Constrained Gene Integration Error

[jeerthik]

Log File:
ArchR-addGeneIntegrationMatrix-dcc6b48f59a-Date-2023-05-31_Time-04-15-42.log

I am running constrained integration with the ArchR tutorial hematopoiesis dataset. When adding the gene integration matrix using a groupList, which is a nested SimpleList, I get the following error:

ArchR logging to : ArchRLogs/ArchR-addGeneIntegrationMatrix-dcc6b48f59a-Date-2023-05-31_Time-04-15-42.log
If there is an issue, please report to github with logFile!
2023-05-31 04:15:42 : Running Seurat's Integration Stuart* et al 2019, 0.003 mins elapsed.
2023-05-31 04:15:43 : Checking ATAC Input, 0.007 mins elapsed.
2023-05-31 04:15:43 : Checking RNA Input, 0.016 mins elapsed.
2023-05-31 04:15:55 : Found 18601 overlapping gene names from gene scores and rna matrix!, 0.215 mins elapsed.
2023-05-31 04:15:55 : Creating Integration Blocks, 0.215 mins elapsed.
2023-05-31 04:15:55 : Prepping Interation Data, 0.219 mins elapsed.
2023-05-31 04:15:57 : Computing Integration in 2 Integration Blocks!, 0 mins elapsed.
Warning: 1 function calls resulted in an errorError in .safelapply(seq_along(blockList), function(i) { : 
Error Found Iteration 2 : 
	[1] "Error in as(x, \"matrix\")[, j, drop = drop] : subscript out of bounds\n"
	<subscriptOutOfBoundsError in as(x, "matrix")[, j, drop = drop]: subscript out of bounds>

This issue occurred with the tutorial hematopoiesis dataset. The commands I used were as follows:

groupList <- SimpleList(
    TNK = SimpleList(
        ATAC = projHeme2$cellNames[projHeme2$Clusters %in% clustTNK],
        RNA = rnaTNK
    ),
    NonTNK = SimpleList(
        ATAC = projHeme2$cellNames[projHeme2$Clusters %in% clustNonTNK],
        RNA = rnaNonTNK
    )    
)

projHeme2 <- addGeneIntegrationMatrix(
    ArchRProj = projHeme2, 
    useMatrix = "GeneScoreMatrix",
    matrixName = "GeneIntegrationMatrix",
    reducedDims = "IterativeLSI",
    seRNA = seRNA,
    addToArrow = FALSE, 
    groupList = groupList,
    groupRNA = "BioClassification",
    nameCell = "predictedCell_Co",
    nameGroup = "predictedGroup_Co",
    nameScore = "predictedScore_Co"
)

I expected the output to be the following, as according to the full tutorial.

## ArchR logging to : ArchRLogs/ArchR-addGeneIntegrationMatrix-f663618b2629-Date-2020-04-15_Time-10-12-35.log
## If there is an issue, please report to github with logFile!
## 2020-04-15 10:12:36 : Running Seurat’s Integration Stuart* et al 2019, 0.014 mins elapsed.
## 2020-04-15 10:12:36 : Checking ATAC Input, 0.027 mins elapsed.
## 2020-04-15 10:12:36 : Checking RNA Input, 0.027 mins elapsed.
## 2020-04-15 10:12:48 : Creating Integration Blocks, 0.218 mins elapsed.
## 2020-04-15 10:12:48 : Prepping Interation Data, 0.222 mins elapsed.
## 2020-04-15 10:12:49 : Computing Integration in 2 Integration Blocks!, 0 mins elapsed.
## 2020-04-15 10:15:24 : Completed Integration with RNA Matrix, 2.574 mins elapsed.
## ArchR logging successful to : ArchRLogs/ArchR-addGeneIntegrationMatrix-f663618b2629-Date-2020-04-15_Time-10-12-35.log

I am running ArchR on a Terra Bio Google Cloud server. ArchR on the server is the latest version. I saw similar posts related to this, but have not been able to find an answer to fix the error I'm running into. Any help is appreciated. Thank you!