Error while run.zinba - Githubissues

1) What operating system are you using?
Linux
2) What error message was displayed?
Processing "chrM"
    Initializing to length 0
    Mapping reads to chromosome......
    Getting alignability info from:
        /run/user/1003/gvfs/smb-share:server=licrfileserver,share=all_labs/Andre/ZIMBA/ResultsATAC/"chrM".wig
Unable to open alignability file 
/run/user/1003/gvfs/smb-share:server=licrfileserver,share=all_labs/Andre/ZIMBA/R
esultsATAC/"chrM".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 '/run/user/1003/gvfs/smb-share:server=licrfileserver,share=all_labs/Andre/ZIMBA/zinba_peaks_norandom/dsRedOEneg2_files/dsRedOEneg2.list': No such file or directory

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

run.zinba()

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

> run.zinba(
e/ZIMBA/BED FILES/Modified Bed 
Files/dsRedOEneg2.bed',server,share=all_labs/Andr 
+   input="none",
+   filetype="bed",
ndre/ZIMBA/mm9(1).2bit",03/gvfs/smb-share:server=licrfileserver,share=all_labs/A

+   winSize=300,
+   offset=75,
+   extension=456,
_labs/Andre/ZIMBA/BED FILES/Modified Bed 
Files/dsRedOEneg2.basecount',,share=all 
dre/ZIMBA/ResultsATAC/',3/gvfs/smb-share:server=licrfileserver,share=all_labs/An

+   selectmodel=F, 
+   formula= exp_count ~ 1,
+   formulaE= exp_count ~ 1,
+   formulaZ= exp_count ~ align_perc,
+   interaction=F,
+   threshold=0.05,
+   refinepeaks=1,
+   numProc=25,
+   winGap=0,   
+   FDR=F,
Andre/ZIMBA/zinba_peaks_norandom/dsRedOEneg2",ver=licrfileserver,share=all_labs/

+   printFullOut=1,
+   method="mixture",
+   peakconfidence=0.8
+ )
[1] "parameters in effect:"
$filelist
NULL

$formula
exp_count ~ 1

$formulaE
exp_count ~ 1

$formulaZ
exp_count ~ align_perc

$outfile
[1] 
"/run/user/1003/gvfs/smb-share:server=licrfileserver,share=all_labs/Andre/ZIMBA/
zinba_peaks_norandom/dsRedOEneg2"

$seq
[1] 
"/run/user/1003/gvfs/smb-share:server=licrfileserver,share=all_labs/Andre/ZIMBA/
BED FILES/Modified Bed Files/dsRedOEneg2.bed"

$align
[1] 
"/run/user/1003/gvfs/smb-share:server=licrfileserver,share=all_labs/Andre/ZIMBA/
ResultsATAC/"

$input
[1] "none"

$twoBit
[1] 
"/run/user/1003/gvfs/smb-share:server=licrfileserver,share=all_labs/Andre/ZIMBA/
mm9(1).2bit"

$winSize
[1] 300

$offset
[1] 75

$cnvWinSize
[1] 1e+05

$cnvOffset
[1] 0

$basecountfile
[1] 
"/run/user/1003/gvfs/smb-share:server=licrfileserver,share=all_labs/Andre/ZIMBA/
BED FILES/Modified Bed Files/dsRedOEneg2.basecount"

$threshold
[1] 0.05

$peakconfidence
[1] 0.8

$tol
[1] 1e-05

$numProc
[1] 25

$buildwin
[1] 1

$winGap
[1] 0

$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] 456

$cleanup
[1] FALSE

$selectmodel
[1] FALSE

$selectchr
NULL

$selecttype
[1] "dirty"

$selectcovs
NULL

$FDR
[1] FALSE

--------BEGIN BUILDING WINDOW DATA-------- 2014-06-03 15:43:57 

Importing reads from file 
/run/user/1003/gvfs/smb-share:server=licrfileserver,share=all_labs/Andre/ZIMBA/B
ED FILES/Modified Bed Files/dsRedOEneg2.bed 
    Filetype is bed 
    Extension is 456 
    Getting chromosome lengths from .2bit file: /run/user/1003/gvfs/smb-share:server=licrfileserver,share=all_labs/Andre/ZIMBA/mm9(1).2bit
        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 5876116 reads
    Imported 5876110 reads
    Sorting reads ...COMPLETE

Building window data

Processing "chrM"
    Initializing to length 0
    Mapping reads to chromosome......
    Getting alignability info from:
        /run/user/1003/gvfs/smb-share:server=licrfileserver,share=all_labs/Andre/ZIMBA/ResultsATAC/"chrM".wig
Unable to open alignability file 
/run/user/1003/gvfs/smb-share:server=licrfileserver,share=all_labs/Andre/ZIMBA/R
esultsATAC/"chrM".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 '/run/user/1003/gvfs/smb-share:server=licrfileserver,share=all_labs/Andre/ZIMBA/zinba_peaks_norandom/dsRedOEneg2_files/dsRedOEneg2.list': No such file or directory
Original issue reported on code.google.com by Alentejo...@gmail.com on 3 Jun 2014 at 1:52
sivarajankumar / zinba

Error while run.zinba #62
