Error addGeneIntegrationMatrix "Error in .getPartialMatrix(getArrowFiles(subProj)"

[ZayaAyush]

Hi @rcorces

I tried to integration scRNA and scATAC, but I get the following error:

• seuratRNA_2 An object of class Seurat 31053 features across 7264 samples within 1 assay Active assay: RNA (31053 features, 0 variable features) 1 layer present: counts
• projATAC5 class: ArchRProject outputDirectory: /Users/ArchRanalysisofscATAC/All samples(2): 1_atac 2_atac sampleColData names(1): ArrowFiles cellColData names(22): Sample TSSEnrichment ... ReadsInPeaks FRIP numberOfCells(1): 17364 medianTSS(1): 17.781 medianFrags(1): 7101

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!

[rcorces]

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.
It is worth noting that there are very few actual bugs in ArchR. If you are getting an error, it is probably something specific to your dataset, usage, or computational environment, all of which are extremely challenging to troubleshoot. As such, we require reproducible examples (preferably using the tutorial dataset) from users who want assistance. If you cannot reproduce your error, we will not be able to help. Before going through the work of making a reproducible example, search the previous Issues, Discussions, function definitions, or the ArchR manual and you will likely find the answers you are looking for. If your post does not contain a reproducible example, it is unlikely to receive a response.
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