Entering edit mode
3.8 years ago
jahanshahi.amin
•
0
I'm running sequence alignment on a .fasta file (which had been converted from .fastq file) by google colab using biopython library. when running the following script, I face an error which I send it after the script.
script:
from Bio.Blast import NCBIWWW
fasta_string = open("6449.fasta").read()
result_handle = NCBIWWW.qblast("blastn", "nt", fasta_string)
here's the error I face with:
HTTPError Traceback (most recent call last)
<ipython-input-13-d04b8f20a0cf> in <module>()
from Bio.Blast import NCBIWWW
fasta_string = open("6449.fasta").read()
----> result_handle = NCBIWWW.qblast("blastn", "nt", fasta_string)
/usr/lib/python3.6/urllib/request.py in http_error_default(self, req, fp, code, msg, hdrs)
class HTTPDefaultErrorHandler(BaseHandler):
def http_error_default(self, req, fp, code, msg, hdrs):
--> raise HTTPError(req.full_url, code, msg, hdrs, fp)
class HTTPRedirectHandler(BaseHandler):
HTTPError: HTTP Error 500: Internal Server Error
As far as I know, error number 500 is related to the server issues (ncbiwww server), isn't it? How can I solve it please? Thank you.