Not producing loom file output

[dr-sayyadhury]

Hi, I am wondering why my command is not producing a loom output for an ncv run. Instead its giving me a .csv file instead.

I am running the command line on python. Here is my code.

Code

out_path1 = '/dir_path/out/segmentation/baysor/Control_1A_0005511/baysor_segmented' out_path2 = '/dir_path/out/segmentation/baysor/Control_1A_0005511/ncv'

for path, dir, files in os.walk('/dir_path/out/segmentation/baysor/Control_1A_0005511/fov_segments'): for file in files: print(file) command = [ '/home/shamini/.julia/bin/baysor', 'run', '-c', '/dir_path/baysor_processing/baysor.toml', '-x', 'x_location', '-y', 'y_location', '-z', 'z_location', '-g', 'feature_name', '-s', '9', '--save-polygons', 'geojson', '--prior-segmentation-confidence', '0.5', '-o', os.path.join(out_path1, file), os.path.join(path,file) ] subprocess.run(command, check=True)

    command = [
    '/home/shamini/.julia/bin/baysor', 'segfree',
    '-c', '/dir_path/baysor_processing/baysor.toml',
    '-x', 'x_location',
    '-y', 'y_location',
    #'-z', 'z_location',
    '-g', 'feature_name',
    #'-s', '9',
    #'--save-polygons', 'geojson',
    #'--prior-segmentation-confidence', '0.5',
    '-o', os.path.join(out_path2, file),
    os.path.join(path,file)
    ]
    subprocess.run(command, check=True)