zinba crashes with error: cannot open file 'peaks_files/peaks.list': No such file or directory

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1) What operating system are you using?
Ubuntu 14.04 64 bit

2) What error message was displayed?
        For chrY_random length is 58682461
    Importing bed formatted reads
    Skipped 26202212 reads
    Imported 0 reads
    Sorting reads ...COMPLETE

Building window data

--------BUILD WINDOWS COMPLETE-------

Error in file(file, "r") : cannot open the connection
Calls: zinba -> run.zinba -> scan -> file
In addition: Warning message:
In file(file, "r") :
  cannot open file 'peaks_files/peaks.list': No such file or directory
Execution halted

3) What was the exact command you used that resulted in the error?
path_reads="/alignments/map1.bed"
path_map="/home/data/mm9/mapability/zinba/map36_mm9"
path_align="/home/data/mm9/mapability/zinba/alignability/"
path_twoBit="/home/local/data/mm9/mm9.2bit"

zinba(
  refinepeaks=0, #refine peaks? 1 for yes, 0 for no
  seq=path_reads, #path to mapped experimental reads
  input="none", #path to mapped input reads if available (default is "none")
  filetype="bed", #either 'bed', 'bowtie', or 'tagAlign'
  threshold=0.05, #FDR threshold, default is 0.05
  align=path_align, #path to alignability directory
  numProc=10, #number of CPUs to use, must be less than max available   (default 1)
  twoBit=path_twoBit, #path to genome build in .2bit format
  outfile="peaks", #prefix for outputted files
  extension=200, #average fragment library length (size selected)
)

4) Please copy and paste any additional screen output that resulted from
running the command

sessionInfo()
R version 2.15.0 (2012-03-30)
Platform: x86_64-unknown-linux-gnu (64-bit)

attached base packages:
[1] stats     graphics  grDevices utils     datasets  base     

other attached packages:
[1] zinba_2.01.1

Original issue reported on code.google.com by bionob...@gmail.com on 25 Sep 2014 at 6:03

[GoogleCodeExporter]

Please, delete this issue. After installing the latest version, I no longer had 
this problem.

Original comment by bionob...@gmail.com on 25 Sep 2014 at 9:27

[GoogleCodeExporter]

Original comment by homer...@gmail.com on 26 Jan 2015 at 4:33

• Changed state: Invalid