Cannot run anim in pyani 0.3.0-alpha using provided data, on macosx 12.6, nucmer fails. about pyani

[widdowquinn]

Thanks for the very detailed report @joneson

I think this may be due to an issue with the conda-provided mummer. I see this issue, myself.

 % conda list | grep mummer                                                                      [3:21:36]
mummer                    3.23                h6de7cb9_11    bioconda
% nucmer --version                                                                              [3:22:38]
nucmer
NUCmer (NUCleotide MUMmer) version 3.1
% head /opt/anaconda3/envs/pyani_py310/bin/nucmer                                               [3:26:48]
#!/usr/bin/perl
[...]
% mamba install mummer=3.23=h589c0e0_12 -y
% conda list | grep mummer                                                                      [3:24:40]
mummer                    3.23                h589c0e0_12    bioconda
% nucmer --version                                                                              [3:24:58]
zsh: /opt/anaconda3/envs/pyani_py310/bin/nucmer: bad interpreter: /usr/local/bin/perl: no such file or directory
% head /opt/anaconda3/envs/pyani_py310/bin/nucmer                                               [3:25:08]
#!/usr/local/bin/perl
[...]

This has been reported as an issue at bioconda (bioconda/bioconda-recipes#28209), but remains unfixed 18mo later. The problem is with bioconda-recipes, and the workaround for now is to downgrade the conda mummer with:

% conda install mummer=3.23=h6de7cb9_11

If this remains unfixed, I may have to pin mummer to a specific build in the requirements*.txt files.

[joneson]

Great! Thank-you much. Downgrading mummer got me through "pyani anim" as expected. After this I wasn't able to run "pyani report" for either --formats html or excel until after I installed jinja2 and openpyxl in the environment, and then re-installing pyani. After that I am able to get through the First Analysis with expected results.

[liamfriar]

Hi. I just want to confirm that I had the same problem and the downgrade also appears to have fixed it. I am running v 0.2.12 via a conda install. So, this might also be the solution to this old issue #93 .

[widdowquinn]

Thanks for the info @liamfriar - i'm a little reluctant to pin a mummer version, in case of updates, but I should make a FAQ page or something in the docs.

Cheers,

L.