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jtlovell / GENESPACE

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HOG path not getting set? #163

Closed hyphaltip closed 1 month ago

hyphaltip commented 1 month ago

orthofinder completes successfully but the search for the files seems to be failing

I've been able to run genespace successfully for a while but had to install new package with a new R upgrade and now I am getting this failure:

Error in if (is.na(gsParam$synteny$hogs)) { : argument is of length zero

I don't see where you set the subfolders for these only that resultsDir is used in the set_syntenyParams.R so not sure if it just isn't traversing the subfolders or if something else is wrong.

Running: OrthoFinder version 2.5.5 and GENESPACE v1.3.1

jtlovell commented 1 month ago

OK - Thanks for this ... I haven't check forward compatibility to the newer R versions. Thats something I'm planning for next month. But, I wonder what would cause this. ... this errors out right at the beginning of the GENESPACE run, eh?

hyphaltip commented 1 month ago

Yeah right at the beginning, this R 4.3.0 - I'll just go back to an older R if that is the solution

hyphaltip commented 1 month ago

Okay I think the issues was a leftover 'results' folder!