-
Notifications
You must be signed in to change notification settings - Fork 11
Description
I am using the web application as well, and I keep running into the same error.
"There was an error while parsing your data. Please ensure your OTU and mapping files follow the format explained in the documentation. OTU tables must be the json version of biom."
The file was made through Qiime2, referenced against Greengenes 97%. The biom file has been merged with the metadata file.
I have tried using multiple formats from: http://biom-format.org/documentation/biom_conversion.html
including the following suggestions found on other issues.
biom convert -i table.biom -o table.from_biom.txt --to-tsv
biom convert -i table.txt -o table.from_txt_json.biom --table-type="OTU table" --to-json
To add the metadata, the following code was used:
biom add-metadata -i feature-table.biom -o table-with-metadata.biom --observation-metadata-fp taxonomy.tsv --sc-separated taxonomy --sample-metadata-fp metadata.txt --output-as-json
I also tried reinforcing the data type using:
biom convert -i table-with-metadata.biom -o table-with-metadata-r.biom --table-type="OTU table" --to-json
If anyone has time to help troubleshoot, I would greatly appreciate it.