#21 Minimus2 Failure on Large Contigs with Ns

[Matthew Scholz]

I have a large data set, (see included stats), that has been consistently failing on the new (AMOS-3.1.0) minimus2 run. I have tried varying several parameters, including using a nucmer that has been compiled to treat N-N matches as a +3 match, rather than 0, in all cases it appears to fail during make-consensus.

This is the only data set I have found this failure to occur on, however it is also the only data set with Ns or >500KB contigs.

File statistics for contigs:
Contigs_number: 72168
N50: 5728
N90: 1555
Max: 872151
Min: 200
Total_bases: 220067786