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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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Error in sprintf(">50% of celltypes missing. %s celltypes\n in ctd but %s in results file.\n Did you provide the correct annotLevel?", : 参数数目太少 #151

Closed hardworkandworkhard closed 1 week ago

hardworkandworkhard commented 3 months ago

Hi, I am trying to run MAGMA.Celltyping::celltype_associations_pipeline with the following code: MAGMA_results <- MAGMA.Celltyping::celltype_associations_pipeline( magma_dirs = trait_path, ctd = ctd, ctd_species = "human", ctd_levels = 1, ctd_name = "test", run_linear = TRUE, run_top10 = TRUE, save_dir = result_path) ctd is the output of MAGMA.Celltyping::get_ctd("ctd_allKI",storage_dir=storage_dir) The error I encounter all the time is: Error in sprintf(">50% of celltypes missing. %s celltypes\n in ctd but %s in results file.\n Did you provide the correct annotLevel?", : 参数数目太少, same GWAS summary statistics can generate output by setting the ctd as the output of MAGMA.Celltyping::get_ctd("ctd_BlueLake2018_FrontalCortexOnly",storage_dir=storage_dir). This issue also meet when using ctd established by myself via:

ctd_lung <- EWCE::generate_celltype_data(
  exp = lung_list_modify$exp,
  annotLevels = annotLevels,
  groupName = "lung", ##generate file named "ctd_lung.rda" if setting so
  no_cores = 1,
  input_species = "human",
  output_species = "human",
  savePath="E:/move/disk_document/Projects_documents/05.allergic_diseases_mental_disorders/01.allergic_diseases_anxiety/04.MAGMA/MAGMA_celltype_enrichment/single_cell_dataset")

Do you have any idea how to solve this issue?

Thanks!!!!!!! ![Uploading error info.jpg…]()

lfz-123qweasd commented 2 weeks ago

I have the same problem!!!! ======= 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 Importing precomputed MAGMA results. magma_cmd and geneCovarFile will be set to NULL. Reading enrichment results file into R. Error in sprintf(">50% of celltypes missing. %s celltypes\n in ctd but %s in results file.\n Did you provide the correct annotLevel?", : 参数数目太少

I have slove the problem by： MAGMA_results <- MAGMA.Celltyping::celltype_associations_pipeline( magma_dirs = magma_dirs, ctd = ctd, ctd_levels = 1, ctd_name = "Zeisel2018", run_linear = TRUE, run_top10 = TRUE)

By this ：https://github.com/neurogenomics/MAGMA_Celltyping/issues/130

bschilder commented 2 weeks ago

@hardworkandworkhard can you please submit the Bug issue template so that I can have the information necessary to assess the problem?

bschilder commented 2 weeks ago

@lfz-123qweasd I can't really help much without a complete bug report. https://github.com/neurogenomics/MAGMA_Celltyping/issues/new?assignees=&labels=bug&projects=&template=bug_report.md&title=

In the meantime, please see the answer to the question in #130