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GreenleafLab / ArchR

ArchR : Analysis of Regulatory Chromatin in R (www.ArchRProject.com)
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addDoubletsScores : Error in H5Fopen(file, flags = flags, fapl = fapl, native = native) : HDF5. File accessibility. Unable to open file. #1581

Closed matteozoia4 closed 2 years ago

matteozoia4 commented 2 years ago

Attach your log file arrowfiles log : ArchR-createArrows-10a5f145ba289-Date-2022-08-22_Time-22-10-42.log

doubscore log : ArchR-addDoubletScores-10a5f62d31d9f-Date-2022-08-23_Time-09-40-44.log

Describe the bug

doubScores <- addDoubletScores(
     input = inputFiles,
     k = 10,
     knnMethod = "UMAP", 
     LSIMethod = 1)

ArchR logging to : ArchRLogs/ArchR-addDoubletScores-10a5f62d31d9f-Date-2022-08-23_Time-09-40-44.log If there is an issue, please report to github with logFile! 2022-08-23 09:40:44 : Batch Execution w/ safelapply!, 0 mins elapsed. Error in H5Fopen(file, flags = flags, fapl = fapl, native = native) : HDF5. File accessibility. Unable to open file.>

To Reproduce I so far didn't had time to test your provided files, I was trying to fix the bug by looking at previous discussion and issues on the topic (without positive outcome though). 

library(ArchR)
ArchR::installExtraPackages()

library(ArchR)
library(nloptr)
library(parallel)
library(stringi)
library(rhdf5)

library(BSgenome.Mmusculus.UCSC.mm10)
genomeAnnotation <- createGenomeAnnotation(genome = BSgenome.Mmusculus.UCSC.mm10)

library(TxDb.Mmusculus.UCSC.mm10.ensGene)
library(org.Mm.eg.db)
geneAnnotation <- createGeneAnnotation(TxDb = TxDb.Mmusculus.UCSC.mm10.ensGene, OrgDb = org.Mm.eg.db)
geneAnnotation

geneAnnotation <- createGeneAnnotation(
  TSS = geneAnnotation$TSS, 
  exons = geneAnnotation$exons, 
  genes = geneAnnotation$genes
)

inputFiles <- c(scATAC_E9.5="~/Documents/220325_PhD_MZ_back-up/Thesis_Project/In_progress/Multiom_Analysis/Files_for_ArchR/9.5_atac_fragments.tsv.gz", 
                scATAC_E10.5="~/Documents/220325_PhD_MZ_back-up/Thesis_Project/In_progress/Multiom_Analysis/Files_for_ArchR/10.5_atac_fragments.tsv.gz", 
                scATAC_E11.5="~/Documents/220325_PhD_MZ_back-up/Thesis_Project/In_progress/Multiom_Analysis/Files_for_ArchR/11.5_atac_fragments.tsv.gz")
inputFiles 

addArchRThreads(threads = 1)
addArchRGenome("mm10")

ArrowFiles <- createArrowFiles(
  inputFiles = inputFiles,
  sampleNames = names(inputFiles),
  minTSS = 4, 
  minFrags = 1000, 
  addTileMat = TRUE,
  addGeneScoreMat = TRUE
)

ArrowFiles

doubScores <- addDoubletScores(
  input = inputFiles,
  k = 10, 
  knnMethod = = "UMAP",
  LSIMethod = 1
  )>

Expected behavior I would like to add the doubletscores to the 3 ATAC samples I produced the arrow files for.

Screenshots (Not applicable)

Session Info R version 4.2.1 (2022-06-23) Platform: x86_64-apple-darwin17.0 (64-bit) Running under: macOS Monterey 12.0.1

Matrix products: default LAPACK: /Library/Frameworks/R.framework/Versions/4.2/Resources/lib/libRlapack.dylib

Random number generation: RNG: L'Ecuyer-CMRG Normal: Inversion Sample: Rejection

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

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

other attached packages: [1] Rsamtools_2.12.0 org.Mm.eg.db_3.15.0 TxDb.Mmusculus.UCSC.mm10.ensGene_3.4.0 [4] GenomicFeatures_1.48.3 AnnotationDbi_1.58.0 BSgenome.Mmusculus.UCSC.mm10_1.4.3
[7] BSgenome_1.64.0 rtracklayer_1.56.1 Biostrings_2.64.1
[10] XVector_0.36.0 stringi_1.7.8 nloptr_2.0.3
[13] rhdf5_2.40.0 SummarizedExperiment_1.26.1 Biobase_2.56.0
[16] MatrixGenerics_1.8.1 Rcpp_1.0.9 Matrix_1.4-1
[19] GenomicRanges_1.48.0 GenomeInfoDb_1.32.3 IRanges_2.30.1
[22] S4Vectors_0.34.0 BiocGenerics_0.42.0 matrixStats_0.62.0
[25] data.table_1.14.2 stringr_1.4.1 plyr_1.8.7
[28] magrittr_2.0.3 ggplot2_3.3.6 gtable_0.3.0
[31] gtools_3.9.3 gridExtra_2.3 ArchR_1.0.2

loaded via a namespace (and not attached): [1] utf8_1.2.2 reticulate_1.25 tidyselect_1.1.2 RSQLite_2.2.16 htmlwidgets_1.5.4
[6] BiocParallel_1.30.3 Rtsne_0.16 devtools_2.4.4 munsell_0.5.0 codetools_0.2-18
[11] ica_1.0-3 future_1.27.0 miniUI_0.1.1.1 withr_2.5.0 spatstat.random_2.2-0
[16] colorspace_2.0-3 progressr_0.10.1 filelock_1.0.2 rstudioapi_0.13 Seurat_4.1.1
[21] ROCR_1.0-11 tensor_1.5 listenv_0.8.0 labeling_0.4.2 GenomeInfoDbData_1.2.8
[26] harmony_0.1.0 polyclip_1.10-0 farver_2.1.1 bit64_4.0.5 pheatmap_1.0.12
[31] parallelly_1.32.1 vctrs_0.4.1 generics_0.1.3 BiocFileCache_2.4.0 R6_2.5.1
[36] doParallel_1.0.17 clue_0.3-61 bitops_1.0-7 rhdf5filters_1.8.0 spatstat.utils_2.3-1
[41] cachem_1.0.6 DelayedArray_0.22.0 assertthat_0.2.1 BiocIO_1.6.0 promises_1.2.0.1
[46] scales_1.2.1 rgeos_0.5-9 Cairo_1.6-0 globals_0.16.0 processx_3.7.0
[51] goftest_1.2-3 rlang_1.0.4 GlobalOptions_0.1.2 splines_4.2.1 lazyeval_0.2.2
[56] spatstat.geom_2.4-0 yaml_2.3.5 BiocManager_1.30.18 reshape2_1.4.4 abind_1.4-5
[61] httpuv_1.6.5 tools_4.2.1 usethis_2.1.6 ellipsis_0.3.2 spatstat.core_2.4-4
[66] RColorBrewer_1.1-3 sessioninfo_1.2.2 ggridges_0.5.3 progress_1.2.2 zlibbioc_1.42.0
[71] purrr_0.3.4 RCurl_1.98-1.8 ps_1.7.1 prettyunits_1.1.1 rpart_4.1.16
[76] deldir_1.0-6 pbapply_1.5-0 GetoptLong_1.0.5 cowplot_1.1.1 urlchecker_1.0.1
[81] zoo_1.8-10 SeuratObject_4.1.0 ggrepel_0.9.1 cluster_2.1.3 fs_1.5.2
[86] scattermore_0.8 circlize_0.4.15 lmtest_0.9-40 RANN_2.6.1 fitdistrplus_1.1-8
[91] pkgload_1.3.0 hms_1.1.2 patchwork_1.1.2 mime_0.12 xtable_1.8-4
[96] XML_3.99-0.10 shape_1.4.6 biomaRt_2.52.0 compiler_4.2.1 tibble_3.1.8
[101] KernSmooth_2.23-20 crayon_1.5.1 htmltools_0.5.3 mgcv_1.8-40 later_1.3.0
[106] tidyr_1.2.0 DBI_1.1.3 dbplyr_2.2.1 ComplexHeatmap_2.12.1 rappdirs_0.3.3
[111] MASS_7.3-58.1 cli_3.3.0 igraph_1.3.4 pkgconfig_2.0.3 GenomicAlignments_1.32.1 [116] sp_1.5-0 plotly_4.10.0 spatstat.sparse_2.1-1 xml2_1.3.3 foreach_1.5.2
[121] callr_3.7.2 digest_0.6.29 sctransform_0.3.4 RcppAnnoy_0.0.19 spatstat.data_2.2-0
[126] leiden_0.4.2 uwot_0.1.14 curl_4.3.2 restfulr_0.0.15 shiny_1.7.2
[131] rjson_0.2.21 lifecycle_1.0.1 nlme_3.1-159 jsonlite_1.8.0 Rhdf5lib_1.18.2
[136] viridisLite_0.4.1 fansi_1.0.3 pillar_1.8.1 lattice_0.20-45 KEGGREST_1.36.3
[141] fastmap_1.1.0 httr_1.4.4 pkgbuild_1.3.1 survival_3.4-0 glue_1.6.2
[146] remotes_2.4.2 png_0.1-7 shinythemes_1.2.0 rhandsontable_0.3.8 iterators_1.0.14
[151] bit_4.0.4 presto_1.0.0 profvis_0.3.7 blob_1.2.3 memoise_2.0.1
[156] dplyr_1.0.9 irlba_2.3.5 future.apply_1.9.0

Additional context Nothing to add.

Many thanks for your help! MZ

rcorces commented 2 years ago

Hi @matteozoia4! Thanks for using ArchR! Please make sure that your post belongs in the Issues section. Only bugs and error reports belong in the Issues section. Usage questions and feature requests should be posted in the Discussions section, not in Issues.
Before we help you, you must respond to the following questions unless your original post already contained this information: 1. If you've encountered an error, have you already searched previous Issues to make sure that this hasn't already been solved? 2. Can you recapitulate your error using the tutorial code and dataset? If so, provide a reproducible example. 3. Did you post your log file? If not, add it now. 4. Remove any screenshots that contain text and instead copy and paste the text using markdown's codeblock syntax (three consecutive backticks). You can do this by editing your original post.

matteozoia4 commented 2 years ago

Dear rcorces,

I managed to run the addDoubletsScores by re-setting the input files path (as shown below), is that what I was missing as step?

input <- c(scATAC_E9.5="~/Documents/220325_PhD_MZ_back-up/Thesis_Project/In_progress/Multiom_Analysis/Files_for_ArchR/scATAC_E9.5.arrow", 
           scATAC_E10.5="~/Documents/220325_PhD_MZ_back-up/Thesis_Project/In_progress/Multiom_Analysis/Files_for_ArchR/scATAC_E10.5.arrow", 
           scATAC_E11.5="~/Documents/220325_PhD_MZ_back-up/Thesis_Project/In_progress/Multiom_Analysis/Files_for_ArchR/scATAC_E11.5.arrow")

doubScores <- addDoubletScores(
  input = input,
  k = 10, #Refers to how many cells near a "pseudo-doublet" to count.
  knnMethod = "UMAP", #Refers to the embedding to use for nearest neighbor search with doublet projection.
  LSIMethod = 1
  )

Is the out-put correct?

ArchR logging to : ArchRLogs/ArchR-addDoubletScores-10a5f45314c2d-Date-2022-08-23_Time-11-49-56.log
If there is an issue, please report to github with logFile!
2022-08-23 11:49:57 : Batch Execution w/ safelapply!, 0 mins elapsed.
2022-08-23 11:49:57 : scATAC_E9.5 (1 of 3) :  Computing Doublet Statistics, 0 mins elapsed.
Filtering 1 dims correlated > 0.75 to log10(depth + 1)
scATAC_E9.5 (1 of 3) : UMAP Projection R^2 = 0.99321
2022-08-23 11:57:59 : scATAC_E10.5 (2 of 3) :  Computing Doublet Statistics, 8.046 mins elapsed.
scATAC_E10.5 (2 of 3) : UMAP Projection R^2 = 0.99673
2022-08-23 12:02:41 : scATAC_E11.5 (3 of 3) :  Computing Doublet Statistics, 12.746 mins elapsed.
Filtering 1 dims correlated > 0.75 to log10(depth + 1)
scATAC_E11.5 (3 of 3) : UMAP Projection R^2 = 0.99166
ArchR logging successful to : ArchRLogs/ArchR-addDoubletScores-10a5f45314c2d-Date-2022-08-23_Time-11-49-56.log

Many thanks for your time and patience! MZ

rcorces commented 2 years ago

Please read the full manual and all relevant function documentation before posting. As illustrated in the manual and in the function documentation, the input to addDoubletScores() is not a vector of fragment files.

https://www.archrproject.com/bookdown/inferring-scatac-seq-doublets-with-archr.html https://www.archrproject.com/reference/addDoubletScores.html

input | An ArchRProject object or a character vector containing the paths to the ArrowFiles to be used. -- | --