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RAiSD: software to detect positive selection based on multiple signatures of a selective sweep and SNP vectors
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Assertion `RSDDataset->numberOfSamples>=1' #51

Open ChrisK1988 opened 5 months ago

ChrisK1988 commented 5 months ago

Hello,

I have been using RAiSD on a modern human dataset with ~4100 individuals to assess positive selection segments across the genome. I have separated my VCFs by population and am getting an error with only one population. It errors out on the following command with the below issue and I am not sure how to fix it.

Command: ./RAiSD -n FIN -I Path/to/VCF/FIN_only.ALLChroms.vcf -R

RAiSD: sources/RAiSD_Dataset.c:1806: RSDDataset_getNumberOfSamples_vcf: Assertion `RSDDataset->numberOfSamples>=1' failed. Aborted

The VCF files were created at different times but from the same original data source. They followed the same construction commands so I am not sure why this specific population is throwing an error. Based on the error it is suggesting that I have some issues with the samples, but that is not the case as the samples appear to be correct and have corresponding phased genotypes (like the rest of the data did).

Thank you for your help!

Chris

alachins commented 3 months ago

Hi Chris, This error might be caused when the vcf contains no samples or no SNPs. There has to be at least one valid SNP in your data to prevent this assertion from failing. Nikos

On Fri, Apr 12, 2024 at 6:37 PM ChrisK1988 @.***> wrote:

Hello,

I have been using RAiSD on a modern human dataset with ~4100 individuals to assess positive selection segments across the genome. I have separated my VCFs by population and am getting an error with only one population. It errors out on the following command with the below issue and I am not sure how to fix it.

Command: ./RAiSD -n FIN -I Path/to/VCF/FIN_only.ALLChroms.vcf -R

RAiSD: sources/RAiSD_Dataset.c:1806: RSDDataset_getNumberOfSamples_vcf: Assertion `RSDDataset->numberOfSamples>=1' failed. Aborted

The VCF files were created at different times but from the same original data source. They followed the same construction commands so I am not sure why this specific population is throwing an error.

Thank you for your help!

Chris

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ChrisK1988 commented 2 months ago

Hi. Sorry for the very late comment back. The VCF file does contain samples and SNPs. I am not sure the underlying mechanics behind it, but it seems like the issue was resolved by updating a version of some of the dependencies, which is interesting because it worked before without the update.

At any rate, it is resolved and I appreciate the response.