If you see the error samtools: error while loading shared libraries: libcrypto.so.1.0.0: 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.
Then,
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
.