Assembling large sequences

Simon Andrews simon.andrews at bbsrc.ac.uk
Wed Jan 16 08:19:56 EST 2002


[copy sent to staden-package at mrc-lmb.cam.ac.uk]

Whilst playing with Staden 2001 I've found that something I hoped would
have been changed hasn't.

I'm trying to assemble some large genomic sequence fragments (100kb -
300kb) using Staden.  The program will not read these and keeps
crashing.

If I try to bring the files in using Normal Shotgun assembly, then gap
crashes and disappears. 

The following message is sent to the shell;

"Serious problem encountered entering sequence into database:
al603651.sdn"

and the last entry in the log is;

"Wed 16 Jan 13:08:25 2002 [18196] Too much data. Maximum possible =
30000, input stopped there"

I've also tried bringing the sequences in, but turning off the "permit
joins" function.  This again crashes the program, but produces a
different death cry...

Wed 16 Jan 13:10:41 2002 signal_handler: Program terminated unexpectedly
with signal 11.
Wed 16 Jan 13:10:41 2002 signal_handler: This is probably a bug.
Wed 16 Jan 13:10:41 2002 signal_handler: Please email all bug reports to
staden-package at mrc-lmb.cam.ac.uk.


I've tried increasing the maxseq and maxdb parameters, but to no
effect.  Could the maximum sequence size not be increased beyond 30kb? 
It is very useful to bring long genomic contigs into an assembly, but
this seems not to be possible at present.

Thanks for any help anyone can offer.

Simon.




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