#334 'Segmentation fault' during 8-consensus

[Luohao Xu]

I was running with wgs-8.3rc2, and I crashed for the last partition in 8-consensus:

GetAlignmentTrace()-- Overlap ACCEPTED! accept=1000.000000 lScore=0.015327 (7287 vs 7177) aScore=0.140000 (27886 vs 27900) bScore=0.190000 (-30423 v
DP_Compare found overlap between 27582 (U) and 886587 (R) ahang: 27886, bhang: -30423 (expected hang was 27900)
Alignment params: 27800 28000 200 200 0 0.20 1e-06 30 1
-- e/l = 336/7287 = 4.61%
A -----+------+----> []
B 27886 -------> 30423 []
Could (really) not find overlap between 27582 (U) and 3060972 (R) estimated ahang: 35077 (ejecting frag 3060972 from contig)
Could (really) not find overlap between 27582 (U) and 3080153 (R) estimated ahang: 35157 (ejecting frag 3080153 from contig)
Could (really) not find overlap between 27582 (U) and 1583666 (R) estimated ahang: 35179 (ejecting frag 1583666 from contig)
Could (really) not find overlap between 27582 (U) and 1385772 (R) estimated ahang: 35197 (ejecting frag 1385772 from contig)

Failed with 'Segmentation fault'

Backtrace (mangled):

/datalow/zhouqi/soft/wgs-8.3rc2/Linux-amd64/bin/ctgcns(_Z17AS_UTL_catchCrashiP7siginfoPv+0x2a)[0x40b47a]
/lib64/libpthread.so.0[0x3e62c0f710]
/datalow/zhouqi/soft/wgs-8.3rc2/Linux-amd64/bin/ctgcns(_Z12AbacusRefineP6MANodeii15CNS_RefineLevelP11CNS_Options+0x433)[0x43e193]
/datalow/zhouqi/soft/wgs-8.3rc2/Linux-amd64/bin/ctgcns(_Z16MultiAlignContigP11MultiAlignTP7gkStoreP11CNS_Options+0x1a3f)[0x42a4bf]
/datalow/zhouqi/soft/wgs-8.3rc2/Linux-amd64/bin/ctgcns(main+0x62f)[0x4098ff]
/lib64/libc.so.6(__libc_start_main+0xfd)[0x3e6201ed1d]
/datalow/zhouqi/soft/wgs-8.3rc2/Linux-amd64/bin/ctgcns[0x408fa5]

Backtrace (demangled):

[0] /datalow/zhouqi/soft/wgs-8.3rc2/Linux-amd64/bin/ctgcns::AS_UTL_catchCrash(int, siginfo, void) + 0x2a [0x40b47a]
[1] /lib64/libpthread.so.0() [0x3e62c0f710]
[2] /datalow/zhouqi/soft/wgs-8.3rc2/Linux-amd64/bin/ctgcns::AbacusRefine(MANode, int, int, CNS_RefineLevel, CNS_Options) + 0x433 [0x43e193]
[3] /datalow/zhouqi/soft/wgs-8.3rc2/Linux-amd64/bin/ctgcns::MultiAlignContig(MultiAlignT, gkStore, CNS_Options*) + 0x1a3f [0x42a4bf]
[4] /datalow/zhouqi/soft/wgs-8.3rc2/Linux-amd64/bin/ctgcns::(null) + 0x62f [0x4098ff]
[5] /lib64/libc.so.6::(null) + 0xfd [0x3e6201ed1d]
[6] /datalow/zhouqi/soft/wgs-8.3rc2/Linux-amd64/bin/ctgcns() [0x408fa5]

GDB:

[Luohao Xu]

So I took only 25X corrected reads, and changed some options such as ovlHashBlockLength and ovlRefBlockSize, then it worked, although I got some warmings like
ERROR! Column ci=14065 has a next pointer (14066)

[Brian Walenz]

We're not maintaining this anymore, and trying to not provide support, sorry.

If it ran to completion, even with those errors reported, I'd declare success!

The supported assembler for PacBio is https://github.com/marbl/canu. You can reassemble your raw reads from scratch (it'll do both correction and assembly) or just assemble your corrected reads. Or neither. If you have the time and CPU, I'd suggest reassembly from scratch, but there haven't (yet) been significant improvements in the algorithms.