when i use cnvnator first step :cnanator - root 1.root - tree 1.bam it showed that:

There was a crash. This is the entire stack trace of all threads:

0 0x00007f1f602f24fc in waitpid () from /lib64/libc.so.6

1 0x00007f1f6026ff62 in do_system () from /lib64/libc.so.6

2 0x00007f1f61becc44 in TUnixSystem::StackTrace() () from /home/zhangweiwei/miniconda3/envs/cnvnator_env/bin/../lib/libCore.so.6.20

3 0x00007f1f61bef77e in TUnixSystem::DispatchSignals(ESignals) () from /home/zhangweiwei/miniconda3/envs/cnvnator_env/bin/../lib/libCore.so.6.20

4 5 0x00007f1f60388e78 in __memmove_ssse3_back () from /lib64/libc.so.6

6 0x0000556fcb9fc924 in std::cxx11::basic_string<char, std::char_traits, std::allocator >::_M_assign(std::cxx11::basic_string<char, std::char_traits, std::allocator > const&) ()

7 0x0000556fcba4012d in HisMaker::produceTrees(std::**cxx11::basic_string<char, std::char_traits, std::allocator >*, int, std::**cxx11::basic_string<char, std::char_traits, std::allocator >*, int, bool) ()

8 0x0000556fcb9f94e9 in main ()

===========================================================

The lines below might hint at the cause of the crash. You may get help by asking at the ROOT forum http://root.cern.ch/forum Only if you are really convinced it is a bug in ROOT then please submit a report at http://root.cern.ch/bugs Please post the ENTIRE stack trace from above as an attachment in addition to anything else that might help us fixing this issue.

5 0x00007f1f60388e78 in __memmove_ssse3_back () from /lib64/libc.so.6

6 0x0000556fcb9fc924 in std::cxx11::basic_string<char, std::char_traits, std::allocator >::_M_assign(std::cxx11::basic_string<char, std::char_traits, std::allocator > const&) ()

7 0x0000556fcba4012d in HisMaker::produceTrees(std::**cxx11::basic_string<char, std::char_traits, std::allocator >*, int, std::**cxx11::basic_string<char, std::char_traits, std::allocator >*, int, bool) ()

8 0x0000556fcb9f94e9 in main ()

and i do not know how to deal with it ,can anyone help me ?

Hello, looks like the crash is caused by ROOT. Are you able to start ROOT on its own?

Alexej Abyzov, Ph.D. Senior Associate Consultant, Associate Professor of Biomedical Informatics, Department of Quantitative Health Sciences, Center for Individualized Medicine, Mayo Clinic

Mayo Clinic, 200 1st street SW, Harwick 3-12 Rochester, MN 55905 www.abyzovlab.orghttp://www.abyzovlab.org tel: +1-(507)-538-0978

On Jan 3, 2022, at 1:26 AM, 1147843025 @.**@.>> wrote:

when i use cnvnator first step :cnanator - root 1.root - tree 1.bam it showed that:

There was a crash. This is the entire stack trace of all threads:

0 0x00007f1f602f24fc in waitpid () from /lib64/libc.so.6

1https://github.com/abyzovlab/CNVnator/pull/1 0x00007f1f6026ff62 in do_system () from /lib64/libc.so.6

2https://github.com/abyzovlab/CNVnator/pull/2 0x00007f1f61becc44 in TUnixSystem::StackTrace() () from /home/zhangweiwei/miniconda3/envs/cnvnator_env/bin/../lib/libCore.so.6.20

3https://github.com/abyzovlab/CNVnator/issues/3 0x00007f1f61bef77e in TUnixSystem::DispatchSignals(ESignals) () from /home/zhangweiwei/miniconda3/envs/cnvnator_env/bin/../lib/libCore.so.6.20

4https://github.com/abyzovlab/CNVnator/issues/4

5https://github.com/abyzovlab/CNVnator/pull/5 0x00007f1f60388e78 in __memmove_ssse3_back () from /lib64/libc.so.6

6https://github.com/abyzovlab/CNVnator/issues/6 0x0000556fcb9fc924 in std::cxx11::basic_string<char, std::char_traits, std::allocator >::_M_assign(std::cxx11::basic_string<char, std::char_traits, std::allocator > const&) ()

7https://github.com/abyzovlab/CNVnator/issues/7 0x0000556fcba4012d in HisMaker::produceTrees(std::cxx11::basic_string<char, std::char_traits, std::allocator >, int, std::cxx11::basic_string<char, std::char_traits, std::allocator >, int, bool) ()

8https://github.com/abyzovlab/CNVnator/issues/8 0x0000556fcb9f94e9 in main ()