calculate_diversity.R Issues

Microbial community profiling MetaPhlAn
1

I am having trouble running alpha and beta diversity on my MetaPhlAn output. I have a .tsv file of all outputs and tried running it through the calculate_diversity.R script, but received this warning: “380 samples with 100% unknown species were removed from the input table” which is the total number of samples.

Is there further processing I should have performed on the file? Should I restrict the clade name column to species only?

Thank you for your help!

2

Hi @edenardo,

Could you tell me more on how you have merged the files? Did you use the merge_metaphlan_tables.py utility?
Also, can you confirm that in the output you had detected some species?

3

Yes, I merged the files using merge_metaphlan_tables.py - the output did detect a number of species.

4

I am not sure what could be the issue here, could you copy here the first 10 lines of the file? Or attach the full file if the data is not private. Thanks