Inconsistent Merging windows

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1) What operating system are you using?
Unix Cluster

2) What error message was displayed?
There is no error. The importing of wins files is highly inconsistent and fails 
to call peaks for  number of chromosomes.. I have run this on the same data 
several times and it's never the same missing wins files.

looks like the win files for some chrs are missing

3) What was the exact command you used that resulted in the error?

run.zinba(
    outfile="/XXXXX/ZINBA_PEAK",
    seq="/XXXXX/temp.Nsorted.bed",
    basecountfile="/XXXXX/temp.Nsorted.bed.basecount",
    align="/XXXXX/ZINBA_ALIGNABILITY_HG19_MAP50",
    twoBit="/XXXXX/hg19.2bit",
  numProc=12,
    winSize=300,  
    offset=75,  
    filetype="bed",
    buildwin=1,
    selectmodel=0,
    formula=exp_count~1,
    formulaE=exp_count~1,
    formulaZ=exp_count~align_perc,
    refinepeaks=0,
    printFullOut=1,
    extension=1,
    method="mixture",
    cleanup=0
    )
4) Please copy and paste any additional screen output that resulted from
running the command

eg. an example missing chrs 1,2 and 3

--------MERGE WINDOWS -------- 2014-03-23 22:28:10 
There are 1 thresholds: 
0.8 
High threshold= 0.8
    Importing windows from FILEPATH/ZINBA_PEAK_chr4.wins...
    Importing windows from FILEPATH/ZINBA_PEAK_chr5.wins...
    Importing windows from FILEPATH/ZINBA_PEAK_chr6.wins...
    Importing windows from FILEPATH/ZINBA_PEAK_chr7.wins...
    Importing windows from FILEPATH/ZINBA_PEAK_chrX.wins...
    Importing windows from FILEPATH/ZINBA_PEAK_chr8.wins...
    Importing windows from FILEPATH/ZINBA_PEAK_chr9.wins...
    Importing windows from FILEPATH/ZINBA_PEAK_chr10.wins...
    Importing windows from FILEPATH/ZINBA_PEAK_chr11.wins...
    Importing windows from FILEPATH/ZINBA_PEAK_chr12.wins...
    Importing windows from FILEPATH/ZINBA_PEAK_chr13.wins...
    Importing windows from FILEPATH/ZINBA_PEAK_chr14.wins...
    Importing windows from FILEPATH/ZINBA_PEAK_chr15.wins...
    Importing windows from FILEPATH/ZINBA_PEAK_chr16.wins...
    Importing windows from FILEPATH/ZINBA_PEAK_chr17.wins...
    Importing windows from FILEPATH/ZINBA_PEAK_chr18.wins...
    Importing windows from FILEPATH/ZINBA_PEAK_chr20.wins...
    Importing windows from FILEPATH/ZINBA_PEAK_chr19.wins...
    Importing windows from FILEPATH/ZINBA_PEAK_chr22.wins...
    Importing windows from FILEPATH/ZINBA_PEAK_chr21.wins...

Imported 47592 coordinates
Processing threshold 0.8
    47592 coords at this threshold
    Collapsed to 11813 regions

Original issue reported on code.google.com by doc2...@gmail.com on 24 Mar 2014 at 2:07