Segmentation fault error

[srbehera]

I am running PCA for 1kGP merged SV vcf files and I am getting the seg fault error when I run the PBS script with 150G memory. The run command is in the last line. It worked fine when I extracted a single chromosome (chr21) from the VCF and run the same script.

Input: bcftool_merge.sv_chr1_22_maf_ge0.05.annotated.vcf.gz
MAF lower bound: 0
Thin: 1
Number principle components: 20
Reading data...
1793 samples
Kept 2028657 markers out of 2028657
/var/spool/torque/mom_priv/jobs/3377732.sug-moab.SC: line 12: 11059 Segmentation fault      /hgsc_software/akt/akt-0.3.3/bin/akt pca ${vcf}.vcf.gz --force -Oz -o ${vcf}.pca.cf.gz > ${vcf}.txt

[jaredo]

You are running out of memory, 2,028,657 markers is far too many for a PCA.

You could try removing rare variants and/or LD pruning.

[srbehera]

I got it. Yes, it's merged SVs of all 3,202 so it contains too many variants. I actually extracted the variants with MAF > 0.05 (using bcftools). I think the MAF input parameter option in AKT is not working although I see some lines in the source code.