METAPHLAN: Getting genus level resolution but not family level

Question

[dpc]

Hi 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

Due to this, STAMP software is showing some ERROR and not importing my stamp formatted profile file (.spf file). Why am I not getting family but getting genus level resolution? Isn’t it strange???

Thanks, DC7

[cpad0112]

f stands for family and g stands for genus in example line. IN example line 6 levels of information is present. I guess 7th level, species is not pasted. Please post the some error here to understand what is going on. please also post few lines output from metaphlan and the how you are executing stamps.

[dpc]

Hi... here, order is clostridiales, genus is lawsonibacter... Right? what is the family then?

Thanks, DC7

[cpad0112]

f__Clostridiales_unclassified

[dpc]

yes... that's where my confusion is. The family is not specified. But, the genus is. How is this possible? How, a child level taxa can be classified without being sured of parent level? while importing in STAMP, getting the following error for following classification:

classification: k__Bacteria|p__Firmicutes|c__Bacilli|o__Bacillales|f__Bacillales_unclassified|g__Gemella

error: "Child g__Gemella has an unclassified parent."

[antonioggsousa]

This seems to be related with the taxonomic database used for the taxonomic profile with METAPHLAN.

Which database did you use? Do you know?

Sorry, but I never use myself.

António

[cpad0112]

did you use biom to sff convert script provided by stamp team?

[dpc]

I am not getting any script to merge all the metaphlan .biom outputs which I should do prior to conversion into .spf file.

Thanks, DC7