Cannot merge metaphlan output files

Microbial community profiling MetaPhlAn
1

Hi,

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?

2

Hi @ahmedbar
Could you please share the content of the folder you are running the command on?

3

Sure @aitor.blancomiguez
Here you are! I uploaded only two.
sorted_bamfilt_trimmed_254_ProRIDE__A_1296__V350144121_L1-2-3-4_59_R1_profiled_metagenome.txt (21.3 KB)
sorted_bamfilt_trimmed_254_ProRIDE__A_1326__V350144121_L1-2-3-4_62_R1_profiled_metagenome.txt (11.3 KB)

4

HI @ahmedbar
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