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Kurt-Hetrick / CIDR_DATA_ARCHIVING

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ValidateSam throwing non-zero exit codes #257

Closed Kurt-Hetrick closed 4 years ago

Kurt-Hetrick commented 4 years ago

don't know why. started happening after I did some bug fixes and changed the output path for the output cram file, but this also occuring on files that i made the bug fixes for...for now.

Kurt-Hetrick commented 4 years ago

the files appear fine. the log looks right, but at the very end it sends.

"To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp"

might try to see what happens on a cram file from a newer version of picard.

Kurt-Hetrick commented 4 years ago

looks like this is the wonkiness of files generated via HaplotypeCaller. The artificial haplotype reads break specs but they are still workable. annoying, but going to close for now and revisit when i come across a "normal" bam/cram file.