[MUMmer-help] Nucmer problem - ERROR: postnuc returned non-zero

[Felipe L. <fel...@ya...>]

I think that you can help me.

The output and command line at terminal is:

$ nucmer --prefix=8A_8B contigs_copd8A.fasta contigs_copd8B.fasta 
1: PREPARING DATA
2,3: RUNNING mummer AND CREATING CLUSTERS
# reading input file "8A_8B.ntref" of length 1976286
# construct suffix tree for sequence of length 1976286
# (maximum reference length is 536870908)
# (maximum query length is 4294967295)
# process 19762 characters per dot
#....................................................................................................
# CONSTRUCTIONTIME /usr/bin/mummer 8A_8B.ntref 0.44
# reading input file "/media/Iomega_HDD/snps_copd8/contigs_copd8B.fasta" of length 1900897
# matching query-file "/media/Iomega_HDD/snps_copd8/contigs_copd8B.fasta"
# against subject-file "8A_8B.ntref"
# COMPLETETIME /usr/bin/mummer 8A_8B.ntref 1.51
# SPACE /usr/bin/mummer 8A_8B.ntref 3.78
4: FINISHING DATA
ERROR: Could not parse input from 'Query File'. 
Please check the filename and format, or file a bug report
ERROR: postnuc returned non-zero


The error file contains:

20131022|121048|  4492| ERROR: postnuc returned non-zero


The .delta file contains:

/media/Iomega_HDD/snps_copd8/contigs_copd8A.fasta /media/Iomega_HDD/snps_copd8/contigs_copd8B.fasta
NUCMER

The .nucmer file

>allcontigs /media/Iomega_HDD/snps_copd8/contigs_copd8A.fasta
tgcccgccgagccagcgttcgagatggtcgaggaccgcccggtcggcttcgtcgagatcc
tcgcgggccgcctctgcggcatagcggaacacctcgcgatcctgcaccgagcgaccgcag
ataccgcccagggtcaggtcgcggctggccaggtcggcccgcgccacccgcaaaagaccc

tgggcgaggttctccaggtcaccggcgaggcttcccgccaggaccagttggc....



 
Felipe Lira
Spanish National Center of Biotechnology - CNB/ CSIC
Microbial Biotechnology Department
Fellow of http://obrasocial.lacaixa.es/

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