Question: Integer overflow issue with ChIPQC
2
gravatar for Nitesh Kumar Singh
3 months ago by
CCMB, Hyderabad, India
Nitesh Kumar Singh30 wrote:

Hi, I have recently started working on ChIP-seq data. So after mapping using Bowtie and calling peak caller using MACS2, I wanted to do check the quality of peaks. For this, I used ChIPQC but I was getting error with ChIPQCreport. On checking I realized that ChipQCsample was returning nothing for "Fragment Length Cross-coverage" and "Relative Cross-Coverage". ChIPQCsample ran without any error but it did give warnings like "In x * w : NAs produced by integer overflow". I think this is the reason for the whole mess. I dont know why this is happening? For debugging I tried running ChIPQCsample with only bam as input, which again gave me error. I tried with my single end ChIP-seq data, other ChIP-seq data from my lab, other RNAseq data (single end and paired end, to see if there is issue with my peak caller) but all gave me same error. Only bam that ran successfully was this ex1.bam from Rsamtools package. I dont know what is the issue here, I checked online if anyone reported similar issues and find few recent mentions of this problem, so it could be a version issue, not sure. But there was no solution. I am on Ubutnu 18.04.2 LTS and my session info is given below

R version 3.6.0 (2019-04-26)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 18.04.2 LTS

Matrix products: default
BLAS:   /usr/local/lib/R/lib/libRblas.so
LAPACK: /usr/local/lib/R/lib/libRlapack.so

locale:
 [1] LC_CTYPE=en_IN.UTF-8       LC_NUMERIC=C               LC_TIME=en_IN.UTF-8        LC_COLLATE=en_IN.UTF-8     LC_MONETARY=en_IN.UTF-8   
 [6] LC_MESSAGES=en_IN.UTF-8    LC_PAPER=en_IN.UTF-8       LC_NAME=C                  LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_IN.UTF-8 LC_IDENTIFICATION=C       

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

other attached packages:
 [1] ChIPQC_1.20.0               DiffBind_2.12.0             SummarizedExperiment_1.14.0 DelayedArray_0.10.0         BiocParallel_1.18.0        
 [6] matrixStats_0.54.0          Biobase_2.44.0              GenomicRanges_1.36.0        GenomeInfoDb_1.20.0         IRanges_2.18.1             
[11] S4Vectors_0.22.0            BiocGenerics_0.30.0         ggplot2_3.2.0              

loaded via a namespace (and not attached):
  [1] amap_0.8-17                               colorspace_1.4-1                          rjson_0.2.20                             
  [4] hwriter_1.3.2                             XVector_0.24.0                            rstudioapi_0.10                          
  [7] ggrepel_0.8.1                             bit64_0.9-7                               AnnotationDbi_1.46.0                     
 [10] splines_3.6.0                             TxDb.Rnorvegicus.UCSC.rn4.ensGene_3.2.2   Nozzle.R1_1.1-1                          
 [13] Rsamtools_2.0.0                           annotate_1.62.0                           GO.db_3.8.2                              
 [16] pheatmap_1.0.12                           graph_1.62.0                              TxDb.Hsapiens.UCSC.hg18.knownGene_3.2.2  
 [19] BiocManager_1.30.4                        compiler_3.6.0                            httr_1.4.0                               
 [22] GOstats_2.50.0                            backports_1.1.4                           assertthat_0.2.1                         
 [25] Matrix_1.2-17                             lazyeval_0.2.2                            TxDb.Hsapiens.UCSC.hg19.knownGene_3.2.2  
 [28] limma_3.40.2                              prettyunits_1.0.2                         tools_3.6.0                              
 [31] gtable_0.3.0                              glue_1.3.1                                GenomeInfoDbData_1.2.1                   
 [34] Category_2.50.0                           reshape2_1.4.3                            systemPipeR_1.18.2                       
 [37] dplyr_0.8.3                               batchtools_0.9.11                         rappdirs_0.3.1                           
 [40] ShortRead_1.42.0                          Rcpp_1.0.1                                TxDb.Dmelanogaster.UCSC.dm3.ensGene_3.2.2
 [43] TxDb.Mmusculus.UCSC.mm9.knownGene_3.2.2   Biostrings_2.52.0                         gdata_2.18.0                             
 [46] rtracklayer_1.44.0                        TxDb.Mmusculus.UCSC.mm10.knownGene_3.4.7  stringr_1.4.0                            
 [49] gtools_3.8.1                              XML_3.98-1.20                             edgeR_3.26.5                             
 [52] zlibbioc_1.30.0                           scales_1.0.0                              BSgenome_1.52.0                          
 [55] VariantAnnotation_1.30.1                  hms_0.5.0                                 RBGL_1.60.0                              
 [58] RColorBrewer_1.1-2                        yaml_2.2.0                                memoise_1.1.0                            
 [61] biomaRt_2.40.1                            latticeExtra_0.6-28                       stringi_1.4.3                            
 [64] RSQLite_2.1.1                             genefilter_1.66.0                         checkmate_1.9.4                          
 [67] GenomicFeatures_1.36.4                    caTools_1.17.1.2                          chipseq_1.34.0                           
 [70] rlang_0.4.0                               pkgconfig_2.0.2                           bitops_1.0-6                             
 [73] TxDb.Celegans.UCSC.ce6.ensGene_3.2.2      lattice_0.20-38                           purrr_0.3.2                              
 [76] GenomicAlignments_1.20.1                  bit_1.1-14                                tidyselect_0.2.5                         
 [79] GSEABase_1.46.0                           AnnotationForge_1.26.0                    plyr_1.8.4                               
 [82] magrittr_1.5                              R6_2.4.0                                  gplots_3.0.1.1                           
 [85] base64url_1.4                             DBI_1.0.0                                 pillar_1.4.2                             
 [88] withr_2.1.2                               survival_2.44-1.1                         RCurl_1.95-4.12                          
 [91] tibble_2.1.3                              crayon_1.3.4                              KernSmooth_2.23-15                       
 [94] progress_1.2.2                            locfit_1.5-9.1                            grid_3.6.0                               
 [97] data.table_1.12.2                         blob_1.2.0                                Rgraphviz_2.28.0                         
[100] digest_0.6.20                             xtable_1.8-4                              brew_1.0-6                               
[103] munsell_0.5.0
chipqc rstudio • 145 views
ADD COMMENTlink written 3 months ago by Nitesh Kumar Singh30
1

I have the exact same error. It's strange that some BAM file will work, but other will not. Did you figure out how to fix this?

ADD REPLYlink written 9 weeks ago by zhenfeng.liu110

I have exactly the same problem. Did you figure out what was wrong?

ADD REPLYlink written 9 weeks ago by anishazaveri0

I haven't figured out what's wrong, but when I reverted back to version 1.18.2, the error went away.

ADD REPLYlink written 9 weeks ago by zhenfeng.liu110

I tried to run the older version 1.18.2 on R 3.5, but had an issue with DiffBind dependencies (amap doesn't seem to be compatible with 3.5)

ADD REPLYlink written 5 weeks ago by ryleehackley0

update for anyone experiencing the same issues as me, reverting back to R 3.5, installing Rtools, and building and missing packages from the cran archive did the trick. My working session info and package versions are below.

> packageurl <- "https://cran.r-project.org/src/contrib/Archive/amap/amap_0.8-16.tar.gz"
> install.packages(packageurl, repos=NULL, type="source")

> sessionInfo()
R version 3.5.1 (2018-07-02)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 17763)

Matrix products: default

locale:
[1] LC_COLLATE=English_United States.1252  LC_CTYPE=English_United States.1252    LC_MONETARY=English_United States.1252
[4] LC_NUMERIC=C                           LC_TIME=English_United States.1252    

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

other attached packages:
 [1] DiffBind_2.10.0             SummarizedExperiment_1.12.0 DelayedArray_0.8.0          BiocParallel_1.16.6         matrixStats_0.54.0         
 [6] Biobase_2.42.0              GenomicRanges_1.34.0        GenomeInfoDb_1.18.2         IRanges_2.16.0              S4Vectors_0.20.1           
[11] BiocGenerics_0.28.0         amap_0.8-16                

loaded via a namespace (and not attached):
 [1] Category_2.48.1          bitops_1.0-6             bit64_0.9-7              RColorBrewer_1.1-2       progress_1.2.2           httr_1.4.1              
 [7] Rgraphviz_2.26.0         tools_3.5.1              backports_1.1.4          R6_2.4.0                 KernSmooth_2.23-15       DBI_1.0.0               
[13] lazyeval_0.2.2           colorspace_1.4-1         tidyselect_0.2.5         prettyunits_1.0.2        bit_1.1-14               compiler_3.5.1          
[19] sendmailR_1.2-1          graph_1.60.0             rtracklayer_1.42.2       checkmate_1.9.4          caTools_1.17.1.2         scales_1.0.0            
[25] BatchJobs_1.8            genefilter_1.64.0        RBGL_1.58.2              stringr_1.4.0            digest_0.6.20            Rsamtools_1.34.1        
[31] AnnotationForge_1.24.0   XVector_0.22.0           base64enc_0.1-3          pkgconfig_2.0.2          limma_3.38.3             rlang_0.4.0             
[37] rstudioapi_0.10          RSQLite_2.1.2            BBmisc_1.11              GOstats_2.48.0           hwriter_1.3.2            gtools_3.8.1            
[43] dplyr_0.8.3              RCurl_1.95-4.12          magrittr_1.5             GO.db_3.7.0              GenomeInfoDbData_1.2.0   Matrix_1.2-14           
[49] Rcpp_1.0.2               munsell_0.5.0            stringi_1.4.3            edgeR_3.24.3             zlibbioc_1.28.0          gplots_3.0.1.1          
[55] grid_3.5.1               blob_1.2.0               ggrepel_0.8.1            gdata_2.18.0             crayon_1.3.4             lattice_0.20-35         
[61] splines_3.5.1            Biostrings_2.50.2        GenomicFeatures_1.34.8   annotate_1.60.1          hms_0.5.1                locfit_1.5-9.1          
[67] zeallot_0.1.0            pillar_1.4.2             rjson_0.2.20             systemPipeR_1.16.1       biomaRt_2.38.0           XML_3.98-1.20           
[73] glue_1.3.1               ShortRead_1.40.0         latticeExtra_0.6-28      data.table_1.12.2        BiocManager_1.30.4       vctrs_0.2.0             
[79] gtable_0.3.0             purrr_0.3.2              assertthat_0.2.1         ggplot2_3.2.1            xtable_1.8-4             survival_2.42-3         
[85] pheatmap_1.0.12          tibble_2.1.3             GenomicAlignments_1.18.1 AnnotationDbi_1.44.0     memoise_1.1.0            brew_1.0-6              
[91] GSEABase_1.44.0     

> package.version("ChIPQC"); package.version("DiffBind")
[1] "1.18.2"
[1] "2.10.0"
ADD REPLYlink written 5 weeks ago by ryleehackley0

The problem is caused by single end data which would not return fragment length. I fixed it in my fork project. And I contacted the author and hope they will fix it in their next release.

https://github.com/shengqh/ChIPQC

ADD REPLYlink written 5 weeks ago by shengqh0
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