Error Running runGenie3 in R

Dear all,

Thanks for sharing this amazing tool.

Unfortunately, while running SCENIC in R, I encountered the following error:

runGenie3(exprMat_filtered_log, scenicOptions) Using 18 TFs as potential regulators... Running GENIE3 part 1 Running GENIE3 part 10 Running GENIE3 part 2 Running GENIE3 part 3 Running GENIE3 part 4 Error in gzfile(file, mode) : all connections are in use

Do you have any recommendations for addressing this problem?

sessionInfo() R version 4.2.2 (2022-10-31 ucrt) Platform: x86_64-w64-mingw32/x64 (64-bit) Running under: Windows 10 x64 (build 22621)

Matrix products: default

locale: [1] LC_COLLATE=Italian_Italy.utf8 LC_CTYPE=Italian_Italy.utf8 LC_MONETARY=Italian_Italy.utf8 LC_NUMERIC=C LC_TIME=Italian_Italy.utf8

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

other attached packages: [1] snow_0.4-4 ComplexHeatmap_2.14.0 data.table_1.14.10 ggplot2_3.4.4 BiocParallel_1.32.6 KernSmooth_2.23-20 RcisTarget_1.18.2 AUCell_1.20.2
[9] SCENIC_1.3.1

loaded via a namespace (and not attached): [1] bitops_1.0-7 matrixStats_1.2.0 bit64_4.0.5 doParallel_1.0.17 RColorBrewer_1.1-3 httr_1.4.7
[7] GenomeInfoDb_1.34.9 tools_4.2.2 utf8_1.2.4 R6_2.5.1 DBI_1.2.1 BiocGenerics_0.44.0
[13] colorspace_2.1-0 GetoptLong_1.0.5 withr_3.0.0 tidyselect_1.2.0 bit_4.0.5 compiler_4.2.2
[19] graph_1.76.0 cli_3.6.2 Biobase_2.58.0 DelayedArray_0.24.0 scales_1.3.0 arrow_14.0.0.2
[25] digest_0.6.33 R.utils_2.12.3 XVector_0.38.0 pkgconfig_2.0.3 htmltools_0.5.7 sparseMatrixStats_1.10.0
[31] MatrixGenerics_1.10.0 fastmap_1.1.1 rlang_1.1.2 GlobalOptions_0.1.2 rstudioapi_0.15.0 RSQLite_2.3.5
[37] shiny_1.8.0 DelayedMatrixStats_1.20.0 shape_1.4.6 generics_0.1.3 dplyr_1.1.4 R.oo_1.26.0
[43] RCurl_1.98-1.14 magrittr_2.0.3 GenomeInfoDbData_1.2.9 Matrix_1.6-4 Rcpp_1.0.11 munsell_0.5.0
[49] S4Vectors_0.36.2 fansi_1.0.6 lifecycle_1.0.4 R.methodsS3_1.8.2 SummarizedExperiment_1.28.0 zlibbioc_1.44.0
[55] blob_1.2.4 parallel_4.2.2 promises_1.2.1 ggrepel_0.9.4 crayon_1.5.2 lattice_0.20-45
[61] Biostrings_2.66.0 annotate_1.76.0 circlize_0.4.15 KEGGREST_1.38.0 pillar_1.9.0 GenomicRanges_1.50.2
[67] rjson_0.2.21 codetools_0.2-18 stats4_4.2.2 XML_3.99-0.16.1 glue_1.6.2 png_0.1-8
[73] vctrs_0.6.5 tzdb_0.4.0 httpuv_1.6.13 foreach_1.5.2 gtable_0.3.4 purrr_1.0.2
[79] clue_0.3-65 assertthat_0.2.1 cachem_1.0.8 mime_0.12 xtable_1.8-4 later_1.3.2
[85] tibble_3.2.1 iterators_1.0.14 AnnotationDbi_1.60.2 memoise_2.0.1 IRanges_2.32.0 cluster_2.1.4

Everything was run on an HP Windows machine: Intel(R) Xeon(R) Platinum 8260 CPU @ 2.40GHz, 2394 Mhz, 24 core (2x).

aertslab / SCENIC

Error Running runGenie3 in R #441