Re: [wgs-assembler-users] Unitig splitter failed

[Ole K. T. <o.k...@ib...>]

Hi Hiroaki.

You can skip the unitig splitter. I'm not sure what effects that will have
for your assembly, but I've done it a couple of times and it looks good.

You have to create the files splitUnitigs.out and consensus-fix.out in
the 5-consensus-split folder ("touch splitUnitigs.out; touch
consensus-fix.out"), and restart CA. Then CA will skip the splitting.

Ole


On 11 April 2013 13:31, Hiroaki Sakai <hir...@af...> wrote:

> 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...
>
>
>
>
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