error when merging two VCFs

[Dayzu Quinto]

This is the command I am running:

rtg vcfmerge -F --no-merge-records -o 40054_merged.vcf.gz 40054_Sentieon.vcf.gz 40054.renamed.cnv.vcf.gz

And this is the error I see:

/shared/gb-vault/ancestry_toolbox/rtg-tools-3.12.1/rtg: line 299:  4334 Killed                  "$RTG_JAVA" -Djava.library.path="$THIS_DIR" -XX:ErrorFile=$HSLOG "${RTG_JAVA_OPTS_ARRAY[@]}" "$RTG_REFERENCES_DIR" "$RTG_MODELS_DIR" "${RTG_USAGE_ARRAY[@]}" "${RTG_PROXY_ARRAY[@]}" "${RTG_DEFAULT_THREADS_ARRAY[@]}" $RTG_TALKBACK "${RTG_MEM_ARRAY[@]}" -jar "$RTG_JAR" "$@"

[Sean Irvine]

Hi Dayzu,

That looks like the process was killed by the operating system, most likely because you ran out of memory on the machine where you ran the command.

Normally a merge would not require much RAM, so possibly you had other tasks running that were occupying memory?

You can try forcing more or less memory with something like:

rtg RTG_MEM=48g -F --no-merge-records -o 40054_merged.vcf.gz 40054_Sentieon.vcf.gz 40054.renamed.cnv.vcf.gz

where you replace the 48 with some appropriate number based on the available RAM you have.

Sean.

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