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GreenleafLab / ArchR

ArchR : Analysis of Regulatory Chromatin in R (www.ArchRProject.com)
MIT License
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Error occurs when running addReproduciblePeakSet() #492

Closed zhijunyuu closed 3 years ago

zhijunyuu commented 3 years ago

Attach your log file ArchR-addReproduciblePeakSet-ef5e40415715-Date-2021-01-14_Time-12-24-41.log

Describe the bug Hello ArchR people, many thanks for this nice tool. I meet the error when I use addReproduciblePeakSet() to call peaks:

HCA_pse <-addReproduciblePeakSet(
  ArchRProj = HCA_pse, 
  groupBy = "predictedGroup_Un", 
  pathToMacs2 = pathToMacs2
)

This is the error:

ArchR logging to : ArchRLogs/ArchR-addReproduciblePeakSet-ef5e40415715-Date-2021-01-14_Time-12-24-41.log
If there is an issue, please report to github with logFile!
2021-01-14 12:24:41 : Peak Calling Parameters!, 0.006 mins elapsed.
                            Group nCells nCellsUsed nReplicates nMin nMax maxPeaks
B cells                   B cells   9947       1500           3  500  500   150000
Epithelial cells Epithelial cells    393        379           2   41  338   150000
Mast cells             Mast cells    231        231           3   49   95   115500
Myeloids                 Myeloids    487        487           3  114  209   150000
Stromal cells       Stromal cells   2672       1500           3  500  500   150000
T cells                   T cells   5511       1500           3  500  500   150000
2021-01-14 12:24:41 : Batching Peak Calls!, 0.007 mins elapsed.
2021-01-14 12:24:41 : Batch Execution w/ safelapply!, 0 mins elapsed.
2021-01-14 12:24:41 : Group 1 of 17, Calling Peaks with MACS2!, 0 mins elapsed.
2021-01-14 12:24:59 : Group 2 of 17, Calling Peaks with MACS2!, 0.297 mins elapsed.
2021-01-14 12:25:56 : Group 3 of 17, Calling Peaks with MACS2!, 1.241 mins elapsed.
2021-01-14 12:27:06 : Group 4 of 17, Calling Peaks with MACS2!, 2.42 mins elapsed.
2021-01-14 12:28:07 : Group 5 of 17, Calling Peaks with MACS2!, 3.437 mins elapsed.
2021-01-14 12:29:16 : Group 6 of 17, Calling Peaks with MACS2!, 4.577 mins elapsed.
2021-01-14 12:29:41 : Group 7 of 17, Calling Peaks with MACS2!, 4.994 mins elapsed.
2021-01-14 12:30:21 : Group 8 of 17, Calling Peaks with MACS2!, 5.663 mins elapsed.
2021-01-14 12:31:45 : Group 9 of 17, Calling Peaks with MACS2!, 7.068 mins elapsed.
2021-01-14 12:32:57 : Group 10 of 17, Calling Peaks with MACS2!, 8.266 mins elapsed.
2021-01-14 12:33:35 : Group 11 of 17, Calling Peaks with MACS2!, 8.903 mins elapsed.
2021-01-14 12:34:00 : Group 12 of 17, Calling Peaks with MACS2!, 9.316 mins elapsed.
2021-01-14 12:34:55 : Group 13 of 17, Calling Peaks with MACS2!, 10.232 mins elapsed.
2021-01-14 12:35:09 : Group 14 of 17, Calling Peaks with MACS2!, 10.467 mins elapsed.
2021-01-14 12:35:27 : Group 15 of 17, Calling Peaks with MACS2!, 10.76 mins elapsed.
2021-01-14 12:36:14 : Group 16 of 17, Calling Peaks with MACS2!, 11.553 mins elapsed.
2021-01-14 12:36:27 : Group 17 of 17, Calling Peaks with MACS2!, 11.77 mins elapsed.
2021-01-14 12:37:28 : Identifying Reproducible Peaks!, 12.783 mins elapsed.

************************************************************
2021-01-14 12:37:28 : ERROR Found in .identifyReproduciblePeaks for Rep. Peaks Group (1 of 6) : 
LogFile = ArchRLogs/ArchR-addReproduciblePeakSet-ef5e40415715-Date-2021-01-14_Time-12-24-41.log

<simpleError in `[[<-`(`*tmp*`, name, value = "B cells._.223"): 1 elements in value to replace 0 elements>

************************************************************

Error in .logError(e, fn = ".identifyReproduciblePeaks", info = prefix,  : 
  Exiting See Error Above
In addition: Warning messages:
1: In data.table::fread(summitsFile, select = c(1, 2, 3, 5)) :
  File '/hpc/pmc_stunnenberg/Zhijun/projects/202101/12/ArchR_output/PeakCalls/InsertionBeds/B.cells._.223-1_summits.bed' has size 0. Returning a NULL data.table.
2: In data.table::fread(summitsFile, select = c(1, 2, 3, 5)) :
  File '/hpc/pmc_stunnenberg/Zhijun/projects/202101/12/ArchR_output/PeakCalls/InsertionBeds/Stromal.cells._.176-13_summits.bed' has size 0. Returning a NULL data.table.
3: In data.table::fread(summitsFile, select = c(1, 2, 3, 5)) :
  File '/hpc/pmc_stunnenberg/Zhijun/projects/202101/12/ArchR_output/PeakCalls/InsertionBeds/Stromal.cells._.223-14_summits.bed' has size 0. Returning a NULL data.table.
4: In data.table::fread(summitsFile, select = c(1, 2, 3, 5)) :
  File '/hpc/pmc_stunnenberg/Zhijun/projects/202101/12/ArchR_output/PeakCalls/InsertionBeds/T.cells._.223-16_summits.bed' has size 0. Returning a NULL data.table.

Expected behavior I am not sure how to solve the issue, whether it's related to the version of R.

Session Info

R version 4.0.3 (2020-10-10)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Debian GNU/Linux 10 (buster)

Matrix products: default
BLAS:   /usr/lib/x86_64-linux-gnu/atlas/libblas.so.3.10.3
LAPACK: /usr/lib/x86_64-linux-gnu/atlas/liblapack.so.3.10.3

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C               LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8     LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8    LC_PAPER=en_US.UTF-8      
 [8] LC_NAME=C                  LC_ADDRESS=C               LC_TELEPHONE=C             LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

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

other attached packages:
 [1] BSgenome.Hsapiens.UCSC.hg38_1.4.3 BSgenome_1.58.0                   rtracklayer_1.50.0                Biostrings_2.58.0                 XVector_0.30.0                   
 [6] presto_1.0.0                      Rcpp_1.0.5                        SeuratDisk_0.0.0.9013             Seurat_3.9.9.9026                 ArchR_1.0.0                      
[11] magrittr_2.0.1                    rhdf5_2.34.0                      data.table_1.13.6                 DelayedArray_0.16.0               Matrix_1.2-18                    
[16] SummarizedExperiment_1.20.0       Biobase_2.50.0                    GenomicRanges_1.42.0              GenomeInfoDb_1.26.2               IRanges_2.24.1                   
[21] S4Vectors_0.28.1                  BiocGenerics_0.36.0               MatrixGenerics_1.2.0              matrixStats_0.57.0                ggplot2_3.3.3                    

loaded via a namespace (and not attached):
  [1] plyr_1.8.6               igraph_1.2.6             lazyeval_0.2.2           splines_4.0.3            BiocParallel_1.24.1      listenv_0.8.0            scattermore_0.7         
  [8] usethis_1.6.3            digest_0.6.27            htmltools_0.5.1          fansi_0.4.1              memoise_1.1.0            tensor_1.5               cluster_2.1.0           
 [15] ROCR_1.0-11              remotes_2.2.0            globals_0.14.0           prettyunits_1.1.1        colorspace_2.0-0         ggrepel_0.9.0            dplyr_1.0.2             
 [22] callr_3.5.1              crayon_1.3.4             RCurl_1.98-1.2           jsonlite_1.7.2           spatstat_1.64-1          spatstat.data_1.7-0      survival_3.2-7          
 [29] zoo_1.8-8                glue_1.4.2               polyclip_1.10-0          gtable_0.3.0             zlibbioc_1.36.0          leiden_0.3.6             pkgbuild_1.2.0          
 [36] Rhdf5lib_1.12.0          future.apply_1.7.0       abind_1.4-5              scales_1.1.1             miniUI_0.1.1.1           viridisLite_0.3.0        xtable_1.8-4            
 [43] reticulate_1.18          bit_4.0.4                rsvd_1.0.3               htmlwidgets_1.5.3        httr_1.4.2               RColorBrewer_1.1-2       ellipsis_0.3.1          
 [50] ica_1.0-2                pkgconfig_2.0.3          XML_3.99-0.5             farver_2.0.3             uwot_0.1.10              deldir_0.2-3             tidyselect_1.1.0        
 [57] labeling_0.4.2           rlang_0.4.10             reshape2_1.4.4           later_1.1.0.1            munsell_0.5.0            tools_4.0.3              cli_2.2.0               
 [64] generics_0.1.0           devtools_2.3.2           ggridges_0.5.3           stringr_1.4.0            fastmap_1.0.1            goftest_1.2-2            fs_1.5.0                
 [71] processx_3.4.5           bit64_4.0.5              fitdistrplus_1.1-3       purrr_0.3.4              RANN_2.6.1               pbapply_1.4-3            future_1.21.0           
 [78] nlme_3.1-150             mime_0.9                 hdf5r_1.3.3              compiler_4.0.3           rstudioapi_0.13          curl_4.3                 plotly_4.9.3            
 [85] png_0.1-7                testthat_3.0.1           spatstat.utils_1.20-2    tibble_3.0.4             stringi_1.5.3            ps_1.5.0                 desc_1.2.0              
 [92] lattice_0.20-41          vctrs_0.3.6              pillar_1.4.7             lifecycle_0.2.0          rhdf5filters_1.2.0       BiocManager_1.30.10      lmtest_0.9-38           
 [99] RcppAnnoy_0.0.18         cowplot_1.1.1            bitops_1.0-6             irlba_2.3.3              httpuv_1.5.4             patchwork_1.1.0.9000     R6_2.5.0                
[106] promises_1.1.1           KernSmooth_2.23-18       gridExtra_2.3            parallelly_1.23.0        sessioninfo_1.1.1        codetools_0.2-18         pkgload_1.1.0           
[113] MASS_7.3-53              gtools_3.8.2             assertthat_0.2.1         rprojroot_2.0.2          withr_2.3.0              GenomicAlignments_1.26.0 sctransform_0.3.2       
[120] Rsamtools_2.6.0          GenomeInfoDbData_1.2.4   mgcv_1.8-33              grid_4.0.3               rpart_4.1-15             tidyr_1.1.2              Cairo_1.5-12.2          
[127] Rtsne_0.15               shiny_1.5.0
rcorces commented 3 years ago

I'm not sure about this one. I thought we had fixed this but maybe it has something to do with including spaces in your group names?

Can you confirm that the tutorial code and data work on your setup for addReproduciblePeakSet()

Are there files in this directory and do they have anything in them? /hpc/pmc_stunnenberg/Zhijun/projects/202101/12/ArchR_output/PeakCalls/ReplicateCalls/

zhijunyuu commented 3 years ago

Thanks for the quick reply. I was also wondering the space maybe the problem, I will use the removed one for a try.

I am running the tutorial now, but meet the error in addUMAP which I didn't meet when running my own data, that's a bit weird.

> projHeme2 <- addUMAP(
+   ArchRProj = projHeme2, 
+   reducedDims = "IterativeLSI", 
+   name = "UMAP", 
+   nNeighbors = 30, 
+   minDist = 0.5, 
+   metric = "cosine"
+ )
16:27:10 UMAP embedding parameters a = 0.583 b = 1.334
16:27:10 Read 10251 rows and found 30 numeric columns
16:27:10 Using Annoy for neighbor search, n_neighbors = 30
16:27:10 Building Annoy index with metric = cosine, n_trees = 50
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
16:27:12 Writing NN index file to temp file /tmp/RtmpfcmBHI/fileef5e3938b10b
16:27:12 Searching Annoy index using 36 threads, search_k = 3000
16:27:14 Annoy recall = 100%
16:27:16 Commencing smooth kNN distance calibration using 36 threads
16:27:18 Initializing from normalized Laplacian + noise
16:27:18 Commencing optimization for 200 epochs, with 468490 positive edges
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
16:27:25 Optimization finished
Error in model$nn_index$save(nn_tmpfname) : attempt to apply non-function

There are files in this directory and they do have something in them

(base) [zyu@hpcs04 ReplicateCalls]$ pwd
/hpc/pmc_stunnenberg/Zhijun/projects/202101/12/ArchR_output/PeakCalls/ReplicateCalls
(base) [zyu@hpcs04 ReplicateCalls]$ ls -l
total 10273
-rw-r--r--. 1 zyu pmc_research 530850 Jan 14 12:25 B.cells._.176-summits.rds
-rw-r--r--. 1 zyu pmc_research 645082 Jan 14 12:27 B.cells._.183-summits.rds
-rw-r--r--. 1 zyu pmc_research    422 Jan 14 12:24 B.cells._.223-summits.rds
-rw-r--r--. 1 zyu pmc_research 636362 Jan 14 12:29 Epithelial.cells._.176-summits.rds
-rw-r--r--. 1 zyu pmc_research 515800 Jan 14 12:28 Epithelial.cells._.223-summits.rds
-rw-r--r--. 1 zyu pmc_research 795099 Jan 14 12:31 Mast.cells._.176-summits.rds
-rw-r--r--. 1 zyu pmc_research 211979 Jan 14 12:29 Mast.cells._.183-summits.rds
-rw-r--r--. 1 zyu pmc_research 349497 Jan 14 12:30 Mast.cells._.223-summits.rds
-rw-r--r--. 1 zyu pmc_research 336941 Jan 14 12:33 Myeloids._.176-summits.rds
-rw-r--r--. 1 zyu pmc_research 215038 Jan 14 12:34 Myeloids._.183-summits.rds
-rw-r--r--. 1 zyu pmc_research 675746 Jan 14 12:32 Myeloids._.223-summits.rds
-rw-r--r--. 1 zyu pmc_research    422 Jan 14 12:35 Stromal.cells._.176-summits.rds
-rw-r--r--. 1 zyu pmc_research 455723 Jan 14 12:34 Stromal.cells._.183-summits.rds
-rw-r--r--. 1 zyu pmc_research    422 Jan 14 12:35 Stromal.cells._.223-summits.rds
-rw-r--r--. 1 zyu pmc_research 432845 Jan 14 12:36 T.cells._.176-summits.rds
-rw-r--r--. 1 zyu pmc_research 560363 Jan 14 12:37 T.cells._.183-summits.rds
-rw-r--r--. 1 zyu pmc_research    422 Jan 14 12:36 T.cells._.223-summits.rds
rcorces commented 3 years ago

This was addressed in #424 Its caused by a change in the more recent versions of uwot. You can either downgrade your uwot install or upgrade your ArchR install to the development release 1.0.1

devtools::install_github("GreenleafLab/ArchR", ref="release_1.0.1", repos = BiocManager::repositories())

zhijunyuu commented 3 years ago

I upgraded ArchR to 1.0.1

And I tried the tutorial code, but I got the same error:

> projHeme4 <- addReproduciblePeakSet(
+   ArchRProj = projHeme4, 
+   groupBy = "Clusters2", 
+   pathToMacs2 = pathToMacs2
+ )
ArchR logging to : ArchRLogs/ArchR-addReproduciblePeakSet-176932a95a523-Date-2021-01-18_Time-14-35-13.log
If there is an issue, please report to github with logFile!
2021-01-18 14:35:14 : Peak Calling Parameters!, 0.012 mins elapsed.
                Group nCells nCellsUsed nReplicates nMin nMax maxPeaks
B                   B    421        416           2  164  252   150000
CD4.M           CD4.M    566        565           2   79  486   150000
CD4.N           CD4.N   1277        540           2   40  500   150000
CLP               CLP    396        396           2   92  304   150000
Erythroid   Erythroid    876        718           2  218  500   150000
GMP               GMP   1211        882           2  382  500   150000
Mono             Mono   2517       1000           2  500  500   150000
NK                 NK    954        806           2  306  500   150000
pDC               pDC    290        280           2  134  146   140000
PreB             PreB    349        349           2   40  309   150000
Progenitor Progenitor   1393        642           2  142  500   150000
2021-01-18 14:35:14 : Batching Peak Calls!, 0.012 mins elapsed.
2021-01-18 14:35:14 : Batch Execution w/ safelapply!, 0 mins elapsed.
2021-01-18 14:35:14 : Group 1 of 22, Calling Peaks with MACS2!, 0 mins elapsed.
2021-01-18 14:36:08 : Group 2 of 22, Calling Peaks with MACS2!, 0.896 mins elapsed.
2021-01-18 14:36:55 : Group 3 of 22, Calling Peaks with MACS2!, 1.682 mins elapsed.
2021-01-18 14:37:17 : Group 4 of 22, Calling Peaks with MACS2!, 2.046 mins elapsed.
2021-01-18 14:39:32 : Group 5 of 22, Calling Peaks with MACS2!, 4.291 mins elapsed.
2021-01-18 14:40:38 : Group 6 of 22, Calling Peaks with MACS2!, 5.399 mins elapsed.
2021-01-18 14:41:33 : Group 7 of 22, Calling Peaks with MACS2!, 6.321 mins elapsed.
2021-01-18 14:42:43 : Group 8 of 22, Calling Peaks with MACS2!, 7.477 mins elapsed.
2021-01-18 14:45:07 : Group 9 of 22, Calling Peaks with MACS2!, 9.882 mins elapsed.
2021-01-18 14:45:27 : Group 10 of 22, Calling Peaks with MACS2!, 10.217 mins elapsed.
2021-01-18 14:46:20 : Group 11 of 22, Calling Peaks with MACS2!, 11.105 mins elapsed.
2021-01-18 14:48:39 : Group 12 of 22, Calling Peaks with MACS2!, 13.422 mins elapsed.
2021-01-18 14:49:01 : Group 13 of 22, Calling Peaks with MACS2!, 13.788 mins elapsed.
2021-01-18 14:50:44 : Group 14 of 22, Calling Peaks with MACS2!, 15.497 mins elapsed.
2021-01-18 14:52:07 : Group 15 of 22, Calling Peaks with MACS2!, 16.878 mins elapsed.
2021-01-18 14:53:37 : Group 16 of 22, Calling Peaks with MACS2!, 18.389 mins elapsed.
2021-01-18 14:54:33 : Group 17 of 22, Calling Peaks with MACS2!, 19.323 mins elapsed.
2021-01-18 14:55:21 : Group 18 of 22, Calling Peaks with MACS2!, 20.112 mins elapsed.
2021-01-18 14:56:08 : Group 19 of 22, Calling Peaks with MACS2!, 20.898 mins elapsed.
2021-01-18 14:57:14 : Group 20 of 22, Calling Peaks with MACS2!, 22.001 mins elapsed.
2021-01-18 14:58:46 : Group 21 of 22, Calling Peaks with MACS2!, 23.529 mins elapsed.
2021-01-18 15:00:51 : Group 22 of 22, Calling Peaks with MACS2!, 25.61 mins elapsed.
2021-01-18 15:01:21 : Identifying Reproducible Peaks!, 26.128 mins elapsed.
[1] "/hpc/pmc_stunnenberg/Zhijun/projects/202101/18/HemeTutorial/PeakCalls/B-reproduciblePeaks.gr.rds"

************************************************************
2021-01-18 15:01:27 : ERROR Found in .identifyReproduciblePeaks for Rep. Peaks Group (2 of 11) : 
LogFile = ArchRLogs/ArchR-addReproduciblePeakSet-176932a95a523-Date-2021-01-18_Time-14-35-13.log

<simpleError in `[[<-`(`*tmp*`, name, value = "CD4.M._.scATAC_PBMC_R1"): 1 elements in value to replace 0 elements>

************************************************************

Error in .logError(e, fn = ".identifyReproduciblePeaks", info = prefix,  : 
  Exiting See Error Above
In addition: Warning messages:
1: In data.table::fread(summitsFile, select = c(1, 2, 3, 5)) :
  File '/hpc/pmc_stunnenberg/Zhijun/projects/202101/18/HemeTutorial/PeakCalls/InsertionBeds/CD4.M._.scATAC_PBMC_R1-3_summits.bed' has size 0. Returning a NULL data.table.
2: In data.table::fread(summitsFile, select = c(1, 2, 3, 5)) :
  File '/hpc/pmc_stunnenberg/Zhijun/projects/202101/18/HemeTutorial/PeakCalls/InsertionBeds/Erythroid._.scATAC_CD34_BMMC_R1-9_summits.bed' has size 0. Returning a NULL data.table.
3: In data.table::fread(summitsFile, select = c(1, 2, 3, 5)) :
  File '/hpc/pmc_stunnenberg/Zhijun/projects/202101/18/HemeTutorial/PeakCalls/InsertionBeds/GMP._.scATAC_BMMC_R1-12_summits.bed' has size 0. Returning a NULL data.table.

Seems it's not the problem of the spaces in the cluster names, but some systematic problems.

Log file:

ArchR-addReproduciblePeakSet-176932a95a523-Date-2021-01-18_Time-14-35-13.log

Session information 

R version 4.0.3 (2020-10-10)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Debian GNU/Linux 10 (buster)

Matrix products: default
BLAS:   /usr/lib/x86_64-linux-gnu/atlas/libblas.so.3.10.3
LAPACK: /usr/lib/x86_64-linux-gnu/atlas/liblapack.so.3.10.3

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C               LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8     LC_MONETARY=en_US.UTF-8   
 [6] LC_MESSAGES=en_US.UTF-8    LC_PAPER=en_US.UTF-8       LC_NAME=C                  LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

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

other attached packages:
 [1] BSgenome.Hsapiens.UCSC.hg19_1.4.3 BSgenome_1.58.0                   rtracklayer_1.50.0                Biostrings_2.58.0                
 [5] XVector_0.30.0                    gtable_0.3.0                      circlize_0.4.12                   ComplexHeatmap_2.7.4             
 [9] harmony_1.0                       gridExtra_2.3                     uwot_0.1.10                       nabor_0.5.0                      
[13] presto_1.0.0                      Rcpp_1.0.5                        SeuratDisk_0.0.0.9013             Seurat_3.9.9.9027                
[17] ArchR_1.0.1                       magrittr_2.0.1                    rhdf5_2.34.0                      data.table_1.13.6                
[21] DelayedArray_0.16.0               Matrix_1.2-18                     SummarizedExperiment_1.20.0       Biobase_2.50.0                   
[25] GenomicRanges_1.42.0              GenomeInfoDb_1.26.2               IRanges_2.24.1                    S4Vectors_0.28.1                 
[29] BiocGenerics_0.36.0               MatrixGenerics_1.2.0              matrixStats_0.57.0                ggplot2_3.3.3                    

loaded via a namespace (and not attached):
  [1] plyr_1.8.6               igraph_1.2.6             lazyeval_0.2.2           splines_4.0.3            BiocParallel_1.24.1     
  [6] listenv_0.8.0            scattermore_0.7          digest_0.6.27            htmltools_0.5.1          magick_2.5.2            
 [11] fansi_0.4.1              tensor_1.5               cluster_2.1.0            ROCR_1.0-11              globals_0.14.0          
 [16] colorspace_2.0-0         ggrepel_0.9.0            dplyr_1.0.2              crayon_1.3.4             RCurl_1.98-1.2          
 [21] jsonlite_1.7.2           spatstat_1.64-1          spatstat.data_1.7-0      survival_3.2-7           zoo_1.8-8               
 [26] glue_1.4.2               polyclip_1.10-0          zlibbioc_1.36.0          leiden_0.3.6             GetoptLong_1.0.5        
 [31] Rhdf5lib_1.12.0          future.apply_1.7.0       shape_1.4.5              abind_1.4-5              scales_1.1.1            
 [36] miniUI_0.1.1.1           viridisLite_0.3.0        xtable_1.8-4             clue_0.3-58              reticulate_1.18         
 [41] bit_4.0.4                rsvd_1.0.3               htmlwidgets_1.5.3        httr_1.4.2               RColorBrewer_1.1-2      
 [46] ellipsis_0.3.1           ica_1.0-2                farver_2.0.3             XML_3.99-0.5             pkgconfig_2.0.3         
 [51] deldir_0.2-3             labeling_0.4.2           tidyselect_1.1.0         rlang_0.4.10             reshape2_1.4.4          
 [56] later_1.1.0.1            munsell_0.5.0            tools_4.0.3              cli_2.2.0                generics_0.1.0          
 [61] ggridges_0.5.3           stringr_1.4.0            fastmap_1.0.1            goftest_1.2-2            bit64_4.0.5             
 [66] fitdistrplus_1.1-3       purrr_0.3.4              RANN_2.6.1               pbapply_1.4-3            future_1.21.0           
 [71] nlme_3.1-150             mime_0.9                 hdf5r_1.3.3              compiler_4.0.3           rstudioapi_0.13         
 [76] plotly_4.9.3             png_0.1-7                spatstat.utils_1.20-2    tibble_3.0.4             stringi_1.5.3           
 [81] RSpectra_0.16-0          lattice_0.20-41          vctrs_0.3.6              pillar_1.4.7             lifecycle_0.2.0         
 [86] rhdf5filters_1.2.0       lmtest_0.9-38            GlobalOptions_0.1.2      RcppAnnoy_0.0.18         cowplot_1.1.1           
 [91] bitops_1.0-6             irlba_2.3.3              httpuv_1.5.5             patchwork_1.1.0.9000     R6_2.5.0                
 [96] promises_1.1.1           KernSmooth_2.23-18       parallelly_1.23.0        codetools_0.2-18         gtools_3.8.2            
[101] MASS_7.3-53              assertthat_0.2.1         rjson_0.2.20             withr_2.3.0              GenomicAlignments_1.26.0
[106] sctransform_0.3.2        Rsamtools_2.6.0          GenomeInfoDbData_1.2.4   mgcv_1.8-33              rpart_4.1-15            
[111] tidyr_1.1.2              Cairo_1.5-12.2           Rtsne_0.15               shiny_1.5.0
rcorces commented 3 years ago

what version of macs2 are you running? /hpc/pmc_stunnenberg/Zhijun/miniconda3/bin/macs2 --version

zhijunyuu commented 3 years ago

it's macs2 2.2.7.1

rcorces commented 3 years ago

ok thats definitely not the problem then. Sorry - I'm not sure what is the problem but hopefully we can figure it out. are there any files in this folder after the error? /hpc/pmc_stunnenberg/Zhijun/projects/202101/18/HemeTutorial/PeakCalls/InsertionBeds/

zhijunyuu commented 3 years ago

No, I don't have any files in that folder after the error.

rcorces commented 3 years ago

have you run addGroupCoverages()? This is a prerequisite for peak calling

zhijunyuu commented 3 years ago

Yes, that's making Pseudo-bulk Replicates step.

rcorces commented 3 years ago

Maybe @jgranja24 has thoughts?

zhijunyuu commented 3 years ago

The problem solved, it's not a bug from ArchR. It's because the singularity and macs2 I used were not under the same environment.

NinaJiangL commented 3 years ago

hi I am having the similar problem with addReproduciblePeakSet. I am using "Tiles" for peaks calling instead of using findMacs2 as I am running ArchR on a window-base system (can not install Masc2) I am running the tutorial file and code : projHemeTmp <- addReproduciblePeakSet( ArchRProj = projHeme4, groupBy = "Clusters2", peakMethod = "Tiles", method = "p" ) but the error occurs: ArchR logging to : ArchRLogs\ArchR-addReproduciblePeakSet-447425335ffa-Date-2021-01-22_Time-10-57-17.log If there is an issue, please report to github with logFile! Group Coverages Already Computed Returning Groups, Set force = TRUE to Recompute! List of length 11 names(11): B CD4.M CD4.N CLP Erythroid GMP Mono NK pDC PreB Progenitor 2021-01-22 10:57:18 : Peak Calling Parameters!, 0.019 mins elapsed. Group nCells nCellsUsed nReplicates nMin nMax maxPeaks B B 446 440 2 171 269 150000 CD4.M CD4.M 642 604 2 104 500 150000 CD4.N CD4.N 1286 549 2 49 500 150000 CLP CLP 317 317 2 40 277 150000 Erythroid Erythroid 891 731 2 231 500 150000 GMP GMP 1078 800 2 300 500 150000 Mono Mono 2604 1000 2 500 500 150000 NK NK 1117 971 2 471 500 150000 pDC pDC 289 280 2 124 156 140000 PreB PreB 436 436 2 40 396 150000 Progenitor Progenitor 1555 645 2 145 500 150000 2021-01-22 10:57:30 : Computing Total Accessibility Across All Features, 0.22 mins elapsed. 2021-01-22 10:57:35 : Computing Pseudo-Grouped Tile Matrix, 0.316 mins elapsed. 2021-01-22 10:58:57 : Created Pseudo-Grouped Tile Matrix (0.484 GB), 1.678 mins elapsed. 2021-01-22 10:58:58 : Computing Peaks from Tile Matrix Group (1 of 11), 1.685 mins elapsed. 2021-01-22 10:59:19 : Computing Peaks from Tile Matrix Group (2 of 11), 2.045 mins elapsed. 2021-01-22 10:59:23 : Computing Peaks from Tile Matrix Group (3 of 11), 2.111 mins elapsed. 2021-01-22 10:59:27 : Computing Peaks from Tile Matrix Group (4 of 11), 2.173 mins elapsed. 2021-01-22 10:59:31 : Computing Peaks from Tile Matrix Group (5 of 11), 2.237 mins elapsed. 2021-01-22 10:59:35 : Computing Peaks from Tile Matrix Group (6 of 11), 2.309 mins elapsed. 2021-01-22 10:59:40 : Computing Peaks from Tile Matrix Group (7 of 11), 2.389 mins elapsed. 2021-01-22 10:59:44 : Computing Peaks from Tile Matrix Group (8 of 11), 2.463 mins elapsed. 2021-01-22 10:59:49 : Computing Peaks from Tile Matrix Group (9 of 11), 2.54 mins elapsed. 2021-01-22 10:59:53 : Computing Peaks from Tile Matrix Group (10 of 11), 2.604 mins elapsed. 2021-01-22 10:59:57 : Computing Peaks from Tile Matrix Group (11 of 11), 2.669 mins elapsed. 2021-01-22 11:00:02 : Creating Group Peak Sets with Annotations!, 2.763 mins elapsed. Error in gzfile(file, mode) : cannot open the connection In addition: Warning message: In gzfile(file, mode) : cannot open compressed file 'C:\Users\A\Documents\HemeTutorial/PeakCalls/B-reproduciblePeaks.gr.rds', probable reason 'No such file or directory'

There has no PeakCalls file in my path , so I am wondering where can I get the "B-reproduciblePeaks.gr.rds" file , do I need to re-download it ? is there any possible to use "Tiles" with R on window's system?

rcorces commented 3 years ago

@zhijunyuu - glad this is solved. my original intuition was that there was a problem with macs2 so that makes sense to me. Thanks for letting us know

@NinaJiangL - sorry but we arent currently supporting windows. There are too many bugs and not a large enough user base for this to be a priority at the moment. I'll make this more clear on the website in a future update.

yding9 commented 3 years ago

@zhijunyuu Hi, can you share how you solve this issue? I meet the similar problem but I guess ArchR and macs2 are in the same environment?

@rcorces Sorry I tried several methods to install macs2 but I always see the following bugs. My InsertionBeds folder is empty; The ReplicateCalls folder has several rds objects with size of 1 KB. And those 1 KB rds objects are causing troubles:

ArchR logging to : ArchRLogs/ArchR-addReproduciblePeakSet-349d8b90c77-Date-2021-02-08_Time-22-07-37.log If there is an issue, please report to github with logFile! 2021-02-08 22:07:39 : Peak Calling Parameters!, 0.03 mins elapsed. Group nCells nCellsUsed nReplicates nMin nMax maxPeaks C1 C1 648 648 2 214 434 150000 C2 C2 113 113 2 49 64 56500 C3 C3 427 427 2 178 249 150000 C4 C4 346 346 2 148 198 150000 C5 C5 166 166 2 72 94 83000 C6 C6 1254 985 2 485 500 150000 C7 C7 224 224 2 108 116 112000 C8 C8 978 789 2 289 500 150000 C9 C9 1172 1000 2 500 500 150000 C10 C10 738 738 2 337 401 150000 C11 C11 1452 1000 2 500 500 150000 C12 C12 230 230 2 40 190 115000 C13 C13 410 410 2 127 283 150000 C14 C14 656 656 2 258 398 150000 C15 C15 3270 540 2 40 500 150000 C16 C16 414 414 2 40 374 150000 C17 C17 239 239 2 40 199 119500 C18 C18 356 356 2 59 297 150000 C19 C19 1749 1000 2 500 500 150000 C20 C20 476 476 2 230 246 150000 C21 C21 2471 611 2 111 500 150000 C22 C22 999 644 2 144 500 150000 C23 C23 263 263 2 40 223 131500 C24 C24 1056 540 2 40 500 150000 C25 C25 250 250 2 40 210 125000 2021-02-08 22:07:39 : Batching Peak Calls!, 0.031 mins elapsed. 2021-02-08 22:07:39 : Batch Execution w/ safelapply!, 0 mins elapsed. 2021-02-08 22:07:39 : Group 1 of 50, Calling Peaks with MACS2!, 0.001 mins elapsed. 2021-02-08 22:07:39 : Group 2 of 50, Calling Peaks with MACS2!, 0.001 mins elapsed. 2021-02-08 22:07:39 : Group 3 of 50, Calling Peaks with MACS2!, 0.002 mins elapsed. 2021-02-08 22:07:39 : Group 4 of 50, Calling Peaks with MACS2!, 0.002 mins elapsed. 2021-02-08 22:07:39 : Group 5 of 50, Calling Peaks with MACS2!, 0.002 mins elapsed. 2021-02-08 22:07:39 : Group 6 of 50, Calling Peaks with MACS2!, 0.003 mins elapsed. 2021-02-08 22:07:39 : Group 7 of 50, Calling Peaks with MACS2!, 0.003 mins elapsed. 2021-02-08 22:07:40 : Group 8 of 50, Calling Peaks with MACS2!, 0.004 mins elapsed. 2021-02-08 22:07:40 : Group 9 of 50, Calling Peaks with MACS2!, 0.004 mins elapsed. 2021-02-08 22:07:40 : Group 10 of 50, Calling Peaks with MACS2!, 0.005 mins elapsed. 2021-02-08 22:07:40 : Group 11 of 50, Calling Peaks with MACS2!, 0.005 mins elapsed. 2021-02-08 22:07:40 : Group 12 of 50, Calling Peaks with MACS2!, 0.005 mins elapsed. 2021-02-08 22:07:40 : Group 13 of 50, Calling Peaks with MACS2!, 0.006 mins elapsed. 2021-02-08 22:07:40 : Group 14 of 50, Calling Peaks with MACS2!, 0.006 mins elapsed. 2021-02-08 22:07:40 : Group 15 of 50, Calling Peaks with MACS2!, 0.007 mins elapsed. 2021-02-08 22:07:40 : Group 16 of 50, Calling Peaks with MACS2!, 0.007 mins elapsed. 2021-02-08 22:12:08 : Group 17 of 50, Calling Peaks with MACS2!, 4.473 mins elapsed. 2021-02-08 22:12:35 : Group 18 of 50, Calling Peaks with MACS2!, 4.928 mins elapsed. 2021-02-08 22:12:43 : Group 19 of 50, Calling Peaks with MACS2!, 5.064 mins elapsed. 2021-02-08 22:13:20 : Group 20 of 50, Calling Peaks with MACS2!, 5.677 mins elapsed. 2021-02-08 22:13:25 : Group 21 of 50, Calling Peaks with MACS2!, 5.762 mins elapsed. 2021-02-08 22:13:37 : Group 22 of 50, Calling Peaks with MACS2!, 5.966 mins elapsed. 2021-02-08 22:13:38 : Group 23 of 50, Calling Peaks with MACS2!, 5.973 mins elapsed. 2021-02-08 22:13:49 : Group 24 of 50, Calling Peaks with MACS2!, 6.158 mins elapsed. 2021-02-08 22:13:52 : Group 25 of 50, Calling Peaks with MACS2!, 6.214 mins elapsed. 2021-02-08 22:13:52 : Group 26 of 50, Calling Peaks with MACS2!, 6.215 mins elapsed. 2021-02-08 22:14:12 : Group 27 of 50, Calling Peaks with MACS2!, 6.553 mins elapsed. 2021-02-08 22:14:30 : Group 28 of 50, Calling Peaks with MACS2!, 6.85 mins elapsed. 2021-02-08 22:15:03 : Group 29 of 50, Calling Peaks with MACS2!, 7.397 mins elapsed. 2021-02-08 22:17:13 : Group 30 of 50, Calling Peaks with MACS2!, 9.566 mins elapsed. 2021-02-08 22:18:17 : Group 31 of 50, Calling Peaks with MACS2!, 10.631 mins elapsed. 2021-02-08 22:18:41 : Group 32 of 50, Calling Peaks with MACS2!, 11.032 mins elapsed. 2021-02-08 22:20:01 : Group 33 of 50, Calling Peaks with MACS2!, 12.369 mins elapsed. 2021-02-08 22:22:18 : Group 34 of 50, Calling Peaks with MACS2!, 14.643 mins elapsed. 2021-02-08 22:22:47 : Group 35 of 50, Calling Peaks with MACS2!, 15.128 mins elapsed. 2021-02-08 22:22:57 : Group 36 of 50, Calling Peaks with MACS2!, 15.292 mins elapsed. 2021-02-08 22:23:04 : Group 37 of 50, Calling Peaks with MACS2!, 15.413 mins elapsed. 2021-02-08 22:24:02 : Group 38 of 50, Calling Peaks with MACS2!, 16.384 mins elapsed. 2021-02-08 22:25:35 : Group 39 of 50, Calling Peaks with MACS2!, 17.921 mins elapsed. 2021-02-08 22:25:47 : Group 40 of 50, Calling Peaks with MACS2!, 18.121 mins elapsed. 2021-02-08 22:25:51 : Group 41 of 50, Calling Peaks with MACS2!, 18.191 mins elapsed. 2021-02-08 22:26:05 : Group 42 of 50, Calling Peaks with MACS2!, 18.429 mins elapsed. 2021-02-08 22:26:13 : Group 43 of 50, Calling Peaks with MACS2!, 18.568 mins elapsed. 2021-02-08 22:26:28 : Group 44 of 50, Calling Peaks with MACS2!, 18.808 mins elapsed. 2021-02-08 22:27:16 : Group 45 of 50, Calling Peaks with MACS2!, 19.62 mins elapsed. 2021-02-08 22:27:28 : Group 46 of 50, Calling Peaks with MACS2!, 19.806 mins elapsed. 2021-02-08 22:27:30 : Group 47 of 50, Calling Peaks with MACS2!, 19.838 mins elapsed. 2021-02-08 22:27:46 : Group 48 of 50, Calling Peaks with MACS2!, 20.112 mins elapsed. 2021-02-08 22:27:54 : Group 49 of 50, Calling Peaks with MACS2!, 20.245 mins elapsed. 2021-02-08 22:29:05 : Group 50 of 50, Calling Peaks with MACS2!, 21.434 mins elapsed. 2021-02-08 22:36:55 : Identifying Reproducible Peaks!, 29.299 mins elapsed. [1] "/allen/programs/celltypes/workgroups/rnaseqanalysis/YiDing/New_Folder/Multiome_H19.30.004/test-minFrags1-maxFrags107-TSS0/PeakCalls/C23-reproduciblePeaks.gr.rds"

2021-02-08 22:37:03 : ERROR Found in .identifyReproduciblePeaks for Rep. Peaks Group (17 of 25) : LogFile = ArchRLogs/ArchR-addReproduciblePeakSet-349d8b90c77-Date-2021-02-08_Time-22-07-37.log

<simpleError in [[<-(*tmp*, name, value = "C24._.Rep1"): 1 elements in value to replace 0 elements>

[1] "/allen/programs/celltypes/workgroups/rnaseqanalysis/YiDing/New_Folder/Multiome_H19.30.004/test-minFrags1-maxFrags107-TSS0/PeakCalls/C2-reproduciblePeaks.gr.rds" [1] "/allen/programs/celltypes/workgroups/rnaseqanalysis/YiDing/New_Folder/Multiome_H19.30.004/test-minFrags1-maxFrags107-TSS0/PeakCalls/C16-reproduciblePeaks.gr.rds" [1] "/allen/programs/celltypes/workgroups/rnaseqanalysis/YiDing/New_Folder/Multiome_H19.30.004/test-minFrags1-maxFrags107-TSS0/PeakCalls/C1-reproduciblePeaks.gr.rds" [1] "/allen/programs/celltypes/workgroups/rnaseqanalysis/YiDing/New_Folder/Multiome_H19.30.004/test-minFrags1-maxFrags107-TSS0/PeakCalls/C12-reproduciblePeaks.gr.rds"

2021-02-08 22:37:10 : ERROR Found in .identifyReproduciblePeaks for Rep. Peaks Group (22 of 25) : LogFile = ArchRLogs/ArchR-addReproduciblePeakSet-349d8b90c77-Date-2021-02-08_Time-22-07-37.log

<simpleError in [[<-(*tmp*, name, value = "C6._.H19.30.004.ANG.Multiome"): 1 elements in value to replace 0 elements>

[1] "/allen/programs/celltypes/workgroups/rnaseqanalysis/YiDing/New_Folder/Multiome_H19.30.004/test-minFrags1-maxFrags107-TSS0/PeakCalls/C17-reproduciblePeaks.gr.rds" [1] "/allen/programs/celltypes/workgroups/rnaseqanalysis/YiDing/New_Folder/Multiome_H19.30.004/test-minFrags1-maxFrags107-TSS0/PeakCalls/C15-reproduciblePeaks.gr.rds" [1] "/allen/programs/celltypes/workgroups/rnaseqanalysis/YiDing/New_Folder/Multiome_H19.30.004/test-minFrags1-maxFrags107-TSS0/PeakCalls/C18-reproduciblePeaks.gr.rds"

2021-02-08 22:37:12 : ERROR Found in .identifyReproduciblePeaks for Rep. Peaks Group (24 of 25) : LogFile = ArchRLogs/ArchR-addReproduciblePeakSet-349d8b90c77-Date-2021-02-08_Time-22-07-37.log

<simpleError in [[<-(*tmp*, name, value = "C8._.H19.30.004.MEC.Multiome"): 1 elements in value to replace 0 elements>

[1] "/allen/programs/celltypes/workgroups/rnaseqanalysis/YiDing/New_Folder/Multiome_H19.30.004/test-minFrags1-maxFrags107-TSS0/PeakCalls/C21-reproduciblePeaks.gr.rds" [1] "/allen/programs/celltypes/workgroups/rnaseqanalysis/YiDing/New_Folder/Multiome_H19.30.004/test-minFrags1-maxFrags107-TSS0/PeakCalls/C22-reproduciblePeaks.gr.rds" [1] "/allen/programs/celltypes/workgroups/rnaseqanalysis/YiDing/New_Folder/Multiome_H19.30.004/test-minFrags1-maxFrags107-TSS0/PeakCalls/C11-reproduciblePeaks.gr.rds" [1] "/allen/programs/celltypes/workgroups/rnaseqanalysis/YiDing/New_Folder/Multiome_H19.30.004/test-minFrags1-maxFrags107-TSS0/PeakCalls/C25-reproduciblePeaks.gr.rds" [1] "/allen/programs/celltypes/workgroups/rnaseqanalysis/YiDing/New_Folder/Multiome_H19.30.004/test-minFrags1-maxFrags107-TSS0/PeakCalls/C20-reproduciblePeaks.gr.rds" [1] "/allen/programs/celltypes/workgroups/rnaseqanalysis/YiDing/New_Folder/Multiome_H19.30.004/test-minFrags1-maxFrags107-TSS0/PeakCalls/C13-reproduciblePeaks.gr.rds" [1] "/allen/programs/celltypes/workgroups/rnaseqanalysis/YiDing/New_Folder/Multiome_H19.30.004/test-minFrags1-maxFrags107-TSS0/PeakCalls/C10-reproduciblePeaks.gr.rds" [1] "/allen/programs/celltypes/workgroups/rnaseqanalysis/YiDing/New_Folder/Multiome_H19.30.004/test-minFrags1-maxFrags107-TSS0/PeakCalls/C19-reproduciblePeaks.gr.rds" [1] "/allen/programs/celltypes/workgroups/rnaseqanalysis/YiDing/New_Folder/Multiome_H19.30.004/test-minFrags1-maxFrags107-TSS0/PeakCalls/C14-reproduciblePeaks.gr.rds" [1] "/allen/programs/celltypes/workgroups/rnaseqanalysis/YiDing/New_Folder/Multiome_H19.30.004/test-minFrags1-maxFrags107-TSS0/PeakCalls/C4-reproduciblePeaks.gr.rds" [1] "/allen/programs/celltypes/workgroups/rnaseqanalysis/YiDing/New_Folder/Multiome_H19.30.004/test-minFrags1-maxFrags107-TSS0/PeakCalls/C5-reproduciblePeaks.gr.rds" [1] "/allen/programs/celltypes/workgroups/rnaseqanalysis/YiDing/New_Folder/Multiome_H19.30.004/test-minFrags1-maxFrags107-TSS0/PeakCalls/C7-reproduciblePeaks.gr.rds" [1] "/allen/programs/celltypes/workgroups/rnaseqanalysis/YiDing/New_Folder/Multiome_H19.30.004/test-minFrags1-maxFrags107-TSS0/PeakCalls/C3-reproduciblePeaks.gr.rds" [1] "/allen/programs/celltypes/workgroups/rnaseqanalysis/YiDing/New_Folder/Multiome_H19.30.004/test-minFrags1-maxFrags107-TSS0/PeakCalls/C9-reproduciblePeaks.gr.rds" Error in .safelapply(seq_along(outSummitList), function(i) { : Error Found Iteration 17 : [1] "Error in .logError(e, fn = \".identifyReproduciblePeaks\", info = prefix, : \n Exiting See Error Above\n" <simpleError in .logError(e, fn = ".identifyReproduciblePeaks", info = prefix, errorList = errorList, logFile = logFile): Exiting See Error Above> Error Found Iteration 22 : [1] "Error in .logError(e, fn = \".identifyReproduciblePeaks\", info = prefix, : \n Exiting See Error Above\n" <simpleError in .logError(e, fn = ".identifyReproduciblePeaks", info = prefix, errorList = errorList, logFile = logFile): Exiting See Error Above> Error Found Iteration 24 : [1] "Error in .logError(e, fn = \".identifyReproduciblePeaks\", info = prefix, : \n Exiting See Error Above\n" <simpleError in .logError(e, fn = ".identifyReproduciblePeaks", info = prefix, errorList = errorList, logFile = logFile): Exiting See Error Above> In addition: Warning message: In mclapply(..., mc.cores = threads, mc.preschedule = preschedule) : 3 function calls resulted in an error ArchR-addReproduciblePeakSet-349d8b90c77-Date-2021-02-08_Time-22-07-37.log

rcorces commented 3 years ago

@yding9 - In addition to knowing what isnt working, its always helpful for us to know what IS working. Have you run the standard tutorial and does peak calling work for you on the tutorial data with the tutorial code?

yding9 commented 3 years ago

@rcorces Thank you for getting back to me so quickly! Yes, I tried the standard tutorial and peak calling works for me on the tutorial data with the tutorial code! But this function doesn't work for my archr object. Initially, I thought it would be something wrong with my archr object so I used another new dataset to retry peak calling. The similar error came: My InsertionBeds folder is empty; The ReplicateCalls folder has several rds objects with size of 1 KB. And those 1 KB rds objects are causing troubles.

I'm using macs2 2.2.7.1 installed by pip under python 3.8. By the way, ArchR's native peak caller (TileMatrix) works well without any error. I'm currently using TileMatrix as a workaround while getting this fixed.

rcorces commented 3 years ago

That seems very odd. You ran the tutorial data and your own data in the same computational environment and the tutorial worked but your data doesnt? That seems fishy to me. I think in order to help you, we will need a reproducible example.

rcorces commented 3 years ago

Closing due to inactivity. Feel free to comment again here and I will re-open if you still need help.

zhijunyuu commented 3 years ago

@yding9 Hi, sorry for late reply. For my case, I installed ArchR and macs2 under my own conda environment, then the problem solved.