[AMOS-help] Error with 454 reads

[George T. <gts...@gm...>]

Dear all,

I have Sanger and 454 mixed (from 2 different organisms) sequences that I
try to map on a reference bacterial sequence. When I use only the Sanger
sequences everything goes smoothly but when I have a hybrid with Sanger+454
I get the following error

gtsiamis@gtsiamis-server[All] AMOScmp-shortReads WGS_454_Sanger       [
6:14PM]
The log file is: WGS_454_Sanger.runAmos.log
Doing step 10:  Building AMOS bank
Doing step 20:  Collecting clear range sequences
Doing step 30:  Running nucmer
Command: /usr/bin/nucmer --maxmatch --prefix=WGS_454_Sanger -l 20 -c 20
WGS_454_Sanger.1con WGS_454_Sanger.seq exited with status: 1


The message from the file nucmer.error is

20101125|224904| 26318| ERROR: mummer and/or mgaps returned non-zero


Please note that the size of the afg file is big 17.3GB


Any suggestions?

Thanx in advance

George



George Tsiamis, Ph.D.
Lecturer in Environmental Microbiology
Department of Environmental and Natural Resources Management
University of Ioannina
2 Seferi str., Agrinio
30100, Greece
e-mail: gts...@cc..., gts...@gm...
tel. +302641074149, fax. +302641033716