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No results on ChromosomeV or X in C. elegans #48

Open GoogleCodeExporter opened 8 years ago

GoogleCodeExporter commented 8 years ago 
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