Question: DEXSeqHTML parallelization error
0
gravatar for Neel Aluru
3.8 years ago by
Neel Aluru450
United States
Neel Aluru450 wrote:

Hello,

I am trying to generate HTML report for DEXSeq results and encountering parallelization error (at least I think it is a parallelization error). Any help in solving this problem will be highly appreciated.

Thank you,

Neel

Here is my code and session Info()

>library("DEXSeq")
>setwd("~/Desktop/RNAseq/LiverDEXseq")
>countFiles=list.files(pattern="dexseq.txt$")
>flattenedFile=list.files(pattern="gff$")
>sampleTable= data.frame(row.names=c("CL1", "CL2","CL3", "CL4","PL1","PL2","PL3","PL4"), >condition=c("Control","Control","Control","Control","PCB126","PCB126","PCB126","PCB126"))
>dxd = DEXSeqDataSetFromHTSeq(countFiles, sampleData=sampleTable, design= ~sample+exon+condition:exon,flattenedfile=flattenedFile)
>colData(dxd)
>sampleAnnotation(dxd)
>dxd = estimateSizeFactors(dxd)

>library("BiocParallel", lib.loc="/Library/Frameworks/R.framework/Versions/3.2/Resources/library")
>BPPARAM = MulticoreParam(workers=8)
>dxd = estimateDispersions(dxd, BPPARAM=BPPARAM)

>plotDispEsts(dxd)
>dxd = testForDEU(dxd, BPPARAM = BPPARAM)
>dxd=estimateExonFoldChanges(dxd, fitExpToVar = "condition", BPPARAM = BPPARAM)
>dxr1=DEXSeqResults(dxd)
>dxr1

>DEXSeqHTML(dxr1)
Error in unserialize(socklist[[n]]) : error reading from connection

> DEXSeqHTML(object=dxr1, BPPARAM = BPPARAM)
Error in unserialize(socklist[[n]]) : error reading from connection

> sessionInfo()
R version 3.2.2 (2015-08-14)
Platform: x86_64-apple-darwin13.4.0 (64-bit)
Running under: OS X 10.10.5 (Yosemite)

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] stats4    parallel  stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
 [1] DEXSeq_1.16.3              DESeq2_1.10.0              RcppArmadillo_0.6.200.2.0  Rcpp_0.12.2                SummarizedExperiment_1.0.1
 [6] GenomicRanges_1.22.1       GenomeInfoDb_1.6.1         IRanges_2.4.4              S4Vectors_0.8.3            Biobase_2.30.0            
[11] BiocGenerics_0.16.1        BiocParallel_1.4.0         BiocInstaller_1.20.1       methylKit_0.9.5           

loaded via a namespace (and not attached):
 [1] genefilter_1.52.0    statmod_1.4.22       locfit_1.5-9.1       reshape2_1.4.1       splines_3.2.2        lattice_0.20-33     
 [7] colorspace_1.2-6     chron_2.3-47         survival_2.38-3      XML_3.98-1.3         foreign_0.8-66       DBI_0.3.1           
[13] RColorBrewer_1.1-2   lambda.r_1.1.7       plyr_1.8.3           stringr_1.0.0        zlibbioc_1.16.0      Biostrings_2.38.2   
[19] munsell_0.4.2        gtable_0.1.2         futile.logger_1.4.1  hwriter_1.3.2        latticeExtra_0.6-26  geneplotter_1.48.0  
[25] biomaRt_2.26.1       AnnotationDbi_1.32.0 proto_0.3-10         acepack_1.3-3.3      xtable_1.8-0         scales_0.3.0        
[31] Hmisc_3.17-0         annotate_1.48.0      XVector_0.10.0       Rsamtools_1.22.0     gridExtra_2.0.0      ggplot2_1.0.1       
[37] digest_0.6.8         stringi_1.0-1        grid_3.2.2           bitops_1.0-6         tools_3.2.2          magrittr_1.5        
[43] RCurl_1.95-4.7       RSQLite_1.0.0        Formula_1.2-1        cluster_2.0.3        futile.options_1.0.0 MASS_7.3-45         
[49] data.table_1.9.6     rpart_4.1-10         nnet_7.3-11  

dexseq parallel dexseqhtml • 821 views
ADD COMMENTlink written 3.8 years ago by Neel Aluru450

I repeated it without BPPARAM and I am still getting the same error!

ADD REPLYlink written 3.8 years ago by Neel Aluru450

Hi Neel, 

Not sure what is the problem, but I have notice had the same error when I run out of memory in my computer. Based on your sessionInfo(), I am guessing that you are probably using a laptop for the analysis. Would you have chance to check in a bigger machine if this happens also there?

Alejandro

ADD REPLYlink written 3.8 years ago by Alejandro Reyes1.7k

Hi Alejandro,

Thanks for the reply. I ran the analysis on a Mac Pro (12-Core Intel Xeon E5, 2.7 GHz, 64 GB memory and 1TB hard drive; there is 250GB free space). I will try to run it on a server as you suggested.

Thank you, Neel

ADD REPLYlink written 3.8 years ago by Neel Aluru450
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