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Shuhua-Group / ArchaicSeeker2.0

ArchaicSeeker is a series of software for detecting archaic introgression sequences and reconstructing introgression history. The latest version of this series, ArchaicSeeker 2.0, has the following three notable improvements compared with the original version of this software. First, it can automatically determine the boundary of each introgressed sequence. Next, it is capable of tracing both known and unknown ancestral sources of a given introgressed sequence. Finally, it has the ability to reconstruct the introgression history with more sophisticated introgression models.
GNU General Public License v3.0
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Error about duplicate sites from Archaic vcf #9

Closed jackzhong1995 closed 1 month ago

jackzhong1995 commented 4 months ago

Hi,

I download ancient vcf files from your protocol suggestion. I want to known how do you deal with the ancient vcf files, as it contain duplicate sites that will cause ArchaicSeeker error? Is there any code can solve it?

image

Best wishes. jackzhong

jackzhong1995 commented 4 months ago

well, I have solved this trouble about duplicated sites using my personal script.

But another problem occured like this after Loading genotype information correctly:

ArchaicSeeker2: seeker.cpp:170: void archaicSeekerHMM(archaicSeekerPar&, const genomePar&): Assertion `popCorrespond.count(data.comPop[i]) failed.

How to solve it?

Best.

yorkklause commented 1 month ago

Hi jackzhong,

I apologize for the late response; I am not on this email list.

Regarding your issue, it seems that the "pop.par" file and the "model.txt" file are inconsistent. Specifically, any populations present in the second column of the "pop.par" file should also be present in the "model.txt" file.

If you could share all your configuration files, we could further diagnose this.

Thank you,

Kai Yuan