Fasta blast alignment error
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Entering edit mode
3.2 years ago

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.

alignment sequencing • 515 views
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