Result visualization error

[Caiguoyu]

I would like to ask，after I finished calculating aBSREL，I imported visualization on the official website，the result showed 'Ouch! Something went wrong when rendering the results page. Please file a bug.'Why???

[spond]

Dear @Caiguoyu,

Does your JSON file load OK usign https://observablehq.com/@spond/displaying-absrel-results-using-branch-censoring? If so, there's probably a version incompatibility somewhere.

Would you mind sharing your JSON file with me for debugging purposes?

Best, Sergei

[Caiguoyu]

Dear @Caiguoyu,

Does your JSON file load OK usign https://observablehq.com/@spond/displaying-absrel-results-using-branch-censoring? If so, there's probably a version incompatibility somewhere.

Would you mind sharing your JSON file with me for debugging purposes?

Best, Sergei

Dear @spond I can share my JSON file with you，But the link（https://observablehq.com/@spond/displaying-absrel-results-using-branch-censoring） you shared with me above cannot be opened，My JSON files are directly generated by computing in Xshell. chai.PML.ABSREL.zip

[bpetros95]

I am having similar difficulties with SLAC. My .json file looks fine. Appreciate any feedback.

hyphy_test_results.txt.zip

[stevenweaver]

Dear @bpetros95,

I was able to reproduce your issue.

@spond @stephenshank,

The error occurs at https://github.com/veg/hyphy-vision/blob/master/src/jsx/slac.jsx#L1171

TypeError: undefined is not an object (evaluating 't[e][n].codon[0]')

Best, Steven

[stephenshank]

A lot of the internal nodes only possess the Nucleotide GTR attribute, see below. They are missing the codon attribute that the aforementioned line expects, as well as the synonymous substitution count and nonsynonymous substitution count attributes expected a few lines below.

I'm not sure why that would be (note that runtime is 2.5.42), but if this is expected behavior from HyPhy I can accommodate.

[spond]

Dear all,

The SLAC JSON is expected to contain more than just the Nucleotide GTR (which seems to be confined to just one "abnormal" node record). There's something odd happening. @bpetros95 : could you please share your input file and run settings? I'ld like to check it with the current version.

Best, Sergei

[bpetros95]

yep, ran it in hyphy v2.5.32, SLAC, universal genetic code, all branches, 100 ancestral state samples, 0.05 p-val inputs.zip

[stephenshank]

Dear @bpetros95,

I ran your dataset with HyPhy 2.5.50, which is our latest version available through bioconda. This issue actually persists, so I believe this might represent an interesting edge case. Thank you for sharing!

We'll discuss internally and follow up.

Regards, Stephen

[bpetros95]

Exciting! Do let me know what you find or if you have visualization suggestions in the meantime.

Brittany

[spond]

Dear @bpetros95,

Add --kill-zero-lengths Constrain to your command line, and the resulting JSON should be viewable. I would also recommend pruning out duplicate sequences:

-------
>[WARNING] This dataset contains 1560 duplicate sequences. Identical
sequences do not contribute any information to the analysis and only
slow down computation. Please consider removing duplicate or 'nearly'
duplicate sequences, e.g. using
https://github.com/veg/hyphy-analyses/tree/master/remove-duplicates
prior to running selection analyses
-------

I'll investigate what happens with the default setting to cause the errors in JSON (it has to do with automatic removal of zero-length branches).

Best, Sergei

[bpetros95]

Thanks, I have it running with the added argument and will let you know how it goes.

[spond]

Dear @bpetros95,

I looked into the issue a bit; I added some bug fixes to the next release. The issue stems from the fact that your input tree (output by NextStrain, looks like) has "single-child" internal nodes in the tree, e.g.

(KP317956_1:0):0.002579999999999999

HyPhy assumes that the input trees will be at least bifurcating, so each internal node has ≥2 children. While technically valid, single-child trees seem to be breaking some logic in the code in non-trivial ways. Let's keep this open until the next release. I need to confirm that my bug fixes deal with the underlying issue.

Best, Sergei

[bpetros95]

confirmed that HyPhy viz works with --kill-zero-lengths Constrain added to the command. thank you!

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