Exporting OTU table from QIIME 2 into PICRUSt

Hi,
I don’t understand how I can import my OTU table from qiime2 to picrust. When I run the commend line :

normalize_by_copy_number.py -i feature-table.biom  -o normalized_otu_v4_v5.biom

An error is displayed :

raise ValueError,"No OTUs match identifiers in precalculated file. PICRUSt requires an OTU table reference/closed picked against GreenGenes.\nExample of the first 5 OTU ids from your table: {0}".format(', '.join(list(ids_to_load)[:5]))
ValueError: No OTUs match identifiers in precalculated file. PICRUSt requires an OTU table reference/closed picked against GreenGenes.
Example of the first 5 OTU ids from your table: k__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus;s__salivarius, k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Ruminococcaceae;g__Ruminococcus;s__albus, k__Bacteria;p__Bacteroidetes;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__Alistipes;s__massiliensis, k__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus;s__, k__Bacteria;p__Actinobacteria;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Atopobium;s__

But after I saw the we had to use a commend line to make the table compatible with Picrust :

filter_otus_from_otu_table.py -i otu_table.biom -o closed_otu_table.biom --negate_ids_to_exclude -e $PWD/gg_13_5_otus/rep_set/97_otus.fasta

But this command is for Qiime 1 , how to do what compatible but going through qiime2.

Thank you for your help :slight_smile:

Hi @ylana_sauvaget!

The error message indicates that the OTU IDs (i.e. feature IDs) in your QIIME 2 exported table don’t match the OTU IDs used in PICRUSt, which are Greengenes OTU IDs by default. QIIME 2 doesn’t provide closed-reference OTU picking at this time, so you’ll need to use another tool (such as QIIME 1’s pick_closed_reference_otus.py) to generate your Greengenes closed-reference OTU table for use with PICRUSt.

Note that we don’t develop the PICRUSt software so if you have more specific questions about PICRUSt, please post to the PICRUSt user support list.

As noted above, the QIIME 2 table won’t be compatible with PICRUSt – it isn’t possible to filter the table to contain Greengenes OTU IDs because the table doesn’t contain any of those IDs.

For future reference, you can filter features from a feature table using qiime feature-table filter-features (there’s a filtering tutorial with examples).

1 Like

This topic was automatically closed 31 days after the last reply. New replies are no longer allowed.