Unable to calculate doublet scores

[asmagen]

Hello,

Most of the ArchR functionality and multithreading is working well on my servers but the doublet score calculation fails with some errors:

>     doubScores <- addDoubletScores(
+         input = ArrowFiles,
+         k = 10, #Refers to how many cells near a "pseudo-doublet" to count.
+         knnMethod = "UMAP", #Refers to the embedding to use for nearest neighbor search with doublet projection.
+         LSIMethod = 1
+     )
ArchR logging to : ArchRLogs/ArchR-addDoubletScores-314793dcedba4-Date-2020-11-13_Time-11-29-27.log
If there is an issue, please report to github with logFile!
2020-11-13 11:29:28 : Batch Execution w/ safelapply!, 0 mins elapsed.
2020-11-13 11:29:28 : T-KP-D21-mm10 (1 of 2) :  Computing Doublet Statistics, 0.001 mins elapsed.
OMP: Error #34: System unable to allocate necessary resources for OMP thread:
OMP: System error #11: Resource temporarily unavailable
OMP: Hint Try decreasing the value of OMP_NUM_THREADS.

************************************************************
2020-11-13 11:33:49 : ERROR Found in Simulate LSI Project Doublets for T-KP-D21-mm10 (1 of 2) :  
LogFile = ArchRLogs/ArchR-addDoubletScores-314793dcedba4-Date-2020-11-13_Time-11-29-27.log

<simpleError in mcfork(detached): unable to fork, possible reason: Resource temporarily unavailable>

************************************************************

************************************************************
2020-11-13 11:33:50 : ERROR Found in .simulateProjectDoublets for T-KP-D21-mm10 (1 of 2) :  
LogFile = ArchRLogs/ArchR-addDoubletScores-314793dcedba4-Date-2020-11-13_Time-11-29-27.log

<simpleError in .logError(e, fn = "Simulate LSI Project Doublets", info = prefix,     errorList = errorList, logFile = logFile): Exiting See Error Above>

************************************************************

Error in .logError(e, fn = ".simulateProjectDoublets", info = prefix,  : 
  Exiting See Error Above
[ArchR-addDoubletScores-314793dcedba4-Date-2020-11-13_Time-11-29-27.log](https://github.com/GreenleafLab/ArchR/files/5538148/ArchR-addDoubletScores-314793dcedba4-Date-2020-11-13_Time-11-29-27.log)

Any advice on how to resolve or debug this?

Thanks

[rcorces]

This looks like an error related to your system, not ArchR. Seems like your system isnt able to allocate the requested resources - looks like you are requesting too many threads with ArchR. I dont think this is something we can help with.

[mirifax]

Hi @asmagen I am having the same error and working in a cluster environment. Just curious if you managed to solve the problem?

[eblchen]

Similar here working in a cluster environment, the doublet scores never finish calculating. Anyone fixed this?