Error when using blastn in biopython
I am trying to use NcbiblastnCommandline from biopython and catching an error:
Bio.Application.ApplicationError: Non-zero return code 1 from 'blastn -out output.csv -outfmt 6 qstart qend length sstrand -query original.fasta -evalue 1000 -word_size 4 -subject original.fasta -strand plus -dust no -perc_identity 100.0', message 'USAGE'
There is no error when I execute the same command from terminal, google search give me nothing about this error and message "USAGE" absolutely non-informative for me. What can cause such error and how can I fix it?
1 answer
Follow this BLAST+ to install BLAST+ on windows and adding it to the path should work.
from Bio.Blast.Applications import NcbiblastnCommandline
blastn = "C:/path_to_blast/blast-BLAST_VERSION+/bin/blastn"
cline = NcbiblastnCommandline(cmd = blastn,query='query.fasta', out='out.tab', outfmt=6, subject='subject.fasta') stdout, stderr = cline()
print("STDOUT: %s" % stdout)
print("STDERR: %s" % stderr)
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I think
6 qstart qend length sstrandneeds to be in quotation marks.In my script it is in quotation marks.
What does it appear like in
cline? It needs to be in" options "in the actual command line.Yes, you right. Thank you. The problem was in quotation marks, but now I am a little confused because yesterday I was writing another script and I was using the same way to customize my output table and all worked without quotation marks in command line. And it works now. In yesterday's script. I checked.
Was that a blast command script? In this case blast needs that option to be in quotes.
Now I understand, but in my yesterday's script
outfmt="6 qseqid sseqid qcovs"works perfectly, whereas todayoutfmt="6 qstart qend length sstrand"is not working butoutfmt="'6 qstart qend length sstrand'"is working.