backtrace report might help to
[...]
WA=0x24c380d0,
R=0x451243b0 "\t\t\t\t\003\003\003\003\001\001\001\001\002\002\002\002\002\002\002\001\002", '\003' <repeats 16 times>, "\001\001\001\001\002\002\002\003\003\003\003\003\003\002\002\002\002\t\002\001\003\003\003\003\003\002", Q=0x4513ca70 "", G=0x2aaaaaae50d8 "\002", sigG=0x0,
P=0x673430, wTr=0x45014898, nWinTr=0x44ff8948, RA=0x230b1010) at stitchWindowAligns.cpp:337
#390 0x0000000000446040 in stitchWindowAligns (iA=0, nA=397, Score=0, WAincl=0x67a8c0, tR2=0, tG2=0, trA=..., Lread=295, WA=0x24c380d0,
R=0x451243b0 "\t\t\t\t\003\003\003\003\001\001\001\001\002\002\002\002\002\002\002\001\002", '\003' <repeats 16 times>, "\001\001\001\001\002\002\002\003\003\003\003\003\003\002\002\002\002\t\002\001\003\003\003\003\003\002", Q=0x4513ca70 "", G=0x2aaaaaae50d8 "\002", sigG=0x0,
P=0x673430, wTr=0x45014898, nWinTr=0x44ff8948, RA=0x230b1010) at stitchWindowAligns.cpp:329
#391 0x000000000042de36 in ReadAlign::stitchPieces (this=0x230b1010, R=0x67b300, Q=0x67b320, G=0x2aaaaaae50d8 "\002", SA=..., Lread=295)
at ReadAlign_stitchPieces.cpp:405
#392 0x000000000042f3d4 in ReadAlign::mapOneRead (this=0x230b1010) at ReadAlign_mapOneRead.cpp:88
#393 0x000000000043f24c in ReadAlign::oneRead (this=0x230b1010) at ReadAlign_oneRead.cpp:67
#394 0x0000000000432660 in ReadAlignChunk::mapChunk (this=0x67a570) at ReadAlignChunk_mapChunk.cpp:25
#395 0x0000000000431f7d in ReadAlignChunk::processChunks (this=0x67a570) at ReadAlignChunk_processChunks.cpp:97
#396 0x000000000040848a in ThreadControl::threadRAprocessChunks (RAchunk=0x67a570) at ThreadControl.h:19
#397 0x0000003435007851 in start_thread () from /lib64/libpthread.so.0
#398 0x0000003434ce767d in clone () from /lib64/libc.so.6