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millanek / Dsuite

Fast calculation of Patterson's D (ABBA-BABA) and the f4-ratio statistics across many populations/species
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Cannot get Dinvestigate to run #91

Closed drew-olson-tmru closed 8 months ago

drew-olson-tmru commented 9 months ago

Hi,

I have another open issue, but I am no longer receiving that error code, I am now receiving this error: There are 3 sets (populations/species) excluding the Outgroup /builddir/build/BUILD/gcc-11.4.1-20230605/obj-x86_64-redhat-linux/x86_64-redhat-linux/libstdc++-v3/include/bits/basic_string.h:1040: std::cxx11::basic_string<_CharT, _Traits, _Alloc>::const_reference std::cxx11::basic_string<_CharT, _Traits, _Alloc>::operator[](std::cxx11::basic_string<_CharT, _Traits, _Alloc>::size_type) const [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator; std::cxx11::basic_string<_CharT, _Traits, _Alloc>::const_reference = const char&; std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::size_type = long unsigned int]: Assertion '__pos <= size()' failed. Aborted (core dumped)

I cannot find any help with troubleshooting. Anything that I can find says that this is an error with the program itself, however, this runs just fine when I use the dataset from the tutorial. Are there any nuances that are not mentioned in the tutorial or documentation for vcf file preparation, splitting of vcf files into chromosomes, etc. I have made sure that the sets and trios files are tab spaced and have no white space or extra lines. I even went through and cleaned up more in the vcf file header and removed extra format info that Dsuite does not use, leaving only the GT to be used. But I can only get this error. Please help me if you can.

EDIT: I have now exhausted almost every option to try and get my vcf file to work in this program. I'm not sure what to do anymore. Everything should be working. Can someone please help me figure this issue out?

drew-olson-tmru commented 9 months ago

Update Dsuite Dtrios also does not run properly. It provides me with a blank txt file.

drew-olson-tmru commented 8 months ago

I am closing this now. I found out the issue in my VCF. It seems to have been due to missing values in the GT field after merging my vcf files using bcftools merge.