Question: ChiPQC: 1Error in 1:(2 * readlength(object)) : NA/NaN argument
0
gravatar for zebasilio
8 months ago by
zebasilio0
zebasilio0 wrote:

Hi!!

I am using ChipQC to check for the quality of a Chipseq experiment we performed in our lab. We have 12 samples (4x input controls, 4x ChipA, 4x ChipB), but unfortunately I get always an error message. Code, error message and session information can be seen below. I thank you in advance for any help you can provide. José

> samples<-read.csv("samples_datasheet.csv")
> BlacklistFile<-"/media/jose/Volume/annotation/black_list/ENCFF001TDO.bed"
#(BlacklistFile downloaded from: ENCFF001TDO (h19 assembly): https://www.encodeproject.org/annotations/ENCSR636HFF/)
> moser_chipseq = ChIPQC(samples,
+                        annotation="hg19",
+                        blacklist = BlacklistFile, chromosomes=NULL)
Myc_A Hela_cells  Myc Myc Myc 1 bed
Myc_B Hela_cells  Myc Myc Myc 2 bed
Myc_C Hela_cells  Myc Myc Myc 3 bed
Myc_D Hela_cells  Myc Myc Myc 4 bed
IKK1_A Hela_cells  IKK1 IKK1 IKK1 1 bed
IKK1_B Hela_cells  IKK1 IKK1 IKK1 2 bed
IKK1_C Hela_cells  IKK1 IKK1 IKK1 3 bed
IKK1_D Hela_cells  IKK1 IKK1 IKK1 4 bed
Compiling annotation...
Computing metrics for 12 samples...
list
Bam file has 25 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

 11list300
Bam file has 25 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 coverage histogram for chr3

Calculating SSD for chr3

Calculating unique positions per strand for chr3

Calculating shift for chr3

 **1Error in 1:(2 * readlength(object)) : NA/NaN argument**

> sessionInfo()
R version 3.5.2 (2018-12-20)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 18.04.1 LTS

Matrix products: default
BLAS: /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.7.1
LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.7.1

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C               LC_TIME=de_AT.UTF-8        LC_COLLATE=en_US.UTF-8     LC_MONETARY=de_AT.UTF-8    LC_MESSAGES=en_US.UTF-8   
 [7] LC_PAPER=de_AT.UTF-8       LC_NAME=C                  LC_ADDRESS=C               LC_TELEPHONE=C             LC_MEASUREMENT=de_AT.UTF-8 LC_IDENTIFICATION=C       

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

other attached packages:
 [1] ChIPQC_1.18.0               DiffBind_2.10.0             SummarizedExperiment_1.12.0 DelayedArray_0.8.0          BiocParallel_1.16.2         matrixStats_0.54.0         
 [7] Biobase_2.42.0              GenomicRanges_1.34.0        GenomeInfoDb_1.18.1         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] backports_1.1.2                           ChIPseeker_1.18.0                         GOstats_2.48.0                            fastmatch_1.1-0                          
  [5] plyr_1.8.4                                igraph_1.2.2                              lazyeval_0.2.1                            GSEABase_1.44.0                          
  [9] splines_3.5.2                             BatchJobs_1.7                             gridBase_0.4-7                            urltools_1.7.1                           
 [13] amap_0.8-16                               digest_0.6.18                             GOSemSim_2.8.0                            viridis_0.5.1                            
 [17] GO.db_3.7.0                               gdata_2.18.0                              magrittr_1.5                              checkmate_1.8.5                          
 [21] memoise_1.1.0                             BBmisc_1.11                               limma_3.38.3                              Nozzle.R1_1.1-1                          
 [25] Biostrings_2.50.1                         annotate_1.60.0                           systemPipeR_1.16.0                        enrichplot_1.2.0                         
 [29] prettyunits_1.0.2                         colorspace_1.3-2                          blob_1.1.1                                ggrepel_0.8.0                            
 [33] dplyr_0.7.8                               crayon_1.3.4                              RCurl_1.95-4.11                           jsonlite_1.6                             
 [37] TxDb.Hsapiens.UCSC.hg19.knownGene_3.2.2   graph_1.60.0                              chipseq_1.32.0                            genefilter_1.64.0                        
 [41] bindr_0.1.1                               sendmailR_1.2-1                           brew_1.0-6                                survival_2.43-3                          
 [45] glue_1.3.0                                gtable_0.2.0                              zlibbioc_1.28.0                           XVector_0.22.0                           
 [49] UpSetR_1.3.3                              Rgraphviz_2.26.0                          scales_1.0.0                              DOSE_3.8.0                               
 [53] pheatmap_1.0.10                           DBI_1.0.0                                 edgeR_3.24.1                              TxDb.Mmusculus.UCSC.mm9.knownGene_3.2.2  
 [57] Rcpp_1.0.0                                plotrix_3.7-4                             viridisLite_0.3.0                         xtable_1.8-3                             
 [61] progress_1.2.0                            units_0.6-2                               gridGraphics_0.3-0                        bit_1.1-14                               
 [65] europepmc_0.3                             AnnotationForge_1.24.0                    httr_1.4.0                                fgsea_1.8.0                              
 [69] gplots_3.0.1                              RColorBrewer_1.1-2                        pkgconfig_2.0.2                           XML_3.98-1.16                            
 [73] farver_1.1.0                              locfit_1.5-9.1                            ggplotify_0.0.3                           tidyselect_0.2.5                         
 [77] rlang_0.3.0.1                             reshape2_1.4.3                            AnnotationDbi_1.44.0                      munsell_0.5.0                            
 [81] tools_3.5.2                               RSQLite_2.1.1                             ggridges_0.5.1                            stringr_1.3.1                            
 [85] bit64_0.9-7                               caTools_1.17.1.1                          purrr_0.2.5                               ggraph_1.0.2                             
 [89] bindrcpp_0.2.2                            RBGL_1.58.1                               TxDb.Rnorvegicus.UCSC.rn4.ensGene_3.2.2   DO.db_2.9                                
 [93] xml2_1.2.0                                biomaRt_2.38.0                            compiler_3.5.2                            rstudioapi_0.8                           
 [97] tibble_1.4.2                              tweenr_1.0.0                              stringi_1.2.4                             TxDb.Hsapiens.UCSC.hg18.knownGene_3.2.2  
[101] GenomicFeatures_1.34.1                    lattice_0.20-38                           Matrix_1.2-15                             pillar_1.3.0                             
[105] BiocManager_1.30.4                        triebeard_0.3.0                           TxDb.Mmusculus.UCSC.mm10.knownGene_3.4.4  data.table_1.11.8                        
[109] cowplot_0.9.3                             bitops_1.0-6                              TxDb.Celegans.UCSC.ce6.ensGene_3.2.2      rtracklayer_1.42.1                       
[113] qvalue_2.14.0                             R6_2.3.0                                  latticeExtra_0.6-28                       hwriter_1.3.2                            
[117] ShortRead_1.40.0                          KernSmooth_2.23-15                        gridExtra_2.3                             boot_1.3-20                              
[121] MASS_7.3-51.1                             gtools_3.8.1                              assertthat_0.2.0                          Category_2.48.0                          
[125] rjson_0.2.20                              withr_2.1.2                               GenomicAlignments_1.18.0                  Rsamtools_1.34.0                         
[129] GenomeInfoDbData_1.2.0                    hms_0.4.2                                 grid_3.5.2                                TxDb.Dmelanogaster.UCSC.dm3.ensGene_3.2.2
[133] rvcheck_0.1.3                             ggforce_0.1.3                             base64enc_0.1-3
chipqc • 278 views
ADD COMMENTlink written 8 months ago by zebasilio0

Does anyone have any idea how could I solve this? Any help is very appreciated. Best, José

ADD REPLYlink modified 7 months ago • written 7 months ago by zebasilio0

hi,

I suspect this may be caused by some peaks being very close to chromosome start or ends. I will put in a fix for this case tonight and that may solve this issue. Would you be able to share your bed files with me? If you can send a link to me at tcarroll(at)rockefeller.edu, then I could test that this solved the problem.

Thanks,

tom

ADD REPLYlink written 7 months ago by Thomas Carroll400

hi,

I suspect this may be caused by some peaks being very close to chromosome start or ends. I will put in a fix for this case tonight and that may solve this issue. Would you be able to share your bed files with me? If you can send a link to me at tcarroll(at)rockefeller.edu, then I could test that this solved the problem.

Thanks,

tom

ADD REPLYlink written 7 months ago by Thomas Carroll400

Dear Prof. Carroll, I have sent you the bed files as you requested.

Thank you so much for your effort. Best Regards, José Basílio

ADD REPLYlink written 7 months ago by zebasilio0

hi, I have added some code to remove peaks close to chromosome edges (within distance of window defined in profileWin parameter) and report number removed. Hopefully this is the issue.

This is in release ChIPQC version 1.18.2.

thank you for report,

tom

ADD REPLYlink written 7 months ago by Thomas Carroll400

hi, I have added some code to remove peaks close to chromosome edges (within distance of window defined in profileWin parameter) and report number removed. Hopefully this is the issue.

This is in release ChIPQC version 1.18.2.

thank you for report,

tom

ADD REPLYlink written 7 months ago by Thomas Carroll400
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