The bioBakery help forum

PICRUSt error and missing pathway name

feature-table.json.biom (144.3 KB)
meta-predic.tsv (2.2 MB)

From: fx363@nyu.edu

We used https://huttenhower.sph.harvard.edu/galaxy/ to run PICRUSt but kept getting the error message below from the “Normalize by Copy Number” step. The input file we used was the biom file(feature-table.json.biom) generated by QIIME2 with Greengenes database, which is attached.

Could you please see the error message below and our input biom table attached and let us know what we could do with that? Is that anything wrong with the biom table?

This biom table worked in http://galaxy.morganlangille.com/ but the final outputs we got didn’t show the pathway name and the OTU id. What’s the difference between those two websites to run PICRUSt? and What are the possible reasons we did not get the pathway name in the tsv file(attached: meta-predic.tsv) we converted?

A lot thanks for your help.

Tool execution generated the following error message:

Traceback (most recent call last): File “/galaxy-central/tools/picrust/scripts/normalize_by_copy_number.py”, line 146, in main() File “/galaxy-central/tools/picrust/scripts/normalize_by_copy_number.py”, line 69, in main otu_table=parse_classic_table_to_rich_table(open(opts.input_otu_fp,‘U’),None,None,None,DenseOTUTable) File “/galaxy_venv/local/lib/python2.7/site-packages/biom/parse.py”, line 647, in parse_classic_table_to_rich_table **kwargs) File “/galaxy_venv/local/lib/python2.7/site-packages/biom/parse.py”, line 735, in parse_classic_table md_name = header[-1] IndexError: list index out of range

Best,

Fangxi

Hello Fangxi,
The version of Picrust we have in our Galaxy is a bit outdated, we are in the process of upgrading it. In the mean time, may I suggest you use the version of the authors.
Best regards,
George Weingart PhD
Huttenhower Lab