TSSEnrichment error

[hjyshane]

I am working with multiomics data (ATAC and scRNA).
When I run TSSenrichment, I get this error message. I tried multiple different approaches but keep getting the error message from TSSenrichment function.

PTZ_1hr_seurat <- TSSEnrichment(PTZ_1hr_seurat, fast = FALSE, verbose = TRUE)
Extracting TSS positions
Finding + strand cut sites
Error in h(simpleError(msg, call)) :
error in evaluating the argument 'y' in selecting a method for function 'intersect': [internal] bgzf_seek() failed

Here is the code I am running.

h5_data_PTZ_1hr <- Read10X_h5("/igm/projects/210907_Bedrosian_cellranger-arc-count/PTZ-1hr/outs/filtered_feature_bc_matrix.h5")

annotations <- GetGRangesFromEnsDb(ensdb = EnsDb.Mmusculus.v79)
genome(annotations) <- "mm10"
seqlevelsStyle(annotations) <- 'UCSC'

PTZ_1hr_seurat <-
CreateSeuratObject(counts = h5_data_PTZ_1hr$Gene Expression,
assay = "RNA",
project = "10x_multiomics", meta.data = "/igm/projects/210907_Bedrosian_cellranger-arc-count/PTZ-1hr/outs/per_barcode_metrics.csv") %>%
PercentageFeatureSet(pattern = "^mt-",
col.name = "percent_mt_rna",
assay = "RNA",)

PTZ_1hr_seurat[["ATAC"]] <-
CreateChromatinAssay(counts = h5_data_PTZ_1hr$Peaks,
sep = c(":", "-"),
fragments = "/igm/projects/210907_Bedrosian_cellranger-arc-count/PTZ-1hr/outs/atac_fragments.tsv.gz",
min.cells = 5,
annotation = annotations)
DefaultAssay(PTZ_1hr_seurat) <- "ATAC"
PTZ_1hr_seurat <- TSSEnrichment(PTZ_1hr_seurat, fast = FALSE, verbose = TRUE)

And this is the session info
R version 4.3.3 (2024-02-29)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Amazon Linux 2

Matrix products: default
BLAS: /igm/apps/R/R-4.3.3_install/lib64/R/lib/libRblas.so
LAPACK: /igm/apps/R/R-4.3.3_install/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 LC_COLLATE=en_US.UTF-8 LC_MONETARY=en_US.UTF-8
[6] LC_MESSAGES=en_US.UTF-8 LC_PAPER=en_US.UTF-8 LC_NAME=C LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C

time zone: America/New_York
tzcode source: system (glibc)

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

other attached packages:
[1] EnsDb.Mmusculus.v79_2.99.0 ensembldb_2.26.0 AnnotationFilter_1.26.0 GenomicFeatures_1.54.4 AnnotationDbi_1.64.1
[6] Biobase_2.62.0 DoubletFinder_2.0.4 fields_15.2 viridisLite_0.4.2 spam_2.10-0
[11] ROCR_1.0-11 glmGamPoi_1.14.3 sctransform_0.4.1 Matrix_1.6-5 cowplot_1.1.3
[16] plyr_1.8.9 clustree_0.5.1 ggraph_2.2.1 hdf5r_1.3.10 patchwork_1.2.0
[21] Signac_1.13.0 Seurat_5.1.0 lubridate_1.9.3 forcats_1.0.0 stringr_1.5.1
[26] dplyr_1.1.4 purrr_1.0.2 readr_2.1.5 tidyr_1.3.1 tibble_3.2.1
[31] ggplot2_3.5.1 tidyverse_2.0.0 rrrSingleCellUtils_0.10.1 nichenetr_2.1.0 SeuratObject_5.0.2
[36] sp_2.1-4 GenomicRanges_1.54.1 GenomeInfoDb_1.38.8 IRanges_2.36.0 S4Vectors_0.40.2
[41] BiocGenerics_0.48.1

loaded via a namespace (and not attached):
[1] dichromat_2.0-0.1 progress_1.2.3 nnet_7.3-19 goftest_1.2-3 Biostrings_2.70.3
[6] vctrs_0.6.5 spatstat.random_3.2-3 RApiSerialize_0.1.2 digest_0.6.36 png_0.1-8
[11] shape_1.4.6.1 proxy_0.4-27 ggrepel_0.9.5 deldir_2.0-4 parallelly_1.37.1
[16] MASS_7.3-60.0.1 reshape2_1.4.4 httpuv_1.6.15 foreach_1.5.2 withr_3.0.0
[21] xfun_0.45 ggpubr_0.6.0 survival_3.6-4 memoise_2.0.1 zoo_1.8-12
[26] GlobalOptions_0.1.2 pbapply_1.7-2 Formula_1.2-5 prettyunits_1.2.0 KEGGREST_1.42.0
[31] promises_1.3.0 httr_1.4.7 restfulr_0.0.15 rstatix_0.7.2 globals_0.16.3
[36] fitdistrplus_1.1-11 stringfish_0.16.0 rstudioapi_0.16.0 miniUI_0.1.1.1 generics_0.1.3
[41] base64enc_0.1-3 curl_5.2.1 zlibbioc_1.48.2 polyclip_1.10-6 randomForest_4.7-1.1
[46] GenomeInfoDbData_1.2.11 SparseArray_1.2.4 xtable_1.8-4 doParallel_1.0.17 evaluate_0.24.0
[51] S4Arrays_1.2.1 BiocFileCache_2.10.2 hms_1.1.3 irlba_2.3.5.1 qs_0.26.1
[56] colorspace_2.1-0 filelock_1.0.3 visNetwork_2.1.2 reticulate_1.38.0 spatstat.data_3.1-2
[61] magrittr_2.0.3 lmtest_0.9-40 later_1.3.2 viridis_0.6.5 lattice_0.22-6
[66] spatstat.geom_3.2-9 future.apply_1.11.2 scattermore_1.2 XML_3.99-0.16.1 shadowtext_0.1.3
[71] matrixStats_1.3.0 RcppAnnoy_0.0.22 class_7.3-22 Hmisc_5.1-2 pillar_1.9.0
[76] nlme_3.1-164 iterators_1.0.14 caTools_1.18.2 compiler_4.3.3 RSpectra_0.16-1
[81] stringi_1.8.4 gower_1.0.1 tensor_1.5 SummarizedExperiment_1.32.0 GenomicAlignments_1.38.2
[86] crayon_1.5.3 abind_1.4-5 BiocIO_1.12.0 graphlayouts_1.1.1 bit_4.0.5
[91] fastmatch_1.1-4 codetools_0.2-20 recipes_1.0.10 e1071_1.7-14 biovizBase_1.50.0
[96] GetoptLong_1.0.5 plotly_4.10.4 mime_0.12 splines_4.3.3 circlize_0.4.16
[101] Rcpp_1.0.12 fastDummies_1.7.3 dbplyr_2.5.0 Rttf2pt1_1.3.12 knitr_1.48
[106] blob_1.2.4 utf8_1.2.4 clue_0.3-65 listenv_0.9.1 checkmate_2.3.1
[111] ggsignif_0.6.4 statmod_1.5.0 tzdb_0.4.0 tweenr_2.0.3 pkgconfig_2.0.3
[116] tools_4.3.3 cachem_1.1.0 RSQLite_2.3.6 DBI_1.2.2 fastmap_1.2.0
[121] rmarkdown_2.27 scales_1.3.0 grid_4.3.3 ica_1.0-3 Rsamtools_2.18.0
[126] broom_1.0.5 VariantAnnotation_1.48.1 dotCall64_1.1-1 carData_3.0-5 RANN_2.6.1
[131] rpart_4.1.23 farver_2.1.2 tidygraph_1.3.1 yaml_2.3.9 MatrixGenerics_1.14.0
[136] DiagrammeR_1.0.11 foreign_0.8-86 rtracklayer_1.62.0 cli_3.6.3 leiden_0.4.3.1
[141] lifecycle_1.0.4 caret_6.0-94 uwot_0.2.2 lava_1.8.0 backports_1.4.1
[146] BiocParallel_1.36.0 timechange_0.3.0 gtable_0.3.5 rjson_0.2.21 ggridges_0.5.6
[151] progressr_0.14.0 pROC_1.18.5 limma_3.58.1 jsonlite_1.8.8 RcppHNSW_0.6.0
[156] bitops_1.0-7 bit64_4.0.5 Rtsne_0.17 spatstat.utils_3.0-5 RcppParallel_5.1.7
[161] timeDate_4032.109 lazyeval_0.2.2 shiny_1.8.1.1 htmltools_0.5.8.1 rappdirs_0.3.3
[166] glue_1.7.0 XVector_0.42.0 RCurl_1.98-1.14 BSgenome_1.70.2 gridExtra_2.3
[171] igraph_2.0.3 extrafontdb_1.0 R6_2.5.1 fdrtool_1.2.17 RcppRoll_0.3.1
[176] cluster_2.1.6 ipred_0.9-14 ProtGenerics_1.34.0 DelayedArray_0.28.0 tidyselect_1.2.1
[181] htmlTable_2.4.2 maps_3.4.2 ggforce_0.4.2 xml2_1.3.6 car_3.1-2
[186] future_1.33.2 ModelMetrics_1.2.2.2 munsell_0.5.1 KernSmooth_2.23-22 data.table_1.15.4
[191] htmlwidgets_1.6.4 ComplexHeatmap_2.18.0 RColorBrewer_1.1-3 biomaRt_2.58.2 rlang_1.1.4
[196] spatstat.sparse_3.1-0 extrafont_0.19 spatstat.explore_3.2-7 ggnewscale_0.4.10 fansi_1.0.6
[201] hardhat_1.3.1 prodlim_2023.08.28

[timoast]

Please see #242