ERROR in Normalize by Copy Number

[Jenessa Winston]

Hello Everyone-

Any help would be GREATLY appreciated.  I have followed the directions online for the "closed reference" OTU table for input into Galaxy.  When I upload and run this file, I am getting the following error:

Traceback (most recent call last): File "/galaxy-central/tools/picrust/scripts/normalize_by_copy_number.py", line 146, in <module> main() File "/galaxy-central/tools/picrust/scripts/normalize_by_copy_number.py", line 74, in main raise ValueEr

 How do I fix this??

Thanks

Jenessa

[Gavin Douglas]

Hey Jenessa,

You’ll have to press the bug icon in galaxy to see the full error message - without that it’s difficult to troubleshoot this error.

However a good bet is that your BIOM table isn’t in JSON format (which is required for PICRUSt v1.0.0, the version hosted on the galaxy website).

You can use a command like this to convert from HDF5 to JSON: 

biom convert -i otu_table.biom -o otu_table_json.biom --table-type="OTU table" --to-json

Cheers,

Gavin

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[Jenessa Winston]

It worked! Thanks!