I have seen the posts about BLAST outfmt and I suspect my mistake to be something really small that I am overlooking. I am blasting a large number of sequences, want just one hit for each, but I want to be able to filter for the word virus in the output.
This is my command line:
blastn -remote -db nr -query ~/path/filename.fa -outfmt "6 field1 field2..." num_alignments 1 -out ~/path/outfilename
I have tried various fields from the list of outfmt options, and I get output for everything EXCEPT stitle or salltitles or any of the other descriptive fields like scientific or common name.
if I use -outfmt "6 qseid sseqid stitle pident" for instance I get output with only 3 columns, not 4. if I use only stitle in that line, I get the std output columns. it is like the word stitle does not exist, yet it does not trigger any error messages.
What am I missing here? Can I not use those fields when I do remote?
Susanne
How about
-outfmt '6 qseid sseqid stitle pident'?Single or double quotes are interchangeable here.
Ok. There are at least two things wrong with your command.
num_alignmentsis irrelevant to outfmt 6I'm surprised it doesn't just return some error. Anyway, perhaps your problem is somehow related to this.
Susanne,
Did you ever get this to work? I'm experiencing the same problem using the following code...
It's as though the subject title (stitle) cannot be retrieved. I'm using blast/2.4.0. Any advice welcome.