'reached elapsed time limit' error on ChIPQC
Entering edit mode
cattapre • 0
Last seen 6.8 years ago


I am trying to run ChIPQC on a 16-sample experiment (with 16 respective controls), but I am getting a message as below. I am running on a Ubuntu cluster running 17 threads for my job.

That's the output I get (included sessionInfo() )

Loading required package: ggplot2
Loading required package: DiffBind
Loading required package: GenomicRanges
Loading required package: methods
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: ‘BiocGenerics’

The following objects are masked from ‘package:parallel’:

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from ‘package:stats’:

    IQR, mad, xtabs

The following objects are masked from ‘package:base’:

    anyDuplicated, append, as.data.frame, cbind, colnames, do.call,
    duplicated, eval, evalq, Filter, Find, get, grep, grepl, intersect,
    is.unsorted, lapply, lengths, Map, mapply, match, mget, order,
    paste, pmax, pmax.int, pmin, pmin.int, Position, rank, rbind,
    Reduce, rownames, sapply, setdiff, sort, table, tapply, union,
    unique, unsplit

Loading required package: S4Vectors
Loading required package: stats4

Attaching package: ‘S4Vectors’

The following objects are masked from ‘package:base’:

    colMeans, colSums, expand.grid, rowMeans, rowSums

Loading required package: IRanges
Loading required package: GenomeInfoDb
Loading required package: SummarizedExperiment
Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

R version 3.3.1 (2016-06-21)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 14.04.3 LTS

 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            

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

other attached packages:
 [1] ChIPQC_1.8.2               DiffBind_2.0.2            
 [3] SummarizedExperiment_1.2.3 Biobase_2.32.0            
 [5] GenomicRanges_1.24.2       GenomeInfoDb_1.8.3        
 [7] IRanges_2.6.1              S4Vectors_0.10.2          
 [9] BiocGenerics_0.18.0        ggplot2_2.1.0             

loaded via a namespace (and not attached):
 [1] edgeR_3.14.0                             
 [2] splines_3.3.1                            
 [3] TxDb.Hsapiens.UCSC.hg18.knownGene_3.2.2  
 [4] TxDb.Mmusculus.UCSC.mm10.knownGene_3.2.2 
 [5] gtools_3.5.0                             
 [6] assertthat_0.1                           
 [7] latticeExtra_0.6-28                      
 [8] amap_0.8-14                              
 [9] RBGL_1.48.1                              
[10] Rsamtools_1.24.0                         
[11] Category_2.38.0                          
[12] RSQLite_1.0.0                            
[13] backports_1.0.3                          
[14] lattice_0.20-33                          
[15] limma_3.28.14                            
[16] digest_0.6.9                             
[17] RColorBrewer_1.1-2                       
[18] XVector_0.12.0                           
[19] checkmate_1.8.1                          
[20] colorspace_1.2-6                         
[21] Matrix_1.2-6                             
[22] plyr_1.8.4                               
[23] GSEABase_1.34.0                          
[24] chipseq_1.22.0                           
[25] XML_3.98-1.4                             
[26] pheatmap_1.0.8                           
[27] ShortRead_1.30.0                         
[28] biomaRt_2.28.0                           
[29] genefilter_1.54.2                        
[30] zlibbioc_1.18.0                          
[31] xtable_1.8-2                             
[32] GO.db_3.3.0                              
[33] scales_0.4.0                             
[34] brew_1.0-6                               
[35] gdata_2.17.0                             
[36] TxDb.Rnorvegicus.UCSC.rn4.ensGene_3.2.2  
[37] BiocParallel_1.6.2                       
[38] tibble_1.1                               
[39] annotate_1.50.0                          
[40] GenomicFeatures_1.24.4                   
[41] survival_2.39-5                          
[42] magrittr_1.5                             
[43] systemPipeR_1.6.2                        
[44] fail_1.3                                 
[45] gplots_3.0.1                             
[46] hwriter_1.3.2                            
[47] GOstats_2.38.1                           
[48] graph_1.50.0                             
[49] tools_3.3.1                              
[50] BBmisc_1.10                              
[51] stringr_1.0.0                            
[52] sendmailR_1.2-1                          
[53] munsell_0.4.3                            
[54] locfit_1.5-9.1                           
[55] AnnotationDbi_1.34.4                     
[56] Biostrings_2.40.2                        
[57] caTools_1.17.1                           
[58] grid_3.3.1                               
[59] RCurl_1.95-4.8                           
[60] TxDb.Celegans.UCSC.ce6.ensGene_3.2.2     
[61] rjson_0.2.15                             
[62] AnnotationForge_1.14.2                   
[63] bitops_1.0-6                             
[64] base64enc_0.1-3                          
[65] gtable_0.2.0                             
[66] DBI_0.4-1                                
[67] reshape2_1.4.1                           
[68] R6_2.1.2                                 
[69] GenomicAlignments_1.8.4                  
[70] Nozzle.R1_1.1-1                          
[71] dplyr_0.5.0                              
[72] rtracklayer_1.32.1                       
[73] KernSmooth_2.23-15                       
[74] stringi_1.1.1                            
[75] TxDb.Hsapiens.UCSC.hg19.knownGene_3.2.2  
[76] BatchJobs_1.6                            
[77] Rcpp_0.12.5                              
[78] TxDb.Dmelanogaster.UCSC.dm3.ensGene_3.2.2
[79] TxDb.Mmusculus.UCSC.mm9.knownGene_3.2.2  
BA_e10-5_1 BA Dlx2 KO e10.5 1 bed
CxCR7_P8_1 CxCR7 Dlx2 KO P8 1 bed
BG_e11-5_1 BG Dlx2 KO e11.5 1 bed
BG_e11-5_2 BG Dlx2 KO e11.5 2 bed
BG_e13-5_R1_1 BG Dlx2 KO e13.5 1 bed
BG_e13-5_R2_1 BG Dlx2 KO e13.5 1 bed
BG_e13-5_R1_2 BG Dlx2 KO e13.5 2 bed
BG_e13-5_R2_2 BG Dlx2 KO e13.5 2 bed
BG_e13-5_R1_3 BG Dlx2 KO e13.5 3 bed
BG_e16-5_1 BG Dlx2 KO e16.5 1 bed
Cx_e16-5_1 Cx Dlx2 KO e16.5 1 bed
Cx_e16-5_2 Cx Dlx2 KO e16.5 2 bed
OB_e16-5_1 OB Dlx2 KO e16.5 1 bed
Cx_P2_1 Cx Dlx2 KO P2 1 bed
Cx_P8_1 Cx Dlx2 KO P8 1 bed
Cx_P8_2 Cx Dlx2 KO P8 2 bed
Compiling annotation...
Computing metrics for 32 samples...
Error: stop worker failed:
  'clear_cluster' receive data failed:
  reached elapsed time limit
Execution halted
job submitted

Could you please help me figure it out? Thanks. Below is my R script


setTimeLimit(cpu = Inf, elapsed = Inf, transient = FALSE)


blacklist.mm9 <- read.table("......../mm9-blacklist.bed")

samples <- read.csv("........./ChIPQC.csv")


sampleset <- ChIPQC(samples, annotation="mm9", chromosomes = NULL, consensus=FALSE, bCount=FALSE, mapQCth = 30, blacklist = blacklist.mm9)

ChIPQCreport(Dlx2, facet=FALSE, reportName="New_ChIPQC", reportFolder="New_report")



ChIPQC • 2.6k views
Entering edit mode
Last seen 20 days ago
United States

I believe that there is an error in analyzing one of  your files, BiocParallel tries to shut the cluster down, but cannot do so in a timely fashion and reports that, rather than the underlying error. You can evaluate your in serial mode to debug the problematic file with

sampleset <- ChIPQC(samples, ...)
Entering edit mode

It worked. Thanks, Martin!


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