Blast Error in Python
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Entering edit mode
3.4 years ago
aldana99 • 0

Hi everyone, i need help with something. Im doing this script:

from Bio.Blast.Applications import NcbiblastpCommandline
from Bio.Blast import NCBIWWW

blastp_cline = NcbiblastpCommandline(cmd='C:\\Program Files\\NCBI\\blast-2.11.0+\\bin\\blastp', query='C:\\Users\\Aldana\\Desktop\\lab\\RA_pred-40aa.fa', db="C:\\Users\\Aldana\\Desktop\\lab\\TriTrypDB-48_TcruziTCC_AnnotatedProteins.fasta", outfmt=5, out='target.out', evalue=0.001,remote=True)

stdout, stderr = blastp_cline()

print(blastp_cline, file=open('outputblast.txt','a'))

And then ive got this error:

ApplicationError: Non-zero return code 2 from '"C:\\Program Files\\NCBI\\blast-2.11.0+\\bin\\blastp" -out target.out -outfmt 5 -query C:\\Users\\Aldana\\Desktop\\lab\\RA_pred-40aa.fa -db C:\\Users\\Aldana\\Desktop\\lab\\TriTrypDB-48_TcruziTCC_AnnotatedProteins.fasta -evalue 0.001 -remote', message "BLAST Database error: 'C:\\Users\\Aldana\\Desktop\\lab\\TriTrypDB-48_TcruziTCC_AnnotatedProteins.fasta' not found on NCBI servers."

I dont know what im doing wrong, if someone can help me i would be so grateful.

blast python genome blastp sequence • 888 views
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Entering edit mode

The remote=True seems out of place since you have a local blast installation.

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