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The mystery of the forbidden names

Simon Andrews simon.andrews at bbsrc.ac.uk
Mon Feb 12 08:12:26 EST 2001


Guy Bottu wrote:
> 
> During an exercise session one of our students used seqed to make a
> nucleic acid sequence file with name "protein". When he tried to run the
> program composition, it took a very long time to run and produced an
> output saying that there are O bases. The program translate stalled.

We don't get the same effect on our system (GCG 10.1 DEC-unix).  Seqed
will happily create a nucleotide sequence called protein, and
composition reads it fine (new also works).  Did you check whether the
student had entered any unusual characters into the sequence.  What was
the sequence type written into the sequence header?

An effect we have seen which produces the sort of output you describe,
is when the user is running out of disk quota (either on their account
or on any temporary space which may be being used).  This often results
in 0 size files.  You may be seeing an artifact of this??

TTFN

Simon.






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