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Bug 622458 - [abrt] crash in bwa-0.5.8a-1.fc13: bwt_cal_width: Process /usr/bin/bwa was killed by signal 11 (SIGSEGV)
[abrt] crash in bwa-0.5.8a-1.fc13: bwt_cal_width: Process /usr/bin/bwa was ki...
Product: Fedora
Classification: Fedora
Component: bwa (Show other bugs)
x86_64 Linux
low Severity medium
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Assigned To: Adam Huffman
Fedora Extras Quality Assurance
Depends On:
  Show dependency treegraph
Reported: 2010-08-09 08:44 EDT by Ian
Modified: 2011-06-28 10:48 EDT (History)
1 user (show)

See Also:
Fixed In Version:
Doc Type: Bug Fix
Doc Text:
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Clone Of:
Last Closed: 2011-06-28 10:48:12 EDT
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Regression: ---
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Verified Versions:
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oVirt Team: ---
RHEL 7.3 requirements from Atomic Host:
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Attachments (Terms of Use)
File: backtrace (7.47 KB, text/plain)
2010-08-09 08:44 EDT, Ian
no flags Details

  None (edit)
Description Ian 2010-08-09 08:44:05 EDT
abrt 1.1.1 detected a crash.

architecture: x86_64
Attached file: backtrace
cmdline: bwa aln -l 25 -k 2 -n 5 -f solid0424_20100706_3_CB_bcut_F3.sai /home/idonaldson/genomes/danRer6/danRer6_chr.fa solid0424_20100706_3_CB_bcut_F3.fastq
component: bwa
crash_function: bwt_cal_width
executable: /usr/bin/bwa
global_uuid: 84a6b51a23311f8e46dfeaf7ee074be7f363bcf8
package: bwa-0.5.8a-1.fc13
rating: 4
reason: Process /usr/bin/bwa was killed by signal 11 (SIGSEGV)
release: Fedora release 13 (Goddard)

There are 37833287 reads in the fastq file.

Output before seg fault was:
[bwa_aln_core] calculate SA coordinate... 0.14 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 262144 sequences have been processed.
[bwa_aln_core] calculate SA coordinate... Segmentation fault (core dumped)

How to reproduce
Command line:
bwa aln -l 25 -k 2 -n 5 -f solid0424_20100706_3_CB_bcut_F3.sai ~/genomes/danRer6/danRer6_chr.fa solid0424_20100706_3_CB_bcut_F3.fastq
Comment 1 Ian 2010-08-09 08:44:07 EDT
Created attachment 437584 [details]
File: backtrace
Comment 2 Bug Zapper 2011-06-01 07:49:31 EDT
This message is a reminder that Fedora 13 is nearing its end of life.
Approximately 30 (thirty) days from now Fedora will stop maintaining
and issuing updates for Fedora 13.  It is Fedora's policy to close all
bug reports from releases that are no longer maintained.  At that time
this bug will be closed as WONTFIX if it remains open with a Fedora 
'version' of '13'.

Package Maintainer: If you wish for this bug to remain open because you
plan to fix it in a currently maintained version, simply change the 'version' 
to a later Fedora version prior to Fedora 13's end of life.

Bug Reporter: Thank you for reporting this issue and we are sorry that 
we may not be able to fix it before Fedora 13 is end of life.  If you 
would still like to see this bug fixed and are able to reproduce it 
against a later version of Fedora please change the 'version' of this 
bug to the applicable version.  If you are unable to change the version, 
please add a comment here and someone will do it for you.

Although we aim to fix as many bugs as possible during every release's 
lifetime, sometimes those efforts are overtaken by events.  Often a 
more recent Fedora release includes newer upstream software that fixes 
bugs or makes them obsolete.

The process we are following is described here: 
Comment 3 Bug Zapper 2011-06-28 10:48:12 EDT
Fedora 13 changed to end-of-life (EOL) status on 2011-06-25. Fedora 13 is 
no longer maintained, which means that it will not receive any further 
security or bug fix updates. As a result we are closing this bug.

If you can reproduce this bug against a currently maintained version of 
Fedora please feel free to reopen this bug against that version.

Thank you for reporting this bug and we are sorry it could not be fixed.

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