mv: cannot move './Input/Condition_2' to './Input/F_140mg/kg_CPA_2cycle_TD229': No such file or directory
/var/spool/sge/scc-tm2/job_scripts/9183579: line 399: cd: /scratch/9183579.1.linga/Input/F_140mg/kg_CPA_2cycle_TD229: No such file or directory
mv: cannot stat '*.out': No such file or directory
mv: cannot stat '*.out_num_mapped_reads.txt': No such file or directory
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Loading required package: stats4
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Loading required package: parallel

Attaching package: 'BiocGenerics'

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    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
    tapply, union, unique, unsplit, which, which.max, which.min


Attaching package: 'S4Vectors'

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    expand.grid

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

    Vignettes contain introductory material; view with
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    'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: DelayedArray
Loading required package: matrixStats

Attaching package: 'matrixStats'

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Loading required package: BiocParallel

Attaching package: 'DelayedArray'

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Loading required package: limma

Attaching package: 'limma'

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Error in file(file, "rt") : cannot open the connection
Calls: read.delim2 -> read.table -> file
In addition: Warning message:
In file(file, "rt") :
  cannot open file '/scratch/9183579.1.linga/Input/F_140mg/kg_CPA_2cycle_TD2290.out': No such file or directory
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_F_Placebo_TD229_F_140mg/kg_CPA_2cycle_TD229.txt': No such file or directory
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_F_Placebo_TD229_F_140mg/kg_CPA_2cycle_TD229.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_F_140mg/kg_CPA_2cycle_TD229_G170_M30M31_F_Placebo_TD229_G170_M20M21.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_F_140mg/kg_CPA_2cycle_TD229_G170_M30M31_F_Placebo_TD229_G170_M20M21.txt': No such file or directory
Execution halted
/var/spool/sge/scc-tm2/job_scripts/9183579: line 535: DiffExp_9c_Venn_Tables_F_140mg/kg_CPA_2cycle_TD229_G170_M30M31_F_Placebo_TD229_G170_M20M21.txt: No such file or directory
rm: cannot remove 'Count.Table.*.txt': No such file or directory
cp: cannot stat '/scratch/9183579.1.linga/Input/DiffExp_v2_Intronic_Only_F_Placebo_TD229_F_140mg/kg_CPA_2cycle_TD229.txt': No such file or directory
cp: cannot stat '/scratch/9183579.1.linga/Input/F_140mg/kg_CPA_2cycle_TD229_G170_M30M31_vs_F_Placebo_TD229_G170_M20M21_DiffExp_v2_Intronic_Only_forSEGEXUpload*': No such file or directory
cp: cannot stat '/scratch/9183579.1.linga/Input/*_Genes*.txt': No such file or directory
cp: cannot stat '/scratch/9183579.1.linga/Input/*.png': No such file or directory
cp: cannot stat '/scratch/9183579.1.linga/Input/DiffExp_9c_Venn_Tables_F_140mg/kg_CPA_2cycle_TD229_G170_M30M31_F_Placebo_TD229_G170_M20M21.txt': No such file or directory
mv: cannot stat '*.txt': No such file or directory
mv: cannot stat '*.png': No such file or directory