#36 Mod.SequenceSearcher test_remoteBlast fails

closed-out-of-date
nobody
None
5
2012-02-13
2008-10-17
No

python 2.5
blastall 2.2.15

The local blast still works but the remote blast gives the following traceback::

Traceback (most recent call last):
File "/home/nisusers/rgruenberg/biskit/Biskit/Mod/SequenceSearcher.py", line 919, in test_remoteBlast
self.search( self.searchRemoteBlast )
File "/home/nisusers/rgruenberg/biskit/Biskit/Mod/SequenceSearcher.py", line 878, in search
searchFunction()
File "/home/nisusers/rgruenberg/biskit/Biskit/Mod/SequenceSearcher.py", line 857, in searchRemoteBlast
alignments=50)
File "/home/nisusers/rgruenberg/biskit/Biskit/Mod/SequenceSearcher.py", line 297, in remoteBlast
raise BlastError( str(why) )
BlastError: list index out of range

And further into Bio::

289 (remoteBlast) parsed = NCBIXML.parse( results ).next()
NCBIXML: 572 (parse) None
NCBIXML: 98 (endElement) None
<string>: 0 (?) None
NCBIXML: 216 (_end_BlastOutput_version) None

Discussion

  • Raik Gruenberg

    Raik Gruenberg - 2012-02-13
    • status: open --> closed-out-of-date
     
  • Raik Gruenberg

    Raik Gruenberg - 2012-02-13

    This issue seems to be resolved with a current installation of ncbi tools.

     

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