This was exactly it. Works like a charm now.
jkb at mrc-lmb.cam.ac.uk wrote:
>> In <3E91A9BD.4C844A3B at genome.wi.mit.edu> major <major at genome.wi.mit.edu> writes:
> > I guess I have 2 questions then.
> > #1- How can I resolve the 'Error calculating consensus' error?
>> It's probably the memory allocation. The code ought to automatically work this
> out, but I guess it does not based on your observations.
>> Try calling "DatabaseInfo $io" before hand, as this sets the various size
> variables, or manually "set maxseq 1234567".
>> > #2- When I select 'reject failures' from the normal shotgun GUI, should
> > I expect to have non-aligning reads placed in new contigs. If not, how
> > can I prevent them from being placed in the DB?[Can I hard code 'reject
> > failures' someplace?]
>> This depends on whether you have enter all readings. If you do, then they'll
> be put in separate contigs. If not, then they're placed in the failure file of
> filenames. I think it's the -enter_failure options, but the scripting manual
> should help (http://www.mrc-lmb.cam.ac.uk/pubseq/scripting_manual).
> James Bonfield (jkb at mrc-lmb.cam.ac.uk) Fax: (+44) 01223 213556
> Medical Research Council - Laboratory of Molecular Biology,
> Hills Road, Cambridge, CB2 2QH, England.
> Also see Staden Package WWW site at http://www.mrc-lmb.cam.ac.uk/pubseq/