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Question: ChIPQC reading more samples that it should
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gravatar for C Lin
5 months ago by
C Lin60
United States
C Lin60 wrote:

Hi,

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...

list

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

 

done

Calculating coverage

Calculating Summits on chrY ..[1] 1

list

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)

 

locale:

[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8

[5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 LC_PAPER=en_US.UTF-8 LC_NAME=C

[9] LC_ADDRESS=C LC_TELEPHONE=C LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C

 

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
ADD COMMENTlink modified 4 months ago • written 5 months ago by C Lin60
0
gravatar for Thomas Carroll
5 months ago by
United Kingdom/London/MRC CSC Imperial College London
Thomas Carroll390 wrote:

hi,

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 tc.infomatics@gmail.com).

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 

library(BiocParallel)
register(SerialParam())
proj1 = ChIPQC(samples,annotation = 'hg38',chromosomes = "chrY")

and report the output here?

 

best,

tom

ADD COMMENTlink written 5 months ago by Thomas Carroll390
0
gravatar for C Lin
4 months ago by
C Lin60
United States
C Lin60 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 4 months ago by C Lin60

Okay great.

Thanks for letting us know you resolved this.

ADD REPLYlink written 4 months ago by Thomas Carroll390
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