Fasta blast alignment error
0
0
Entering edit mode
3.8 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 • 601 views
ADD COMMENT

Login before adding your answer.

Traffic: 1759 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6