Lastz is running indefinitely

[aamirwkhan06]

Dear Lastz team

I am running pairwise alignment of the chromosomes from two genomes individually. For other genome combinations, the alignment step ran very quickly, but for one of the genome combinations its running since last one month.

Following is the command I am using:

./Programs/programs/lastz-distrib-1.03.02/src/lastz ./genome1/nibFiles/chr1.nib ./genome2/nibFiles/Chr1.nib --notransition --step=20 --format=lav --inner=2000 --xdrop=9400 --gappedthresh=3000 --hspthresh=2200 --ambiguous=iupac > ./alignments/genome1_genome2/genome1-chr1_genome2-Chr1.lav

Can you please tell few constraints or the reason for this unusual behavior?

Thanks and regards
Aamir