Question: Blast results only print to terminal
0
gravatar for darzenis
2.0 years ago by
darzenis20
darzenis20 wrote:

I am trying to run blastx using the command below, but the output is not a separate file – the results only print to my terminal, rather than to a file. Any advice?

blastx -query filename -task blastx-fast -db nr -evalue 1e-5 -outfmt 5

Notes: I have the blast_nr database downloaded and this command is executed in that directory. I tried the default outfmt and the same thing happened.

Thanks!

blast rna-seq • 671 views
ADD COMMENTlink modified 2.0 years ago • written 2.0 years ago by darzenis20

Thank you! That worked.

ADD REPLYlink written 2.0 years ago by darzenis20

You should use -out real_outputfile_name as the proper option for blast suite of programs in your command line.

ADD REPLYlink modified 2.0 years ago • written 2.0 years ago by genomax77k
1
gravatar for Joe
2.0 years ago by
Joe16k
United Kingdom
Joe16k wrote:

Either use the -out flag or simply issue a STDOUT redirection at the end of your command:

blastx [my command] > output.txt
ADD COMMENTlink modified 2.0 years ago • written 2.0 years ago by Joe16k
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