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
Original issue reported on code.google.com by
Alentejo...@gmail.com
on 3 Jun 2014 at 1:52