Help with Consed contig joining problem?

Amy Kistler amylkistler at yahoo.com
Wed Mar 17 07:45:20 EST 2004

I have been using Consed for sequence assembly with great enthusiasm.
However, I recently have had a problem joining contigs with
significant chunks of sequence match.  I have tried to join such
contigs via clicking on the sequence match regions in the assembly
view, then selecting the region which comes up in the sequence matches
window, which brings me to the compare contigs window.  When I click
on the "join contigs" button, I get an hour glass symbol and "Wait"
message in the consed window.  The program freezes in this state
indefinitely.  In my command line window, I get the following message:

Error from consed:  segmentation fault.  Attempting to continue can't
establish setjmp for handler of segmentation faults2.

While I understand the error message, I do not understand why I am
having this problem.  I can do the joining exercise in the consed
quicktour, no problem.  Moreover, the regions in the contigs are
typically >95% similar (even happens with regions of 100%

Am I doing something wrong or out of sequence (e.g., in the quick
tour, you tear the contigs before joining;  wasn't clear if this is a
required step to do before joining)?  Has anyone else run across this
problem?  Can anyone help?

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