[MUMmer-help] PROmer running time

[Savita K. <ks...@ib...>]

Dear MUMmer users,

I have a question about the running time of MUMmer.

I'm using MUMer's PROmer tool to compare selected sequences from a draft
genome to another genome, to analyse high level synteny.

The program has been running for around 27 days now, on a
server with 94GB memory. The input file sizes are 26566 sequences-512MB
and 9 sequences-360MB. I wanted to know approximately how long would you
expect PROmer to run for files of this size? Also, I was wondering if
there was an option to run PROmer in a multithreaded way?

FYI, the .mgap output file is being updated regularly
and the command I used was:
promer --prefix=refBv_qryAh data/Bv.fa data/Ah_scaff.fa --maxmatch --matrix=2

Any help greatly appreciated.

Many thanks,
Savita Karthikeyan
Research Assistant,
Institute of Bioinformatics and Applied Biotechnology,
Biotech Park
Electronics City Phase I
Bangalore 560 100
India