ANGSD beagle generation returning empty file

Question

[DanielEB_fisk]

Hello Biostars community,

I am struggling quite a bit with ANGSD these days as it seems that no code I provide to the machine is working as intended. I want now to produce a beagle file but the following script is returning me an empty file

#!/bin/bash
#SBATCH --account GRINFISH
#SBATCH -c 10
#SBATCH --mem 64g
#SBATCH --output ../logs/make-beagle.out
#SBATCH --error ../logs/make-beagle.err
#SBATCH --time 20:00:00

REF=../refs/In-mtDNA/genome-mtDNA-reference.fa

angsd -out batch1_batch3 -ref $REF \
-SNP_pval 0.01 -doMaf 1 -bam bam-list.txt -uniqueOnly 1 -remove_bads 1 -only_proper_pairs 1 \
-trim 0 -C 50 -minMapQ 20 -minQ 20 -setMinDepth 1 -setMaxDepth 6 -doCounts 1 -GL 1 -doGlf 2 \
-doMajorMinor 1 -doPost 2 -nThreads 10

I feel that I may be committing a mistake in the code, this is, a flag parameter that should not be used when producing a beagle file, or I am lacking a flag that must be used. I am not receiving any errors in the log however.

Any help will be greatly appreciated.

Thank you,