Raise embedded.RRuntimeError(_rinterface._geterrmessage())

Dear Lefse development team,

I want to compare my bacterial abundance across eight depths. Only one sample was sampled from each depth, so I only have eight samples.

Here I want to see the differential bacterial taxa of depth2,3,4,5,6,7,8 comparing with the 1st depth using lefse, respectively, using the command line below. An error happened.
#command line
module load tools #pre for miniconda3/4.12.0
module load miniconda3/4.12.0
module load intel/perflibs/64/2020_update2
module load gcc/7.4.0
module load R/4.2.0
conda activate lefse
for r in Phylum Class Order Family Genus Species ;
lefse_format_input.py ${tsv_dir}${r}_proportion1.tsv ${diff_dir}${r}proportion1.in -c 2 -s 1 -u 3 -o 1000000
lefse_run.py ${diff_dir}${r}_proportion1.in ${diff_dir}${r}_proportion1.res -a 1.0
lefse_plot_res.py ${diff_dir}${r}_proportion1.res ${diff_dir}${r}_proportion1.pdf --feature_font_size 8 --title_font_size 8 --class_legend_font_size 8 --format pdf --dpi 300
conda deactivate


#Tsv file
DATA.tsv (910 Bytes)

Could you give some suggestions?

Thank you very much.



What I want is a left-right barplot, with all taxa more enriched in this sample and all taxa more enriched in that sample. No need to be significantly differential.

Hello Bing,
I think LEfSe isn’t the best tool for this task; since you only have one sample per group it is likely creating problems for the statistical analysis portion of LEfSe and it’s not possible to skip that portion. I’d recommend using a different data visualization package (e.g. ggplot2 in R) to create the barplot.