Source: kallisto
Followup-For: Bug #1118526
X-Debbugs-Cc: [email protected]
Single-stepping got to the abort point:
3828 cout << "CompactedDBG::construct(): Before split: " <<
unitigsBefore << " unitigs" << endl;
(gdb) n
CompactedDBG::construct(): Before split: 41 unitigs
3829 cout << "CompactedDBG::construct(): After split (1/" <<
(reference_mode ? "1" : "2" ) << "): " << unitigsAfter1 << " unitigs" << endl;
(gdb) n
CompactedDBG::construct(): After split (1/1): 26 unitigs
3831 cout << "CompactedDBG::construct(): Unitigs split: " <<
unitigSplit.first << endl;
(gdb) n
CompactedDBG::construct(): Unitigs split: 0
3832 cout << "CompactedDBG::construct(): Unitigs deleted: " <<
unitigSplit.second << endl;
(gdb) n
CompactedDBG::construct(): Unitigs deleted: 15
3834 cout << endl << "CompactedDBG::construct(): Joining unitigs" <<
endl;
(gdb) n
CompactedDBG::construct(): Joining unitigs
CompactedDBG<void, void>::construct (this=this@entry=0x7fffffff9140, opt=...,
bf=..., r=..., nb_unique_minimizers=nb_unique_minimizers@entry=22,
nb_non_unique_minimizers=<optimized out>) at
./ext/bifrost/src/KmerHashTable.hpp:170
170 inline size_t size() const {
(gdb) n
CompactedDBG<void, void>::construct (this=this@entry=0x7fffffff9140, opt=...,
bf=..., r=..., nb_unique_minimizers=nb_unique_minimizers@entry=22,
nb_non_unique_minimizers=<optimized out>) at
./ext/bifrost/src/CompactedDBG.tcc:3839
3839 const int unitigsAfter3 = size();
(gdb) n
3843 cout << "CompactedDBG::construct(): After join: " <<
unitigsAfter3 << " unitigs" << endl;
(gdb) n
3839 const int unitigsAfter3 = size();
(gdb) n
3843 cout << "CompactedDBG::construct(): After join: " <<
unitigsAfter3 << " unitigs" << endl;
(gdb) n
CompactedDBG::construct(): After join: 26 unitigs
3844 cout << "CompactedDBG::construct(): Joined " << joined << "
unitigs" << endl;
(gdb) n
CompactedDBG::construct(): Joined 0 unitigs
3862 }
(gdb) n
CompactedDBG<void, void>::construct (this=this@entry=0x7fffffff9140, opt=...,
bf=..., r=..., nb_unique_minimizers=nb_unique_minimizers@entry=22,
nb_non_unique_minimizers=<optimized out>) at
/usr/include/c++/15/bits/new_allocator.h:104
104 ~__new_allocator() _GLIBCXX_USE_NOEXCEPT { }
(gdb) n
CompactedDBG<void, void>::build (this=this@entry=0x7fffffff9140, opt=...) at
./ext/bifrost/src/CompactedDBG.tcc:709
709 r.clear();
(gdb) n
711 }
(gdb) n
corrupted size vs. prev_size
Thread 1 "kallisto" received signal SIGABRT, Aborted.
