postnuc: postnuc.cc:1427: long int revC(long int, long int): Assertion `Len - Coord + 1 > 0' failed.

[yhsYhsYhs]

dnadiff sequence.fasta reads.fasta -p 50long
Building alignments
1: PREPARING DATA
2,3: RUNNING mummer AND CREATING CLUSTERS
# reading input file "50long.ntref" of length 4641653
# construct suffix tree for sequence of length 4641653
# (maximum reference length is 536870908)
# (maximum query length is 4294967295)
# process 46416 characters per dot
#....................................................................................................
# CONSTRUCTIONTIME /usr/bin/mummer 50long.ntref 2.31
# reading input file "/50long/e.coli.correctedReads.fasta" of length 112457574
# matching query-file "/50long/e.coli.correctedReads.fasta"
# against subject-file "50long.ntref"
# COMPLETETIME /usr/bin/mummer 50long.ntref 126.30
# SPACE /usr/bin/mummer 50long.ntref 112.41
4: FINISHING DATA
postnuc: postnuc.cc:1427: long int revC(long int, long int): Assertion `Len - Coord + 1 > 0' failed.
Aborted (core dumped)
ERROR: postnuc returned non-zero
ERROR: Failed to run nucmer, aborting.

[skoren]

Most likely this is a name collision in the read names. Check the input for duplicate read names (up to the first space) and rename them to see if it fixes the error (see also https://sourceforge.net/p/mummer/mailman/message/27154776/).

[yhsYhsYhs]

hello;
I had changed the reads id 1…n-1,and this problem occured still.

thinkstation# dnadiff  sequence.fasta reads.fasta -p mha
Building alignments

1: PREPARING DATA
2,3: RUNNING mummer AND CREATING CLUSTERS
# reading input file "mha.ntref" of length 4641653
# construct suffix tree for sequence of length 4641653
# (maximum reference length is 536870908)
# (maximum query length is 4294967295)
# process 46416 characters per dot
#....................................................................................................
# CONSTRUCTIONTIME /usr/bin/mummer mha.ntref 2.01
# reading input file "reads.fasta" of length 172911839
# matching query-file "reads.fasta"
# against subject-file "mha.ntref"
# COMPLETETIME /usr/bin/mummer mhap.ntref 156.73
# SPACE /usr/bin/mummer mhap.ntref 169.75
4: FINISHING DATA
postnuc: postnuc.cc:1427: long int revC(long int, long int): Assertion `Len - Coord + 1 > 0' failed.
Aborted (core dumped)
ERROR: postnuc returned non-zero
ERROR: Failed to run nucmer, aborting.

[aphillippy]

Best option may be to switch to nucmer4, which is in beta release and shouldn't have such name collision problems: https://mummer4.github.io

[peflanag]

Hi I had the same issue and have removed the old MUMmer and updated to MUMmer4. I am trying to run the following command to get a delta file to process in the web application Assemblytics but MUMmer4 doesnt seem to want to run. This is the script I want to run from the Assemblytics website

nucmer -maxmatch -l 100 -c 500 REFERENCE.fa ASSEMBLY.fa -prefix OUT

But it wont work and I have tried a few variations. Im not command line savvy so any help would be great. I'm a novice!

Cheers

Peter

[peflanag]

UPDATE: I used the script

nucmer -p ref.seq qry.seq

and a new error has been thrown out. Any ideas?

Cheers,

P