invalid distance between adjacent sites

[etwatson]

Greetings!

I ran into an error running the ngsLD software and get the below output. I use the beagle input, and I have converted the positions in the file from de novo RAD sites to where these sites map to the reference genome. Maybe I have made an error in converting the site coordinates, so some help in understanding this error would do wonders.

Thanks,
Eric

--> Input Arguments:
geno: RILs.refpos.beagle.gz
probs: true
log_scale: false
n_ind: 71
n_sites: 7586
pos: RILs.refpos.beagle.sites
max_kb_dist (kb): 5
max_snp_dist: 0
min_maf: 0.001000
ignore_miss_data: false
call_geno: false
N_thresh: 0.000000
call_thresh: 0.000000
rnd_sample: 1.000000
seed: 1565042370
extend_out: false
out: RILs.ld
n_threads: 30
verbose: 1
version: 1.1.0 (Aug 1 2019 @ 14:12:13)
--> GZIP input file (not BINARY)
-> Reading data from file..
--> Calculating MAF for all sites...
--> Getting sites coordinates

ERROR: [read_pos] invalid distance between adjacent sites!

Numerical result out of range

[Morgan-McCarthy]

Hey did you find out what the problem was here? I've run into the same issue.

[fgvieira]

It usually means that the sites are not sorted, so the distance between sites is negative.

[Morgan-McCarthy]

Thanks for the follow up!