Command-line blastn results in "Too many positional arguments" error
2
0
Entering edit mode
23 months ago
langziv ▴ 70

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 • 1.1k views
ADD COMMENT
0
Entering edit mode

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

ADD REPLY
0
Entering edit mode

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

ADD REPLY
2
Entering edit mode
23 months ago
Jack Tierney ▴ 410

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 :)

ADD COMMENT
1
Entering edit mode
23 months ago
GenoMax 147k

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.

ADD COMMENT

Login before adding your answer.

Traffic: 1635 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6