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I want to save the output of the below command:

start C:\Users\Desktop\putty.exe -ssh server_ip  -l username -pw password -m <path of the command file> 

I used the "> <output_file>" at the end of the above command but it didn't work out.

How to get the logs saved in a file ?

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Once you redirect the output, like so: ls > output.txt

Perform pwd, output.txt will get stored in the present working directory.

If you want to store in local system then go to Settings -> Session -> Logging -> log file name.

You can store the complete session in the file in your local system

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