[wgs-assembler-users] segmentation fault, olap-from-seeds

[Richard B. <r....@qm...>]

Hi all,

I am running CABOG for the first time on 4.3X 454 coverage of an 880Mb plant genome. It has stopped working at the end of the 79th iteration of "olap-from-seeds", due to a "segmentation fault". Can anyone advise me how to resume the assembly, please? I have tried restarting it but the problem recurs.

The end of my standard output was:

/home/btw434/work-yearly/Celera/wgs-7.0/Linux-amd64/bin/AshCelera1/0-overlaptrim-overlap/olap-from-seeds.sh 77 > /home/btw434/work-yearly/Celera/wgs-7.0/Linux-amd64/bin/AshCelera1/0-overlaptrim-overlap/olaps/0077.err 2>&1
/home/btw434/work-yearly/Celera/wgs-7.0/Linux-amd64/bin/AshCelera1/0-overlaptrim-overlap/olap-from-seeds.sh 78 > /home/btw434/work-yearly/Celera/wgs-7.0/Linux-amd64/bin/AshCelera1/0-overlaptrim-overlap/olaps/0078.err 2>&1
/home/btw434/work-yearly/Celera/wgs-7.0/Linux-amd64/bin/AshCelera1/0-overlaptrim-overlap/olap-from-seeds.sh 79 > /home/btw434/work-yearly/Celera/wgs-7.0/Linux-amd64/bin/AshCelera1/0-overlaptrim-overlap/olaps/0079.err 2>&1
----------------------------------------END CONCURRENT Wed Apr 24 12:32:33 2013 (1582382 seconds)
================================================================================

runCA failed.

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

 at ./runCA line 1237.
        main::caFailure('olap-from-seeds failed.  See *.err in /home/btw434/work-yearl...', undef) called at ./runCA line 3200
        main::merOverlapper('trim') called at ./runCA line 3258
        main::createOverlapJobs('trim') called at ./runCA line 3647
        main::overlapTrim() called at ./runCA line 5876

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

olap-from-seeds failed.  See *.err in /home/btw434/work-yearly/Celera/wgs-7.0/Linux-amd64/bin/AshCelera1/0-overlaptrim-overlap.


The tail of /home/btw434/work-yearly/Celera/wgs-7.0/Linux-amd64/bin/AshCelera1/0-overlaptrim-overlap/olaps/0079.err read: 

Thread 1 processed 1170163 olaps at Wed Apr 24 12:21:07 2013
Thread 0 processed 1174288 olaps at Wed Apr 24 12:21:11 2013
Extracted 12711 of 12711 fragments in iid range 5900001 .. 5912794
Thread 1 processed 1374622 olaps at Wed Apr 24 12:29:16 2013
Thread 0 processed 1383950 olaps at Wed Apr 24 12:29:20 2013
Thread 1 processed 224905 olaps at Wed Apr 24 12:30:49 2013
Thread 0 processed 229187 olaps at Wed Apr 24 12:30:51 2013
                   Failed overlaps = 106922508
Start analyzing multi-alignments  Num_Frags = 62794
/home/btw434/work-yearly/Celera/wgs-7.0/Linux-amd64/bin/AshCelera1/0-overlaptrim-overlap/olap-from-seeds.sh: line 63: 40962 Segmentation fault      $bin/olap-from-seeds -a -b -t 2 -S /home/btw434/work-yearly/Celera/wgs-7.0/Linux-amd64/bin/AshCelera1/0-overlaptrim-overlap/Ash1.merStore -G -o /home/btw434/work-yearly/Celera/wgs-7.0/Linux-amd64/bin/AshCelera1/0-overlaptrim-overlap/olaps/$jobid.ovb.WORKING.gz /home/btw434/work-yearly/Celera/wgs-7.0/Linux-amd64/bin/AshCelera1/Ash1.gkpStore $minid $maxid

Do you know how I might solve this problem, please? 

many thanks

Richard


_______
Dr Richard Buggs | Senior Lecturer | School of Biological and Chemical Sciences, Queen Mary University of London, E1 4NS, United Kingdom | email: r....@qm... | website: http://www.sbcs.qmul.ac.uk/staff/richardbuggs.html | office: +44(0)207 882 3058 | mobile: +44(0)772 992 0401 | twitter: @RJABuggs