Problem with ChIPQC
1
0
Entering edit mode
@lionelferrato-20039
Last seen 5.1 years ago

Hi,

I try to run ChIPQC on a sample. I get this error message:

> ChIPQC("/Users/lionelferrato/chip_seq/output/NRF1_sample_sheet_without_peaks.csv", bCount=TRUE, consensus=TRUE, blacklist = "/Users/lionelferrato/chip_seq/output/blacklist/mm10.blacklist.bed")
NRF1_CHIP_WT_1 ESC NRF1 WT none 1 bed
Checking chromosomes:
[1] "chr1"
Adding controls...
Counting reads in consensus peakset...
Computing metrics for 2 samples...
list
Bam file has 22 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  ..[1] 1
list
Bam file has 22 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  ..[1] 1
Samples: 2 : NRF1_CHIP_WT_1 NRF1_INPUT_WT 
               Tissue  Factor Condition Treatment Replicate Peaks
NRF1_CHIP_WT_1    ESC    NRF1        WT      none         1 10173
NRF1_INPUT_WT     ESC Control        WT      none        c1 10173
                 Reads Map%  Filt% Dup% ReadL FragL RelCC   SSD  RiP%  RiBL%
NRF1_CHIP_WT_1 3116621  100 0.0737    0    50   103  1.53 2.130 5.830 0.0346
NRF1_INPUT_WT  1886330  100 0.0775    0    50   108  1.53 0.566 0.201 0.0188
    Warning messages:
    1: In if is.na(peaks)) peaks = NULL :
  the condition has length > 1 and only the first element will be used
    2: In if is.na(peaks)) peaks = NULL :
  the condition has length > 1 and only the first element will be used

My sample sheets looks like this:

SampleID,Tissue,Factor,Condition,Treatment,Replicate,bamReads,ControlID,bamControl,Peaks,PeakCaller
NRF1_CHIP_WT_1,ESC,NRF1,WT,none,1,/Users/lionelferrato/chip_seq/output/BAM/NRF1_CHIP_WT_1.bam,NRF1_INPUT_WT,/Users/lionelferrato/chip_seq/output/BAM/NRF1_INPUT_WT.bam,/Users/lionelferrato/chip_seq/output/peaks/NRF1_peaks_macs.bed,bed

My sessionInfo() looks like this:

R version 3.5.2 (2018-12-20)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS Sierra 10.12.6

Matrix products: default
BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libRlapack.dylib

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

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

other attached packages:
 [1] ChIPQC_1.18.1               DiffBind_2.10.0             SummarizedExperiment_1.12.0
 [4] DelayedArray_0.8.0          BiocParallel_1.16.6         matrixStats_0.54.0         
 [7] Biobase_2.42.0              GenomicRanges_1.34.0        GenomeInfoDb_1.18.2        
[10] IRanges_2.16.0              S4Vectors_0.20.1            BiocGenerics_0.28.0        
[13] ggplot2_3.1.0              

loaded via a namespace (and not attached):
  [1] amap_0.8-16                               colorspace_1.4-0                         
  [3] rjson_0.2.20                              hwriter_1.3.2                            
  [5] XVector_0.22.0                            base64enc_0.1-3                          
  [7] rstudioapi_0.9.0                          ggrepel_0.8.0                            
  [9] bit64_0.9-7                               AnnotationDbi_1.44.0                     
 [11] splines_3.5.2                             TxDb.Rnorvegicus.UCSC.rn4.ensGene_3.2.2  
 [13] Nozzle.R1_1.1-1                           Rsamtools_1.34.1                         
 [15] annotate_1.60.0                           GO.db_3.7.0                              
 [17] pheatmap_1.0.12                           graph_1.60.0                             
 [19] TxDb.Hsapiens.UCSC.hg18.knownGene_3.2.2   BiocManager_1.30.4                       
 [21] compiler_3.5.2                            httr_1.4.0                               
 [23] GOstats_2.48.0                            backports_1.1.3                          
 [25] assertthat_0.2.0                          Matrix_1.2-15                            
 [27] lazyeval_0.2.1                            TxDb.Hsapiens.UCSC.hg19.knownGene_3.2.2  
 [29] limma_3.38.3                              prettyunits_1.0.2                        
 [31] tools_3.5.2                               gtable_0.2.0                             
 [33] glue_1.3.0                                GenomeInfoDbData_1.2.0                   
 [35] Category_2.48.0                           reshape2_1.4.3                           
 [37] systemPipeR_1.16.1                        dplyr_0.8.0.1                            
 [39] ShortRead_1.40.0                          Rcpp_1.0.0                               
 [41] TxDb.Dmelanogaster.UCSC.dm3.ensGene_3.2.2 TxDb.Mmusculus.UCSC.mm9.knownGene_3.2.2  
 [43] Biostrings_2.50.2                         gdata_2.18.0                             
 [45] rtracklayer_1.42.1                        TxDb.Mmusculus.UCSC.mm10.knownGene_3.4.4 
 [47] stringr_1.4.0                             gtools_3.8.1                             
 [49] XML_3.98-1.17                             edgeR_3.24.3                             
 [51] zlibbioc_1.28.0                           scales_1.0.0                             
 [53] hms_0.4.2                                 RBGL_1.58.1                              
 [55] RColorBrewer_1.1-2                        BBmisc_1.11                              
 [57] memoise_1.1.0                             biomaRt_2.38.0                           
 [59] latticeExtra_0.6-28                       stringi_1.3.1                            
 [61] RSQLite_2.1.1                             genefilter_1.64.0                        
 [63] checkmate_1.9.1                           GenomicFeatures_1.34.3                   
 [65] caTools_1.17.1.1                          chipseq_1.32.0                           
 [67] rlang_0.3.1                               pkgconfig_2.0.2                          
 [69] BatchJobs_1.7                             bitops_1.0-6                             
 [71] lattice_0.20-38                           TxDb.Celegans.UCSC.ce6.ensGene_3.2.2     
 [73] purrr_0.3.0                               GenomicAlignments_1.18.1                 
 [75] bit_1.1-14                                tidyselect_0.2.5                         
 [77] GSEABase_1.44.0                           AnnotationForge_1.24.0                   
 [79] plyr_1.8.4                                magrittr_1.5                             
 [81] sendmailR_1.2-1                           R6_2.4.0                                 
 [83] gplots_3.0.1.1                            DBI_1.0.0                                
 [85] pillar_1.3.1                              withr_2.1.2                              
 [87] survival_2.43-3                           RCurl_1.95-4.11                          
 [89] tibble_2.0.1                              crayon_1.3.4                             
 [91] KernSmooth_2.23-15                        progress_1.2.0                           
 [93] locfit_1.5-9.1                            grid_3.5.2                               
 [95] data.table_1.12.0                         blob_1.1.1                               
 [97] Rgraphviz_2.26.0                          digest_0.6.18                            
 [99] xtable_1.8-3                              brew_1.0-6                               
[101] munsell_0.5.0

Why am I getting this error ?

Thanks in advance.

software error • 667 views
ADD COMMENT
0
Entering edit mode

hi lionel,

This is not an error but a warning and your ChIPQC object has been returned and printed to screen successfully.

The warning is nothing to do with your data and something we will remove from future versions of ChIPQC.

tom

ADD REPLY
1
Entering edit mode
@lionelferrato-20039
Last seen 5.1 years ago

Thank you very much for your answer, I am reassured.

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