First of all, thank you for making this plugin
though, while process I'm kept on facing the same error (or perhaps I'm doing something wrong I'm very new at GitHub system)
so following steps in GitHub - vitorheidrich/q2-srs: QIIME 2 plugin for microbiome count data normalization by scaling with ranked subsampling (SRS)
at 2) Running SRS step, when I type in
I get this
Could you please tell me what could be the reason why I get these returned non-zero exit status 1?
I'm kept on seeing this non-zero exit status 1
Thank you so much for your help in advance.
Thanks for using q2-srs. I see that you are using the latest qiime2 release. Because I didn't test q2-srs in this latest release, I just reran this tutorial using qiime2-2021.8 just to be sure your issue is not being caused by an incompatibility of some kind. And it isn't, still works fine.
Now my first guess is that there is something wrong/different with your data that SRS is not being able to deal with. Can you send me this
table.qza file of yours? It would be easier for me to debug this issue if I am able to reproduce this error.
Sorry for this inconvenience,
This is the file you have requested
again, Thank you so much for your help!!
Thank you for providing your feature-table. As I suspected, your table is a bit unusual because it contains spaces in feature names (eg "OTU 1" instead of OTU_1"). The version of q2-srs you used would only work for feature-tables with feature names without spaces. Even though most of the feature-tables generated within qiime will not contain spaces in feature names, we have no interest in complicating your life, so I am considering that a q2-srs bug (thanks for pointing this out ), which is now fixed.
So please just reinstall q2-srs and you already will have the updated/fixed plugin.
- deactivate your qiime env
- cd into your qiime env directory (in my case, located at
rm -r bin/SRS* lib/python3.8/site-packages/*srs* conda-meta/q2_srs*
- follow the installation instructions provided here
Let me know if this works for you!