Error when running Integrating scRNA-seq and scATAC-seq data vignette

[realmungmung]

Hi all,
I'm running this Integrating scRNA-seq and scATAC-seq data vignette and I was able to run through the tutorial until this command:
gene.activities <- GeneActivity(pbmc.atac, features = VariableFeatures(pbmc.rna))

where I got a huge error:

gene.activities <- GeneActivity(pbmc.atac, features = VariableFeatures(pbmc.rna))
Extracting gene coordinates
Extracting reads overlapping genomic regions
| | 0 % ~calculating [E::bgzf_read_block] Failed to read BGZF header at offset 1416828390
[E::hts_itr_next] Failed to seek to offset 92869838159767: Illegal seek
[E::hts_itr_next] Failed to seek to offset 92902743745887: Illegal seek
[E::hts_itr_next] Failed to seek to offset 92916919541141: Illegal seek
[E::hts_itr_next] Failed to seek to offset 93381738192310: Illegal seek
[E::hts_itr_next] Failed to seek to offset 93413213899239: Illegal seek
[E::hts_itr_next] Failed to seek to offset 93516938894158: Illegal seek
[E::hts_itr_next] Failed to seek to offset 93609721460164: Illegal seek
[E::hts_itr_next] Failed to seek to offset 93629593997030: Illegal seek
[E::hts_itr_next] Failed to seek to offset 93633988935576: Illegal seek
[E::hts_itr_next] Failed to seek to offset 93643503715391: Illegal seek
......

my session info is:

sessionInfo()
R version 4.4.2 (2024-10-31)
Platform: aarch64-apple-darwin20
Running under: macOS Sonoma 14.6.1

Matrix products: default
BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libRlapack.dylib; LAPACK version 3.12.0

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

time zone: America/Los_Angeles
tzcode source: internal

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

other attached packages:
[1] cowplot_1.1.3 ggplot2_3.5.1 EnsDb.Hsapiens.v86_2.99.0 ensembldb_2.30.0 AnnotationFilter_1.30.0
[6] GenomicFeatures_1.58.0 AnnotationDbi_1.68.0 Biobase_2.66.0 GenomicRanges_1.58.0 GenomeInfoDb_1.42.1
[11] IRanges_2.40.1 S4Vectors_0.44.0 BiocGenerics_0.52.0 Signac_1.14.0 Seurat_5.1.0
[16] SeuratObject_5.0.2 sp_2.1-4 pbmcMultiome.SeuratData_0.1.4 SeuratData_0.2.2.9001

loaded via a namespace (and not attached):
[1] RcppAnnoy_0.0.22 splines_4.4.2 later_1.4.1 BiocIO_1.16.0 bitops_1.0-9 tibble_3.2.1
[7] polyclip_1.10-7 rpart_4.1.23 XML_3.99-0.18 fastDummies_1.7.4 lifecycle_1.0.4 globals_0.16.3
[13] lattice_0.22-6 MASS_7.3-63 backports_1.5.0 magrittr_2.0.3 rmarkdown_2.29 Hmisc_5.2-1
[19] plotly_4.10.4 yaml_2.3.10 httpuv_1.6.15 sctransform_0.4.1 spam_2.11-0 spatstat.sparse_3.1-0
[25] reticulate_1.40.0 pbapply_1.7-2 DBI_1.2.3 RColorBrewer_1.1-3 abind_1.4-8 zlibbioc_1.52.0
[31] Rtsne_0.17 purrr_1.0.2 biovizBase_1.54.0 RCurl_1.98-1.16 nnet_7.3-20 VariantAnnotation_1.52.0
[37] rappdirs_0.3.3 GenomeInfoDbData_1.2.13 ggrepel_0.9.6 irlba_2.3.5.1 listenv_0.9.1 spatstat.utils_3.1-1
[43] goftest_1.2-3 RSpectra_0.16-2 spatstat.random_3.3-2 fitdistrplus_1.2-1 parallelly_1.41.0 leiden_0.4.3.1
[49] codetools_0.2-20 DelayedArray_0.32.0 RcppRoll_0.3.1 tidyselect_1.2.1 UCSC.utils_1.2.0 farver_2.1.2
[55] base64enc_0.1-3 matrixStats_1.4.1 spatstat.explore_3.3-3 GenomicAlignments_1.42.0 jsonlite_1.8.9 Formula_1.2-5
[61] progressr_0.15.1 ggridges_0.5.6 survival_3.8-3 tools_4.4.2 ica_1.0-3 Rcpp_1.0.13-1
[67] glue_1.8.0 gridExtra_2.3 SparseArray_1.6.0 xfun_0.49 MatrixGenerics_1.18.0 dplyr_1.1.4
[73] withr_3.0.2 fastmap_1.2.0 digest_0.6.37 R6_2.5.1 mime_0.12 colorspace_2.1-1
[79] scattermore_1.2 tensor_1.5 dichromat_2.0-0.1 spatstat.data_3.1-4 RSQLite_2.3.9 tidyr_1.3.1
[85] generics_0.1.3 data.table_1.16.4 rtracklayer_1.66.0 httr_1.4.7 htmlwidgets_1.6.4 S4Arrays_1.6.0
[91] uwot_0.2.2 pkgconfig_2.0.3 gtable_0.3.6 blob_1.2.4 lmtest_0.9-40 XVector_0.46.0
[97] htmltools_0.5.8.1 dotCall64_1.2 ProtGenerics_1.38.0 scales_1.3.0 png_0.1-8 spatstat.univar_3.1-1
[103] knitr_1.49 rstudioapi_0.17.1 reshape2_1.4.4 rjson_0.2.23 checkmate_2.3.2 nlme_3.1-166
[109] curl_6.0.1 zoo_1.8-12 cachem_1.1.0 stringr_1.5.1 KernSmooth_2.23-26 parallel_4.4.2
[115] miniUI_0.1.1.1 foreign_0.8-87 restfulr_0.0.15 pillar_1.10.0 grid_4.4.2 vctrs_0.6.5
[121] RANN_2.6.2 promises_1.3.2 xtable_1.8-4 cluster_2.1.8 htmlTable_2.4.3 evaluate_1.0.1
[127] cli_3.6.3 compiler_4.4.2 Rsamtools_2.22.0 rlang_1.1.4 crayon_1.5.3 future.apply_1.11.3
[133] labeling_0.4.3 plyr_1.8.9 stringi_1.8.4 viridisLite_0.4.2 deldir_2.0-4 BiocParallel_1.40.0
[139] munsell_0.5.1 Biostrings_2.74.1 lazyeval_0.2.2 spatstat.geom_3.3-4 Matrix_1.7-1 BSgenome_1.74.0
[145] RcppHNSW_0.6.0 patchwork_1.3.0 bit64_4.5.2 future_1.34.0 KEGGREST_1.46.0 shiny_1.10.0
[151] SummarizedExperiment_1.36.0 ROCR_1.0-11 igraph_2.1.2 memoise_2.0.1 fastmatch_1.1-6 bit_4.5.0.1

Please let me know if you have any suggestions thank you so much!

[timoast]

It looks like you have some issue with your fragment file. Make sure that this file is compressed with bgzip and indexed using tabix, and if you alter the file you need to ensure that the index is updated. How did you create the fragment file?