Dear Lefse development team,
I ran the already installed lefse on our HPC server. Error happened when running the lefse_run.py.
module load tools
module load ngs
module load anaconda3/2022.10
module load intel/perflibs/64/2020_update2
module load gcc/7.4.0
module load R/4.2.0
export LD_LIBRARY_PATH=/services/tools/R/4.2.0
tsv_dir=/relative_proportion_tsv/
diff_dir=/differential_analysis/
lefse_format_input.py ${tsv_dir}proportion1.tsv ${diff_dir}proportion1.in -c 1 -s 3 -u 2 -o 1000000
lefse_run.py ${diff_dir}proportion1.in ${diff_dir}proportion1.res
Could you give some hints to solve the problem according to your experience?
Best,
Bing
Update
It works now after reinstallation under my own directory on HPC.
Reinstallation
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
Create lefse environment
conda create -n lefse
Activate lefse environment
conda activate lefse
Install lefse through bioconda channel
conda install -c conda-forge -c bioconda lefse
Command lines
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}proportion.tsv ${diff_dir}${r}proportion.in -c 2 -s 1 -u 3 -o 1000000
lefse_run.py ${diff_dir}${r}proportion.in ${diff_dir}${r}proportion.res
lefse_plot_res.py ${diff_dir}${r}proportion.res ${diff_dir}${r}proportion.pdf --feature_font_size 8 --title_font_size 8 --class_legend_font_size 8 --format pdf --dpi 300
lefse_plot_cladogram.py ${diff_dir}${r}proportion.res ${diff_dir}${r}proportion_cladogram.pdf --format pdf
done
Best,
Bing
Hello Bing,
Thank you for the update and I’m glad you were able to find a solution.
Best,
Meg
