GATK version: 184.108.40.206 (installed via conda)
gatk MarkDuplicatesSpark \
-I input.bam \
-O output.bam \
openjdk version: 8.0.192
I have a problem with MarkDuplicatesSpark function. I tried to run the GATK pipeline on HPC cluster. It worked for small bam files (e.g. 507 Mb) but didn't work for big bam files (e.g. 9.6 Gb). I have uploaded the log file. Do you have any idea about the problem? How can I solve this?
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