DiffBind: GreyListChIP error: Error: $ operator is invalid for atomic vectors
Entering edit mode
millerh1 ▴ 10
Last seen 14 months ago
United States

Hello! I am currently using DiffBind 3.6.1 and encountering the following error when attempting to analyze my data:

> dba <- dba.contrast(dba, design = "~Condition")
Computing results names...
> dba <- dba.analyze(dba)
Applying Blacklist/Greylists...
Genome detected: Hsapiens.UCSC.hg38
Applying blacklist...
Removed: 276 of 43183 intervals.
Counting control reads for greylist...
Blacklist error: Error in value[[3L]](cond): GreyListChIP error: Error: $ operator is invalid for atomic vectors

Unable to apply Blacklist/Greylist.

Do you know what might be the issue?

Here is my sessionInfo():

> 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/blas/libblas.so.3.9.0
LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.9.0

 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C               LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8    LC_PAPER=en_US.UTF-8       LC_NAME=C                 

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

other attached packages:
 [1] RLSeq_1.2.0                 DiffBind_3.6.1              SummarizedExperiment_1.26.1 Biobase_2.56.0             
 [5] MatrixGenerics_1.8.0        matrixStats_0.62.0          GenomicRanges_1.48.0        GenomeInfoDb_1.32.1        
 [9] IRanges_2.30.0              S4Vectors_0.34.0            BiocGenerics_0.42.0         forcats_0.5.1              
[13] stringr_1.4.0               dplyr_1.0.9                 purrr_0.3.4                 readr_2.1.2                
[17] tidyr_1.2.0                 tibble_3.1.7                ggplot2_3.3.6               tidyverse_1.3.1            

loaded via a namespace (and not attached):
  [1] utf8_1.2.2                    tidyselect_1.1.2              RSQLite_2.2.14                AnnotationDbi_1.58.0         
  [5] htmlwidgets_1.5.4             grid_4.2.0                    BiocParallel_1.30.3           aws.signature_0.6.0          
  [9] pROC_1.18.0                   munsell_0.5.0                 codetools_0.2-18              systemPipeR_2.2.2            
 [13] future_1.25.0                 withr_2.5.0                   colorspace_2.0-3              filelock_1.0.2               
 [17] rstudioapi_0.13               listenv_0.8.0                 bbmle_1.0.25                  GenomeInfoDbData_1.2.8       
 [21] mixsqp_0.3-43                 hwriter_1.3.2.1               bit64_4.0.5                   coda_0.19-4                  
 [25] parallelly_1.31.1             vctrs_0.4.1                   generics_0.1.2                ipred_0.9-12                 
 [29] BiocFileCache_2.4.0           regioneR_1.28.0               R6_2.5.1                      apeglm_1.18.0                
 [33] invgamma_1.1                  locfit_1.5-9.5                bitops_1.0-7                  cachem_1.0.6                 
 [37] DelayedArray_0.22.0           assertthat_0.2.1              vroom_1.5.7                   promises_1.2.0.1             
 [41] BiocIO_1.6.0                  scales_1.2.0                  nnet_7.3-17                   gtable_0.3.0                 
 [45] valr_0.6.4                    globals_0.15.0                processx_3.5.3                timeDate_3043.102            
 [49] rlang_1.0.2                   genefilter_1.78.0             splines_4.2.0                 rtracklayer_1.56.0           
 [53] ModelMetrics_1.2.2.2          broom_0.8.0                   RLHub_1.2.0                   BiocManager_1.30.17          
 [57] yaml_2.3.5                    reshape2_1.4.4                modelr_0.1.8                  GenomicFeatures_1.48.0       
 [61] backports_1.4.1               httpuv_1.6.5                  caret_6.0-92                  tools_4.2.0                  
 [65] lava_1.6.10                   ellipsis_0.3.2                gplots_3.1.3                  RColorBrewer_1.1-3           
 [69] Rcpp_1.0.8.3                  plyr_1.8.7                    base64enc_0.1-3               progress_1.2.2               
 [73] zlibbioc_1.42.0               RCurl_1.98-1.6                ps_1.7.0                      prettyunits_1.1.1            
 [77] rpart_4.1.16                  pbapply_1.5-0                 ashr_2.2-54                   haven_2.5.0                  
 [81] ggrepel_0.9.1                 fs_1.5.2                      magrittr_2.0.3                data.table_1.14.2            
 [85] caretEnsemble_2.0.1           reprex_2.0.1                  truncnorm_1.0-8               mvtnorm_1.1-3                
 [89] SQUAREM_2021.1                amap_0.8-18                   hms_1.1.1                     mime_0.12                    
 [93] xtable_1.8-4                  XML_3.99-0.9                  emdbook_1.3.12                jpeg_0.1-9                   
 [97] readxl_1.4.0                  gridExtra_2.3                 compiler_4.2.0                biomaRt_2.52.0               
[101] bdsmatrix_1.3-4               KernSmooth_2.23-20            crayon_1.5.1                  htmltools_0.5.2              
[105] later_1.3.0                   tzdb_0.3.0                    geneplotter_1.74.0            aws.s3_0.3.21                
[109] lubridate_1.8.0               DBI_1.1.2                     ExperimentHub_2.4.0           dbplyr_2.1.1                 
[113] MASS_7.3-57                   rappdirs_0.3.3                ShortRead_1.54.0              Matrix_1.4-1                 
[117] cli_3.3.0                     parallel_4.2.0                gower_1.0.0                   pkgconfig_2.0.3              
[121] GenomicAlignments_1.32.0      numDeriv_2016.8-1.1           recipes_0.2.0                 xml2_1.3.3                   
[125] foreach_1.5.2                 annotate_1.74.0               hardhat_0.2.0                 XVector_0.36.0               
[129] prodlim_2019.11.13            rvest_1.0.2                   callr_3.7.0                   digest_0.6.29                
[133] Biostrings_2.64.0             cellranger_1.1.0              restfulr_0.0.13               GreyListChIP_1.28.0          
[137] curl_4.3.2                    shiny_1.7.1                   Rsamtools_2.12.0              gtools_3.9.2                 
[141] rjson_0.2.21                  lifecycle_1.0.1               nlme_3.1-157                  jsonlite_1.8.0               
[145] limma_3.52.0                  BSgenome_1.64.0               fansi_1.0.3                   pillar_1.7.0                 
[149] lattice_0.20-45               KEGGREST_1.36.0               fastmap_1.1.0                 httr_1.4.3                   
[153] survival_3.2-13               interactiveDisplayBase_1.34.0 glue_1.6.2                    png_0.1-7                    
[157] iterators_1.0.14              BiocVersion_3.15.2            bit_4.0.4                     class_7.3-20                 
[161] stringi_1.7.6                 blob_1.2.3                    DESeq2_1.36.0                 AnnotationHub_3.4.0          
[165] latticeExtra_0.6-29           caTools_1.18.2                memoise_2.0.1                 irlba_2.3.5                  
[169] future.apply_1.9.0
DiffBind • 767 views
Entering edit mode

I would welcome the opportunity to debug this issue if you were willing to send me your DBA object dba and a link to a place I could access the control reads.

In the meantime, you can turn off greylist generation by either setting bGreylist=FALSE when calling dba.analyze() or setting

dba$config$doGreylist <- FALSE

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