Question: Integer overflow issue with ChIPQC
0
gravatar for Nitesh Kumar Singh
5 days ago by
CCMB, Hyderabad, India
Nitesh Kumar Singh10 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] LCCTYPE=enIN.UTF-8 LCNUMERIC=C LCTIME=enIN.UTF-8 LCCOLLATE=enIN.UTF-8 LCMONETARY=enIN.UTF-8
[6] LC
MESSAGES=enIN.UTF-8 LCPAPER=enIN.UTF-8 LCNAME=C LCADDRESS=C LCTELEPHONE=C
[11] LCMEASUREMENT=enIN.UTF-8 LC_IDENTIFICATION=C

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

other attached packages: [1] ChIPQC1.20.0 DiffBind2.12.0 SummarizedExperiment1.14.0 DelayedArray0.10.0 BiocParallel1.18.0
[6] matrixStats
0.54.0 Biobase2.44.0 GenomicRanges1.36.0 GenomeInfoDb1.20.0 IRanges2.18.1
[11] S4Vectors0.22.0 BiocGenerics0.30.0 ggplot2_3.2.0

loaded via a namespace (and not attached): [1] amap0.8-17 colorspace1.4-1 rjson0.2.20
[4] hwriter
1.3.2 XVector0.24.0 rstudioapi0.10
[7] ggrepel0.8.1 bit640.9-7 AnnotationDbi1.46.0
[10] splines
3.6.0 TxDb.Rnorvegicus.UCSC.rn4.ensGene3.2.2 Nozzle.R11.1-1
[13] Rsamtools2.0.0 annotate1.62.0 GO.db3.8.2
[16] pheatmap
1.0.12 graph1.62.0 TxDb.Hsapiens.UCSC.hg18.knownGene3.2.2
[19] BiocManager1.30.4 compiler3.6.0 httr1.4.0
[22] GOstats
2.50.0 backports1.1.4 assertthat0.2.1
[25] Matrix1.2-17 lazyeval0.2.2 TxDb.Hsapiens.UCSC.hg19.knownGene3.2.2
[28] limma
3.40.2 prettyunits1.0.2 tools3.6.0
[31] gtable0.3.0 glue1.3.1 GenomeInfoDbData1.2.1
[34] Category
2.50.0 reshape21.4.3 systemPipeR1.18.2
[37] dplyr0.8.3 batchtools0.9.11 rappdirs0.3.1
[40] ShortRead
1.42.0 Rcpp1.0.1 TxDb.Dmelanogaster.UCSC.dm3.ensGene3.2.2 [43] TxDb.Mmusculus.UCSC.mm9.knownGene3.2.2 Biostrings2.52.0 gdata2.18.0
[46] rtracklayer
1.44.0 TxDb.Mmusculus.UCSC.mm10.knownGene3.4.7 stringr1.4.0
[49] gtools3.8.1 XML3.98-1.20 edgeR3.26.5
[52] zlibbioc
1.30.0 scales1.0.0 BSgenome1.52.0
[55] VariantAnnotation1.30.1 hms0.5.0 RBGL1.60.0
[58] RColorBrewer
1.1-2 yaml2.2.0 memoise1.1.0
[61] biomaRt2.40.1 latticeExtra0.6-28 stringi1.4.3
[64] RSQLite
2.1.1 genefilter1.66.0 checkmate1.9.4
[67] GenomicFeatures1.36.4 caTools1.17.1.2 chipseq1.34.0
[70] rlang
0.4.0 pkgconfig2.0.2 bitops1.0-6
[73] TxDb.Celegans.UCSC.ce6.ensGene3.2.2 lattice0.20-38 purrr0.3.2
[76] GenomicAlignments
1.20.1 bit1.1-14 tidyselect0.2.5
[79] GSEABase1.46.0 AnnotationForge1.26.0 plyr1.8.4
[82] magrittr
1.5 R62.4.0 gplots3.0.1.1
[85] base64url1.4 DBI1.0.0 pillar1.4.2
[88] withr
2.1.2 survival2.44-1.1 RCurl1.95-4.12
[91] tibble2.1.3 crayon1.3.4 KernSmooth2.23-15
[94] progress
1.2.2 locfit1.5-9.1 grid3.6.0
[97] data.table1.12.2 blob1.2.0 Rgraphviz2.28.0
[100] digest
0.6.20 xtable1.8-4 brew1.0-6
[103] munsell_0.5.0

chipqc rstudio • 24 views
ADD COMMENTlink written 5 days ago by Nitesh Kumar Singh10
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 276 users visited in the last hour