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eblerjana / pangenie

Pangenome-based genome inference
MIT License
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Error for PanGenie-index #65

Open dtx282000 opened 10 months ago

dtx282000 commented 10 months ago

Description:

I'm encountering an issue when running the following command:

PanGenie-index -v pangenome.vcf -r GXFZ.fa -t 8 -o pangenome

The error message I'm receiving is:

image image

Here, pangenome.vcf file is as follows:

image

So, how can I handle it?

eblerjana commented 10 months ago

This is described in detail in the README secion "Required input files": https://github.com/eblerjana/pangenie#required-input-files . See especially "What should I do if my input VCF contains overlapping variants?"

dtx282000 commented 10 months ago

Thanks four your response. Now, I have solved it. But, I have a new error when running the script:

image

So, how can I handle it?

eblerjana commented 9 months ago

This does not look like any error related to PanGenie, rather something related to bgzip. Did you write the PanGenie-genotyping.shscript? What happens internally?