Reading data from file... Killed

[mayroberts]

Hi there, I have been trying to run ngsLD using the code below:

BASENAME=DTR_dedup_bams_mindp100_maxdp590_minind13_minq20
BEAGLE=$BASEDIR/DTR_dedup_bams_mindp100_maxdp590_minind13_minq20.beagle.gz
POS=$BASEDIR/DTR_dedup_bams_mindp100_maxdp590_minind13_minq20.pos.gz

module load ngsLD

ngsLD \
--geno $BEAGLE \
--posH $POS \
--probs \
--n_ind 132 \
--n_sites 22573846 \
--max_kb_dist 0 \
--n_threads 24 \
--outH ${BASENAME}.ld

I get the message :

`==> Input Arguments: geno: /hb/groups/bernardi_lab/may/DTR/population-analysis/angsd//DTR_dedup_bams_mindp100_maxdp590_minind13_minq20.beagle.gz probs: true log_scale: false n_ind: 132 n_sites: 22573846 pos: /hb/groups/bernardi_lab/may/DTR/population-analysis/angsd//DTR_dedup_bams_mindp100_maxdp590_minind13_minq20.pos.gz (WITH header) max_kb_dist (kb): 0 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: 1662233690 extend_out: false out: DTR_dedup_bams_mindp100_maxdp590_minind13_minq20.ld (WITH header) n_threads: 24 verbose: 1 version: 1.1.1 (Jun 30 2022 @ 17:42:53)

==> GZIP input file (not BINARY)

Reading data from file... /var/spool/slurmd/job169158/slurm_script: line 30: 29359 Killed ngsLD --geno $BEAGLE --posH $POS --probs --n_ind 132 --n_sites 22573846 --max_kb_dist 0 --n_threads 24 --outH ${BASENAME}.ld`

It seems to be an issue not with the parameter on line 30 necessarily - I swapped the order of the inputs and it was always this last line. Do you have an idea of where I am going wrong? Thanks so much.

[mayroberts]

Figured it out! I had not realized I needed to reformat my beagle.gz and pos.gz file by removing the header and columns for the beagle.gz and last column of the pos.gz file.