#16 nucmer fails on FASTA input with no line-wrapping

[Leighton Pritchard]

postnuc fails when input FASTA nucleotide sequences are not wrapped, possibly as a consequence of a FASTA sequence parsing problem.

This command line fails:

$ nucmer -mum -p halomonas_anim/H_stevensii_vs_H_spBC04 genome_fna_files/H_stevensii.fna genome_fna_files/H_spBC04.fna
1: PREPARING DATA
2,3: RUNNING mummer AND CREATING CLUSTERS
# reading input file "halomonas_anim/H_stevensii_vs_H_spBC04.ntref" of length 3693798
# construct suffix tree for sequence of length 3693798
# (maximum input length is 536870908)
# process 36937 characters per dot
#....................................................................................................
# CONSTRUCTIONTIME /opt/mummer/mummer halomonas_anim/H_stevensii_vs_H_spBC04.ntref 2.16
# reading input file "/Users/lpritc/Documents/Ad_hoc_Work/2014-01-15_ANIm/genome_fna_files/H_spBC04.fna" of length 5921529
# matching query-file "/Users/lpritc/Documents/Ad_hoc_Work/2014-01-15_ANIm/genome_fna_files/H_spBC04.fna"
# against subject-file "halomonas_anim/H_stevensii_vs_H_spBC04.ntref"
# COMPLETETIME /opt/mummer/mummer halomonas_anim/H_stevensii_vs_H_spBC04.ntref 10.42
# SPACE /opt/mummer/mummer halomonas_anim/H_stevensii_vs_H_spBC04.ntref 9.23
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, please file a bug report

Reformatting the file H_spBC04.fna to wrap the input sequences at 60 characters fixes the issue:

$ nucmer -mum -p halomonas_anim/H_stevensii_vs_H_spBC04 genome_fna_files/H_stevensii.fna genome_fna_files/H_spBC04_wrap.fna
1: PREPARING DATA
2,3: RUNNING mummer AND CREATING CLUSTERS
# reading input file "halomonas_anim/H_stevensii_vs_H_spBC04.ntref" of length 3693798
# construct suffix tree for sequence of length 3693798
# (maximum input length is 536870908)
# process 36937 characters per dot
#....................................................................................................
# CONSTRUCTIONTIME /opt/mummer/mummer halomonas_anim/H_stevensii_vs_H_spBC04.ntref 2.31
# reading input file "/Users/lpritc/Documents/Ad_hoc_Work/2014-01-15_ANIm/genome_fna_files/H_spBC04_wrap.fna" of length 5921529
# matching query-file "/Users/lpritc/Documents/Ad_hoc_Work/2014-01-15_ANIm/genome_fna_files/H_spBC04_wrap.fna"
# against subject-file "halomonas_anim/H_stevensii_vs_H_spBC04.ntref"
# COMPLETETIME /opt/mummer/mummer halomonas_anim/H_stevensii_vs_H_spBC04.ntref 11.19
# SPACE /opt/mummer/mummer halomonas_anim/H_stevensii_vs_H_spBC04.ntref 9.33
4: FINISHING DATA