The running time is toooooooo looooooooong

bcgsc / HLAminer

⛏ HLA predictions from NGS shotgun data

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The running time is toooooooo looooooooong #7

Closed zhangyafeng1 closed 4 years ago

zhangyafeng1 commented 4 years ago

The script HPTASRwgs_classI-II.sh have running 7 days ,,,,,, my bam file is 7.9G , OOOOMMMMMGGGGGGG,,,toooooo loooooooooong..........

warrenlr commented 4 years ago

hmm the script HPTASRwgs_classI-II.sh is not processing bam files... so not sure what the relation between the bam file size and this is. Do you mean your input read set?

On thing that would be helpful is to know which step is taking so long. I suspect TASR, which could be addressed by replacing with a faster multi-threaded assembler..