#9 ERROR: mummer and/or mgaps returned non-zero

[Daniel Brami]

Hello,

I was running nucmer with the following options:

nucmer -maxmatch -c 100 -p nucmer reference.fasta query.fasta

The program terminated unexpectedly and did not yield the expected .delta file.
the .error file contained the following message:

20080221|170115| 6021| ERROR: mummer and/or mgaps returned non-zero, please file a bug report

Upon further analysis, I also found this message:

2,3: RUNNING mummer AND CREATING CLUSTERS
# reading input file "nucmer.ntref" of length 851 857 594
# construct suffix tree for sequence of length 851857594
# (maximum input length is 536 870 908)
# process 8518575 characters per dot

My input files are of the following sizes:
reference.fasta -> 893 278 465 B
query.fasta (multi-fasta) -> 23 710 231 B

Other than inversing my queyr and reference files, would you have any sggestions on how to get nucmer to run?

Much appreciated,

Daniel Brami

[Adam Phillippy]

Logged In: YES
user_id=1231950
Originator: NO

The input of length 851,857,594 exceeded the maximum allowed input of 536,870,908 characters.

[LIYY]

Dear Adam:
I have this trouble, too.I got the reason,but How to solve ? Split my sequence?OR change Makerfile?How to change?
Thanks,
LIYY