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Command-line blastn results in "Too many positional arguments" error

Hi.
I'm running the following command

blastn –db nt –query input.txt –out OUTPUT.txt -remote

which results in the error message

Error:  (CArgException::eSynopsis) Too many positional arguments (1), the offending value: –db

I couldn't find a similar issue.
Does anyone have an idea how to deal with this error?
Thanks.

blastn command-line
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updated by Jack Tierney • Jack Tierney • written by langziv • langziv

I believe flags of more than one character (eg. "db") require a '--' rather than a single '-'. It's a bit confusing in the manual because the hyphens merge

edit. I could easily be wrong as I haven't checked it myself. Perhaps I should have posted this as a comment. Apologies

• 0 views • link
written by Jack Tierney • Jack Tierney

Thanks @Jack Tierney, but after adding hyphens the error persists.

• 0 views • link
written by langziv • langziv

2 answers

Apologies yeah I was wrong but I worked it out! The font for the first 3 hyphens in that command is abnormal. This is what made me think they had merged as I came across that before. Instead replace each of those weird hyphens with a regular one and you should be good to go :)

• 0 views • link
written by Jack Tierney • Jack Tierney

Are you using macOS? It is possible that - you are typing are getting converted to smart hyphens. This can also happen if you are copying and pasting the command as is from some other document especially a PDF file.

Please turn off Use smart quotes and dashes option in keyboard section of system preferences.

• 0 views • link
written by GenoMax GenoMax

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