Question: TarSeqQC TargetExperiment() example takes forever
0
gravatar for jls2282
2.8 years ago by
jls22820
United States
jls22820 wrote:

When running TarSeqQC the system hangs with only one rsession thread at 100% for at least 20 minutes (Mac Pro 2 x 3.06 GHz 6-core Intel Xeon processors, 128 GB 1333 MHz DDR3). I stopped it then since this is too long for a simple example, would not work for an amplicon sequencing analysis pipeline. Tried with 18 workers, no difference. The package was installed from source. I am curious to see others' experience.

library(TarSeqQC)
library(BiocParallel)
bpp=BiocParallel::MulticoreParam(4)
bamFile<-system.file("extdata", "mybam.bam", package="TarSeqQC",mustWork=TRUE)
bedFile<-system.file("extdata", "mybed.bed", package="TarSeqQC",mustWork=TRUE)
fastaFile<-system.file("extdata", "myfasta.fa", package="TarSeqQC",mustWork=TRUE)
myPanel<-TargetExperiment(bedFile, bamFile, fastaFile, feature="amplicon", attribute="coverage", BPPARAM=bpp))

sessionInfo()

R version 3.3.1 (2016-06-21)
Platform: x86_64-apple-darwin13.4.0 (64-bit)
Running under: OS X 10.9.5 (Mavericks)

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] BiocParallel_1.8.1   TarSeqQC_1.4.1       openxlsx_3.0.0       plyr_1.8.4           ggplot2_2.2.0        Rsamtools_1.26.1     Biostrings_2.42.1   
 [8] XVector_0.14.0       GenomicRanges_1.26.1 GenomeInfoDb_1.10.1  IRanges_2.8.1        S4Vectors_0.12.1     BiocGenerics_0.20.0 

loaded via a namespace (and not attached):
 [1] Rcpp_0.12.8                RColorBrewer_1.1-2         bitops_1.0-6               tools_3.3.1                zlibbioc_1.20.0           
 [6] digest_0.6.10              rpart_4.1-10               base64_2.0                 tibble_1.2                 gtable_0.2.0              
[11] htmlTable_1.7              lattice_0.20-34            Matrix_1.2-7.1             gridExtra_2.2.1            stringr_1.1.0             
[16] cluster_2.0.5              knitr_1.15.1               cowplot_0.7.0              grid_3.3.1                 nnet_7.3-12               
[21] Biobase_2.34.0             data.table_1.10.0          survival_2.40-1            foreign_0.8-67             latticeExtra_0.6-28       
[26] Formula_1.2-1              reshape2_1.4.2             magrittr_1.5               GenomicAlignments_1.10.0   htmltools_0.3.5           
[31] Hmisc_4.0-1                scales_0.4.1               splines_3.3.1              SummarizedExperiment_1.4.0 assertthat_0.1            
[36] colorspace_1.3-1           stringi_1.1.2              acepack_1.4.1              lazyeval_0.2.0             openssl_0.9.5             
[41] munsell_0.4.3  

 

tarseqqc • 460 views
ADD COMMENTlink modified 2.3 years ago by bioinf10 • written 2.8 years ago by jls22820
Answer: TarSeqQC TargetExperiment() example takes forever
0
gravatar for gmerino
2.8 years ago by
gmerino20
Argentina
gmerino20 wrote:

Hello!

I'm one of the TarSeqQC developers. Currently, I'm working under OS X 10.12.1 (Sierra) and the example runs well. Two months ago I have experimented with a similar problem related to a new version of BiocParallel. When I tried to use more than one worker the cycles never ended.

The solution (here, https://support.bioconductor.org/p/88307/#88874)  was to add options(bphost ="localhost") at the start of my code (or in the .Rprofile) before the calling of the BiocParallel methods. Maybe this could solve your problem too.

Please, let me know if it was solved or not. If was not, I could check the TarSeqQC example in your MacOS version.

Best, 

Gabriela

ADD COMMENTlink written 2.8 years ago by gmerino20

Hello Gabriela,

I also ran into some issue with TargetExperiment(), here are the details TarSeqQC Error- failed to stop SOCKcluster cluster-error writing to connection

I hope if you can help me out.

Thanks!

ADD REPLYlink modified 2.3 years ago • written 2.3 years ago by bioinf10
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