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