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I've been using the ete2 module on very powerful servers for some time. Everything was fine until it started going very slowly (one get_taxid_translator() function per minute), now I cannot even get past ncbi = NCBITaxa() assignment. I have uninstalled and reinstalled anaconda2, tried updating to ete3, everything works fine on our 'development servers' but still cannot get past the ncbi = NCBITaxa() line in any piece of software on our normal servers. Even the following script fails to finish

    #!/usr/bin/env python
    from ete3 import NCBITaxa

    ncbi = NCBITaxa()

    print "Finished"

Has this happened to anyone else? Do I need to downgrade any dependencies? Could it be a permissions issue? When I run the basic script ctrl+c nor ctrl+z will escape the script and I have to use kill -9 <job-id> to kill the script. If I wait too long the process enters an uninterruptible sleep.

Thank you in advance, Alexis.

Python 2.7.12 :: Anaconda custom (64-bit) gcc (GCC) 5.4.0

Alexis Lucattini
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  • A "has anyone else encountered this problem" style question is unlikely to be answered (or be answerable) by the stackoverflow community, especially since you indicate the code works on your development server. At minimum, you should provide a minimal reproducible example so that others can try to reproduce your problem: i.e. a set of commands starting with loading the ete module and ending with the call to `NCBITaxa`. – Scott Ritchie Oct 12 '16 at 03:47
  • Some thoughts on your problem: Have you checked whether the python, library, and dependency versions the same between servers? Does NCBITaxa try to connect to an external database? If so it may be a server configuration/connection issue. – Scott Ritchie Oct 12 '16 at 03:49
  • NCBITaxa() connects to a sqlite3 database. If anaconda base directory is on a network file system, this might be an I/O problem. – jhc Nov 09 '16 at 18:20

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