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zinba memory not mapped #33

Closed GoogleCodeExporter closed 8 years ago

GoogleCodeExporter commented 8 years ago 
1) What operating system are you using?
Ubuntu 12.04
zinba 2.01 et 2.01.1

2) What error message was displayed?

 *** caught segfault ***
address 0x719da5a, cause 'memory not mapped'

3) What was the exact command you used that resulted in the error?

I follow the example of your site for chip-seq

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

zinba(
+   align='align_athresh1_extension200/',
+   numProc=4,
+   seq='data/ctcfGM12878rep3chr22.taf',
+   basecountfile='data/ctcfGM12878rep3chr22.basecount',
+   filetype="tagAlign",
+   outfile="data/ctcf",
+   twoBit="hg18.2bit",
+   extension=200,
+   printFullOut=1,
+   refinepeaks=1,
+   broad=F,
+   input='data/inputGM12878rep3chr22.taf'
+ )
[1] "parameters in effect:"
$filelist
NULL

$formula
NULL

$formulaE
NULL

$formulaZ
NULL

$outfile
[1] "data/ctcf"

$seq
[1] "data/ctcfGM12878rep3chr22.taf"

$align
[1] "align_athresh1_extension200/"

$input
[1] "data/inputGM12878rep3chr22.taf"

$twoBit
[1] "hg18.2bit"

$winSize
[1] 250

$offset
[1] 125

$cnvWinSize
[1] 1e+05

$cnvOffset
[1] 2500

$basecountfile
[1] "data/ctcfGM12878rep3chr22.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] "tagAlign"

$extension
[1] 200

$cleanup
[1] FALSE

$selectmodel
[1] TRUE

$selectchr
[1] "chr22"

$selecttype
[1] "complete"

$selectcovs
[1] "input_count"

$FDR
[1] TRUE

Loading required package: multicore
Loading required package: doMC
Loading required package: foreach
foreach: simple, scalable parallel programming from Revolution Analytics
Use Revolution R for scalability, fault tolerance and more.
http://www.revolutionanalytics.com
Loading required package: iterators

Overwriting previously existing directory data/ctcf_files/

--------BEGIN BUILDING WINDOW DATA-------- 2012-09-12 17:26:41 

Importing reads from file data/ctcfGM12878rep3chr22.taf 
    Filetype is tagAlign 
    Extension is 200 
    Getting chromosome lengths from .2bit file: hg18.2bit
        For chr10 length is 135374737
        For chr10_random length is 113275
        For chr11 length is 134452384
        For chr11_random length is 215294
        For chr12 length is 132349534
        For chr13 length is 114142980
        For chr13_random length is 186858
        For chr14 length is 106368585
        For chr15 length is 100338915
        For chr15_random length is 784346
        For chr16 length is 88827254
        For chr16_random length is 105485
        For chr17 length is 78774742
        For chr17_random length is 2617613
        For chr18 length is 76117153
        For chr18_random length is 4262
        For chr19 length is 63811651
        For chr19_random length is 301858
        For chr1 length is 247249719
        For chr1_random length is 1663265
        For chr20 length is 62435964
        For chr21 length is 46944323
        For chr21_random length is 1679693
        For chr22 length is 49691432
        For chr22_random length is 257318
        For chr22_h2_hap1 length is 63661
        For chr2 length is 242951149
        For chr2_random length is 185571
        For chr3 length is 199501827
        For chr3_random length is 749256
        For chr4 length is 191273063
        For chr4_random length is 842648
        For chr5 length is 180857866
        For chr5_random length is 143687
        For chr5_h2_hap1 length is 1794870
        For chr6 length is 170899992
        For chr6_random length is 1875562
        For chr6_cox_hap1 length is 4731698
        For chr6_qbl_hap2 length is 4565931
        For chr7 length is 158821424
        For chr7_random length is 549659
        For chr8 length is 146274826
        For chr8_random length is 943810
        For chr9 length is 140273252
        For chr9_random length is 1146434
        For chrM length is 16571
        For chrX length is 154913754
        For chrX_random length is 1719168
        For chrY length is 57772954
        For chrY length is 57772954
    Importing tagAlign formatted reads
    Skipped 0 reads
    Imported 231568 reads
    Sorting reads ...COMPLETE

Building window data

Processing 
    Initializing to length 0
    Mapping reads to chromosome......

 *** caught segfault ***
address 0x719da5a, cause 'memory not mapped'

Traceback:
 1: .C("buildWindows", as.character(seq), as.character(input), as.character(align),     as.character(twoBit), as.integer(winSize), as.integer(offset),     as.integer(cnvWinSize), as.integer(cnvOffset), as.character(filetype),     as.character(filelist), as.integer(extension), as.character(outdir),     PACKAGE = "zinba")
 2: buildwindowdata(seq = seq, align = align, input = input, twoBit = twoBit,     winSize = winSize, offset = offset, cnvWinSize = cnvWinSize,     cnvOffset = cnvOffset, filelist = filelist, filetype = filetype,     extension = extension, outdir = outfile_subdir)
 3: run.zinba(align = align, numProc = numProc, seq = seq, input = input,     basecountfile = basecountfile, filetype = filetype, offset = 125,     buildwin = 1, outfile = outfile, threshold = threshold, twoBit = twoBit,     cnvOffset = 2500, pquant = 1, winGap = winGap, cnvWinSize = 1e+05,     initmethod = "count", printFullOut = 1, winSize = 250, diff = 0,     pWinSize = 200, extension = extension, method = "mixture",     refinepeaks = refinepeaks, selectmodel = TRUE, selectchr = "chr22",     selecttype = selecttype, selectcovs = selectcovs, FDR = FDR,     interaction = interaction, peakconfidence = peakconfidence)
 4: zinba(align = "align_athresh1_extension200/", numProc = 4, seq = "data/ctcfGM12878rep3chr22.taf",     basecountfile = "data/ctcfGM12878rep3chr22.basecount", filetype = "tagAlign",     outfile = "data/ctcf", twoBit = "hg18.2bit", extension = 200,     printFullOut = 1, refinepeaks = 1, broad = F, input = "data/inputGM12878rep3chr22.taf")

Possible actions:
1: abort (with core dump, if enabled)
2: normal R exit
3: exit R without saving workspace
4: exit R saving workspace
Selection: 

Thanks for your help

Original issue reported on code.google.com by dubju...@gmail.com on 12 Sep 2012 at 3:28

GoogleCodeExporter commented 8 years ago 
I've tested the new version of zinba 2.02.03, and it works!
Thanks

Original comment by dubju...@gmail.com on 26 Oct 2012 at 2:35

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