Question: Error using BLAST+
0
gravatar for onspotproductions
5.2 years ago by
United States
onspotproductions140 wrote:

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 • 3.3k views
ADD COMMENTlink modified 5 weeks ago by Yanpeng Chen0 • written 5.2 years ago by onspotproductions140
0
gravatar for Philipp Bayer
5.2 years ago by
Philipp Bayer6.9k
Australia/Perth/UWA
Philipp Bayer6.9k wrote:

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 COMMENTlink modified 14 months ago by Ram32k • written 5.2 years ago by Philipp Bayer6.9k
0
gravatar for Yanpeng Chen
5 weeks ago by
China/Chengdu/UESTC
Yanpeng Chen0 wrote:

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 COMMENTlink written 5 weeks ago by Yanpeng Chen0
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