Error in (function (..., threads = 1, preschedule = FALSE) : Error Found Iteration 1 :

[wenhai-cell87]

Thank you very much for developing this tool. However, I encountered a problem while actually running the addReproduciblePeakSet process."

neuron_1 <- addReproduciblePeakSet(
ArchRProj = neuron_1,
groupBy = "Clusters",
peaksPerCell = 500,
pathToMacs2 = pathToMacs2,
force = TRUE)

ArchR logging to : ArchRLogs/ArchR-addReproduciblePeakSet-3a341dbd6075-Date-2024-05-13_Time-21-19-56.889968.log
If there is an issue, please report to github with logFile!

Calling Peaks with Macs2

2024-05-13 21:19:59.1349 : Peak Calling Parameters!, 0.037 mins elapsed.

Group nCells nCellsUsed nReplicates nMin nMax maxPeaks

C1 C1 318 318 4 63 95 150000
C2 C2 1527 1527 4 352 404 150000
C3 C3 61 55 2 34 37 27500
C4 C4 850 850 4 175 264 150000
C5 C5 472 472 4 88 168 150000
C6 C6 790 790 4 151 229 150000
C7 C7 93 81 2 50 50 40500
C8 C8 522 522 4 98 168 150000
C9 C9 543 543 4 113 151 150000
C10 C10 675 675 4 154 182 150000
C11 C11 730 730 4 166 212 150000
C12 C12 846 846 4 202 220 150000
C13 C13 1443 1443 4 327 386 150000
C14 C14 1519 1519 4 269 485 150000
C15 C15 1444 1444 4 328 387 150000
C16 C16 520 520 4 102 154 150000
C17 C17 556 556 4 113 168 150000
C18 C18 735 735 4 164 219 150000
C19 C19 340 340 4 67 98 150000
C20 C20 322 279 3 59 110 139500
C21 C21 1307 1280 4 134 500 150000
C22 C22 247 247 3 53 106 123500
C23 C23 673 673 4 126 201 150000
C24 C24 516 516 4 114 139 150000
C25 C25 649 649 4 137 183 150000
2024-05-13 21:19:59.148482 : Batching Peak Calls!, 0.038 mins elapsed.

2024-05-13 21:19:59.158763 : Batch Execution w/ safelapply!, 0 mins elapsed.

Warning message in mclapply(..., mc.cores = threads, mc.preschedule = preschedule):
“94 function calls resulted in an error”
Error in (function (..., threads = 1, preschedule = FALSE) :
Error Found Iteration 1 :
[1] "Error in data.table::fread(summitsFile, select = c(1, 2, 3, 5)) : \n File '/data/chenwenhai/ATAC5/ATAC_out/PeakCalls/InsertionBeds/C1..WT_M_1101006-1_summits.bed' does not exist or is non-readable. getwd()=='/data/chenwenhai/ATAC5'\n"
<simpleError in data.table::fread(summitsFile, select = c(1, 2, 3, 5)): File '/data/chenwenhai/ATAC5/ATAC_out/PeakCalls/InsertionBeds/C1..WT_M_1101006-1_summits.bed' does not exist or is non-readable. getwd()=='/data/chenwenhai/ATAC5'>
Error Found Iteration 2 :
[1] "Error in data.table::fread(summitsFile, select = c(1, 2, 3, 5)) : \n File '/data/chenwenhai/ATAC5/ATAC_out/PeakCalls/InsertionBeds/C1..CKO_M_1018004-2_summits.bed' does not exist or is non-readable. getwd()=='/data/chenwenhai/ATAC5'\n"
<simpleError in data.table::fread(summitsFile, select = c(1, 2, 3, 5)): File '/data/chenwenhai/ATAC5/ATAC_out/PeakCalls/InsertionBeds/C1..CKO_M_1018004-2_summits.bed' does not exist or is non-readable. getwd()=='/data/chenwenhai/ATAC5'>
......

I would greatly appreciate it if you could provide some suggestions.

here is my packagesVersion

[1] SeuratObject_4.1.4 cacoa_0.4.0
[3] Matrix_1.6-3 sp_2.1-2
[5] ArchRtoSignac_1.0.4 ggsci_3.0.3
[7] ggpubr_0.6.0 hexbin_1.28.3
[9] circlize_0.4.16 ComplexHeatmap_2.15.4
[11] dittoSeq_1.17.0 ggrepel_0.9.5
[13] dplyr_1.1.4 ggrastr_1.0.2
[15] harmony_1.2.0 scuttle_1.12.0
[17] SingleCellExperiment_1.24.0 ggridges_0.5.6
[19] nabor_0.5.0 BSgenome.Mmusculus.UCSC.mm10_1.4.3
[21] BSgenome_1.70.1 rtracklayer_1.62.0
[23] BiocIO_1.12.0 Biostrings_2.70.1
[25] XVector_0.42.0 rhdf5_2.46.1
[27] SummarizedExperiment_1.32.0 Biobase_2.62.0
[29] MatrixGenerics_1.14.0 Rcpp_1.0.12
[31] GenomicRanges_1.54.1 GenomeInfoDb_1.38.1
[33] IRanges_2.36.0 S4Vectors_0.40.2
[35] BiocGenerics_0.48.1 matrixStats_1.2.0
[37] data.table_1.14.10 stringr_1.5.1
[39] plyr_1.8.9 magrittr_2.0.3
[41] ggplot2_3.4.4 gtable_0.3.4
[43] gtools_3.9.5 gridExtra_2.3
[45] ArchR_1.0.2

[rcorces]

Hi @wenhai-cell87! Thanks for using ArchR! Lately, it has been very challenging for me to keep up with maintenance of this package and all of my other
responsibilities as a PI. I have not been responding to issue posts and I have not been pushing updates to the software. We are actively searching to hire
a computational biologist to continue to develop and maintain ArchR and related tools. If you know someone who might be a good fit, please let us know!
In the meantime, your issue will likely go without a reply. Most issues with ArchR right not relate to compatibility. Try reverting to R 4.1 and Bioconductor 3.15.
Newer versions of Seurat and Matrix also are causing issues. Sorry for not being able to provide active support for this package at this time.