1) What operating system are you using?
Ubuntu 14.04
2) What error message was displayed?
Erreur dans covariateselect(file = data, selection = selecttype, loc =
paste(outfile_subpath, :
covselect.R: all models failed after model selection intermediate step
3) What was the exact command you used that resulted in the error?
zinba(
align='results/adipocytes/zinba/sorties_zinba',
numProc=4,
seq='results/adipocytes/hits/faire_3T3L1_day8.hits',
basecountfile='results/adipocytes/zinba/necessary_files/faire_3T3L1_day8.basecount',
filetype="bowtie",
outfile="results/adipocytes/zinba/sorties_zinba/faire_3T3L1_day8",
twoBit="results/adipocytes/zinba/necessary_files/mm9.2bit",
extension=300,
printFullOut=1,
refinepeaks=1,
broad=F,
input="none",
FDR=0.05
)
4) Please copy and paste any additional screen output that resulted from
running the command
> zinba(
+ align='results/adipocytes/zinba/sorties_zinba',
+ numProc=4,
+ seq='results/adipocytes/hits/faire_3T3L1_day8.hits',
+
basecountfile='results/adipocytes/zinba/necessary_files/faire_3T3L1_day8.basecou
nt',
+ filetype="bowtie",
+ outfile="results/adipocytes/zinba/sorties_zinba/faire_3T3L1_day8",
+ twoBit="results/adipocytes/zinba/necessary_files/mm9.2bit",
+ extension=300,
+ printFullOut=1,
+ refinepeaks=1,
+ broad=F,
+ input="none",
+ FDR=0.05
+ )
[1] "parameters in effect:"
$filelist
NULL
$formula
NULL
$formulaE
NULL
$formulaZ
NULL
$outfile
[1] "results/adipocytes/zinba/sorties_zinba/faire_3T3L1_day8"
$seq
[1] "results/adipocytes/hits/faire_3T3L1_day8.hits"
$align
[1] "results/adipocytes/zinba/sorties_zinba"
$input
[1] "none"
$twoBit
[1] "results/adipocytes/zinba/necessary_files/mm9.2bit"
$winSize
[1] 250
$offset
[1] 125
$cnvWinSize
[1] 1e+05
$cnvOffset
[1] 2500
$basecountfile
[1] "results/adipocytes/zinba/necessary_files/faire_3T3L1_day8.basecount"
$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] "bowtie"
$extension
[1] 300
$cleanup
[1] FALSE
$selectmodel
[1] TRUE
$selectchr
[1] "chr22"
$selecttype
[1] "dirty"
$selectcovs
[1] "gcPerc" "align_perc" "exp_cnvwin_log"
$FDR
[1] 0.05
$interaction
[1] TRUE
Overwriting previously existing directory
results/adipocytes/zinba/sorties_zinba/faire_3T3L1_day8_files/
--------BEGIN BUILDING WINDOW DATA-------- 2014-05-15 13:48:35
Importing reads from file results/adipocytes/hits/faire_3T3L1_day8.hits
Filetype is bowtie
Extension is 300
Importing bowtie formatted reads
Skipped 0 reads
Imported 10818457 reads
Sorting reads ...
Building window data
COMPLETE
Processing chr1
Initializing to length 197195432
Mapping reads to chromosome......
Getting alignability info from:
results/adipocytes/zinba/sorties_zinba/chr1.wig
Getting sequence from .2bit file:
results/adipocytes/zinba/necessary_files/mm9.2bit
Getting counts for 100000bp windows..........
Refining boundaries....
Global variance is 3.82822e-06
Refining 6 boundaries
Getting counts for zinba windows..........
Offset 0bp......
Printed out data to results/adipocytes/zinba/sorties_zinba/faire_3T3L1_day8_files/faire_3T3L1_day8_chr1_win250bp_offset0bp.txt
Offset 125bp......
Printed out data to results/adipocytes/zinba/sorties_zinba/faire_3T3L1_day8_files/faire_3T3L1_day8_chr1_win250bp_offset125bp.txt
Processing chr2
Initializing to length 181748087
Mapping reads to chromosome......
Getting alignability info from:
results/adipocytes/zinba/sorties_zinba/chr2.wig
Getting sequence from .2bit file:
results/adipocytes/zinba/necessary_files/mm9.2bit
Getting counts for 100000bp windows..........
Refining boundaries....
Global variance is 0.275908
Refining 1 boundaries
Getting counts for zinba windows..........
Offset 0bp......
Printed out data to results/adipocytes/zinba/sorties_zinba/faire_3T3L1_day8_files/faire_3T3L1_day8_chr2_win250bp_offset0bp.txt
Offset 125bp......
Printed out data to results/adipocytes/zinba/sorties_zinba/faire_3T3L1_day8_files/faire_3T3L1_day8_chr2_win250bp_offset125bp.txt
Processing chr3
Initializing to length 159599783
Mapping reads to chromosome......
Getting alignability info from:
results/adipocytes/zinba/sorties_zinba/chr3.wig
Getting sequence from .2bit file:
results/adipocytes/zinba/necessary_files/mm9.2bit
Getting counts for 100000bp windows..........
Refining boundaries....
Global variance is 7.78757e-05
Refining 2 boundaries
Getting counts for zinba windows..........
Offset 0bp......
Printed out data to results/adipocytes/zinba/sorties_zinba/faire_3T3L1_day8_files/faire_3T3L1_day8_chr3_win250bp_offset0bp.txt
Offset 125bp......
Printed out data to results/adipocytes/zinba/sorties_zinba/faire_3T3L1_day8_files/faire_3T3L1_day8_chr3_win250bp_offset125bp.txt
Processing chr4
Initializing to length 155630120
Mapping reads to chromosome......
Getting alignability info from:
results/adipocytes/zinba/sorties_zinba/chr4.wig
Getting sequence from .2bit file:
results/adipocytes/zinba/necessary_files/mm9.2bit
Getting counts for 100000bp windows..........
Refining boundaries....
Global variance is 0.0207596
Refining 3 boundaries
Getting counts for zinba windows..........
Offset 0bp......
Printed out data to results/adipocytes/zinba/sorties_zinba/faire_3T3L1_day8_files/faire_3T3L1_day8_chr4_win250bp_offset0bp.txt
Offset 125bp......
Printed out data to results/adipocytes/zinba/sorties_zinba/faire_3T3L1_day8_files/faire_3T3L1_day8_chr4_win250bp_offset125bp.txt
Processing chr5
Initializing to length 152537259
Mapping reads to chromosome......
Getting alignability info from:
results/adipocytes/zinba/sorties_zinba/chr5.wig
Getting sequence from .2bit file:
results/adipocytes/zinba/necessary_files/mm9.2bit
Getting counts for 100000bp windows..........
Refining boundaries....
Global variance is 0.000150938
Refining 9 boundaries
Getting counts for zinba windows..........
Offset 0bp......
Printed out data to results/adipocytes/zinba/sorties_zinba/faire_3T3L1_day8_files/faire_3T3L1_day8_chr5_win250bp_offset0bp.txt
Offset 125bp......
Printed out data to results/adipocytes/zinba/sorties_zinba/faire_3T3L1_day8_files/faire_3T3L1_day8_chr5_win250bp_offset125bp.txt
Processing chr6
Initializing to length 149517037
Mapping reads to chromosome......
Getting alignability info from:
results/adipocytes/zinba/sorties_zinba/chr6.wig
Getting sequence from .2bit file:
results/adipocytes/zinba/necessary_files/mm9.2bit
Getting counts for 100000bp windows..........
Refining boundaries....
Global variance is 0.000210308
Refining 3 boundaries
Getting counts for zinba windows..........
Offset 0bp......
Printed out data to results/adipocytes/zinba/sorties_zinba/faire_3T3L1_day8_files/faire_3T3L1_day8_chr6_win250bp_offset0bp.txt
Offset 125bp......
Printed out data to results/adipocytes/zinba/sorties_zinba/faire_3T3L1_day8_files/faire_3T3L1_day8_chr6_win250bp_offset125bp.txt
Processing chr7
Initializing to length 152524553
Mapping reads to chromosome......
Getting alignability info from:
results/adipocytes/zinba/sorties_zinba/chr7.wig
Getting sequence from .2bit file:
results/adipocytes/zinba/necessary_files/mm9.2bit
Getting counts for 100000bp windows..........
Refining boundaries....
Global variance is 0.0372734
Refining 4 boundaries
Getting counts for zinba windows..........
Offset 0bp......
Printed out data to results/adipocytes/zinba/sorties_zinba/faire_3T3L1_day8_files/faire_3T3L1_day8_chr7_win250bp_offset0bp.txt
Offset 125bp......
Printed out data to results/adipocytes/zinba/sorties_zinba/faire_3T3L1_day8_files/faire_3T3L1_day8_chr7_win250bp_offset125bp.txt
Processing chr8
Initializing to length 131738871
Mapping reads to chromosome......
Getting alignability info from:
results/adipocytes/zinba/sorties_zinba/chr8.wig
Getting sequence from .2bit file:
results/adipocytes/zinba/necessary_files/mm9.2bit
Getting counts for 100000bp windows..........
Refining boundaries....
Global variance is 4.99793e-06
Refining 9 boundaries
Getting counts for zinba windows..........
Offset 0bp......
Printed out data to results/adipocytes/zinba/sorties_zinba/faire_3T3L1_day8_files/faire_3T3L1_day8_chr8_win250bp_offset0bp.txt
Offset 125bp......
Printed out data to results/adipocytes/zinba/sorties_zinba/faire_3T3L1_day8_files/faire_3T3L1_day8_chr8_win250bp_offset125bp.txt
Processing chr9
Initializing to length 124076172
Mapping reads to chromosome......
Getting alignability info from:
results/adipocytes/zinba/sorties_zinba/chr9.wig
Getting sequence from .2bit file:
results/adipocytes/zinba/necessary_files/mm9.2bit
Getting counts for 100000bp windows..........
Refining boundaries....
Global variance is 0.026068
Refining 0 boundaries
Getting counts for zinba windows..........
Offset 0bp......
Printed out data to results/adipocytes/zinba/sorties_zinba/faire_3T3L1_day8_files/faire_3T3L1_day8_chr9_win250bp_offset0bp.txt
Offset 125bp......
Printed out data to results/adipocytes/zinba/sorties_zinba/faire_3T3L1_day8_files/faire_3T3L1_day8_chr9_win250bp_offset125bp.txt
Processing chr10
Initializing to length 129993255
Mapping reads to chromosome......
Getting alignability info from:
results/adipocytes/zinba/sorties_zinba/chr10.wig
Getting sequence from .2bit file:
results/adipocytes/zinba/necessary_files/mm9.2bit
Getting counts for 100000bp windows..........
Refining boundaries....
Global variance is 3.93008e-05
Refining 8 boundaries
Getting counts for zinba windows..........
Offset 0bp......
Printed out data to results/adipocytes/zinba/sorties_zinba/faire_3T3L1_day8_files/faire_3T3L1_day8_chr10_win250bp_offset0bp.txt
Offset 125bp......
Printed out data to results/adipocytes/zinba/sorties_zinba/faire_3T3L1_day8_files/faire_3T3L1_day8_chr10_win250bp_offset125bp.txt
Processing chr11
Initializing to length 121843856
Mapping reads to chromosome......
Getting alignability info from:
results/adipocytes/zinba/sorties_zinba/chr11.wig
Getting sequence from .2bit file:
results/adipocytes/zinba/necessary_files/mm9.2bit
Getting counts for 100000bp windows..........
Refining boundaries....
Global variance is 1.85619e-06
Refining 35 boundaries
Getting counts for zinba windows..........
Offset 0bp......
Printed out data to results/adipocytes/zinba/sorties_zinba/faire_3T3L1_day8_files/faire_3T3L1_day8_chr11_win250bp_offset0bp.txt
Offset 125bp......
Printed out data to results/adipocytes/zinba/sorties_zinba/faire_3T3L1_day8_files/faire_3T3L1_day8_chr11_win250bp_offset125bp.txt
Processing chr12
Initializing to length 121257530
Mapping reads to chromosome......
Getting alignability info from:
results/adipocytes/zinba/sorties_zinba/chr12.wig
Getting sequence from .2bit file:
results/adipocytes/zinba/necessary_files/mm9.2bit
Getting counts for 100000bp windows..........
Refining boundaries....
Global variance is 0.0255878
Refining 4 boundaries
Getting counts for zinba windows..........
Offset 0bp......
Printed out data to results/adipocytes/zinba/sorties_zinba/faire_3T3L1_day8_files/faire_3T3L1_day8_chr12_win250bp_offset0bp.txt
Offset 125bp......
Printed out data to results/adipocytes/zinba/sorties_zinba/faire_3T3L1_day8_files/faire_3T3L1_day8_chr12_win250bp_offset125bp.txt
Processing chr13
Initializing to length 120284312
Mapping reads to chromosome......
Getting alignability info from:
results/adipocytes/zinba/sorties_zinba/chr13.wig
Getting sequence from .2bit file:
results/adipocytes/zinba/necessary_files/mm9.2bit
Getting counts for 100000bp windows..........
Refining boundaries....
Global variance is 2.38516e-06
Refining 16 boundaries
Getting counts for zinba windows..........
Offset 0bp......
Printed out data to results/adipocytes/zinba/sorties_zinba/faire_3T3L1_day8_files/faire_3T3L1_day8_chr13_win250bp_offset0bp.txt
Offset 125bp......
Printed out data to results/adipocytes/zinba/sorties_zinba/faire_3T3L1_day8_files/faire_3T3L1_day8_chr13_win250bp_offset125bp.txt
Processing chr14
Initializing to length 125194864
Mapping reads to chromosome......
Getting alignability info from:
results/adipocytes/zinba/sorties_zinba/chr14.wig
Getting sequence from .2bit file:
results/adipocytes/zinba/necessary_files/mm9.2bit
Getting counts for 100000bp windows..........
Refining boundaries....
Global variance is 0.0467922
Refining 6 boundaries
Getting counts for zinba windows..........
Offset 0bp......
Printed out data to results/adipocytes/zinba/sorties_zinba/faire_3T3L1_day8_files/faire_3T3L1_day8_chr14_win250bp_offset0bp.txt
Offset 125bp......
Printed out data to results/adipocytes/zinba/sorties_zinba/faire_3T3L1_day8_files/faire_3T3L1_day8_chr14_win250bp_offset125bp.txt
Processing chr15
Initializing to length 103494974
Mapping reads to chromosome......
Getting alignability info from:
results/adipocytes/zinba/sorties_zinba/chr15.wig
Getting sequence from .2bit file:
results/adipocytes/zinba/necessary_files/mm9.2bit
Getting counts for 100000bp windows..........
Refining boundaries....
Global variance is 1.04787e-06
Refining 51 boundaries
Getting counts for zinba windows..........
Offset 0bp......
Printed out data to results/adipocytes/zinba/sorties_zinba/faire_3T3L1_day8_files/faire_3T3L1_day8_chr15_win250bp_offset0bp.txt
Offset 125bp......
Printed out data to results/adipocytes/zinba/sorties_zinba/faire_3T3L1_day8_files/faire_3T3L1_day8_chr15_win250bp_offset125bp.txt
Processing chr16
Initializing to length 98319150
Mapping reads to chromosome......
Getting alignability info from:
results/adipocytes/zinba/sorties_zinba/chr16.wig
Getting sequence from .2bit file:
results/adipocytes/zinba/necessary_files/mm9.2bit
Getting counts for 100000bp windows..........
Refining boundaries....
Global variance is 5.18728e-07
Refining 51 boundaries
Getting counts for zinba windows..........
Offset 0bp......
Printed out data to results/adipocytes/zinba/sorties_zinba/faire_3T3L1_day8_files/faire_3T3L1_day8_chr16_win250bp_offset0bp.txt
Offset 125bp......
Printed out data to results/adipocytes/zinba/sorties_zinba/faire_3T3L1_day8_files/faire_3T3L1_day8_chr16_win250bp_offset125bp.txt
Processing chr17
Initializing to length 95272651
Mapping reads to chromosome......
Getting alignability info from:
results/adipocytes/zinba/sorties_zinba/chr17.wig
Getting sequence from .2bit file:
results/adipocytes/zinba/necessary_files/mm9.2bit
Getting counts for 100000bp windows..........
Refining boundaries....
Global variance is 3.74818e-05
Refining 3 boundaries
Getting counts for zinba windows..........
Offset 0bp......
Printed out data to results/adipocytes/zinba/sorties_zinba/faire_3T3L1_day8_files/faire_3T3L1_day8_chr17_win250bp_offset0bp.txt
Offset 125bp......
Printed out data to results/adipocytes/zinba/sorties_zinba/faire_3T3L1_day8_files/faire_3T3L1_day8_chr17_win250bp_offset125bp.txt
Processing chr18
Initializing to length 90772031
Mapping reads to chromosome......
Getting alignability info from:
results/adipocytes/zinba/sorties_zinba/chr18.wig
Getting sequence from .2bit file:
results/adipocytes/zinba/necessary_files/mm9.2bit
Getting counts for 100000bp windows..........
Refining boundaries....
Global variance is 4.82354e-07
Refining 36 boundaries
Getting counts for zinba windows..........
Offset 0bp......
Printed out data to results/adipocytes/zinba/sorties_zinba/faire_3T3L1_day8_files/faire_3T3L1_day8_chr18_win250bp_offset0bp.txt
Offset 125bp......
Printed out data to results/adipocytes/zinba/sorties_zinba/faire_3T3L1_day8_files/faire_3T3L1_day8_chr18_win250bp_offset125bp.txt
Processing chr19
Initializing to length 61342430
Mapping reads to chromosome......
Getting alignability info from:
results/adipocytes/zinba/sorties_zinba/chr19.wig
Getting sequence from .2bit file:
results/adipocytes/zinba/necessary_files/mm9.2bit
Getting counts for 100000bp windows..........
Refining boundaries....
Global variance is 1.38932e-06
Refining 18 boundaries
Getting counts for zinba windows..........
Offset 0bp......
Printed out data to results/adipocytes/zinba/sorties_zinba/faire_3T3L1_day8_files/faire_3T3L1_day8_chr19_win250bp_offset0bp.txt
Offset 125bp......
Printed out data to results/adipocytes/zinba/sorties_zinba/faire_3T3L1_day8_files/faire_3T3L1_day8_chr19_win250bp_offset125bp.txt
Processing chrX
Initializing to length 166650296
Mapping reads to chromosome......
Getting alignability info from:
results/adipocytes/zinba/sorties_zinba/chrX.wig
Getting sequence from .2bit file:
results/adipocytes/zinba/necessary_files/mm9.2bit
Getting counts for 100000bp windows..........
Refining boundaries....
Global variance is 0.0180617
Refining 6 boundaries
Getting counts for zinba windows..........
Offset 0bp......
Printed out data to results/adipocytes/zinba/sorties_zinba/faire_3T3L1_day8_files/faire_3T3L1_day8_chrX_win250bp_offset0bp.txt
Offset 125bp......
Printed out data to results/adipocytes/zinba/sorties_zinba/faire_3T3L1_day8_files/faire_3T3L1_day8_chrX_win250bp_offset125bp.txt
Processing chrY
Initializing to length 15902555
Mapping reads to chromosome......
Getting alignability info from:
results/adipocytes/zinba/sorties_zinba/chrY.wig
Getting sequence from .2bit file:
results/adipocytes/zinba/necessary_files/mm9.2bit
Getting counts for 100000bp windows..........
Refining boundaries....
Global variance is 0.00167603
Refining 3 boundaries
Getting counts for zinba windows..........
Offset 0bp......
Printed out data to results/adipocytes/zinba/sorties_zinba/faire_3T3L1_day8_files/faire_3T3L1_day8_chrY_win250bp_offset0bp.txt
Offset 125bp......
Printed out data to results/adipocytes/zinba/sorties_zinba/faire_3T3L1_day8_files/faire_3T3L1_day8_chrY_win250bp_offset125bp.txt
Processing chrM
Initializing to length 16299
Mapping reads to chromosome......
Getting alignability info from:
results/adipocytes/zinba/sorties_zinba/chrM.wig
Getting sequence from .2bit file:
results/adipocytes/zinba/necessary_files/mm9.2bit
Getting counts for 100000bp windows..........
Refining boundaries....
Global variance is 1.92092
Refining 0 boundaries
Getting counts for zinba windows..........
Offset 0bp......
Printed out data to results/adipocytes/zinba/sorties_zinba/faire_3T3L1_day8_files/faire_3T3L1_day8_chrM_win250bp_offset0bp.txt
Offset 125bp......
Printed out data to results/adipocytes/zinba/sorties_zinba/faire_3T3L1_day8_files/faire_3T3L1_day8_chrM_win250bp_offset125bp.txt
--------BUILD WINDOWS COMPLETE-------
--------STARTING MODEL SELECTION-------- 2014-05-15 13:59:36
Specified chromosome not found or specified, using
results/adipocytes/zinba/sorties_zinba/faire_3T3L1_day8_files/faire_3T3L1_day8_c
hrM_win250bp_offset125bp.txt
$`1`
exp_count ~ 1
<environment: 0xc6daef8>
$`2`
exp_count ~ align_perc + 1
<environment: 0xc6daef8>
$`3`
exp_count ~ exp_cnvwin_log + 1
<environment: 0xc6daef8>
$`4`
exp_count ~ gcPerc + 1
<environment: 0xc6daef8>
$`5`
exp_count ~ align_perc + exp_cnvwin_log + 1
<environment: 0xc6daef8>
$`6`
exp_count ~ align_perc + gcPerc + 1
<environment: 0xc6daef8>
$`7`
exp_count ~ exp_cnvwin_log + gcPerc + 1
<environment: 0xc6daef8>
$`8`
exp_count ~ align_perc + exp_cnvwin_log + gcPerc + 1
<environment: 0xc6daef8>
$`9`
exp_count ~ align_perc + exp_cnvwin_log + align_perc:exp_cnvwin_log +
1
<environment: 0xc6daef8>
$`10`
exp_count ~ align_perc + gcPerc + align_perc:gcPerc + 1
<environment: 0xc6daef8>
$`11`
exp_count ~ exp_cnvwin_log + gcPerc + exp_cnvwin_log:gcPerc +
1
<environment: 0xc6daef8>
$`12`
exp_count ~ align_perc + exp_cnvwin_log + gcPerc + align_perc:exp_cnvwin_log +
1
<environment: 0xc6daef8>
$`13`
exp_count ~ align_perc + exp_cnvwin_log + gcPerc + align_perc:gcPerc +
1
<environment: 0xc6daef8>
$`14`
exp_count ~ align_perc + exp_cnvwin_log + gcPerc + exp_cnvwin_log:gcPerc +
1
<environment: 0xc6daef8>
$`15`
exp_count ~ align_perc + exp_cnvwin_log + gcPerc + align_perc:exp_cnvwin_log +
align_perc:gcPerc + 1
<environment: 0xc6daef8>
$`16`
exp_count ~ align_perc + exp_cnvwin_log + gcPerc + align_perc:exp_cnvwin_log +
exp_cnvwin_log:gcPerc + 1
<environment: 0xc6daef8>
$`17`
exp_count ~ align_perc + exp_cnvwin_log + gcPerc + align_perc:gcPerc +
exp_cnvwin_log:gcPerc + 1
<environment: 0xc6daef8>
$`18`
exp_count ~ align_perc + exp_cnvwin_log + gcPerc + align_perc:exp_cnvwin_log +
align_perc:gcPerc + exp_cnvwin_log:gcPerc + 1
<environment: 0xc6daef8>
$`19`
exp_count ~ align_perc + exp_cnvwin_log + gcPerc + align_perc:exp_cnvwin_log +
align_perc:gcPerc + exp_cnvwin_log:gcPerc + align_perc:exp_cnvwin_log:gcPerc +
1
<environment: 0xc6daef8>
Erreur dans covariateselect(file = data, selection = selecttype, loc =
paste(outfile_subpath, :
covselect.R: all models failed after model selection intermediate step
Original issue reported on code.google.com by j.blanch...@gmail.com on 15 May 2014 at 4:34
Original issue reported on code.google.com by
j.blanch...@gmail.com
on 15 May 2014 at 4:34