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neurogenomics / MAGMA_Celltyping

Find causal cell-types underlying complex trait genetics
https://neurogenomics.github.io/MAGMA_Celltyping
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Problem with get_genomeLocFile #101

Closed malosreet closed 2 years ago

malosreet commented 2 years ago

Hello!

I am just starting to use MAGMA.Celltyping and not familiar with GWAS related analysis. I am running into an error with map_snps_to_genes.

First I used import_sumstats from MungeSumstats to download the properly formatted GWAS summary statistics for several studies on Open GWAS. Then I am trying to use map_snps_to_genes, but I get the following error message on Step 1 of the MAGMA analysis. 

ERROR - reading gene location file: too few values on line 1:

        line: {

When I look at the "NCBI37.3.gene.loc" file this is what I see:

{

  "message": "Bad credentials",

  "documentation_url": "https://docs.github.com/rest"

}

I think this is happening because map_snps_to_genes is calling get_genomeLocFile, which calls get_data, which calls pb_download to try to get the appropriate files from the MAGMA.Celltyping respository. But the authentication fails so the download fails.

Perhaps I can change something simple in my set-up to fix this problem. I downloaded the required file directly from the MAGMA website, but I couldn't figure out how to specify to map_snps_to_genes that it should use that file.

Any advice is appreciated!

Malosree

bschilder commented 2 years ago

i think this is a duplicate of #100