#318 fail in 7-2-CGW

[Matt MacManes]

Hi All, Having a failure in 7-2-CGW Of note, I spend 38 days (!!) in 7-0-CGW mostly in logical ckp05-1SM-partial. Continued after editing teh *timing file and manually restarting.

This is 8.3rc2

ScaffoldSanity()-- Contig 17085687 at    766916 +- 5354382     to    768208 +- 5354416      ctg len      1292  gap to next     -1289 +- 17753
ScaffoldSanity()-- Contig  1143896 at    766919 +- 5372168     to    767071 +- 5372172      ctg len       152  gap to next      1117 +- 35569
ScaffoldSanity()-- Contig 17807967 at    768188 +- 5407741     to    768578 +- 5407751      ctg len       390  gap to next      4470 +- 9186
ScaffoldSanity()-- Contig 17314057 at    773048 +- 5416937     to    776572 +- 5417028      ctg len      3524
cgw: CIScaffoldT_CGW.C:1143: void ScaffoldSanity(ScaffoldGraphT*, CIScaffoldT*): Assertion `hasProblems == 0' failed.

Failed with 'Aborted'

Backtrace (mangled):

/share/wgs-assembler/Linux-amd64/bin/cgw(_Z17AS_UTL_catchCrashiP9siginfo_tPv+0x2a)[0x41b5aa]
/lib/x86_64-linux-gnu/libpthread.so.0(+0x10340)[0x7fdfadb70340]
/lib/x86_64-linux-gnu/libc.so.6(gsignal+0x39)[0x7fdfad7cecc9]
/lib/x86_64-linux-gnu/libc.so.6(abort+0x148)[0x7fdfad7d20d8]
/lib/x86_64-linux-gnu/libc.so.6(+0x2fb86)[0x7fdfad7c7b86]
/lib/x86_64-linux-gnu/libc.so.6(+0x2fc32)[0x7fdfad7c7c32]
/share/wgs-assembler/Linux-amd64/bin/cgw(_Z14ScaffoldSanityP14ScaffoldGraphTP9NodeCGW_T+0x946)[0x447786]
/share/wgs-assembler/Linux-amd64/bin/cgw[0x4da07a]
/share/wgs-assembler/Linux-amd64/bin/cgw(_Z9RepeatReziPc+0x76)[0x4dbc66]
/share/wgs-assembler/Linux-amd64/bin/cgw(main+0xdd2)[0x419302]
/lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xf5)[0x7fdfad7b9ec5]
/share/wgs-assembler/Linux-amd64/bin/cgw[0x41a6cc]

Backtrace (demangled):

[0] /share/wgs-assembler/Linux-amd64/bin/cgw::AS_UTL_catchCrash(int, siginfo_t*, void*) + 0x2a  [0x41b5aa]
[1] /lib/x86_64-linux-gnu/libpthread.so.0::(null) + 0x10340  [0x7fdfadb70340]
[2] /lib/x86_64-linux-gnu/libc.so.6::(null) + 0x39  [0x7fdfad7cecc9]
[3] /lib/x86_64-linux-gnu/libc.so.6::(null) + 0x148  [0x7fdfad7d20d8]
[4] /lib/x86_64-linux-gnu/libc.so.6::(null) + 0x2fb86  [0x7fdfad7c7b86]
[5] /lib/x86_64-linux-gnu/libc.so.6::(null) + 0x2fc32  [0x7fdfad7c7c32]
[6] /share/wgs-assembler/Linux-amd64/bin/cgw::ScaffoldSanity(ScaffoldGraphT*, NodeCGW_T*) + 0x946  [0x447786]
[7] /share/wgs-assembler/Linux-amd64/bin/cgw() [0x4da07a]
[8] /share/wgs-assembler/Linux-amd64/bin/cgw::RepeatRez(int, char*) + 0x76  [0x4dbc66]
[9] /share/wgs-assembler/Linux-amd64/bin/cgw::(null) + 0xdd2  [0x419302]
[10] /lib/x86_64-linux-gnu/libc.so.6::(null) + 0xf5  [0x7fdfad7b9ec5]
[11] /share/wgs-assembler/Linux-amd64/bin/cgw() [0x41a6cc]

GDB:

Aborted (core dumped)

Any ideas?