1) What operating system are you using?
CentOs - x64
2) What error message was displayed?
--------BUILD WINDOWS COMPLETE-------
--------STARTING MODEL SELECTION-------- 2014-09-03 20:25:25
Specified chromosome not found or specified, using
/no_backup/so/sjhanwar/ATAC_seq/Peak_calling/output.txt_files/WNN1_6640_AGGCAGA.
sort_chrM_win250bp_offset125bp.txt
$`1`
exp_count ~ 1
<environment: 0x2e3f0c0>
$`2`
exp_count ~ input_count + 1
<environment: 0x2e3f0c0>
Error in covariateselect(file = data, selection = selecttype, loc =
paste(outfile_subpath, :
covselect.R: all models failed after model selection final step
3) What was the exact command you used that resulted in the error?
zinba(align='/no_backup/so/sjhanwar/ATAC_seq/Peak_calling/zinba_outDir/',
numProc=4,
seq='/no_backup/so/sjhanwar/ATAC_seq/Peak_calling/zinba_inputdir/WNN1_6640_AGGCA
GA.sort.bed',
basecountfile='/no_backup/so/sjhanwar/ATAC_seq/Peak_calling/outFile',
filetype="bed",
outfile='/no_backup/so/sjhanwar/ATAC_seq/Peak_calling/output.txt',
twoBit='/no_backup/so/sjhanwar/ATAC_seq/Peak_calling/zinba_map50/mm9.2bit',
extension=200, printFullOut=1, refinepeaks=1, broad=F,
input='/no_backup/so/sjhanwar/ATAC_seq/Peak_calling/zinba_inputdir/input_WNN1_61
46.bed')
4) Please copy and paste any additional screen output that resulted from
running the command
> zinba(
+ align='/no_backup/so/sjhanwar/ATAC_seq/Peak_calling/zinba_outDir/',
numProc=4,
seq='/no_backup/so/sjhanwar/ATAC_seq/Peak_calling/zinba_inputdir/WNN1_6640_AGGCA
GA.sort.bed',
basecountfile='/no_backup/so/sjhanwar/ATAC_seq/Peak_calling/outFile',
filetype="bed",
outfile='/no_backup/so/sjhanwar/ATAC_seq/Peak_calling/output.txt',
twoBit='/no_backup/so/sjhanwar/ATAC_seq/Peak_calling/zinba_map50/mm9.2bit',
extension=200,
+ printFullOut=1,
+ refinepeaks=1, broad=F,
input='/no_backup/so/sjhanwar/ATAC_seq/Peak_calling/zinba_inputdir/input_WNN1_61
46.bed')
[1] "parameters in effect:"
$filelist
NULL
$formula
NULL
$formulaE
NULL
$formulaZ
NULL
$outfile
[1] "/no_backup/so/sjhanwar/ATAC_seq/Peak_calling/output.txt"
$seq
[1]
"/no_backup/so/sjhanwar/ATAC_seq/Peak_calling/zinba_inputdir/WNN1_6640_AGGCAGA.s
ort.bed"
$align
[1] "/no_backup/so/sjhanwar/ATAC_seq/Peak_calling/zinba_outDir/"
$input
[1]
"/no_backup/so/sjhanwar/ATAC_seq/Peak_calling/zinba_inputdir/input_WNN1_6146.bed
"
$twoBit
[1] "/no_backup/so/sjhanwar/ATAC_seq/Peak_calling/zinba_map50/mm9.2bit"
$winSize
[1] 250
$offset
[1] 125
$cnvWinSize
[1] 1e+05
$cnvOffset
[1] 2500
$basecountfile
[1] "/no_backup/so/sjhanwar/ATAC_seq/Peak_calling/outFile"
$threshold
[1] 0.05
$peakconfidence
[1] 0.95
$tol
[1] 1e-05
$numProc
[1] 4
$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] 200
$cleanup
[1] FALSE
$selectmodel
[1] TRUE
$selectchr
[1] "chr22"
$selecttype
[1] "complete"
$selectcovs
[1] "input_count"
$FDR
[1] TRUE
$interaction
[1] TRUE
Loading required package: multicore
WARNING: multicore has been superseded and will be removed shortly
Attaching package: ‘multicore’
The following object is masked from ‘package:R.utils’:
exit
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
--------BEGIN BUILDING WINDOW DATA-------- 2014-09-03 20:14:39
Importing reads from file
/no_backup/so/sjhanwar/ATAC_seq/Peak_calling/zinba_inputdir/WNN1_6640_AGGCAGA.so
rt.bed
Filetype is bed
Extension is 200
Importing bed formatted reads
Skipped 0 reads
Imported 57398993 reads
Sorting reads ...COMPLETE
Building window data
Processing chr1
Initializing to length 197195432
Mapping reads to chromosome......
Getting alignability info from:
/no_backup/so/sjhanwar/ATAC_seq/Peak_calling/zinba_outDir/chr1.wig
Getting sequence from .2bit file:
/no_backup/so/sjhanwar/ATAC_seq/Peak_calling/zinba_map50/mm9.2bit
Getting counts for 100000bp windows..........
Refining boundaries....
Global variance is 2.78148e-06
Refining 102 boundaries
Loading reads from input file /no_backup/so/sjhanwar/ATAC_seq/Peak_calling/zinba_inputdir/input_WNN1_6146.bed.........
Importing bed formatted reads
Skipped 0 reads
Imported 21148196 inpput reads
Sorting reads ...COMPLETE
Mapping input tags to the genome.........
Getting counts for zinba windows..........
Offset 0bp......
Printed out data to /no_backup/so/sjhanwar/ATAC_seq/Peak_calling/output.txt_files/WNN1_6640_AGGCAGA.sort_chr1_win250bp_offset0bp.txt
Offset 125bp......
Printed out data to /no_backup/so/sjhanwar/ATAC_seq/Peak_calling/output.txt_files/WNN1_6640_AGGCAGA.sort_chr1_win250bp_offset125bp.txt
Processing chr2
Initializing to length 181748087
Mapping reads to chromosome......
Getting alignability info from:
/no_backup/so/sjhanwar/ATAC_seq/Peak_calling/zinba_outDir/chr2.wig
Getting sequence from .2bit file:
/no_backup/so/sjhanwar/ATAC_seq/Peak_calling/zinba_map50/mm9.2bit
Getting counts for 100000bp windows..........
Refining boundaries....
Global variance is 0.000140802
Refining 1 boundaries
Mapping input tags to the genome.........
Getting counts for zinba windows..........
Offset 0bp......
Printed out data to /no_backup/so/sjhanwar/ATAC_seq/Peak_calling/output.txt_files/WNN1_6640_AGGCAGA.sort_chr2_win250bp_offset0bp.txt
Offset 125bp......
Printed out data to /no_backup/so/sjhanwar/ATAC_seq/Peak_calling/output.txt_files/WNN1_6640_AGGCAGA.sort_chr2_win250bp_offset125bp.txt
Processing chr3
Initializing to length 159599783
Mapping reads to chromosome......
Getting alignability info from:
/no_backup/so/sjhanwar/ATAC_seq/Peak_calling/zinba_outDir/chr3.wig
Getting sequence from .2bit file:
/no_backup/so/sjhanwar/ATAC_seq/Peak_calling/zinba_map50/mm9.2bit
Getting counts for 100000bp windows..........
Refining boundaries....
Global variance is 2.65444e-06
Refining 85 boundaries
Mapping input tags to the genome.........
Getting counts for zinba windows..........
Offset 0bp......
Printed out data to /no_backup/so/sjhanwar/ATAC_seq/Peak_calling/output.txt_files/WNN1_6640_AGGCAGA.sort_chr3_win250bp_offset0bp.txt
Offset 125bp......
Printed out data to /no_backup/so/sjhanwar/ATAC_seq/Peak_calling/output.txt_files/WNN1_6640_AGGCAGA.sort_chr3_win250bp_offset125bp.txt
Processing chr4
Initializing to length 155630120
Mapping reads to chromosome......
Getting alignability info from:
/no_backup/so/sjhanwar/ATAC_seq/Peak_calling/zinba_outDir/chr4.wig
Getting sequence from .2bit file:
/no_backup/so/sjhanwar/ATAC_seq/Peak_calling/zinba_map50/mm9.2bit
Getting counts for 100000bp windows..........
Refining boundaries....
Global variance is 4.78415e-06
Refining 49 boundaries
Mapping input tags to the genome.........
Getting counts for zinba windows..........
Offset 0bp......
Printed out data to /no_backup/so/sjhanwar/ATAC_seq/Peak_calling/output.txt_files/WNN1_6640_AGGCAGA.sort_chr4_win250bp_offset0bp.txt
Offset 125bp......
Printed out data to /no_backup/so/sjhanwar/ATAC_seq/Peak_calling/output.txt_files/WNN1_6640_AGGCAGA.sort_chr4_win250bp_offset125bp.txt
Processing chr5
Initializing to length 152537259
Mapping reads to chromosome......
Getting alignability info from:
/no_backup/so/sjhanwar/ATAC_seq/Peak_calling/zinba_outDir/chr5.wig
Getting sequence from .2bit file:
/no_backup/so/sjhanwar/ATAC_seq/Peak_calling/zinba_map50/mm9.2bit
Getting counts for 100000bp windows..........
Refining boundaries....
Global variance is 4.14456e-06
Refining 53 boundaries
Mapping input tags to the genome.........
Getting counts for zinba windows..........
Offset 0bp......
Printed out data to /no_backup/so/sjhanwar/ATAC_seq/Peak_calling/output.txt_files/WNN1_6640_AGGCAGA.sort_chr5_win250bp_offset0bp.txt
Offset 125bp......
Printed out data to /no_backup/so/sjhanwar/ATAC_seq/Peak_calling/output.txt_files/WNN1_6640_AGGCAGA.sort_chr5_win250bp_offset125bp.txt
Processing chr6
Initializing to length 149517037
Mapping reads to chromosome......
Getting alignability info from:
/no_backup/so/sjhanwar/ATAC_seq/Peak_calling/zinba_outDir/chr6.wig
Getting sequence from .2bit file:
/no_backup/so/sjhanwar/ATAC_seq/Peak_calling/zinba_map50/mm9.2bit
Getting counts for 100000bp windows..........
Refining boundaries....
Global variance is 3.28221e-06
Refining 69 boundaries
Mapping input tags to the genome.........
Getting counts for zinba windows..........
Offset 0bp......
Printed out data to /no_backup/so/sjhanwar/ATAC_seq/Peak_calling/output.txt_files/WNN1_6640_AGGCAGA.sort_chr6_win250bp_offset0bp.txt
Offset 125bp......
Printed out data to /no_backup/so/sjhanwar/ATAC_seq/Peak_calling/output.txt_files/WNN1_6640_AGGCAGA.sort_chr6_win250bp_offset125bp.txt
Processing chr7
Initializing to length 152524553
Mapping reads to chromosome......
Getting alignability info from:
/no_backup/so/sjhanwar/ATAC_seq/Peak_calling/zinba_outDir/chr7.wig
Getting sequence from .2bit file:
/no_backup/so/sjhanwar/ATAC_seq/Peak_calling/zinba_map50/mm9.2bit
Getting counts for 100000bp windows..........
Refining boundaries....
Global variance is 7.01342e-06
Refining 39 boundaries
Mapping input tags to the genome.........
Getting counts for zinba windows..........
Offset 0bp......
Printed out data to /no_backup/so/sjhanwar/ATAC_seq/Peak_calling/output.txt_files/WNN1_6640_AGGCAGA.sort_chr7_win250bp_offset0bp.txt
Offset 125bp......
Printed out data to /no_backup/so/sjhanwar/ATAC_seq/Peak_calling/output.txt_files/WNN1_6640_AGGCAGA.sort_chr7_win250bp_offset125bp.txt
Processing chr8
Initializing to length 131738871
Mapping reads to chromosome......
Getting alignability info from:
/no_backup/so/sjhanwar/ATAC_seq/Peak_calling/zinba_outDir/chr8.wig
Getting sequence from .2bit file:
/no_backup/so/sjhanwar/ATAC_seq/Peak_calling/zinba_map50/mm9.2bit
Getting counts for 100000bp windows..........
Refining boundaries....
Global variance is 4.37081e-06
Refining 54 boundaries
Mapping input tags to the genome.........
Getting counts for zinba windows..........
Offset 0bp......
Printed out data to /no_backup/so/sjhanwar/ATAC_seq/Peak_calling/output.txt_files/WNN1_6640_AGGCAGA.sort_chr8_win250bp_offset0bp.txt
Offset 125bp......
Printed out data to /no_backup/so/sjhanwar/ATAC_seq/Peak_calling/output.txt_files/WNN1_6640_AGGCAGA.sort_chr8_win250bp_offset125bp.txt
Processing chr9
Initializing to length 124076172
Mapping reads to chromosome......
Getting alignability info from:
/no_backup/so/sjhanwar/ATAC_seq/Peak_calling/zinba_outDir/chr9.wig
Getting sequence from .2bit file:
/no_backup/so/sjhanwar/ATAC_seq/Peak_calling/zinba_map50/mm9.2bit
Getting counts for 100000bp windows..........
Refining boundaries....
Global variance is 5.17432e-06
Refining 45 boundaries
Mapping input tags to the genome.........
Getting counts for zinba windows..........
Offset 0bp......
Printed out data to /no_backup/so/sjhanwar/ATAC_seq/Peak_calling/output.txt_files/WNN1_6640_AGGCAGA.sort_chr9_win250bp_offset0bp.txt
Offset 125bp......
Printed out data to /no_backup/so/sjhanwar/ATAC_seq/Peak_calling/output.txt_files/WNN1_6640_AGGCAGA.sort_chr9_win250bp_offset125bp.txt
Processing chr10
Initializing to length 129993255
Mapping reads to chromosome......
Getting alignability info from:
/no_backup/so/sjhanwar/ATAC_seq/Peak_calling/zinba_outDir/chr10.wig
Getting sequence from .2bit file:
/no_backup/so/sjhanwar/ATAC_seq/Peak_calling/zinba_map50/mm9.2bit
Getting counts for 100000bp windows..........
Refining boundaries....
Global variance is 3.65164e-06
Refining 47 boundaries
Mapping input tags to the genome.........
Getting counts for zinba windows..........
Offset 0bp......
Printed out data to /no_backup/so/sjhanwar/ATAC_seq/Peak_calling/output.txt_files/WNN1_6640_AGGCAGA.sort_chr10_win250bp_offset0bp.txt
Offset 125bp......
Printed out data to /no_backup/so/sjhanwar/ATAC_seq/Peak_calling/output.txt_files/WNN1_6640_AGGCAGA.sort_chr10_win250bp_offset125bp.txt
Processing chr11
Initializing to length 121843856
Mapping reads to chromosome......
Getting alignability info from:
/no_backup/so/sjhanwar/ATAC_seq/Peak_calling/zinba_outDir/chr11.wig
Getting sequence from .2bit file:
/no_backup/so/sjhanwar/ATAC_seq/Peak_calling/zinba_map50/mm9.2bit
Getting counts for 100000bp windows..........
Refining boundaries....
Global variance is 1.53937e-05
Refining 5 boundaries
Mapping input tags to the genome.........
Getting counts for zinba windows..........
Offset 0bp......
Printed out data to /no_backup/so/sjhanwar/ATAC_seq/Peak_calling/output.txt_files/WNN1_6640_AGGCAGA.sort_chr11_win250bp_offset0bp.txt
Offset 125bp......
Printed out data to /no_backup/so/sjhanwar/ATAC_seq/Peak_calling/output.txt_files/WNN1_6640_AGGCAGA.sort_chr11_win250bp_offset125bp.txt
Processing chr12
Initializing to length 121257530
Mapping reads to chromosome......
Getting alignability info from:
/no_backup/so/sjhanwar/ATAC_seq/Peak_calling/zinba_outDir/chr12.wig
Getting sequence from .2bit file:
/no_backup/so/sjhanwar/ATAC_seq/Peak_calling/zinba_map50/mm9.2bit
Getting counts for 100000bp windows..........
Refining boundaries....
Global variance is 4.96169e-06
Refining 38 boundaries
Mapping input tags to the genome.........
Getting counts for zinba windows..........
Offset 0bp......
Printed out data to /no_backup/so/sjhanwar/ATAC_seq/Peak_calling/output.txt_files/WNN1_6640_AGGCAGA.sort_chr12_win250bp_offset0bp.txt
Offset 125bp......
Printed out data to /no_backup/so/sjhanwar/ATAC_seq/Peak_calling/output.txt_files/WNN1_6640_AGGCAGA.sort_chr12_win250bp_offset125bp.txt
Processing chr13
Initializing to length 120284312
Mapping reads to chromosome......
Getting alignability info from:
/no_backup/so/sjhanwar/ATAC_seq/Peak_calling/zinba_outDir/chr13.wig
Getting sequence from .2bit file:
/no_backup/so/sjhanwar/ATAC_seq/Peak_calling/zinba_map50/mm9.2bit
Getting counts for 100000bp windows..........
Refining boundaries....
Global variance is 2.94717e-06
Refining 58 boundaries
Mapping input tags to the genome.........
Getting counts for zinba windows..........
Offset 0bp......
Printed out data to /no_backup/so/sjhanwar/ATAC_seq/Peak_calling/output.txt_files/WNN1_6640_AGGCAGA.sort_chr13_win250bp_offset0bp.txt
Offset 125bp......
Printed out data to /no_backup/so/sjhanwar/ATAC_seq/Peak_calling/output.txt_files/WNN1_6640_AGGCAGA.sort_chr13_win250bp_offset125bp.txt
Processing chr14
Initializing to length 125194864
Mapping reads to chromosome......
Getting alignability info from:
/no_backup/so/sjhanwar/ATAC_seq/Peak_calling/zinba_outDir/chr14.wig
Getting sequence from .2bit file:
/no_backup/so/sjhanwar/ATAC_seq/Peak_calling/zinba_map50/mm9.2bit
Getting counts for 100000bp windows..........
Refining boundaries....
Global variance is 4.95189e-06
Refining 27 boundaries
Mapping input tags to the genome.........
Getting counts for zinba windows..........
Offset 0bp......
Printed out data to /no_backup/so/sjhanwar/ATAC_seq/Peak_calling/output.txt_files/WNN1_6640_AGGCAGA.sort_chr14_win250bp_offset0bp.txt
Offset 125bp......
Printed out data to /no_backup/so/sjhanwar/ATAC_seq/Peak_calling/output.txt_files/WNN1_6640_AGGCAGA.sort_chr14_win250bp_offset125bp.txt
Processing chr15
Initializing to length 103494974
Mapping reads to chromosome......
Getting alignability info from:
/no_backup/so/sjhanwar/ATAC_seq/Peak_calling/zinba_outDir/chr15.wig
Getting sequence from .2bit file:
/no_backup/so/sjhanwar/ATAC_seq/Peak_calling/zinba_map50/mm9.2bit
Getting counts for 100000bp windows..........
Refining boundaries....
Global variance is 4.04847e-06
Refining 46 boundaries
Mapping input tags to the genome.........
Getting counts for zinba windows..........
Offset 0bp......
Printed out data to /no_backup/so/sjhanwar/ATAC_seq/Peak_calling/output.txt_files/WNN1_6640_AGGCAGA.sort_chr15_win250bp_offset0bp.txt
Offset 125bp......
Printed out data to /no_backup/so/sjhanwar/ATAC_seq/Peak_calling/output.txt_files/WNN1_6640_AGGCAGA.sort_chr15_win250bp_offset125bp.txt
Processing chr16
Initializing to length 98319150
Mapping reads to chromosome......
Getting alignability info from:
/no_backup/so/sjhanwar/ATAC_seq/Peak_calling/zinba_outDir/chr16.wig
Getting sequence from .2bit file:
/no_backup/so/sjhanwar/ATAC_seq/Peak_calling/zinba_map50/mm9.2bit
Getting counts for 100000bp windows..........
Refining boundaries....
Global variance is 2.72613e-06
Refining 51 boundaries
Mapping input tags to the genome.........
Getting counts for zinba windows..........
Offset 0bp......
Printed out data to /no_backup/so/sjhanwar/ATAC_seq/Peak_calling/output.txt_files/WNN1_6640_AGGCAGA.sort_chr16_win250bp_offset0bp.txt
Offset 125bp......
Printed out data to /no_backup/so/sjhanwar/ATAC_seq/Peak_calling/output.txt_files/WNN1_6640_AGGCAGA.sort_chr16_win250bp_offset125bp.txt
Processing chr17
Initializing to length 95272651
Mapping reads to chromosome......
Getting alignability info from:
/no_backup/so/sjhanwar/ATAC_seq/Peak_calling/zinba_outDir/chr17.wig
Getting sequence from .2bit file:
/no_backup/so/sjhanwar/ATAC_seq/Peak_calling/zinba_map50/mm9.2bit
Getting counts for 100000bp windows..........
Refining boundaries....
Global variance is 1.58596e-05
Refining 6 boundaries
Mapping input tags to the genome.........
Getting counts for zinba windows..........
Offset 0bp......
Printed out data to /no_backup/so/sjhanwar/ATAC_seq/Peak_calling/output.txt_files/WNN1_6640_AGGCAGA.sort_chr17_win250bp_offset0bp.txt
Offset 125bp......
Printed out data to /no_backup/so/sjhanwar/ATAC_seq/Peak_calling/output.txt_files/WNN1_6640_AGGCAGA.sort_chr17_win250bp_offset125bp.txt
Processing chr18
Initializing to length 90772031
Mapping reads to chromosome......
Getting alignability info from:
/no_backup/so/sjhanwar/ATAC_seq/Peak_calling/zinba_outDir/chr18.wig
Getting sequence from .2bit file:
/no_backup/so/sjhanwar/ATAC_seq/Peak_calling/zinba_map50/mm9.2bit
Getting counts for 100000bp windows..........
Refining boundaries....
Global variance is 2.87558e-06
Refining 44 boundaries
Mapping input tags to the genome.........
Getting counts for zinba windows..........
Offset 0bp......
Printed out data to /no_backup/so/sjhanwar/ATAC_seq/Peak_calling/output.txt_files/WNN1_6640_AGGCAGA.sort_chr18_win250bp_offset0bp.txt
Offset 125bp......
Printed out data to /no_backup/so/sjhanwar/ATAC_seq/Peak_calling/output.txt_files/WNN1_6640_AGGCAGA.sort_chr18_win250bp_offset125bp.txt
Processing chr19
Initializing to length 61342430
Mapping reads to chromosome......
Getting alignability info from:
/no_backup/so/sjhanwar/ATAC_seq/Peak_calling/zinba_outDir/chr19.wig
Getting sequence from .2bit file:
/no_backup/so/sjhanwar/ATAC_seq/Peak_calling/zinba_map50/mm9.2bit
Getting counts for 100000bp windows..........
Refining boundaries....
Global variance is 3.92737e-06
Refining 26 boundaries
Mapping input tags to the genome.........
Getting counts for zinba windows..........
Offset 0bp......
Printed out data to /no_backup/so/sjhanwar/ATAC_seq/Peak_calling/output.txt_files/WNN1_6640_AGGCAGA.sort_chr19_win250bp_offset0bp.txt
Offset 125bp......
Printed out data to /no_backup/so/sjhanwar/ATAC_seq/Peak_calling/output.txt_files/WNN1_6640_AGGCAGA.sort_chr19_win250bp_offset125bp.txt
Processing chrX
Initializing to length 166650296
Mapping reads to chromosome......
Getting alignability info from:
/no_backup/so/sjhanwar/ATAC_seq/Peak_calling/zinba_outDir/chrX.wig
Getting sequence from .2bit file:
/no_backup/so/sjhanwar/ATAC_seq/Peak_calling/zinba_map50/mm9.2bit
Getting counts for 100000bp windows..........
Refining boundaries....
Global variance is 3.06848e-06
Refining 44 boundaries
Mapping input tags to the genome.........
Getting counts for zinba windows..........
Offset 0bp......
Printed out data to /no_backup/so/sjhanwar/ATAC_seq/Peak_calling/output.txt_files/WNN1_6640_AGGCAGA.sort_chrX_win250bp_offset0bp.txt
Offset 125bp......
Printed out data to /no_backup/so/sjhanwar/ATAC_seq/Peak_calling/output.txt_files/WNN1_6640_AGGCAGA.sort_chrX_win250bp_offset125bp.txt
Processing chrY
Initializing to length 15902555
Mapping reads to chromosome......
Getting alignability info from:
/no_backup/so/sjhanwar/ATAC_seq/Peak_calling/zinba_outDir/chrY.wig
Getting sequence from .2bit file:
/no_backup/so/sjhanwar/ATAC_seq/Peak_calling/zinba_map50/mm9.2bit
Getting counts for 100000bp windows..........
Refining boundaries....
Global variance is 2.01893e-08
Refining 1 boundaries
Mapping input tags to the genome.........
Getting counts for zinba windows..........
Offset 0bp......
Printed out data to /no_backup/so/sjhanwar/ATAC_seq/Peak_calling/output.txt_files/WNN1_6640_AGGCAGA.sort_chrY_win250bp_offset0bp.txt
Offset 125bp......
Printed out data to /no_backup/so/sjhanwar/ATAC_seq/Peak_calling/output.txt_files/WNN1_6640_AGGCAGA.sort_chrY_win250bp_offset125bp.txt
Processing chrM
Initializing to length 16299
Mapping reads to chromosome......
Getting alignability info from:
/no_backup/so/sjhanwar/ATAC_seq/Peak_calling/zinba_outDir/chrM.wig
Getting sequence from .2bit file:
/no_backup/so/sjhanwar/ATAC_seq/Peak_calling/zinba_map50/mm9.2bit
Getting counts for 100000bp windows..........
Refining boundaries....
Global variance is 92888.7
Refining 0 boundaries
Mapping input tags to the genome.........
Getting counts for zinba windows..........
Offset 0bp......
Printed out data to /no_backup/so/sjhanwar/ATAC_seq/Peak_calling/output.txt_files/WNN1_6640_AGGCAGA.sort_chrM_win250bp_offset0bp.txt
Offset 125bp......
Printed out data to /no_backup/so/sjhanwar/ATAC_seq/Peak_calling/output.txt_files/WNN1_6640_AGGCAGA.sort_chrM_win250bp_offset125bp.txt
--------BUILD WINDOWS COMPLETE-------
--------STARTING MODEL SELECTION-------- 2014-09-03 20:25:25
Specified chromosome not found or specified, using
/no_backup/so/sjhanwar/ATAC_seq/Peak_calling/output.txt_files/WNN1_6640_AGGCAGA.
sort_chrM_win250bp_offset125bp.txt
$`1`
exp_count ~ 1
<environment: 0x2e3f0c0>
$`2`
exp_count ~ input_count + 1
<environment: 0x2e3f0c0>
Error in covariateselect(file = data, selection = selecttype, loc =
paste(outfile_subpath, :
covselect.R: all models failed after model selection final step
> zinba(
+ + align='/no_backup/so/sjhanwar/ATAC_seq/Peak_calling/zinba_outDir/',
numProc=4,
seq='/no_backup/so/sjhanwar/ATAC_seq/Peak_calling/zinba_inputdir/WNN1_6640_AGGCA
GA.sort.bed',
basecountfile='/no_backup/so/sjhanwar/ATAC_seq/Peak_calling/outFile',
filetype="bed",
outfile='/no_backup/so/sjhanwar/ATAC_seq/Peak_calling/output.txt',
twoBit='/no_backup/so/sjhanwar/ATAC_seq/Peak_calling/zinba_map50/mm9.2bit',
extension=200,
Error: unexpected '=' in:
"zinba(
+ align="
> + printFullOut=1,
Error: unexpected ',' in "+ printFullOut=1,"
> zinba(
+ + align='/no_backup/so/sjhanwar/ATAC_seq/Peak_calling/zinba_outDir/',
numProc=4,
seq='/no_backup/so/sjhanwar/ATAC_seq/Peak_calling/zinba_inputdir/WNN1_6640_AGGCA
GA.sort.bed',
basecountfile='/no_backup/so/sjhanwar/ATAC_seq/Peak_calling/outFile',
filetype="bed",
outfile='/no_backup/so/sjhanwar/ATAC_seq/Peak_calling/output.txt',
twoBit='/no_backup/so/sjhanwar/ATAC_seq/Peak_calling/zinba_map50/mm9.2bit',
extension=200,
Error: unexpected '=' in:
"zinba(
+ align="
> + printFullOut=1,
Error: unexpected ',' in "+ printFullOut=1,"
Please reply
Original issue reported on code.google.com by shalu.jh...@gmail.com on 4 Sep 2014 at 11:16
Original issue reported on code.google.com by
shalu.jh...@gmail.comon 4 Sep 2014 at 11:16