dfguan / despi Goto Github PK

(gdb) bt
#0  0x00007f2b7a01e428 in __GI_raise (sig=sig@entry=6) at ../sysdeps/unix/sysv/linux/raise.c:54
#1  0x00007f2b7a02002a in __GI_abort () at abort.c:89
#2  0x00007f2b7a65884d in __gnu_cxx::__verbose_terminate_handler() () from /usr/lib/x86_64-linux-gnu/libstdc++.so.6
#3  0x00007f2b7a6566b6 in ?? () from /usr/lib/x86_64-linux-gnu/libstdc++.so.6
#4  0x00007f2b7a656701 in std::terminate() () from /usr/lib/x86_64-linux-gnu/libstdc++.so.6
#5  0x00007f2b7a656919 in __cxa_throw () from /usr/lib/x86_64-linux-gnu/libstdc++.so.6
#6  0x00007f2b7a656ebc in operator new(unsigned long) () from /usr/lib/x86_64-linux-gnu/libstdc++.so.6
#7  0x00007f2b7a656f19 in operator new[](unsigned long) () from /usr/lib/x86_64-linux-gnu/libstdc++.so.6
#8  0x0000000000408ef0 in preprocess (refPath=refPath@entry=0x25e1c98 "deSPI-wgs.fa", kmerPath=kmerPath@entry=0x25e1c38 "database.srt", 
    taxonomyNodesPath=taxonomyNodesPath@entry=0x25e1d30 "taxonomy/nodes.dmp", giTaxidPath=giTaxidPath@entry=0x25e1c58 "", bwt_s="", 
    nkmerTID=std::vector of length 0, capacity 0, hash_index=0x7f2b39cdf010) at preprocess.cpp:1100
#9  0x000000000040de30 in build_index (p_opt=p_opt@entry=0x25e1c20) at main.cpp:443
#10 0x0000000000401f4c in main (argc=6, argv=0x7ffec6164a58) at main.cpp:635
(gdb) up 8
#8  0x0000000000408ef0 in preprocess (refPath=refPath@entry=0x25e1c98 "deSPI-wgs.fa", kmerPath=kmerPath@entry=0x25e1c38 "database.srt", 
    taxonomyNodesPath=taxonomyNodesPath@entry=0x25e1d30 "taxonomy/nodes.dmp", giTaxidPath=giTaxidPath@entry=0x25e1c58 "", bwt_s="", 
    nkmerTID=std::vector of length 0, capacity 0, hash_index=0x7f2b39cdf010) at preprocess.cpp:1100
1100            kmersSpchar* _2kmers = new kmersSpchar[endNodeNum*(_kmer - 1)];
(gdb) l
1095            heads.clear();
1096            tails.clear();
1097            //getchar();
1098            fprintf(stderr, "end node is %lu\n",endNodeNum);
1099
1100            kmersSpchar* _2kmers = new kmersSpchar[endNodeNum*(_kmer - 1)];
1101
1102            uint8_t* _2kmers_0p = new uint8_t[endNodeNum];
1103
1104            fprintf(stderr,"outputing... \n");
(gdb) p endNodeNum
$1 = 26732088398
(gdb) p _kmer-1
$2 = 30
(gdb) q