Segmentation fault when running SEEKIN

[vinay-swamy]

Hi there,
I was attempting to run seekin using the following command, using a vcf I generated with vcf-merge
I made sure the resulting file was then converted to gzip format, and ran seekin
./seekin kinship -i $space/test1.vcf.gz -r 0.3 -m 0.05 -d DS -p hom -l 2000 -t 1 -w 1 -o test
This is the output:
SEEKIN: SEquence-based Estimation of kinship
Version 1.01: released on 2017-Oct-10

---

Module kinship

---

Parameters:
-i /home/vinayswamy/Documents/PROJECTS/aldave_lab/wex/variant_samples/test1.vcf.gz
-f []
-o test
-r 0.300000
-m 0.050000
-d DS
-p hom
-s 0
-w 1
-l 2000
-t 1

[Fri Jul 13 11:55:19 2018] Started!
[Fri Jul 13 11:55:19 2018] No individual-specific allele frequency file is specified!
[Fri Jul 13 11:55:19 2018] Use the hom mode with weight function 2MAF(1-MAF)Rsq^2
[Fri Jul 13 11:55:19 2018] BLOCK_SIZE is set to 2000
[Fri Jul 13 11:55:19 2018] THREAD_NUM is set to 1
[Fri Jul 13 11:55:19 2018] MAF filter 0.05
[Fri Jul 13 11:55:19 2018] R2 filter 0.3
[Fri Jul 13 11:55:19 2018] GENOTYPE MODE DS
[Fri Jul 13 11:55:19 2018] Reading the markers in /home/vinayswamy/Documents/PROJECTS/aldave_lab/wex/variant_samples/test1.vcf.gz
Segmentation fault (core dumped)

I also ran the same command, but used the -s 1 argument for small sample sizes

SEEKIN: SEquence-based Estimation of kinship
Version 1.01: released on 2017-Oct-10

---

Module kinship

---

Parameters:
-i /home/vinayswamy/Documents/PROJECTS/aldave_lab/wex/variant_samples/test1.vcf.gz
-f []
-o test.
-r 0.300000
-m 0.050000
-d DS
-p hom
-s 1
-w 1
-l 2000
-t 1

[Fri Jul 13 12:01:49 2018] Started!
[Fri Jul 13 12:01:49 2018] No individual-specific allele frequency file is specified!
[Fri Jul 13 12:01:49 2018] Use the hom mode with weight function 2MAF(1-MAF)Rsq^2
[Fri Jul 13 12:01:49 2018] Start the algorithm model for small sample size, make sure that the individual-specific allele frequency file exists
[Fri Jul 13 12:01:49 2018] BLOCK_SIZE is set to 2000
[Fri Jul 13 12:01:49 2018] THREAD_NUM is set to 1
[Fri Jul 13 12:01:49 2018] MAF filter 0.05
[Fri Jul 13 12:01:49 2018] R2 filter 0.3
[Fri Jul 13 12:01:49 2018] GENOTYPE MODE DS
[Fri Jul 13 12:01:49 2018] Start the algorithm model for small sample size
terminate called after throwing an instance of 'std::runtime_error'
what(): FAIL_IO: Failed to Open [] for r
Aborted (core dumped)

I've attatched the file I used as well. Let me know If there's anything I'm doing wrong, or if there is a fix.
Thank You

test1.vcf.gz

[jinzhuangdou]

Hi, you vcf file does not have the dosage information. You should use the -GT mode to take the genotype.