Metaphlan3 Merged Table Error


I am trying to merge my metaphlan3 output files using the command: *_profile.txt > merged_abundance_table.txt

This is the error I have:

merge_metaphlan_tables found tables without a header including the database version. Exiting.

Where do I go from here? Thank you!


Hi @jlhaller , I ran into a similar issue; turned out the *_profile.txt was inadvertently including some non-metaphlan files. I made of fork of metaphlan with some slightly improved logging and error handling. If you clone that and install it (or just replace the with the one in the repo), it should tell you which file is missing the header. Biobakery team, would this be a helpful PR?