AttributeError version 1.5.6

[kristij249]

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]

@kristij249,

Thanks for trying out Parsnp! It looks like you are using Python 2 which has been deprecated as of January 1, 2020, RIP :skull: 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]

@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]

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

[bkille]

@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]

Thanks Bryce, My apologies for not responding to this sooner, I got pulled onto another project. I appreciate your rapid responses and assistance. Have a good evening, Kristi

Kristi Jones, Ph. D. Biological Scientist Food Animal Reproductive Services Large Animal Clinical Sciences University of Florida Vet Med @.**@.> (352)294-4326

From: Bryce Kille @.> Sent: Thursday, November 18, 2021 5:13 PM To: marbl/parsnp @.> Cc: Jones,Kristi L @.>; Mention @.> Subject: Re: [marbl/parsnp] AttributeError version 1.5.6 (Issue #97)

[External Email]

@kristij249https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_kristij249&d=DwMCaQ&c=sJ6xIWYx-zLMB3EPkvcnVg&r=nCEbTyrGc19OzBBaSxxoNXdB3cuCmG6puk9Nuoc8998&m=LHDDv_XHSmpX4uFaDFBMqrZBUexlbk_kc7NpnrIuaJ3GP-DJ3pYItBAxpzrq9zWk&s=05MFBiPbKyeUINvyrK5QruM0TYrcJIXrA4Iks0Wru0s&e= 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

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