Run frozen at 0%

[brycemash]

I'm in an interactive session on a linux cluster.

$use Java-11 $use R-4.1 $R

d <- readRDS('broad/dunnlab/GBM_Single_Cell/Seurat_files/Integrated_Data_Sets/PanCancer_Final/Pre_Scale/merged.RPCA.int.rds') library(Seurat) library(Matrix) d <- d[, sample(colnames(d), size = 2000, replace=F)]

Extract expression matrix and gene metadata

expression_matrix <- d@assays$RNA@data gene_metadata <- rownames(expression_matrix) output_directory <- "broad/dunnlab/BLM/conda_libraries/compass" sparse_matrix <- Matrix(as.matrix(expression_matrix), sparse = TRUE) writeMM(sparse_matrix, file = paste0(output_directory, "/expression.mtx")) write.table(gene_metadata, file = paste0(output_directory, "/genes.tsv"), sep = "\t", row.names = FALSE, col.names = FALSE, quote = FALSE) quit()

$conda activate /broad/dunnlab/BLM/conda_libraries/compass $#python -m pip install git+https://github.com/yoseflab/Compass.git --upgrade $conda install pandas=1.5.3 $#export PATH=$PATH:/home/unix/mashimo/.local/bin/ #required for pip $#export PATH=$PATH:/broad/dunnlab/BLM/conda_libraries/compass #required for compass $cd /broad/dunnlab/BLM/conda_libraries/compass/ $compass --data-mtx expression.mtx genes.tsv --species homo_sapiens --num-processes 10 Cache for model and media already built Evaluating Reaction Penalties... /broad/dunnlab/BLM/conda_libraries/compass/lib/python3.8/site-packages/compass/compass/penalties.py:158: FutureWarning: iteritems is deprecated and will be removed in a future version. Use .items instead. for name, expression_data in expression.iteritems(): Processing 2000 samples using 10 processes Progress bar will update once the first sample is finished 0%| | 0/2000 [00:00<?, ?it/s]

I'm a bit confused on how you use scRNA data and what the "samples" would mean... would they just be averages of the cells in a sample?

[brycemash]

i tried again with 52 processes and 3 threads and still stuck at 0%