Metaphlan3 Merged Table Error

Hello,

I am trying to merge my metaphlan3 output files using the command:

merge_metaphlan_tables.py *_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!

Jen

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 merge_metaphlan_tables.py with the one in the repo), it should tell you which file is missing the header. Biobakery team, would this be a helpful PR?