[wgs-assembler-users] Unitig splitter failed

[Hiroaki S. <hir...@af...>]

Hi,

I'm working of the de-novo genome assembly of a plant species and trying to
do a hybrid assembly combining PacBio reads (1.9Gbp) corrected by pacBioToCA
and 454 reads (11Gbp) by runCA. I'm using the CSV:

% ./runCA -version
CA version CVS TIP ($Id: AS_GKP_main.c,v 1.105 2012/09/13 17:41:13 skoren
Exp $).
CA version CVS TIP ($Id: AS_CGB_unitigger.c,v 1.45 2011/09/06 02:15:18
mkotelbajcvi Exp $).
CA version CVS TIP ($Id: BuildUnitigs.cc,v 1.88 2012/01/15 23:49:34
brianwalenz Exp $).
Using up to 12 OpenMP threads.
CA version CVS TIP ($Id: AS_CGW_main.c,v 1.116 2012/11/15 05:04:54
brianwalenz Exp $).
CA version CVS TIP ($Id: terminator.C,v 1.17 2012/09/10 08:58:11 brianwalenz
Exp $).

When I ran the runCA, it stopped during 5-consensus-split stage. The error
messages I got were:

----------------------------------------START Thu Apr 11 17:11:18 2013
/tool/wgs/Linux-amd64/bin/utgcnsfix \
 -g /my_genome/454_pacbio/result/vigan_454.gkpStore \
 -t /my_genome/454_pacbio/result/vigan_454.tigStore 2 \
> /my_genome/454_pacbio/result/5-consensus/consensus-fix.out 2>&1
----------------------------------------END Thu Apr 11 18:10:54 2013 (3576
seconds)
----------------------------------------START Thu Apr 11 18:10:54 2013
/tool/wgs/Linux-amd64/bin/tigStore \
 -g /my_genome/454_pacbio/result/vigan_454.gkpStore \
 -t /my_genome/454_pacbio/result/5-consensus-insert-sizes/vigan_454.tigStore
3 \
 -d matepair -U \
> /my_genome/454_pacbio/result/5-consensus-insert-sizes/estimates.out 2>&1
----------------------------------------END Thu Apr 11 18:11:23 2013 (29
seconds)
----------------------------------------START Thu Apr 11 18:11:23 2013
/tool/wgs/Linux-amd64/bin/gatekeeper \
 --edit
/my_genome/454_pacbio/result/5-consensus-insert-sizes/vigan_454.tigStore.dis
tupdate \
        /my_genome/454_pacbio/result/vigan_454.gkpStore \
> /my_genome/454_pacbio/result/5-consensus-insert-sizes/updates.err 2>&1
----------------------------------------END Thu Apr 11 18:12:10 2013 (47
seconds)
----------------------------------------START Thu Apr 11 18:12:10 2013
/tool/wgs/Linux-amd64/bin/splitUnitigs \
 -g /my_genome/454_pacbio/result/vigan_454.gkpStore \
 -t /my_genome/454_pacbio/result/vigan_454.tigStore 3 \
> /my_genome/454_pacbio/result/5-consensus-split/splitUnitigs.out 2>&1
sh: line 3: 63004 Aborted                 (core dumped)
/tool/wgs/Linux-amd64/bin/splitUnitigs -g
/my_genome/454_pacbio/result/vigan_454.gkpStore -t
/my_genome/454_pacbio/result/vigan_454.tigStore 3 >
/my_genome/454_pacbio/result/5-consensus-split/splitUnitigs.out 2>&1
----------------------------------------END Thu Apr 11 18:58:30 2013 (2780
seconds)
ERROR: Failed with signal ABRT (6)
============================================================================
====

runCA failed.

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

 at /tool/wgs/Linux-amd64/bin/runCA line 1390
        main::caFailure('Unitig splitter failed', '/my_genome...') called at
/tool/wgs/Linux-amd64/bin/runCA line 4824
        main::postUnitiggerConsensus() called at
/tool/wgs/Linux-amd64/bin/runCA line 6144
----------------------------------------
Last few lines of the relevant log file
(/my_genome/454_pacbio/result/5-consensus-split/splitUnitigs.out.FAILED):

/lib64/libc.so.6(__libc_start_main+0xfd)[0x309dc1ecdd]
/tool/wgs/Linux-amd64/bin/splitUnitigs[0x408b69]

Backtrace (demangled):

[0] /tool/wgs/Linux-amd64/bin/splitUnitigs::AS_UTL_catchCrash(int, siginfo*,
void*) + 0x27  [0x40f857]
[1] /lib64/libpthread.so.0() [0x309e40f4a0]
[2] /lib64/libc.so.6::(null) + 0x35  [0x309dc32885]
[3] /lib64/libc.so.6::(null) + 0x175  [0x309dc34065]
[4] /lib64/libc.so.6() [0x309dc2b9fe]
[5] /lib64/libc.so.6::(null) + 0  [0x309dc2bac0]
[6] /tool/wgs/Linux-amd64/bin/splitUnitigs::unitigConsensus::alignFragment()
+ 0x3ee  [0x42c28e]
[7] /tool/wgs/Linux-amd64/bin/splitUnitigs::MultiAlignUnitig(MultiAlignT*,
gkStore*, CNS_Options*, int*) + 0x578  [0x42db88]
[8] /tool/wgs/Linux-amd64/bin/splitUnitigs::(null) + 0x2c7b  [0x40b8ab]
[9] /lib64/libc.so.6::(null) + 0xfd  [0x309dc1ecdd]
[10] /tool/wgs/Linux-amd64/bin/splitUnitigs() [0x408b69]

GDB:



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

Unitig splitter failed
----------------------------------------

I would appreciate it if any of you would kindly give me any suggestions.

Best regards,

-------------
Hiroaki Sakai, PhD
National Institute of Agrobiological Sciences, Japan
hir...@af...