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