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SHZ66 / zinba

Automatically exported from code.google.com/p/zinba
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caught segfault when running generateAlignability #39

Open GoogleCodeExporter opened 8 years ago

GoogleCodeExporter commented 8 years ago 
1) What operating system are you using?
Centos OS 6.1

2) What error message was displayed?
Loading align count data from /home/jma/download/ZINBA/Mappability50/temp.wig
    Processing chr10

 *** caught segfault ***
address 0x2aec96c0b000, cause 'memory not mapped'

Traceback:
 1: .C("alignAdjust", as.character(inputfile), as.character(outDir),     as.character(twoBitFile), as.integer(athresh), as.integer(adjustsize),     PACKAGE = "zinba")
 2: alignAdjust(inputfile = paste(mapdir, "temp.wig", sep = ""),     outDir = outdir, twoBitFile = twoBitFile, athresh = athresh,     adjustsize = round(extension/2))
 3: generateAlignability(mapdir = "/home/jma/download/ZINBA/Mappability36/",     outdir = "/home/jma/download/ZINBA/align_athresh1_extension200/",     athresh = 1, extension = 200, twoBitFile = "/home/jma/download/ZINBA/2BIT/hg18.2bit")

3) What was the exact command you used that resulted in the error?
generateAlignability(mapdir = "/home/jma/download/ZINBA/Mappability36/",     
outdir = "/home/jma/download/ZINBA/align_athresh1_extension200/",     athresh = 
1, extension = 200, twoBitFile = "/home/jma/download/ZINBA/2BIT/hg18.2bit")

4) Please copy and paste any additional screen output that resulted from
running the command
I'm using ZINBA version 2.02.03 and I attached the core dump file for you to 
debug

Original issue reported on code.google.com by jing...@gmail.com on 6 Dec 2012 at 10:17

GoogleCodeExporter commented 8 years ago 
(1) the core dump file is >200Mb so it can't be uploaded here.

(2) The error message was:
Loading align count data from /home/jma/download/ZINBA/Mappability36/temp.wig
    Processing chr10

 *** caught segfault ***
address 0x2aec96c0b000, cause 'memory not mapped'

Original comment by jing...@gmail.com on 6 Dec 2012 at 10:35

GoogleCodeExporter commented 8 years ago 
sorry, I figured it out. Your tool is alright.

Original comment by jing...@gmail.com on 7 Dec 2012 at 12:59

GoogleCodeExporter commented 8 years ago 
Great, glad it worked out

Original comment by homer...@gmail.com on 7 Dec 2012 at 1:42

GoogleCodeExporter commented 8 years ago 
I have the same error and have not figured it out. Can you post what you were 
doing incorrectly and how you fixed it?

Original comment by jjaar...@gmail.com on 22 Oct 2013 at 9:39

GoogleCodeExporter commented 8 years ago 
I too have the same error while running generateAlignability(). May I know 
about the problem?

Original comment by ashwini....@gmail.com on 14 Jul 2014 at 9:40

GoogleCodeExporter commented 8 years ago 
Running out of disk space during this process is not uncommon, it may be worth 
checking.

Original comment by homer...@gmail.com on 26 Jan 2015 at 4:10