I ran Metaphlan4 and now I have the output txt files. When I am trying to merge the file using the following command
merge_metaphlan_tables.py *.txt > merged_abundance_table.txt
It gives me
IndexError: list index out of range
Can you please help me with that?
Could you please share the content of the folder you are running the command on?
It seems that there are some warning messages stored at the beginning of your profiles, try to remove the first to WARNING lines and the script should work perfectly. If you don’t have internet connection when running metaphlan, I suggest you to use the --offline flag to avoid this problems