Error using BLAST+
2
0
Entering edit mode
6.5 years ago

I am trying to use BLASTx to query a nucletoide 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

 

blast uniprot protein fasta • 4.5k views
ADD COMMENT
0
Entering edit mode
6.5 years ago

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
ADD COMMENT
0
Entering edit mode
17 months ago
Yanpeng Chen ▴ 10

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
ADD COMMENT

Login before adding your answer.

Traffic: 1674 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6