Assistance with Error during calculate_SP function

[LaurenBertin]

I am getting the following error below while trying to run the calculate_SP function:

Inferring p-values
Please look at vignettes for options on running this locally if you need to run many instances of this command.
Clumping cjI8AV, 905 variants, using EUR population reference
No encoding supplied: defaulting to UTF-8.
Error in mtfrm.default(list(url = "https://api.opengwas.io/api/ld/clump", :
cannot mtfrm
In addition: Warning message:
In TwoSampleMR::format_data(mr_dataX, type = "exposure") :
The following columns are not present but are helpful for harmonisation
eaf

I tried running the following code before running this function as others have used this within the regular Two Sample MR, but it is still not working:

options(ieugwasr_api = 'gwas-api.mrcieu.ac.uk/')

Do you have any other suggestions for how to get this function to work as it is supposed to? Thanks in advance for your time!

Best,
Lauren

[LizaDarrous]

Hi Lauren,
Thank you for using lhcMR! I'm afraid this error is from the TwoSampleMR package as you know, and has been extensively reported here: MRCIEU/TwoSampleMR#495
I'm afraid in a pinch there's nothing I can do now but will see if another clumping method can be used instead (plink) in a future update.
I would urge you to reply to the creator in that thread link above (explodecomputer) with a sample of SNPs that are creating this error so that it can be fixed asap.