Error calculating consensus

major major at genome.wi.mit.edu
Tue Apr 8 03:12:08 EST 2003


Hello-

I am having a problem using the 'assemble_shotgun' command.  I have
several reads I'm trying to load into a DB using this procedure, and
keep getting the following output:
-----------------------------
Automatic sequence assembler
Database is logically consistent
Mon 07 Apr 12:18:48 2003 Error: Error calculating consensus
Mon 07 Apr 12:18:48 2003 signal_handler: Program terminated unexpectedly
with signal 11.
Mon 07 Apr 12:18:48 2003 signal_handler: This is probably a bug.
Mon 07 Apr 12:18:48 2003 signal_handler: Please email all bug reports to
staden-package at mrc-lmb.cam.ac.uk.
Abort process (core dumped)
-----------------------------

I've tried manually setting the consensus parameters before calling
assemble_shotgun, but there was no change.
-------
set consensus_cutoff #.## 
set quality_cutoff # 
set consensus_mode # 
-------


The odd bit is, this add_reads script I'm using will work on newly
created databases, but not ones which have been modified.  Also, I can
open the DB which causes the above error, and manually select the
shotgun_assemble feature with no error.  However, there is a bug here
too I think.  When you use the GUI normal shotgun assemble interface, 
and you select 'reject failures' the non-aligning reads still get placed
in their own contigs.  When specifiying reject failures in the script,
the failures are not added to the database?

I guess I have 2 questions then.  
#1- How can I resolve the 'Error calculating consensus' error?
#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?]

Thanks,
John




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