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%

[wuxiangning]

hello!did u solve this issue. I meet the same issue recently