Has anyone used this program to detect a deletion in 1000 genomes phase 1 samples? I am following this protocol: http://www.broadinstitute.org/software/genomestrip/cookbook-genotyping-novel-site-1000-genomes-phase-1. My vcf file contains 1 deletion, I started a job yesterday and it is still running (for 24 hours already).

Program pulls 1000 genome data from external server. And does not eat much resources. Maybe it is my not so good internet connection?

There is also a progress meter table in log file. It is updating regularly. At the moment last line looks like this:

INFO  15:16:57,625 ProgressMeter -        Starting        0.00e+00   24.2 h     15250.3 w    100.0%        24.2 h     0.0 s

Is 15250.3 remaining time in weeks?

Have anyone used it? How long did it take to run it?