BiocParallel error with ChIPQC
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@8f9d24cc
Last seen 3 days ago
United States

Hi, I just got this error message when using ChIPQC (with a metadata table for 4 bam files with peak info...):

Error: BiocParallel errors 4 remote errors, element index: 1, 2, 3, 4  0 unevaluated and other errors  
first remote error: Error in if (is.na(peaks)) peaks = NULL: the condition has length > 1

With the following command:

chipObj <- ChIPQC(samples)

Show Traceback gives me:

7. stop(.error_bplist(res))
6. .bpinit(manager = manager, X = X, FUN = FUN, ARGS = ARGS, BPPARAM = BPPARAM, 
BPOPTIONS = BPOPTIONS, BPREDO = BPREDO)
5. bplapply(X, FUN, ..., BPREDO = BPREDO, BPPARAM = BPPARAM, BPOPTIONS = BPOPTIONS)
4. bplapply(X, FUN, ..., BPREDO = BPREDO, BPPARAM = BPPARAM, BPOPTIONS = BPOPTIONS)
3. bplapply(samplelist, doChIPQCsample, experiment, chromosomes, 
annotation, mapQCth, blacklist, profileWin, fragmentLength, 
shifts)
2. bplapply(samplelist, doChIPQCsample, experiment, chromosomes, 
annotation, mapQCth, blacklist, profileWin, fragmentLength, 
shifts)
1. ChIPQC(samples)

After getting this error, I tried to run ChIPQC with files that had given me great results in the past (ChIPQC report...) and I got the same error message. I can't analyze these other ChIP-seq datasets anymore. I recently updated a bunch of R packages so my guess would be that the new version of one of the packages is encountering some issue.

I tried to install a previous version of ChIPQC (3.10 or 3.11) with:

BiocManager::install("ChIPQC", version = "3.11")

and kept getting error messages of this type:

Error: Bioconductor version '3.11' requires R version '4.0'; use   `BiocManager::install(version = '3.15')` with R version 4.2; see https://bioconductor.org/install

I already the version 3.15 of BiocManager and the version 4.2 of R so I am not sure how to overcome this error.

A similar ChIPQC issue (from 3.8 years ago) was described here: ChIPQC - can't read in bam files

It was suggested in the comments to try to open the bam files with Rsamtools function open.bamFile(). I just did that and got the following error message:

Error in value[[3L]](cond) : 
failed to open BamFile: unable to find an inherited method for function 'path' for signature '"character"'
6. stop("failed to open BamFile: ", conditionMessage(err))
5. value[[3L]](cond)
4. tryCatchOne(expr, names, parentenv, handlers[[1L]])
3. tryCatchList(expr, classes, parentenv, handlers)
2. tryCatch({
.io_check_exists(path(con))
index <- sub("\\.bai$", "", index(con, asNA = FALSE))
con$.extptr <- .Call(.bamfile_open, path(con), index, "rb") ...
1. open.BamFile("extract_14M_1_PEO1_G9A_1_S4_L002.bam")

Could there be an issue with the latest version of Rsamtools or am I not using Rsamtools correctly?

From another Bioconductor question: DiffBind GreyListChIP error: Error: BiocParallel errors

I tried:

BiocParallel::register(BiocParallel::SerialParam())

And this did not solve my issue.

I also tried a few other things like clearing the workspace, relaunching R, RStudio, my computer, installing the newest version of RStudio, reindexing the bam files... I tried on a different computer that has unfortunately also updated many R packages (it has the version 3.12 of ChIPQC) and got the same error message.

If anyone has any solution or ideas I could try to solve this issue, it would be fantastic and greatly appreciated.

Thank you very much in advance.

Best,

Etienne

sessionInfo( ):

R version 4.2.0 (2022-04-22)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 20.04.4 LTS

Matrix products: default
BLAS:   /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3
LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/liblapack.so.3

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

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

other attached packages:
 [1] BiocParallel_1.31.8         valr_0.6.4                  ChIPseeker_1.32.0           org.Mm.eg.db_3.15.0         ensembldb_2.20.2            AnnotationFilter_1.20.0     GenomicFeatures_1.48.3      AnnotationDbi_1.58.0        AnnotationHub_3.4.0         BiocFileCache_2.4.0        
[11] dbplyr_2.1.1                forcats_0.5.1               stringr_1.4.0               dplyr_1.0.9                 purrr_0.3.4                 readr_2.1.2                 tidyr_1.2.0                 tibble_3.1.7                tidyverse_1.3.1             ChIPQC_1.32.0              
[21] DiffBind_3.6.1              SummarizedExperiment_1.26.1 Biobase_2.56.0              MatrixGenerics_1.8.0        matrixStats_0.62.0          GenomicRanges_1.48.0        GenomeInfoDb_1.32.2         IRanges_2.30.0              S4Vectors_0.34.0            BiocGenerics_0.42.0        
[31] ggplot2_3.3.6              

loaded via a namespace (and not attached):
  [1] utf8_1.2.2                                tidyselect_1.1.2                          RSQLite_2.2.14                            htmlwidgets_1.5.4                         grid_4.2.0                                scatterpie_0.1.7                         
  [7] munsell_0.5.0                             codetools_0.2-18                          systemPipeR_2.2.2                         withr_2.5.0                               colorspace_2.0-3                          GOSemSim_2.22.0                          
 [13] filelock_1.0.2                            knitr_1.39                                rstudioapi_0.13                           DOSE_3.22.0                               bbmle_1.0.25                              GenomeInfoDbData_1.2.8                   
 [19] polyclip_1.10-0                           mixsqp_0.3-43                             hwriter_1.3.2.1                           farver_2.1.0                              bit64_4.0.5                               treeio_1.20.0                            
 [25] coda_0.19-4                               vctrs_0.4.1                               TxDb.Rnorvegicus.UCSC.rn4.ensGene_3.2.2   generics_0.1.2                            xfun_0.31                                 R6_2.5.1                                 
 [31] graphlayouts_0.8.0                        apeglm_1.18.0                             invgamma_1.1                              locfit_1.5-9.5                            gridGraphics_0.5-1                        fgsea_1.22.0                             
 [37] bitops_1.0-7                              cachem_1.0.6                              DelayedArray_0.22.0                       assertthat_0.2.1                          vroom_1.5.7                               promises_1.2.0.1                         
 [43] BiocIO_1.6.0                              scales_1.2.0                              ggraph_2.0.5                              enrichplot_1.16.1                         gtable_0.3.0                              tidygraph_1.2.1                          
 [49] rlang_1.0.2                               splines_4.2.0                             rtracklayer_1.56.0                        lazyeval_0.2.2                            broom_0.8.0                               BiocManager_1.30.18                      
 [55] yaml_2.3.5                                reshape2_1.4.4                            modelr_0.1.8                              TxDb.Dmelanogaster.UCSC.dm3.ensGene_3.2.2 backports_1.4.1                           httpuv_1.6.5                             
 [61] qvalue_2.28.0                             tools_4.2.0                               ggplotify_0.1.0                           ellipsis_0.3.2                            gplots_3.1.3                              RColorBrewer_1.1-3                       
 [67] Rcpp_1.0.8.3                              plyr_1.8.7                                progress_1.2.2                            zlibbioc_1.42.0                           RCurl_1.98-1.7                            prettyunits_1.1.1                        
 [73] viridis_0.6.2                             ashr_2.2-54                               chipseq_1.46.0                            haven_2.5.0                               ggrepel_0.9.1                             fs_1.5.2                                 
 [79] magrittr_2.0.3                            data.table_1.14.2                         TxDb.Hsapiens.UCSC.hg18.knownGene_3.2.2   DO.db_2.9                                 reprex_2.0.1                              truncnorm_1.0-8                          
 [85] mvtnorm_1.1-3                             SQUAREM_2021.1                            amap_0.8-18                               ProtGenerics_1.28.0                       TxDb.Mmusculus.UCSC.mm9.knownGene_3.2.2   patchwork_1.1.1                          
 [91] hms_1.1.1                                 mime_0.12                                 xtable_1.8-4                              XML_3.99-0.10                             emdbook_1.3.12                            jpeg_0.1-9                               
 [97] readxl_1.4.0                              gridExtra_2.3                             compiler_4.2.0                            biomaRt_2.52.0                            bdsmatrix_1.3-4                           shadowtext_0.1.2                         
[103] KernSmooth_2.23-20                        crayon_1.5.1                              htmltools_0.5.2                           ggfun_0.0.6                               later_1.3.0                               tzdb_0.3.0                               
[109] aplot_0.1.6                               lubridate_1.8.0                           DBI_1.1.2                                 tweenr_1.0.2                              MASS_7.3-57                               rappdirs_0.3.3                           
[115] boot_1.3-28                               ShortRead_1.54.0                          Matrix_1.4-1                              cli_3.3.0                                 parallel_4.2.0                            igraph_1.3.2                             
[121] pkgconfig_2.0.3                           TxDb.Hsapiens.UCSC.hg19.knownGene_3.2.2   GenomicAlignments_1.32.0                  numDeriv_2016.8-1.1                       TxDb.Celegans.UCSC.ce6.ensGene_3.2.2      xml2_1.3.3                               
[127] ggtree_3.4.0                              XVector_0.36.0                            rvest_1.0.2                               yulab.utils_0.0.4                         digest_0.6.29                             Biostrings_2.64.0                        
[133] fastmatch_1.1-3                           cellranger_1.1.0                          tidytree_0.3.9                            restfulr_0.0.13                           GreyListChIP_1.28.1                       curl_4.3.2                               
[139] shiny_1.7.1                               Rsamtools_2.12.0                          gtools_3.9.2                              rjson_0.2.21                              nlme_3.1-157                              lifecycle_1.0.1                          
[145] jsonlite_1.8.0                            viridisLite_0.4.0                         limma_3.52.1                              BSgenome_1.64.0                           fansi_1.0.3                               pillar_1.7.0                             
[151] lattice_0.20-45                           Nozzle.R1_1.1-1                           plotrix_3.8-2                             KEGGREST_1.36.2                           fastmap_1.1.0                             httr_1.4.3                               
[157] GO.db_3.15.0                              interactiveDisplayBase_1.34.0             glue_1.6.2                                png_0.1-7                                 BiocVersion_3.15.2                        bit_4.0.4                                
[163] ggforce_0.3.3                             stringi_1.7.6                             blob_1.2.3                                TxDb.Mmusculus.UCSC.mm10.knownGene_3.10.0 latticeExtra_0.6-29                       caTools_1.18.2                           
[169] memoise_2.0.1                             ape_5.6-2                                 irlba_2.3.5
BiocManager ChIPQC RSamtools BiocParallel • 55 views
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