CODEWITHSUNDEEP
biopythonblastncbi
Chaoran
Chaoran

Reputation: 11

BioPython - qblast() timeout every time, running from python shell

I am a new user to BioPython. I have set up my virtual env and installed BioPython via pip inside the venv.

I am following the instructions in the BioPython cookbook/tutorial here.

First, I import the module:

>>>from Bio.Blast import NCBIWWW

Then I set my email, using: >>>[email protected], as the guidelines specify. Finally, I run the query: >>> result_handle = NCBIWWW.qblast("blastn", "nt", "8332116")

Every time I try to send this query, it hangs a really long time. Eventually I get the following warning:

/home/user/python/covid_dna/env/lib/python3.10/site-packages/Bio/Blast/NCBIWWW.py:281: BiopythonWarning: BLAST request BHFD53MJ016 is taking longer than 10 minutes, consider re-issuing it
  warnings.warn(

I expected the query to return a result to result_handle. Instead, either the query fails, or I send keyboard interrupt with ctrl+c as it has hung for over 30 minutes.

Am I using incorrect syntax? Have I failed to set some variable, such as the url_base correctly?

I have run the same BLAST query using the web interface, which returns an expected BLAST search result: web_blast_result

Upvotes: 0

Views: 47

Answers (1)

Chaoran
Chaoran

Reputation: 11

Posting just in case anyone was actually reading this. It turned out to be a DNS or other network connectivity issue, perhaps on the NCBI server side. I ran the same query a few days later and it behaved as expected.

Upvotes: 0

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