Error in .safelapply(seq_along(blockList), function(i)

[AyehSadr]

Hi
I've encountered an error while working with the gene integration matrix creation process, and I'm struggling to resolve it. I. I've provided the log file details and the error messages I received.

projSKNSH2 <- addGeneIntegrationMatrix(
ArchRProj = projSKNSH2,
useMatrix = "GeneScoreMatrix",
matrixName = "GeneIntegrationMatrix",
reducedDims = "IterativeLSI",
seRNA = scRNAseq,
addToArrow = FALSE,
groupRNA = "orig.ident",
nameCell = "predictedCell_Un",
nameGroup = "predictedGroup_Un",
nameScore = "predictedScore_Un"
)

ArchR logging to : ArchRLogs/ArchR-addGeneIntegrationMatrix-3efbae296eaf57-Date-2024-02-29_Time-13-14-07.819371.log
If there is an issue, please report to github with logFile!
2024-02-29 13:14:07.894534 : Running Seurat's Integration Stuart* et al 2019, 0.001 mins elapsed.
2024-02-29 13:14:07.971618 : Checking ATAC Input, 0.003 mins elapsed.
2024-02-29 13:14:08.183277 : Checking RNA Input, 0.006 mins elapsed.
2024-02-29 13:14:13.0876 : Found 19818 overlapping gene names from gene scores and rna matrix!, 0.088 mins elapsed.
2024-02-29 13:14:13.089081 : Creating Integration Blocks, 0.088 mins elapsed.
2024-02-29 13:14:13.632301 : Prepping Interation Data, 0.097 mins elapsed.
2024-02-29 13:14:14.466356 : Computing Integration in 4 Integration Blocks!, 0 mins elapsed.
Error in .safelapply(seq_along(blockList), function(i) { :
Error Found Iteration 1 :
[1] "Error in slot(object = object, name = "features")[[layer]] <- features : \n more elements supplied than there are to replace\n"
<simpleError in slot(object = object, name = "features")[[layer]] <- features: more elements supplied than there are to replace>
Error Found Iteration 2 :
[1] "Error in slot(object = object, name = "features")[[layer]] <- features : \n more elements supplied than there are to replace\n"
<simpleError in slot(object = object, name = "features")[[layer]] <- features: more elements supplied than there are to replace>
Error Found Iteration 3 :
[1] "Error in slot(object = object, name = "features")[[layer]] <- features : \n more elements supplied than there are to replace\n"
<simpleError in slot(object = object, name = "features")[[layer]] <- features: more elements supplied than there are to replace>
Error Found Iteration 4 :
[1] "Error in slot(object = object, name = "features")[[layer]] <- features :
In addition: Warning message:
In mclapply(..., mc.cores = threads, mc.preschedule = preschedule) :
4 function calls resulted in an error
Could you please check the log file and the error, and provide me with some recommendations?

Best Regards
Ayeh
ArchR-addGeneIntegrationMatrix-292756c2df99-Date-2020-06-26_Time-13-18-05.log

[shladyshau]

I have the same issue. Would be grateful if someone could provide feedback on it