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!