[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:
library(QuasR)
library(BSgenome.Mmusculus.UCSC.mm10)
cl <- makeCluster(1)
sampleFile <- "sampleFile.txt"
genomeName <- "BSgenome.Mmusculus.UCSC.mm10"
proj <- qAlign(sampleFile, genome= genomeName, splicedAlignment=TRUE,
clObj=cl)
And I get
> proj <- qAlign(sampleFile, genome= genomeName, splicedAlignment=TRUE,
clObj=cl)
alignment files missing - need to:
create 1 genomic alignment(s)
Testing the compute nodes...OK
Loading QuasR on the compute nodes...OK
Available cores:
nodeNames
ccwsge0155
1
Performing genomic alignments for 1 samples. See progress in the log file:
/scratch/4401022.1.huge/QuasR_log_41394115a102.txt
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.
Ugo
> sessionInfo()
R version 3.0.2 (2013-09-25)
Platform: x86_64-unknown-linux-gnu (64-bit)
locale:
[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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