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HyPhy: Hypothesis testing using Phylogenies
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Error Displaying aBSREL results #1640

Closed Joye-YF-Zhou closed 8 months ago

Joye-YF-Zhou commented 10 months ago

Hello HyPhy team,

I have just recently finished running aBSREL results on a GARD corrected alignment. However, when I try to visualize the results on HyPhy vision, it fails. It tells me to file a bug. Would you be able to give any insights on how this might happen?

Information on how I ran the tests: HyPhy version 2.5.48 GARD command: hyphy gard --type nucleotide --alignment file.fasta --rate-class 4 --mode Faster aBSREL command: hyphy absrel --alignment file.fasta.best-gard.fit.bf --tree MUSCLE_CARP_prot_8-13-23.fasta.contree

I have attached here the json file of the aBSREL results.

Thank you for looking over this problem!

file.fasta.best-gard.fit.bf.ABSREL copy.json.zip

spond commented 10 months ago

Dear @Joye-YF-Zhou,

The output of this analysis seems to have some issues with the JSON file (probably a bug); some of the tree branches are missing required records in the JSON file. Would you be able to share the input files for me to take a more in-depth look?

In the meantime, you may be able to view partial results with https://observablehq.com/@spond/displaying-absrel-results-using-branch-censoring

Best, Sergei

Joye-YF-Zhou commented 10 months ago

Dear Dr. Pond,

Thank you for looking over this issue! I would be more than happy for you to look over my input files. I have sent you an email with the files attached!

Best regards, Joye Zhou

github-actions[bot] commented 8 months ago

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