I have run into a slight issue with exporting my data after running the pipeline. Normally the .tsv file with taxonomy that I have been getting in previous runs doesn't seem to want to generate now. The error that is generate is seen below:
is the addition of my metadata with -m Fungal-Metadata-BLM.tsv. The rest of the code generates the needed files except for this last chunk of code. So I checked the second link. Sadly this is the same attempted fix I did before posting from that other post, Biom add metadata problem, and it didn’t fix the issue either.
Again thank you so much for your help, I am still relatively new to all this so I am likely overlooking something obvious.
I am not sure if this is the issue, but the command I referred to was:
Is there a reason why you are adding --observation-header OTUID,taxonomy,confidence? You should not need this addition if you are editing the headers, as described in both links. I am wondering if this causes things to fail later on?
Not sure why -m Fungal-Metadata-BLM.tsv is being added to this command.
Also, then editing the taxonomy headers I usually replace: Feature ID Taxon Confidence
with this: #OTUID taxonomy confidence
Perhaps you can share your qza files? Hopefully, someone smarter than I will spot the issue.