-
Notifications
You must be signed in to change notification settings - Fork 4
New issue
Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.
By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.
Already on GitHub? Sign in to your account
qiime micom build KeyError: 'd__Bacteria;p__Bacteroidota;c__Bacteroidia;__;__;__' #31
Comments
Hi, the unassigned taxonomy is fine. Your tables look a bit odd though. Can you tell me a bit more how you generated them? Were those all outputs from Qiime 2? Because at least the taxonomy looks like it is misformatted. Usually those have spaces between the |
Hm it does not look like the biom table came from the amplicon distribution. This should have the same IDs as the taxa table (the |
hi Diener, thanks for your reply, I will run the previous steps again with newly installed qiime2 amplicon distribution and put the output here. |
Sounds good. |
Hi Diener, |
Hi, Can you paste the commands you are running? Is the feature table the output from dada2 or did you do something else with it like summarizing on the genus level? For the micom plugin it expects the table directly from dada2. It will collapse on the used rank automatically. |
Hi Diener, |
Hi Diener,
many thanks for your valuable help! |
Hi, the warning shouldn't be a problem if you are using CARVEME. You are right that there aren't that many taxa in there however it does seem to match a good chunk of the abundance so it looks like there aren't that many taxa in the original data? You could also play around with the The infeasibility usually comes from not using the correct medium for the model database (needs to be one built for CARVEME, from the media repository for instance). |
Hi Diener,
![1713936914661](https://private-user-images.githubusercontent.com/32172984/325092601-d6e42b17-d80c-42d6-be7c-0016f232b12b.png?jwt=eyJhbGciOiJIUzI1NiIsInR5cCI6IkpXVCJ9.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.zhHIKbAvFhG2PpX6L2u50fLKhvmCoecHLglumUSkLNg)
I tried to run qiime micom build and had the error in below:
version info: q2cli version 2024.2.0 + QIIME 2 Plugin 'micom' version 0.14.0 (from package 'q2-micom' version 0.14.0)
I am wondering if I should remove all the unassigned taxonomy? or anything else was wrong?
many thanks for your help!
Zhaoju
The text was updated successfully, but these errors were encountered: