Question: ChIPQC stops at chr3 for calculating shift
0
gravatar for psudyant
20 months ago by
psudyant0
psudyant0 wrote:

Hello, 

I am having trouble with ChIPQC function in the ChIPQC package. This function will not analyze all chromosomes and stops at chr3. I have used the older version the same way but did not find this error. I made sure that chrM is not included in chrom_to_test. Please help. 

Below is the output:

analyze_samples <- ChIPQC(samples, consensus = T, bCount = T, summits = 250, annotation = "hg19",
+                           chromosomes = chrom_to_test, blacklist = blacklist.hg19)
H3K27ac_Ctrl_1  Control    1 bed
H3K27ac_Ctrl_2  Control    2 bed
H3K27ac_Ctrl_3  Control    3 bed
H3K27ac_Pter_1  Pter   1 bed
H3K27ac_Pter_2  Pter   2 bed
H3K27ac_Pter_3  Pter   3 bed
Compiling annotation...
Using default blacklist for hg19...
Adding controls...
Counting reads in consensus peakset...
Re-centering peaks...
Computing metrics for 8 samples...
list
Bam file has 84 contigs
Calculating coverage histogram for chr1

Calculating SSD for chr1

Calculating unique positions per strand for chr1

Calculating shift for chr1

 300 / 300
Counting reads in features for chr1

Signal over peaks for chr1

done
Calculating coverage
Calculating Summits on  chr1  ..Calculating coverage histogram for chr2

Calculating SSD for chr2

Calculating unique positions per strand for chr2

Calculating shift for chr2

 300 / 300
Counting reads in features for chr2

Signal over peaks for chr2

done
Calculating coverage
Calculating Summits on  chr2  ..Calculating coverage histogram for chr3

Calculating SSD for chr3

Calculating unique positions per strand for chr3

Calculating shift for chr3

 119 / 300

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(samples, consensus = T, bCount = T, summits = 250, annotation = "hg19", 
       chromosomes = NULL, blacklist = blacklist.hg19)

sessionInfo()
R version 3.4.0 (2017-04-21)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: OS X El Capitan 10.11.6

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  methods   base     

other attached packages:
 [1] ChIPQC_1.12.3              DiffBind_2.4.8             SummarizedExperiment_1.6.4 DelayedArray_0.2.7        
 [5] matrixStats_0.52.2         Biobase_2.36.2             ggplot2_2.2.1              BiocInstaller_1.26.1      
 [9] GenomicRanges_1.28.5       GenomeInfoDb_1.12.2        IRanges_2.10.3             S4Vectors_0.14.4          
[13] BiocGenerics_0.22.0       

loaded via a namespace (and not attached):
 [1] Category_2.42.1                           bitops_1.0-6                             
 [3] bit64_0.9-7                               RColorBrewer_1.1-2                       
 [5] TxDb.Hsapiens.UCSC.hg18.knownGene_3.2.2   tools_3.4.0                              
 [7] backports_1.1.0                           R6_2.2.2                                 
 [9] KernSmooth_2.23-15                        DBI_0.7                                  
[11] lazyeval_0.2.0                            colorspace_1.3-2                         
[13] TxDb.Celegans.UCSC.ce6.ensGene_3.2.2      bit_1.1-12                               
[15] Nozzle.R1_1.1-1                           compiler_3.4.0                           
[17] sendmailR_1.2-1                           graph_1.54.0                             
[19] TxDb.Mmusculus.UCSC.mm10.knownGene_3.4.0  rtracklayer_1.36.4                       
[21] caTools_1.17.1                            scales_0.5.0                             
[23] checkmate_1.8.3                           BatchJobs_1.6                            
[25] genefilter_1.58.1                         RBGL_1.52.0                              
[27] stringr_1.2.0                             digest_0.6.12                            
[29] Rsamtools_1.28.0                          AnnotationForge_1.18.2                   
[31] XVector_0.16.0                            base64enc_0.1-3                          
[33] pkgconfig_2.0.1                           limma_3.32.6                             
[35] rlang_0.1.2                               RSQLite_2.0                              
[37] BBmisc_1.11                               TxDb.Hsapiens.UCSC.hg19.knownGene_3.2.2  
[39] bindr_0.1                                 GOstats_2.42.0                           
[41] hwriter_1.3.2                             BiocParallel_1.10.1                      
[43] gtools_3.5.0                              dplyr_0.7.3                              
[45] RCurl_1.95-4.8                            magrittr_1.5                             
[47] GO.db_3.4.1                               GenomeInfoDbData_0.99.0                  
[49] Matrix_1.2-11                             Rcpp_0.12.12                             
[51] munsell_0.4.3                             stringi_1.1.5                            
[53] edgeR_3.18.1                              zlibbioc_1.22.0                          
[55] gplots_3.0.1                              fail_1.3                                 
[57] plyr_1.8.4                                grid_3.4.0                               
[59] blob_1.1.0                                gdata_2.18.0                             
[61] ggrepel_0.6.5                             lattice_0.20-35                          
[63] Biostrings_2.44.2                         splines_3.4.0                            
[65] GenomicFeatures_1.28.4                    annotate_1.54.0                          
[67] locfit_1.5-9.1                            rjson_0.2.15                             
[69] systemPipeR_1.10.2                        reshape2_1.4.2                           
[71] biomaRt_2.32.1                            XML_3.98-1.9                             
[73] glue_1.1.1                                ShortRead_1.34.1                         
[75] latticeExtra_0.6-28                       gtable_0.2.0                             
[77] amap_0.8-14                               assertthat_0.2.0                         
[79] chipseq_1.26.1                            TxDb.Mmusculus.UCSC.mm9.knownGene_3.2.2  
[81] TxDb.Rnorvegicus.UCSC.rn4.ensGene_3.2.2   xtable_1.8-2                             
[83] survival_2.41-3                           tibble_1.3.4                             
[85] pheatmap_1.0.8                            GenomicAlignments_1.12.2                 
[87] AnnotationDbi_1.38.2                      memoise_1.1.0                            
[89] bindrcpp_0.2                              brew_1.0-6                               
[91] TxDb.Dmelanogaster.UCSC.dm3.ensGene_3.2.2 GSEABase_1.38.1      

Thank you

chipqc • 257 views
ADD COMMENTlink written 20 months ago by psudyant0
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