Parallel problem on serialize

[oandrefonseca]

results <- pipelineCNA(seurat_sample_count, organism = 'human', par_cores = 8, SUBCLONES = FALSE)

[1] " raw data - genes: 17617 cells: 9386"
[1] "1) Filter: cells > 200 genes"
[1] "2) Filter: genes > 10% of cells"
[1] "7525 genes past filtering"
[1] "3) Annotations gene coordinates"
Error in serialize(data, node$con) : error writing to connection

I tried to reduce the par_cores value, but nothing seemed to work.

[AntonioDeFalco]

Hello @oandrefonseca,
Yes this is usually due to a memory problem, what type of machine are you running on? linux? how much ram do you have?

Have you also tried non-parallel execution, with par_cores = 1?

[DGladish]

Just wanted to say that I am also receiving the same error. I am working on my personal laptop, with windows 11 and 16GB of ram. I have an 8 core processor. However, I receive the error after "8) Smoothing data" when specifying par_cores = 8.

Right now I am trying non-parallel execution, and SCEVAN is making it past where I was stuck (currently at "time classify tumor cells") however it is taking a very long time to run (~7 hours now and still going).

EDIT: received the error using non-parallel execution after "found x subclones"