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.
IndelRealigner Crashing, Java Fatal Error
I am receiving the following error when running this script:
java -Xmx32G -Djava.io.tmpdir=/data1/home/nipm/arvin/tmp \
-jar /data1/APPS/gatk_nightly/GenomeAnalysisTK.jar \
-T IndelRealigner \
-R /data1/DATA/REFERENCE/human_g1k_v37_decoy.fasta \
-targetIntervals S14_03B_CHG000251_realignment_targets.list \
-known /data1/DATA/REFERENCE/1000G_phase1.indels.b37.vcf \
-I S14_03B_CHG000251_combined_dedup.bam \
INFO 18:21:42,635 ProgressMeter - 1:184280371 4.010121E7 33.9 m 50.0 s 5.9% 9.6 h 9.0 h
INFO 18:22:12,636 ProgressMeter - 1:187049819 4.0801219E7 34.4 m 50.0 s 6.0% 9.6 h 9.0 h
INFO 18:22:43,558 ProgressMeter - 1:190054021 4.1601238E7 34.9 m 50.0 s 6.1% 9.6 h 9.0 h
INFO 18:23:13,561 ProgressMeter - 1:192972143 4.2301251E7 35.4 m 50.0 s 6.2% 9.6 h 9.0 h
INFO 18:23:20,807 IndelRealigner - Not attempting realignment in interval 1:193831502-193831691 because there are too many reads.
INFO 18:23:43,562 ProgressMeter - 1:195808771 4.3001259E7 35.9 m 50.0 s 6.2% 9.6 h 9.0 h
A fatal error has been detected by the Java Runtime Environment:
SIGSEGV (0xb) at pc=0x00007fec98d8689b, pid=11969, tid=0x00007fec94265700
JRE version: OpenJDK Runtime Environment (8.0_144-b01) (build 1.8.0_144-b01)
Java VM: OpenJDK 64-Bit Server VM (25.144-b01 mixed mode linux-amd64 )
Core dump written. Default location: /data2/travis/WGS-86/CHG000251/core or core.11969
An error report file with more information is saved as:
If you would like to submit a bug report, please visit:
I am running GATK 3.8, nightly build from 09/18/2017
As for java:
openjdk version "1.8.0_144"
OpenJDK Runtime Environment (build 1.8.0_144-b01)
OpenJDK 64-Bit Server VM (build 25.144-b01, mixed mode)
I am trying to use 3.8 because 3.7 keeps crashing at HaplotypeCaller. I am now trying 3.7 using the flag --pair_hmm_implementation LOGLESS_CACHING, as this was a suggestion from my server administrator. She was also running into problems with HaplotypeCaller and this fixed her issue.