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/ATACout/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/ATACout/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/ATACout/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/ATACout/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.

[chenyenchung]

Hi @wenhai-cell87,

We encountered a similar issue as yours with summit files not found. In our case, there's no MACS2 files in the output directory at all (ReplicateCalls). This appeared to be MACS2 not running but ArchR did not notice that MACS2 failed and moved on to run the next step.

If this is the same case as ours, running the macs2 callpeaks command in the log file should fail. It worked out after we made sure MACS2 is functional.