map_snps_to_genes() related error

[barbareyex]

Hi,

I am trying to run the MAGMA.Celltyping::celltype_associations_pipeline with the following code:

MAGMA_results <- MAGMA.Celltyping::celltype_associations_pipeline(magma_dirs = genesOutPath,
                                                                  ctd = ctd,
                                                                  ctd_species = "hsapiens",
                                                                  ctd_name = "louvain6",
                                                                  run_linear = TRUE,
                                                                  run_top10 = TRUE)

genesOutPath is the output of MAGMA.Celltyping::map_snps_to_genes(path_formatted = path_formatted, genome_build = "GRCh37")

The error I encounter all the time is this: Error in stopper(paste0(magmaPaths$filePathPrefix, ".genes.out"), "does not exist. Run map_snps_to_genes() before this function"): /tmp/RtmpZE8Tlp//prospective_memory.ukb.tsv.35UP.10DOWN/MAGMA_Files/prospective_memory.ukb.tsv.genes.out.35UP.10DOWN/prospective_memory.ukb.tsv.genes.out.35UP.10DOWN.genes.out does not exist. Run map_snps_to_genes() before this function, but it doesn't make sense because I have already run the map_snps_to_genes function. Also, as the path it says in the error is not the same as genesOutPath, I copied the files in genesOutPath (including the file.genes.out), but I still have the same issue.

Do you have any idea how to solve this?

Thanks!