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Bin-Chen-Lab / spider

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Error when running SPIDER_predict, associated with ExperimentHub #1

Open LiuCanidk opened 1 week ago

LiuCanidk commented 1 week ago

Hi, thanks for developing this nice tool I was trying this tool on my own dataset but encountered the following error. Hope someone could help

My code

SPIDER_predict ( seurat_data = sce, tissue = 'hela', disease = 'cell_line', SPIDER_model_file_path = paste0(prefix, '/SPIDER_python/SPIDER_weight/'), use_cell_type = 'SingleR', protein = 'All', use_pretrain = 'T', #Using pretrained SPIDER save_path = paste0(prefix, '/SPIDER_results/'), use_python_path = '/work/home/liucan666/software/mamba/mambaforge/envs/SPIDER/lib/python39.zip', scarches_path = paste0(prefix, '/scarches-0.4.0/'))

My seurat object

An object of class Seurat 26271 features across 74253 samples within 1 assay Active assay: RNA (26271 features, 2000 variable features) 3 layers present: counts, data, scale.data 6 dimensional reductions calculated: pca, umap, harmony, umap_harmony, umap_sct, umap_sct_harmony

Error report

Cannot connect to ExperimentHub server, using 'localHub=TRUE' instead Error in .updateHubDB(hub_bfc, .class, url, proxy, localHub) : Invalid Cache: sqlite file Hub has not been added to cache Run again with 'localHub=FALSE' Calls: SPIDER_predict ... ExperimentHub -> .Hub -> .create_cache -> .updateHubDB In addition: Warning message: package ‘dplyr’ was built under R version 4.1.3 Execution halted

How can I fix this, I run this code on a distributed server, which cannot connect to internet when running in computing node, is this problem associated with internet connection?

Thanks in advance

Ruoqiao2020 commented 1 week ago

It seems that the error you encountered is similar to the error shown in this link: https://support.bioconductor.org/p/9155330/. Probably you'll need to set proxy information to allow ExperimentHub access. Would you try if this works: Accessing behind a proxy

LiuCanidk commented 1 week ago

Hi, I fixed it by running hub() in the registering node. It was relevant to the internet proxy in the computing nodes. And running hub() in the normal internet access can help load the cache of the ExperimentHub package.