Error in h(simpleError(msg, call)) : There was an error evaluating the 'y' argument while selecting a method for the 'intersect' function: [internal] bgzf_seek() failed

[Syayaq]

Hello!

I am merging 2 scATACsec data using the vignette "Merging objects"
(https://stuartlab.org/signac/articles/merging.html)
the error is reported as below:

`library(pheatmap)
library(SingleR)
library(celldex)
library(devtools)
library(Seurat)
library(dplyr)
library(patchwork)
library(Signac)
library(Matrix)
library(magrittr)
library(readr)
library(tidyr)
library(harmony)
library(EnsDb.Hsapiens.v86)
library(ggplot2)
library(cowplot)
library(hdf5r)
library(spatstat.geom)
library(Matrix)
library(Seurat)
library(Rtsne)
library(umap)
library(Matrix)
library(Metrics)
library(biovizBase)
library(SeuratObject)
library(GenomicRanges)
library(future)

peaks1 <- read.table(
file = "D:/ATAC-seq/ATAC_GBM/GSM4119513/peaks.bed"
)
a<-peaks1[,1]
c<-gsub("-",":",a)
b<-strsplit(c,split = ':')
d<-as.data.frame(b)
e<-as.data.frame(t(d))
colnames(e)<-c("chr", "start", "end")
row.names(e)<-1:nrow(e)
peaks1<-e

peaks2 <- read.table(
file = "D:/ATAC-seq/ATAC_GBM/GSM4119515/peaks.bed",
)
a<-peaks2[,1]
c<-gsub("-",":",a)
b<-strsplit(c,split = ':')
d<-as.data.frame(b)
e<-as.data.frame(t(d))
colnames(e)<-c("chr", "start", "end")
row.names(e)<-1:nrow(e)
peaks2<-e

convert to genomic ranges

gr1 <- makeGRangesFromDataFrame(peaks1)
gr2<- makeGRangesFromDataFrame(peaks2)

combined.peaks <- reduce(x = c(gr1, gr2))
peakwidths <- width(combined.peaks)
combined.peaks <- combined.peaks[peakwidths < 10000 & peakwidths > 20]

md1<-read.table(
file = "D:/大三下/ATAC-seq/ATAC_GBM/GSM4119513/barcodes.tsv"
)
md2<-read.table(
file = "D:/大三下/ATAC-seq/ATAC_GBM/GSM4119515/barcodes.tsv"
)

create fragment objects

frags1<- CreateFragmentObject(
path = "D:/大三下/ATAC-seq/ATAC_GBM/GSM4119513/fragment.bed.gz",
cells = md1[,1]
)
frags2<- CreateFragmentObject(
path = "D:/大三下/ATAC-seq/ATAC_GBM/GSM4119515/fragment.bed.gz",
cells = md2[,1]
)

pbmc1.counts <- FeatureMatrix(
fragments = frags1,
features = combined.peaks,
cells = md1[,1]
)

Error in h(simpleError(msg, call)) :
在为'intersect'函数选择方法时评估'y'参数出了错: [internal] bgzf_seek() failed

`

sessionInfo()
R version 4.3.2 (2023-10-31 ucrt)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 11 x64 (build 22631)

Matrix products: default

locale:
[1] LC_COLLATE=Chinese (Simplified)_China.utf8 LC_CTYPE=Chinese (Simplified)_China.utf8
[3] LC_MONETARY=Chinese (Simplified)_China.utf8 LC_NUMERIC=C
[5] LC_TIME=Chinese (Simplified)_China.utf8

time zone: Asia/Shanghai
tzcode source: internal

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

other attached packages:
[1] future_1.33.1 biovizBase_1.50.0 Metrics_0.1.4
[4] umap_0.2.10.0 Rtsne_0.17 spatstat.geom_3.2-8
[7] spatstat.data_3.0-4 hdf5r_1.3.9 cowplot_1.1.3
[10] ggplot2_3.4.4 EnsDb.Hsapiens.v86_2.99.0 ensembldb_2.26.0
[13] AnnotationFilter_1.26.0 GenomicFeatures_1.54.3 AnnotationDbi_1.64.1
[16] harmony_1.2.0 Rcpp_1.0.12 tidyr_1.3.1
[19] readr_2.1.5 magrittr_2.0.3 Matrix_1.6-5
[22] Signac_1.12.0 patchwork_1.2.0 dplyr_1.1.4
[25] Seurat_5.0.1 SeuratObject_5.0.1 sp_2.1-3
[28] devtools_2.4.5 usethis_2.2.2 celldex_1.12.0
[31] SingleR_2.4.1 SummarizedExperiment_1.32.0 Biobase_2.62.0
[34] GenomicRanges_1.54.1 GenomeInfoDb_1.38.5 IRanges_2.36.0
[37] S4Vectors_0.40.2 BiocGenerics_0.48.1 MatrixGenerics_1.14.0
[40] matrixStats_1.2.0 pheatmap_1.0.12

loaded via a namespace (and not attached):
[1] fs_1.6.3 ProtGenerics_1.34.0 spatstat.sparse_3.0-3
[4] bitops_1.0-7 httr_1.4.7 RColorBrewer_1.1-3
[7] backports_1.4.1 profvis_0.3.8 tools_4.3.2
[10] sctransform_0.4.1 utf8_1.2.4 R6_2.5.1
[13] lazyeval_0.2.2 uwot_0.1.16 withr_3.0.0
[16] urlchecker_1.0.1 prettyunits_1.2.0 gridExtra_2.3
[19] progressr_0.14.0 cli_3.6.2 spatstat.explore_3.2-6
[22] fastDummies_1.7.3 askpass_1.2.0 ggridges_0.5.6
[25] pbapply_1.7-2 Rsamtools_2.18.0 foreign_0.8-86
[28] dichromat_2.0-0.1 parallelly_1.36.0 sessioninfo_1.2.2
[31] BSgenome_1.70.1 rstudioapi_0.15.0 RSQLite_2.3.5
[34] generics_0.1.3 BiocIO_1.12.0 ica_1.0-3
[37] spatstat.random_3.2-2 fansi_1.0.6 abind_1.4-5
[40] lifecycle_1.0.4 yaml_2.3.8 SparseArray_1.2.3
[43] BiocFileCache_2.10.1 grid_4.3.2 blob_1.2.4
[46] promises_1.2.1 ExperimentHub_2.10.0 crayon_1.5.2
[49] miniUI_0.1.1.1 lattice_0.22-5 beachmat_2.18.0
[52] KEGGREST_1.42.0 knitr_1.45 pillar_1.9.0
[55] rjson_0.2.21 future.apply_1.11.1 codetools_0.2-19
[58] fastmatch_1.1-4 leiden_0.4.3.1 glue_1.7.0
[61] data.table_1.15.0 remotes_2.4.2.1 vctrs_0.6.5
[64] png_0.1-8 spam_2.10-0 gtable_0.3.4
[67] cachem_1.0.8 xfun_0.41 S4Arrays_1.2.0
[70] mime_0.12 survival_3.5-7 RcppRoll_0.3.0
[73] interactiveDisplayBase_1.40.0 ellipsis_0.3.2 fitdistrplus_1.1-11
[76] ROCR_1.0-11 nlme_3.1-164 bit64_4.0.5
[79] progress_1.2.3 filelock_1.0.3 RcppAnnoy_0.0.22
[82] irlba_2.3.5.1 rpart_4.1.23 KernSmooth_2.23-22
[85] Hmisc_5.1-1 colorspace_2.1-0 DBI_1.2.1
[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_4.10.4
[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_0.6.34 goftest_1.2-3 spatstat.utils_3.0-4
[106] rmarkdown_2.25 XVector_0.42.0 base64enc_0.1-3
[109] htmltools_0.5.7 pkgconfig_2.0.3 sparseMatrixStats_1.14.0
[112] dbplyr_2.4.0 fastmap_1.1.1 rlang_1.1.3
[115] htmlwidgets_1.6.4 shiny_1.8.0 DelayedMatrixStats_1.24.0
[118] zoo_1.8-12 jsonlite_1.8.8 BiocParallel_1.36.0
[121] VariantAnnotation_1.48.1 BiocSingular_1.18.0 RCurl_1.98-1.14
[124] Formula_1.2-5 GenomeInfoDbData_1.2.11 dotCall64_1.1-1
[127] munsell_0.5.0 reticulate_1.35.0 stringi_1.8.3
[130] zlibbioc_1.48.0 MASS_7.3-60.0.1 AnnotationHub_3.10.0
[133] plyr_1.8.9 pkgbuild_1.4.3 parallel_4.3.2
[136] listenv_0.9.1 ggrepel_0.9.5 deldir_2.0-2
[139] Biostrings_2.70.2 splines_4.3.2 tensor_1.5
[142] hms_1.1.3 igraph_2.0.1.1 RcppHNSW_0.6.0
[145] reshape2_1.4.4 biomaRt_2.58.2 ScaledMatrix_1.10.0
[148] pkgload_1.3.4 BiocVersion_3.18.1 XML_3.99-0.16.1
[151] evaluate_0.23 BiocManager_1.30.22 tzdb_0.4.0
[154] httpuv_1.6.14 openssl_2.1.1 RANN_2.6.1
[157] purrr_1.0.2 polyclip_1.10-6 scattermore_1.2
[160] rsvd_1.0.5 xtable_1.8-4 restfulr_0.0.15
[163] RSpectra_0.16-1 later_1.3.2 viridisLite_0.4.2
[166] tibble_3.2.1 memoise_2.0.1 GenomicAlignments_1.38.2
[169] cluster_2.1.6 globals_0.16.2

Hope for your help!

[timoast]

Please see #242