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Download the latest Picard release at https://github.com/broadinstitute/picard/releases.
GATK version 4.beta.3 (i.e. the third beta release) is out. See the GATK4 beta page for download and details.

Picard tools MarkDuplicates without swap usage

Hi,
I've been trying to run MarkDuplicates on a shared cluster and I keep getting the job killed because of swap usage. I'm trying to figure out a way to use MarkDuplicates without just throwing tonnes of ram at it. To get more ram, I need to request more cores which means lower priority in the queuing system.

I've been using the command:
java -Xmx40g -Djavaio.tmpdir=/home/gowens/tmp -jar $picard MarkDuplicates I=${name}.bam O=${name}.dup.bam M=${name}.dupmetrics.txt CREATE_INDEX=TRUE TMP_DIR=/home/gowens/tmp MAX_RECORDS_IN_RAM=5000000;

I've tried changing MAX_RECORDS_IN_RAM up or down but I'm not sure if thats helping or hurting the problem. For reference, the BAM files I'm marking are 2G to 23G in size and the issue is with the ones on the larger size.

Issue · Github
by Sheila

Issue Number
1411
State
closed
Last Updated
Assignee
Array
Milestone
Array
Closed By
vdauwera

Answers

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