different values with same settings

[albodrug]

Hello SEEKIN developers!

I was wondering why SEEKIN gives different values with the same command. The discrepancy is quite large as i go from -0.29 to 0.0 , and some other values in between.

Below is a while loop with three identical runs of SEEKIN giving out three different values in the kinship.kin file

> while true; do rm kinship.*; ./seekin kinship -i temp/kinship_merge.vcf -r 0.3 -m 0.05 -d GT -p hom -t 10 -w 1 -o kinship ; cat kinship.kin ; sleep 5s; done

SEEKIN: SEquence-based Estimation of kinship
Version 1.01: released on 2017-Oct-10
********************
Module kinship
********************
Parameters: 
 -i temp/kinship_merge.vcf 
 -f [] 
 -o kinship 
 -r 0.300000 
 -m 0.050000 
 -d GT 
 -p hom 
 -s 0 
 -w 1 
 -l 10000 
 -t 10 

[Wed May 26 15:50:12 2021] Started!
[Wed May 26 15:50:12 2021] No individual-specific allele frequency file is specified!
[Wed May 26 15:50:12 2021] Use the hom mode with weight function 2MAF(1-MAF)Rsq^2
[Wed May 26 15:50:12 2021] BLOCK_SIZE is set to 10000
[Wed May 26 15:50:12 2021] THREAD_NUM is set to 10
[Wed May 26 15:50:12 2021] MAF filter 0.05
[Wed May 26 15:50:12 2021] R2 filter 0.3
[Wed May 26 15:50:12 2021] GENOTYPE MODE  GT
[Wed May 26 15:50:12 2021] Reading the markers in temp/kinship_merge.vcf
[Wed May 26 15:50:13 2021] ...Scanning 12399 markers and overlapping markers 10000.
[Wed May 26 15:50:13 2021] ...Scanning 25077 markers and overlapping markers 20000.
[Wed May 26 15:50:13 2021] ...Scanning 37268 markers and overlapping markers 30000.
[Wed May 26 15:50:13 2021] ...Scanning 49084 markers and overlapping markers 40000.
[Wed May 26 15:50:13 2021] ...Scanning 60771 markers and overlapping markers 50000.
[Wed May 26 15:50:13 2021] ...Scanning 73180 markers and overlapping markers 60000.
[Wed May 26 15:50:13 2021] ...Scanning 86315 markers and overlapping markers 70000.
[Wed May 26 15:50:13 2021] ...Scanning 98624 markers and overlapping markers 80000.
[Wed May 26 15:50:13 2021] ...Scanning 111214 markers and overlapping markers 90000.
[Wed May 26 15:50:13 2021] ...Scanning 123567 markers and overlapping markers 100000.
[Wed May 26 15:50:13 2021] ...Scanning 135186 markers and overlapping markers 110000.
[Wed May 26 15:50:13 2021] ...Scanning 140926 markers and overlapping markers 114670.
[Wed May 26 15:50:13 2021] Write results to "kinship.*"
[Wed May 26 15:50:13 2021] Finished!
ind1	ind2	nsnp	kinship
EXA210119_S1	EXA210121_S3	114670	-0.2909

SEEKIN: SEquence-based Estimation of kinship
Version 1.01: released on 2017-Oct-10
********************
Module kinship
********************
Parameters: 
 -i temp/kinship_merge.vcf 
 -f [] 
 -o kinship 
 -r 0.300000 
 -m 0.050000 
 -d GT 
 -p hom 
 -s 0 
 -w 1 
 -l 10000 
 -t 10 

[Wed May 26 15:50:18 2021] Started!
[Wed May 26 15:50:18 2021] No individual-specific allele frequency file is specified!
[Wed May 26 15:50:18 2021] Use the hom mode with weight function 2MAF(1-MAF)Rsq^2
[Wed May 26 15:50:18 2021] BLOCK_SIZE is set to 10000
[Wed May 26 15:50:18 2021] THREAD_NUM is set to 10
[Wed May 26 15:50:18 2021] MAF filter 0.05
[Wed May 26 15:50:18 2021] R2 filter 0.3
[Wed May 26 15:50:18 2021] GENOTYPE MODE  GT
[Wed May 26 15:50:18 2021] Reading the markers in temp/kinship_merge.vcf
[Wed May 26 15:50:18 2021] ...Scanning 12399 markers and overlapping markers 10000.
[Wed May 26 15:50:18 2021] ...Scanning 25077 markers and overlapping markers 20000.
[Wed May 26 15:50:18 2021] ...Scanning 37268 markers and overlapping markers 30000.
[Wed May 26 15:50:18 2021] ...Scanning 49084 markers and overlapping markers 40000.
[Wed May 26 15:50:18 2021] ...Scanning 60771 markers and overlapping markers 50000.
[Wed May 26 15:50:18 2021] ...Scanning 73180 markers and overlapping markers 60000.
[Wed May 26 15:50:18 2021] ...Scanning 86315 markers and overlapping markers 70000.
[Wed May 26 15:50:18 2021] ...Scanning 98624 markers and overlapping markers 80000.
[Wed May 26 15:50:18 2021] ...Scanning 111214 markers and overlapping markers 90000.
[Wed May 26 15:50:18 2021] ...Scanning 123567 markers and overlapping markers 100000.
[Wed May 26 15:50:18 2021] ...Scanning 135186 markers and overlapping markers 110000.
[Wed May 26 15:50:18 2021] ...Scanning 140926 markers and overlapping markers 114670.
[Wed May 26 15:50:18 2021] Write results to "kinship.*"
[Wed May 26 15:50:18 2021] Finished!
ind1	ind2	nsnp	kinship
EXA210119_S1	EXA210121_S3	114670	-0.2871

SEEKIN: SEquence-based Estimation of kinship
Version 1.01: released on 2017-Oct-10
********************
Module kinship
********************
Parameters: 
 -i temp/kinship_merge.vcf 
 -f [] 
 -o kinship 
 -r 0.300000 
 -m 0.050000 
 -d GT 
 -p hom 
 -s 0 
 -w 1 
 -l 10000 
 -t 10 

[Wed May 26 15:50:23 2021] Started!
[Wed May 26 15:50:23 2021] No individual-specific allele frequency file is specified!
[Wed May 26 15:50:23 2021] Use the hom mode with weight function 2MAF(1-MAF)Rsq^2
[Wed May 26 15:50:23 2021] BLOCK_SIZE is set to 10000
[Wed May 26 15:50:23 2021] THREAD_NUM is set to 10
[Wed May 26 15:50:23 2021] MAF filter 0.05
[Wed May 26 15:50:23 2021] R2 filter 0.3
[Wed May 26 15:50:23 2021] GENOTYPE MODE  GT
[Wed May 26 15:50:23 2021] Reading the markers in temp/kinship_merge.vcf
[Wed May 26 15:50:23 2021] ...Scanning 12399 markers and overlapping markers 10000.
[Wed May 26 15:50:24 2021] ...Scanning 25077 markers and overlapping markers 20000.
[Wed May 26 15:50:24 2021] ...Scanning 37268 markers and overlapping markers 30000.
[Wed May 26 15:50:24 2021] ...Scanning 49084 markers and overlapping markers 40000.
[Wed May 26 15:50:24 2021] ...Scanning 60771 markers and overlapping markers 50000.
[Wed May 26 15:50:24 2021] ...Scanning 73180 markers and overlapping markers 60000.
[Wed May 26 15:50:24 2021] ...Scanning 86315 markers and overlapping markers 70000.
[Wed May 26 15:50:24 2021] ...Scanning 98624 markers and overlapping markers 80000.
[Wed May 26 15:50:24 2021] ...Scanning 111214 markers and overlapping markers 90000.
[Wed May 26 15:50:24 2021] ...Scanning 123567 markers and overlapping markers 100000.
[Wed May 26 15:50:24 2021] ...Scanning 135186 markers and overlapping markers 110000.
[Wed May 26 15:50:24 2021] ...Scanning 140926 markers and overlapping markers 114670.
[Wed May 26 15:50:24 2021] Write results to "kinship.*"
[Wed May 26 15:50:24 2021] Finished!
ind1	ind2	nsnp	kinship
EXA210119_S1	EXA210121_S3	114670	0.0000

Thanks for any info!
Cheers,
Alex