'memory not mapped' happens during running basealigncount and ZINBA pipeline function

[GoogleCodeExporter]

1) What operating system are you using?
Linux 64bit
2) What error message was displayed?
 *** caught segfault ***
address 0x2aaaf1be9000, cause 'memory not mapped'

3) What was the exact command you used that resulted in the error?
zinba(align = aligndir, numProc = 9, seq = sample, basecountfile = countfile,   
  filetype = "bed", outfile = marker, twoBit = twoBit, extension = extension,   
  printFullOut = 1, refinepeaks = 1, broad = broad, input = control)

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

 *** caught segfault ***
address 0x2aaaf1be9000, 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 = aligndir, numProc = 9, seq = sample, basecountfile = countfile,     filetype = "bed", outfile = marker, twoBit = twoBit, extension = extension,     printFullOut = 1, refinepeaks = 1, broad = broad, input = control)
aborting ...

Original issue reported on code.google.com by ntthong1...@gmail.com on 5 Aug 2011 at 11:56

[GoogleCodeExporter]

A few questions before proceeding

1) What version of ZINBA have you downloaded and installed (2.0 or 2.01)?

2) Are you running your commands on a high performance computing cluster?

3) please do the following:
  a) paste all of your zinba commands into a file and save it in "zinbacode.R"
  b) execute the following command at the terminal
        R CMD BATCH zinbacode.R
  c) This should produce a zinbacode.Rout file.  Please attach this file to your reply (see just below the comment box when making your reply for the attach link)

Original comment by homer...@gmail.com on 5 Aug 2011 at 12:43

[GoogleCodeExporter]

Hi

1) What version of ZINBA have you downloaded and installed (2.0 or 2.01)?
2.01

2) Are you running your commands on a high performance computing cluster?
Yes, I submitted the jobs using qsub on a Sun Grid Engine system.

3) I have attached two files corresponding to error and output.

This bug however is not consistent that when I try to re-run, it may disappear.

Original comment by ntthong1...@gmail.com on 5 Aug 2011 at 1:00

Attachments:

• ZB.Rep1HmecCtcf.o499828
• ZB.Rep1HmecCtcf.e499828

[GoogleCodeExporter]

We've seen this issue before occurring on high performance computing clusters.  
I am currently working on an update to resolve these issues by this weekend, 
will keep you posted. 

Original comment by homer...@gmail.com on 5 Aug 2011 at 1:48

[GoogleCodeExporter]

Original comment by homer...@gmail.com on 5 Aug 2011 at 2:01

• Changed state: Accepted

[GoogleCodeExporter]

Original comment by homer...@gmail.com on 9 Aug 2011 at 7:28

• Changed state: Done

[GoogleCodeExporter]

Hi,
   I met the same problem while running the zinba(), but I didn't running commands on a high performance computing cluster, just on the Desktop, and I'm looking forward to the updated version.

Thanks!

Original comment by liaoxin...@genomics.org.cn on 21 Dec 2011 at 6:23

[GoogleCodeExporter]

I can provide more input if you can answer the following questions

1) What version of ZINBA are you using?  

2) What genome are you trying to analyze?

3) Can you paste/attach the commands and corresponding screen output of all the 
commands that have resulted in the error?

Original comment by homer...@gmail.com on 21 Dec 2011 at 3:28

[GoogleCodeExporter]

Great!
1) What version of ZINBA are you using?
  zinba_2.01.1.tar.gz
2) What genome are you trying to analyze?
  hg18
3)Can you paste/attach the commands and corresponding screen output of all the 
commands that have resulted in the error?
 I have attached files needed.

Many Thanks!

Original comment by liaoxin...@genomics.org.cn on 22 Dec 2011 at 2:19

Attachments:

• my_commands.txt

[GoogleCodeExporter]

I sorry, forget to attach the scren output file.

Original comment by liaoxin...@genomics.org.cn on 22 Dec 2011 at 2:20

Attachments:

• screen_output.txt

[GoogleCodeExporter]

I'm a bit stumped when I look at your output, as nothing seems to be out of 
place.  I am asking the other developer to take a look to see what the issue 
might be.  In the mean time, could you send me the following output:

1) head test.bed 
2) ls -l align_result/*
3) tail test.basecount

Sorry for any inconvenience this may have caused

Original comment by homer...@gmail.com on 23 Dec 2011 at 6:31

[GoogleCodeExporter]

Tahnks for your reply!
Please check attachment for information you needed. 

Original comment by liaoxin...@genomics.org.cn on 24 Dec 2011 at 4:35

Attachments:

• file_information.txt

[GoogleCodeExporter]

I dont see any potential issues with your files, unfortunately.  Could you 
confirm to me that this issue also occurs with the data data and code available 
on the "UsingZinba" wiki page?  This will help us rule out any system-specific 
issues.  The exact step-by-step testing directions corresponding to the test 
dataset can be found here:  
http://code.google.com/p/zinba/wiki/UsingZINBA#FAIRE-seq_example

Thanks you!

Original comment by homer...@gmail.com on 27 Dec 2011 at 7:41

[GoogleCodeExporter]

    I have re-run it with data provided on the "UsingZinba" wiki page, and I have attached the files.

Many Thanks !

Original comment by liaoxin...@genomics.org.cn on 29 Dec 2011 at 3:48

Attachments:

• before_running_command.txt
• after_running_commamds.txt
• screen_output.txt