mkdir: cannot create directory 'jingyi_pipeline/': File exists
mkdir: cannot create directory 'jingyi_pipeline/filtering/': File exists
mkdir: cannot create directory 'jingyi_pipeline/filtering/': File exists
mkdir: cannot create directory 'jingyi_pipeline/filtering/': File exists
mkdir: cannot create directory 'jingyi_pipeline/filtering/': File exists
mkdir: cannot create directory 'jingyi_pipeline/filtering/': File exists
mkdir: cannot create directory 'jingyi_pipeline/filtering/': File exists
mkdir: cannot create directory 'jingyi_pipeline/filtering/': File exists
mkdir: cannot create directory 'jingyi_pipeline/': File exists
[1] "Start Quanlity Control for input file"
[1] "Input file pass QC"
[1] "The new sample masterlist write to  jingyi_pipeline/temp_mvl_20171117"
[1] "Start to looking for if duplicate sample existed"
[1] "Duplicate samples are:"
                  V1                 V2 V3
1 MGH_NA17-473-tumor MGH_NA17-482-tumor  5
2 MGH_NA17-476-tumor MGH_NA17-482-tumor  5
3 MGH_NA17-482-tumor MGH_NA17-473-tumor  5
4 MGH_NA17-482-tumor MGH_NA17-476-tumor  5
Error in read.table(args[2], header = FALSE, sep = "\t", fill = FALSE,  :
  no lines available in input
Execution halted
[1] "Find multi genes annotation and replace with protein coding genes only"
[1] "All multi genes are replaced."
Error in if (is.na(CurrentTable[j, n + 1]) == TRUE) { :
  argument is of length zero
Calls: FindCurrentSymbolWithPos
In addition: Warning message:
In is.na(CurrentTable[j, n + 1]) :
  is.na() applied to non-(list or vector) of type 'NULL'
Execution halted
[1] "Replace Gene Length based on isoform"
[1] "All samples have CTCL subtype"
Warning message:
In is.na(mvl$QUARTILE) :
  is.na() applied to non-(list or vector) of type 'NULL'
Error in fix.by(by.x, x) : 'by' must specify a uniquely valid column
Calls: MutationRate -> merge -> merge.data.frame -> fix.by
Execution halted