[MUMmer-help] promer error: not enough memory (when nucmer works fine)

[Rong S. <rs...@bc...>]

The reference fasta file is about 190M size, the query fasta file is 
about 400M in size. I ran the nucmer script without a problem. But with 
the same data set, promer failed with "not enough memory" error. The 
machine I ran it on has 48G RAM and about 20G is free when I ran promer, 
so it's weird why promer would fail to allocate memory. I thought both 
nucmer and promer used exactly same alignment tools, which seems odd 
that one would fail when the other works fine?

Here's the error output of promer:
[rshe@rshe01]$ promer -p DP0001_promer 
/home/pubseq/seqdev/Assembly_project/DP0001/T_castaneum/T_castaneum_CM_chromosomes.fa 
DP0001-contigs.fa
1: PREPARING DATA
2,3: RUNNING mummer AND CREATING CLUSTERS
# reading input file "DP0001_promer.aaref" of length 374989958
# construct suffix tree for sequence of length 374989958
# (maximum reference length is 536870908)
# (maximum query length is 4294967295)
# process 3749899 characters per dot
file "construct.c", line 878:  allocandusespaceviaptr(4,562484938) 
failed:not enough memory
ERROR: mummer and/or mgaps returned non-zero

Rong