rcorces
commented
12 months ago Hi @ZayaAyush! Thanks for using ArchR! Please make sure that your post belongs in the Issues section. Only bugs and error reports belong in the Issues section. Usage questions and feature requests should be posted in the Discussions section, not in Issues.
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Hi @rcorces
I tried to integration scRNA and scATAC, but I get the following error:
projATAC5 <- addGeneIntegrationMatrix( ArchRProj = projATAC5, useMatrix = "GeneScoreMatrix", matrixName = "GeneIntegrationMatrix", reducedDims = "IterativeLSI", seRNA = seuratRNA_2, addToArrow = FALSE, force = TRUE, verbose = FALSE, groupRNA = "seurat_clusters", nameCell = "predictedCell_Un", nameGroup = "predictedGroup_Un", nameScore = "predictedScore_Un" )
ArchR logging to : ArchRLogs/ArchR-addGeneIntegrationMatrix-30132f52ce93-Date-2023-11-26_Time-19-51-58.38178.log If there is an issue, please report to github with logFile! 2023-11-26 19:52:05.883285 : Found 21915 overlapping gene names from gene scores and rna matrix!, 0.125 mins elapsed. Error in .safelapply(seq_along(blockList), function(i) { : Error Found Iteration 1 : [1] "Error in .getPartialMatrix(getArrowFiles(subProj), featureDF = geneDF[geneDF$name %in% : \n Error not all cellNames found in partialMatrix\n" <simpleError in .getPartialMatrix(getArrowFiles(subProj), featureDF = geneDF[geneDF$name %in% genesUse, ], threads = 1, cellNames = subProj$cellNames, useMatrix = useMatrix, verbose = FALSE): Error not all cellNames found in partialMatrix> Error Found Iteration 2 : [1] "Error in .getPartialMatrix(getArrowFiles(subProj), featureDF = geneDF[geneDF$name %in% : \n Error not all cellNames found in partialMatrix\n" <simpleError in .getPartialMatrix(getArrowFiles(subProj), featureDF = geneDF[geneDF$name %in% genesUse, ], threads = 1, cellNames = subProj$cellNames, useMatrix = useMatrix, verbose = FALSE): Error not all cellNames found in partialMatrix> In addition: Warning message: In mclapply(..., mc.cores = threads, mc.preschedule = preschedule) : 2 function calls resulted in an error
Here you can find the .log file. ArchR-addGeneIntegrationMatrix-30132f52ce93-Date-2023-11-26_Time-19-51-58.38178.log
Any idea of what's causing this?
Thank you!