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knights-lab / BugBase

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json formatting issue #12

Open Ellierein opened 5 years ago

Ellierein commented 5 years ago

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.

Biancabrown commented 5 years ago

Hello,

I'm also having in this issue. My data is in json format. I double checked the file form

"{"id": "None","format": "Biological Observation Matrix 1.0.0","format_url": "http://biom-format.org""

My mapping file is also in the correct form.

However, I am getting an error message on bugbase saying that my files are formatted incorrect:

"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."

Any suggestions?