Multi-trait analysis of GWAS (mtag) doesn't work
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Entering edit mode
10 weeks ago

Good morning, I'm making my first attempt to run Multi-trait analysis of GWAS (aka mtag) package (https://github.com/JonJala/mtag/wiki/Tutorial-1:-The-Basics). I'm not so confident with python, so probably I'm missing something. Indeed, after the activation of the environment, when i run the current script:

python mtag.py \
    --sumstats CC_preMTAG.txt,Non_cancer_illness_code_self_reported_type_2_diabetes_preMTAG.txt \
    --out tutorial_results_1.1NS \
    --n_min 0.0 \
      --stream_stdout &

It gives me the following errors:

mtag.py: error: unrecognized arguments: \

(myenv) C:\Users\Salvatore\Desktop\CC_MTAG\mtag>--sumstats CC_preMTAG,Non_cancer_illness_code_self_reported_type_2_diabetes_preMTAG \
"--sumstats" is not recognized as an internal or external command,
 an executable program or batch file.

(myenv) C:\Users\Salvatore\Desktop\CC\CC_MTAG\mtag>--out tutorial_results_1.1NS \
"--out" is not recognized as an internal or external command,
 an executable program or batch file.

(myenv) C:\Users\Salvatore\Desktop\CC_MTAG\mtag>--n_min 0.0 \
"--n_min" is not recognized as an internal or external command,
 an executable program or a batch file.

(myenv) C:\Users\Salvatore\Desktop\CC_MTAG\mtag> --stream_stdout &
"--stream_stdout" is not recognized as an internal or external command,
 an executable program, or a batch file.

Any suggestions?

python GWAS mtag • 318 views
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0
Entering edit mode
9 weeks ago

It might be because you have a lot of backslashes in there, which it can't interpret. It's in the wiki like that to signify a new line in a script, but if you are pasting it into the terminal in one line then try removing the backslashes. Your output file needs to be a path, so I added ./ Try this:

python mtag.py --sumstats CC_preMTAG.txt,Non_cancer_illness_code_self_reported_type_2_diabetes_preMTAG.txt --out ./tutorial_results_1.1NS --n_min 0.0 --stream_stdout &
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