Hello,
I am trying to run simpleRNASeq on some FastQs in an HPC system at NYU. I tried to run some scripts which ran perfectly a few months ago (I wrote the pipeline in the summer). However, now execution halts, for reasons that are still mysterious to me. Nothing in the script has changed since it ran perfectly well several times this summer.
The Error Messages are below, followed by the commands I ran. Please let me know if you have a solution. Thank you.
ERRORS:
Execution halted: Error in checkForRemoteErrors(val) :
4 nodes produced errors; first error: error in evaluating the argument 'query' in selecting a method for function 'countOverlaps': Error in grng[strand(grng) == "+"] :
error in evaluating the argument 'i' in selecting a method for function '[': Error in windowrep.int(x, ceiling(length.out/n)), 1, length.out) :
error in evaluating the argument 'x' in selecting a method for function 'window': Error in rep.int(x, ceiling(length.out/n)) :
attempt to replicate an object of type 'S4'
Calls: rep.int -> rep.int
Calls: == ... eval -> eval -> == -> == -> rep -> rep -> .local -> window
Calls: simpleRNASeq ... clusterApply -> staticClusterApply -> checkForRemoteErrors
COMMANDS:
#!/usr/bin/env Rscript
#This R script runs simpleRNASeq on BAM alignments stored in the pipeline's directory structure of 'alignments.1'
#It produces a table of counts for features (genes) for the samples
#This script needs the Bioconductor core packages and easyRNASeq package to be installed in order to run.
#get arguments
args<-commandArgs(trailingOnly=TRUE)
#load easyRNASeq
library(easyRNASeq)
#get bam filenames from arguments
filenames<-c(args[2:length(args)])
#assing to bamFiles object
bamFiles<-getBamFileList(filenames)
#set parameters for annotaion, bam files
annotParam <- AnnotParam(datasource=args[1], type="gff3")
bamParam <- BamParam(stranded=FALSE)
#set parameters for RNASeq experiment; incorporates annotParam, bamParam
rnaSeqParam <- RnaSeqParam(countBy="genes", annotParam=annotParam, bamParam=bamParam)
#get summarized experiment object, which contains counts
sexp <- simpleRNASeq(bamFiles=bamFiles,
param=rnaSeqParam,
nnodes = 8,
verbose=TRUE
)
#use assay function to extract count table from summarized experiment; assign to count.table object
count.table<-assay(sexp)
#print preview of count table
print("Printing the head of assay of the count table")
head(count.table)
#'count.table' R object printed to a text file
write.table(count.table,file="count.table.txt",col.names=NA,quote=F,sep="\t
