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Subinoy Biswas
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@subinoy-biswas-6708
Last seen 5.8 years ago
I am doing a quality check of my ATAC-Seq peaks with ChIPQC package but I am getting an error.
Error in names(res) <- c("Reads", "Map%", "Filt%", "Dup%", "ReadL", "FragL", :
'names' attribute [9] must be the same length as the vector [7]
So, I need help to solve the issue. Below is my sample sheet.
> sampleid Tissue Factor Condition Treatment Replicate bamReads ControlID bamControl Peaks PeakCaller
> BD24 Tumor Eight 2018 1 bam_reads/BD24_bam.bam BD03 bam_reads/BD03_bam.bam peaks_BD03_ref_data/q_05/BD24_peaks.narrowPeak macs
> BD28 Tumor Eight 2018 2 bam_reads/BD28_bam.bam BD031 bam_reads/BD03_bam.bam peaks_BD03_ref_data/q_05/BD28_peaks.narrowPeak macs
> BD07 Tumor Twelve 2016 1 bam_reads/BD07_bam.bam BD032 bam_reads/BD03_bam.bam peaks_BD03_ref_data/q_05/BD07_peaks.narrowPeak macs
> BD11 Tumor Twelve 2017 2 bam_reads/BD11_bam.bam BD033 bam_reads/BD03_bam.bam peaks_BD03_ref_data/q_05/BD11_peaks.narrowPeak macs
Here is my code
library(DiffBind)
library(ChIPseeker)
library(org.Mm.eg.db)
library(bedr)
library(ChIPQC)
library(BiocParallel)
register(SerialParam())
samples <- read.csv("cd4_meta_8_12_BD03_q_05_test.csv", header = T)
proj1 = ChIPQC(samples,annotation = 'mm10',chromosomes = "chrY")
proj1
proj1 = ChIPQC(samples,annotation = 'mm10',chromosomes = "chrY")
1 Tumor Eight 2018 1 macs
2 Tumor Eight 2018 2 macs
3 Tumor Twelve 2016 1 macs
4 Tumor Twelve 2017 2 macs
Compiling annotation...
Computing metrics for 5 samples...
list
Bam file has 138 contigs
Calculating coverage histogram for chrY
Calculating SSD for chrY
Calculating unique positions per strand for chrY
Calculating shift for chrY
300 / 300
Counting reads in features for chrY
Signal over peaks for chrY
done
Calculating coverage
Calculating Summits on chrY ..[1] 1
list
Bam file has 138 contigs
Calculating coverage histogram for chrY
Calculating SSD for chrY
Calculating unique positions per strand for chrY
Calculating shift for chrY
300 / 300
Counting reads in features for chrY
Signal over peaks for chrY
done
Calculating coverage
Calculating Summits on chrY ..[1] 1
list
Bam file has 138 contigs
Calculating coverage histogram for chrY
Calculating SSD for chrY
Calculating unique positions per strand for chrY
Calculating shift for chrY
300 / 300
Counting reads in features for chrY
Signal over peaks for chrY
done
Calculating coverage
Calculating Summits on chrY ..[1] 1
list
Bam file has 138 contigs
Calculating coverage histogram for chrY
Calculating SSD for chrY
Calculating unique positions per strand for chrY
Calculating shift for chrY
300 / 300
Counting reads in features for chrY
Signal over peaks for chrY
done
Calculating coverage
Calculating Summits on chrY ..[1] 1
list
Bam file has 138 contigs
Calculating coverage histogram for chrY
Calculating SSD for chrY
Calculating unique positions per strand for chrY
Calculating shift for chrY
300 / 300
Counting reads in features for chrY
[1] 1
**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
3: In if is.na(peaks)) peaks = NULL :
the condition has length > 1 and only the first element will be used
4: In if is.na(peaks)) peaks = NULL :
the condition has length > 1 and only the first element will be used
**proj1**
> Samples: 5 : 1 2 3 4 BD03
> Tissue Condition Treatment Control Replicate Peaks
> 1 Tumor Eight 2018 BD03 1 14156
> 2 Tumor Eight 2018 BD031 2 4052
> 3 Tumor Twelve 2016 BD032 1 3968
> 4 Tumor Twelve 2017 BD033 2 14339
**Error in names(res) <- c("Reads", "Map%", "Filt%", "Dup%", "ReadL", "FragL", :
'names' attribute [9] must be the same length as the vector [7]**
> sessionInfo()
R version 3.5.1 (2018-07-02)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS High Sierra 10.13.6
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] 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] org.Mm.eg.db_3.7.0 AnnotationDbi_1.44.0 ChIPQC_1.18.0 ggplot2_3.1.0
[5] bindrcpp_0.2.2 bedr_1.0.6 ChIPseeker_1.18.0 TCseq_1.6.0
[9] rmarkdown_1.11 DiffBind_2.10.0 SummarizedExperiment_1.12.0 DelayedArray_0.8.0
[13] BiocParallel_1.16.2 matrixStats_0.54.0 Biobase_2.42.0 GenomicRanges_1.34.0
[17] GenomeInfoDb_1.18.1 IRanges_2.16.0 S4Vectors_0.20.1 BiocGenerics_0.28.0
loaded via a namespace (and not attached):
[1] R.utils_2.7.0 tidyselect_0.2.5
[3] RSQLite_2.1.1 htmlwidgets_1.3
[5] grid_3.5.1 BatchJobs_1.7
[7] munsell_0.5.0 units_0.6-2
[9] systemPipeR_1.16.0 withr_2.1.2
[11] colorspace_1.4-0 GOSemSim_2.8.0
[13] Category_2.48.0 knitr_1.21
[15] rstudioapi_0.9.0 DOSE_3.8.0
[17] labeling_0.3 urltools_1.7.1
[19] GenomeInfoDbData_1.2.0 hwriter_1.3.2
[21] bit64_0.9-7 farver_1.1.0
[23] pheatmap_1.0.12 TxDb.Rnorvegicus.UCSC.rn4.ensGene_3.2.2
[25] lambda.r_1.2.3 xfun_0.4
[27] R6_2.3.0 locfit_1.5-9.1
[29] bitops_1.0-6 fgsea_1.8.0
[31] gridGraphics_0.3-0 assertthat_0.2.0
[33] scales_1.0.0 ggraph_1.0.2
[35] nnet_7.3-12 enrichplot_1.2.0
[37] gtable_0.2.0 rlang_0.3.1
[39] genefilter_1.64.0 BBmisc_1.11
[41] splines_3.5.1 rtracklayer_1.42.1
[43] lazyeval_0.2.1 acepack_1.4.1
[45] europepmc_0.3 brew_1.0-6
[47] checkmate_1.9.0 yaml_2.2.0
[49] reshape2_1.4.3 TxDb.Dmelanogaster.UCSC.dm3.ensGene_3.2.2
[51] GenomicFeatures_1.34.1 backports_1.1.3
[53] qvalue_2.14.0 Hmisc_4.1-1
[55] RBGL_1.58.1 tools_3.5.1
[57] ggplotify_0.0.3 gridBase_0.4-7
[59] gplots_3.0.1 RColorBrewer_1.1-2
[61] ggridges_0.5.1 Rcpp_1.0.0
[63] plyr_1.8.4 base64enc_0.1-3
[65] progress_1.2.0 zlibbioc_1.28.0
[67] purrr_0.2.5 RCurl_1.95-4.11
[69] prettyunits_1.0.2 rpart_4.1-13
[71] viridis_0.5.1 cowplot_0.9.4
[73] chipseq_1.32.0 ggrepel_0.8.0
[75] cluster_2.0.7-1 magrittr_1.5
[77] TxDb.Hsapiens.UCSC.hg18.knownGene_3.2.2 data.table_1.12.0
[79] futile.options_1.0.1 DO.db_2.9
[81] triebeard_0.3.0 amap_0.8-16
[83] TxDb.Mmusculus.UCSC.mm9.knownGene_3.2.2 hms_0.4.2
[85] evaluate_0.12 xtable_1.8-3
[87] XML_3.98-1.16 VennDiagram_1.6.20
[89] gridExtra_2.3 testthat_2.0.1
[91] compiler_3.5.1 biomaRt_2.38.0
[93] tibble_2.0.1 KernSmooth_2.23-15
[95] crayon_1.3.4 R.oo_1.22.0
[97] htmltools_0.3.6 GOstats_2.48.0
[99] Formula_1.2-3 geneplotter_1.60.0
[101] sendmailR_1.2-1 DBI_1.0.0
[103] tweenr_1.0.1 formatR_1.5
[105] MASS_7.3-51.1 boot_1.3-20
[107] ShortRead_1.40.0 Matrix_1.2-15
[109] R.methodsS3_1.7.1 gdata_2.18.0
[111] bindr_0.1.1 igraph_1.2.2
[113] pkgconfig_2.0.2 TxDb.Hsapiens.UCSC.hg19.knownGene_3.2.2
[115] rvcheck_0.1.3 GenomicAlignments_1.18.0
[117] foreign_0.8-71 TxDb.Celegans.UCSC.ce6.ensGene_3.2.2
[119] xml2_1.2.0 annotate_1.60.0
[121] XVector_0.22.0 AnnotationForge_1.24.0
[123] stringr_1.3.1 digest_0.6.18
[125] graph_1.60.0 Biostrings_2.50.1
[127] fastmatch_1.1-0 htmlTable_1.13.1
[129] edgeR_3.24.2 GSEABase_1.44.0
[131] Rsamtools_1.34.0 gtools_3.8.1
[133] rjson_0.2.20 jsonlite_1.6
[135] futile.logger_1.4.3 viridisLite_0.3.0
[137] limma_3.38.3 pillar_1.3.1
[139] Nozzle.R1_1.1-1 lattice_0.20-38
[141] httr_1.4.0 plotrix_3.7-4
[143] survival_2.43-3 GO.db_3.7.0
[145] glue_1.3.0 UpSetR_1.3.3
[147] bit_1.1-14 Rgraphviz_2.26.0
[149] ggforce_0.1.3 class_7.3-15
[151] stringi_1.2.4 blob_1.1.1
[153] TxDb.Mmusculus.UCSC.mm10.knownGene_3.4.4 DESeq2_1.22.1
[155] latticeExtra_0.6-28 caTools_1.17.1.1
[157] memoise_1.1.0 dplyr_0.7.8
[159] e1071_1.7-0
--------------------
Please suggest me how to solve this error.
Thanks, SB
Thanks, @James W. MacDonald for properly formatting the query.
Got the same error. Is there any update?
Got the same error. Any resolution?
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