samtools / bbmap conda conflict

If you see the error samtools: error while loading shared libraries: cannot open shared object file: No such file or directory it is probably a bbmap conflict.

As of the time of writing, bbmap installs samtools version 1.7, but samtools 1.14 is available, and there were some significant changes around version 1.9 that changed the SSL libraries samtools uses.

There are lots of github issues and biostars posts about this. Here is my simple solution:

mamba uninstall samtools

This will tell you what depends on samtools, and it will remove it too! If your samtools is an earlier version, then you will also see that here.


mamba install samtools

Now you are up to date. Once you have confirmed this version of samtools works, you can try installing the offending package (that was removed alongside samtools) and see it tries to downgrade your samtools version. For me, that was bbmap.