summarize_miso not recognizing my directories

Question

[lavanya.kannan]

I am trying to run the function "miso_summary" of MISO software (https://miso.readthedocs.io/en/fastmiso/#)

summarize_miso ‐‐summarize‐samples miso_output/SE/sample1 outputdir

but the command does not seem to recognize its arguments - in this case, they are input and output directories. I have made this work before by luck, but cannot understand what I am missing.

This is the output I get:

[kannal01@phoenix2 Monica]$ summarize_miso miso_output/SE/8711/ miso_output/SE/sample_summaries/
MISO (Mixture of Isoforms model)
Summarize MISO output to get Psi values and confidence intervals.
Use --help argument to view options.

[GenoMax]

Looking at the help page you need to run the command at the directory level where all samples are present. summarize_miso ‐‐summarize‐samples miso_output/ outputdir or summarize_miso ‐‐summarize‐samples miso_output/SE/ outputdir

[lavanya.kannan]

miso_output/SE/sample1 is the directory where I store all the miso --run results. I tried summarize_miso ‐‐summarize‐samples miso_output/SE/sample1, summarize_miso ‐‐summarize‐samples miso_output/SE/ and also summarize_miso ‐‐summarize‐samples miso_output/ with no luck.

miso_output/SE/ is the directory where I store results of all samples - but it should not matter for this command.

Perhaps, the folder miso_output/SE/sample1 must be checked for missing files/ folders?