search

broadinstitute / gatk

Official code repository for GATK versions 4 and up
https://software.broadinstitute.org/gatk
Other
1.64k stars 581 forks source link

HaplotypeCaller: Java invalid pointer in native Smith-Waterman implementation #7187

Open RWilton opened 3 years ago

RWilton commented 3 years ago

Bug Report

Affected tool(s) or class(es)

HaplotypeCaller

Affected version(s)

Description

HaplotypeCaller fails with the following java error:

*** Error in `java': munmap_chunk(): invalid pointer: 0x00007f1da5980f00 *** ======= Backtrace: ========= /lib64/libc.so.6(+0x7f3e4)[0x7f1daaec73e4] /var/tmp/rwilton/libgkl_smithwaterman14257239252565866950.so(_Z21runSWOnePairBT_avx512iiiiPhS_iiaPcPs+0x338)[0x7f05b3b50f48] /var/tmp/rwilton/libgkl_smithwaterman14257239252565866950.so(Java_com_intel_gkl_smithwaterman_IntelSmithWaterman_alignNative+0xd8)

Steps to reproduce

Using properly-aligned paired-end reads from GIAB reference sample HG002 (NA24385) with GRCh38.p12.

Please see the attached log file for parameterization and stderr log: vcall.swbug.log

Expected behavior

No error.

Actual behavior

See above and attached log file.

Thank you in advance for having a look at this!

Richard Wilton Johns Hopkins University

droazen commented 3 years ago

@RWilton There is a new version of the Intel GKL that we hope will resolve this issue -- we are in the process of moving GATK to it, and hope that it will be included in the next GATK release. @lbergelson and/or @Kmannth may have further details.