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sivarajankumar / zinba

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generateAlignability-Segementation Fault #20

Closed GoogleCodeExporter closed 8 years ago

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

 Ubuntu 11.10 (Desktop)

2) What error message was displayed?

*** glibc detected *** /usr/lib/R/bin/exec/R: malloc(): smallbin double linked 
list corrupted: 0x0000000002815a00 ***

 *** caught segfault ***
Segmentation fault

I had tried (zinba_2.01) and (zinba_2.02.03), both display the a similar error 
related to Segmentation fault, mer length used is 50

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

library(zinba)
generateAlignability(
mapdir="/home/davidu/Documents/Mappability_Map/map_Arab",
outdir="/home/davidu/Documents/map_arab_alignability",
athresh=6,
extension=200,
twoBitFile="/home/davidu/Documents/TAIR10/TAIR10.2bit"
)

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

R.methodsS3 v1.2.1 (2010-09-18) successfully loaded. See ?R.methodsS3 for help.
R.oo v1.8.1 (2011-07-10) successfully loaded. See ?R.oo for help.
R.utils v1.8.1 (2011-09-19) successfully loaded. See ?R.utils for help.

Processing chr1b.out .......
    chr1 .......

Processing chr2b.out .......
    chr2 .......

Processing chr3b.out .......
    chr3 .......

Processing chr4b.out .......
    chr4 .......

Processing chr5b.out .......
    chr5 .......

Processing chrCb.out .......
    chrC .......

Processing chrMb.out .......
    chrM .......

Processing chrMb.out .......
    chrM .......
Loading align count data from 
/home/davidu/Documents/Mappability_Map/map_Arab/temp.wig
    Processing chr1
*** glibc detected *** /usr/lib/R/bin/exec/R: malloc(): smallbin double linked 
list corrupted: 0x0000000002815a00 ***

 *** caught segfault ***
Segmentation fault

Original issue reported on code.google.com by daugo...@gmail.com on 17 Apr 2012 at 3:52

GoogleCodeExporter commented 8 years ago

Original comment by daugo...@gmail.com on 17 Apr 2012 at 3:54

Attachments:

GoogleCodeExporter commented 8 years ago 
Sorry for the delay in response.  We haven't encountered anyone using 
Arabidopsis yet so this may be related to to the way in which the mappability 
files were generated.  Which build of the Arabidopsis genome where you using?  
I will try to generate an alignability directory with my own code and see if I 
get the same issue

Original comment by homer...@gmail.com on 28 May 2012 at 6:30

GoogleCodeExporter commented 8 years ago 
I'm using the TAIR10 built, I download the fasta files from here 
(ftp://ftp.arabidopsis.org/home/tair/Sequences/whole_chromosomes/) and built 
the .2bit with:

fatotwobit(faFile='TAIR10.fasta',outFile='TAIR10.2bit')

The mappability files were generated using code from Peakseq.

I will appreciated if you can generate the alignability directory and tell me 
what was wrong.

Original comment by daugo...@gmail.com on 29 May 2012 at 1:07

GoogleCodeExporter commented 8 years ago 
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