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/