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stuart-lab / signac

R toolkit for the analysis of single-cell chromatin data
https://stuartlab.org/signac/
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fragments.tsv.gz.tbi issue? When running the TSSEnrichment function #350

Closed sqsun closed 3 years ago

sqsun commented 3 years ago

fragments.tsv.gz.tbi and fragments.tsv.gz files were automatically generated by 10x CellRanger

I was following the pipline: https://satijalab.org/signac/articles/pbmc_vignette.html, with the issue:

pbmc <- TSSEnrichment(object = pbmc, fast = FALSE) Extracting TSS positions Finding + strand cut sites Error in .headerTabix(file, ...) : [internal] bgzf_seek() failed

traceback() 7: .headerTabix(file, ...) 6: seqnamesTabix(file = tabix.file) 5: seqnamesTabix(file = tabix.file) 4: intersect(x = seqlevels(x = regions), y = seqnamesTabix(file = tabix.file)) 3: MultiRegionCutMatrix(regions = plus.strand, object = object, assay = assay, cells = cells, verbose = FALSE) 2: CreateRegionPileupMatrix(object = object, regions = tss.positions, assay = assay, cells = cells, verbose = verbose) 1: TSSEnrichment(object = pbmc, fast = FALSE)

sessionInfo() R version 3.6.3 (2020-02-29) Platform: x86_64-pc-linux-gnu (64-bit) Running under: CentOS Linux 7 (Core)

Matrix products: default BLAS: /opt/R-3.6.3/lib64/R/lib/libRblas.so LAPACK: /opt/R-3.6.3/lib64/R/lib/libRlapack.so

locale: [1] LC_CTYPE=zh_CN.UTF-8 LC_NUMERIC=C
[3] LC_TIME=zh_CN.UTF-8 LC_COLLATE=zh_CN.UTF-8
[5] LC_MONETARY=zh_CN.UTF-8 LC_MESSAGES=zh_CN.UTF-8
[7] LC_PAPER=zh_CN.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=zh_CN.UTF-8 LC_IDENTIFICATION=C

attached base packages: [1] stats4 parallel stats graphics grDevices utils datasets [8] methods base

other attached packages: [1] motifmatchr_1.8.0 BSgenome.Hsapiens.UCSC.hg38_1.4.1 [3] BSgenome_1.54.0 rtracklayer_1.46.0
[5] Biostrings_2.54.0 XVector_0.26.0
[7] TFBSTools_1.24.0 JASPAR2018_1.1.1
[9] ggplot2_3.3.2 data.table_1.13.0
[11] EnsDb.Hsapiens.v75_2.99.0 ensembldb_2.10.2
[13] AnnotationFilter_1.10.0 GenomicFeatures_1.38.2
[15] AnnotationDbi_1.48.0 Biobase_2.46.0
[17] GenomicRanges_1.38.0 GenomeInfoDb_1.22.1
[19] IRanges_2.20.2 S4Vectors_0.24.4
[21] BiocGenerics_0.32.0 Seurat_3.2.2
[23] Signac_1.1.0

loaded via a namespace (and not attached): [1] R.utils_2.10.1 reticulate_1.18
[3] tidyselect_1.1.0 poweRlaw_0.70.6
[5] RSQLite_2.2.1 htmlwidgets_1.5.2
[7] grid_3.6.3 BiocParallel_1.20.1
[9] Rtsne_0.15 munsell_0.5.0
[11] codetools_0.2-18 ica_1.0-2
[13] future_1.20.1 miniUI_0.1.1.1
[15] withr_2.3.0 colorspace_2.0-0
[17] OrganismDbi_1.28.0 knitr_1.30
[19] rstudioapi_0.13 ROCR_1.0-11
[21] tensor_1.5 listenv_0.8.0
[23] GenomeInfoDbData_1.2.2 polyclip_1.10-0
[25] bit64_4.0.5 farver_2.0.3
[27] parallelly_1.21.0 vctrs_0.3.4
[29] generics_0.1.0 xfun_0.17
[31] biovizBase_1.34.1 BiocFileCache_1.10.2
[33] lsa_0.73.2 ggseqlogo_0.1
[35] R6_2.5.0 rsvd_1.0.3
[37] hdf5r_1.3.3 bitops_1.0-6
[39] spatstat.utils_1.17-0 reshape_0.8.8
[41] DelayedArray_0.12.3 assertthat_0.2.1
[43] promises_1.1.1 scales_1.1.1
[45] nnet_7.3-14 gtable_0.3.0
[47] globals_0.13.1 goftest_1.2-2
[49] ggbio_1.34.0 seqLogo_1.52.0
[51] rlang_0.4.7 RcppRoll_0.3.0
[53] splines_3.6.3 lazyeval_0.2.2
[55] dichromat_2.0-0 checkmate_2.0.0
[57] BiocManager_1.30.10 reshape2_1.4.4
[59] abind_1.4-5 backports_1.2.0
[61] httpuv_1.5.4 Hmisc_4.4-1
[63] RBGL_1.62.1 tools_3.6.3
[65] ellipsis_0.3.1 RColorBrewer_1.1-2
[67] ggridges_0.5.2 Rcpp_1.0.5
[69] plyr_1.8.6 base64enc_0.1-3
[71] progress_1.2.2 zlibbioc_1.32.0
[73] purrr_0.3.4 RCurl_1.98-1.2
[75] prettyunits_1.1.1 rpart_4.1-15
[77] openssl_1.4.2 deldir_0.2-3
[79] pbapply_1.4-3 cowplot_1.1.0
[81] zoo_1.8-8 SummarizedExperiment_1.16.1 [83] ggrepel_0.8.2 cluster_2.1.0
[85] magrittr_1.5 lmtest_0.9-38
[87] RANN_2.6.1 SnowballC_0.7.0
[89] ProtGenerics_1.18.0 fitdistrplus_1.1-1
[91] matrixStats_0.56.0 hms_0.5.3
[93] patchwork_1.1.0 mime_0.9
[95] xtable_1.8-4 XML_3.99-0.3
[97] jpeg_0.1-8.1 gridExtra_2.3
[99] compiler_3.6.3 biomaRt_2.42.1
[101] tibble_3.0.3 KernSmooth_2.23-18
[103] crayon_1.3.4 R.oo_1.24.0
[105] htmltools_0.5.0 mgcv_1.8-33
[107] later_1.1.0.1 Formula_1.2-4
[109] tidyr_1.1.2 DBI_1.1.0
[111] tweenr_1.0.1 dbplyr_1.4.4
[113] MASS_7.3-53 rappdirs_0.3.1
[115] readr_1.3.1 Matrix_1.2-18
[117] R.methodsS3_1.8.1 igraph_1.2.5
[119] pkgconfig_2.0.3 TFMPvalue_0.0.8
[121] GenomicAlignments_1.22.1 foreign_0.8-75
[123] plotly_4.9.2.1 annotate_1.64.0
[125] DirichletMultinomial_1.32.0 stringr_1.4.0
[127] VariantAnnotation_1.32.0 digest_0.6.25
[129] pracma_2.2.9 sctransform_0.3.1
[131] RcppAnnoy_0.0.16 CNEr_1.22.0
[133] graph_1.64.0 spatstat.data_1.5-2
[135] leiden_0.3.5 fastmatch_1.1-0
[137] htmlTable_2.1.0 uwot_0.1.9
[139] curl_4.3 gtools_3.8.2
[141] shiny_1.5.0 Rsamtools_2.2.3
[143] lifecycle_0.2.0 nlme_3.1-149
[145] jsonlite_1.7.1 viridisLite_0.3.0
[147] askpass_1.1 pillar_1.4.6
[149] lattice_0.20-41 GGally_2.0.0
[151] KEGGREST_1.26.1 GO.db_3.10.0
[153] fastmap_1.0.1 httr_1.4.2
[155] survival_3.2-7 glue_1.4.2
[157] spatstat_1.64-1 png_0.1-7
[159] bit_4.0.4 ggforce_0.3.2
[161] stringi_1.5.3 blob_1.2.1
[163] caTools_1.18.0 latticeExtra_0.6-29
[165] memoise_1.1.0 dplyr_1.0.2
[167] irlba_2.3.3 future.apply_1.6.0 

# insert reproducible example here
timoast commented 3 years ago

Try re-indexing the fragment file, and other suggestions here: #242