knights-lab / BugBase

37 stars 11 forks source link

BIOM format issue #5

Open microDM opened 6 years ago

microDM commented 6 years ago

I have used biom file (hdf5) created by qiime pipeline as input. But BugBase is throwing error. Then I created biom file in json format using command biom convert -i input.biom -o output.biom --to-json Result of head -c 80 output.biom is {"id": "No Table ID","format": "Biological Observation Matrix 1.0.0","format_url

It is in json format (v 1.0.0) The standalone throwing me error like: Error in scan(file = file, what = what, sep = sep, quote = quote, dec = dec, : line 2 did not have 8 elements Calls: load.inputs -> read.table -> scan Execution halted

And I tried webserver also....which is prompting me check biom file format.

jingao-yu commented 6 years ago

Have you tried converting the biom file to tsv format befor converting again to json format ?