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gagneurlab / FRASER

FRASER - Find RAre Splicing Events in RNA-seq
MIT License
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In countNonSplicedReads stucked for no error report #82

Closed tlz4320 closed 3 years ago

tlz4320 commented 3 years ago

When I use countNonSplicedReads, it showed subread logo. And after waited for 1 day, it still keep running, but the cpu usage is very low. Because of no any error showed from it, I can't know what happened. Could you please add more information for better diagnosis。

tlz4320 commented 3 years ago

I have found what problem it have. In countNonSplicedReads, it will generate a temp file as genome in work directory. And I thought you haven't sort it first, therefore when use that temp file without sort, the disk performance should be very very high so that can hold random access. Therefore a ssd is necessary for using that method. And another way to solve that is change work directory to a ssd, if your ssd is not big enough to put all your data in.