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icbi-lab / nextNEOpi

nextNEOpi: a comprehensive pipeline for computational neoantigen prediction
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immunogenicity_scoring #11

Closed beijish closed 2 years ago

beijish commented 2 years ago

Good evening,

pipeline completed but immunogenicity_scoring vails... I was wondering if you've been able to resolve " // TODO: check why sometimes this fails: workaround ignore errors errorStrategy 'ignore'" ?

I suspect we're stuck with the same bit here. Happy to send more Information if useful. BW

SV

riederd commented 2 years ago

Hi,

good to hear that the pipeline completed now. I must admit that until now we did not come around to dig into this issue, as far as I remember it is an issue with the GBM model R code we use from https://github.com/vincentlaboratories/neoag/ If you can post the content of the work folder from the immunogenicity_scoring process I will see if I find some time to look into this.