Error in if (is.na(gsParam$synteny$hogs))

jtlovell / GENESPACE

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Error in if (is.na(gsParam$synteny$hogs)) #85

Closed xiaoyezao closed 1 year ago

xiaoyezao commented 1 year ago

Hi,

I got the following error in GENESPACE v1.2:

1. Running orthofinder (or parsing existing results)
    Checking for existing orthofinder results ...
    ... found existing run, not re-running orthofinder
Error in if (is.na(gsParam$synteny$hogs)) { : argument is of length zero
Calls: run_genespace
Execution halted

I run orthofinder independently and used the -y option (Split paralogous clades below root of a HOG into separate HOGs). Could this be the issue?

Thank you.

jtlovell commented 1 year ago

I have not written anything to support orthofinder -y and I don't plan to. Does it run using the default method? If not, I'll check and see what might be causing this.

jtlovell commented 1 year ago

I'm going to close this, but re-open if you have issues. John