1) What operating system are you using?
OSX, 10.6.8
2) What error message was displayed?
The resulting bed file has no results for C. elegans chromosome V and X; I have
changed the window and offset sizes from 300 and 75 respectively, and also ran
with and without refinement.
3) What was the exact command you used that resulted in the error?
run.zinba(
filelist="/Users/acd13/Desktop/ZINBA/set2s/EMB/B/set2_EMB_B.ce10Mito.filelist",
outfile="/Users/acd13/Desktop/ZINBA/set2s/EMB/B/set2_EMB_B.ce10Mito_w300_o75_refined.ZINBA_retry",
seq="/Users/acd13/Desktop/Mapped/set2_emb_B.ce10Mito_noSpace.hits",
basecountfile="/Users/acd13/Desktop/ZINBA/set2s/EMB/B/set2_emb_B.ce10Mito_noSpace.sbpc",
align="/Users/acd13/Desktop/ZINBA/Mappabilities/ce10_100bp/",
twoBit="/Users/acd13/Desktop/ZINBA/Ce10Files/ce10.2bit",
numProc=4,
winSize=200,
offset=50,
filetype="bowtie",
buildwin=1,
#filelist="/Users/acd13/Desktop/ZINBA/set2s/EMB/B/set2_EMB_B.ce10Mito.list",
selectmodel=0,
formula=exp_count~1,
formulaE=exp_count~1,
formulaZ=exp_count~align_perc,
refinepeaks=0,
printFullOut=1,
extension=1,
method="mixture",
cleanup=0
)
4) Please copy and paste any additional screen output that resulted from
running the command
[1] "parameters in effect:"
$filelist
[1] "/Users/acd13/Desktop/ZINBA/set2s/EMB/B/set2_EMB_B.ce10Mito.filelist"
$formula
exp_count ~ 1
$formulaE
exp_count ~ 1
$formulaZ
exp_count ~ align_perc
$outfile
[1]
"/Users/acd13/Desktop/ZINBA/set2s/EMB/B/set2_EMB_B.ce10Mito_w300_o75_refined.ZIN
BA_retry"
$seq
[1] "/Users/acd13/Desktop/Mapped/set2_emb_B.ce10Mito_noSpace.hits"
$align
[1] "/Users/acd13/Desktop/ZINBA/Mappabilities/ce10_100bp/"
$input
[1] "none"
$twoBit
[1] "/Users/acd13/Desktop/ZINBA/Ce10Files/ce10.2bit"
$winSize
[1] 200
$offset
[1] 50
$cnvWinSize
[1] 1e+05
$cnvOffset
[1] 0
$basecountfile
[1] "/Users/acd13/Desktop/ZINBA/set2s/EMB/B/set2_emb_B.ce10Mito_noSpace.sbpc"
$threshold
[1] 0.01
$peakconfidence
[1] 0.8
$tol
[1] 1e-05
$numProc
[1] 4
$buildwin
[1] 1
$winGap
[1] 0
$pWinSize
[1] 200
$pquant
[1] 1
$refinepeaks
[1] 0
$printFullOut
[1] 1
$method
[1] "mixture"
$initmethod
[1] "count"
$diff
[1] 0
$filetype
[1] "bowtie"
$extension
[1] 1
$cleanup
[1] 0
$selectmodel
[1] 0
$selectchr
NULL
$selecttype
[1] "dirty"
$selectcovs
NULL
$FDR
[1] FALSE
--------BEGIN BUILDING WINDOW DATA-------- 2013-06-20 12:20:04
Importing reads from file
/Users/acd13/Desktop/Mapped/set2_emb_B.ce10Mito_noSpace.hits
Filetype is bowtie
Extension is 1
Getting chromosome lengths from .2bit file: /Users/acd13/Desktop/ZINBA/Ce10Files/ce10.2bit
For chrI length is 15072423
For chrII length is 15279345
For chrIII length is 13783700
For chrIV length is 17493793
For chrV length is 20924149
For chrX length is 17718866
For chrM length is 13794
For chrM length is 13794
Importing bowtie formatted reads
Skipped 0 reads
Imported 20838734 reads
Sorting reads ...
Building window data
COMPLETE
Processing chrI
Initializing to length 15072423
Mapping reads to chromosome......
Getting alignability info from:
/Users/acd13/Desktop/ZINBA/Mappabilities/ce10_100bp/chrI.wig
Getting sequence from .2bit file:
/Users/acd13/Desktop/ZINBA/Ce10Files/ce10.2bit
Getting counts for 100000bp windows..........
Refining boundaries....
Global variance is 0.000619728
Refining 143 boundaries
Getting counts for zinba windows..........
Offset 0bp......
Printed out data to /Users/acd13/Desktop/ZINBA/set2s/EMB/B/set2_EMB_B.ce10Mito_w300_o75_refined.ZINBA_retry_files/set2_emb_B.ce10Mito_noSpace_chrI_win200bp_offset0bp.txt
Offset 50bp......
Printed out data to /Users/acd13/Desktop/ZINBA/set2s/EMB/B/set2_EMB_B.ce10Mito_w300_o75_refined.ZINBA_retry_files/set2_emb_B.ce10Mito_noSpace_chrI_win200bp_offset50bp.txt
Offset 100bp......
Printed out data to /Users/acd13/Desktop/ZINBA/set2s/EMB/B/set2_EMB_B.ce10Mito_w300_o75_refined.ZINBA_retry_files/set2_emb_B.ce10Mito_noSpace_chrI_win200bp_offset100bp.txt
Offset 150bp......
Printed out data to /Users/acd13/Desktop/ZINBA/set2s/EMB/B/set2_EMB_B.ce10Mito_w300_o75_refined.ZINBA_retry_files/set2_emb_B.ce10Mito_noSpace_chrI_win200bp_offset150bp.txt
Processing chrII
Initializing to length 15279345
Mapping reads to chromosome......
Getting alignability info from:
/Users/acd13/Desktop/ZINBA/Mappabilities/ce10_100bp/chrII.wig
Getting sequence from .2bit file:
/Users/acd13/Desktop/ZINBA/Ce10Files/ce10.2bit
Getting counts for 100000bp windows..........
Refining boundaries....
Global variance is 0.000597679
Refining 147 boundaries
Getting counts for zinba windows..........
Offset 0bp......
Printed out data to /Users/acd13/Desktop/ZINBA/set2s/EMB/B/set2_EMB_B.ce10Mito_w300_o75_refined.ZINBA_retry_files/set2_emb_B.ce10Mito_noSpace_chrII_win200bp_offset0bp.txt
Offset 50bp......
Printed out data to /Users/acd13/Desktop/ZINBA/set2s/EMB/B/set2_EMB_B.ce10Mito_w300_o75_refined.ZINBA_retry_files/set2_emb_B.ce10Mito_noSpace_chrII_win200bp_offset50bp.txt
Offset 100bp......
Printed out data to /Users/acd13/Desktop/ZINBA/set2s/EMB/B/set2_EMB_B.ce10Mito_w300_o75_refined.ZINBA_retry_files/set2_emb_B.ce10Mito_noSpace_chrII_win200bp_offset100bp.txt
Offset 150bp......
Printed out data to /Users/acd13/Desktop/ZINBA/set2s/EMB/B/set2_EMB_B.ce10Mito_w300_o75_refined.ZINBA_retry_files/set2_emb_B.ce10Mito_noSpace_chrII_win200bp_offset150bp.txt
Processing chrIII
Initializing to length 13783700
Mapping reads to chromosome......
Getting alignability info from:
/Users/acd13/Desktop/ZINBA/Mappabilities/ce10_100bp/chrIII.wig
Getting sequence from .2bit file:
/Users/acd13/Desktop/ZINBA/Ce10Files/ce10.2bit
Getting counts for 100000bp windows..........
Refining boundaries....
Global variance is 0.00073081
Refining 131 boundaries
Getting counts for zinba windows..........
Offset 0bp......
Printed out data to /Users/acd13/Desktop/ZINBA/set2s/EMB/B/set2_EMB_B.ce10Mito_w300_o75_refined.ZINBA_retry_files/set2_emb_B.ce10Mito_noSpace_chrIII_win200bp_offset0bp.txt
Offset 50bp......
Printed out data to /Users/acd13/Desktop/ZINBA/set2s/EMB/B/set2_EMB_B.ce10Mito_w300_o75_refined.ZINBA_retry_files/set2_emb_B.ce10Mito_noSpace_chrIII_win200bp_offset50bp.txt
Offset 100bp......
Printed out data to /Users/acd13/Desktop/ZINBA/set2s/EMB/B/set2_EMB_B.ce10Mito_w300_o75_refined.ZINBA_retry_files/set2_emb_B.ce10Mito_noSpace_chrIII_win200bp_offset100bp.txt
Offset 150bp......
Printed out data to /Users/acd13/Desktop/ZINBA/set2s/EMB/B/set2_EMB_B.ce10Mito_w300_o75_refined.ZINBA_retry_files/set2_emb_B.ce10Mito_noSpace_chrIII_win200bp_offset150bp.txt
Processing chrIV
Initializing to length 17493793
Mapping reads to chromosome......
Getting alignability info from:
/Users/acd13/Desktop/ZINBA/Mappabilities/ce10_100bp/chrIV.wig
Getting sequence from .2bit file:
/Users/acd13/Desktop/ZINBA/Ce10Files/ce10.2bit
Getting counts for 100000bp windows..........
Refining boundaries....
Global variance is 0.000698683
Refining 169 boundaries
Getting counts for zinba windows..........
Offset 0bp......
Printed out data to /Users/acd13/Desktop/ZINBA/set2s/EMB/B/set2_EMB_B.ce10Mito_w300_o75_refined.ZINBA_retry_files/set2_emb_B.ce10Mito_noSpace_chrIV_win200bp_offset0bp.txt
Offset 50bp......
Printed out data to /Users/acd13/Desktop/ZINBA/set2s/EMB/B/set2_EMB_B.ce10Mito_w300_o75_refined.ZINBA_retry_files/set2_emb_B.ce10Mito_noSpace_chrIV_win200bp_offset50bp.txt
Offset 100bp......
Printed out data to /Users/acd13/Desktop/ZINBA/set2s/EMB/B/set2_EMB_B.ce10Mito_w300_o75_refined.ZINBA_retry_files/set2_emb_B.ce10Mito_noSpace_chrIV_win200bp_offset100bp.txt
Offset 150bp......
Printed out data to /Users/acd13/Desktop/ZINBA/set2s/EMB/B/set2_EMB_B.ce10Mito_w300_o75_refined.ZINBA_retry_files/set2_emb_B.ce10Mito_noSpace_chrIV_win200bp_offset150bp.txt
Processing chrV
Initializing to length 20924149
Mapping reads to chromosome......
Getting alignability info from:
/Users/acd13/Desktop/ZINBA/Mappabilities/ce10_100bp/chrV.wig
Getting sequence from .2bit file:
/Users/acd13/Desktop/ZINBA/Ce10Files/ce10.2bit
Getting counts for 100000bp windows..........
Refining boundaries....
Global variance is 0.00127926
Refining 206 boundaries
Getting counts for zinba windows..........
Offset 0bp......
Printed out data to /Users/acd13/Desktop/ZINBA/set2s/EMB/B/set2_EMB_B.ce10Mito_w300_o75_refined.ZINBA_retry_files/set2_emb_B.ce10Mito_noSpace_chrV_win200bp_offset0bp.txt
Offset 50bp......
Printed out data to /Users/acd13/Desktop/ZINBA/set2s/EMB/B/set2_EMB_B.ce10Mito_w300_o75_refined.ZINBA_retry_files/set2_emb_B.ce10Mito_noSpace_chrV_win200bp_offset50bp.txt
Offset 100bp......
Printed out data to /Users/acd13/Desktop/ZINBA/set2s/EMB/B/set2_EMB_B.ce10Mito_w300_o75_refined.ZINBA_retry_files/set2_emb_B.ce10Mito_noSpace_chrV_win200bp_offset100bp.txt
Offset 150bp......
Printed out data to /Users/acd13/Desktop/ZINBA/set2s/EMB/B/set2_EMB_B.ce10Mito_w300_o75_refined.ZINBA_retry_files/set2_emb_B.ce10Mito_noSpace_chrV_win200bp_offset150bp.txt
Processing chrX
Initializing to length 17718866
Mapping reads to chromosome......
Getting alignability info from:
/Users/acd13/Desktop/ZINBA/Mappabilities/ce10_100bp/chrX.wig
Getting sequence from .2bit file:
/Users/acd13/Desktop/ZINBA/Ce10Files/ce10.2bit
Getting counts for 100000bp windows..........
Refining boundaries....
Global variance is 0.000447204
Refining 170 boundaries
Getting counts for zinba windows..........
Offset 0bp......
Printed out data to /Users/acd13/Desktop/ZINBA/set2s/EMB/B/set2_EMB_B.ce10Mito_w300_o75_refined.ZINBA_retry_files/set2_emb_B.ce10Mito_noSpace_chrX_win200bp_offset0bp.txt
Offset 50bp......
Printed out data to /Users/acd13/Desktop/ZINBA/set2s/EMB/B/set2_EMB_B.ce10Mito_w300_o75_refined.ZINBA_retry_files/set2_emb_B.ce10Mito_noSpace_chrX_win200bp_offset50bp.txt
Offset 100bp......
Printed out data to /Users/acd13/Desktop/ZINBA/set2s/EMB/B/set2_EMB_B.ce10Mito_w300_o75_refined.ZINBA_retry_files/set2_emb_B.ce10Mito_noSpace_chrX_win200bp_offset100bp.txt
Offset 150bp......
Printed out data to /Users/acd13/Desktop/ZINBA/set2s/EMB/B/set2_EMB_B.ce10Mito_w300_o75_refined.ZINBA_retry_files/set2_emb_B.ce10Mito_noSpace_chrX_win200bp_offset150bp.txt
Processing chrM
Initializing to length 13794
Mapping reads to chromosome......
Getting alignability info from:
/Users/acd13/Desktop/ZINBA/Mappabilities/ce10_100bp/chrM.wig
Getting sequence from .2bit file:
/Users/acd13/Desktop/ZINBA/Ce10Files/ce10.2bit
Getting counts for 100000bp windows..........
Refining boundaries....
Global variance is nan
Refining 0 boundaries
Getting counts for zinba windows..........
Offset 0bp......
Printed out data to /Users/acd13/Desktop/ZINBA/set2s/EMB/B/set2_EMB_B.ce10Mito_w300_o75_refined.ZINBA_retry_files/set2_emb_B.ce10Mito_noSpace_chrM_win200bp_offset0bp.txt
Offset 50bp......
Printed out data to /Users/acd13/Desktop/ZINBA/set2s/EMB/B/set2_EMB_B.ce10Mito_w300_o75_refined.ZINBA_retry_files/set2_emb_B.ce10Mito_noSpace_chrM_win200bp_offset50bp.txt
Offset 100bp......
Printed out data to /Users/acd13/Desktop/ZINBA/set2s/EMB/B/set2_EMB_B.ce10Mito_w300_o75_refined.ZINBA_retry_files/set2_emb_B.ce10Mito_noSpace_chrM_win200bp_offset100bp.txt
Offset 150bp......
--------BUILD WINDOWS COMPLETE-------
Printed out data to /Users/acd13/Desktop/ZINBA/set2s/EMB/B/set2_EMB_B.ce10Mito_w300_o75_refined.ZINBA_retry_files/set2_emb_B.ce10Mito_noSpace_chrM_win200bp_offset150bp.txt
--------GETTING ENRICHED WINDOWS-------- 2013-06-20 12:22:34
--------WINDOW ANALYSIS COMPLETE-------- 2013-06-20 12:26:57
--------MERGE WINDOWS -------- 2013-06-20 12:26:57
There are 1 thresholds:
0.8
High threshold= 0.8
Importing windows from /Users/acd13/Desktop/ZINBA/set2s/EMB/B/set2_EMB_B.ce10Mito_w300_o75_refined.ZINBA_retry_files/set2_EMB_B.ce10Mito_w300_o75_refined.ZINBA_retry_chrI.wins...
Importing windows from /Users/acd13/Desktop/ZINBA/set2s/EMB/B/set2_EMB_B.ce10Mito_w300_o75_refined.ZINBA_retry_files/set2_EMB_B.ce10Mito_w300_o75_refined.ZINBA_retry_chrII.wins...
Importing windows from /Users/acd13/Desktop/ZINBA/set2s/EMB/B/set2_EMB_B.ce10Mito_w300_o75_refined.ZINBA_retry_files/set2_EMB_B.ce10Mito_w300_o75_refined.ZINBA_retry_chrIII.wins...
Importing windows from /Users/acd13/Desktop/ZINBA/set2s/EMB/B/set2_EMB_B.ce10Mito_w300_o75_refined.ZINBA_retry_files/set2_EMB_B.ce10Mito_w300_o75_refined.ZINBA_retry_chrIV.wins...
Imported 20579 coordinates
Processing threshold 0.8
20579 coords at this threshold
Collapsed to 2978 regions
--------ZINBA COMPLETE-------- 2013-06-20 12:27:00
Time difference of 6.929521 mins
Original issue reported on code.google.com by acdaughe...@gmail.com on 20 Jun 2013 at 7:28
Original issue reported on code.google.com by
acdaughe...@gmail.com
on 20 Jun 2013 at 7:28