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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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The sample is in the VCF but not assigned in the SETS.txt #82

Open ScooLida opened 10 months ago

ScooLida commented 10 months ago

Hi! I can't understand. I have file like this. Why Dsuite can't find sample. SAmple is in same directory as SETS.txt file 1k.sort.bam tanaicus 5k.sort.bam tanaicus 3k.sort.bam tanaicus SRR10012547.sort.bam europaeus SRR17908653.sort.bam europaeus SRR12518920.sort.bam europaeus SRR17908654.sort.bam europaeus SRR10011655.sort.bam europaeus SRR6485265.sort.bam americanus SRR11020211.sort.bam americanus .. /mss_users/ltursunova/cow/new2/och.fasta Outgroup

Error Did not find the sample: "mss_users/ltursunova/cow/new2/och.fasta" 1k,5k,SRR10012547,SRR11020211,SRR17044867,SRR17908655,SRR5949621,SRR5949630,SRR6485240,SRR6485284,3k,SRR10082089,SRR11020300,SRR17908653,SRR5949623,SRR5949632,SRR10011655,SRR10082097,SRR12518920,SRR17908654,SRR17908659,SRR5949624,SRR5949634,SRR6485281 Did not find any samples in the VCF for "Outgroup" Dsuite: Dsuite_common.cpp:28: void SetInformation::linkSetsAndVCFpositions(const std::vector<std::__cxx11::basic_string >&): Assertion `!spPos.empty()' failed. Aborted (core dumped)

wuyh0328 commented 8 months ago

I have the same problem. Have you solved it?

ScooLida commented 8 months ago

I have the same problem. Have you solved it?

Yes, there is two mistake. Outgroup also must be in .bam file, not .fasta. And I don't have to write .sort.bam. For list number and group is enough.

1k tanaicus 5k tanaicus

wuyh0328 commented 8 months ago

But I don't have either of those mistakes. It still can't find a sample. Do you know how to solve it? 1703664569973

ScooLida commented 8 months ago

But I don't have either of those mistakes. It still can't find a sample. Do you know how to solve it? 1703664569973

Do you have this sample at all(MDe2A)? Cheсk your data

wuyh0328 commented 8 months ago

Thank you! YES,You can see it in the sample list below。(I use the module Dquartets).

ScooLida commented 8 months ago

Thank you! YES,You can see it in the sample list below。(I use the module Dquartets).

May be MDe2A appears twice in sets. There's nothing more I can help

wuyh0328 commented 8 months ago

Ok, thank you very much. I will check again.

wuyh0328 commented 8 months ago

Thank you! YES,You can see it in the sample list below。(I use the module Dquartets).

May be MDe2A appears twice in sets. There's nothing more I can help

I seem to have found the problem. In my SETS.txt file, there are Spaces after the sample ID.