Question: ChIPQC reading more samples that it should
gravatar for C T
2.4 years ago by
C T90
United States
C T90 wrote:


I am trying to run ChIPQC. In my samples sheet I have 3 samples with the same input file and 2 samples with the same input file. So the total of files is 5 samples + 2 input. However, ChIPQC is "Computing metrics for 8 samples...". I am guessing this is why the error message is triggered at the end. Any idea?

This is my samples sheet:

SampleID Tissue Factor Condition ControlID Replicate

6 ES2_shHOTAIR_H3K27M3_1 ES2_shHOTAIR H3K27M3 ES2_shHOT ES2_shHOTAIR_Input 1

7 ES2_shHOTAIR_H3K4M1_1 ES2_shHOTAIR H3K4M1 ES2_shHOT ES2_shHOTAIR_Input 1

8 ES2_shHOTAIR_H3K4M2_1 ES2_shHOTAIR H3K4M2 ES2_shHOT ES2_shHOTAIR_Input 1

9 hMSC_GFP_H3K27M2_1 hMSC_GFP H3K27M2 MSC_ctrl hMSC_GFP_Input 1

10 hMSC_GFP_H3K27M3_1 hMSC_GFP H3K27M3 MSC_ctrl hMSC_GFP_Input 1

bamReads bamControl

6 sam_2/DNSES2shHOTH3K27M3-1_S10_L004_R1_001_remdup.bam sam_2/DNSES2HOTInput-1_S4_L001_R1_001_remdup.bam 

7 sam_2/DNSES2HOTH3K4M1-1_S5_L001_R1_001_remdup.bam sam_2/DNSES2HOTInput-1_S4_L001_R1_001_remdup.bam

8 sam_2/DNSES2HOTH3K4M2-1_S6_L001_R1_001_remdup.bam sam_2/DNSES2HOTInput-1_S4_L001_R1_001_remdup.bam

9 sam_2/DNSMSCGFPH3K27M2-1_S6_L003_R1_001_remdup.bam sam_2/DNSMSCGFPInput-1_S1_L002_R1_001_remdup.bam

10 sam_2/DNSMSCGFPH3K27M3-1_S6_L004_R1_001_remdup.bam sam_2/DNSMSCGFPInput-1_S1_L002_R1_001_remdup.bam

Peaks PeakCaller

6 sam_2/ES2shHOT_H3K27M3_peaks.xls macs

7 sam_2/ES2shHOT_H3K4M1_peaks.xls macs

8 sam_2/ES2shHOT_H3K4M2_peaks.xls macs

9 sam_2/MSCGFP_H3K27M2_peaks.xls macs

10 sam_2/MSCGFP_H3K27M3_peaks.xls macs

Below is the error message 

> proj1 = ChIPQC(samples,annotation = 'hg38',chromosomes = "chrY")

ES2_shHOTAIR_H3K27M3_1 ES2_shHOTAIR H3K27M3 ES2_shHOT 1 macs

ES2_shHOTAIR_H3K4M1_1 ES2_shHOTAIR H3K4M1 ES2_shHOT 1 macs

ES2_shHOTAIR_H3K4M2_1 ES2_shHOTAIR H3K4M2 ES2_shHOT 1 macs

hMSC_GFP_H3K27M2_1 hMSC_GFP H3K27M2 MSC_ctrl 1 macs

hMSC_GFP_H3K27M3_1 hMSC_GFP H3K27M3 MSC_ctrl 1 macs

Compiling annotation...

Computing metrics for 8 samples...


Bam file has 25 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



Calculating coverage

Calculating Summits on chrY ..[1] 1


Error in names(res) <- nms :

'names' attribute [8] must be the same length as the vector [6]

In addition: Warning message:

stop worker failed:

'clear_cluster' receive data failed:

reached elapsed time limit

> sessionInfo()

R version 3.3.0 (2016-05-03)

Platform: x86_64-pc-linux-gnu (64-bit)

Running under: CentOS release 6.6 (Final)







attached base packages:

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


other attached packages:

[1] ChIPQC_1.8.9 DiffBind_2.0.9 SummarizedExperiment_1.2.3 Biobase_2.32.0

[5] GenomicRanges_1.24.3 GenomeInfoDb_1.8.7 IRanges_2.6.1 S4Vectors_0.10.3

[9] BiocGenerics_0.18.0 ggplot2_2.2.1 RevoUtilsMath_3.2.5


loaded via a namespace (and not attached):

[1] edgeR_3.14.0 splines_3.3.0

[3] TxDb.Hsapiens.UCSC.hg18.knownGene_3.2.2 TxDb.Mmusculus.UCSC.mm10.knownGene_3.2.2

[5] gtools_3.5.0 assertthat_0.1

[7] latticeExtra_0.6-28 amap_0.8-14

[9] RBGL_1.48.1 Rsamtools_1.24.0

[11] Category_2.38.0 RSQLite_1.1-2

[13] backports_1.0.5 lattice_0.20-33

[15] limma_3.28.21 digest_0.6.12

[17] RColorBrewer_1.1-2 XVector_0.12.1

[19] checkmate_1.8.2 colorspace_1.3-2

[21] Matrix_1.2-6 plyr_1.8.4

[23] GSEABase_1.34.1 chipseq_1.22.0

[25] TxDb.Hsapiens.UCSC.hg38.knownGene_3.1.3 XML_3.98-1.6

[27] pheatmap_1.0.8 ShortRead_1.30.0

[29] biomaRt_2.28.0 genefilter_1.54.2

[31] zlibbioc_1.18.0 xtable_1.8-2

[33] GO.db_3.3.0 scales_0.4.1

[35] brew_1.0-6 gdata_2.17.0

[37] TxDb.Rnorvegicus.UCSC.rn4.ensGene_3.2.2 BiocParallel_1.6.6

[39] tibble_1.2 annotate_1.50.1

[41] GenomicFeatures_1.24.5 lazyeval_0.2.0

[43] survival_2.41-3 magrittr_1.5

[45] memoise_1.0.0 systemPipeR_1.6.4

[47] fail_1.3 gplots_3.0.1

[49] hwriter_1.3.2 GOstats_2.38.1

[51] graph_1.50.0 tools_3.3.0

[53] BBmisc_1.11 stringr_1.2.0

[55] sendmailR_1.2-1 munsell_0.4.3

[57] locfit_1.5-9.1 AnnotationDbi_1.34.4

[59] Biostrings_2.40.2 caTools_1.17.1

[61] grid_3.3.0 RCurl_1.95-4.8

[63] TxDb.Celegans.UCSC.ce6.ensGene_3.2.2 rjson_0.2.15

[65] AnnotationForge_1.14.2 bitops_1.0-6

[67] base64enc_0.1-3 gtable_0.2.0

[69] DBI_0.6 reshape2_1.4.2

[71] R6_2.2.0 GenomicAlignments_1.8.4

[73] Nozzle.R1_1.1-1 dplyr_0.5.0

[75] rtracklayer_1.32.2 KernSmooth_2.23-15

[77] TxDb.Hsapiens.UCSC.hg19.knownGene_3.2.2 stringi_1.1.3

[79] BatchJobs_1.6 Rcpp_0.12.10

[81] TxDb.Dmelanogaster.UCSC.dm3.ensGene_3.2.2 TxDb.Mmusculus.UCSC.mm9.knownGene_3.2.2
chipqc • 566 views
ADD COMMENTlink modified 2.4 years ago • written 2.4 years ago by C T90
Answer: ChIPQC reading more samples that it should
gravatar for Thomas Carroll
2.4 years ago by
United States/New York/The Rockefeller University
Thomas Carroll400 wrote:


It is not clear to me what the issue is here. 

Could you share your SampleSheet as an RData object so I can take a look? (Send to

Secondly, It may be worth running in serial as I am not sure what the error with parallelizing is here (stop worker failed:'clear_cluster' receive data failed:reached elapsed time limit). 

Could you try 

proj1 = ChIPQC(samples,annotation = 'hg38',chromosomes = "chrY")

and report the output here?




ADD COMMENTlink written 2.4 years ago by Thomas Carroll400
Answer: ChIPQC reading more samples that it should
gravatar for C T
2.4 years ago by
C T90
United States
C T90 wrote:

Thank you, Thomas for your reply. I figured out the issue.

Turns out, some of the path to bamReads and bamControl have extra spaces causing the error above.

ADD COMMENTlink written 2.4 years ago by C T90

Okay great.

Thanks for letting us know you resolved this.

ADD REPLYlink written 2.4 years ago by Thomas Carroll400
Please log in to add an answer.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 169 users visited in the last hour