Error using BLAST+

Question

[onspotproductions]

I am trying to use BLASTx to query a nucleotide sequence against a protein database and I wanted to add the encoded protein information to the output dataset. I however keep getting this error

blastx -db UniprotConus -query /Users/evanclark/Desktop/Cone_Snail_Assembly_split/aaaa-Cone_Snail_Assembly.txt -outfmt qseqid pident length mismatch gapopen qstart qend sstart send evalue bitscore sseq qseq 6 -out result1.txt
Error: Too many positional arguments (1), the offending value: sseqid
Error:  (CArgException::eSynopsis) Too many positional arguments (1), the offending value: sseqid

Answer 1

[Philipp Bayer]

You may want to put " or ' around your formatting arguments:

blastx -db UniprotConus -query /Users/evanclark/Desktop/Cone_Snail_Assembly_split/aaaa-Cone_Snail_Assembly.txt -outfmt "qseqid pident length mismatch gapopen qstart qend sstart send evalue bitscore sseq qseq 6" -out result1.txt

If that doesn't work, put the 6 before the other arguments:

blastx -db UniprotConus -query /Users/evanclark/Desktop/Cone_Snail_Assembly_split/aaaa-Cone_Snail_Assembly.txt -outfmt "6 qseqid pident length mismatch gapopen qstart qend sstart send evalue bitscore sseq qseq" -out result1.txt

Answer 2

[Yanpeng Chen]

more concise with:

blastx -db UniprotConus -query /Users/evanclark/Desktop/Cone_Snail_Assembly_split/aaaa-Cone_Snail_Assembly.txt -outfmt "6 std sseq qseq" -out result1.txt