Missing python library "pysam"

[fpusan]

Hi! I'm getting this warning after running the test_install.pl script:

WARNING: Some SqueezeMeta dependencies could not be found in your environment!

• Missing python library "pysam"

Could somebody help me? Thanks in advanced!

Originally posted by @emagallong in https://github.com/jtamames/SqueezeMeta/issues/258#issuecomment-1533388417

[fpusan]

How did you install SqueezeMeta? If using conda, have you activated the right environment?

[emagallong]

Thanks, for your quick response!! Yes, I used conda and I'm on the SqueezeMeta environment...

[fpusan]

pysam should be present in that environment. What is the output of which python?

[emagallong]

It's python3.6.15

[emagallong]

/home/usuario/miniconda3/envs/SqueezeMeta/bin/python

[fpusan]

Ok then it is a bit weird, it should be present. What happens if you manually install it with mamba install -c bioconda pysam

[emagallong]

This is the output: Looking for: ['pysam']

warning libmamba Could not parse state fileCould not load cache state: [json.exception.type_error.302] type must be number, but is null warning libmamba Could not parse state fileCould not load cache state: [json.exception.type_error.302] type must be number, but is null warning libmamba Could not parse state fileCould not load cache state: [json.exception.type_error.302] type must be number, but is null warning libmamba Could not parse state fileCould not load cache state: [json.exception.type_error.302] type must be number, but is null warning libmamba Could not parse state fileCould not load cache state: [json.exception.type_error.302] type must be number, but is null warning libmamba Could not parse state fileCould not load cache state: [json.exception.type_error.302] type must be number, but is null warning libmamba Could not parse state fileCould not load cache state: [json.exception.type_error.302] type must be number, but is null warning libmamba Could not parse state fileCould not load cache state: [json.exception.type_error.302] type must be number, but is null bioconda/noarch 4.2MB @ 3.8MB/s 1.7s bioconda/linux-64 4.6MB @ 2.8MB/s 2.4s pkgs/main/linux-64 5.6MB @ 2.3MB/s 3.6s pkgs/r/linux-64 1.4MB @ 384.1kB/s 1.4s pkgs/main/noarch 822.9kB @ 209.5kB/s 2.8s pkgs/r/noarch 1.3MB @ 312.4kB/s 2.5s r/linux-64 770.6kB @ 183.4kB/s 0.5s r/noarch 864.2kB @ 201.3kB/s 0.6s conda-forge/noarch 12.1MB @ 2.7MB/s 6.7s conda-forge/linux-64 31.2MB @ 3.0MB/s 16.0s

Pinned packages:

• python 3.6.*

Transaction

Prefix: /home/usuario/miniconda3/envs/SqueezeMeta

All requested packages already installed

[emagallong]

I already run the test_install.pl and I got the same issue...

[fpusan]

So it thinks it is already installed (also there is something weird going on with your conda) What happens if you open python and type import pysam?

[fpusan]

Also what is the output of which python3 (note that now there is a 3 in the end)

[emagallong]

This is the output for which python3 : /home/usuario/miniconda3/envs/SqueezeMeta/bin/python3 This is the output for import pysam :

Python 3.6.15 | packaged by conda-forge | (default, Dec 3 2021, 18:49:41) [GCC 9.4.0] on linux Type "help", "copyright", "credits" or "license" for more information.

import pysam Traceback (most recent call last): File "", line 1, in File "/home/usuario/miniconda3/envs/SqueezeMeta/lib/python3.6/site-packages/pysam/init.py", line 5, in from pysam.libchtslib import * ImportError: libhts.so.2: cannot open shared object file: No such file or directory

[fpusan]

Ok, pysam itself is installed, but it is missing a dependency.

I see that pysam was recently updated in bioconda, apparently this broke our package. I expect this to keep happening in the future, so I will look into pinning package versions as suggested to me in #638. I am afraid that not allowing conda to solve packages on its own may also be problematic in a different way, but I'll see what I find out.

In any case, I just made a new release that fixes this particular issue. You will need to reinstall SqueezeMeta, then pysam and test_install.pl will hopefully work. Let me know what happens.

[emagallong]

Ok, I'll try and I'll keep you posted! Thanks ;)

[emagallong]

So far, everything is running pretty good. The issue was fixed. Thanks a lot, Fernando! I'm excited to run SqueezeMeta!

[fpusan]

Excellent! Good luck with your analyses, you know where to find us