ReduceReads is blocked
Posted in Ask the GATK team | Last updated on

Comments (3)

Hello ! 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. Muriel

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