Merge_metaphlan_tables.py doesn't work after converting to GTDB taxonomy

The merge_metaphlan_tables.py script doesnt work if when metaphlan output has been converted using the sgb_to_gtdb_profile.py utility script. I suspect this is to do with the lower number of headers and columns.

This is what an example of my converted metaphlan output looks like:

#mpa_vJan21_CHOCOPhlAnSGB_202103
#clade_name     relative_abundance
d__Bacteria     100.00001
d__Bacteria;p__Actinobacteriota 25.292869999999997
d__Bacteria;p__Proteobacteria   12.73789
d__Bacteria;p__Firmicutes_A     38.49073
d__Bacteria;p__Bacteroidota     18.188679999999998
d__Bacteria;p__Firmicutes       4.95885
d__Bacteria;p__Firmicutes_C     0.28645
d__Bacteria;p__Firmicutes_B     0.04454

The error code in the merged output is:
merge_metaphlan_tables: wrong header format for “13-6929606_metaphlan_gtdb.txt”, please check your profiles.

Any ideas on how to fix this?

Hi @sxh1136
Yes, currently the merge_metaphlan_tables.py does not work with the profiles produced by the sgb_to_gtdb_profile.py. However, in the following days, we are going to push version 4.0.2 that will include new utilities and, between them, the merging of gtdb-transformed profiles

Thanks for the quick reply. Good to hear that a fix is coming soon. Would you recommend that I even convert SGB taxonomy to GTDB if I’m just using the metaphlan data to plot relative abundance stacked bar charts?

Hi @sxh1136
We just pushed version 4.0.2 fixing this problem (now, for GTDB profiles you will need to use the --gtdb_profiles parameter)