skkanlei
commented
7 months ago sessionInfo() R version 4.3.2 (2023-10-31) Platform: x86_64-pc-linux-gnu (64-bit) Running under: CentOS Linux 7 (Core)
Matrix products: default BLAS: /opt/software/R-4.3/lib64/R/lib/libRblas.so LAPACK: /opt/software/R-4.3/lib64/R/lib/libRlapack.so; LAPACK version 3.11.0
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C LC_TIME=en_US.UTF-8
[4] 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
[10] LC_TELEPHONE=C LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
time zone: Asia/Shanghai tzcode source: system (glibc)
attached base packages: [1] grid stats4 stats graphics grDevices utils datasets methods base
other attached packages:
[1] patchwork_1.1.3 ggplot2_3.4.4 SeuratWrappers_0.2.0
[4] SeuratObject_4.1.3 Seurat_4.3.0 Signac_1.11.0
[7] cicero_1.3.9 Gviz_1.46.1 monocle3_1.3.4
[10] SingleCellExperiment_1.24.0 SummarizedExperiment_1.32.0 GenomicRanges_1.54.1
[13] GenomeInfoDb_1.38.4 IRanges_2.36.0 S4Vectors_0.40.2
[16] MatrixGenerics_1.14.0 matrixStats_1.2.0 Biobase_2.62.0
[19] BiocGenerics_0.48.1
loaded via a namespace (and not attached):
[1] ProtGenerics_1.34.0 spatstat.sparse_3.0-3 bitops_1.0-7
[4] httr_1.4.7 RColorBrewer_1.1-3 tools_4.3.2
[7] sctransform_0.4.1 backports_1.4.1 utf8_1.2.4
[10] R6_2.5.1 lazyeval_0.2.2 uwot_0.1.16
[13] withr_2.5.2 sp_2.1-2 prettyunits_1.2.0
[16] gridExtra_2.3 progressr_0.14.0 cli_3.6.2
[19] spatstat.explore_3.2-5 spatstat.data_3.0-3 ggridges_0.5.5
[22] pbapply_1.7-2 Rsamtools_2.18.0 foreign_0.8-85
[25] dichromat_2.0-0.1 parallelly_1.36.0 BSgenome_1.70.1
[28] VGAM_1.1-9 rstudioapi_0.15.0 RSQLite_2.3.4
[31] generics_0.1.3 BiocIO_1.12.0 ica_1.0-3
[34] spatstat.random_3.2-2 dplyr_1.1.4 Matrix_1.6-1
[37] interp_1.1-6 fansi_1.0.6 abind_1.4-5
[40] terra_1.7-65 lifecycle_1.0.4 yaml_2.3.8
[43] SparseArray_1.2.3 BiocFileCache_2.10.1 Rtsne_0.17
[46] blob_1.2.4 promises_1.2.1 crayon_1.5.2
[49] miniUI_0.1.1.1 lattice_0.21-9 cowplot_1.1.2
[52] GenomicFeatures_1.54.1 KEGGREST_1.42.0 pillar_1.9.0
[55] knitr_1.45 rjson_0.2.21 boot_1.3-28.1
[58] future.apply_1.11.1 codetools_0.2-19 fastmatch_1.1-4
[61] leiden_0.4.3.1 glue_1.6.2 remotes_2.4.2.1
[64] data.table_1.14.10 vctrs_0.6.5 png_0.1-8
[67] gtable_0.3.4 cachem_1.0.8 xfun_0.41
[70] S4Arrays_1.2.0 mime_0.12 survival_3.5-7
[73] RcppRoll_0.3.0 ellipsis_0.3.2 fitdistrplus_1.1-11
[76] ROCR_1.0-11 nlme_3.1-163 bit64_4.0.5
[79] progress_1.2.3 filelock_1.0.3 RcppAnnoy_0.0.21
[82] irlba_2.3.5.1 KernSmooth_2.23-22 rpart_4.1.21
[85] colorspace_2.1-0 DBI_1.2.0 Hmisc_5.1-1
[88] nnet_7.3-19 tidyselect_1.2.0 bit_4.0.5
[91] compiler_4.3.2 curl_5.2.0 htmlTable_2.4.2
[94] xml2_1.3.6 DelayedArray_0.28.0 plotly_4.10.3
[97] rtracklayer_1.62.0 checkmate_2.3.1 scales_1.3.0
[100] lmtest_0.9-40 rappdirs_0.3.3 stringr_1.5.1
[103] digest_0.6.33 goftest_1.2-3 spatstat.utils_3.0-4
[106] minqa_1.2.6 rmarkdown_2.25 XVector_0.42.0
[109] htmltools_0.5.7 pkgconfig_2.0.3 jpeg_0.1-10
[112] base64enc_0.1-3 lme4_1.1-35.1 dbplyr_2.4.0
[115] fastmap_1.1.1 ensembldb_2.26.0 rlang_1.1.2
[118] htmlwidgets_1.6.4 shiny_1.8.0 zoo_1.8-12
[121] jsonlite_1.8.8 BiocParallel_1.36.0 VariantAnnotation_1.48.1
[124] RCurl_1.98-1.13 magrittr_2.0.3 Formula_1.2-5
[127] GenomeInfoDbData_1.2.11 munsell_0.5.0 Rcpp_1.0.11
[130] reticulate_1.34.0 stringi_1.8.3 zlibbioc_1.48.0
[133] MASS_7.3-60 plyr_1.8.9 parallel_4.3.2
[136] listenv_0.9.0 ggrepel_0.9.4 deldir_2.0-2
[139] Biostrings_2.70.1 splines_4.3.2 tensor_1.5
[142] hms_1.1.3 igraph_1.6.0 spatstat.geom_3.2-7
[145] reshape2_1.4.4 biomaRt_2.58.0 XML_3.99-0.16
[148] evaluate_0.23 latticeExtra_0.6-30 biovizBase_1.50.0
[151] BiocManager_1.30.22 nloptr_2.0.3 httpuv_1.6.13
[154] RANN_2.6.1 tidyr_1.3.0 purrr_1.0.2
[157] polyclip_1.10-6 future_1.33.1 scattermore_1.2
[160] rsvd_1.0.5 xtable_1.8-4 restfulr_0.0.15
[163] AnnotationFilter_1.26.0 later_1.3.2 viridisLite_0.4.2
[166] tibble_3.2.1 memoise_2.0.1 AnnotationDbi_1.64.1
[169] GenomicAlignments_1.38.0 cluster_2.1.4 globals_0.16.2
hpliner
While running code "run_cicero", I keep getting "The previous R session was abnormally terminated due to an unexpected crash"
I don't know what to do,I also test the other data, meet the same issue!
Here is my code
library(cicero) library(Signac) library(Seurat) library(SeuratWrappers) library(ggplot2) library(patchwork) library(monocle3)
bone.cds <- as.cell_data_set(x = bone, assay = "ATAC") bone.cds <- monocle3::detect_genes(bone.cds)
Ensure there are no peaks included with zero reads
bone.cds <- bone.cds[Matrix::rowSums(exprs(bone.cds)) != 0,] bone.cds <- detect_genes(bone.cds) bone.cds <- estimate_size_factors(bone.cds) bone.cds <- preprocess_cds(bone.cds, method = "LSI") bone.cds <- reduce_dimension(bone.cds, reduction_method = "UMAP", preprocess_method = "LSI") bone.cicero <- make_cicero_cds(bone.cds,reduced_coordinates = reducedDims(bone.cds)$UMAP)
genome <- seqlengths(bone@assays$ATAC@annotation@seqinfo)
use chromosome 1 to save some time
omit this step to run on the whole genome
genome <- genome[30]
convert chromosome sizes to a dataframe
genome.df <- data.frame("chr" = names(genome), "length" = genome)
run cicero
conns <- run_cicero(bone.cicero, genomic_coords = genome.df, sample_num = 100)