segfault calling zinba

[GoogleCodeExporter]

1) What operating system are you using?
Debian

2) What error message was displayed?

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

 *** caught segfault ***
address (nil), cause 'unknown'

Traceback:
 1: gc()
 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(align = "cre5-athresh4_extension134/", numProc = 4, seq = "data/ITNY-2340.6.1873.CGATGT.merge.unique.collapse.sorted.bed",     basecountfile = "data/ITNY-2340.6.1873.CGATGT.merge.unique.collapse.sorted.basecount",     filetype = "bed", outfile = "data/faireITNY", twoBit = "cre5.2bit",     extension = 134, printFullOut = 1, refinepeaks = 1, broad = F,     input = "none")

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

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

zinba(
  align='cre5-athresh4_extension134/',
  numProc=4,
  seq='data/ITNY-2340.6.1873.CGATGT.merge.unique.collapse.sorted.bed',
  basecountfile='data/ITNY-2340.6.1873.CGATGT.merge.unique.collapse.sorted.basecount',
  filetype="bed",
  outfile="data/faireITNY",
  twoBit="cre5.2bit",
  extension=134,
  printFullOut=1,
  refinepeaks=1,
  broad=F,
  input="none"
)

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

Original issue reported on code.google.com by CHW...@lbl.gov on 9 May 2012 at 12:56

[GoogleCodeExporter]

Could you paste the output of the following command:

head data/ITNY-2340.6.1873.CGATGT.merge.unique.collapse.sorted.bed

Also, try installing http://zinba.googlecode.com/files/zinba_2.02.01.tar.gz to 
see if the problem persists.  It may simply be in issue with the input file 
that you are using. 

Original comment by homer...@gmail.com on 28 May 2012 at 6:35

[GoogleCodeExporter]

Could you paste the output of the following command:

head data/ITNY-2340.6.1873.CGATGT.merge.unique.collapse.sorted.bed

Also, try installing http://zinba.googlecode.com/files/zinba_2.02.01.tar.gz to 
see if the problem persists.  It may simply be in issue with the input file 
that you are using. 

Original comment by homer...@gmail.com on 28 May 2012 at 6:35

[GoogleCodeExporter]

Why would downgrading from 2.02.03 to 2.02.01 solve the issue?

head data/ITNY-2340.6.1873.CGATGT.merge.unique.collapse.sorted.bed
chromosome_1    3453    3503    2340:6:2208:6900:122792 37      -
chromosome_1    3454    3504    2340:6:2207:6231:195982 37      -
chromosome_1    3456    3506    2340:6:2301:20388:183433        37      +
chromosome_1    3468    3518    2340:6:2205:8731:59037  37      -
chromosome_1    3488    3538    2340:6:2103:14735:140619        37      -
chromosome_1    9075    9125    2340:6:1306:11594:4885  13      +
chromosome_1    10274   10324   2340:6:2108:12512:169892        37      +
chromosome_1    11237   11287   2340:6:2303:14922:83303 17      -
chromosome_1    11244   11294   2340:6:1207:15513:77030 20      +
chromosome_1    11245   11295   2340:6:1202:15826:19295 20      -

Original comment by CHW...@lbl.gov on 30 May 2012 at 11:47

[GoogleCodeExporter]

Your first column pertaining to the chromosome should be formatted as "chr1" 
and similarly for the rest of the chromosomes.  More detail on the UCSC "bed" 
format can be found here: http://genome.ucsc.edu/FAQ/FAQformat#format1

Original comment by homer...@gmail.com on 31 May 2012 at 12:43

[GoogleCodeExporter]

Different model organism does not necessarily name the chromosome in the same 
way. Any chance to take away such restriction?

Original comment by CHW...@lbl.gov on 31 May 2012 at 12:50

[GoogleCodeExporter]

the chromosome name should match the nomenclature in the .2bit file that you 
use, otherwise chromosome assignment will not be possible

Original comment by homer...@gmail.com on 3 Oct 2012 at 1:43

[GoogleCodeExporter]

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

• Changed state: Verified