Question: ChIPQC Error in names(res) <- nms
0
gravatar for gavrielmatt
9 months ago by
United States
gavrielmatt0 wrote:

Hello,

I am trying to run ChIPQC on 3 experimental samples and 1 control sample. When I run ChIPQC I get an error message when ChIPQC tries to analyze the 3rd scaffold. Here is the ChIPQC command I ran and the corresponding output.

> Experiment_ChIPQC <- ChIPQC(ExperimentTable, chromosomes = NULL)
Sample1     NA bed
Sample2     NA bed
Sample3     NA bed
Computing metrics for 4 samples...
list
Bam file has 434 contigs
Calculating coverage histogram for scaffold_1

Calculating SSD for scaffold_1

Calculating unique positions per strand for scaffold_1

Calculating shift for scaffold_1

 300 / 300
Counting reads in features for scaffold_1

Signal over peaks for scaffold_1

done
Calculating coverage
Calculating Summits on  scaffold_1  ..Calculating coverage histogram for scaffold_2

Calculating SSD for scaffold_2

Calculating unique positions per strand for scaffold_2

Calculating shift for scaffold_2

 300 / 300
Counting reads in features for scaffold_2

Signal over peaks for scaffold_2

done
Calculating coverage
Calculating Summits on  scaffold_2  ..Calculating coverage histogram for scaffold_3

Calculating SSD for scaffold_3

Calculating unique positions per strand for scaffold_3

Calculating shift for scaffold_3

 100Error in names(res) <- nms : 
  'names' attribute [4] must be the same length as the vector [2]
In addition: Warning message:
stop worker failed:
  'clear_cluster' receive data failed:
  reached elapsed time limit 

 

Here is the traceback

> traceback()
5: bplapply(X, FUN, ..., BPREDO = BPREDO, BPPARAM = BPPARAM)
4: bplapply(X, FUN, ..., BPREDO = BPREDO, BPPARAM = BPPARAM)
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(ExperimentTable, chromosomes = NULL)

 

Here is the session info

> sessionInfo()
R version 3.4.3 (2017-11-30)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS High Sierra 10.13.6

Matrix products: default
BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libRlapack.dylib

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

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

other attached packages:
 [1] ChIPQC_1.14.0              DiffBind_2.6.6            
 [3] SummarizedExperiment_1.8.1 DelayedArray_0.4.1        
 [5] matrixStats_0.54.0         Biobase_2.38.0            
 [7] GenomicRanges_1.30.3       GenomeInfoDb_1.14.0       
 [9] IRanges_2.12.0             S4Vectors_0.16.0          
[11] BiocGenerics_0.24.0        ggplot2_3.0.0             

loaded via a namespace (and not attached):
  [1] amap_0.8-16                              
  [2] colorspace_1.3-2                         
  [3] rjson_0.2.20                             
  [4] hwriter_1.3.2                            
  [5] XVector_0.18.0                           
  [6] base64enc_0.1-3                          
  [7] rstudioapi_0.7                           
  [8] ggrepel_0.8.0                            
  [9] bit64_0.9-7                              
 [10] AnnotationDbi_1.40.0                     
 [11] splines_3.4.3                            
 [12] TxDb.Rnorvegicus.UCSC.rn4.ensGene_3.2.2  
 [13] Nozzle.R1_1.1-1                          
 [14] Rsamtools_1.30.0                         
 [15] annotate_1.56.2                          
 [16] GO.db_3.5.0                              
 [17] pheatmap_1.0.10                          
 [18] graph_1.56.0                             
 [19] TxDb.Hsapiens.UCSC.hg18.knownGene_3.2.2  
 [20] compiler_3.4.3                           
 [21] httr_1.3.1                               
 [22] GOstats_2.44.0                           
 [23] backports_1.1.2                          
 [24] assertthat_0.2.0                         
 [25] Matrix_1.2-14                            
 [26] lazyeval_0.2.1                           
 [27] TxDb.Hsapiens.UCSC.hg19.knownGene_3.2.2  
 [28] limma_3.34.9                             
 [29] prettyunits_1.0.2                        
 [30] tools_3.4.3                              
 [31] bindrcpp_0.2.2                           
 [32] gtable_0.2.0                             
 [33] glue_1.3.0                               
 [34] GenomeInfoDbData_1.0.0                   
 [35] Category_2.44.0                          
 [36] reshape2_1.4.3                           
 [37] systemPipeR_1.12.0                       
 [38] dplyr_0.7.6                              
 [39] ShortRead_1.36.1                         
 [40] Rcpp_0.12.18                             
 [41] TxDb.Dmelanogaster.UCSC.dm3.ensGene_3.2.2
 [42] TxDb.Mmusculus.UCSC.mm9.knownGene_3.2.2  
 [43] Biostrings_2.46.0                        
 [44] gdata_2.18.0                             
 [45] rtracklayer_1.38.3                       
 [46] TxDb.Mmusculus.UCSC.mm10.knownGene_3.4.0 
 [47] stringr_1.3.1                            
 [48] gtools_3.8.1                             
 [49] XML_3.98-1.10                            
 [50] edgeR_3.20.9                             
 [51] zlibbioc_1.24.0                          
 [52] scales_1.0.0                             
 [53] hms_0.4.2                                
 [54] RBGL_1.54.0                              
 [55] RColorBrewer_1.1-2                       
 [56] BBmisc_1.11                              
 [57] memoise_1.1.0                            
 [58] biomaRt_2.34.2                           
 [59] latticeExtra_0.6-28                      
 [60] stringi_1.2.4                            
 [61] RSQLite_2.1.1                            
 [62] genefilter_1.60.0                        
 [63] RMySQL_0.10.15                           
 [64] checkmate_1.8.5                          
 [65] GenomicFeatures_1.30.3                   
 [66] caTools_1.17.1.1                         
 [67] BiocParallel_1.12.0                      
 [68] chipseq_1.28.0                           
 [69] rlang_0.2.2                              
 [70] pkgconfig_2.0.2                          
 [71] BatchJobs_1.7                            
 [72] bitops_1.0-6                             
 [73] TxDb.Celegans.UCSC.ce6.ensGene_3.2.2     
 [74] lattice_0.20-35                          
 [75] purrr_0.2.5                              
 [76] bindr_0.1.1                              
 [77] GenomicAlignments_1.14.2                 
 [78] bit_1.1-14                               
 [79] tidyselect_0.2.4                         
 [80] GSEABase_1.40.1                          
 [81] AnnotationForge_1.20.0                   
 [82] plyr_1.8.4                               
 [83] magrittr_1.5                             
 [84] sendmailR_1.2-1                          
 [85] R6_2.2.2                                 
 [86] gplots_3.0.1                             
 [87] DBI_1.0.0                                
 [88] pillar_1.3.0                             
 [89] withr_2.1.2                              
 [90] survival_2.42-6                          
 [91] RCurl_1.95-4.11                          
 [92] tibble_1.4.2                             
 [93] crayon_1.3.4                             
 [94] KernSmooth_2.23-15                       
 [95] progress_1.2.0                           
 [96] locfit_1.5-9.1                           
 [97] grid_3.4.3                               
 [98] data.table_1.11.4                        
 [99] blob_1.1.1                               
[100] Rgraphviz_2.22.0                         
[101] digest_0.6.15                            
[102] xtable_1.8-2                             
[103] brew_1.0-6                               
[104] munsell_0.5.0   

 

Can anyone explain why I would be getting the error message above?

Thanks so much

chipqc • 136 views
ADD COMMENTlink written 9 months ago by gavrielmatt0
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