Strange output for metaphlan! Parent level taxa unclassified, but getting child level taxa resolution

Hi community (@fbeghini ) I am using MetaPhlAn3 and getting some output like:

k__Bacteria|p__Firmicutes|c__Clostridia|o__Clostridiales|f__Clostridiales_unclassified|g__Lawsonibacter 2|1239|186801|186802||2172004 0.46367

Here, we are getting genus level classification “Lawsonibacter”, but the family remains unclassified (same thing happened for many other taxa as well). This is leading to downstream analysis problem. When I tried to load it in STAMP software, it is showing some ERROR and not importing my stamp compatible profile file ( .spf file ) :

 Error reading profile file
 Child g__Gemella has an unclassified parent.

The same type of profiling problemWhy am I not getting family but getting genus level resolution? Isn’t it strange???


This is a result of a known genus not having a nicely defined parent family in the NCBI taxonomy. When this happens, MetaPhlAn fills in a family using the name of the next highest taxonomic rank (in this case the order Clostridiales). STAMP must be flagging the string “unclassified” in the family name automatically. One option would be to use sed to replace “unclassified” with another string that won’t raise a flag for STAMP.

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