[wgs-assembler-users] Crash in CGW, allocing a negative amount of memory

SourceForge Headquarters 225 Broadway Suite 1600 San Diego, CA 92101 +1 (858) 422-6466

Hi,
cgw crashes trying to allocate a negative amount of memory. This is 
with CA 8.1. I've tried -recomputegaps, but that didn't help (it ended 
in the second crash below).

First crash:
Could not malloc memory (-47244640206 bytes)
cgw: AS_UTL_alloc.C:65: void* safe_malloc(size_t): Assertion `p != 
__null' failed.

Failed with 'Aborted'

Backtrace (mangled):

/projects/cees/bin/celera/wgs-8.1/Linux-amd64/bin/cgw(_Z17AS_UTL_catchCrashiP7siginfoPv+0x27)[0x41cbb7]
/lib64/libpthread.so.0[0x3810a0f500]
/lib64/libc.so.6(gsignal+0x35)[0x380fe328a5]
/lib64/libc.so.6(abort+0x175)[0x380fe34085]
/lib64/libc.so.6[0x380fe2ba1e]
/lib64/libc.so.6(__assert_perror_fail+0x0)[0x380fe2bae0]
/projects/cees/bin/celera/wgs-8.1/Linux-amd64/bin/cgw[0x4cdaf7]
/projects/cees/bin/celera/wgs-8.1/Linux-amd64/bin/cgw(_Z27ReLoadMultiAlignTFromStreamP8_IO_FILEP11MultiAlignT+0x75)[0x4e8425]
/projects/cees/bin/celera/wgs-8.1/Linux-amd64/bin/cgw(_Z25LoadMultiAlignTFromStreamP8_IO_FILE+0x24)[0x4e8ae4]
/projects/cees/bin/celera/wgs-8.1/Linux-amd64/bin/cgw(_ZN15MultiAlignStore14loadMultiAlignEib+0x20b)[0x43f09b]
/projects/cees/bin/celera/wgs-8.1/Linux-amd64/bin/cgw(_Z12GetConsensusP10GraphCGW_TiP12VarArrayTypeS2_+0x8b)[0x46b68b]
/projects/cees/bin/celera/wgs-8.1/Linux-amd64/bin/cgw[0x469a53]
/projects/cees/bin/celera/wgs-8.1/Linux-amd64/bin/cgw(_Z13OverlapChunksP10GraphCGW_Tii10PairOrientiidi+0x145)[0x46a695]
/projects/cees/bin/celera/wgs-8.1/Linux-amd64/bin/cgw[0x4e696c]
/projects/cees/bin/celera/wgs-8.1/Linux-amd64/bin/cgw(_Z17check_consistencyP15Scaffold_Fill_tii+0x8b2)[0x4e7322]
/projects/cees/bin/celera/wgs-8.1/Linux-amd64/bin/cgw(_Z9Fill_GapsPcii+0x498)[0x435f78]
/projects/cees/bin/celera/wgs-8.1/Linux-amd64/bin/cgw(main+0x1bfd)[0x41a7ed]
/lib64/libc.so.6(__libc_start_main+0xfd)[0x380fe1ecdd]
/projects/cees/bin/celera/wgs-8.1/Linux-amd64/bin/cgw[0x418899]

Backtrace (demangled):

[0] 
/projects/cees/bin/celera/wgs-8.1/Linux-amd64/bin/cgw::AS_UTL_catchCrash(int, 
siginfo*, void*) + 0x27  [0x41cbb7]
[1] /lib64/libpthread.so.0() [0x3810a0f500]
[2] /lib64/libc.so.6::(null) + 0x35  [0x380fe328a5]
[3] /lib64/libc.so.6::(null) + 0x175  [0x380fe34085]
[4] /lib64/libc.so.6() [0x380fe2ba1e]
[5] /lib64/libc.so.6::(null) + 0  [0x380fe2bae0]
[6] /projects/cees/bin/celera/wgs-8.1/Linux-amd64/bin/cgw() [0x4cdaf7]
[7] 
/projects/cees/bin/celera/wgs-8.1/Linux-amd64/bin/cgw::ReLoadMultiAlignTFromStream(_IO_FILE*, 
MultiAlignT*) + 0x75  [0x4e8425]
[8] 
/projects/cees/bin/celera/wgs-8.1/Linux-amd64/bin/cgw::LoadMultiAlignTFromStream(_IO_FILE*) 
+ 0x24  [0x4e8ae4]
[9] 
/projects/cees/bin/celera/wgs-8.1/Linux-amd64/bin/cgw::MultiAlignStore::loadMultiAlign(int, 
bool) + 0x20b  [0x43f09b]
[10] 
/projects/cees/bin/celera/wgs-8.1/Linux-amd64/bin/cgw::GetConsensus(GraphCGW_T*, 
int, VarArrayType*, VarArrayType*) + 0x8b  [0x46b68b]
[11] /projects/cees/bin/celera/wgs-8.1/Linux-amd64/bin/cgw() [0x469a53]
[12] 
/projects/cees/bin/celera/wgs-8.1/Linux-amd64/bin/cgw::OverlapChunks(GraphCGW_T*, 
int, int, PairOrient, int, int, double, int) + 0x145  [0x46a695]
[13] /projects/cees/bin/celera/wgs-8.1/Linux-amd64/bin/cgw() [0x4e696c]
[14] 
/projects/cees/bin/celera/wgs-8.1/Linux-amd64/bin/cgw::check_consistency(Scaffold_Fill_t*, 
int, int) + 0x8b2  [0x4e7322]
[15] 
/projects/cees/bin/celera/wgs-8.1/Linux-amd64/bin/cgw::Fill_Gaps(char*, 
int, int) + 0x498  [0x435f78]
[16] /projects/cees/bin/celera/wgs-8.1/Linux-amd64/bin/cgw::(null) + 
0x1bfd  [0x41a7ed]
[17] /lib64/libc.so.6::(null) + 0xfd  [0x380fe1ecdd]
[18] /projects/cees/bin/celera/wgs-8.1/Linux-amd64/bin/cgw() [0x418899]

GDB:

And with -recompute gaps.

Could not malloc memory (-4928055532461031424 bytes)
cgw: AS_UTL_alloc.C:65: void* safe_malloc(size_t): Assertion `p != 
__null' failed.

Failed with 'Aborted'

Backtrace (mangled):

/projects/cees/bin/celera/wgs-8.1/Linux-amd64/bin/cgw(_Z17AS_UTL_catchCrashiP7siginfoPv+0x27)[0x41cbb7]
/lib64/libpthread.so.0[0x3810a0f500]
/lib64/libc.so.6(gsignal+0x35)[0x380fe328a5]
/lib64/libc.so.6(abort+0x175)[0x380fe34085]
/lib64/libc.so.6[0x380fe2ba1e]
/lib64/libc.so.6(__assert_perror_fail+0x0)[0x380fe2bae0]
/projects/cees/bin/celera/wgs-8.1/Linux-amd64/bin/cgw[0x4cdaf7]
/projects/cees/bin/celera/wgs-8.1/Linux-amd64/bin/cgw(_Z27ReLoadMultiAlignTFromStreamP8_IO_FILEP11MultiAlignT+0x75)[0x4e8425]
/projects/cees/bin/celera/wgs-8.1/Linux-amd64/bin/cgw(_Z25LoadMultiAlignTFromStreamP8_IO_FILE+0x24)[0x4e8ae4]
/projects/cees/bin/celera/wgs-8.1/Linux-amd64/bin/cgw(_ZN15MultiAlignStore14loadMultiAlignEib+0x20b)[0x43f09b]
/projects/cees/bin/celera/wgs-8.1/Linux-amd64/bin/cgw(_Z12GetConsensusP10GraphCGW_TiP12VarArrayTypeS2_+0x8b)[0x46b68b]
/projects/cees/bin/celera/wgs-8.1/Linux-amd64/bin/cgw[0x469a53]
/projects/cees/bin/celera/wgs-8.1/Linux-amd64/bin/cgw(_Z13OverlapChunksP10GraphCGW_Tii10PairOrientiidi+0x145)[0x46a695]
/projects/cees/bin/celera/wgs-8.1/Linux-amd64/bin/cgw[0x492286]
/projects/cees/bin/celera/wgs-8.1/Linux-amd64/bin/cgw[0x495be6]
/projects/cees/bin/celera/wgs-8.1/Linux-amd64/bin/cgw(_Z24LeastSquaresGapEstimatesP14ScaffoldGraphTP9NodeCGW_Tjj+0x135)[0x497865]
/projects/cees/bin/celera/wgs-8.1/Linux-amd64/bin/cgw(main+0x10f7)[0x419ce7]
/lib64/libc.so.6(__libc_start_main+0xfd)[0x380fe1ecdd]
/projects/cees/bin/celera/wgs-8.1/Linux-amd64/bin/cgw[0x418899]

Backtrace (demangled):

[0] 
/projects/cees/bin/celera/wgs-8.1/Linux-amd64/bin/cgw::AS_UTL_catchCrash(int, 
siginfo*, void*) + 0x27  [0x41cbb7]
[1] /lib64/libpthread.so.0() [0x3810a0f500]
[2] /lib64/libc.so.6::(null) + 0x35  [0x380fe328a5]
[3] /lib64/libc.so.6::(null) + 0x175  [0x380fe34085]
[4] /lib64/libc.so.6() [0x380fe2ba1e]
[5] /lib64/libc.so.6::(null) + 0  [0x380fe2bae0]
[6] /projects/cees/bin/celera/wgs-8.1/Linux-amd64/bin/cgw() [0x4cdaf7]
[7] 
/projects/cees/bin/celera/wgs-8.1/Linux-amd64/bin/cgw::ReLoadMultiAlignTFromStream(_IO_FILE*, 
MultiAlignT*) + 0x75  [0x4e8425]
[8] 
/projects/cees/bin/celera/wgs-8.1/Linux-amd64/bin/cgw::LoadMultiAlignTFromStream(_IO_FILE*) 
+ 0x24  [0x4e8ae4]
[9] 
/projects/cees/bin/celera/wgs-8.1/Linux-amd64/bin/cgw::MultiAlignStore::loadMultiAlign(int, 
bool) + 0x20b  [0x43f09b]
[10] 
/projects/cees/bin/celera/wgs-8.1/Linux-amd64/bin/cgw::GetConsensus(GraphCGW_T*, 
int, VarArrayType*, VarArrayType*) + 0x8b  [0x46b68b]
[11] /projects/cees/bin/celera/wgs-8.1/Linux-amd64/bin/cgw() [0x469a53]
[12] 
/projects/cees/bin/celera/wgs-8.1/Linux-amd64/bin/cgw::OverlapChunks(GraphCGW_T*, 
int, int, PairOrient, int, int, double, int) + 0x145  [0x46a695]
[13] /projects/cees/bin/celera/wgs-8.1/Linux-amd64/bin/cgw() [0x492286]
[14] /projects/cees/bin/celera/wgs-8.1/Linux-amd64/bin/cgw() [0x495be6]
[15] 
/projects/cees/bin/celera/wgs-8.1/Linux-amd64/bin/cgw::LeastSquaresGapEstimates(ScaffoldGraphT*, 
NodeCGW_T*, unsigned int, unsigned int) + 0x135  [0x497865]
[16] /projects/cees/bin/celera/wgs-8.1/Linux-amd64/bin/cgw::(null) + 
0x10f7  [0x419ce7]
[17] /lib64/libc.so.6::(null) + 0xfd  [0x380fe1ecdd]
[18] /projects/cees/bin/celera/wgs-8.1/Linux-amd64/bin/cgw() [0x418899]

GDB:

Brian, do you know what might be wrong here, and how I can fix it?

Thank you,