addReproduciblePeakSet Error: object 'ArchRProj' not found

[grimmem1]

addReproduciblePeakSet is throwing an error (below) where I am told "Error: object 'ArchRProj' not found" when using a multiomic ArchRProj object that 1) is straight from addGroupCoverages and 2) appears to be fine. No log file is generated in ArchRLogs. Any advice is appreciated.

> pathToMacs2 <- "/usr/local/anaconda3/bin/macs2"
> proj.comb <- addReproduciblePeakSet(
+   ArchRProj = proj.comb,
+   groupBy = "Clusters",
+   peakMethod = "Macs2",
+   reproducibility = "2",
+   peaksPerCell = 500,
+   maxPeaks = 150000,
+   minCells = 25,
+   excludeChr = c("chrM", "chrY"),
+   pathToMacs2 = pathToMacs2,
+   genomeSize = NULL,
+   shift = -75,
+   extsize = 150,
+   method = "p",
+   cutOff = 0.1,
+   additionalParams = "--nomodel --nolambda",
+   extendSummits = 250,
+   promoterRegion = c(2000, 100),
+   genomeAnnotation = getGenomeAnnotation(ArchRProj),
+   geneAnnotation = getGeneAnnotation(ArchRProj),
+   plot = TRUE,
+   threads = getArchRThreads(),
+   parallelParam = NULL,
+   force = TRUE,
+   verbose = TRUE,
+   logFile = createLogFile("addReproduciblePeakSet")
+ )
Error: object 'ArchRProj' not found

> proj.comb

           ___      .______        ______  __    __  .______      
          /   \     |   _  \      /      ||  |  |  | |   _  \     
         /  ^  \    |  |_)  |    |  ,----'|  |__|  | |  |_)  |    
        /  /_\  \   |      /     |  |     |   __   | |      /     
       /  _____  \  |  |\  \\___ |  `----.|  |  |  | |  |\  \\___.
      /__/     \__\ | _| `._____| \______||__|  |__| | _| `._____|
    
class: ArchRProject 
outputDirectory: /gstore/scratch/u/grimmem1/Yauch/Proj_SMARCA/MULTIOME/20210701_Multiome_CMO_test2/ArchROutput 
samples(4): hto07 hto08 hto09 hto10
sampleColData names(1): ArrowFiles
cellColData names(19): Sample TSSEnrichment ... Gex_RiboRatio Clusters
numberOfCells(1): 7840
medianTSS(1): 13.377
medianFrags(1): 12204.5

> sessionInfo()
R version 4.1.0 (2021-05-18)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS Catalina 10.15.7

Matrix products: default
BLAS:   /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/4.1/Resources/lib/libRlapack.dylib

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
 [1] parallel  stats4    grid      stats     graphics  grDevices utils     datasets  methods  
[10] base     

other attached packages:
 [1] gridExtra_2.3                     SeuratObject_4.0.2               
 [3] Seurat_4.0.3                      forcats_0.5.1                    
 [5] stringr_1.4.0                     dplyr_1.0.7                      
 [7] purrr_0.3.4                       readr_2.0.1                      
 [9] tidyverse_1.3.1                   ggpubr_0.4.0                     
[11] BSgenome.Hsapiens.UCSC.hg38_1.4.3 BSgenome_1.60.0                  
[13] rtracklayer_1.52.1                Biostrings_2.60.2                
[15] XVector_0.32.0                    ComplexHeatmap_2.8.0             
[17] ArchR_1.0.1                       magrittr_2.0.1                   
[19] rhdf5_2.36.0                      Matrix_1.3-4                     
[21] SummarizedExperiment_1.22.0       Biobase_2.52.0                   
[23] GenomicRanges_1.44.0              GenomeInfoDb_1.28.1              
[25] IRanges_2.26.0                    S4Vectors_0.30.0                 
[27] BiocGenerics_0.38.0               MatrixGenerics_1.4.2             
[29] matrixStats_0.60.0                ggplot2_3.3.5                    
[31] RColorBrewer_1.1-2                viridis_0.6.1                    
[33] viridisLite_0.4.0                 colorspace_2.0-2                 
[35] pheatmap_1.0.12                   tidyr_1.1.3                      
[37] tibble_3.1.3                      data.table_1.14.0                
[39] openxlsx_4.2.4                   

loaded via a namespace (and not attached):
  [1] utf8_1.2.2               reticulate_1.20          tidyselect_1.1.1        
  [4] htmlwidgets_1.5.3        BiocParallel_1.26.1      Rtsne_0.15              
  [7] munsell_0.5.0            codetools_0.2-18         ica_1.0-2               
 [10] future_1.21.0            miniUI_0.1.1.1           withr_2.4.2             
 [13] rstudioapi_0.13          ROCR_1.0-11              tensor_1.5              
 [16] ggsignif_0.6.2           listenv_0.8.0            labeling_0.4.2          
 [19] GenomeInfoDbData_1.2.6   polyclip_1.10-0          farver_2.1.0            
 [22] parallelly_1.27.0        vctrs_0.3.8              generics_0.1.0          
 [25] R6_2.5.0                 doParallel_1.0.16        clue_0.3-59             
 [28] spatstat.utils_2.2-0     bitops_1.0-7             rhdf5filters_1.4.0      
 [31] DelayedArray_0.18.0      assertthat_0.2.1         promises_1.2.0.1        
 [34] BiocIO_1.2.0             scales_1.1.1             gtable_0.3.0            
 [37] Cairo_1.5-12.2           globals_0.14.0           goftest_1.2-2           
 [40] rlang_0.4.11             GlobalOptions_0.1.2      splines_4.1.0           
 [43] rstatix_0.7.0            lazyeval_0.2.2           spatstat.geom_2.2-2     
 [46] broom_0.7.9              reshape2_1.4.4           yaml_2.2.1              
 [49] abind_1.4-5              modelr_0.1.8             backports_1.2.1         
 [52] httpuv_1.6.2             tools_4.1.0              spatstat.core_2.3-0     
 [55] ellipsis_0.3.2           ggridges_0.5.3           Rcpp_1.0.7              
 [58] plyr_1.8.6               zlibbioc_1.38.0          RCurl_1.98-1.4          
 [61] rpart_4.1-15             deldir_0.2-10            pbapply_1.4-3           
 [64] GetoptLong_1.0.5         cowplot_1.1.1            zoo_1.8-9               
 [67] haven_2.4.3              ggrepel_0.9.1            cluster_2.1.2           
 [70] fs_1.5.0                 RSpectra_0.16-0          scattermore_0.7         
 [73] circlize_0.4.13          lmtest_0.9-38            reprex_2.0.1            
 [76] RANN_2.6.1               fitdistrplus_1.1-5       hms_1.1.0               
 [79] patchwork_1.1.1          mime_0.11                xtable_1.8-4            
 [82] XML_3.99-0.7             rio_0.5.27               readxl_1.3.1            
 [85] shape_1.4.6              compiler_4.1.0           KernSmooth_2.23-20      
 [88] crayon_1.4.1             htmltools_0.5.1.1        mgcv_1.8-36             
 [91] later_1.3.0              tzdb_0.1.2               lubridate_1.7.10        
 [94] DBI_1.1.1                dbplyr_2.1.1             MASS_7.3-54             
 [97] car_3.0-11               cli_3.0.1                igraph_1.2.6            
[100] pkgconfig_2.0.3          GenomicAlignments_1.28.0 foreign_0.8-81          
[103] spatstat.sparse_2.0-0    plotly_4.9.4.1           xml2_1.3.2              
[106] foreach_1.5.1            rvest_1.0.1              digest_0.6.27           
[109] sctransform_0.3.2        RcppAnnoy_0.0.19         spatstat.data_2.1-0     
[112] cellranger_1.1.0         leiden_0.3.9             uwot_0.1.10             
[115] restfulr_0.0.13          curl_4.3.2               gtools_3.9.2            
[118] shiny_1.6.0              Rsamtools_2.8.0          rjson_0.2.20            
[121] nlme_3.1-152             lifecycle_1.0.0          jsonlite_1.7.2          
[124] Rhdf5lib_1.14.2          carData_3.0-4            fansi_0.5.0             
[127] pillar_1.6.2             lattice_0.20-44          fastmap_1.1.0           
[130] httr_1.4.2               survival_3.2-12          glue_1.4.2              
[133] zip_2.2.0                png_0.1-7                iterators_1.0.13        
[136] stringi_1.7.3            irlba_2.3.3              future.apply_1.8.1    

[rcorces]

I have never seen this reported before. Seems very odd. Are you able to reproduce this on the tutorial dataset or in any other situation? I think I would try the dumb things like restarting your R session and perhaps reinstalling ArchR.

[grimmem1]

Thanks. I tried the dumb things before posting and can recreate the error with the PBMC data (below). Importantly, this happens on my local machine (R 4.1.0) as well as on a remote HPC (R 4.0.0):

> pathToMacs2 <- "/usr/local/anaconda3/bin/macs2" # local machine
> proj

           ___      .______        ______  __    __  .______      
          /   \     |   _  \      /      ||  |  |  | |   _  \     
         /  ^  \    |  |_)  |    |  ,----'|  |__|  | |  |_)  |    
        /  /_\  \   |      /     |  |     |   __   | |      /     
       /  _____  \  |  |\  \\___ |  `----.|  |  |  | |  |\  \\___.
      /__/     \__\ | _| `._____| \______||__|  |__| | _| `._____|
    
class: ArchRProject 
outputDirectory: /path/to/ArchROutput 
samples(1): PBMC_10k
sampleColData names(1): ArrowFiles
cellColData names(18): Sample TSSEnrichment ... Gex_RiboRatio Clusters
numberOfCells(1): 10939
medianTSS(1): 18.015
medianFrags(1): 12425
> proj.peaks <- addReproduciblePeakSet(
+   ArchRProj = proj,
+   groupBy = "Clusters",
+   peakMethod = "Macs2",
+   reproducibility = "2",
+   peaksPerCell = 500,
+   maxPeaks = 150000,
+   minCells = 25,
+   excludeChr = c("chrM", "chrY"),
+   #pathToMacs2 = if (tolower(peakMethod) == "Macs2") findMacs2() else NULL,
+   pathToMacs2 = pathToMacs2,
+   genomeSize = NULL,
+   shift = -75,
+   extsize = 150,
+   #method = if (tolower(peakMethod) == "Macs2") "q" else "p",
+   method = "p",
+   cutOff = 0.1,
+   additionalParams = "--nomodel --nolambda",
+   extendSummits = 250,
+   promoterRegion = c(2000, 100),
+   genomeAnnotation = getGenomeAnnotation(ArchRProj),
+   geneAnnotation = getGeneAnnotation(ArchRProj),
+   plot = TRUE,
+   threads = getArchRThreads(),
+   parallelParam = NULL,
+   force = TRUE,
+   verbose = TRUE,
+   logFile = createLogFile("addReproduciblePeakSet")
+ )
Error: object 'ArchRProj' not found

I haven't been able to attempt the same for the Hematopoiesis dataset because it is not found:

> inputFiles <- getTutorialData("Hematopoiesis")
> inputFiles
named character(0)

Other upstream functions that work fine, suggesting my v1.0.1 install is fine:
getInputFiles, ArchRProject, import10xFeatureMatrix, addGeneExpressionMatrix, addIterativeLSI, addCombinedDims, addUMAP, addClusters, plotEmbedding, addGroupCoverages

[rcorces]

I think this should be moved to an Issue instead of a Discussions post. Please create a post under Issues and make sure to show all of the code you use to reproduce this behavior using the tutorial PBMC data.