Question: Using Rscript to run DEXSeq on Linux cluster
0
gravatar for Christopher T Gregg
7.9 years ago by
Christopher T Gregg210 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=""> [[alternative HTML version deleted]]
dexseq • 814 views
ADD COMMENTlink modified 7.9 years ago by Wolfgang Huber13k • written 7.9 years ago by Christopher T Gregg210
Answer: Using Rscript to run DEXSeq on Linux cluster
0
gravatar for Steve Lianoglou
7.9 years ago by
Denali
Steve Lianoglou12k wrote:
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? -steve 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: w="" ww.neuro.utah.edu="" labs="" gregg="" index.html=""> > > > > ? ? ? ?[[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor > -- 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
ADD COMMENTlink written 7.9 years ago by Steve Lianoglou12k
Answer: Using Rscript to run DEXSeq on Linux cluster
0
gravatar for Wolfgang Huber
7.9 years ago by
EMBL European Molecular Biology Laboratory
Wolfgang Huber13k wrote:
Dear Chris some things to check: - does your script try to open an X11 device? - does Rscript on your system invoke the same version of R as when you start R interactively (this could depend on your $PATH, other environment variables, or shell alias settings) - does Rscript read the same settings for .Renviron and run the same initialisation commands in .Rprofile as your R? best wishes Wolfgang On 11/23/11 8:04 PM, Christopher T Gregg 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: w="" ww.neuro.utah.edu="" labs="" gregg="" index.html=""> > > > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor -- Best wishes Wolfgang Wolfgang Huber EMBL http://www.embl.de/research/units/genome_biology/huber
ADD COMMENTlink written 7.9 years ago by Wolfgang Huber13k
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