404 Not Found error in FELLA
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sergi.picart ▴ 20
@sergipicart-11865
Last seen 2.4 years ago
Germany

I have received several inquiries about a recent error in FELLA. The message, after calling buildGraphFromKEGGREST, looks like the following:

Error in .getUrl(url, .listParser, nameColumn = 1, valueColumn = 2) :

Not Found (HTTP 404)

This is due to our dependency KEGGREST, so we must wait for a fix on their behalf. In the meantime, we have shared some FELLA databases for common organisms here.

You just need to download the database of your organism of choice, unzip it (e.g. to ~/Downloads/fella-hsa here) and then

library(FELLA)

FELLAdata <- loadKEGGdata("~/Downloads/fella-hsa", internalDir = FALSE)

# KEGG release
cat(getInfo(FELLAdata))

# ... and resume your analysis

We hope this helps, and apologise if your organism is missing in our list.

EDIT1: KEGGREST is now fixed, and the error persists. As noted in https://www.genome.jp/kegg/module.html,

The MODULE flat file no longer contains organism-specific versions of complete modules. All modules, complete or incomplete and reference or organism-specific, continue to be available in the module map (show_module) interface. Posted on September 12, 2019

This breaks down the module listing, now organism-agnostic as opposed to prior organism-specific names. Expect a fix by this week, as I need to double check no artifacts are introduced by making modules organism-agnostic.

Thank you for you patience.

FELLA software error • 1.2k views
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2
Entering edit mode
sergi.picart ▴ 20
@sergipicart-11865
Last seen 2.4 years ago
Germany

A fix has been pushed, so it should be available soon. KEGG still keeps organism-specific modules, but not within keggList(). Now organism-specific modules are determined by imposing that at least one organismal gene must lie within them. Some small tests on hsa and sce suggest that this should have little (if any) impact in practice, with respect to prior versions.

Thank you, and do not hesitate to report any issues you might encounter

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