Hi,
I’ve tried to calculate unifrac of merged SGB table from metaphlan v4.0.6 by using utils/calculate_diversity.R.
but I’ve got an error message:
Error in FUN(X[[i]], ...) : attempt to set index 30210/30210 in SET_STRING_ELT
Calls: <Anonymous> -> lapply -> FUN
Execution halted
my metaphlan database version & nwk version both are equal to vOct22.
There was no errors when calculate other diversity metrics.
I have no idea to resolve this error.
my command:
Rscript ~/miniconda3/envs/biobakery/lib/python3.10/site-packages/metaphlan/utils/calculate_diversity.R \
-f mpa_merge.tsv -o diversity/beta/ -d beta -m weighted-unifrac \
-t ~/miniconda3/envs/biobakery/lib/python3.10/site-packages/metaphlan/utils/mpa_vOct22_CHOCOPhlAnSGB_202212.nwk
please advise me.
Thanks 