Closed ryobon-dev closed 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
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)
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
— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/ngs-fzb/MTBseq_source/issues/61#issuecomment-772559193 , or unsubscribe https://github.com/notifications/unsubscribe-auth/ASU6F6TRM576WFKBAOL2B4DS5FN73ANCNFSM4WZ2HGLQ .
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