Question about calculate_diversity.R

Microbial community profiling MetaPhlAn
1

MetaPhlAn version 4.0.6 (1 Mar 2023):

–Describe the issue

I tried to use calcaulate_diversity.R for alpha and beta diversity. I have some issue with command line from tutorials.

When I ran metaphlan4, I had only two txt files: 1) bowtie2.txt and 2) profile.txt.

In the tutorial, however, tsv file is used. My question is how I can produce tsv file from metaphlan run.

Another question is when I used profile.txt file for calculate_diversity.R, I got the following errors.

Warning: unable to access index for repository http://cran.us.r-project.org/src/contrib:
Line starting ' install.packages → available.packages → readRDS
In addition: Warning message:
package âoptparseâ is not available (for R version 3.5.1)
Execution halted

Would someone please let me know how to calculate alpha and beta diversity from output of metaphlan?

Thanks.

2

Hi and sorry for the late reply!

Regarding the first point, the metaphlan run produces a profile.txt file for each sample, you can then merge the single profiles with the script merge_metaphlan_tables.py (here the tutorial: MetaPhlAn 4 · biobakery/MetaPhlAn Wiki · GitHub) to obtain a .tsv table on which you can then calculate alpha and beta diveristy.
Regarding the error message from R, are you running the script calculate_diversity.R inside a conda environment with metaphlan4? (here the installation tutorial MetaPhlAn 4 · biobakery/MetaPhlAn Wiki · GitHub), like that you should already have the requirements installed.