Version 2.4.3 of Bowtie does not work
The latest version of bowtie2, 2.4.3, has performance issues. The version 2.4.2 had issues with TBB and this has been replaced in 2.4.3 with C++ threads, but this results on our system in an infinite run with a lot of kernel cpu, where it should take a minute to process a single sample. Now it hangs for >76 hours! (reported by agaat)
Currently the environment is pinned at bowtie 2.4.2 with TBB 2020.2.
Next is to see why 2.4.3 does not work. If this is a bowtie2 issue, conda, or our (conda) setup.