command used:
c) Entire program log:
Have run this script many times previously but problem occurred with the 4.3.0 update
After BwaAndMarkDuplicatesPipelineSpark need to SortSam and then to BuildBamIndex
Error log said the bam Index had been written couldn't find file anywhere
Fixed by adding and explicit --OUTPUT to create the file in the proper directory. Sorry, didn't save the error log.
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