Markduplicate error in picard

Question

[rj.rezwan]

Hi, I tried to mark duplicates in the ABC_sorted.bam file using the following command but received the attached error. Could someone guide me on how to solve this error and what changes I should make to get the results?

picard MarkDuplicates I=ABC_sorted.bam O=duplicate_ABC.bam METRICS_FILE=metrics_ABC.txt VALIDATION_STRINGENCY=SILENT CREATE_INDEX=TRUE

Answer 1

[barslmn]

Try increasing the allocated memory with -Xmx parameter. It's the second question in their FAQ. https://broadinstitute.github.io/picard/faq.html

[rj.rezwan]

I have used the following script of picard for mark duplication by incorporating the @barslmn suggestion:

picard -Xmx24G MarkDuplicates I=fixmate_sorted.bam O=markduplicate.bam M=markdup_metrics.txt ASSUME_SORTED=true VALIDATION_STRINGENCY=LENIENT CREATE_INDEX=TRUE

"ASSUME_SORTED=true" is mentioned in the markduplication script for those files which are sorted by the samtools