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pangenome / pggb

the pangenome graph builder
https://doi.org/10.1101/2023.04.05.535718
MIT License
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run without errors and outputs #388

Closed Gon1976 closed 3 months ago

Gon1976 commented 3 months ago

Hi I am trying to run pggb. I make a fasta with 7 chromosomes i want to compare of 7 species. I names using PanSN I run with the basic comand ./pggb -i test.fa -o out I have not ouput

Also I tried the examples command lines and I cant run it because PanSN not match: ./pggb -i data/HLA/DRB1-3123.fa.gz -p 70 -s 3000 -G 2000 -n 10 -t 16 -o out -M -m [pggb] warning: there are sequence names (like 'gi|568815592:32578768-32589835') that do not match the Pangenome Sequence Naming (PanSN) any idea? Thanks Gonzalo

AndreaGuarracino commented 3 months ago

PanSN warning should not prevent graph building, but just variant calling, as PanSN became mandatory in recent versions of VG.

Can you share your (bgzipped) sequences? or at least your log file, to check what is going on?

From: Gon1976 @.> Sent: Tuesday, April 9, 2024 07:50 To: pangenome/pggb @.> Cc: Subscribed @.***> Subject: [pangenome/pggb] run without errors and outputs (Issue #388)

Hi I am trying to run pggb. I make a fasta with 7 chromosomes i want to compare of 7 species. I names using PanSN I run with the basic comand ./pggb -i test.fa -o out I have not ouput

Also I tried the examples command lines and I cant run it because PanSN not match: ./pggb -i data/HLA/DRB1-3123.fa.gz -p 70 -s 3000 -G 2000 -n 10 -t 16 -o out -M -m [pggb] warning: there are sequence names (like 'gi|568815592:32578768-32589835') that do not match the Pangenome Sequence Naming (PanSN) any idea? Thanks Gonzalo

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Gon1976 commented 3 months ago

I have not log file. I send my compressed fasta

test.fa.gz

AndreaGuarracino commented 3 months ago

Thx! How did you install PGGB? Which version?

Gon1976 commented 3 months ago

Thanks, the version is: ./pggb --version pggb v0.6.0-0-gd500639

I download from github: git clone --recursive https://github.com/pangenome/pggb cd pggb and try using: ./pggb

AndreaGuarracino commented 3 months ago

In that way you've just downloaded the PGGB script, but to be able to run it, you have to install also its components (wfmash, seqwish, ...). The fact that it is not saying anything as error message is a known issue for me, that's silly, I will fix it. Try to install PGGB with Docker/Singularity/Bioconda (https://github.com/pangenome/pggb?tab=readme-ov-file#installation).

Gon1976 commented 3 months ago

ok, i will try, thanks for your support

Gon1976 commented 3 months ago

I installed tools, and use singularity to run. Works fine thanks