Hi i ran to this error when i want to try the tool on my dataset
Error in names(x) <- value :
'names' attribute [2] must be the same length as the vector [1]
Calls: get_cellfracs_seuratv3 -> colnames<-
Execution halted
Traceback (most recent call last):
File "/Users/alextran/miniconda3/envs/cytospace/bin/cytospace", line 8, in
sys.exit(run_cytospace())
File "/Users/alextran/miniconda3/envs/cytospace/lib/python3.8/site-packages/cytospace/cytospace.py", line 683, in run_cytospace
main_cytospace(**arguments)
File "/Users/alextran/miniconda3/envs/cytospace/lib/python3.8/site-packages/cytospace/cytospace.py", line 520, in main_cytospace
read_data(scRNA_path, cell_type_path,
File "/Users/alextran/miniconda3/envs/cytospace/lib/python3.8/site-packages/cytospace/cytospace.py", line 33, in read_data
cell_type_fraction_estimation_path = estimate_cell_type_fractions(scRNA_path, cell_type_path, st_data_outpath, output_path, output_prefix)
File "/Users/alextran/miniconda3/envs/cytospace/lib/python3.8/site-packages/cytospace/common/common.py", line 79, in estimate_cell_type_fractions
out = subprocess.run(run_args, check=True)
File "/Users/alextran/miniconda3/envs/cytospace/lib/python3.8/subprocess.py", line 516, in run
raise CalledProcessError(retcode, process.args,
subprocess.CalledProcessError: Command '['Rscript', '/Users/alextran/miniconda3/envs/cytospace/lib/python3.8/site-packages/cytospace/get_cellfracs_seuratv3.R', '--scrna-path', '//Users/alextran/Downloads/mouse/SC.txt', '--ct-path', '/Users/alextran/Downloads/mouse/SC_other.txt', '--st-path', '/Users/alextran/cytospace/cytospace_results/ST_expression.txt', '--outdir', '/Users/alextran/cytospace/cytospace_results', '--prefix', '']' returned non-zero exit status 1.
Hi i ran to this error when i want to try the tool on my dataset
Error in names(x) <- value : 'names' attribute [2] must be the same length as the vector [1] Calls: get_cellfracs_seuratv3 -> colnames<- Execution halted Traceback (most recent call last): File "/Users/alextran/miniconda3/envs/cytospace/bin/cytospace", line 8, in
sys.exit(run_cytospace())
File "/Users/alextran/miniconda3/envs/cytospace/lib/python3.8/site-packages/cytospace/cytospace.py", line 683, in run_cytospace
main_cytospace(**arguments)
File "/Users/alextran/miniconda3/envs/cytospace/lib/python3.8/site-packages/cytospace/cytospace.py", line 520, in main_cytospace
read_data(scRNA_path, cell_type_path,
File "/Users/alextran/miniconda3/envs/cytospace/lib/python3.8/site-packages/cytospace/cytospace.py", line 33, in read_data
cell_type_fraction_estimation_path = estimate_cell_type_fractions(scRNA_path, cell_type_path, st_data_outpath, output_path, output_prefix)
File "/Users/alextran/miniconda3/envs/cytospace/lib/python3.8/site-packages/cytospace/common/common.py", line 79, in estimate_cell_type_fractions
out = subprocess.run(run_args, check=True)
File "/Users/alextran/miniconda3/envs/cytospace/lib/python3.8/subprocess.py", line 516, in run
raise CalledProcessError(retcode, process.args,
subprocess.CalledProcessError: Command '['Rscript', '/Users/alextran/miniconda3/envs/cytospace/lib/python3.8/site-packages/cytospace/get_cellfracs_seuratv3.R', '--scrna-path', '//Users/alextran/Downloads/mouse/SC.txt', '--ct-path', '/Users/alextran/Downloads/mouse/SC_other.txt', '--st-path', '/Users/alextran/cytospace/cytospace_results/ST_expression.txt', '--outdir', '/Users/alextran/cytospace/cytospace_results', '--prefix', '']' returned non-zero exit status 1.