Using needle command with no output to the terminal
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3.7 years ago
Jacob ▴ 10

I'm am using the needle command and would just like there to be no output to the terminal

For example this is what I run

needle -asequence seq1.fna -bsequence seq2.fna -gapopen 0 -gapextend 2 -outfile file.needle          
Needleman-Wunsch global alignment of two sequences

And I would just like the line Needleman-Wunsch global alignment of two sequences to not print.

needle emboss silent • 1.4k views
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2
Entering edit mode
3.7 years ago
Charles Plessy ★ 2.7k

The -auto option just does that. Quoting from the manual:

The -auto qualifier will turn off any prompting of the user. It will try to run the program with all the default settings that are defined in the ACD file. If a parameter does not have a default value and it is flagged as required, the program will stop and produce an error message.

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