First try with progressiveMauve, and I got this error.
I'm trying to align two de novo assembly genome of Brassica napus on its reference (850 MB). It seems that something goes wrong on the first steps.
./progressiveMauve --seed-family --seed-weight 41 $REF_FASTA $ASS_PATH/aviso.fa $ASS_PATH/tower.fa > run.log 2> run.err
This list makes reference to memory or version pb for this error. I launched the command on a cluster with a lot of memory.
./progressiveMauve --version progressiveMauve build date Feb 13 2015 at 05:57:13
I tried with default size for seed-weight, it didn't change the error.
Any help ?
Storing raw sequence at /tmp/rawseq11609.000 Sequence loaded successfully. Brassica_napus_v4.1.chromosomes.fasta 850292103 base pairs. Storing raw sequence at /tmp/rawseq11609.001 Sequence loaded successfully. aviso.fa 699132284 base pairs. Storing raw sequence at /tmp/rawseq11609.002 Sequence loaded successfully. tower.fa 690335263 base pairs. Creating sorted mer list
Error creating sorted mer list terminate called after throwing an instance of 'genome::gnException' (code error 134)