If you happen to see a question you know the answer to, please do chime in and help your fellow community members. We encourage our fourm members to be more involved, jump in and help out your fellow researchers with their questions. GATK forum is a community forum and helping each other with using GATK tools and research is the cornerstone of our success as a genomics research community.We appreciate your help!
Test-drive the GATK tools and Best Practices pipelines on Terra
Check out this blog post to learn how you can get started with GATK and try out the pipelines in preconfigured workspaces (with a user-friendly interface!) without having to install anything.
We will be out of the office on October 14, 2019, due to the U.S. holiday. We will return to monitoring the forum on October 15.
GATK 3.8-0 PrintReads fatal error
Could you please help me to figure out this fatal error in running PrintReads?
After I updated GATK to version 3.8-0. I kept getting this fatal error in running PrintReads. I can skip this step and run HaplotypeCaller with -BQSR option.
parsing sample: SRR098333
INFO 17:12:12,287 HelpFormatter - ---------------------------------------------------------------------------------- INFO 17:12:12,289 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.8-0-ge9d806836, Compiled 2017/07/28 21:26:50 INFO 17:12:12,289 HelpFormatter - Copyright (c) 2010-2016 The Broad Institute INFO 17:12:12,289 HelpFormatter - For support and documentation go to https://software.broadinstitute.org/gatk INFO 17:12:12,289 HelpFormatter - [Sat Sep 09 17:12:12 EDT 2017] Executing on Linux 2.6.32-358.23.2.el6.x86_64 amd64 INFO 17:12:12,289 HelpFormatter - Java HotSpot(TM) 64-Bit Server VM 1.8.0_65-b17 INFO 17:12:12,293 HelpFormatter - Program Args: -T PrintReads -nct 8 -R ./refs/GATK_Resource_Bundle/b37/human_g1k_v37.fasta -BQSR SRR098333.recal_data.table -I SRR098333.bwa_mem.sorted_dups_removed_indelrealigner.bam -o SRR098333.bwa_mem.sorted_dups_removed_indelrealigner_BQSR.bam ... INFO 17:43:53,363 ProgressMeter - 3:83180289 4.6776207E7 31.7 m 40.0 s 18.6% 2.8 h 2.3 h # # A fatal error has been detected by the Java Runtime Environment: # # SIGSEGV (0xb) at pc=0x00007fe6c2da3f8b, pid=1932, tid=140629048932096 # # JRE version: Java(TM) SE Runtime Environment (8.0_65-b17) (build 1.8.0_65-b17) # Java VM: Java HotSpot(TM) 64-Bit Server VM (25.65-b01 mixed mode linux-amd64 ) # Problematic frame: # V [libjvm.so+0x64bf8b] InstanceKlass::oop_follow_contents(ParCompactionManager*, oopDesc*)+0x16b # # Core dump written. Default location: core or core.1932 # # An error report file with more information is saved as: # hs_err_pid1932.log # # If you would like to submit a bug report, please visit: # http://bugreport.java.com/bugreport/crash.jsp # /var/spool/slurmd/job465052/slurm_script: line 18: 1932 Aborted (core dumped) java -Xms16g -Xmx200g -jar /home/apps/GATK/GenomeAnalysisTK-3.8.0/GenomeAnalysisTK.jar -T PrintReads -nct 8 -R ./refs/GATK_Resource_Bundle/b37/human_g1k_v37.fasta -BQSR SRR09833$SLURM_ARRAY_TASK_ID.recal_data.table -I SRR09833$SLURM_ARRAY_TASK_ID.bwa_mem.sorted_dups_removed_indelrealigner.bam -o SRR09833$SLURM_ARRAY_TASK_ID.bwa_mem.sorted_dups_removed_indelrealigner_BQSR.bam