The bioBakery help forum

HUMAnN v3 joint taxonomic profile

There is a problem with the output format of humann_reduce_table. To reproduce,

$ metaphlan --version; humann --version
MetaPhlAn version 3.0 (20 Mar 2020)
humann v3.0.0.alpha.1

$ metaphlan --input_type fasta -t rel_ab --nproc 12 SRS014459-Stool.fasta.gz profiled_metagenome.tsv

$ humann_join_tables -i . --file_name profiled_metagenome.tsv -o joined_profiled_metagenome.tsv

$ humann_reduce_table -i joined_profiled_metagenome.tsv -o max_profiled_metagenome.tsv --function max --sort-by level

$ humann --input SRS014459-Stool.fasta.gz --output test.out --taxonomic-profile max_profiled_metagenome.tsv

ERROR: The MetaPhlAn2 taxonomic profile provided was not generated with the expected database version. Please update your version of MetaPhlAn2 to v3.0.

MetaPhlAn 3.0 output has an additional field, “additional_species”, so append tab to each line of max profile.

sed -i 's//\t/’ max_profiled_metagenome.tsv

$ humann --input SRS014459-Stool.fasta.gz --output test.out --taxonomic-profile max_profiled_metagenome.tsv

ERROR: The MetaPhlAn2 taxonomic profile provided was not generated with the database version v30 . Please update your version of MetaPhlAn2 to v3.0.

Prepend first line of profiled_metagenome.tsv to max_profiled_metagenome.tsv
#mpa_v30_CHOCOPhlAn_201901

Now it works!

Thanks for pointing this out - we built in the database version check to the main software now that there are multiple versions floating around, but these changes have not necessarily made it into the suite of utility scripts yet. Assuming your MetaPhlAn profiles were generated on v30 then this is a good short-term hack. :slight_smile: