You should better turn off the option that actually causes the problem (-nopermissions or -nopreservetime).

See the documentation for the error:
Upload of file .. was successful, but error occurred while setting the permissions and/or timestamp. If the problem persists, turn off setting permissions or preserving timestamp. Alternatively you can turn on ‘Ignore permission errors’ option.

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For an answer to your literal question, please read How do I configure site, transfer and/or any other settings for which there are no script commands?

Hi,

I am getting the below error while uploading a file through scripting.

Upload of file 'test.txt' was successful, but error occurred while setting the permissions and/or timestamp. If the problem persists, turn on 'Ignore permission errors' option

Can someone help me on this? How can I use 'Ignore permission errors' in script?

Many thanks,