rcorces
commented
1 year ago Hi @dpwlek1997! Thanks for using ArchR! Please make sure that your post belongs in the Issues section. Only bugs and error reports belong in the Issues section. Usage questions and feature requests should be posted in the Discussions section, not in Issues.
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ybaeus
Hi, i currently perform multiome analysis (scATACseq+scRNAseq) based on https://greenleaflab.github.io/ArchR_2020/Ex-Analyze-Multiome.html and the master branch. I faced an issue during peak calling (using MACS2).
Error ArchR logging to : ArchRLogs/ArchR-addReproduciblePeakSet-4e6b1c6ac4a6-Date-2023-03-12_Time-15-59-16.log If there is an issue, please report to github with logFile! Calling Peaks with Macs2 2023-03-12 15:59:17 : Peak Calling Parameters!, 0.017 mins elapsed. 2023-03-12 15:59:17 : Batching Peak Calls!, 0.021 mins elapsed. 2023-03-12 15:59:17 : Batch Execution w/ safelapply!, 0 mins elapsed. Error in base::try(featureplot_topmofic, silent = TRUE) : object 'featureplot_topmofic' not found
log file ArchR-addIterativeLSI-f7043b715d39-Date-2023-03-09_Time-17-26-43.log
Describe the bug It said that the object 'featureplot_topmofic' is not found, but still trying to figure out where to start for debugging.
And, this was the command i used. pathToMacs2 <- findMacs2() #python3.8.10 , python3.10 only work for macs3 proj <- addReproduciblePeakSet( ArchRProj = proj, groupBy = "Clusters", pathToMacs2 = pathToMacs2, peaksPerCell = 500, # default, number of peaks per cell maxPeaks = 150000, # default, total peaks per cell minCells = 25 # default )
Session Info R version 4.1.0 (2021-05-18) Platform: x86_64-pc-linux-gnu (64-bit) Running under: CentOS Linux 7 (Core)
Matrix products: default BLAS/LAPACK: /depot/rhel/easybuild/software/OpenBLAS/0.3.12-GCC-10.2.0/lib/libopenblas_haswellp-r0.3.12.so
Random number generation: RNG: L'Ecuyer-CMRG Normal: Inversion Sample: Rejection
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
[7] LC_PAPER=en_US.UTF-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 grid stats graphics grDevices utils datasets methods base
other attached packages: [1] ArchR_1.0.2 BSgenome.Hsapiens.UCSC.hg38_1.4.4 BSgenome_1.62.0 rtracklayer_1.54.0
[5] Biostrings_2.62.0 XVector_0.34.0 EnsDb.Hsapiens.v86_2.99.0 ensembldb_2.18.4
[9] AnnotationFilter_1.18.0 GenomicFeatures_1.46.5 AnnotationDbi_1.56.2 Signac_1.9.0
[13] ArchRtoSignac_1.0.2 forcats_0.5.2 dplyr_1.1.0 purrr_1.0.0
[17] readr_2.1.3 tidyr_1.2.1 tibble_3.1.8 tidyverse_1.3.2
[21] readxl_1.4.1 reticulate_1.28 rhdf5_2.38.1 SummarizedExperiment_1.24.0
[25] Biobase_2.54.0 MatrixGenerics_1.6.0 Rcpp_1.0.9 Matrix_1.5-3
[29] GenomicRanges_1.46.1 GenomeInfoDb_1.30.1 IRanges_2.28.0 S4Vectors_0.32.4
[33] BiocGenerics_0.40.0 matrixStats_0.63.0 data.table_1.14.6 stringr_1.5.0
[37] plyr_1.8.8 magrittr_2.0.3 ggplot2_3.4.0 gtable_0.3.1
[41] gtools_3.9.4 gridExtra_2.3
loaded via a namespace (and not attached): [1] utf8_1.2.3 R.utils_2.12.2 tidyselect_1.2.0 RSQLite_2.2.20 htmlwidgets_1.6.1 BiocParallel_1.28.3
[7] devtools_2.4.5 munsell_0.5.0 codetools_0.2-18 interp_1.1-3 miniUI_0.1.1.1 future_1.30.0
[13] withr_2.5.0 RcisTarget_1.14.0 colorspace_2.0-3 progressr_0.12.0 filelock_1.0.2 knitr_1.42
[19] rstudioapi_0.14 listenv_0.9.0 GenomeInfoDbData_1.2.7 farver_2.1.1 bit64_4.0.5 rprojroot_2.0.3
[25] parallelly_1.33.0 vctrs_0.5.2.9000 generics_0.1.3 xfun_0.37 biovizBase_1.42.0 timechange_0.1.1
[31] BiocFileCache_2.2.1 R6_2.5.1 arrow_6.0.1 bitops_1.0-7 rhdf5filters_1.6.0 cachem_1.0.6
[37] DelayedArray_0.20.0 assertthat_0.2.1 promises_1.2.0.1 BiocIO_1.4.0 scales_1.2.1 nnet_7.3-18
[43] googlesheets4_1.0.1 Cairo_1.6-0 globals_0.16.2 processx_3.8.0 rlang_1.0.6 RcppRoll_0.3.0
[49] splines_4.1.0 lazyeval_0.2.2 gargle_1.2.1 dichromat_2.0-0.1 broom_1.0.2 checkmate_2.1.0
[55] BiocManager_1.30.19 yaml_2.3.6 modelr_0.1.10 backports_1.4.1 httpuv_1.6.9 Hmisc_4.7-2
[61] usethis_2.1.6 tools_4.1.0 ellipsis_0.3.2 RColorBrewer_1.1-3 sessioninfo_1.2.2 base64enc_0.1-3
[67] progress_1.2.2 zlibbioc_1.40.0 RCurl_1.98-1.9 ps_1.7.2 prettyunits_1.1.1 rpart_4.1.19
[73] deldir_1.0-6 pbapply_1.6-0 urlchecker_1.0.1 SeuratObject_4.1.3 haven_2.5.1 cluster_2.1.4
[79] fs_1.5.2 reprex_2.0.2 googledrive_2.0.0 ProtGenerics_1.26.0 pkgload_1.3.2 mime_0.12
[85] hms_1.1.2 patchwork_1.1.2 evaluate_0.20 xtable_1.8-4 XML_3.99-0.13 jpeg_0.1-10
[91] AUCell_1.16.0 compiler_4.1.0 biomaRt_2.50.3 crayon_1.5.2 R.oo_1.25.0 htmltools_0.5.4
[97] later_1.3.0 tzdb_0.3.0 Formula_1.2-4 lubridate_1.9.0 DBI_1.1.3.9007 dbplyr_2.3.1
[103] rappdirs_0.3.3 cli_3.6.0 R.methodsS3_1.8.2 igraph_1.3.5 pkgconfig_2.0.3 GenomicAlignments_1.30.0 [109] foreign_0.8-84 sp_1.5-1 xml2_1.3.3 annotate_1.72.0 rvest_1.0.3 callr_3.7.3
[115] VariantAnnotation_1.40.0 digest_0.6.31 graph_1.72.0 rmarkdown_2.20 cellranger_1.1.0 fastmatch_1.1-3
[121] htmlTable_2.4.1 GSEABase_1.56.0 restfulr_0.0.15 curl_4.3.3 shiny_1.7.4 Rsamtools_2.10.0
[127] rjson_0.2.21 lifecycle_1.0.3 jsonlite_1.8.4 Rhdf5lib_1.16.0 desc_1.4.2 fansi_1.0.4
[133] pillar_1.8.1 lattice_0.20-45 pkgbuild_1.4.0 KEGGREST_1.34.0 fastmap_1.1.0 httr_1.4.4
[139] survival_3.4-0 remotes_2.4.2 glue_1.6.2 png_0.1-8 bit_4.0.5 profvis_0.3.7
[145] stringi_1.7.8 blob_1.2.3 latticeExtra_0.6-30 memoise_2.0.1 irlba_2.3.5.1 future.apply_1.10.0
Thank you so much for the great software and your time. Much appreciated it! I don't think this is a bug but need more information (not sure how to change the labels haha)