Error in smith waterman native library
open | Created 2019-02-19 | Last updated 2019-05-15| Posted by byoo | See in Github


NativeLibraries bug


Mutect2 (GATK 4.1.0.0) fails occasionally in smith waterman native library as below. stderr is attached. I can also provide core dump if necessary.

stderr.tar.gz

07:30:59.335 INFO  ProgressMeter -          17:78451657            627.7               1223980           1950.0
*** Error in `java': munmap_chunk(): invalid pointer: 0x00002ba8e50b7740 ***
======= Backtrace: =========
/lib64/libc.so.6(+0x7ab54)[0x2ba8df926b54]
/gpfs/data/software/cromwell/log/cromwell-executions/Mutect2/2cebc7be-fe23-4787-9095-9b91227c6526/call-M2/shard-13/attempt-2/tmp.945f1f83/libgkl_smithwaterman5575294852416409537.so(_Z19runSWOnePairBT_avx2iiiiPhS_iiaPcPs+0x338)[0x2ba9aee21fa8]
/gpfs/data/software/cromwell/log/cromwell-executions/Mutect2/2cebc7be-fe23-4787-9095-9b91227c6526/call-M2/shard-13/attempt-2/tmp.945f1f83/libgkl_smithwaterman5575294852416409537.so(Java_com_intel_gkl_smithwaterman_IntelSmithWaterman_alignNative+0xd8)[0x2ba9aee21bf8]
[0x2ba8e8f6675a]
======= Memory map: ========
00400000-00401000 r-xp 00000000 08:03 5769910                            /usr/lib/jvm/java-1.8.0-openjdk-1.8.0.111-1.b15.el7_2.x86_64/jre/bin/java
00600000-00601000 r--p 00000000 08:03 5769910                            /usr/lib/jvm/java-1.8.0-openjdk-1.8.0.111-1.b15.el7_2.x86_64/jre/bin/java
...

Return to top