GreenleafLab
Not All Seqnames Identical!
Hi all, I am having an issue with addIterativeLSI , using TileMatrix , I get this error:
ArchR logging to : ArchRLogs/ArchR-addIterativeLSI-34f754ef9709-Date-2024-08-12_Time-22-18-58.603256.log If there is an issue, please report to github with logFile! Error in .availableSeqnames(ArrowFiles, subGroup = useMatrix) : Not All Seqnames Identical!
R version 4.3.1 (2023-06-16) Platform: x86_64-pc-linux-gnu (64-bit) Running under: Ubuntu 22.04.3 LTS Matrix products: default BLAS: /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3 LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblasp-r0.3.20.so; LAPACK version 3.10.0 Random number generation: RNG: L'Ecuyer-CMRG Normal: Inversion Sample: Rejection locale: [1] LC_CTYPE=C.UTF-8 LC_NUMERIC=C LC_TIME=C.UTF-8 LC_COLLATE=C.UTF-8 [5] LC_MONETARY=C.UTF-8 LC_MESSAGES=C.UTF-8 LC_PAPER=C.UTF-8 LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C LC_MEASUREMENT=C.UTF-8 LC_IDENTIFICATION=C time zone: Etc/UTC tzcode source: system (glibc) attached base packages: [1] parallel stats4 grid stats graphics grDevices utils datasets methods base other attached packages: [1] hexbin_1.28.3 harmony_1.2.0 [3] uwot_0.2.2 ggridges_0.5.6 [5] BSgenome.Hsapiens.UCSC.hg38_1.4.5 BSgenome_1.70.2 [7] rtracklayer_1.62.0 BiocIO_1.12.0 [9] Biostrings_2.70.3 XVector_0.42.0 [11] nabor_0.5.0 Seurat_5.0.1 [13] SeuratObject_5.0.0 sp_2.1-4 [15] rhdf5_2.46.1 SummarizedExperiment_1.32.0 [17] Biobase_2.62.0 MatrixGenerics_1.14.0 [19] Rcpp_1.0.12 Matrix_1.6-1 [21] GenomicRanges_1.54.1 GenomeInfoDb_1.38.8 [23] IRanges_2.36.0 S4Vectors_0.40.2 [25] BiocGenerics_0.48.1 matrixStats_1.3.0 [27] data.table_1.15.4 stringr_1.5.1 [29] plyr_1.8.9 magrittr_2.0.3 [31] ggplot2_3.4.0 gtable_0.3.5 [33] gtools_3.9.5 gridExtra_2.3 [35] ArchR_1.0.2 loaded via a namespace (and not attached): [1] RcppAnnoy_0.0.22 splines_4.3.1 later_1.3.2 [4] bitops_1.0-7 tibble_3.2.1 polyclip_1.10-6 [7] XML_3.99-0.16.1 fastDummies_1.7.3 lifecycle_1.0.4 [10] doParallel_1.0.17 globals_0.16.3 lattice_0.21-8 [13] MASS_7.3-60 plotly_4.10.4 yaml_2.3.8 [16] remotes_2.5.0 httpuv_1.6.15 sctransform_0.4.1 [19] spam_2.10-0 sessioninfo_1.2.2 pkgbuild_1.4.4 [22] spatstat.sparse_3.0-3 reticulate_1.37.0 cowplot_1.1.3 [25] pbapply_1.7-2 RColorBrewer_1.1-3 abind_1.4-5 [28] pkgload_1.3.4 zlibbioc_1.48.2 Rtsne_0.17 [31] purrr_1.0.2 RCurl_1.98-1.14 circlize_0.4.16 [34] GenomeInfoDbData_1.2.11 ggrepel_0.9.5 irlba_2.3.5.1 [37] listenv_0.9.1 spatstat.utils_3.0-5 goftest_1.2-3 [40] RSpectra_0.16-1 spatstat.random_3.2-3 fitdistrplus_1.1-11 [43] parallelly_1.37.1 leiden_0.4.3.1 codetools_0.2-19 [46] DelayedArray_0.28.0 shape_1.4.6.1 tidyselect_1.2.1 [49] farver_2.1.2 spatstat.explore_3.2-7 GenomicAlignments_1.38.2 [52] jsonlite_1.8.8 GetoptLong_1.0.5 ellipsis_0.3.2 [55] progressr_0.14.0 iterators_1.0.14 survival_3.5-5 [58] foreach_1.5.2 tools_4.3.1 ica_1.0-3 [61] glue_1.7.0 SparseArray_1.2.4 usethis_2.2.3 [64] dplyr_1.1.4 withr_3.0.0 BiocManager_1.30.23 [67] fastmap_1.2.0 rhdf5filters_1.14.1 fansi_1.0.6 [70] digest_0.6.35 R6_2.5.1 mime_0.12 [73] colorspace_2.1-0 scattermore_1.2 Cairo_1.6-2 [76] tensor_1.5 spatstat.data_3.0-4 utf8_1.2.4 [79] tidyr_1.3.1 generics_0.1.3 httr_1.4.7 [82] htmlwidgets_1.6.4 S4Arrays_1.2.1 pkgconfig_2.0.3 [85] ComplexHeatmap_2.18.0 lmtest_0.9-40 htmltools_0.5.8.1 [88] profvis_0.3.8 dotCall64_1.1-1 clue_0.3-65 [91] scales_1.3.0 png_0.1-8 rstudioapi_0.16.0 [94] reshape2_1.4.4 rjson_0.2.21 nlme_3.1-162 [97] GlobalOptions_0.1.2 zoo_1.8-12 cachem_1.1.0 [100] KernSmooth_2.23-21 miniUI_0.1.1.1 restfulr_0.0.15 [103] pillar_1.9.0 vctrs_0.6.5 RANN_2.6.1 [106] urlchecker_1.0.1 promises_1.3.0 xtable_1.8-4 [109] cluster_2.1.4 cli_3.6.3 compiler_4.3.1 [112] Rsamtools_2.18.0 rlang_1.1.4 crayon_1.5.2 [115] future.apply_1.11.2 labeling_0.4.3 fs_1.6.4 [118] stringi_1.8.4 viridisLite_0.4.2 deldir_2.0-4 [121] BiocParallel_1.36.0 munsell_0.5.1 lazyeval_0.2.2 [124] devtools_2.4.5 spatstat.geom_3.2-9 RcppHNSW_0.6.0 [127] patchwork_1.2.0 future_1.33.2 Rhdf5lib_1.24.2 [130] shiny_1.8.1.1 ROCR_1.0-11 igraph_2.0.3 [133] memoise_2.0.1
| >
Any suggestions please how to fix that? Thank you!
Hi @Aya-Balbaa-72! 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.
I got a same error, too.
ArchR logging to : ArchRLogs/ArchR-getGroupBW-5dd927c8fd40-Date-2024-08-22_Time-20-10-58.log If there is an issue, please report to github with logFile! Error in .availableSeqnames(head(getArrowFiles(ArchRProj))) : Not All Seqnames Identical!
Also got the same error. I inspected the seqnames in each arrow files and they are the same. Was there any fix found?
I also got this error when I used addGroupCoverages on a subset created by subsetArchRProject. I used the arrow files of the subset to create a new project and found that the number of cell was different form the subset. When I subset data，I have set dropCells = TRUE and force = TRUE. Could you please take a look and see where the problem lies? I'm looking forward to your reply.
