summarize_miso not recognizing my directories
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.
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Pierre Lindenbaum
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lavanya.kannan •
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lavanya.kannan •
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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/ outputdirorsummarize_miso ‐‐summarize‐samples miso_output/SE/ outputdirmiso_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?