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sivarajankumar / zinba

Automatically exported from code.google.com/p/zinba
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Error creating .bpcount file #21

Closed GoogleCodeExporter closed 8 years ago

GoogleCodeExporter commented 8 years ago 
1) What operating system are you using?
Tried on both Linux Fedora Core 13 64-bit Desktop and RHEL Server

2) What error message was displayed?

"Error in peakbound(bpprofile = bpout, output = peakout, pwinSize = pWinSize,  
: 
  Error, file pertaining to SBP for merged regions does not exist.  Check .winlist file for errors.
Calls: run.zinba -> getrefinedpeaks -> peakbound
Execution halted"

3) What was the exact command you used that resulted in the error?
run.zinba(seq='chr19.bed', 
filetype='bed',twoBit='mm9.2bit',winSize=500,offset=250,extension=200,basecountf
ile='chr19.basecount',align='alignability',selectmodel=F,formula= exp_count ~ 
gcPerc + align_perc + exp_cnvwin_log,formulaE= exp_count ~ gcPerc + align_perc 
+ exp_cnvwin_log, formulaZ= exp_count ~ gcPerc + align_perc + exp_cnvwin_log, 
threshold=0.05,refinepeaks=1, 
numProc=4,winGap=0,FDR=TRUE,outfile=outfilename,printFullOut=1,method="mixture")

4) Please copy and paste any additional screen output that resulted from
running the command

"""
[1] "parameters in effect:"
$filelist
NULL

$formula
exp_count ~ gcPerc + align_perc + exp_cnvwin_log

$formulaE
exp_count ~ gcPerc + align_perc + exp_cnvwin_log

$formulaZ
exp_count ~ gcPerc + align_perc + exp_cnvwin_log

$outfile
[1] "faire_zimba_chr19"

$seq
[1] "chr19.bed"

$align
[1] "alignability"

$input
[1] "none"

$twoBit
[1] "mm9.2bit"

$winSize
[1] 500

$offset
[1] 250

$cnvWinSize
[1] 1e+05

$cnvOffset
[1] 0

$basecountfile
[1] "chr19.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] "bed"

$extension
[1] 200

$cleanup
[1] FALSE

$selectmodel
[1] FALSE

$selectchr
NULL

$selecttype
[1] "dirty"

$selectcovs
NULL

$FDR
[1] TRUE

$interaction
[1] TRUE

Loading required package: multicore
Loading required package: doMC
Loading required package: foreach
Loading required package: iterators
Loading required package: codetools
Loading required package: R.methodsS3
R.methodsS3 v1.2.2 (2010-11-17) successfully loaded. See ?R.methodsS3 for help.
Loading required package: R.oo
R.oo v1.9.3 (2012-03-18) successfully loaded. See ?R.oo for help.
R.utils v1.12.1 (2012-03-20) successfully loaded. See ?R.utils for help.

Overwriting previously existing directory 
/home/shira/jiannew0312/bed/bychr/faire_zimba_chr19_files/

--------BEGIN BUILDING WINDOW DATA-------- 2012-04-23 13:41:06 

Importing reads from file /home/shira/jiannew0312/bed/bychr/chr19.bed 
    Filetype is bed 
    Extension is 200 
    Importing bed formatted reads
    Skipped 0 reads
    Imported 1328416 reads
    Sorting reads ...COMPLETE

Building window data

Processing chr19
    Initializing to length 61342430
    Mapping reads to chromosome......
    Getting alignability info from:
        /home/shira/Downloads/zinba/chr19.wig
    Getting sequence from .2bit file:
        mm9.2bit
    Getting counts for 100000bp windows..........
        Refining boundaries....
            Global variance is 8.89003e-06
            Refining 576 boundaries
    Getting counts for zinba windows..........
        Offset 0bp......
    Printed out data to /home/shira/jiannew0312/bed/bychr/faire_zimba_chr19_files/chr19_chr19_win500bp_offset0bp.txt
        Offset 250bp......
    Printed out data to /home/shira/jiannew0312/bed/bychr/faire_zimba_chr19_files/chr19_chr19_win500bp_offset250bp.txt

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

--------GETTING ENRICHED WINDOWS-------- 2012-04-23 13:41:30 

...........................................................................
Processed 
/home/shira/jiannew0312/bed/bychr/faire_zimba_chr19_files/chr19_chr19_win500bp_o
ffset0bp.txt
    Selected number of peaks: 1636
    2012-04-23 13:49:55 .....................................................................
Processed 
/home/shira/jiannew0312/bed/bychr/faire_zimba_chr19_files/chr19_chr19_win500bp_o
ffset250bp.txt
    Selected number of peaks: 1520
    2012-04-23 13:57:02 
Time difference of 15.55760 mins
--------WINDOW ANALYSIS COMPLETE-------- 2012-04-23 13:57:03 

--------MERGE WINDOWS AND REFINE PEAKS (no parallelization)-------- 2012-04-23 
13:57:03 

Threshold is 0.05
Assuming uncompressed version of basecount file (file in path does not have 
.bin.gz extension used for compressed files

Getting significant windows from 
/home/shira/jiannew0312/bed/bychr/faire_zimba_chr19_files/faire_zimba_chr19.winl
ist
    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 /home/shira/jiannew0312/bed/bychr/faire_zimba_chr19_files/faire_zimba_chr19_chr19.wins...
    Skipping line, /home/shira/jiannew0312/bed/bychr/faire_zimba_chr19_files/faire_zimba_chr19_chr19.wins

Imported 3109 coordinates

Collapsed to 1642 non-overlapping regions

Getting basecount data for all
    For chr1 length is 197195432
    For chr2 length is 181748087
    For chr3 length is 159599783
    For chr4 length is 155630120
    For chr5 length is 152537259
    For chr6 length is 149517037
    For chr7 length is 152524553
    For chr8 length is 131738871
    For chr9 length is 124076172
    For chr10 length is 129993255
    For chr11 length is 121843856
    For chr12 length is 121257530
    For chr13 length is 120284312
    For chr14 length is 125194864
    For chr15 length is 103494974
    For chr16 length is 98319150
    For chr17 length is 95272651
    For chr18 length is 90772031
    For chr19 length is 61342430
    For chrX length is 166650296
    For chrY length is 15902555
    For chrM length is 16299
    For chr13_random length is 400311
    For chr16_random length is 3994
    For chr17_random length is 628739
    For chr1_random length is 1231697
    For chr3_random length is 41899
    For chr4_random length is 160594
    For chr5_random length is 357350
    For chr7_random length is 362490
    For chr8_random length is 849593
    For chr9_random length is 449403
    For chrUn_random length is 5900358
    For chrX_random length is 1785075
    For chrY_random length is 58682461

Getting basecount data from /home/shira/jiannew0312/bed/bychr/chr19.basecount
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        Starting position in chromosome is 1
    Processing: fixedStep chrom=127 start=1 step=1
        Loading data for 127
        Initializing length of 0
        Starting position in chromosome is 1
    Processing: fixedStep chrom=130 start=1 step=1
        Loading data for 130
        Initializing length of 0
        Starting position in chromosome is 1
    Processing: fixedStep chrom=138 start=1 step=1
        Loading data for 138
        Initializing length of 0
        Starting position in chromosome is 1
    Processing: fixedStep chrom=143 start=1 step=1
        Loading data for 143
        Initializing length of 0
        Starting position in chromosome is 1
    Processing: fixedStep chrom=148 start=1 step=1
        Loading data for 148
        Initializing length of 0
        Starting position in chromosome is 1
    Processing: fixedStep chrom=154 start=1 step=1
        Loading data for 154
        Initializing length of 0
        Starting position in chromosome is 1
    Processing: fixedStep chrom=160 start=1 step=1
        Loading data for 160
        Initializing length of 0
        Starting position in chromosome is 1
    Processing: fixedStep chrom=166 start=1 step=1
        Loading data for 166
        Initializing length of 0
        Starting position in chromosome is 1
    Processing: fixedStep chrom=168 start=1 step=1
        Loading data for 168
        Initializing length of 0
        Starting position in chromosome is 1
    Processing: fixedStep chrom=169 start=1 step=1
        Loading data for 169
        Initializing length of 0
        Starting position in chromosome is 1
    Processing: fixedStep chrom=171 start=1 step=1
        Loading data for 171
        Initializing length of 0
        Starting position in chromosome is 1
    Processing: fixedStep chrom=173 start=1 step=1
        Loading data for 173
        Initializing length of 0
        Starting position in chromosome is 1
    Processing: fixedStep chrom=170 start=1 step=1
        Loading data for 170
        Initializing length of 0
        Starting position in chromosome is 1
    Processing: fixedStep chrom=165 start=1 step=1
        Loading data for 165
        Initializing length of 0
        Starting position in chromosome is 1
    Processing: fixedStep chrom=163 start=1 step=1
        Loading data for 163
        Initializing length of 0
        Starting position in chromosome is 1
    Processing: fixedStep chrom=149 start=1 step=1
        Loading data for 149
        Initializing length of 0
        Starting position in chromosome is 1
    Processing: fixedStep chrom=142 start=1 step=1
        Loading data for 142
        Initializing length of 0
        Starting position in chromosome is 1
    Processing: fixedStep chrom=136 start=1 step=1
        Loading data for 136
        Initializing length of 0
        Starting position in chromosome is 1
    Processing: fixedStep chrom=133 start=1 step=1
        Loading data for 133
        Initializing length of 0
        Starting position in chromosome is 1
    Processing: fixedStep chrom=126 start=1 step=1
        Loading data for 126
        Initializing length of 0
        Starting position in chromosome is 1
    Processing: fixedStep chrom=120 start=1 step=1
        Loading data for 120
        Initializing length of 0
        Starting position in chromosome is 1
    Processing: fixedStep chrom=125 start=1 step=1
        Loading data for 125
        Initializing length of 0
        Starting position in chromosome is 1

getSeqCountProfile COMPLETED SUCCESSFULLY
Error in peakbound(bpprofile = bpout, output = peakout, pwinSize = pWinSize,  : 
  Error, file pertaining to SBP for merged regions does not exist.  Check .winlist file for errors.
Calls: run.zinba -> getrefinedpeaks -> peakbound
Execution halted
"""

Original issue reported on code.google.com by songtre...@gmail.com on 24 Apr 2012 at 6:31

GoogleCodeExporter commented 8 years ago 
There seems to be an issues with the basecount processing step. Try installing 
the following version to see if the problem is repeated:  
http://zinba.googlecode.com/files/zinba_2.02.01.tar.gz

Original comment by homer...@gmail.com on 28 May 2012 at 6:33

GoogleCodeExporter commented 8 years ago 
It also appears that the formatting may be off for your basecount file, as the 
chromosome names are not being read properly.  This file follows the "wig" 
format so it must start with a fixedstep line (see 
http://genome.ucsc.edu/goldenPath/help/wiggle.html).  If you left this line out 
at the beginning of your basecount file then this is probably the issue. Try 
running 

head 'chr19.basecount'

to check

Original comment by homer...@gmail.com on 30 May 2012 at 4:33

GoogleCodeExporter commented 8 years ago 
we are currently incorporating these issues into a new zinba version, check 
back soon for a comprehensive update

Original comment by homer...@gmail.com on 20 Nov 2012 at 8:54