rcorces
commented
8 months ago Hi @jinbufan! 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.
xiangsui5
Hi, I encountered an error when I tried to subset project by sample names, here is the code:
dd=split(proj2@cellColData,proj2$Libname) for (i in names(dd)){
subsetArchRProject( ArchRProj = proj2, cells = getCellNames(proj2[proj2$Libname==i,]),
outputDirectory = i, dropCells = TRUE, logFile = NULL, threads = getArchRThreads(), force = TRUE)}
Here is the logfile: Copying ArchRProject to new outputDirectory : /data/work/01.human_brain/03.额叶/subGroup/sample/T599T600-1
Copying Arrow Files...
Copying Arrow Files (1 of 1)
Getting ImputeWeights
No imputeWeights found, returning NULL
Copying Other Files...
Copying Other Files (1 of 18): 00.peak_file
Copying Other Files (2 of 18): 01.clustering_har
Copying Other Files (3 of 18): addp2g.FineClust.qvalue.noFilter.rds
Copying Other Files (4 of 18): Annotations
Copying Other Files (5 of 18): ArchRLogs
Copying Other Files (6 of 18): Background-Peaks.rds
Copying Other Files (7 of 18): Embeddings
Copying Other Files (8 of 18): file_ArchRProject_addp2g.FineClust.qvalue.Filter.20240306.rds
Copying Other Files (9 of 18): file_Full_p2gGR_cCRE_not_merge_and_filter.rds
Copying Other Files (10 of 18): file_p2gGR_cCRE_merge_and_filter.rds
Copying Other Files (11 of 18): FineClust.rds
Copying Other Files (12 of 18): GroupCoverages
Copying Other Files (13 of 18): IterativeLSI
Copying Other Files (14 of 18): markerPeaks_FineClust.rds
Copying Other Files (15 of 18): Peak2GeneLinks
Copying Other Files (16 of 18): PeakCalls
Copying Other Files (17 of 18): Plots
Copying Other Files (18 of 18): RNAIntegration
Error in saveArchRProject(ArchRProj = ArchRProj[cells, ], outputDirectory = outputDirectory, : all(file.exists(zfiles)) is not TRUE Traceback:
My R session: R version 4.2.2 (2022-10-31) Platform: x86_64-conda-linux-gnu (64-bit) Running under: CentOS Linux 7 (Core)
Matrix products: default BLAS/LAPACK: /opt/conda/lib/libopenblasp-r0.3.23.so
Random number generation: RNG: L'Ecuyer-CMRG Normal: Inversion Sample: Rejection
locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=en_US.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
attached base packages: [1] stats4 grid stats graphics grDevices utils datasets [8] methods base
other attached packages: [1] rhdf5_2.42.1 SummarizedExperiment_1.28.0 [3] Biobase_2.58.0 MatrixGenerics_1.10.0
[5] Rcpp_1.0.10 Matrix_1.5-4.1
[7] GenomicRanges_1.50.2 GenomeInfoDb_1.34.9
[9] IRanges_2.32.0 S4Vectors_0.36.2
[11] BiocGenerics_0.44.0 matrixStats_1.0.0
[13] data.table_1.14.8 stringr_1.5.0
[15] plyr_1.8.8 magrittr_2.0.3
[17] ggplot2_3.4.2 gtable_0.3.3
[19] gtools_3.9.4 gridExtra_2.3
[21] ArchR_1.0.2
loaded via a namespace (and not attached): [1] lattice_0.21-8 listenv_0.9.0 digest_0.6.31
[4] utf8_1.2.3 parallelly_1.36.0 IRdisplay_1.1
[7] R6_2.5.1 repr_1.1.6 evaluate_0.21
[10] pillar_1.9.0 zlibbioc_1.44.0 rlang_1.1.1
[13] uuid_1.1-0 RCurl_1.98-1.12 munsell_0.5.0
[16] DelayedArray_0.24.0 compiler_4.2.2 pkgconfig_2.0.3
[19] base64enc_0.1-3 globals_0.16.2 htmltools_0.5.5
[22] tidyselect_1.2.0 tibble_3.2.1 GenomeInfoDbData_1.2.9 [25] codetools_0.2-19 fansi_1.0.4 future_1.32.0
[28] crayon_1.5.2 dplyr_1.1.2 withr_2.5.0
[31] bitops_1.0-7 rhdf5filters_1.10.1 jsonlite_1.8.5
[34] lifecycle_1.0.3 scales_1.2.1 future.apply_1.11.0
[37] cli_3.6.1 stringi_1.7.12 XVector_0.38.0
[40] generics_0.1.3 vctrs_0.6.3 IRkernel_1.3.2
[43] Rhdf5lib_1.20.0 tools_4.2.2 glue_1.6.2
[46] parallel_4.2.2 fastmap_1.1.1 colorspace_2.1-0
[49] pbdZMQ_0.3-9
I also tried to change dropCells = FALSE but it still get error.