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mummer4 / mummer

Mummer alignment tool
Artistic License 2.0
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Error running nucmer #42

Open giantoni opened 6 years ago

giantoni commented 6 years ago

Hey guys!

I am trying to run nucmer for a large genomes, I have installed the 64 bits version, but I always get this error after a while:

1: PREPARING DATA 2,3: RUNNING mummer AND CREATING CLUSTERS

reading input file "alignments.ntref" of length 3784490948

construct suffix tree for sequence of length 3784490948

(maximum reference length is 18446744073709551612)

(maximum query length is 18446744073709551615)

process 37844909 characters per dot

....................................................................................................

CONSTRUCTIONTIME /raid/genevol/users/gisele/assembly_optmization/MUMmer3.23/mummer alignments.ntref 5648.63

reading input file "/raid/genevol/users/gisele/assembly_optmization/todos/assemblies_cat.contig" of length 3784490947

matching query-file "/raid/genevol/users/gisele/assembly_optmization/todos/assemblies_cat.contig"

against subject-file "alignments.ntref"

ERROR: mummer and/or mgaps returned non-zero

Any thoughts?

Best! Gisele

gmarcais commented 6 years ago

This is the output of version 3. I only maintain version 4 of the software.

shiyi-pan commented 2 years ago

Hey guys!

I am trying to run nucmer for a large genomes, I have installed the 64 bits version, but I always get this error after a while:

1: PREPARING DATA 2,3: RUNNING mummer AND CREATING CLUSTERS

reading input file "alignments.ntref" of length 3784490948

construct suffix tree for sequence of length 3784490948

(maximum reference length is 18446744073709551612)

(maximum query length is 18446744073709551615)

process 37844909 characters per dot

....................................................................................................

CONSTRUCTIONTIME /raid/genevol/users/gisele/assembly_optmization/MUMmer3.23/mummer alignments.ntref 5648.63

reading input file "/raid/genevol/users/gisele/assembly_optmization/todos/assemblies_cat.contig" of length 3784490947

matching query-file "/raid/genevol/users/gisele/assembly_optmization/todos/assemblies_cat.contig"

against subject-file "alignments.ntref"

ERROR: mummer and/or mgaps returned non-zero

Any thoughts?

Best! Gisele

Hi, I met the same problem , could you solve it?