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tlemane / kmtricks

modular k-mer count matrix and Bloom filter construction for large read collections
GNU Affero General Public License v3.0
72 stars 7 forks source link

Killed after receive Segmentation fault:SIGSEGV(11) signal #38

Open shenweima opened 1 month ago

shenweima commented 1 month ago 
Compute SuperK   [==========================>                       ] [02h:53m:13s]                                                                                                         
Compute SuperK   [==========================>                       ] [02h:53m:13s]                                                                                                         
Compute SuperK   [==========================>                       ] [02h:53m:13s]                                                                                                         
Compute SuperK   [==========================>                       ] [02h:53m:13s]                                                                                                         
Compute SuperK   [==========================>                       ] [02h:53m:13s]                                                                                                         
Count partitions [==========================>                       ] [02h:53m:13s]                                                                                                         
[2024-07-22 20:20:44.859] [error] Killed after receive Segmentation fault:SIGSEGV(11) signal. Demangled backtrace dumped at ./kmtricks_backtrace.log. If the problem persists, please open an issue with the return of 'kmtricks infos' and the content of ./kmtricks_backtrace.log
terminate called without an active exception
[2024-07-22 20:20:44.921] [error] Killed after receive Aborted:SIGABRT(6) signal. Demangled backtrace dumped at ./kmtricks_backtrace.log. If the problem persists, please open an issue with the return of 'kmtricks infos' and the content of ./kmtricks_backtrace.log

Contents of kmtricks_backtrace.log:

Backtrace:
1 0x00002aff282b1400 (null) + 47275378938880
2 0x00002aff282b1387 gsignal + 55
3 0x00002aff282b2a78 abort + 328
4 0x00002aff27e4df9e __gnu_cxx::__verbose_terminate_handler() + 192
5 0x00002aff27e4c4e2 (null) + 47275374331106
6 0x00002aff27e462e3 std::unexpected() + 0
7 0x0000557b38bcd705 (null) + 93987721238277
8 0x00002aff282b4ce9 (null) + 47275378953449
9 0x00002aff282b4d37 (null) + 47275378953527
10 0x0000557b38c8f92a (null) + 93987722033450
11 0x00002aff282b1400 (null) + 47275378938880
12 0x0000557b38f812d1 gatb::core::bank::impl::BankFasta::Iterator::get_next_seq_from_file(gatb::core::tools::misc::Vector<char>&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >&, int, gatb::core::bank::impl::BankFasta::Iterator::CommentMode_e) + 2449
13 0x0000557b38f8187c gatb::core::bank::impl::BankFasta::Iterator::get_next_seq(gatb::core::tools::misc::Vector<char>&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >&, gatb::core::bank::impl::BankFasta::Iterator::CommentMode_e) + 92
14 0x0000557b38f8195d gatb::core::bank::impl::BankFasta::Iterator::next() + 77
15 0x0000557b38f7760a (null) + 93987725080074
16 0x0000557b38d35a30 (null) + 93987722713648
17 0x0000557b38bf9fa4 (null) + 93987721420708
18 0x00002aff27e69b55 (null) + 47275374451541
19 0x00002aff2797dea5 (null) + 47275369291429
20 0x00002aff2837996d clone + 109