Unable to open alignability file outdirAlignability/.wig

[GoogleCodeExporter]

1) What operating system are you using?
ubuntu linux 12.04 64bit

2) What error message was displayed?
Building window data

Processing 
        Initializing to length 0
        Mapping reads to chromosome......
        Getting alignability info from:
                outdirAlignability/.wig
Unable to open alignability file outdirAlignability/.wig
ERROR: building windows was unsuccssful

3) What was the exact command you used that resulted in the error?
zinba(refinepeaks=1, basecountfile='test_ip.basecount',
  seq='../bowtie/test_ip.bed', 
  input='../bowtie/test_input.bed',   filetype='bed',
  align='outdirAlignability', numProc=4, 
  twoBit='sacCer3.2bit', 
  outfile='outfileZinba', extension=140, 
  broad=T, printFullOut=1,   mode='peaks')

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

[1] "parameters in effect:"
$filelist
NULL

$formula
NULL

$formulaE
NULL

$formulaZ
NULL

$outfile
[1] "outfileZinba"

$seq
[1] "../bowtie/test_ip.bed"

$align
[1] "outdirAlignability"

$input
[1] "../bowtie/test_input.bed"

$twoBit
[1] "sacCer3.2bit"

$winSize
[1] 250

$offset
[1] 125

$cnvWinSize
[1] 1e+05

$cnvOffset
[1] 2500

$basecountfile
[1] "test_ip.basecount"

$threshold
[1] 0.05

$peakconfidence
[1] 0.95

$tol
[1] 1e-05

$numProc
[1] 4

$buildwin
[1] 1

$winGap
[1] 5000

$pWinSize
[1] 200

$pquant
[1] 1

$refinepeaks
[1] 1

$printFullOut
[1] 1

$method
[1] "mixture"

$initmethod
[1] "count"

$diff
[1] 0

$filetype
[1] "bed"

$extension
[1] 140

$cleanup
[1] FALSE

$selectmodel
[1] TRUE

$selectchr
[1] "chr22"

$selecttype
[1] "complete"

$selectcovs
[1] "input_count"

$FDR
[1] TRUE

Loading required package: multicore
Loading required package: doMC
Loading required package: foreach
foreach: simple, scalable parallel programming from Revolution Analytics
Use Revolution R for scalability, fault tolerance and more.
http://www.revolutionanalytics.com
Loading required package: iterators
Loading required package: parallel

Attaching package: ‘parallel’

The following object is masked from ‘package:multicore’:

    mclapply, mcparallel, pvec

Overwriting previously existing directory outfileZinba_files/

--------BEGIN BUILDING WINDOW DATA-------- 2014-04-02 14:48:32

Importing reads from file ../bowtie/test_ip.bed
        Filetype is bed
        Extension is 140
        Getting chromosome lengths from .2bit file: sacCer3.2bit
                For chrI length is 230218
                For chrII length is 813184
                For chrIII length is 316620
                For chrIV length is 1531933
                For chrIX length is 439888
                For chrV length is 576874
                For chrVI length is 270161
                For chrVII length is 1090940
                For chrVIII length is 562643
                For chrX length is 745751
                For chrXI length is 666816
                For chrXII length is 1078177
                For chrXIII length is 924431
                For chrXIV length is 784333
                For chrXV length is 1091291
                For chrXVI length is 948066
                For chrM length is 85779
                For chrM length is 85779
        Importing bed formatted reads
        Skipped 0 reads
        Imported 9382159 reads
        Sorting reads ...COMPLETE

Building window data

Processing
        Initializing to length 0
        Mapping reads to chromosome......
        Getting alignability info from:
                outdirAlignability/.wig
Unable to open alignability file outdirAlignability/.wig
ERROR: building windows was unsuccssful

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

*** glibc detected *** /usr/lib/R/bin/exec/R: corrupted double-linked list: 
0x00000000025b5ca0 ***

Original issue reported on code.google.com by zongzhi....@gmail.com on 2 Apr 2014 at 8:56