simpleRNASeq stopped running (related to S4 vectors?)
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@michaeldhar-9369
Last seen 5.8 years ago

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

simplernaseq easyrnaseq s4vectors • 895 views
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@nicolas-delhomme-6252
Last seen 2.9 years ago
Sweden

Hej Michael! Can you run sessionInfo() and copy paste the results. One you have installed and loaded easyRNASeq. It could be that the issues disappear once you have the latest version of all softwares. If not let me know and I'll look into it.

Cheers, Nico

---------------------------------------------------------------
Nicolas Delhomme, PhD
Acting Manager
UPSC bioinformatics core facility
Umeå Plant Science Center,
Swedish University for Agricultural Sciences (SLU) and Umeå University
Tel: +46 90 786 5478
Email: nicolas.delhomme@umu.se
SLU - Umeå universitet Umeå S-901 87 Sweden
​---------------------------------------------------------------
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