Error when running zinba : can't open file

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Hi all, I have a problem when I run zinba.

1) What operating system are you using?

Ubuntu 12.04
I use zinba 2.01.1 because the other version prevent me to run 
"generateAlignability" correctly

2) What error message was displayed?

Error in file(file, "r") : can't open connexion
Furthermore : Warning :
In file(file, "r") : can't open file 
'/home/julie/PeakCallerComparaison/H3K36me3_files/H3K36me3.list' : no such file 
or directory

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

zinba(
+   refinepeaks=0, #refine peaks? 1 for yes, 0 for no
+   
seq="/home/julie/PeakCallerComparaison/GSM535746_3T3L1t1.H3K36me3.aligned.txt", 
#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="/home/julie/PeakCallerComparaison/Zinba/proccessedFiles/", #path to 
alignability directory
+   numProc=6, #number of CPUs to use, must be less than max available   
(default 1)
+   twoBit="/home/julie/PeakCallerComparaison/Zinba/mm9.2bit", #path to genome 
build in .2bit format
+   outfile="/home/julie/PeakCallerComparaison/H3K36me3", #prefix for outputted 
files
+   extension=200, #average fragment library length (size selected)
+   broad=TRUE)

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] "/home/julie/PeakCallerComparaison/H3K36me3"

$seq
[1] "/home/julie/PeakCallerComparaison/GSM535746_3T3L1t1.H3K36me3.aligned.txt"

$align
[1] "/home/julie/PeakCallerComparaison/Zinba/proccessedFiles/"

$input
[1] "none"

$twoBit
[1] "/home/julie/PeakCallerComparaison/Zinba/mm9.2bit"

$winSize
[1] 250

$offset
[1] 125

$cnvWinSize
[1] 1e+05

$cnvOffset
[1] 2500

$basecountfile
NULL

$threshold
[1] 0.05

$peakconfidence
[1] 0.95

$tol
[1] 1e-05

$numProc
[1] 6

$buildwin
[1] 1

$winGap
[1] 5000

$pWinSize
[1] 200

$pquant
[1] 1

$refinepeaks
[1] 0

$printFullOut
[1] 1

$method
[1] "mixture"

$initmethod
[1] "count"

$diff
[1] 0

$filetype
[1] "bed"

$extension
[1] 200

$cleanup
[1] FALSE

$selectmodel
[1] TRUE

$selectchr
[1] "chr22"

$selecttype
[1] "dirty"

$selectcovs
[1] "gcPerc"     "align_perc"

$FDR
[1] TRUE

Overwriting previously existing directory 
/home/julie/PeakCallerComparaison/H3K36me3_files/

--------BEGIN BUILDING WINDOW DATA-------- 2012-09-12 11:30:28 

Importing reads from file 
/home/julie/PeakCallerComparaison/GSM535746_3T3L1t1.H3K36me3.aligned.txt 
    Filetype is bed 
    Extension is 200 
        For chr1 length is 197195432
        For chr2 length is 181748087
        For chr3 length is 159599783
        For chr4 length is 155630120
        For chr5 length is 152537259
        For chr6 length is 149517037
        For chr7 length is 152524553
        For chr8 length is 131738871
        For chr9 length is 124076172
        For chr10 length is 129993255
        For chr11 length is 121843856
        For chr12 length is 121257530
        For chr13 length is 120284312
        For chr14 length is 125194864
        For chr15 length is 103494974
        For chr16 length is 98319150
        For chr17 length is 95272651
        For chr18 length is 90772031
        For chr19 length is 61342430
        For chrX length is 166650296
        For chrY length is 15902555
        For chrM length is 16299
        For chr13_random length is 400311
        For chr16_random length is 3994
        For chr17_random length is 628739
        For chr1_random length is 1231697
        For chr3_random length is 41899
        For chr4_random length is 160594
        For chr5_random length is 357350
        For chr7_random length is 362490
        For chr8_random length is 849593
        For chr9_random length is 449403
        For chrUn_random length is 5900358
        For chrX_random length is 1785075
        For chrY_random length is 58682461
        For chrY_random length is 58682461
    Importing bed formatted reads
    Skipped 11730017 reads
    Imported 0 reads
    Sorting reads ...COMPLETE

Building window data

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

Error in file(file, "r") : can't open connexion
Furthermore : Warning :
In file(file, "r") : can't open file 
'/home/julie/PeakCallerComparaison/H3K36me3_files/H3K36me3.list' : no such file 
or directory

Thanks for your help

Original issue reported on code.google.com by dubju...@gmail.com on 12 Sep 2012 at 9:43

[GoogleCodeExporter]

I have been tried this with the 2.01 version of zinba and the error is the same.

Original comment by dubju...@gmail.com on 12 Sep 2012 at 9:53

[GoogleCodeExporter]

It's resolved! my file was not a real bed file. One colonn was misplaced

Original comment by dubju...@gmail.com on 12 Sep 2012 at 1:55

[GoogleCodeExporter]

Original comment by homer...@gmail.com on 3 Oct 2012 at 1:27

• Changed state: Invalid