NUCmer error

[nehaverma]

Hi there,

I am very new to MUMmer/NUCmer. When I am trying to run NUCmer I am getting following error. I am using multi fasta query/ref files.

Usage: NUCmer <ref> <query>

Error message:

1: PREPARING DATA
2,3: RUNNING mummer AND CREATING CLUSTERS
# reading input file "out.ntref" of length 521077706
# construct suffix tree for sequence of length 521077706
# (maximum reference length is 536870908)
# (maximum query length is 4294967295)
# process 5210777 characters per dot
#.......................................................................ERROR: mummer and/or mgaps returned non-zero

Can you let me know why I am getting this error?? And what should I do?

Thanks
Neha

[SES]

That error is not very descriptive so it's hard say. Based on the size of your reference and query it could be a memory issue. Are you running this job on a machine with plenty of memory and disk space?