ArchR
ArchR copied to clipboard
GreenleafLab
error in addGroupCoverages(ArchRProj = mp, groupBy = "Sample")
Hello, I found an error in this mp<-addGroupCoverages(ArchRProj = mp, groupBy = "Sample") command.
Here is the code and the error message
mp <- addGroupCoverages(ArchRProj = mp, groupBy = "Sample") ArchR logging to : ArchRLogs/ArchR-addGroupCoverages-199f6f5b278588-Date-2023-09-03_Time-23-42-10.log If there is an issue, please report to github with logFile! 2023-09-03 23:42:11 : Creating Coverage Files!, 0.017 mins elapsed. 2023-09-03 23:42:11 : Batch Execution w/ safelapply!, 0.017 mins elapsed. 2023-09-03 23:43:02 : Adding Kmer Bias to Coverage Files!, 0.865 mins elapsed. Error in .safelapply(seq_along(availableChr), function(x) { : Error Found Iteration 1 : [1] "Error in .logError(e, fn = ".addKmerBiasToCoverage", info = "", errorList = errorList, : \n Exiting See Error Above\n" <simpleError in .logError(e, fn = ".addKmerBiasToCoverage", info = "", errorList = errorList, logFile = logFile): Exiting See Error Above> Error Found Iteration 2 : [1] "Error in .logError(e, fn = ".addKmerBiasToCoverage", info = "", errorList = errorList, : \n Exiting See Error Above\n" <simpleError in .logError(e, fn = ".addKmerBiasToCoverage", info = "", errorList = errorList, logFile = logFile): Exiting See Error Above> Error Found Iteration 3 : [1] "Error in .logError(e, fn = ".addKmerBiasToCoverage", info = "", errorList = errorList, : \n Exiting See Error Above\n" <simpleError in .logError(e, fn = ".addKmerBiasToCoverage", info = "", errorList = errorList, logFile = logFile): Exiting See Error Above> Error Found Iteration 4 : [1] "Error in .logError(e, fn = ".addKmerBiasToCoverag 此外: Warning message: In mclapply(..., mc.cores = threads, mc.preschedule = preschedule) : 21 function calls resulted in an error
and traceback() information
traceback() 6: stop(errorMsg) 5: .safelapply(seq_along(availableChr), function(x) { .logMessage(sprintf("Kmer Bias %s (%s of %s)", availableChr[x], x, length(availableChr)), logFile = logFile) message(availableChr[x], " ", appendLF = FALSE) chrBS <- BSgenome[[availableChr[x]]] exp <- Biostrings::oligonucleotideFrequency(chrBS, width = kmerLength) obsList <- lapply(seq_along(coverageFiles), function(y) { .logMessage(sprintf("Coverage File %s (%s of %s)", availableChr[x], y, length(coverageFiles)), logFile = logFile) tryCatch({ obsx <- .getCoverageInsertionSites(coverageFiles[y], availableChr[x]) %>% { BSgenome::Views(chrBS, IRanges(start = . - floor(kmerLength/2), width = kmerLength)) } %>% { Biostrings::oligonucleotideFrequency(., width = kmerLength, simplify.as = "collapsed") } tryCatch({ gc() }, error = function(e) { }) obsx }, error = function(e) { errorList <- list(y = y, coverageFile = coverageFiles[y], chr = availableChr[x], iS = tryCatch({ .getCoverageInsertionSites(coverageFiles[y], availableChr[x]) }, error = function(e) { "Error .getCoverageInsertionSites" })) .logError(e, fn = ".addKmerBiasToCoverage", info = "", errorList = errorList, logFile = logFile) }) }) %>% SimpleList names(obsList) <- names(coverageFiles) SimpleList(expected = exp, observed = obsList) }, threads = threads) 4: SimpleList(.) 3: .safelapply(seq_along(availableChr), function(x) { .logMessage(sprintf("Kmer Bias %s (%s of %s)", availableChr[x], x, length(availableChr)), logFile = logFile) message(availableChr[x], " ", appendLF = FALSE) chrBS <- BSgenome[[availableChr[x]]] exp <- Biostrings::oligonucleotideFrequency(chrBS, width = kmerLength) obsList <- lapply(seq_along(coverageFiles), function(y) { .logMessage(sprintf("Coverage File %s (%s of %s)", availableChr[x], y, length(coverageFiles)), logFile = logFile) tryCatch({ obsx <- .getCoverageInsertionSites(coverageFiles[y], availableChr[x]) %>% { BSgenome::Views(chrBS, IRanges(start = . - floor(kmerLength/2), width = kmerLength)) } %>% { Biostrings::oligonucleotideFrequency(., width = kmerLength, simplify.as = "collapsed") } tryCatch({ gc() }, error = function(e) { }) obsx }, error = function(e) { errorList <- list(y = y, coverageFile = coverageFiles[y], chr = availableChr[x], iS = tryCatch({ .getCoverageInsertionSites(coverageFiles[y], availableChr[x]) }, error = function(e) { "Error .getCoverageInsertionSites" })) .logError(e, fn = ".addKmerBiasToCoverage", info = "", errorList = errorList, logFile = logFile) }) }) %>% SimpleList names(obsList) <- names(coverageFiles) SimpleList(expected = exp, observed = obsList) }, threads = threads) %>% SimpleList 2: .addKmerBiasToCoverage(coverageMetadata = coverageMetadata, genome = getGenome(ArchRProj), kmerLength = kmerLength, threads = threads, verbose = FALSE, logFile = logFile) 1: addGroupCoverages(ArchRProj = mp, groupBy = "Sample")
here is the session information
sessionInfo() R version 4.0.5 (2021-03-31) Platform: x86_64-pc-linux-gnu (64-bit) Running under: Ubuntu 20.04.2 LTS
Matrix products: default
BLAS: /usr/lib/x86_64-linux-gnu/openblas-serial/libblas.so.3
LAPACK: /usr/lib/x86_64-linux-gnu/openblas-serial/liblapack.so.3
locale:
[1] LC_CTYPE=zh_CN.UTF-8 LC_NUMERIC=C 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 LC_PAPER=zh_CN.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C LC_MEASUREMENT=zh_CN.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] parallel stats4 stats graphics grDevices utils datasets methods base
other attached packages:
[1] ArchR_1.0.2 patchwork_1.1.3 harmony_1.0
[4] Rcpp_1.0.11 SingleR_1.4.1 lubridate_1.9.2
[7] forcats_1.0.0 stringr_1.5.0 dplyr_1.1.2
[10] purrr_1.0.2 readr_2.1.4 tidyr_1.3.0
[13] tibble_3.2.1 tidyverse_2.0.0 SeuratObject_4.1.3
[16] Seurat_4.3.0.1 BiocManager_1.30.22 BSgenome.Mmusculus.UCSC.mm10_1.4.0
[19] BSgenome_1.58.0 rtracklayer_1.50.0 Biostrings_2.58.0
[22] XVector_0.30.0 magrittr_2.0.3 rhdf5_2.34.0
[25] Matrix_1.6-1 data.table_1.14.8 SummarizedExperiment_1.20.0
[28] Biobase_2.50.0 GenomicRanges_1.42.0 GenomeInfoDb_1.26.7
[31] IRanges_2.24.1 S4Vectors_0.32.4 BiocGenerics_0.40.0
[34] MatrixGenerics_1.2.1 matrixStats_1.0.0 ggplot2_3.4.3
[37] installr_0.23.4
loaded via a namespace (and not attached):
[1] utf8_1.2.3 spatstat.explore_3.2-1 reticulate_1.31
[4] tidyselect_1.2.0 htmlwidgets_1.6.2 grid_4.0.5
[7] BiocParallel_1.24.1 Rtsne_0.16 devtools_2.4.5
[10] munsell_0.5.0 codetools_0.2-19 ica_1.0-3
[13] future_1.31.0 miniUI_0.1.1.1 withr_2.5.0
[16] spatstat.random_3.1-5 colorspace_2.1-0 progressr_0.14.0
[19] rstudioapi_0.15.0 ROCR_1.0-11 tensor_1.5
[22] listenv_0.9.0 GenomeInfoDbData_1.2.4 polyclip_1.10-4
[25] pheatmap_1.0.12 parallelly_1.34.0 vctrs_0.6.3
[28] generics_0.1.3 timechange_0.2.0 R6_2.5.1
[31] clue_0.3-64 rsvd_1.0.5 cachem_1.0.8
[34] bitops_1.0-7 rhdf5filters_1.2.1 spatstat.utils_3.0-3
[37] DelayedArray_0.20.0 promises_1.2.1 scales_1.2.1
[40] gtable_0.3.4 beachmat_2.10.0 Cairo_1.6-1
[43] globals_0.16.2 processx_3.8.2 goftest_1.2-3
[46] rlang_1.1.1 GlobalOptions_0.1.2 splines_4.0.5
[49] lazyeval_0.2.2 spatstat.geom_3.2-4 reshape2_1.4.4
[52] abind_1.4-5 httpuv_1.6.11 rsconnect_1.0.2
[55] usethis_2.2.2 tools_4.0.5 ellipsis_0.3.2
[58] RColorBrewer_1.1-3 sessioninfo_1.2.2 ggridges_0.5.4
[61] plyr_1.8.8 sparseMatrixStats_1.2.1 zlibbioc_1.36.0
[64] RCurl_1.98-1.12 prettyunits_1.1.1 ps_1.7.5
[67] deldir_1.0-9 pbapply_1.7-2 GetoptLong_1.0.5
[70] urlchecker_1.0.1 cowplot_1.1.1 zoo_1.8-12
[73] ggrepel_0.9.3 cluster_2.1.4 fs_1.6.3
[76] scattermore_1.2 circlize_0.4.15 lmtest_0.9-40
[79] RANN_2.6.1 fitdistrplus_1.1-11 pkgload_1.3.2.1
[82] hms_1.1.3 mime_0.12 xtable_1.8-4
[85] XML_3.99-0.14 gridExtra_2.3 shape_1.4.6
[88] compiler_4.0.5 KernSmooth_2.23-22 crayon_1.5.2
[91] htmltools_0.5.6 later_1.3.1 tzdb_0.4.0
[94] DBI_1.1.3 ComplexHeatmap_2.6.2 MASS_7.3-60
[97] cli_3.6.1 igraph_1.5.1 pkgconfig_2.0.3
[100] GenomicAlignments_1.26.0 sp_2.0-0 plotly_4.10.2
[103] spatstat.sparse_3.0-2 BSgenome.Hsapiens.UCSC.hg38_1.4.3 callr_3.7.3
[106] digest_0.6.33 sctransform_0.3.5 RcppAnnoy_0.0.21
[109] spatstat.data_3.0-1 leiden_0.4.3 uwot_0.1.16
[112] DelayedMatrixStats_1.12.3 curl_5.0.2 shiny_1.7.5
[115] Rsamtools_2.6.0 gtools_3.9.4 rjson_0.2.21
[118] lifecycle_1.0.3 nlme_3.1-163 jsonlite_1.8.7
[121] Rhdf5lib_1.12.1 BiocNeighbors_1.8.2 viridisLite_0.4.2
[124] fansi_1.0.4 pillar_1.9.0 lattice_0.21-8
[127] pkgbuild_1.4.2 fastmap_1.1.1 httr_1.4.7
[130] survival_3.5-7 remotes_2.4.2.1 glue_1.6.2
[133] shinythemes_1.2.0 rhandsontable_0.3.8 png_0.1-8
[136] presto_1.0.0 profvis_0.3.8 stringi_1.7.12
[139] BiocSingular_1.6.0 memoise_2.0.1 irlba_2.3.5.1
[142] future.apply_1.10.0
I don't know how to solve this problem. Could you please take a look and help me? Thank you very much. ArchR-addGroupCoverages-199f6f6e5b436b-Date-2023-09-03_Time-23-01-27.log
Hi @yangchao4! 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.
It is worth noting that there are very few actual bugs in ArchR. If you are getting an error, it is probably something specific to your dataset, usage, or computational environment, all of which are extremely challenging to troubleshoot. As such, we require reproducible examples (preferably using the tutorial dataset) from users who want assistance. If you cannot reproduce your error, we will not be able to help.
Before going through the work of making a reproducible example, search the previous Issues, Discussions, function definitions, or the ArchR manual and you will likely find the answers you are looking for.
If your post does not contain a reproducible example, it is unlikely to receive a response.
__In addition to a reproducible example, you must do the following things before we help you, 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. Did you post your log file? If not, add it now.
3. 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.
Thank you for your response. I have included the error message, code snippets, log files, and version information, and I am also trying to reproduce this issue using the tutorial files.