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I am using ReduceReads but it gets blocked always at the same amount of reads reduced !
For instance, I tried several times on one individual and it is blocked after 19.8 %, another one after 72%. I tried on the cluster and also locally on my computer, I have the same result.
However, there is no error and it seems that it is still running, but not advancing anymore...
I validated my Bam file with ValidateSamFile before performing this step and there is no error.
Any idea on what's going on ?
I am using the version 2.3.6 because I read that the last version that is installed on the cluster I use (2.6.5) has a bug. I can't install new software and in particular the new version, however, all the old versions are still available and I read that the 2.3 didn't have the bug.
Thanks for our help.