start 2026-09-27T20:55:25Z host n3457 window=CM196829.1:25000001-50000000
	-> angsd version: 0.940-dirty (htslib: 1.24) build(Dec 15 2024 09:11:59)
	-> angsd -b output/06_angsd_structure/samples/bam.list -ref output/05_realign_xbOstLuri2/reference/GCA_061535525.1_xbOstLuri2_USDA-ARS_PSRF_primary_genomic.fna -r CM196829.1:25000001-50000000 -out output/06_angsd_structure/gl/016_CM196829.1_25000001-50000000 -GL 1 -doGlf 2 -doMajorMinor 1 -doMaf 1 -doCounts 1 -SNP_pval 1e-6 -minMaf 0.05 -minMapQ 20 -minQ 20 -uniqueOnly 1 -remove_bads 1 -only_proper_pairs 1 -C 50 -baq 1 -minInd 87 -setMinDepth 253 -setMaxDepth 1537 -P 8 
	-> Inputtype is BAM/CRAM
[multiReader] 109 samples in 109 input files
	-> Reading fasta: output/05_realign_xbOstLuri2/reference/GCA_061535525.1_xbOstLuri2_USDA-ARS_PSRF_primary_genomic.fna
	-> SNP-filter using a pvalue: 1.000000e-06 correspond to 23.928127 likelihood units
	-> Parsing 109 number of samples 
	-> Region lookup 1/1
	-> Allocated ~ 10 million nodes to the nodepool, this is not an estimate of the memory usage
	-> Allocated ~ 20 million nodes to the nodepool, this is not an estimate of the memory usage
	-> Allocated ~ 30 million nodes to the nodepool, this is not an estimate of the memory usage
	-> Allocated ~ 40 million nodes to the nodepool, this is not an estimate of the memory usage
	-> Allocated ~ 50 million nodes to the nodepool, this is not an estimate of the memory usage
	-> Allocated ~ 60 million nodes to the nodepool, this is not an estimate of the memory usage
	-> Allocated ~ 70 million nodes to the nodepool, this is not an estimate of the memory usage
	-> Allocated ~ 80 million nodes to the nodepool, this is not an estimate of the memory usage
	-> Allocated ~ 90 million nodes to the nodepool, this is not an estimate of the memory usage
	-> Allocated ~ 100 million nodes to the nodepool, this is not an estimate of the memory usage
	-> Allocated ~ 110 million nodes to the nodepool, this is not an estimate of the memory usage
	-> Allocated ~ 120 million nodes to the nodepool, this is not an estimate of the memory usage
	-> Allocated ~ 130 million nodes to the nodepool, this is not an estimate of the memory usage
	-> Allocated ~ 140 million nodes to the nodepool, this is not an estimate of the memory usage
	-> Allocated ~ 150 million nodes to the nodepool, this is not an estimate of the memory usage
	-> Allocated ~ 160 million nodes to the nodepool, this is not an estimate of the memory usage
	-> Done reading data waiting for calculations to finish
	-> Done waiting for threads
	-> Output filenames:
		->"output/06_angsd_structure/gl/016_CM196829.1_25000001-50000000.arg"
		->"output/06_angsd_structure/gl/016_CM196829.1_25000001-50000000.beagle.gz"
		->"output/06_angsd_structure/gl/016_CM196829.1_25000001-50000000.mafs.gz"
	-> Sun Sep 27 15:06:31 2026
	-> Arguments and parameters for all analysis are located in .arg file
	-> Total number of sites analyzed: 24498725
	-> Number of sites retained after filtering: 186566 
	[ALL done] cpu-time used =  5740.18 sec
	[ALL done] walltime used =  4266.00 sec
end 2026-09-27T22:06:32Z window=CM196829.1:25000001-50000000 sites=186566