PICRUSt command

[Harry (Harry Batsang)]

Hi,

May I know after this (Picrust support?), what command should be used to get the PICRUSt format biom file?

I use the command from this discussion (How to create a feature table with qiime2 for PICRUST with the taxonomic assignment?), specifically: biom add-metadata -i ExportedTableForPICRUSt/feature-table.biom -o table-with-taxonomy.biom --observation-metadata-fp 97_otu_taxonomy.txt --sc-separated taxonomy

But it does not work, and gives me the errors:
Traceback (most recent call last):
File “/Users/ranranhu/miniconda3/envs/qiime2-2018.4/bin/biom”, line 6, in
sys.exit(biom.cli.cli())
File “/Users/ranranhu/miniconda3/envs/qiime2-2018.4/lib/python3.5/site-packages/click/core.py”, line 722, in call
return self.main(*args, **kwargs)
File “/Users/ranranhu/miniconda3/envs/qiime2-2018.4/lib/python3.5/site-packages/click/core.py”, line 697, in main
rv = self.invoke(ctx)
File “/Users/ranranhu/miniconda3/envs/qiime2-2018.4/lib/python3.5/site-packages/click/core.py”, line 1066, in invoke
return _process_result(sub_ctx.command.invoke(sub_ctx))
File “/Users/ranranhu/miniconda3/envs/qiime2-2018.4/lib/python3.5/site-packages/click/core.py”, line 895, in invoke
return ctx.invoke(self.callback, **ctx.params)
File “/Users/ranranhu/miniconda3/envs/qiime2-2018.4/lib/python3.5/site-packages/click/core.py”, line 535, in invoke
return callback(*args, **kwargs)
File “/Users/ranranhu/miniconda3/envs/qiime2-2018.4/lib/python3.5/site-packages/biom_format-2.1.6-py3.5-macosx-10.7-x86_64.egg/biom/cli/metadata_adder.py”, line 107, in add_metadata
float_fields, sample_header, observation_header)
File “/Users/ranranhu/miniconda3/envs/qiime2-2018.4/lib/python3.5/site-packages/biom_format-2.1.6-py3.5-macosx-10.7-x86_64.egg/biom/cli/metadata_adder.py”, line 174, in _add_metadata
header=observation_header)
File “/Users/ranranhu/miniconda3/envs/qiime2-2018.4/lib/python3.5/site-packages/biom_format-2.1.6-py3.5-macosx-10.7-x86_64.egg/biom/parse.py”, line 527, in from_file
raise BiomParseException("No header line was found in mapping "
biom.exception.BiomParseException: No header line was found in mapping file

By the way, I used dada2 to denoise.

Thank you so much!

[Nicholas_Bokulich]

@Harry

By the way, I used dada2 to denoise.

It is fine to use dada2 for initial denoising — but if performing a picrust analysis you must then perform closed-reference OTU picking agains the picrust database using vsearch, as described in the thread that you linked to. Since you mention dada2, I just want to make sure that you saw the vsearch step in that linked protocol.

@Harry

biom.exception.BiomParseException: No header line was found in mapping file

Check out this thread, it looks like you are having the same error:

Adding qiime2 taxonomy data to a .biom file

Hello! I’ve been trying these steps in order to import the biom file to Qiime1 and summarize the taxa barplot by categories. The export parts worked fine, I think, but when trying to add the metadata values to the biom file this error is returned: _ biom.exception.BiomParseException: No header line was found in mapping file. _ I have changed the biom-taxonomy.tsv file header line in order to reproduce what you wrote on your answer, like this: #OTUID taxonomy confidence This way, when …

The error seems fairly clear: there is a formatting issue with your metadata file (i.e., 97_otu_taxonomy.txt) that needs to be fixed.

Note that biom-format and picrust are external software and we cannot really provide support for them on this forum, though we will do what we can to help.

Let me know if fixing the header line in your metadata file helps!

[Harry (Harry Batsang)]

Thank you so much Nicholas, it works.

BUT, PICRUSt galaxy server (http://galaxy.morganlangille.com/) seems down, I have not got a chance to test the biom file. I will update here as soon as the server resumes working.

[Harry (Harry Batsang)]

Hi @Nicholas_Bokulich,

The galaxy resumes working, and I tested the biom file. IT WORKS!

The taxonomy file needs to be modified

The 97_otu_taxonomy.txt file needs to add “#OTUID taxonomy” at the top, but should be Tab instead of space.