SHZ66 / zinba

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segfault error with the 2.03.1 version of zinba #80

Open GoogleCodeExporter opened 8 years ago

GoogleCodeExporter commented 8 years ago
1) What operating system are you using?
OS X Yosemite

2) What error message was displayed?
 *** caught segfault ***
address 0x7fa6280b0524, cause 'memory not mapped'

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

zinba(refinepeaks=0, seq="##/freshSub_noMTsorted.bed",input="none", 
filetype="bed",threshold=0.01, 
align="##/RefGenome/alignability_atresh1_extension174_zinba", numProc=1, 
twoBit= "##/RefGenome/hg19.2bit", 
outfile="##/Zinba_peakcalls/zinba_peakcalls_freshSub_noMT.bed",extension=174, 
broad=FALSE, printFullOut=1, interaction=TRUE, mode="peaks",FDR=TRUE)

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

Loading required package: doParallel
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
Loading required package: parallel
Loading required package: doMC
Loading required package: R.utils
Loading required package: R.oo
Loading required package: R.methodsS3
R.methodsS3 v1.7.0 (2015-02-19) successfully loaded. See ?R.methodsS3 for help.
R.oo v1.19.0 (2015-02-27) successfully loaded. See ?R.oo for help.

Attaching package: 'R.oo'

The following objects are masked from 'package:methods':

    getClasses, getMethods

The following objects are masked from 'package:base':

    attach, detach, gc, load, save

R.utils v2.1.0 (2015-05-27) successfully loaded. See ?R.utils for help.

Attaching package: 'R.utils'

The following object is masked from 'package:utils':

    timestamp

The following objects are masked from 'package:base':

    cat, commandArgs, getOption, inherits, isOpen, parse, warnings

Loading required package: quantreg
Loading required package: SparseM

Attaching package: 'SparseM'

The following object is masked from 'package:base':

    backsolve

--------BEGIN BUILDING WINDOW DATA-------- 2015-08-18 13:12:11 

Importing reads from file /##/bams/freshSub_noMTsorted.bed 
    Filetype is bed 
    Extension is 174 
    Importing bed formatted reads
    Skipped 0 reads
    Imported 6356249 reads
    Sorting reads ...COMPLETE

Building window data

Processing 1
    Initializing to length 0
    Mapping reads to chromosome......

 *** caught segfault ***
address 0x7fa6280b0524, 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),     as.integer(binary), 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, numProc = numProc)
 3: run.zinba(align = align, numProc = numProc, seq = seq, input = input,     basecountfile = basecountfile, filetype = filetype, offset = offset,     buildwin = 1, outfile = outfile, threshold = threshold, twoBit = twoBit,     cnvOffset = cnvOffset, pquant = 1, winGap = winGap, cnvWinSize = cnvWinSize,     initmethod = "count", printFullOut = printFullOut, winSize = winSize,     diff = 0, pWinSize = 200, extension = extension, method = "mixture",     refinepeaks = refinepeaks, selectmodel = TRUE, selectchr = selectchr,     selecttype = selecttype, selectcovs = selectcovs, FDR = FDR,     interaction = interaction)
 4: zinba(refinepeaks = 0, seq = "/Users/irishelenejonkers/Documents/UMCG/ATAC-seq/bams/freshSub_noMTsorted.bed",     input = "none", filetype = "bed", threshold = 0.01, align = "/##/RefGenome/alignability_atresh1_extension174_zinba",     numProc = 1, twoBit = "/##/RefGenome/hg19.2bit",     outfile = "/##/Zinba_peakcalls/zinba_peakcalls_freshSub_noMT.bed",     extension = 174, broad = FALSE, printFullOut = 1, interaction = TRUE,     mode = "peaks", FDR = TRUE)

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: 3
Warning messages:
1: package 'doParallel' was built under R version 3.1.2 
2: package 'foreach' was built under R version 3.1.2 
3: package 'iterators' was built under R version 3.1.2 
4: package 'doMC' was built under R version 3.1.2 
5: package 'R.utils' was built under R version 3.1.3 
6: package 'R.oo' was built under R version 3.1.3 
7: package 'R.methodsS3' was built under R version 3.1.2 
8: package 'quantreg' was built under R version 3.1.2 
9: package 'SparseM' was built under R version 3.1.2 

Additional comment: I have used the 2.03.1 version of zinba, after finding out 
that multicore was not available for R 3.1.x. Still, this doesn't work with the 
same errors as before using the 2.03.1 version. 

Thanks,
Iris

Original issue reported on code.google.com by iris.jon...@gmail.com on 18 Aug 2015 at 12:09