[MUMmer-help] Error message with PROMER and NUCMER

[Andy K. <and...@yo...>]

Hi

I am trying to run both nucmer and promer commands on two files.  The
reference file contains a single contig.  The query file contains multiple
contigs.

I keep getting the following error message;
*
1: PREPARING DATA
2,3: RUNNING mummer AND CREATING CLUSTERS
# reading input file "promer.aaref" of length 1389932
# construct suffix tree for sequence of length 1389932
# (maximum reference length is 536870908)
# (maximum query length is 4294967295)
# process 13899 characters per dot
#....................................................................................................
# CONSTRUCTIONTIME /biol/cnap/people/ak533/MUMmer/MUMmer3_23/mummer
promer.aaref 0.56
# reading input file "promer.aaqry" of length 840869
# matching query-file "promer.aaqry"
# against subject-file "promer.aaref"
# COMPLETETIME /biol/cnap/people/ak533/MUMmer/MUMmer3_23/mummer
promer.aaref 1.01
# SPACE /biol/cnap/people/ak533/MUMmer/MUMmer3_23/mummer promer.aaref 2.16
4: FINISHING DATA
Jcr4S000
ERROR: Could not parse input from 'Query File'.
Please check the filename and format, or file a bug report
ERROR: postpro returned non-zero
*

the mummer command works fine.

Thanks

Andy