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
tsv_dir=/tsv_dir/
diff_dir=/differential_analysis/
for r in Phylum Class Order Family Genus Species ;
do
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
done
conda deactivate
#Error
#Tsv file
DATA.tsv (910 Bytes)
Could you give some suggestions?
Thank you very much.
Best,
Bing