[MUMmer-help] nucmer error when running amosvalidate

[Alan T. <twa...@gm...>]

Hello,

     I am trying to use the amosvalidate function and I receive the
following error:

!!! 2010-10-25 15:01:09  Doing step 620
!!! 2010-10-25 15:01:09  Running: /usr/bin/nucmer --prefix=KS07038_1
KS07038_1.fasta KS07038_1.singletons.seq
1: PREPARING DATA

USAGE: /usr/lib/mummer/prenuc  [options]  <reference>

Try '/usr/lib/mummer/prenuc -h' for more information.
ERROR: prenuc returned non-zero
!!! 2010-10-25 15:01:09  Command: /usr/bin/nucmer --prefix=KS07038_1
KS07038_1.fasta KS07038_1.singletons.seq exited with status: 1
!!! END - Elapsed time: 0d 0h 0m 2s

This is the second time that I have received this error in the AMOS package
- the first time when using the AMOScmp command. I resolved the AMOScmp
error by providing all of the flies in the command line arguments, not just
the prefix to the files. I'm assuming that this is the case with this error
in amosvalidate; however I don't know what files are needed when using
amosvalidate, therefore I don't know what files to pass. So I have two
questions:

1) What are the files that I would need to pass as command line arguments?
2) Is there a way to manipulate the code of prenuc/nucmer to rid of this
error and accept the prefix to the files?

Thank you all in advance!

-- 

Alan Twaddle, B.S.
MUC class of 2010