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!

[bschilder]

Hi @RRRReyes, sorry about that, I think this was a typo in some edits i made recently. I just pushed a fix (v2.0.11); can you try reinstalling MAGMA.Celltyping and rerunning the code after restarting your session?

[barbareyex]

Hi @bschilder, I installed the version 2.0.11 and re-run the pipeline. It seems it advances more in the code of the celltype_association_pipeline(), but finally it doesn't show up any result (the output of MAGMA_results is NULL, and it shows the same error:

Preparing CellTypeDataset.
Converting to sparse matrix.
Converting to sparse matrix.
Checking CTD: level 1
WARNING: 4 columns (cell-types) have less than the expected number of quantile bins (40).
This may be due to an excessive sparsity or insufficient variation in your CellTypeDataset.

Checking CTD: level 2
WARNING: 2 columns (cell-types) have less than the expected number of quantile bins (40).
This may be due to an excessive sparsity or insufficient variation in your CellTypeDataset.

Checking CTD: level 1
Checking CTD: level 2
prospective_memory.ukb.tsv.35UP.10DOWN.genes.out

======= Calculating celltype associations: linear mode =======
Installed MAGMA version: v1.10
Skipping MAGMA installation.
The desired_version of MAGMA is currently installed: v1.10
Using: magma_v1.10
Error in stopper(paste0(magmaPaths$filePathPrefix, ".genes.out"), "does not exist. Run map_snps_to_genes() before this function"): /tmp/RtmpXLwcbP/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

[sophk1]

Hello,
I just wanted to check and see if this issue has been fixed. I tried to run the analysis using v2.0.11 yesterday and ran into the following error, which is the same as the error above I believe:

Preparing CellTypeDataset. Converting to sparse matrix. Checking CTD: level 1 Checking CTD: level 1 SLE_munged.txt.35UP.10DOWN.genes.out ======= Calculating celltype associations: linear mode ======= Installed MAGMA version: v1.10 Skipping MAGMA installation. The desired_version of MAGMA is currently installed: v1.10 Using: magma_v1.10_win Error in stopper(paste0(magmaPaths$filePathPrefix, ".genes.out"), "does not exist. Run map_snps_to_genes() before this function"): C:\Users\sck11\Downloads\SLE_munged.txt.35UP.10DOWN\MAGMA_Files\SLE_munged.txt.genes.out.35UP.10DOWN\SLE_munged.txt.genes.out.35UP.10DOWN.genes.out does not exist. Run map_snps_to_genes() before this function

I was just wondering if there is a fix yet to this issue? Thanks!

[bschilder]

@NathanSkene would it be ok if we asked @Tomrrr1 (or another lab member) to have a look at this? I'm afraid I don't have any time atm with writing my thesis and the papers.

[bschilder]

@NathanSkene can you make a plan of who within your lab is going to maintain MAGMA.Celltyping (and your other packages) now that I've left the lab?