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Output is not generated in the SortSam (Picard)

nithanitha indiaMember

Hi,

I had completed MarkDuplicate step by aligned .sam. When I try to do sorting the .bam file generated from the previous step using SortSam (Picard) the job had run completely but when I check the output the file size was 0. Initially, I thought it may be due to disk space, but I had created 1TB space and repeated this step but still its 0 file size.

Command used:
/gatk-4.1.2.0/gatk SortSam --INPUT MarkDuplicate.bam --OUTPUT sortsam.bam --TMP_DIR --SORT_ORDER=coordinate"

File size:

BWA-mem =aligned.sam (172G); MarkDuplicate: _markduplicate.bam (80G)

gatkversion: 4.1.2.0

Could you please tell why this issue occurs?

Thank you.

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