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aertslab / SCENIC

SCENIC is an R package to infer Gene Regulatory Networks and cell types from single-cell RNA-seq data.
http://scenic.aertslab.org
GNU General Public License v3.0
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runSCENIC_3_scoreCells() error #425

Open alisyedraza1 opened 7 months ago

alisyedraza1 commented 7 months ago

Hi folks,

I am running the SCENIC pipeline. And when running runSCENIC_3_scoreCells(), I encounter the following error:

"Error in seq.int(rx[1L], rx[2L], length.out = nb) : 'from' must be a finite number"

Could someone please help regarding this? My object is fairly big. And the sessionsInfo() is as below:

R version 4.3.0 (2023-04-21) Platform: x86_64-pc-linux-gnu (64-bit) Running under: Rocky Linux 8.7 (Green Obsidian)

Matrix products: default BLAS/LAPACK: /usr/local/intel/2022.1.2.146/mkl/2022.0.2/lib/intel64/libmkl_rt.so.2; LAPACK version 3.9.0

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: America/New_York tzcode source: system (glibc)

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

other attached packages: [1] doRNG_1.8.6 foreach_1.5.2 [3] gridBase_0.4-7 ComplexHeatmap_2.18.0 [5] KernSmooth_2.23-22 svglite_2.1.2 [7] GOplot_1.0.2 gridExtra_2.3 [9] ggdendro_0.1.23 DOSE_3.28.0 [11] clusterProfiler_4.10.0 MAST_1.28.0 [13] rsvd_1.0.5 TxDb.Hsapiens.UCSC.hg19.knownGene_3.2.2 [15] knitr_1.45 GGally_2.1.2 [17] EnhancedVolcano_1.20.0 reticulate_1.34.0 [19] NMF_0.26 synchronicity_1.3.5 [21] bigmemory_4.6.1 cluster_2.1.4 [23] rngtools_1.5.2 registry_0.5-1 [25] ggalluvial_0.12.5 loomR_0.2.1.9000 [27] hdf5r_1.3.8 R6_2.5.1 [29] anndata_0.7.5.6 GeneOverlap_1.38.0 [31] enrichR_3.2 BiocParallel_1.36.0 [33] Augur_1.0.3 clustree_0.5.1 [35] ggraph_2.1.0 scDblFinder_1.16.0 [37] celldex_1.12.0 scCATCH_3.2.2 [39] presto_1.0.0 gprofiler2_0.2.2 [41] scProportionTest_0.0.0.9000 phateR_1.0.7 [43] SeuratData_0.2.2 SeuratDisk_0.0.0.9020 [45] harmony_1.1.0 Rcpp_1.0.11 [47] DoubletFinder_2.0.3 RcisTarget_1.20.0 [49] AUCell_1.24.0 GENIE3_1.24.0 [51] SCENIC_1.3.1 SCopeLoomR_0.13.0 [53] scTenifoldKnk_1.0.2 synapserutils_1.0.0.15 [55] synapser_1.1.0.119 SeuratWrappers_0.3.1 [57] remotes_2.4.2.1 scTenifoldNet_1.3 [59] FactoMineR_2.9 maSigPro_1.74.0 [61] EnsDb.Hsapiens.v86_2.99.0 biomaRt_2.58.0 [63] org.Hs.eg.db_3.18.0 GSEABase_1.64.0 [65] graph_1.80.0 annotate_1.80.0 [67] XML_3.99-0.15 pathview_1.42.0 [69] enrichplot_1.22.0 GOSemSim_2.28.0 [71] annotables_0.2.0 multtest_2.58.0 [73] multcomp_1.4-25 TH.data_1.1-2 [75] MASS_7.3-60 survival_3.5-7 [77] mvtnorm_1.2-3 nlme_3.1-163 [79] future_1.33.0 qlcMatrix_0.9.7 [81] sparsesvd_0.2-2 slam_0.1-50 [83] gplots_3.1.3 gganimate_1.0.8 [85] igraph_1.5.1 rmarkdown_2.25 [87] plotly_4.10.3 kableExtra_1.3.4 [89] SingleR_2.4.0 DEGreport_1.38.0 [91] monocle_2.30.0 DDRTree_0.1.5 [93] irlba_2.3.5.1 VGAM_1.1-9 [95] monocle3_1.3.1 data.table_1.14.8 [97] RColorBrewer_1.1-3 DESeq2_1.42.0 [99] png_0.1-8 apeglm_1.24.0 [101] pheatmap_1.0.12 SingleCellExperiment_1.24.0 [103] SummarizedExperiment_1.32.0 MatrixGenerics_1.14.0 [105] matrixStats_1.1.0 reshape2_1.4.4 [107] Matrix.utils_0.9.8 ensembldb_2.26.0 [109] AnnotationFilter_1.26.0 GenomicFeatures_1.54.1 [111] AnnotationDbi_1.64.1 Biobase_2.62.0 [113] GenomicRanges_1.54.1 GenomeInfoDb_1.38.1 [115] IRanges_2.36.0 S4Vectors_0.40.1 [117] AnnotationHub_3.10.0 BiocFileCache_2.10.1 [119] dbplyr_2.4.0 BiocGenerics_0.48.1 [121] scales_1.2.1 RCurl_1.98-1.13 [123] gridGraphics_0.5-1 edgeR_4.0.1 [125] hablar_0.3.2 limma_3.58.1 [127] speckle_1.2.0 ggrepel_0.9.4 [129] Azimuth_0.4.6 shinyBS_0.61.1 [131] WGCNA_1.72-1 fastcluster_1.2.3 [133] dynamicTreeCut_1.63-1 viridis_0.6.4 [135] viridisLite_0.4.2 patchwork_1.1.3 [137] cowplot_1.1.1 Matrix_1.6-3 [139] lubridate_1.9.3 forcats_1.0.0 [141] stringr_1.5.1 dplyr_1.1.3 [143] purrr_1.0.2 readr_2.1.4 [145] tidyr_1.3.0 tibble_3.2.1 [147] ggplot2_3.4.4 tidyverse_2.0.0 [149] Seurat_5.0.0 SeuratObject_5.0.0 [151] sp_2.1-1

loaded via a namespace (and not attached): [1] httr_1.4.7 jsonlite_1.8.7 scuttle_1.12.0 [4] gtools_3.9.4 Formula_1.2-5 blob_1.2.4 [7] googlesheets4_1.1.1 RSQLite_2.3.3 pillar_1.9.0 [10] XVector_0.42.0 promises_1.2.1 polyclip_1.10-6 [13] gson_0.1.0 recipes_1.0.8 plyr_1.8.9 [16] R.oo_1.25.0 emdbook_1.3.13 tidytree_0.4.5 [19] tweenr_2.0.2 terra_1.7-55 tester_0.1.7 [22] timechange_0.2.0 usethis_2.2.2 shinyjs_2.1.0 [25] cachem_1.0.8 ROCR_1.0-11 cli_3.6.1 [28] deldir_1.0-9 memoise_2.0.1 evaluate_0.23 [31] R.methodsS3_1.8.2 parallelly_1.36.0 foreign_0.8-85 [34] tools_4.3.0 GlobalOptions_0.1.2 BiocIO_1.12.0 [37] HPO.db_0.99.2 locfit_1.5-9.8 compiler_4.3.0 [40] multcompView_0.1-9 caTools_1.18.2 ggridges_0.5.4 [43] gtable_0.3.4 fastmap_1.1.1 future.apply_1.11.0 [46] uwot_0.1.16 metapod_1.10.0 Rgraphviz_2.46.0 [49] fastDummies_1.7.3 lmtest_0.9-40 urlchecker_1.0.1 [52] BiocSingular_1.18.0 sass_0.4.7 ConsensusClusterPlus_1.66.0 [55] RhpcBLASctl_0.23-42 leiden_0.4.3 prodlim_2023.08.28 [58] shadowtext_0.1.2 dqrng_0.3.1 progress_1.2.2 [61] backports_1.4.1 lattice_0.22-5 beachmat_2.18.0 [64] checkmate_2.3.0 qvalue_2.34.0 minqa_1.2.6 [67] rvest_1.0.3 ggfun_0.1.3 colorspace_2.1-0 [70] preprocessCore_1.64.0 psych_2.3.9 WriteXLS_6.4.0 [73] timeDate_4022.108 devtools_2.4.5 GetoptLong_1.0.5 [76] zlibbioc_1.48.0 GO.db_3.18.0 tensor_1.5 [79] RSpectra_0.16-1 gower_1.0.1 lme4_1.1-35.1 [82] combinat_0.0-8 ellipsis_0.3.2 nnet_7.3-19 [85] mclust_6.0.1 mime_0.12 KEGGgraph_1.62.0 [88] fs_1.6.3 class_7.3-22 progressr_0.14.0 [91] scater_1.30.0 profvis_0.3.8 hms_1.1.3 [94] HDO.db_0.99.1 rsample_1.2.0 RcppHNSW_0.5.0 [97] SparseArray_1.2.2 DelayedArray_0.28.0 rlang_1.1.2 [100] iterators_1.0.14 yardstick_1.2.0 RcppAnnoy_0.0.21 [103] goftest_1.2-3 base64enc_0.1-3 bitops_1.0-7 [106] ExperimentHub_2.10.0 abind_1.4-5 bit_4.0.5 [109] filelock_1.0.2 clue_0.3-65 rprojroot_2.0.4 [112] Hmisc_5.1-1 ggbeeswarm_0.7.2 stringi_1.8.1 [115] scran_1.30.0 sparseMatrixStats_1.14.0 maps_3.4.1.1 [118] tidygraph_1.2.3 logging_0.10-108 here_1.0.1 [121] statmod_1.5.0 sessioninfo_1.2.2 pkgconfig_2.0.3 [124] xtable_1.8-4 spatstat.explore_3.2-5 ggplotify_0.1.2 [127] ScaledMatrix_1.10.0 Rtsne_0.16 lava_1.7.3 [130] tzdb_0.4.0 googledrive_2.1.1 KEGGREST_1.42.0 [133] docopt_0.7.1 spatstat.random_3.2-1 xgboost_1.7.5.1 [136] furrr_0.3.1 mnormt_2.1.1 doParallel_1.0.17 [139] MPO.db_0.99.7 ica_1.0-3 shinydashboard_0.7.2 [142] fitdistrplus_1.1-11 ggtree_3.10.0 Biostrings_2.70.1 [145] flashClust_1.01-2 rjson_0.2.21 bigmemory.sri_0.1.6 [148] miniUI_0.1.1.1 GenomicAlignments_1.38.0 bdsmatrix_1.3-6 [151] pals_1.8 mapproj_1.2.11 coda_0.19-4 [154] pkgload_1.3.3 bit64_4.0.5 DelayedMatrixStats_1.24.0 [157] dotCall64_1.1-0 BiocManager_1.30.22 yulab.utils_0.1.0 [160] cellranger_1.1.0 spatstat.geom_3.2-7 yaml_2.3.7 [163] impute_1.76.0 globals_0.16.2 numDeriv_2016.8-1.1 [166] bbmle_1.0.25 uuid_1.1-1 sandwich_3.0-2 [169] httpuv_1.6.12 fastICA_1.2-3 spatstat.sparse_3.0-3 [172] listenv_0.9.0 webshot_0.5.5 RANN_2.6.1 [175] htmlTable_2.4.2 admisc_0.33 generics_0.1.3 [178] ps_1.7.5 fansi_1.0.5 pkgbuild_1.4.2 [181] doMC_1.3.8 lifecycle_1.0.4 gargle_1.5.2 [184] munsell_0.5.0 callr_3.7.3 systemfonts_1.0.5 [187] rstudioapi_0.15.0 htmlwidgets_1.6.2 leaps_3.1 [190] S4Arrays_1.2.0 restfulr_0.0.15 reshape_0.8.9 [193] DBI_1.1.3 zoo_1.8-12 utf8_1.2.4 [196] treeio_1.26.0 shape_1.4.6 vctrs_0.6.4 [199] R.utils_2.12.2 bslib_0.5.1 shiny_1.7.5.1 [202] assertthat_0.2.1 interactiveDisplayBase_1.40.0 Rsamtools_2.18.0 [205] vipor_0.4.5 GenomeInfoDbData_1.2.11 BiocVersion_3.18.0 [208] ipred_0.9-14 glue_1.6.2 digest_0.6.33 [211] hardhat_1.3.0 htmltools_0.5.7 HSMMSingleCell_1.22.0 [214] broom_1.0.5 venn_1.11 processx_3.8.2 [217] later_1.3.1 ggforce_0.4.1 spatstat.utils_3.0-4 [220] emmeans_1.8.9 parsnip_1.1.1 grr_0.9.5 [223] farver_2.1.1 DT_0.30 withr_2.5.2 [226] leidenbase_0.1.25 pbapply_1.7-2 lazyeval_0.2.2 [229] magrittr_2.0.3 crayon_1.5.2 estimability_1.4.1 [232] bluster_1.12.0 xml2_1.3.5 beeswarm_0.4.0 [235] prettyunits_1.2.0 aplot_0.2.2 jquerylib_0.1.4 [238] pbmcapply_1.5.1 nloptr_2.0.3 scattermore_1.2 [241] BiocNeighbors_1.20.0 dichromat_2.0-0.1 circlize_0.4.16 [244] spam_2.10-0 rappdirs_0.3.3 arrow_13.0.0.1 [247] boot_1.3-28.

alisyedraza1 commented 7 months ago

When instead of using the wrapper function [runSCENIC_3_scoreCells()], I follow the entire pipeline from the webpage (https://github.com/aertslab/SCENIC/blob/master/R/runSCENIC_3_scoreCells.R), I usually get stuck around inability to open the .openDev function for some reason. It says it couldn't find the openDev function.

Could anyone help me with this please? Thanks.

alisyedraza1 commented 7 months ago

So I increased the number of cores and memory for the process and the runSCENIC_3_scoreCells() wrapper function worked fine and finished running AUCell. However, it got stuck at the plotting heatmap. It gives the following error with plotting heatmap function:

12:55 Plotting heatmap... Error in par(plt = gridPLT(), new = TRUE) : invalid value specified for graphical parameter "plt" In addition: There were 14 warnings (use warnings() to see them)

Any clues about this? Thanks.

ManarHashemTaha commented 1 month ago

which the ncores and ram you have used ?

So I increased the number of cores and memory for the process and the runSCENIC_3_scoreCells() wrapper function worked fine and finished running AUCell. However, it got stuck at the plotting heatmap. It gives the following error with plotting heatmap function:

12:55 Plotting heatmap... Error in par(plt = gridPLT(), new = TRUE) : invalid value specified for graphical parameter "plt" In addition: There were 14 warnings (use warnings() to see them)

Any clues about this? Thanks.