[Biopython] Entrez.efetch Service unavailable!

Kevin Lam aboulia at gmail.com
Tue Dec 15 22:52:36 EST 2009


Hi I have been trying to use
Entrez.efetch
to download ~1000 bacteria genomes
I read in the docs that biopython will auto take care of the delay and fetch
via the preferred site for download scripts
but I have been getting service unavailable  errors at GMT +8 1100am
is this normal? Or should i edit the source to give a larger delay buffer?
So far I have only managed to get 3 fasta sequences out

Or should I bring this up to NCBI instead?

Traceback (most recent call last):
  File "../retr-fasta.py", line 15, in ?
    handle = Entrez.efetch(db="genome", id=uid, rettype="fasta")
  File
"/home/k/lib/biopython-biopython-9a41381/build/lib.linux-x86_64-2.4/Bio/Entrez/__init__.py",
line 105, in efetch
    return _open(cgi, variables)
  File
"/home/k/lib/biopython-biopython-9a41381/build/lib.linux-x86_64-2.4/Bio/Entrez/__init__.py",
line 343, in _open
    raise IOError("Service unavailable!")
IOError: Service unavailable!


Cheers
Kevin


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