search

pangenome / pggb

the pangenome graph builder
https://doi.org/10.1038/s41592-024-02430-3
MIT License
368 stars 41 forks source link

Behaviour of PGGB when resuming #119

Closed brettChapman closed 2 years ago

brettChapman commented 3 years ago

Hi

After PGGB completes, I'm intending to add spliced regions to my seqwish graph using vg rna and then adding it back in to resume from the smoothxg step to normalise the splice regions.

I was wondering, to resume, do I need to specify the same parameters again, or will PGGB read the yaml file to infer which parameters to resume with? So I could basically just run pggb -r -o output_folder. Thanks.

subwaystation commented 3 years ago

Hi @brettChapman

PGGB scans the given files in the output_folder. If a file is present, it won't be created again. In order for this to work, please run your initial command line adding --resume. Just replace the seqwish file with the new one. It must have the same name, or it won't work.

Best, Simon

subwaystation commented 3 years ago

@brettChapman Are you happy with the current resume function?

AndreaGuarracino commented 2 years ago

pggb does not read the YAML file, but always uses command line parameters to create filenames and, if --resume is specified, deduce which files not to create again. So you have to specify the whole original command line each time for resuming the run.

ekg commented 2 years ago

Note that you can also change parameters of later steps and resume based off of earlier ones. For instance you can change the smoothxg parameters without redoing the wfmash alignment so long as you don't change the wfmash parameters.

On Mon, Nov 22, 2021, 19:32 Andrea Guarracino @.***> wrote:

Closed #119 https://github.com/pangenome/pggb/issues/119.

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub https://github.com/pangenome/pggb/issues/119#event-5655971235, or unsubscribe https://github.com/notifications/unsubscribe-auth/AABDQEJCZQZTVEZTXNTK2CTUNKEDTANCNFSM5AIBM3LQ . Triage notifications on the go with GitHub Mobile for iOS https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675 or Android https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub.