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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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ArchaicSeeker2: data.cpp:500: void genome::vcfsLoad(const std::vector<std::__cxx11::basic_string<char> >&): Assertion `tpos > prePos' failed. #3

Closed rabbitdsy closed 10 months ago

rabbitdsy commented 2 years ago

When I followed the SOP from CELL STAR PROTOCALs "Detecting archaic introgression and modeling multiple-wave admixture with ArchaicSeeker 2.0", the problem occered when running the script ./ArchaicSeeker2 -v test/vcf.par -r test/remap.par -p test/pop.par -X test/outgroup.par -A test/anc.par -m test/model.txt -o test/EAS]

I downloaded the Neanderthal, Denisovan, and YRI vcfs from the links in your manuscript, and without any further change. I wonder do I need do any formatting or use other softwares to make the downloaded genotypes consistent with the input?

Zhang-Rui-2018 commented 2 years ago

Please make sure that the physical positions are strictly increasing and not be duplicated.

imdanique commented 1 year ago

@rabbitdsy Hi! Sorry, I know that it's been a while since your question, but did you manage to solve it? I have the same problem. Thanks!