[BioC] Using Rscript to run DEXSeq on Linux cluster

Steve Lianoglou mailinglist.honeypot at gmail.com
Wed Nov 23 21:26:38 CET 2011

Hi Chris,

Quick question: does the script only bomb when its running on a cluster node?

I mean, does the script run normally if you run it from your own/local machine?

Can you run a more mundane Rscript file from the cluster?


On Wed, Nov 23, 2011 at 2:04 PM, Christopher T Gregg
<chris.gregg at neuro.utah.edu> wrote:
> Hi,
> We have been running DEXSeq on our linux cluster.  To submit jobs to compute nodes we generate a shell script that calls on R to run a file that contains all of the commands to complete the DEXSeq analysis.  The command file has been tested on the cluster through an interactive session using R and works fine within R.  However, when we evoke Rscript to run at the command line or in a shell script we get the following error:
> ------------------------------------------------------------------------
> $Rscript /path/to/DEXSeq_script.R
> $ cat DEXseq.e136397
> Loading required package: Biobase
> Welcome to Bioconductor
>  Vignettes contain introductory material. To view, type
>  'browseVignettes()'. To cite Bioconductor, see
>  'citation("Biobase")' and for packages 'citation("pkgname")'.
> Execution halted
> --------------------------------------------------------------------------
> I would appreciate any thoughts as to why the Rscript approach fails to run DEXSeq from the command line.
> Note that we have worked around this problem by running R in an interactive job through Screen on the cluster and this has been a good solution.
> Thank you!
> best wishes,
> Chris
> Christopher Gregg, PhD.
> Assistant Professor, Neurobiology and Anatomy
> Adjunct Professor, Human Genetics
> 323 Wintrobe Bldg 530
> University of Utah, School of Medicine
> 20 North 1900 East, 401 MREB
> Salt Lake City, Utah 84132-3401
> phone: (801) 581-8212
> fax: (801) 585-9736
> ------------------------------------
> Gregg Lab Website: www.neuro.utah.edu/labs/gregg/index.html<http://www.neuro.utah.edu/labs/gregg/index.html>
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Steve Lianoglou
Graduate Student: Computational Systems Biology
 | Memorial Sloan-Kettering Cancer Center
 | Weill Medical College of Cornell University
Contact Info: http://cbio.mskcc.org/~lianos/contact

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