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lionel.ferrato
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@lionelferrato-20039
Last seen 5.8 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.
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