#252 Unitig consensus fixer assert(0) reached

consensus
closed-fixed
None
5
2015-02-03
2013-08-05
eernst
No

5-consensus/consensus-fix.out.FAILED:

Fixing unitig 20879488 (17 fragments remain)
Testing new unitig 26774528 with 17 fragments (0 remain)
Added unitig 26774528 with 17 fragments.

Evaluating unitig 20879489 of length 22729 with 4682 fragments
utgcnsfix: MultiAlignUnitig.C:99: int MANode2Array(MANode*, char, int32, int32): Assertion `0' failed.

Failed with 'Aborted'

Backtrace (mangled):
...

Backtrace (demangled):

[0] /bluearc/home/martienssen/eernst/src/wgs-dev/Linux-amd64/bin/utgcnsfix::AS_UTL_catchCrash(int, siginfo, void) + 0x27 [0x40c4a7]
[1] /lib64/libpthread.so.0() [0x32ade0f500]
[2] /lib64/libc.so.6::(null) + 0x35 [0x39c2a328a5]
[3] /lib64/libc.so.6::(null) + 0x175 [0x39c2a34085]
[4] /lib64/libc.so.6() [0x39c2a2ba1e]
[5] /lib64/libc.so.6::(null) + 0 [0x39c2a2bae0]
[6] /bluearc/home/martienssen/eernst/src/wgs-dev/Linux-amd64/bin/utgcnsfix::unitigConsensus::generateConsensus() + 0x16c8 [0x429988]
[7] /bluearc/home/martienssen/eernst/src/wgs-dev/Linux-amd64/bin/utgcnsfix::MultiAlignUnitig(MultiAlignT, gkStore, CNS_Options, int) + 0x5a0 [0x42b740]
[8] /bluearc/home/martienssen/eernst/src/wgs-dev/Linux-amd64/bin/utgcnsfix::(null) + 0x511 [0x408d41]
[9] /lib64/libc.so.6::(null) + 0xfd [0x39c2a1ecdd]
[10] /bluearc/home/martienssen/eernst/src/wgs-dev/Linux-amd64/bin/utgcnsfix() [0x408769]

Discussion

  • Brian Walenz

    Brian Walenz - 2013-08-06
    • status: open --> pending-fixed
    • assigned_to: Brian Walenz
     
  • Brian Walenz

    Brian Walenz - 2013-08-06

    Fixed in r4380.

    In your case, I'd suggest backing up and rerunning 5-consensus. There is a chance that a utgcns job failed with the same error, resulting in the fixer doing all the work of that job.

    Delete tigStore/v003*, the output of utgcnsfix.

    Then rerun all of the consensus.sh jobs. Jobs that finished successfully will finish quickly; they will not recompute existing results.

    The fixer will work, and should generate the same result, it'll just be very slow compared to rerunning consensus.sh.

     
  • eernst

    eernst - 2013-08-07

    Thanks, Brian! That sorted it out.

    Also had to run upgrade-v9-to-v10 in the gkpStore dir to get things going again.

     
  • Brian Walenz

    Brian Walenz - 2015-02-03

    Closing old resolved case.

     
  • Brian Walenz

    Brian Walenz - 2015-02-03
    • status: pending-fixed --> closed-fixed
     

Get latest updates about Open Source Projects, Conferences and News.

Sign up for the SourceForge newsletter:





No, thanks