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tinnlab / DeconBenchmark

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errors in runDeconvolution for some methods #2

Open fatemehkordevani opened 2 weeks ago

fatemehkordevani commented 2 weeks ago

Hi,

I have installed DeconBenchmark in a conda environment on our HPC cluster. It has the singularity connection as I have checked with: babelwhale::test_singularity_installation(detailed = TRUE) I have ran runDeconvolution with other methods and it works just fine, however, some other methods it throws different errors when I run. 

1-
runDeconvolution(methods = "digitalDLSorter", bulk = as.matrix(zeiser_psdblk), singleCellExpr = as.matrix(sc_exp_zeiser), singleCellLabels = as.character(ordered.ctypes.zeiser$obj_zeiser.active.ident), containerEngine = "singularity", seed = 1)
Error:
Error in library(digitalDLSorteR) : 
  there is no package called 'digitalDLSorteR'
Calls: suppressMessages -> withCallingHandlers
Execution halted
2- 
runDeconvolution(methods = "AdRoit", bulk = as.matrix(zeiser_psdblk), singleCellExpr = as.matrix(sc_exp_zeiser), singleCellLabels = as.character(ordered.ctypes.zeiser$obj_zeiser.active.ident), containerEngine = "singularity")
Error:
Error in ref.build(args$singleCellExpr, args$singleCellLabels, rownames(args$singleCellExpr),  : 
object 'mapper' not found
Calls: ref.build -> paste0
Execution halted
3- 
runDeconvolution(methods = "DESeq2", bulk = as.matrix(zeiser_psdblk), cellTypeExpr = celltypeexpression, containerEngine = "singularity")
Error in optim(par = rep(1, ncol(pure)), fn = sumLossVST, gr = NULL, i,  : 
                  L-BFGS-B needs finite values of 'fn'
                Calls: unmix -> lapply -> lapply -> FUN -> optim

                In addition: 
                  Warning message:                  
                 In sqrt(alpha * q) :
                  NaNs produced                
                Execution halted

Would it be better if I downloaded the docker repository content and ran everything locally? (The possibility to change the source codes, etc)

khoindd2000 commented 2 weeks ago

Hi @fatemehkordevani,

Thank you for your feedback. We are investigating the issues you mentioned and will notify you of a new push to solve these as soon as possible.

fatemehkordevani commented 1 week ago

Thanks for your response @khoindd2000 , a little update here, DESeq2 works now! the problem was from the dataset on my side, but for the other two methods (DigitalDLsorter and Adroit) the issue persists.