[MUMmer-help] error when using the whole genome, no error when split it (nucmer)

[Seyed M. <smi...@uc...>]

Hello

I have some difficulties for using nucmer to map two plant genomes against
each other. I first tried to map all the query contigs against all the
reference contigs and it generated error after a while ( during the dot
production phase).  I split the reference to two files, each of them
consists of half of the contigs and mapped the query against them
separately. This time it worked very well.
The original reference file has about 40,000 contigs and total length of
them is about 500,000,000 bps.  The query has about 2,000 contigs and its
total length is almost half of the length of the reference. I used nucmer
with its default parameters and run it on a computer with a huge memory.
Can you help me find the possible sources of the error?

Thank you.