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FastaAlternativeReferenceMaker Full thread dump

kamkam HarvardMember

I'm trying to run the FastaAlternativeReferenceMaker tool to generate a masked genome. I've run it a few times now, and each time it crashes with a full thread dump. I attached the full log file to this post.

Could I ask if anyone has encountered this? Do you have any advice to solve this or work around the problem? Thanks!

Issue · Github
by Sheila

Issue Number
Last Updated


  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie

    @kam We haven't seen anything like this previously; it looks like a Java crash rather than a GATK problem. Can you run other tools successfully? And can you try running on the same files but a different machine? That would help narrow down the source of the problem.

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