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cgroza / GraffiTE

GraffiTE is a pipeline that finds polymorphic transposable elements in genome assemblies and/or long reads, and genotypes the discovered polymorphisms in read sets using genome-graphs.
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Error for PanGenie-index #19

Closed dtx282000 closed 9 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: https://private-user-images.githubusercontent.com/24269804/300379928-55105a77-470e-4216-91e5-1ca02ff4decc.png?jwt=eyJhbGciOiJIUzI1NiIsInR5cCI6IkpXVCJ9.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.6O0tLJA1oM935GJ4ROz_T3uzJdwk_EUcIUnI7bZajtU https://private-user-images.githubusercontent.com/24269804/300379990-e6160b36-8c80-47d0-9d81-4b50561d0384.png?jwt=eyJhbGciOiJIUzI1NiIsInR5cCI6IkpXVCJ9.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.Jf80qTBPsT8JxUS1JpKwPh7A2tOk7GanTxhVG45ELbA

Here, pangenome.vcf file is as follows:

https://private-user-images.githubusercontent.com/24269804/300380587-ec64c1fc-1f47-4ba3-8a62-4f4d61cd7c92.png?jwt=eyJhbGciOiJIUzI1NiIsInR5cCI6IkpXVCJ9.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.0P-sdiE4-iXqQeCUTSNVhW1QCyfR28Hu4bhVGuPgL1E

So, how can I handle it?

clemgoub commented 10 months ago

Hello!

Unfortunately I cannot see the screenshots you posted. Could you double check their links? Also, could you show the command you use to run GraffiTE as well as some basic description of the machine(s) you are using?

Thanks a lot!

Clément

dtx282000 commented 10 months ago

Thanks! I have solved it.

clemgoub commented 9 months ago

Thank you! If you have the time, I'd be curious to know what was the issue. This could help other users! Cheers!