SweeD seems stucked with vcf 481 individuals and 6991 sites

[guanruo]

Hi,

I am using SweeD 4.0.0 to detect the selective sweep with vcf format. As the screenshot showed, the vcf have 481 samples and 6991 sites, but it seems stucked more than 10 minutes, the output is empty. But when use OmegaPlus to run with the same vcf, it give me result less than 1s.

Here is my install code for SweeD

git clone http://github.com/alachins/sweed.git

cd sweed

make -f Makefile_MPFR.PTHREADS.gcc

mv SweeD-P SweeD_MPFR-P

SweeD_MPFR-P -input ./Chr1.vcf -grid 200 -folded -osfs chr1.sfs -name chr1 -threads 8

For OmegaPlus:

OmegaPlus-M -input ../Chr1.vcf -name test -threads 4 -grid 200 -minwin 1 -maxwin 50000 -seed 12345

[Nikolaos Alachiotis]

Hi there,

I dont think its stuck. It takes some time to compute the sfs from the data before producing results. This time increases with the number of sequences. Let it run longer than 10 minutes.

Nikos

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Nikolaos Alachiotis

[guanruo]

Thanks for the reply. After 100 mins, SweeD successfully finished the analysis.

在 2018年10月11日星期四 UTC+8下午9:19:11，N.Alachiotis写道：