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Dear Team,
I am using hla-la for ONT WGS data. When I used hla-la with CRAM file without unmapped reads. It executed successfully. But now I am using CRAM file with unmapped reads, pipeline is stuck at one point for 23 hours, I can not see any progress also as "remapped..a.bam.unsorted" file size is 0 bytes.
Can you please suggest me reason of this problem? Please find attached screen shot of code as well as log:
Memory used by me: cpu-per-task=24, memory=100G
Thank you
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