Force a time out on long running blast.pdb() jobs

Issue #79 resolved
Barry Grant created an issue

Running blast.pdb() on large databases when the NCBI server load is high can take an unreasonable amount of time. I suggest we have an optional time.out=90 seconds with a warning and a link to the server results.

Comments (7)

  1. Lars Skjærven

    hmm.. why would timing out be helpful? I anyway need the blast results, and if I don't I can just Crtl-C to stop it. Instead, could we write some meaningful output to the user after some time with the never ending dots (e.g. some server results..?)

  2. Barry Grant reporter

    because I run it in a script and want it to exit so I am can continue without babysitting...

  3. Xinqiu Yao

    How about setting time.out=90 and try=3? We try three times to re-connect to the server and then stop if all of them fail.

  4. Lars Skjærven

    the timeout is a bit annoying since I anyway need to fetch the blast results in order to continue the analysis. can we have no timeout as default?

  5. Barry Grant reporter

    OK, let's have NULL or -1 as default but keep the option to timeout. I have been using the HMMer 3 server quite a bit recently and think it could make a nice alternative for single sequence and 'fasta' 'pdbs' multiple sequence search.

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