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Old 10-30-2016, 10:07 PM   #1
nkalsi
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Location: Atlanta, US

Join Date: Oct 2016
Posts: 1
Exclamation LASTZ error

Hi,
I'm trying to do a lift over between two versions of M. zebra, for which I need a chain file. I'm trying to do a whole genome alignment using LASTZ, and then chaining using axtChain.

But I'm getting an error with LASTZ. Well not exactly an error: it seems to run forever and there's no output. The command I'm using is

lastz GCF_000238955.2_M_zebra_UMD1_genomic.fna[multiple] M_zebra_v0.assembly.fasta --format=axt --strand=both --nochain --gapped --gap=400,30 --inner=2000 --hspthresh=2200 --gappedthresh=6000 --seed=12of19 --notransition --ydrop=3400 --scores=HoxD55.q

I noticed that when I run the command with --chain, it runs. But with the --nochain option, the command runs forever and no output is produced.
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