DEseq2: RData file not found

/cluster/project8/vyp/pontikos/People/JessicaGardner/output/cluster/R/deseq_JessicaGardner_X.out
WARNING: unknown option '--keep.sex=FALSE'

WARNING: unknown option '--support.frame=input-trimmed.txt'

WARNING: unknown option '--keep.dups=FALSE'

WARNING: unknown option '--code=JessicaGardner_X'

WARNING: unknown option '--annotation.file=/scratch2/vyp-scratch2/reference_datasets/RNASeq/Human_hg38/biomart_annotations_human.tab'

WARNING: unknown option '--iFolder=/cluster/project8/vyp/pontikos/People/JessicaGardner/output'

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R_LIBS:
R_PROFILE:
During startup - Warning message:
In library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called 'devtools'
> library(DESeq2)
Loading required package: S4Vectors
Loading required package: stats4
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, xtabs

The following objects are masked from 'package:base':

    anyDuplicated, append, as.data.frame, as.vector, cbind, colnames,
    do.call, duplicated, eval, evalq, Filter, Find, get, grep, grepl,
    intersect, is.unsorted, lapply, lengths, Map, mapply, match, mget,
    order, paste, pmax, pmax.int, pmin, pmin.int, Position, rank,
    rbind, Reduce, rownames, sapply, setdiff, sort, table, tapply,
    union, unique, unlist, unsplit

Loading required package: IRanges
Loading required package: GenomicRanges
Loading required package: GenomeInfoDb
Loading required package: SummarizedExperiment
Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: Rcpp
Loading required package: RcppArmadillo
>
> getArgs <- function() {
+   myargs.list <- strsplit(grep("=",gsub("--","",commandArgs()),value=TRUE),"=")
+   myargs <- lapply(myargs.list,function(x) x[2] )
+   names(myargs) <- lapply(myargs.list,function(x) x[1])
+   return (myargs)
+ }
>
> ### Just for debugging
> support.frame <- "/cluster/project8/vyp/Tabrizi_Huntington_RNASeq/support/htt_support2.txt"
> code <- "htt"
> keep.dups <- FALSE
> annotation.file <- "/cluster/project8/vyp/vincent/Software/RNASeq_pipeline/bundle/human/biomart/biomart_annotations_human.tab"
> iFolder <- "/scratch2/vyp-scratch2/Tabrizi_Huntington_RNASeq/processed/Nov2014/"
>
>
> ## vincent debugging
> support.frame <- "data/TDP43_m323k.tab"
> code <- "m323k"
> annotation.file <- "/cluster/project8/vyp/vincent/Software/RNASeq_pipeline/bundle/mouse/biomart/biomart_annotations_mouse.tab"
> iFolder <- "/scratch2/vyp-scratch2/IoN_RNASeq/Fratta_RNASeq/brain/m323k"
> keep.dups <- FALSE
> keep.sex <- FALSE
>
> ########################## read arguments
>
> myArgs <- getArgs()
> if ('support.frame' %in% names(myArgs)) support.frame <- myArgs[['support.frame']]
> if ('code' %in% names(myArgs)) code <- myArgs[['code']]
> if ('iFolder' %in% names(myArgs)) iFolder <- myArgs[['iFolder']]
> if ('annotation.file' %in% names(myArgs)) annotation.file <- myArgs[['annotation.file']]
> if ('keep.dups' %in% names(myArgs)) keep.dups <- as.logical(myArgs[['keep.dups']])
> if ('keep.sex' %in% names(myArgs)) keep.sex <- as.logical(myArgs[['keep.sex']])
>
> extra.plots <- TRUE
> remove.hb   <- FALSE
>
> message("Should I keep the sex chromosomes? Option set is ", keep.sex)
Should I keep the sex chromosomes? Option set is FALSE
>
> ###check input files and data frame
> message('Now reading ', support.frame)
Now reading input-trimmed.txt
> support <- read.table(support.frame, header = TRUE, stringsAsFactors = FALSE)
> list.conditions <- grep(names(support), pattern = '^condition.*', value  = TRUE)
> list.covars <- grep(names(support), pattern = '^covar.*', value  = TRUE)
>
>
> annotation <- read.table(annotation.file, header = TRUE, sep = '\t', na.string = c('', 'NA'), quote = "" )
> names(annotation) <- ifelse (names(annotation) == "external_gene_name", "external_gene_id", names(annotation)) # trying to agree on the column names
>
>
> ### deseq output folders and files
> deseq2.folder <- paste(iFolder, '/deseq2', sep = '')
> for (folder in c(deseq2.folder)) {
+   if (! file.exists(folder)) dir.create(folder)
+ }
>
>
> ########## load the count data
>
> if (keep.dups) deseq.counts <- paste(deseq2.folder, '/deseq_counts_', code, '_keep_dups.RData', sep = '')
> if (!keep.dups) deseq.counts <- paste(deseq2.folder, '/deseq_counts_', code, '.RData', sep = '')
> load(deseq.counts)
Error in readChar(con, 5L, useBytes = TRUE) : cannot open the connection
Calls: load -> readChar
In addition: Warning message:
In readChar(con, 5L, useBytes = TRUE) :
  cannot open compressed file '/cluster/project8/vyp/pontikos/People/JessicaGardner/output/deseq2/deseq_counts_JessicaGardner_X.RData', probable reason 'No such file or directory'
Execution halted
I'll look into this now.
plagnollab / RNASeq_pipeline

DEseq2: RData file not found #9
