How long can the ANGSD relatedness analysis take?

[juanfmasello]

Hi,

the following code has been running for the last 260 hours. It is running on 95 genomes (short-read Illumina sequencing; genome size ~1.15 GB; mean coverage 18.4). See the code below for more information. Is this normal? How long could it take?

The *.glf.gz file keeps growing in size. Currently, it is ~35 GB. However, the .arg file has shown 0 bytes since the beginning.

Thank you. Cheers,
Juan

#!/bin/bash
#PBS -l select=1:ncpus=24
#PBS -q smp
#PBS -o /mnt/lustre/users/jmasello/mapping_against_belcheri/ANGSD_relatedness_against_belcheri_3.out
#PBS -e /mnt/lustre/users/jmasello/mapping_against_belcheri/ANGSD_relatedness_against_belcheri_3.err
#PBS -m abe

module load chpc/BIOMODULES
module load angsd/0.940

angsd -b bamlist_clean.txt -ref /mnt/lustre/users/jmasello/assemblies/P_belcheri_scaffolded_assembly_both_haplotypes/bpacbel_hap1.scaffolds.fasta -GL 1 -domajorminor 1 -snp_pval 1e-6 -domaf 2 -minmaf 0.005 -doGlf 3 -minQ 25 -minMapQ 30 -minInd 86 -doCounts 1 -only_proper_pairs 1 -baq 1 -setMinDepthInd 3 -skipTriallelic 1 -out Pachyptila_Relatedness_against_bel_3