Hi there,
I hope this is a trivial question, but haven’t found a way around it by myself …
I’m trying to filter my feature table to get a table that contains only the negative control samples, and then summarize the resulting controls table so I can view it. The commands I am using are:
qiime feature-table filter-samples --i-table final_with_healthy_noC_table.qza --m-metadata-file map_Matilda_2017.txt --p-where "Control='Y'" --o-filtered-table final_with_healthy_noC_controls_table.qza
qiime feature-table summarize --i-table final_with_healthy_noC_controls_table.qza --o-visualization final_with_healthy_noC_controls_table.qzv
The first command to filter the table runs fine, but then the summarize
command returns an error:
Plugin error from feature-table: cannot convert float NaN to integer
I have noticed other users have found a similar error using gneiss
when there are zeroes, but not in feature-table
before.
I have checked my mapping file for zeroes and blank cells and there aren’t any.
Next I tried to export the feature table created with filter-samples
using qiime tools export
, so I could try to see where the NaN values were. This worked, but when I tried to convert the output BIOM file to TSV to look at it, I got another error:
biom convert -i final_with_healthy_noC_controls_table/feature-table.biom -o final_with_healthy_noC_controls_table/feature-table.txt --to-tsv
Error: biom.exception.TableException: Cannot delimit self if I don't have data...
What else can I try? Thank you!
PS I am using version 2017.12 because I already did the bulk of my analysis for this project in that version and thought it would be best to keep it consistent …