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
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?