RnBeads error on HPC - Githubissues

Hi, I am getting this below error while running Rnbeads script on HPC.


Error in dev.control(displaylist = "enable") :
  dev.control() called without an open graphics device
Calls: rnb.run.analysis ... new -> initialize -> initialize -> .local -> dev.control
In addition: There were 50 or more warnings (use warnings() to see the first 50)
Execution halted

RnBeads code;

#Set rnbeads options

rnb.options(analysis.name = "example")

rnb.options(logging = TRUE)

rnb.options(assembly = "hg19")

rnb.options(identifiers.column = "Sample_ID")

rnb.options2xml(pretty=TRUE)

rnb.options(min.group.size = 1)

###### modules

rnb.options(import = TRUE)

rnb.options(preprocessing = TRUE)

rnb.options(qc = TRUE)

rnb.options(inference = FALSE)

rnb.options(exploratory = TRUE)

rnb.options(differential = TRUE)

##############some selected options (see more at help("rnb.options"))

#rnb.options(import.default.data.type = "infinium.idat.dir") # NGS: "bs.bed.dir"

#rnb.options(import.table.separator = ",") # for TABdel: "\t"

#rnb.options(import.gender.prediction = FALSE) # only for array datasets

#normalization

rnb.options(normalization = NULL)

rnb.options(normalization.method = "wm.dasen")

rnb.options(normalization.background.method = "none")

rnb.options(normalization.plot.shifts = TRUE)

#qc

rnb.options(qc.boxplots = TRUE)

rnb.options(qc.barplots = TRUE)

rnb.options(qc.negative.boxplot = TRUE)

rnb.options(qc.snp.distances = TRUE)

rnb.options(qc.snp.boxplot = TRUE)

rnb.options(qc.snp.barplot = TRUE)

rnb.options(qc.sample.batch.size = 50)

rnb.options(qc.coverage.plots = FALSE)

rnb.options(qc.coverage.threshold.plot = 1:10)

rnb.options(qc.coverage.histograms = FALSE)

rnb.options(qc.coverage.violins = FALSE)

#filtering

rnb.options(filtering.whitelist = NULL)

rnb.options(filtering.blacklist = NULL)

rnb.options(filtering.snp = "3")

rnb.options(filtering.cross.reactive = FALSE)

rnb.options(filtering.greedycut = TRUE)

rnb.options(filtering.greedycut.pvalue.threshold = 0.05)

rnb.options(filtering.greedycut.rc.ties = "row")

rnb.options(filtering.sex.chromosomes.removal = TRUE)

rnb.options(filtering.missing.value.quantile = 0.8)

rnb.options(filtering.coverage.threshold = 5)

rnb.options(filtering.low.coverage.masking = FALSE)

rnb.options(filtering.high.coverage.outliers = FALSE)

rnb.options(filtering.deviation.threshold = 0)

#regions

rnb.load.annotation.from.db("ensembleRegBuildBPall")

rnb.load.annotation.from.db("ensembleRegBuildBPproximal")

rnb.load.annotation.from.db("ensembleRegBuildBPdistal")

rnb.options(region.types=c("promoters","genes","cpgislands","tiling","ensembleRegBuildBPall","ensembleRegBuildBPproximal","ensembleRegBuildBPdistal")) 

#differential analysis

rnb.options(differential.site.test.method = "ttest") #limma"

rnb.options(differential.comparison.columns = c("Sample_Group", "Treatment")) #Set column used for differential comparision

rnb.options(covariate.adjustment.columns = NULL)

rnb.options(differential.adjustment.sva = TRUE)

rnb.options(differential.adjustment.celltype = FALSE)

rnb.options(differential.enrichment.go = TRUE)

rnb.options(differential.enrichment.lola = FALSE)

rnb.options(differential.variability = FALSE)

rnb.options(differential.report.sites = TRUE)

rnb.options(export.to.bed = TRUE)

rnb.options(export.to.trackhub = c("bigBed","bigWig"))

rnb.options(export.to.csv = TRUE) #default = FALSE #creates big tables

rnb.options(export.to.ewasher = FALSE)

rnb.options(export.types = "sites")

rnb.options(disk.dump.big.matrices = TRUE)

rnb.options(enforce.memory.management = TRUE)

rnb.options(enforce.destroy.disk.dumps = TRUE)

##############################################################################

##### Run Analysis

rnb.run.analysis(dir.reports=report.dir,

                   sample.sheet=sample.annotation,

                   data.dir=idat.dir,

                   data.type="infinium.idat.dir")

Many thanks, nabiyogesh

epigen / RnBeads

RnBeads error on HPC #30