#339 utgcnsfix failed

[wangyugui]

Source Revision: 564

Message:
Evaluating unitig 277102 of length 1357 with 457 fragments
MultiAlignUnitig()-- failed to align fragment 264513270 in unitig 277102.
MultiAlignUnitig()-- unitig 277102 FAILED.

• Fixing unitig 277102 with 457 fragments
• save fragment idx=155 ident=264513270 for next pass
• Testing new unitig 16879804 with 456 fragments (1 remain for next pass)
• Saved new unitig with 456 fragments.
• Fixing unitig 277102 with 1 fragments
• Testing new unitig 16879804 with 1 fragments
• Saved new unitig with 1 fragments.
  utgcnsfix: MultiAlign.C:1142: int32 GetMultiAlignLength(MultiAlignT*, bool): Assertion `len > 0' failed.

Failed with 'Aborted'

Backtrace (mangled):

/usr/hpc-bio/celera-8.3-svn/Linux-amd64/bin/utgcnsfix(_Z17AS_UTL_catchCrashiP9siginfo_tPv+0x2a)[0x40d20a]
/lib64/libpthread.so.0(+0xf100)[0x7f7fbe0f3100]
/lib64/libc.so.6(gsignal+0x37)[0x7f7fbdd585f7]
/lib64/libc.so.6(abort+0x148)[0x7f7fbdd59ce8]
/lib64/libc.so.6(+0x2e566)[0x7f7fbdd51566]
/lib64/libc.so.6(+0x2e612)[0x7f7fbdd51612]
/usr/hpc-bio/celera-8.3-svn/Linux-amd64/bin/utgcnsfix(_Z19GetMultiAlignLengthP11MultiAlignTb+0xdb)[0x41536b]
/usr/hpc-bio/celera-8.3-svn/Linux-amd64/bin/utgcnsfix(_Z22DumpMultiAlignForHumanP8_IO_FILEP11MultiAlignTb+0x77)[0x4154f7]
/usr/hpc-bio/celera-8.3-svn/Linux-amd64/bin/utgcnsfix(main+0x9e6)[0x4099b6]
/lib64/libc.so.6(__libc_start_main+0xf5)[0x7f7fbdd44b15]
/usr/hpc-bio/celera-8.3-svn/Linux-amd64/bin/utgcnsfix[0x409e05]

Backtrace (demangled):

[0] /usr/hpc-bio/celera-8.3-svn/Linux-amd64/bin/utgcnsfix::AS_UTL_catchCrash(int, siginfo_t, void) + 0x2a [0x40d20a]
[1] /lib64/libpthread.so.0::(null) + 0xf100 [0x7f7fbe0f3100]
[2] /lib64/libc.so.6::(null) + 0x37 [0x7f7fbdd585f7]
[3] /lib64/libc.so.6::(null) + 0x148 [0x7f7fbdd59ce8]
[4] /lib64/libc.so.6::(null) + 0x2e566 [0x7f7fbdd51566]
[5] /lib64/libc.so.6::(null) + 0x2e612 [0x7f7fbdd51612]
[6] /usr/hpc-bio/celera-8.3-svn/Linux-amd64/bin/utgcnsfix::GetMultiAlignLength(MultiAlignT, bool) + 0xdb [0x41536b]
[7] /usr/hpc-bio/celera-8.3-svn/Linux-amd64/bin/utgcnsfix::DumpMultiAlignForHuman(_IO_FILE, MultiAlignT*, bool) + 0x77 [0x4154f7]
[8] /usr/hpc-bio/celera-8.3-svn/Linux-amd64/bin/utgcnsfix::(null) + 0x9e6 [0x4099b6]
[9] /lib64/libc.so.6::(null) + 0xf5 [0x7f7fbdd44b15]
[10] /usr/hpc-bio/celera-8.3-svn/Linux-amd64/bin/utgcnsfix() [0x409e05]

[wangyugui]

the right source Revision: 4656

[wangyugui]

the server have 768G memory ,36 cnsConcurrency, and other cns default option, so the memory seems enough.

[wangyugui]

8 of 124 job failed with the same error.

and the max memory usages is less than 20%.

[Brian Walenz]

Hopefully you have some experience editing source code and compiling and etc.

In file src/AS_CNS/MultiAlign.C, comment out line 1142, the assert(). Rerun one of the failing jobs. I'll pick this one. Look in the output for unitig 16879804. Reply with that result.

[wangyugui]

I haved remove Line 1142, and change other parm, it will take about 1 week to finish.

[wangyugui]

I'm sorry that it is so late to update this info.

When I changed the kmer to 31 and overlap size to 50, only 2 of 24 job have this error.

I will try kmer 31 and overlap size 75(1/2 of the 150 bp read length) again.

Error Info:
Evaluating unitig 16326701 of length 88 with 2 fragments
MultiAlignUnitig()-- failed to align fragment 359570520 in unitig 16326701.
MultiAlignUnitig()-- unitig 16326701 FAILED.

• Fixing unitig 16326701 with 2 fragments
• save fragment idx=1 ident=359570520 for next pass
• Testing new unitig 16584486 with 1 fragments (1 remain for next pass)
• Saved new unitig with 1 fragments.
• Fixing unitig 16326701 with 1 fragments
• Testing new unitig 16584486 with 1 fragments
• Saved new unitig with 1 fragments. -

[wangyugui]

I tried kmer 31 and overlap size 60, and there still have

Reading layouts from '/biowrk/celera/juglans.regian/PRJNA291087.DNA/5-consensus/juglans.fixes'.
MultiAlignStore::insertMultiAlign()-- Added new unitig 16122030
INSERTING unitig 16122030
MultiAlignStore::insertMultiAlign()-- Added new unitig 16122031
INSERTING unitig 16122031
DELETING unitig 288676
MultiAlignStore::insertMultiAlign()-- Added new unitig 16122032
INSERTING unitig 16122032
MultiAlignStore::insertMultiAlign()-- Added new unitig 16122033
INSERTING unitig 16122033
DELETING unitig 15759807
MultiAlignStore::insertMultiAlign()-- Added new unitig 16122034
INSERTING unitig 16122034
MultiAlignStore::insertMultiAlign()-- Added new unitig 16122035
INSERTING unitig 16122035
DELETING unitig 15983005
MultiAlignStore::insertMultiAlign()-- Added new unitig 16122036
INSERTING unitig 16122036
MultiAlignStore::insertMultiAlign()-- Added new unitig 16122037
INSERTING unitig 16122037
DELETING unitig 16052761
Reading layouts from '/biowrk/celera/juglans.regian/PRJNA291087.DNA/5-consensus/juglans.fixes' completed.