GATK v3.8 GKL memory issues?

[sooheelee]

Could I get a consult on GATK user questions at https://gatkforums.broadinstitute.org/gatk/discussion/10353/gatk-3-8-0-printreads-fatal-error#latest?

Users are experiencing issues for v3.8 of GATK, which implements the GKL by default. I'm not sure if the issues are related to GKL, and if they are what are the guidelines we should provide users experiencing such issues.

Thanks.

[sooheelee]

Could @erniebrau or @pnvaidya please forward this issue to relevant persons? I've just grabbed your handles because you appear active in this repo. Much appreciated.

[gspowley]

@sooheelee, We are looking into the issues reported in the GATK discussion list. If GKL is causing the issues, then users should add the -jdk_deflater and -jdk_inflater options to GATK until we resolve the issue.

[sooheelee]

Thank you. We look forward to hearing back from you and your team.

[lbergelson]

Another similar report in picard. broadinstitute/picard#975