When I try to visualize alpha diversity from core metrics I get an error.
qiime diversity alpha-group-significance \
--i-alpha-diversity core-metrics-results/evenness_vector.qza \
--m-metadata-file metadata.txt \
Plugin error from diversity:
[Errno 2] No such file or directory: '/var/folders/db/86v8zfn53qv_z90t36yc24sc0000gn/T/qiime2-temp-xjx2t6fe/kruskal-wallis-pairwise-Average%20number%20of%20bathes/showers%20per%20week.csv'
Debug info has been saved to /var/folders/db/86v8zfn53qv_z90t36yc24sc0000gn/T/qiime2-q2cli-err-y069_ef5.log
I’ve never had this problem before. What’s going on?
Hi @prestcat - it looks like the
/ in your metadata column label
Average number of bathes / showers per week is causing things to go crazy. I have opened an issue to fix this, but in the meantime, I think if you change that label to remove the slash, you should be okay (something like
Average number of bathes or showers per week, for example). Thanks, and stay tuned, we will update this thread when a fix is released!
Thank you! I'm not sure if this is related, but there's nothing in my alpha diversity visualizations. For example: faith-pd-group-significance.qzv (574.4 KB)
I thought maybe I made a mistake with chimera removal or trimming, but the beta diversity metrics all seem fine.
Hey @prestcat, I think you found another bug! Two for the price of one! Sorry, but it looks like this visualization isn’t interacting as expected on q2view. I was able to view it locally running
qiime tools view faith-pd-group-significance.qzv, so please give that a shot for now.
I opened up a ticket for the q2view issue here. Stay tuned, and I am really sorry, two separate bugs is pretty unfortunate.
I’m glad it’s not an issue with my data! I was able to view my visualizations with your work around. Thank you!
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