Question: Ncbi Entrez Server Issues
0
gravatar for heath
7.4 years ago by
heath20
United States
heath20 wrote:

Dear All, I am using entrez protein data base for searching a list 40 000 of protein ids, I set stop time (0.3) to keep ncbi server happy my program runs OK at first, but after running 1hrs or so..it shows

 File "snpinfo_new.py", line 31, in <module>
    fg=Entrez.efetch(db='protein', id=uid, rettype='fasta').read()
  File "/opt/python-2.7/lib/python2.7/site-packages/Bio/Entrez/__init__.py", line 113, in efetch
    return _open(cgi, variables)
  File "/opt/python-2.7/lib/python2.7/site-packages/Bio/Entrez/__init__.py", line 360, in _open
    raise exception
urllib2.HTTPError: HTTP Error 500: Internal Server Error

..how I fix this?

Thanks a lot!

ncbi protein dbsnp biopython entrez • 2.7k views
ADD COMMENTlink modified 6.5 years ago by Peter5.8k • written 7.4 years ago by heath20
1

see retrieving FASTA sequences from ncbi using biopython

ADD REPLYlink modified 7.3 years ago by Istvan Albert ♦♦ 84k • written 7.4 years ago by a.zielezinski9.2k

Thanks a lot :-) !!

ADD REPLYlink written 7.4 years ago by heath20
0
gravatar for Peter
6.5 years ago by
Peter5.8k
Scotland, UK
Peter5.8k wrote:

Like any web-based API, you will sometimes get intermittent errors from Entrez - the standard approach would be to wrap the call in a try/except block and retry it (e.g. three retries, with a pause between each).

ADD COMMENTlink written 6.5 years ago by Peter5.8k
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