Loading required package: S4Vectors
Loading required package: methods
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 object is masked from 'package:stats':

    xtabs

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

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, as.vector, cbind, colnames, do.call, duplicated,
    eval, evalq, get, intersect, is.unsorted, lapply, mapply, match,
    mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind,
    rep.int, 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: Rcpp
Loading required package: RcppArmadillo
Warning messages:
1: replacing previous import by 'ggplot2::Position' when loading 'DESeq2' 
2: replacing previous import by 'ggplot2::arrow' when loading 'Hmisc' 
3: replacing previous import by 'ggplot2::unit' when loading 'Hmisc' 
4: replacing previous import by 'scales::alpha' when loading 'Hmisc' 
Loading required package: limma

Attaching package: 'limma'

The following object is masked from 'package:DESeq2':

    plotMA

The following object is masked from 'package:BiocGenerics':

    plotMA

Warning messages:
1: In x/(unlist(mappedReadsNum) * 1e-09 * totalLength) :
  longer object length is not a multiple of shorter object length
2: In x/(unlist(mappedReadsNum) * 1e-09 * totalLength) :
  longer object length is not a multiple of shorter object length
Warning messages:
1: In x/(unlist(mappedReadsNum) * 1e-09 * totalLength) :
  longer object length is not a multiple of shorter object length
2: In x/(unlist(mappedReadsNum) * 1e-09 * totalLength) :
  longer object length is not a multiple of shorter object length
converting counts to integer mode
all samples have 0 counts for all genes. check the counting script.
all genes have equal values for all samples. will not be able to perform differential analysis
estimating size factors
Error in estimateSizeFactorsForMatrix(counts(object), locfunc = locfunc,  : 
  every gene contains at least one zero, cannot compute log geometric means
Execution halted
Error in file(file, "rt") : cannot open the connection
Calls: read.table -> file
In addition: Warning message:
In file(file, "rt") :
  cannot open file 'DiffExp_v2_Intronic_Only_Male_3h_Vehicle_Male_3h_TCPOBOP.txt': No such file or directory
Execution halted
Loading required package: grid
Loading required package: futile.logger
Error in file(file, "rt") : cannot open the connection
Calls: read.table -> file
In addition: Warning message:
In file(file, "rt") :
  cannot open file 'Down_Genes_DESeq_Intronic_Only_Male_3h_TCPOBOP_G123_M3M4_Male_3h_Vehicle_G123_M1M2.txt': No such file or directory
Execution halted
Loading required package: grid
Loading required package: futile.logger
Error in file(file, "rt") : cannot open the connection
Calls: read.table -> file
In addition: Warning message:
In file(file, "rt") :
  cannot open file 'Up_Genes_DESeq_Intronic_Only_Male_3h_TCPOBOP_G123_M3M4_Male_3h_Vehicle_G123_M1M2.txt': No such file or directory
Execution halted
cat: Count.Table.*.txt: No such file or directory
rm: cannot remove `Count.Table.*.txt': No such file or directory
mv: cannot stat `DiffExp_v2_Intronic_Only_Male_3h_Vehicle_Male_3h_TCPOBOP.txt': No such file or directory
cp: cannot stat `/scratch/2973744.1.linga/Input/DiffExp_v2_Intronic_Only_Male_3h_TCPOBOP_G123_M3M4_Male_3h_Vehicle_G123_M1M2.txt': No such file or directory
cp: cannot stat `/scratch/2973744.1.linga/Input/Male_3h_TCPOBOP_G123_M3M4_vs_Male_3h_Vehicle_G123_M1M2_DiffExp_v2_Intronic_Only_forSEGEXUpload*': No such file or directory
cp: cannot stat `/scratch/2973744.1.linga/Input/*_Genes*.txt': No such file or directory
cp: cannot stat `/scratch/2973744.1.linga/Input/*.png': No such file or directory
mv: cannot stat `*.png': No such file or directory