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#204 Segmentation error while generating ASM file

terminator
closed-duplicate
Brian Walenz
Crash (103)
5
2013-04-01
2012-03-17
Anonymous
No

Here is the error I get. I have tried with 72 GB RAM. I have also tried to compile the assembler. I am using 2 big libraries from illumina. 1 mate pair and one paired. The spec file detains are given in the end.
/bubo/glob/g1/mayank/WGS/wgs-7.0/Linux-amd64/bin/terminator -g /bubo/home/h1/mayank/glob/nCJuql4/nCJuql4.gkpStore -t /bubo/home/h1/mayank/glob/nCJuql4/nCJuql4.tigStore 36 -c /bubo/home/h1/mayank/glob/nCJuql4/7-CGW/nCJuql4 35 -o /bubo/home/h1/mayank/glob/nCJuql4/9-terminator/nCJuql4 > /bubo/home/h1/mayank/glob/nCJuql4/9-terminator/nCJuql4.asm.err
====> Reading /bubo/home/h1/mayank/glob/nCJuql4/7-CGW/nCJuql4.ckp.35 at Sat Mar 17 16:39:03 2012
* ScaffoldGraph Memory Report:
* numElements AllocatedElements AllocatedSize
VA 192 bytes; elements: 3 active; 3 allocated; 64 bytes; 'Dists'
VA 2856195648 bytes; elements: 29752038 active; 29752038 allocated; 96 bytes; 'CIFrags'
VA 634200168 bytes; elements: 3775001 active; 3775001 allocated; 168 bytes; 'CIs '
VA 520341216 bytes; elements: 5420221 active; 5420221 allocated; 96 bytes; 'CIEdges'
VA 634686192 bytes; elements: 3777894 active; 3777894 allocated; 168 bytes; 'Contigs '
VA 520439520 bytes; elements: 5421245 active; 5421245 allocated; 96 bytes; 'ConEdges'
VA 270480 bytes; elements: 1610 active; 1610 allocated; 168 bytes; 'Scaffolds'
VA 1146336 bytes; elements: 11941 active; 11941 allocated; 96 bytes; 'SEdges'
* TotalMemorySize = 5167279752
Writing assembly file
writeMDI()--
writeAFGFromCGW()--
writeAMP()--
writeUTGFromCGW()--
writeULK()--
writeCCO()--
sh: line 1: 31600 Segmentation fault (core dumped) /bubo/glob/g1/mayank/WGS/wgs-7.0/Linux-amd64/bin/terminator -g /bubo/home/h1/mayank/glob/nCJuql4/nCJuql4.gkpStore -t /bubo/home/h1/mayank/glob/nCJuql4/nCJuql4.tigStore 36 -c /bubo/home/h1/mayank/glob/nCJuql4/7-CGW/nCJuql4 35 -o /bubo/home/h1/mayank/glob/nCJuql4/9-terminator/nCJuql4 > /bubo/home/h1/mayank/glob/nCJuql4/9-terminator/nCJuql4.asm.err
----------------------------------------END Sat Mar 17 16:41:37 2012 (155 seconds)
ERROR: Failed with signal SEGV (11)
================================================================================

runCA failed.

----------------------------------------
Stack trace:

at /bubo/home/h1/mayank/glob/WGS/wgs-7.0/Linux-amd64/bin/runCA line 1237
main::caFailure('terminator failed', '/bubo/home/h1/mayank/glob/nCJuql4/9-terminator/terminator.err') called at /bubo/home/h1/mayank/glob/WGS/wgs-7.0/Linux-amd64/bin/runCA line 5246
main::terminate() called at /bubo/home/h1/mayank/glob/WGS/wgs-7.0/Linux-amd64/bin/runCA line 5886

----------------------------------------
Failure message:

terminator failed

Spec file
-----------------------------------
useGrid=0
scriptOnGrid=0

ovlRefBlockSize=7630000
frgCorrBatchSize=4000000

frgMinLen=75
ovlMinLen=45
gkpFixInsertSizes=1
ovlStoreMemory=3072
ovlHashBits=24
ovlHashBlockLength=300000000
merylMemory=2048
doChimeraDetection=off
dncMPlibraries=Ill3kbp
unitigger=bogart
bogBadMateDepth=5
createACE=1
cleanup=aggressive
doToggle=1

PE.frg
MP.frg

Discussion

  • Brian Walenz
    Brian Walenz
    2013-01-23

    Can you recompile with debugging enabled and generate a stack trace?

    % gmake BUILDDEBUG=1

    % gdb --args terminator (options but no redirect of output)
    (gdb) run
    [wait for crash]
    (gdb) where

    I see one bug fix to this module. At line 63 in terminator.C, change the 'if' to a 'while'. You might try this first.

     
  • Jason Miller
    Jason Miller
    2013-03-08

    Any response?

     
  • Jason Miller
    Jason Miller
    2013-03-08

    • assigned_to: nobody --> brianwalenz
    • status: open --> pending
     
  • Brian Walenz
    Brian Walenz
    2013-04-01

    • status: pending --> closed-duplicate