mummer4/mummer

delta-filter takes a lot of time and nothing happened when I used option -1

pjx1990 opened this issue · 4 comments

pjx1990 commented

It takes five days to run filter.delta and nothing happened when I used option delta-filter -1. My out.delta file size is about 2Gb. I'd like to if this is normal and how much time it will take?
my command is：
nucmer -maxmatch -c 90 -l 40 $ref $qry
delta-filter -1 out.delta >filter.delta
Thank you!

dongyangzheng commented

hi did you solved this problem?

Huyuxi08 commented

@pjx1990 @dongyangzheng

Hi, it seems that we have encountered the same problem. I have run filter.delta for a week with nothing output, and my out.delta file is about 790M.

Have you solved this problem?

dongyangzheng commented

I use lastz software, using the parameter nogap, no transition, sacrificing accuracy and gaining time, I think this is enough to use.

Huyuxi08 commented

I use lastz software, using the parameter nogap, no transition, sacrificing accuracy and gaining time, I think this is enough to use.

Got it! Thanks so much!