marbl/parsnp

AttributeError version 1.5.6

Closed this issue · 5 comments

kristij249 commented

New to all of this, but I just installed parsnp version 1.5.6 and when running the code ./parsnp -r (insert my reference file with path) -d (insert my directory of genomes to align with the path), I get the following error message:

|--Parsnp 1.5.6--|
For detailed documentation please see --> http://harvest.readthedocs.org/en/latest
Traceback (most recent call last):
File "./parsnp", line 604, in
if shutil.which(exe) is None:
AttributeError: 'module' object has no attribute 'which'

bkille commented

@kristij249,

Thanks for trying out Parsnp! It looks like you are using Python 2 which has been deprecated as of January 1, 2020, RIP 💀 You will need to be running Python 3.

I'd strongly suggest installing conda via miniconda. Once you install miniconda and update your channels, you can install parsnp via:

conda install parsnp

This is the preferred method of installation, and will also make it easier to keep up with new updates.

kristij249 commented

@bkille Thank you for your rapid response. It took a while but I did get that. I noticed though that the version of parsnp that is downloaded that way is still version 1.2 in the bin folder? is there a way to update this or am I in the wrong folder for execution?

bkille commented

Of course, happy to help. Have you installed via conda? Could you show me the output you're observing?

bkille commented

@kristij249 I'm closing this issue as a stale issue. It seems that you've installed parsnp via conda, but are seeing the old version of conda in the bin/ folder. This is because the version of parsnp that you obtained via conda is in ${CONDA_PREFIX}/bin.

Let me know if you still have questions!

-Bryce

kristij249 commented