BSmooth - Error in env[[as.character(i)]] <- value : wrong args for environment subassignment

[ciganche]

I'm coming across a problem while trying to analyze WGBS data from CD4 and CD8 T cells (3 vs 3 samples). I used the following code:

bsseq_obj  = BSseq(chr = chr, pos = position, M = M, Cov = C, sampleNames = sample_names)
replicate = c(seq(1,length(group1_sample_list)), seq(1,length(group2_sample_list)))
bsseq::pData(bsseq_obj) = data.frame(row.names = sample_names, replicate, tissue)
bsseq_obj = renameSeqlevels(bsseq_obj, mapSeqlevels(seqlevels(bsseq_obj), "UCSC"))
bsseq_obj = bsseq_obj[seqnames(bsseq_obj)=="chr19",]
bs.fit = BSmooth(bsseq_obj)

For testing purposes, I am only focusing on chr 19 with 1057376 CpG sites in total. The error appears after calling BSmooth:

Error in env[[as.character(i)]] <- value : 
  wrong args for environment subassignment
In addition: Warning message:
In parallel::mccollect(wait = FALSE, timeout = 1) :
  1 parallel job did not deliver a result

BiocManager::valid() returns TRUE.

R version 4.1.3 (2022-03-10)
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

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   
 [6] 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] HDF5Array_1.22.1            rhdf5_2.38.1                DelayedArray_0.20.0         Matrix_1.4-1                bsseq_1.30.0               
 [6] SummarizedExperiment_1.24.0 Biobase_2.54.0              MatrixGenerics_1.6.0        matrixStats_0.61.0          GenomicRanges_1.46.1       
[11] GenomeInfoDb_1.30.1         IRanges_2.28.0              S4Vectors_0.32.4            ExperimentHub_2.2.1         AnnotationHub_3.2.2        
[16] BiocFileCache_2.2.1         dbplyr_2.1.1                BiocGenerics_0.40.0         DMRcate_2.8.5              

loaded via a namespace (and not attached):
  [1] utf8_1.2.2                                          R.utils_2.11.0                                     
  [3] tidyselect_1.1.2                                    RSQLite_2.2.12                                     
  [5] AnnotationDbi_1.56.2                                htmlwidgets_1.5.4                                  
  [7] grid_4.1.3                                          BiocParallel_1.28.3                                
  [9] munsell_0.5.0                                       codetools_0.2-18                                   
 [11] preprocessCore_1.56.0                               statmod_1.4.36                                     
 [13] colorspace_2.0-3                                    filelock_1.0.2                                     
 [15] knitr_1.38                                          rstudioapi_0.13                                    
 [17] GenomeInfoDbData_1.2.7                              bit64_4.0.5                                        
 [19] vctrs_0.4.0                                         generics_0.1.2                                     
 [21] xfun_0.30                                           biovizBase_1.42.0                                  
 [23] R6_2.5.1                                            illuminaio_0.36.0                                  
 [25] locfit_1.5-9.5                                      AnnotationFilter_1.18.0                            
 [27] bitops_1.0-7                                        rhdf5filters_1.6.0                                 
 [29] cachem_1.0.6                                        reshape_0.8.8                                      
 [31] assertthat_0.2.1                                    promises_1.2.0.1                                   
 [33] BiocIO_1.4.0                                        IlluminaHumanMethylation450kanno.ilmn12.hg19_0.6.0 
 [35] scales_1.1.1                                        nnet_7.3-17                                        
 [37] gtable_0.3.0                                        ensembldb_2.18.4                                   
 [39] rlang_1.0.2                                         genefilter_1.76.0                                  
 [41] splines_4.1.3                                       rtracklayer_1.54.0                                 
 [43] lazyeval_0.2.2                                      DSS_2.42.0                                         
 [45] GEOquery_2.62.2                                     dichromat_2.0-0                                    
 [47] checkmate_2.0.0                                     BiocManager_1.30.16                                
 [49] yaml_2.3.5                                          GenomicFeatures_1.46.5                             
 [51] backports_1.4.1                                     httpuv_1.6.5                                       
 [53] Hmisc_4.6-0                                         tools_4.1.3                                        
 [55] nor1mix_1.3-0                                       ggplot2_3.3.5                                      
 [57] ellipsis_0.3.2                                      RColorBrewer_1.1-3                                 
 [59] siggenes_1.68.0                                     Rcpp_1.0.8.3                                       
 [61] plyr_1.8.7                                          base64enc_0.1-3                                    
 [63] sparseMatrixStats_1.6.0                             progress_1.2.2                                     
 [65] zlibbioc_1.40.0                                     purrr_0.3.4                                        
 [67] RCurl_1.98-1.6                                      prettyunits_1.1.1                                  
 [69] rpart_4.1.16                                        openssl_2.0.0                                      
 [71] bumphunter_1.36.0                                   cluster_2.1.3                                      
 [73] magrittr_2.0.3                                      data.table_1.14.2                                  
 [75] ProtGenerics_1.26.0                                 IlluminaHumanMethylationEPICanno.ilm10b4.hg19_0.6.0
 [77] missMethyl_1.28.0                                   hms_1.1.1                                          
 [79] mime_0.12                                           xtable_1.8-4                                       
 [81] XML_3.99-0.9                                        jpeg_0.1-9                                         
 [83] mclust_5.4.9                                        gridExtra_2.3                                      
 [85] compiler_4.1.3                                      biomaRt_2.50.3                                     
 [87] minfi_1.40.0                                        tibble_3.1.6                                       
 [89] crayon_1.5.1                                        R.oo_1.24.0                                        
 [91] htmltools_0.5.2                                     later_1.3.0                                        
 [93] tzdb_0.3.0                                          Formula_1.2-4                                      
 [95] tidyr_1.2.0                                         DBI_1.1.2                                          
 [97] MASS_7.3-56                                         rappdirs_0.3.3                                     
 [99] readr_2.1.2                                         permute_0.9-7                                      
[101] cli_3.2.0                                           quadprog_1.5-8                                     
[103] R.methodsS3_1.8.1                                   parallel_4.1.3                                     
[105] Gviz_1.38.3                                         pkgconfig_2.0.3                                    
[107] GenomicAlignments_1.30.0                            foreign_0.8-82                                     
[109] xml2_1.3.3                                          foreach_1.5.2                                      
[111] annotate_1.72.0                                     rngtools_1.5.2                                     
[113] multtest_2.50.0                                     beanplot_1.2                                       
[115] XVector_0.34.0                                      doRNG_1.8.2                                        
[117] scrime_1.3.5                                        stringr_1.4.0                                      
[119] VariantAnnotation_1.40.0                            digest_0.6.29                                      
[121] Biostrings_2.62.0                                   base64_2.0                                         
[123] htmlTable_2.4.0                                     edgeR_3.36.0                                       
[125] DelayedMatrixStats_1.16.0                           restfulr_0.0.13                                    
[127] curl_4.3.2                                          shiny_1.7.1                                        
[129] Rsamtools_2.10.0                                    gtools_3.9.2                                       
[131] rjson_0.2.21                                        lifecycle_1.0.1                                    
[133] nlme_3.1-157                                        Rhdf5lib_1.16.0                                    
[135] askpass_1.1                                         limma_3.50.1                                       
[137] BSgenome_1.62.0                                     fansi_1.0.3                                        
[139] pillar_1.7.0                                        lattice_0.20-45                                    
[141] KEGGREST_1.34.0                                     fastmap_1.1.0                                      
[143] httr_1.4.2                                          survival_3.3-1                                     
[145] interactiveDisplayBase_1.32.0                       glue_1.6.2                                         
[147] png_0.1-7                                           iterators_1.0.14                                   
[149] BiocVersion_3.14.0                                  bit_4.0.4                                          
[151] stringi_1.7.6                                       blob_1.2.2                                         
[153] org.Hs.eg.db_3.14.0                                 latticeExtra_0.6-29                                
[155] memoise_2.0.1                                       dplyr_1.0.8

 

Thank you very much for your time.

[PeteHaitch]

The root cause is this:

In parallel::mccollect(wait = FALSE, timeout = 1) :
  1 parallel job did not deliver a result

which means that one of the parallel jobs failed. This can sometimes happen on HPC due to a job being killed (e.g., exceeding memory limits or running time). What was the value of BiocParallel::bpparam() when you ran this code (this would've been used as the default value of BPPARAM in your call to BSmooth())? You might try BSmooth(bsseq_obj, BPPARAM = BiocParallel::SerialParam()) to see if the code works when run without parallelisation.

[kasperdanielhansen]

Could you call traceback() right after the error and send the output?

On Tue, Apr 5, 2022 at 5:35 AM Aleksa Krsmanović @.***> wrote:

I'm coming across a problem while trying to analyze WGBS data from CD4 and CD8 T cells (3 vs 3 samples). I used the following code:

bsseq_obj = BSseq(chr = chr, pos = position, M = M, Cov = C, sampleNames = sample_names) replicate = c(seq(1,length(group1_sample_list)), seq(1,length(group2_sample_list))) bsseq::pData(bsseq_obj) = data.frame(row.names = sample_names, replicate, tissue) bsseq_obj = renameSeqlevels(bsseq_obj, mapSeqlevels(seqlevels(bsseq_obj), "UCSC")) bsseq_obj = bsseq_obj[seqnames(bsseq_obj)=="chr19",] bs.fit = BSmooth(bsseq_obj)

For testing purposes, I am only focusing on chr 19 with 1057376 CpG sites in total. The error appears after calling BSmooth:

Error in env[[as.character(i)]] <- value : wrong args for environment subassignment In addition: Warning message: In parallel::mccollect(wait = FALSE, timeout = 1) : 1 parallel job did not deliver a result

BiocManager::valid() returns TRUE. I am using Ubuntu 20.04 with R version 4.1.3

Thank you very much for your time.

— Reply to this email directly, view it on GitHub https://github.com/hansenlab/bsseq/issues/110, or unsubscribe https://github.com/notifications/unsubscribe-auth/ABF2DH34LYWEB77CFYR3P5TVDQCODANCNFSM5SSEOAXA . You are receiving this because you are subscribed to this thread.Message ID: @.***>

-- Best, Kasper