PCAngsd didn't converge

[NeethuCherukuri]

ood.discovery.neu.edu_pun_sys_dashboard_files_fs__work_seedpod_test_pcangsd_41265911.out.pdf
sbatch script that I'm using!! echo "Job started at: $(date)"

module load singularity/3.10.3

Define paths

DATA_DIR="/work/seedpod/output/angsd_spal2/angsd_result.beagle.gz"
OUT_PREFIX="/work/seedpod/output/pcangsd/pcangsd_spal"
SINGULARITY_IMAGE="/work/seedpod/test/seedpod_latest.sif"

echo "Running pcangsd inside Singularity container..."
singularity exec -B "/work:/work" $SINGULARITY_IMAGE /opt/miniconda/bin/pcangsd -b $DATA_DIR -o $OUT_PREFIX -t 32 -e 1 --maf 0.01 --iter 3000 --tole 1e-7

echo "Job finished at: $(date)"

Output file:
Job started at: Mon Mar 4 13:00:36 EST 2024
Running pcangsd inside Singularity container...

PCAngsd v1.21
Jonas Meisner and Anders Albrechtsen.
Using 32 thread(s).

Parsing Beagle file.
Loaded 730243 sites and 374 individuals.
Estimating minor allele frequencies.
EM (MAF) converged at iteration: 213
Number of sites after MAF filtering (0.01): 730243
Estimating covariance matrix.
Using 1 principal components (manually selected).
Individual allele frequencies estimated (1).
Individual allele frequencies estimated (2). RMSE=0.103376299
Individual allele frequencies estimated (3). RMSE=0.103394873
Individual allele frequencies estimated (4). RMSE=0.001676962
Individual allele frequencies estimated (5). RMSE=0.001336438
Individual allele frequencies estimated (6). RMSE=0.001089854
Individual allele frequencies estimated (7). RMSE=0.000904074
Individual allele frequencies estimated (8). RMSE=0.00076122
.
.
.
Individual allele frequencies estimated (2996). RMSE=6.68e-07
Individual allele frequencies estimated (2997). RMSE=6.48e-07
Individual allele frequencies estimated (2998). RMSE=6.67e-07
Individual allele frequencies estimated (2999). RMSE=6.62e-07
Individual allele frequencies estimated (3000). RMSE=6.12e-07
Individual allele frequencies estimated (3001). RMSE=6.31e-07
PCAngsd did not converge!
Saved covariance matrix as /work/seedpod/output/pcangsd/pcangsd_spal.cov

Total elapsed time: 74m53s
Job finished at: Mon Mar 4 14:15:30 EST 2024