I’m trying to filter AGP metadata that I’ve pulled down from redbiom. I first filter the table features for minimum frequency of 10. I then tried to filter the samples where mental_illness=‘FALSE’ and I get an empty table in return. I’ve checked that there are samples with mental_illness as FALSE, I’ve checked that the sample names match for the feature table and the metadata. I’m at a loss as to what else the issue could be. I’m using qiime2-2019.7
Here’s the command I ran:
qiime feature-table filter-samples
–i-table agp_10_table.qza
–m-metadata-file 2019-08-22_agp_metadata.txt
–p-where “[mental_illness]=‘FALSE’”
–o-filtered-table agp_10_table_filt_test.qza
Looks like none of the samples actually have a mental_illness value of FALSE:
# grab the mental_health column | trim header | sort | get unique vals
cut -f578 2019-08-22_agp_metadata.txt | sed -n '1!p' | sort | uniq
false
No
not applicable
Not provided
true
Yes
So, the simplest solution is to change FALSE to false in your query:
Thank you! This definitely fixed it. I believe this is due to the way the metadata was pulled down from redbiom, but I had been trying to find this error for way too long.