[MUMmer-help] Nucmer and Ubuntu 13.10 problems

[Richard S. <ric...@ls...>]

Hi

I have been using nucmer through RATT but since a recent upgrade of 
Ubuntu from 13.04 to 13.10 I have started to encounter problems.

However I have traced it to the header of the test sample.
Ok, to run
$nucmer ref.fasta test.fasta

if the header in the test.fasta is
>test
-- doesn't work

1: PREPARING DATA
2,3: RUNNING mummer AND CREATING CLUSTERS
# reading input file "out.ntref" of length 4290253
# construct suffix tree for sequence of length 4290253
# (maximum reference length is 536870908)
# (maximum query length is 4294967295)
# process 42902 characters per dot
#....................................................................................................
# CONSTRUCTIONTIME /usr/bin/mummer out.ntref 1.25
# reading input file "/home/richard/work/gnb/temp/630.tst" of length 4290252
# matching query-file "/home/richard/work/gnb/temp/630.tst"
# against subject-file "out.ntref"
# COMPLETETIME /usr/bin/mummer out.ntref 3.64
# SPACE /usr/bin/mummer out.ntref 8.39
4: FINISHING DATA
*ERROR: Could not parse input from 'Query File'. **
*Please check the filename and format, or file a bug report
ERROR: postnuc returned non-zero

However if the header has a second work separeted by a space it works!
>test something
-- this works
>test_something
-- this doesn't work

Can this be fixed as I don't want to have to edit all my fasta files?

Many thanks

Richard