ryobon-dev commented 3 years ago

When start using GATK PrintReads for Test-20_MTBSeq_nextseq_151bp... a fatal error has been detected by the Java Runtime Environment. The messages are in below.

A fatal error has been detected by the Java Runtime Environment: #

SIGSEGV (0xb) at pc=0x0000000114ae66f7, pid=7410, tid=0x0000000000002503

#

JRE version: OpenJDK Runtime Environment (8.0_152-b12) (build 1.8.0_152-release-1056-b12)

Java VM: OpenJDK 64-Bit Server VM (25.152-b12 mixed mode bsd-amd64 compressed oops)

Problematic frame:

C [libgkl_compression3719787253608670960.dylib+0x76f7] deflate_medium+0x867

#

Failed to write core dump. Core dumps have been disabled. To enable core dumping, try "ulimit -c unlimited" before starting Java again

#

An error report file with more information is saved as:

/Users/tomotada/Desktop/iwamoto/MTB_test/hs_err_pid7410.log

#

If you would like to submit a bug report, please visit:

http://bugreport.java.com/bugreport/crash.jsp

The crash happened outside the Java Virtual Machine in native code.

See problematic frame for where to report the bug.

# gatk3 -T --analysis_type PrintReads --reference_sequence /Users/tomotada/miniconda3/envs/MTBseq/share/mtbseq-1.0.4-1/var/ref/M._tuberculosis_H37Rv_2015-11-13.fasta --input_file /Users/tomotada/Desktop/iwamoto/MTB_test/GATK_Bam/Test-20_MTBSeq_nextseq_151bp.realigned.bam --BQSR /Users/tomotada/Desktop/iwamoto/MTB_test/GATK_Bam/Test-20_MTBSeq_nextseq_151bp.gatk.grp --num_cpu_threads_per_data_thread 1 --out /Users/tomotada/Desktop/iwamoto/MTB_test/GATK_Bam/Test-20_MTBSeq_nextseq_151bp.gatk.bam 2>> /Users/tomotada/Desktop/iwamoto/MTB_test/GATK_Bam/Test-20_MTBSeq_nextseq_151bp.gatk.bamlog failed: 64000

hs_err_pid7410.log

TaKohl commented 3 years ago

Hello ryobon-dev,

sorry to say, this seems to be a problem with the gatk tool called by the pipeline. It might be a good idea to contact your local support for the java implementation in your system. And maybe just do a test run with gatk on its own.

best, Thomas

ryobon-dev commented 3 years ago

Thanks for your reply.

I will try to fix this problem.

Best regards,

Tomotada

From: TaKohl notifications@github.com Sent: Wednesday, February 3, 2021 11:41 PM To: ngs-fzb/MTBseq_source MTBseq_source@noreply.github.com Cc: ryobon-dev kx2t-iwmt@asahi-net.or.jp; Author author@noreply.github.com Subject: Re: [ngs-fzb/MTBseq_source] A fatal error has been detected by the Java Runtime Environment: (#61)