Error in parse (test = x) unexpected end of input

GoogleCodeExporter commented 8 years ago

> zinba(
+ align='alignability/',
+ numProc=1,
+ seq='data/GSM480157_dm3-S2-H3K27me3.bed',
+ basecountfile='data/GSM480157_dm3-S2-H3K27me3.basecount',
+ filetype="bed",
+ outfile="output/out",
+ twoBit="lib/dm3.2bit",
+ extension=200,
+ printFullOut=1,
+ refinepeaks=1,
+ broad=F
+ )
[1] "parameters in effect:"
$filelist
NULL

$formula
NULL

$formulaE
NULL

$formulaZ
NULL

$outfile
[1] "output/out"

$seq
[1] "data/GSM480157_dm3-S2-H3K27me3.bed"

$align
[1] "alignability/"

$input
[1] "none"

$twoBit
[1] "lib/dm3.2bit"

$winSize
[1] 250

$offset
[1] 125

$cnvWinSize
[1] 1e+05

$cnvOffset
[1] 2500

$basecountfile
[1] "data/GSM480157_dm3-S2-H3K27me3.basecount"

$threshold
[1] 0.05

$peakconfidence
[1] 0.95

$tol
[1] 1e-05

$numProc
[1] 1

$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] "dirty"

$selectcovs
[1] "gcPerc"         "align_perc"     "exp_cnvwin_log"

$FDR
[1] TRUE

--------BEGIN BUILDING WINDOW DATA-------- 2011-09-29 16:36:23 

Importing reads from file data/GSM480157_dm3-S2-H3K27me3.bed 
        Filetype is bed 
        Extension is 200 
        Getting chromosome lengths from .2bit file: lib/dm3.2bit
                For chr2L length is 23011544
                For chr2LHet length is 368872
                For chr2R length is 21146708
                For chr2RHet length is 3288761
                For chr3L length is 24543557
                For chr3LHet length is 2555491
                For chr3R length is 27905053
                For chr3RHet length is 2517507
                For chr4 length is 1351857
                For chrM length is 19517
                For chrUextra length is 29004656
                For chrU length is 10049037
                For chrX length is 22422827
                For chrXHet length is 204112
                For chrYHet length is 347038
                For chrYHet length is 347038
        Importing bed formatted reads
        Skipped 0 reads
        Imported 2819791 reads
        Sorting reads ...COMPLETE

Building window data

Processing chr2L
        Initializing to length 23011544
        Mapping reads to chromosome......
        Getting alignability info from:
                alignability/chr2L.wig
        Getting sequence from .2bit file:
                lib/dm3.2bit
        Getting counts for 100000bp windows..........
                Refining boundaries....
                        Global variance is 2.64019e-05
                        Refining 33 boundaries
        Getting counts for zinba windows..........
                Offset 0bp......
        Printed out data to output/out_files/GSM480157_dm3-S2-H3K27me3_chr2L_win250bp_offset0bp.txt
                Offset 125bp......
        Printed out data to output/out_files/GSM480157_dm3-S2-H3K27me3_chr2L_win250bp_offset125bp.txt

Processing chr2LHet
        Initializing to length 368872
        Mapping reads to chromosome......
        Getting alignability info from:
                alignability/chr2LHet.wig
        Getting sequence from .2bit file:
                lib/dm3.2bit
        Getting counts for 100000bp windows..........
                Refining boundaries....
                        Global variance is 9.46937e-07
                        Refining 0 boundaries
        Getting counts for zinba windows..........
                Offset 0bp......
        Printed out data to output/out_files/GSM480157_dm3-S2-H3K27me3_chr2LHet_win250bp_offset0bp.txt
                Offset 125bp......
        Printed out data to output/out_files/GSM480157_dm3-S2-H3K27me3_chr2LHet_win250bp_offset125bp.txt

Processing chr2R
        Initializing to length 21146708
        Mapping reads to chromosome......
        Getting alignability info from:
                alignability/chr2R.wig
        Getting sequence from .2bit file:
                lib/dm3.2bit
        Getting counts for 100000bp windows..........
                Refining boundaries....
                        Global variance is 2.59047e-05
                        Refining 30 boundaries
        Getting counts for zinba windows..........
                Offset 0bp......
        Printed out data to output/out_files/GSM480157_dm3-S2-H3K27me3_chr2R_win250bp_offset0bp.txt
                Offset 125bp......
        Printed out data to output/out_files/GSM480157_dm3-S2-H3K27me3_chr2R_win250bp_offset125bp.txt

Processing chr2RHet
        Initializing to length 3288761
        Mapping reads to chromosome......
        Getting alignability info from:
                alignability/chr2RHet.wig
        Getting sequence from .2bit file:
                lib/dm3.2bit
        Getting counts for 100000bp windows..........
                Refining boundaries....
                        Global variance is 1.59678e-05
                        Refining 0 boundaries
        Getting counts for zinba windows..........
                Offset 0bp......
        Printed out data to output/out_files/GSM480157_dm3-S2-H3K27me3_chr2RHet_win250bp_offset0bp.txt
                Offset 125bp......
        Printed out data to output/out_files/GSM480157_dm3-S2-H3K27me3_chr2RHet_win250bp_offset125bp.txt

Processing chr3L
        Initializing to length 24543557
        Mapping reads to chromosome......
        Getting alignability info from:
                alignability/chr3L.wig
        Getting sequence from .2bit file:
                lib/dm3.2bit
        Getting counts for 100000bp windows..........
                Refining boundaries....
                        Global variance is 2.0648e-05
                        Refining 36 boundaries
        Getting counts for zinba windows..........
                Offset 0bp......
        Printed out data to output/out_files/GSM480157_dm3-S2-H3K27me3_chr3L_win250bp_offset0bp.txt
                Offset 125bp......
        Printed out data to output/out_files/GSM480157_dm3-S2-H3K27me3_chr3L_win250bp_offset125bp.txt

Processing chr3LHet
        Initializing to length 2555491
        Mapping reads to chromosome......
        Getting alignability info from:
                alignability/chr3LHet.wig
        Getting sequence from .2bit file:
                lib/dm3.2bit
        Getting counts for 100000bp windows..........
                Refining boundaries....
                        Global variance is 1.11304e-05
                        Refining 1 boundaries
        Getting counts for zinba windows..........
                Offset 0bp......
        Printed out data to output/out_files/GSM480157_dm3-S2-H3K27me3_chr3LHet_win250bp_offset0bp.txt
                Offset 125bp......
        Printed out data to output/out_files/GSM480157_dm3-S2-H3K27me3_chr3LHet_win250bp_offset125bp.txt

Processing chr3R
        Initializing to length 27905053
        Mapping reads to chromosome......
        Getting alignability info from:
                alignability/chr3R.wig
        Getting sequence from .2bit file:
                lib/dm3.2bit
        Getting counts for 100000bp windows..........
                Refining boundaries....
                        Global variance is 4.6984e-05
                        Refining 31 boundaries
        Getting counts for zinba windows..........
                Offset 0bp......
        Printed out data to output/out_files/GSM480157_dm3-S2-H3K27me3_chr3R_win250bp_offset0bp.txt
                Offset 125bp......
        Printed out data to output/out_files/GSM480157_dm3-S2-H3K27me3_chr3R_win250bp_offset125bp.txt

Processing chr3RHet
        Initializing to length 2517507
        Mapping reads to chromosome......
        Getting alignability info from:
                alignability/chr3RHet.wig
        Getting sequence from .2bit file:
                lib/dm3.2bit
        Getting counts for 100000bp windows..........
                Refining boundaries....
                        Global variance is 6.41861e-06
                        Refining 0 boundaries
        Getting counts for zinba windows..........
                Offset 0bp......
        Printed out data to output/out_files/GSM480157_dm3-S2-H3K27me3_chr3RHet_win250bp_offset0bp.txt
                Offset 125bp......
        Printed out data to output/out_files/GSM480157_dm3-S2-H3K27me3_chr3RHet_win250bp_offset125bp.txt

Processing chr4
        Initializing to length 1351857
        Mapping reads to chromosome......
        Getting alignability info from:
                alignability/chr4.wig
        Getting sequence from .2bit file:
                lib/dm3.2bit
        Getting counts for 100000bp windows..........
                Refining boundaries....
                        Global variance is 2.08513e-05
                        Refining 2 boundaries
        Getting counts for zinba windows..........
                Offset 0bp......
        Printed out data to output/out_files/GSM480157_dm3-S2-H3K27me3_chr4_win250bp_offset0bp.txt
                Offset 125bp......
        Printed out data to output/out_files/GSM480157_dm3-S2-H3K27me3_chr4_win250bp_offset125bp.txt

Processing chrX
        Initializing to length 22422827
        Mapping reads to chromosome......
        Getting alignability info from:
                alignability/chrX.wig
        Getting sequence from .2bit file:
                lib/dm3.2bit
        Getting counts for 100000bp windows..........
                Refining boundaries....
                        Global variance is 8.60003e-06
                        Refining 26 boundaries
        Getting counts for zinba windows..........
                Offset 0bp......
        Printed out data to output/out_files/GSM480157_dm3-S2-H3K27me3_chrX_win250bp_offset0bp.txt
                Offset 125bp......
        Printed out data to output/out_files/GSM480157_dm3-S2-H3K27me3_chrX_win250bp_offset125bp.txt

Processing chrXHet
        Initializing to length 204112
        Mapping reads to chromosome......
        Getting alignability info from:
                alignability/chrXHet.wig
        Getting sequence from .2bit file:
                lib/dm3.2bit
        Getting counts for 100000bp windows..........
                Refining boundaries....
                        Global variance is 0.0011744
                        Refining 0 boundaries
        Getting counts for zinba windows..........
                Offset 0bp......
        Printed out data to output/out_files/GSM480157_dm3-S2-H3K27me3_chrXHet_win250bp_offset0bp.txt
                Offset 125bp......
        Printed out data to output/out_files/GSM480157_dm3-S2-H3K27me3_chrXHet_win250bp_offset125bp.txt

Processing chrYHet
        Initializing to length 347038
        Mapping reads to chromosome......
        Getting alignability info from:
                alignability/chrYHet.wig
        Getting sequence from .2bit file:
                lib/dm3.2bit
        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 output/out_files/GSM480157_dm3-S2-H3K27me3_chrYHet_win250bp_offset0bp.txt
                Offset 125bp......
        Printed out data to output/out_files/GSM480157_dm3-S2-H3K27me3_chrYHet_win250bp_offset125bp.txt

--------BUILD WINDOWS COMPLETE-------

--------STARTING MODEL SELECTION-------- 2011-09-29 16:37:23 

Specified chromosome not found or specified, using 
output/out_files/GSM480157_dm3-S2-H3K27me3_chrYHet_win250bp_offset125bp.txt 
$`1`
exp_count ~ 1
<environment: 0x961a9e0>

$`2`
exp_count ~ align_perc + 1
<environment: 0x961a9e0>

$`3`
exp_count ~ exp_cnvwin_log + 1
<environment: 0x961a9e0>

$`4`
exp_count ~ gcPerc + 1
<environment: 0x961a9e0>

$`5`
exp_count ~ align_perc + exp_cnvwin_log + 1
<environment: 0x961a9e0>

$`6`
exp_count ~ align_perc + gcPerc + 1
<environment: 0x961a9e0>

$`7`
exp_count ~ exp_cnvwin_log + gcPerc + 1
<environment: 0x961a9e0>

$`8`
exp_count ~ align_perc + exp_cnvwin_log + gcPerc + 1
<environment: 0x961a9e0>

$`9`
exp_count ~ align_perc + exp_cnvwin_log + align_perc:exp_cnvwin_log + 
    1
<environment: 0x961a9e0>

$`10`
exp_count ~ align_perc + gcPerc + align_perc:gcPerc + 1
<environment: 0x961a9e0>

$`11`
exp_count ~ exp_cnvwin_log + gcPerc + exp_cnvwin_log:gcPerc + 
    1
<environment: 0x961a9e0>

$`12`
exp_count ~ align_perc + exp_cnvwin_log + gcPerc + align_perc:exp_cnvwin_log + 
    1
<environment: 0x961a9e0>

$`13`
exp_count ~ align_perc + exp_cnvwin_log + gcPerc + align_perc:gcPerc + 
    1
<environment: 0x961a9e0>

$`14`
exp_count ~ align_perc + exp_cnvwin_log + gcPerc + exp_cnvwin_log:gcPerc + 
    1
<environment: 0x961a9e0>

$`15`
exp_count ~ align_perc + exp_cnvwin_log + gcPerc + align_perc:exp_cnvwin_log + 
    align_perc:gcPerc + 1
<environment: 0x961a9e0>

$`16`
exp_count ~ align_perc + exp_cnvwin_log + gcPerc + align_perc:exp_cnvwin_log + 
    exp_cnvwin_log:gcPerc + 1
<environment: 0x961a9e0>

$`17`
exp_count ~ align_perc + exp_cnvwin_log + gcPerc + align_perc:gcPerc + 
    exp_cnvwin_log:gcPerc + 1
<environment: 0x961a9e0>

$`18`
exp_count ~ align_perc + exp_cnvwin_log + gcPerc + align_perc:exp_cnvwin_log + 
    align_perc:gcPerc + exp_cnvwin_log:gcPerc + 1
<environment: 0x961a9e0>

$`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: 0x961a9e0>

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................................................................................
.............................................Error in parse(text = x) : 
  <text>:2:0: unexpected end of input
1: exp_count~ 
  ^
>

Original issue reported on code.google.com by gatorg...@gmail.com on 29 Sep 2011 at 8:47

GoogleCodeExporter commented 8 years ago

It appears that your reads pertain to the drosophila genome.  Is there anything 
in particular with the chrYhet chromosome that may make it unsuitable for 
analysis (many repetitive regions, etc)?  For this genome ZINBA picks the last 
chromosome in its chromosome list and uses that for model selection.  For these 
smaller genomes also, the alignability covariate may be close to 1 (perfect 
alignability for all windows) and this may be causing problems in the model 
selection. 

If you can paste/attach the following output, that would help me diagnose the 
issue further: 

1) head -100 output/out_files/*model
2) head 
output/out_files/GSM480157_dm3-S2-H3K27me3_chrYHet_win250bp_offset125bp.txt
3) tail 
output/out_files/GSM480157_dm3-S2-H3K27me3_chrYHet_win250bp_offset125bp.txt

If all seems ok with these files, I will have to go back and alter ZINBA to use 
genome-specific default parameters.  For example, smaller genomes would benefit 
from smaller window sizes. Thank you for you assistance.

Original comment by homer...@gmail.com on 29 Sep 2011 at 9:16

GoogleCodeExporter commented 8 years ago

yes, chrYHet has considerable amount of repetitive regions.  I have attached 
the *.model file and GSM480157_dm3-S2-H3K27me3_chrYHet_win250bp_offset125bp.txt 
file.

Original comment by gatorg...@gmail.com on 29 Sep 2011 at 9:34

Attachments:

GoogleCodeExporter commented 8 years ago

Just looked at the files and it appears we may need to make some 
genome-specific changes to zinba to handle smaller genomes (it is optimized for 
larger ones currently). I have contacted a colleague of mine that works with 
drosophila to see what has worked best with his data.  I will let you know when 
the package is updated.

Original comment by homer...@gmail.com on 30 Sep 2011 at 2:23

GoogleCodeExporter commented 8 years ago

that is perfect, thanks!

Original comment by gatorg...@gmail.com on 30 Sep 2011 at 9:38

GoogleCodeExporter commented 8 years ago

Try installing and running this beta version of the next ZINBA release.  When 
you are running the zinba() command, add the additional option 

genome="dm"

to specify that you are using the drosophila genome. Let me know how it goes 
for you.

Original comment by homer...@gmail.com on 10 Oct 2011 at 2:52

Attachments:

zinba_2.01.2.tar.gz

GoogleCodeExporter commented 8 years ago

Original comment by homer...@gmail.com on 21 Oct 2011 at 5:57

Changed state: Done

GoogleCodeExporter commented 8 years ago

Sorry for the delay, I finally got time to try this version. 

The output files include a ".list", ".model", ".winlist" file, and ".wins" file 
for each chrom, and several "offset0bp.txt", "offset40bp.txt" .... files

But there seems no file contains the peak/enrichment regions.

Original comment by jyhe...@gmail.com on 3 Nov 2011 at 1:26

GoogleCodeExporter commented 8 years ago

Great, so we were able to get past the initial issue.  The output files will 
not be in the *_files/ directory that is generated by zinba, as it is made to 
hold intermediate files and can be deleted if desired.  The output files will 
be .peaks and .bed files in the directory containing the *_files/ folder.  If 
you dont see any output still, send me the latest screen output from your run 
in addition to the following:

ls -l outputpath_files/

where output path is the output prefix parameter used to run zinba.

Original comment by homer...@gmail.com on 3 Nov 2011 at 3:35

GoogleCodeExporter commented 8 years ago

I could not find the .peaks and .bed files.  Zinba gives the following message 
on my end.

...........................
Processed output/out_files/GSM480157_dm3-S2-H3K27me3_chr4_win200bp_offset0bp.txt
    Selected number of peaks: 0
    2011-10-26 23:07:49 ......................
Processed 
output/out_files/GSM480157_dm3-S2-H3K27me3_chr4_win200bp_offset40bp.txt
    Selected number of peaks: 0
    2011-10-26 23:08:58 ......................
Processed 
output/out_files/GSM480157_dm3-S2-H3K27me3_chr4_win200bp_offset80bp.txt
    Selected number of peaks: 0
    2011-10-26 23:10:06 ......................
Processed 
output/out_files/GSM480157_dm3-S2-H3K27me3_chr4_win200bp_offset120bp.txt
    Selected number of peaks: 0
    2011-10-26 23:11:15 ......................
Processed 
output/out_files/GSM480157_dm3-S2-H3K27me3_chr4_win200bp_offset160bp.txt
    Selected number of peaks: 0
    2011-10-26 23:12:25 
Time difference of 6.034036 mins
........................
Processed output/out_files/GSM480157_dm3-S2-H3K27me3_chrX_win200bp_offset0bp.txt
    Selected number of peaks: 0
    2011-10-26 23:17:02 ...................
Processed 
output/out_files/GSM480157_dm3-S2-H3K27me3_chrX_win200bp_offset40bp.txt
    Selected number of peaks: 0
    2011-10-26 23:20:18 ...................
Processed 
output/out_files/GSM480157_dm3-S2-H3K27me3_chrX_win200bp_offset80bp.txt
    Selected number of peaks: 0
    2011-10-26 23:23:32 ...................
Processed 
output/out_files/GSM480157_dm3-S2-H3K27me3_chrX_win200bp_offset120bp.txt
    Selected number of peaks: 0
    2011-10-26 23:26:38 ...................
Processed 
output/out_files/GSM480157_dm3-S2-H3K27me3_chrX_win200bp_offset160bp.txt
    Selected number of peaks: 0
    2011-10-26 23:29:45 
Time difference of 17.35578 mins
.....[1] "The estimated proportion of enrichment for   
output/out_files/GSM480157_dm3-S2-H3K27me3_chrXHet_win200bp_offset0bp.txt  has 
exceeded 0.5, suggesting difficulty in estimating enrichment.  Switching to 
more conservative model"
[1] "using ICL existing model file"
.....[1] "The estimated proportion of enrichment for   
output/out_files/GSM480157_dm3-S2-H3K27me3_chrXHet_win200bp_offset0bp.txt  has 
exceeded 0.5, suggesting difficulty in estimating enrichment.  Switching to 
more conservative model"
[1] "defaulting enrichment to intercept"
.....[1] "The estimated proportion of enrichment for   
output/out_files/GSM480157_dm3-S2-H3K27me3_chrXHet_win200bp_offset0bp.txt  has 
exceeded 0.5, suggesting difficulty in estimating enrichment.  Switching to 
more conservative model"
[1] "The estimated proportion of enrichment for   
output/out_files/GSM480157_dm3-S2-H3K27me3_chrXHet_win200bp_offset40bp.txt  has 
exceeded 0.5, suggesting difficulty in estimating enrichment.  Switching to 
more conservative model"
[1] "using ICL existing model file"
[1] "The estimated proportion of enrichment for   
output/out_files/GSM480157_dm3-S2-H3K27me3_chrXHet_win200bp_offset40bp.txt  has 
exceeded 0.5, suggesting difficulty in estimating enrichment.  Switching to 
more conservative model"
[1] "defaulting enrichment to intercept"
[1] "The estimated proportion of enrichment for   
output/out_files/GSM480157_dm3-S2-H3K27me3_chrXHet_win200bp_offset40bp.txt  has 
exceeded 0.5, suggesting difficulty in estimating enrichment.  Switching to 
more conservative model"
[1] "The estimated proportion of enrichment for   
output/out_files/GSM480157_dm3-S2-H3K27me3_chrXHet_win200bp_offset80bp.txt  has 
exceeded 0.5, suggesting difficulty in estimating enrichment.  Switching to 
more conservative model"
[1] "using ICL existing model file"
[1] "The estimated proportion of enrichment for   
output/out_files/GSM480157_dm3-S2-H3K27me3_chrXHet_win200bp_offset80bp.txt  has 
exceeded 0.5, suggesting difficulty in estimating enrichment.  Switching to 
more conservative model"
[1] "defaulting enrichment to intercept"
[1] "The estimated proportion of enrichment for   
output/out_files/GSM480157_dm3-S2-H3K27me3_chrXHet_win200bp_offset80bp.txt  has 
exceeded 0.5, suggesting difficulty in estimating enrichment.  Switching to 
more conservative model"
[1] "The estimated proportion of enrichment for   
output/out_files/GSM480157_dm3-S2-H3K27me3_chrXHet_win200bp_offset120bp.txt  
has exceeded 0.5, suggesting difficulty in estimating enrichment.  Switching to 
more conservative model"
[1] "using ICL existing model file"
[1] "The estimated proportion of enrichment for   
output/out_files/GSM480157_dm3-S2-H3K27me3_chrXHet_win200bp_offset120bp.txt  
has exceeded 0.5, suggesting difficulty in estimating enrichment.  Switching to 
more conservative model"
[1] "defaulting enrichment to intercept"
[1] "The estimated proportion of enrichment for   
output/out_files/GSM480157_dm3-S2-H3K27me3_chrXHet_win200bp_offset120bp.txt  
has exceeded 0.5, suggesting difficulty in estimating enrichment.  Switching to 
more conservative model"
[1] "The estimated proportion of enrichment for   
output/out_files/GSM480157_dm3-S2-H3K27me3_chrXHet_win200bp_offset160bp.txt  
has exceeded 0.5, suggesting difficulty in estimating enrichment.  Switching to 
more conservative model"
.....[1] "The estimated proportion of enrichment for   
output/out_files/GSM480157_dm3-S2-H3K27me3_chrYHet_win200bp_offset0bp.txt  has 
exceeded 0.5, suggesting difficulty in estimating enrichment.  Switching to 
more conservative model"
[1] "using ICL existing model file"
.....[1] "The estimated proportion of enrichment for   
output/out_files/GSM480157_dm3-S2-H3K27me3_chrYHet_win200bp_offset0bp.txt  has 
exceeded 0.5, suggesting difficulty in estimating enrichment.  Switching to 
more conservative model"
[1] "defaulting enrichment to intercept"
.....[1] "The estimated proportion of enrichment for   
output/out_files/GSM480157_dm3-S2-H3K27me3_chrYHet_win200bp_offset0bp.txt  has 
exceeded 0.5, suggesting difficulty in estimating enrichment.  Switching to 
more conservative model"
[1] "The estimated proportion of enrichment for   
output/out_files/GSM480157_dm3-S2-H3K27me3_chrYHet_win200bp_offset40bp.txt  has 
exceeded 0.5, suggesting difficulty in estimating enrichment.  Switching to 
more conservative model"
[1] "using ICL existing model file"
[1] "The estimated proportion of enrichment for   
output/out_files/GSM480157_dm3-S2-H3K27me3_chrYHet_win200bp_offset40bp.txt  has 
exceeded 0.5, suggesting difficulty in estimating enrichment.  Switching to 
more conservative model"
[1] "defaulting enrichment to intercept"
[1] "The estimated proportion of enrichment for   
output/out_files/GSM480157_dm3-S2-H3K27me3_chrYHet_win200bp_offset40bp.txt  has 
exceeded 0.5, suggesting difficulty in estimating enrichment.  Switching to 
more conservative model"
[1] "The estimated proportion of enrichment for   
output/out_files/GSM480157_dm3-S2-H3K27me3_chrYHet_win200bp_offset80bp.txt  has 
exceeded 0.5, suggesting difficulty in estimating enrichment.  Switching to 
more conservative model"
[1] "using ICL existing model file"
[1] "The estimated proportion of enrichment for   
output/out_files/GSM480157_dm3-S2-H3K27me3_chrYHet_win200bp_offset80bp.txt  has 
exceeded 0.5, suggesting difficulty in estimating enrichment.  Switching to 
more conservative model"
[1] "defaulting enrichment to intercept"
[1] "The estimated proportion of enrichment for   
output/out_files/GSM480157_dm3-S2-H3K27me3_chrYHet_win200bp_offset80bp.txt  has 
exceeded 0.5, suggesting difficulty in estimating enrichment.  Switching to 
more conservative model"
[1] "The estimated proportion of enrichment for   
output/out_files/GSM480157_dm3-S2-H3K27me3_chrYHet_win200bp_offset120bp.txt  
has exceeded 0.5, suggesting difficulty in estimating enrichment.  Switching to 
more conservative model"
[1] "using ICL existing model file"
[1] "The estimated proportion of enrichment for   
output/out_files/GSM480157_dm3-S2-H3K27me3_chrYHet_win200bp_offset120bp.txt  
has exceeded 0.5, suggesting difficulty in estimating enrichment.  Switching to 
more conservative model"
[1] "defaulting enrichment to intercept"
[1] "The estimated proportion of enrichment for   
output/out_files/GSM480157_dm3-S2-H3K27me3_chrYHet_win200bp_offset120bp.txt  
has exceeded 0.5, suggesting difficulty in estimating enrichment.  Switching to 
more conservative model"
[1] "The estimated proportion of enrichment for   
output/out_files/GSM480157_dm3-S2-H3K27me3_chrYHet_win200bp_offset160bp.txt  
has exceeded 0.5, suggesting difficulty in estimating enrichment.  Switching to 
more conservative model"
--------WINDOW ANALYSIS COMPLETE-------- 2011-10-26 23:30:02 

--------MERGE WINDOWS AND REFINE PEAKS (no parallelization)-------- 2011-10-26 
23:30:02 

Threshold is 0.05

Getting significant windows from output/out_files/out.winlist
    Threshold is 0.050000
    Using qvalue as threshold
    Data generated using mixture
    Data format is expanded
    Distance to collapse windows is 0
Getting significant regions from mixture run
    Importing windows from output/out_files/out_chr2L.wins...
    Importing windows from output/out_files/out_chr2R.wins...
    Importing windows from output/out_files/out_chr2RHet.wins...
    Importing windows from output/out_files/out_chr3L.wins...
    Importing windows from output/out_files/out_chr3LHet.wins...
    Importing windows from output/out_files/out_chr3R.wins...
    Importing windows from output/out_files/out_chr3RHet.wins...
    Importing windows from output/out_files/out_chr4.wins...
    Importing windows from output/out_files/out_chrX.wins...
    Skipping line, output/out_files/out_chrX.wins

Imported 0 coordinates
*** glibc detected *** /usr/lib64/R/bin/exec/R: double free or corruption 
(out): 0x00007ffff26e2490 ***
======= Backtrace: =========
/lib/libc.so.6(+0x774b6)[0x7f3f6bf0d4b6]
/lib/libc.so.6(cfree+0x73)[0x7f3f6bf13c83]
/home/guangyao/R/x86_64-pc-linux-gnu-library/2.11/zinba/libs/zinba.so(_ZNSt4list
I6coord2SaIS0_EE5eraseESt14_List_iteratorIS0_E+0x2d)[0x7f3f69031b2d]
/home/guangyao/R/x86_64-pc-linux-gnu-library/2.11/zinba/libs/zinba.so(_ZN8analys
is12importCoordsEPKcdS1_iii+0x19f)[0x7f3f690315df]
/home/guangyao/R/x86_64-pc-linux-gnu-library/2.11/zinba/libs/zinba.so(getSeqCoun
tProfile+0x115)[0x7f3f6907e535]
/usr/lib64/R/lib/libR.so(+0xb60ff)[0x7f3f6c2cf0ff]
/usr/lib64/R/lib/libR.so(Rf_eval+0x77b)[0x7f3f6c2fc66b]
/usr/lib64/R/lib/libR.so(+0xe54c0)[0x7f3f6c2fe4c0]
/usr/lib64/R/lib/libR.so(Rf_eval+0x543)[0x7f3f6c2fc433]
/usr/lib64/R/lib/libR.so(+0xe563c)[0x7f3f6c2fe63c]
/usr/lib64/R/lib/libR.so(Rf_eval+0x543)[0x7f3f6c2fc433]
/usr/lib64/R/lib/libR.so(Rf_applyClosure+0x2fa)[0x7f3f6c2fff3a]
/usr/lib64/R/lib/libR.so(Rf_eval+0x418)[0x7f3f6c2fc308]
/usr/lib64/R/lib/libR.so(+0xe563c)[0x7f3f6c2fe63c]
/usr/lib64/R/lib/libR.so(Rf_eval+0x543)[0x7f3f6c2fc433]
/usr/lib64/R/lib/libR.so(Rf_applyClosure+0x2fa)[0x7f3f6c2fff3a]
/usr/lib64/R/lib/libR.so(Rf_eval+0x418)[0x7f3f6c2fc308]
/usr/lib64/R/lib/libR.so(+0xe563c)[0x7f3f6c2fe63c]
/usr/lib64/R/lib/libR.so(Rf_eval+0x543)[0x7f3f6c2fc433]
======= Memory map: ========
00400000-00401000 r-xp 00000000 08:21 4458476                            
/usr/lib/R/bin/exec/R
00600000-00601000 r--p 00000000 08:21 4458476                            
/usr/lib/R/bin/exec/R
00601000-00602000 rw-p 00001000 08:21 4458476                            
/usr/lib/R/bin/exec/R
0180f000-02f3a000 rw-p 00000000 00:00 0                                  [heap]
7f3f64000000-7f3f64021000 rw-p 00000000 00:00 0 
7f3f64021000-7f3f68000000 ---p 00000000 00:00 0 
7f3f688e7000-7f3f688ec000 r-xp 00000000 08:21 8389056                    
/usr/lib/R/library/MASS/libs/MASS.so
7f3f688ec000-7f3f68aeb000 ---p 00005000 08:21 8389056                    
/usr/lib/R/library/MASS/libs/MASS.so
7f3f68aeb000-7f3f68aec000 r--p 00004000 08:21 8389056                    
/usr/lib/R/library/MASS/libs/MASS.so
7f3f68aec000-7f3f68aed000 rw-p 00005000 08:21 8389056                    
/usr/lib/R/library/MASS/libs/MASS.so
7f3f68aed000-7f3f68af0000 r-xp 00000000 08:21 1835739                    
/home/guangyao/R/x86_64-pc-linux-gnu-library/2.11/multicore/libs/multicore.so
7f3f68af0000-7f3f68cef000 ---p 00003000 08:21 1835739                    
/home/guangyao/R/x86_64-pc-linux-gnu-library/2.11/multicore/libs/multicore.so
7f3f68cef000-7f3f68cf0000 r--p 00002000 08:21 1835739                    
/home/guangyao/R/x86_64-pc-linux-gnu-library/2.11/multicore/libs/multicore.so
7f3f68cf0000-7f3f68cf1000 rw-p 00003000 08:21 1835739                    
/home/guangyao/R/x86_64-pc-linux-gnu-library/2.11/multicore/libs/multicore.so
7f3f68cf1000-7f3f68dd9000 r-xp 00000000 08:21 4198011                    
/usr/lib/libstdc++.so.6.0.14
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/usr/lib/libstdc++.so.6.0.14
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/usr/lib/libstdc++.so.6.0.14
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/usr/lib/libstdc++.so.6.0.14
7f3f68fe2000-7f3f68ff7000 rw-p 00000000 00:00 0 
7f3f68ff7000-7f3f69102000 r-xp 00000000 08:21 1836683                    
/home/guangyao/R/x86_64-pc-linux-gnu-library/2.11/zinba/libs/zinba.so
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/home/guangyao/R/x86_64-pc-linux-gnu-library/2.11/zinba/libs/zinba.so
7f3f69301000-7f3f69302000 r--p 0010a000 08:21 1836683                    
/home/guangyao/R/x86_64-pc-linux-gnu-library/2.11/zinba/libs/zinba.so
7f3f69302000-7f3f69321000 rw-p 0010b000 08:21 1836683                    
/home/guangyao/R/x86_64-pc-linux-gnu-library/2.11/zinba/libs/zinba.so
7f3f69321000-7f3f69337000 rw-p 00000000 00:00 0 
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/usr/lib/R/library/stats/libs/stats.so
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/lib/libnss_files-2.12.1.so
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/lib/libnss_files-2.12.1.so
7f3f69ee5000-7f3f69ee6000 rw-p 0000c000 08:21 7340285                    
/lib/libnss_files-2.12.1.so
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/lib/libnss_nis-2.12.1.so
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/lib/libnss_nis-2.12.1.so
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/lib/libnss_nis-2.12.1.so
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/lib/libnss_nis-2.12.1.so
7f3f6a0f1000-7f3f6a108000 r-xp 00000000 08:21 7340284                    
/lib/libnsl-2.12.1.soAborted
guangyao@IRER:~/projects/chromatin_boundary/output_new/ZINBA$

Original comment by gatorg...@gmail.com on 3 Nov 2011 at 8:58

GoogleCodeExporter commented 8 years ago

it looks like at the default threshold you aren't picking up any peaks.  We 
basically designed this for human data, so for smaller genomes we may need to 
use smaller windows in order to get the heterogeneity in signal that can help 
distinguish signal from one window to another.  If you could zip and attach 
your ,model and chr2L.wins files I'll take a look at this.

Original comment by chat4eve...@gmail.com on 4 Nov 2011 at 12:13

SHZ66 / zinba

Error in parse (test = x) unexpected end of input #7