copycat memory issue

[Yubin]

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I ran into memory issue when I ran the copycat. The gene and cell number are shown below. I was wondering if there is a general guide on the number of cells for this method. Many thanks!!

[1] "running copykat v1.1.0"
[1] "step1: read and filter data ..."
[1] "22318 genes, 73901 cells in raw data"
[1] "8197 genes past LOW.DR filtering"
[1] "step 2: annotations gene coordinates ..."
[1] "start annotation ..."
[1] "step 3: smoothing data with dlm ..."
WARNING:rpy2.rinterface_lib.callbacks:R[write to console]: Error in mcfork() : 
  unable to fork, possible reason: Cannot allocate memory
Calls: <Anonymous> ... <Anonymous> -> copykat -> <Anonymous> -> lapply -> FUN -> mcfork

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[Yubin]

I reduced the number of jobs and now it works.

[Gregor Sturm]

Hi @YubinXie, as infercnvpy is just a thin wrapper around the copycat function, it's best to ask this question in the copykat repo!

Cheers,
Gregor