[BioC] QuasR on Linux Cluster

Ugo Borello ugo.borello at inserm.fr
Fri Oct 18 13:56:52 CEST 2013

Hi all,
I am trying to use QuasR on a Linux Cluster:1 machine/multiple cores.

I run:

cl <- makeCluster(1)

sampleFile <- "sampleFile.txt"

genomeName <- "BSgenome.Mmusculus.UCSC.mm10"

proj <- qAlign(sampleFile, genome= genomeName, splicedAlignment=TRUE,

And I get
> proj <- qAlign(sampleFile, genome= genomeName, splicedAlignment=TRUE,
alignment files missing - need to:
    create 1 genomic alignment(s)
Testing the compute nodes...OK
Loading QuasR on the compute nodes...OK
Available cores:
Performing genomic alignments for 1 samples. See progress in the log file:
Error in unserialize(node$con) : error reading from connection
Calls: qAlign ... FUN -> recvData -> recvData.SOCKnode -> unserialize
Execution halted

I also tryied to modify the multicore option

cl <- makeCluster(detectCores())

And my job is killed because it uses more memory ( Max vmem = 17.118G) than
allowed (16G)

Any suggestions. I am pretty stuck.

Thank you in advance for your help.

> sessionInfo()
R version 3.0.2 (2013-09-25)
Platform: x86_64-unknown-linux-gnu (64-bit)

[1] C

attached base packages:
[1] parallel  stats     graphics  grDevices utils     datasets  methods
[8] base     

other attached packages:
 [1] TxDb.Mmusculus.UCSC.mm10.knownGene_2.10.1
 [2] GenomicFeatures_1.14.0
 [3] AnnotationDbi_1.24.0
 [4] Biobase_2.22.0
 [5] BSgenome.Mmusculus.UCSC.mm10_1.3.19
 [6] BSgenome_1.30.0
 [7] Biostrings_2.30.0
 [8] QuasR_1.2.0   
 [9] Rbowtie_1.2.0 
[10] GenomicRanges_1.14.1
[11] XVector_0.2.0 
[12] IRanges_1.20.0
[13] BiocGenerics_0.8.0

loaded via a namespace (and not attached):
 [1] BiocInstaller_1.12.0 DBI_0.2-7            RColorBrewer_1.0-5
 [4] RCurl_1.95-4.1       RSQLite_0.11.4       Rsamtools_1.14.1
 [7] ShortRead_1.20.0     XML_3.98-1.1         biomaRt_2.18.0
[10] bitops_1.0-6         grid_3.0.2           hwriter_1.3
[13] lattice_0.20-24      latticeExtra_0.6-26  rtracklayer_1.22.0
[16] stats4_3.0.2         tools_3.0.2          zlibbioc_1.8.0

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