BBsplit tasks taking forever and very often failing

[GothamTx]

Hi there,

I am running some PDX samples RNAseq, I use my regular CE with which I have no problem and runs smoothly on regular bulk RNAseq data (nonPDX). WIth these, I am running BBsplit using mm10 (I have an s3 bucket with mm10). The BBsplit jobs take an extremely long time to process and in some cases just end up failing.
Creating an alternative CE without Spot instances helped solve a bit the problem, but for the bigger files I just end up getting failed processes.
Am I the only one with BBsplit being so slow? Or is this known? Any idea how to increase the processing on this task? Or maybe is there an alternative RNASeq pipeline I could call for PDX samples? (I run the regular nf-core RNAseq pipeline).

Many thanks for your help