Local rule: insufficient memory for the Java Runtime Environment

[samarth8392]

Issue

The contamination_paired rule runs as a localrule and since it's not submitted to the cluster and instead executed on the host node, is running into Out of Memory Error

Snippet from the error:

#
# There is insufficient memory for the Java Runtime Environment to continue.
# Cannot create GC thread. Out of system resources.
# Possible reasons:
#   The system is out of physical RAM or swap space
#   The process is running with CompressedOops enabled, and the Java Heap may be blocking the growth of the native heap
# Possible solutions:
#   Reduce memory load on the system
#   Increase physical memory or swap space
#   Check if swap backing store is full
#   Decrease Java heap size (-Xmx/-Xms)
#   Decrease number of Java threads
#   Decrease Java thread stack sizes (-Xss)
#   Set larger code cache with -XX:ReservedCodeCacheSize=
# This output file may be truncated or incomplete.
#
#  Out of Memory Error (gcTaskThread.cpp:48), pid=383637, tid=0x000015555417b700
#
# JRE version:  (8.0_292-b10) (build )
# Java VM: OpenJDK 64-Bit Server VM (25.292-b10 mixed mode linux-amd64 compressed oops)
# Core dump written. Default location: /vf/users/BandayLab/CABO-exome-seq-Andrea/mathurs2/ccbr1332/exome/uc_only_paired/paired_uc_Only/core or core.38
3637 (max size 1 kB). To ensure a full core dump, try "ulimit -c unlimited" before starting Java again


VM Arguments:
jvm_args: -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 
java_command: /opt2/gatk-4.2.2.0/gatk-package-4.2.2.0-local.jar CalculateContamination -I /vf/users/BandayLab/CABO-exome-seq-Andrea/mathurs2/ccbr1332/exome/uc_only_paired/paired_uc_Only/somatic_paired/SNP_Indels/mutect2_out/pileup_summaries/13_CBPC_AU_0029_001_S19_tumor.pileup.table --matched-normal /vf/users/BandayLab/CABO-exome-seq-Andrea/mathurs2/ccbr1332/exome/uc_only_paired/paired_uc_Only/somatic_paired/SNP_Indels/mutect2_out/pileup_summaries/13_CBPC_AU_0029_001_S19_normal.pileup.table -O /vf/users/BandayLab/CABO-exome-seq-Andrea/mathurs2/ccbr1332/exome/uc_only_paired/paired_uc_Only/somatic_paired/qc/gatk_contamination/13_CBPC_AU_0029_001_S19.contamination.table
java_class_path (initial): /opt2/gatk-4.2.2.0/gatk-package-4.2.2.0-local.jar
Launcher Type: SUN_STANDARD

Proposed solution

Run contamination_paired as a regular rule that runs as a job on a compute node.