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iqbal-lab-org / gramtools

Genome inference from a population reference graph
MIT License
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Error while running gramtools #165

Open khodor14 opened 2 years ago

khodor14 commented 2 years ago

Hello,

I tried to use gramtools build. I passed a complete ecoli genome and a vcf. I'm using the singularity image of gramtools. I got the following error

Executing build command
Loading integer encoded PRG
Number of characters in integer encoded linear PRG: 5082025
Generating coverage graph
Checking ref is first path in prg...OK
Number of variant sites: 0
No variant sites found.
Exiting 1
2022-03-04 14:32:28,262 gramtools    ERROR    while running backend build:

Could you provide more insight on how to solve this.

bricoletc commented 2 years ago

Hi @khodor14 , what is the FILTER status of the calls in your VCF? gramtools will only put variants with FILTER set to PASS in the constructed graph.

khodor14 commented 2 years ago

Hi @bricoletc thanks for your reply. It has been a while, sorry for that . I will double check the filter and let you know.