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Terim1 / zinba

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alignability incomplete in test data (no chr22.wig file) #51

Open GoogleCodeExporter opened 8 years ago

GoogleCodeExporter commented 8 years ago 
1) What operating system are you using?
Linux (on Ubuntu virtual machine)

2) What error message was displayed?

Processing chr22
    Initializing to length 49691432
    Mapping reads to chromosome......
    Getting alignability info from:
        align_athresh4_extension134/chr22.wig
Unable to open alignability file align_athresh4_extension134/chr22.wig
ERROR: building windows was unsuccssful

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

Error in file(file, "r") : cannot open the connection
In addition: Warning message:
In file(file, "r") :
  cannot open file 'data/faire_files/faire.list': No such file or directory

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

> 
zinba(align='align_athresh4_extension134/',numProc=4,seq='data/faireGM12878rep1c
hr22.taf',basecountfile='data/faireGM12878rep1chr22.basecount',filetype="tagAlig
n",outfile="data/faire",twoBit="hg18.2bit",extension=134,printFullOut=1,refinepe
aks=1,broad=F,input="none")

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

When I scrolled through the previous commands, I noticed that the 
generateAlignability process hadn't completed (exact command below).
It processed all the chr#b.out files, but only "printed out" and created the 
.wig files for chr10-chr19 (output below).

> 
generateAlignability(mapdir='map36/',outdir='align_athresh4_extension134/',athre
sh=4,extension=134,twoBitFile='hg18.2bit')

.  
.
.

Loading align count data from map36/temp.wig
    Processing chr10
        Printing output to: align_athresh4_extension134/chr10.wig
    Processing chr11
        Printing output to: align_athresh4_extension134/chr11.wig
    Processing chr12
        Printing output to: align_athresh4_extension134/chr12.wig
    Processing chr13
        Printing output to: align_athresh4_extension134/chr13.wig
    Processing chr14
        Printing output to: align_athresh4_extension134/chr14.wig
    Processing chr15
        Printing output to: align_athresh4_extension134/chr15.wig
    Processing chr16
        Printing output to: align_athresh4_extension134/chr16.wig
    Processing chr17
        Printing output to: align_athresh4_extension134/chr17.wig
    Processing chr18
        Printing output to: align_athresh4_extension134/chr18.wig
    Processing chr19
        Printing output to: align_athresh4_extension134/chr19.wig

---------------- ALIGN ADJUST COMPLETED SUCCESSFULLY ----------------

Original issue reported on code.google.com by liz.goos...@gmail.com on 30 Oct 2013 at 4:35