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

converting counts to integer mode
estimating size factors
estimating dispersions
gene-wise dispersion estimates
mean-dispersion relationship
final dispersion estimates
fitting model and testing
-- replacing outliers and refitting for 6236 genes
-- DESeq argument 'minReplicatesForReplace' = 7 
-- original counts are preserved in counts(dds)
estimating dispersions
fitting model and testing
Error in lookupTableSplitted[[i]] : subscript out of bounds
Calls: sapply ... FUN -> paste -> standardGeneric -> eval -> eval -> eval
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_GeneBody_Hepatocyte_NKCell.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_GeneBody_NKCell_SRR_9_Hepatocyte_SRR_11.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_GeneBody_NKCell_SRR_9_Hepatocyte_SRR_11.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_GeneBody_Hepatocyte_NKCell.txt': No such file or directory
cp: cannot stat `/scratch/9022418.1.linga/Input/DiffExp_v2_GeneBody_NKCell_SRR_9_Hepatocyte_SRR_11.txt': No such file or directory
cp: cannot stat `/scratch/9022418.1.linga/Input/NKCell_SRR_9_vs_Hepatocyte_SRR_11_DiffExp_v2_GeneBody_forSEGEXUpload*': No such file or directory
cp: cannot stat `/scratch/9022418.1.linga/Input/*_Genes*.txt': No such file or directory
cp: cannot stat `/scratch/9022418.1.linga/Input/*.png': No such file or directory
mv: cannot stat `*.png': No such file or directory