Crash with CNVnator and root

[alanorth]

One of my users is trying to use root (6.08.06) via a bioinformatics tool called cnvnator (0.3.3). The invocation and crash are:

$ cnvnator -root out.root -genome genome.fna -unique  -tree  sample-sorted.bam
...
...
===========================================================
There was a crash.
This is the entire stack trace of all threads:
===========================================================
#0  0x00007f26e792527c in waitpid () from /usr/lib64/libc.so.6
#1  0x00007f26e78a8c72 in do_system () from /usr/lib64/libc.so.6
#2  0x00007f26ea241b19 in TUnixSystem::StackTrace (this=0xd27900) at /tmp/root-6.08.06/core/unix/src/TUnixSystem.cxx:2405
#3  0x00007f26ea2443ec in TUnixSystem::DispatchSignals (this=0xd27900, sig=kSigSegmentationViolation) at /tmp/root-6.08.06/core/unix/src/TUnixSystem.cxx:3625
#4  <signal handler called>
#5  0x00007f26e863fd77 in ?? () from /usr/lib64/libstdc++.so.6
#6  0x00007f26e864104e in std::string::assign(std::string const&) () from /usr/lib64/libstdc++.so.6
#7  0x000000000043ae90 in HisMaker::produceTrees(std::string*, int, std::string*, int, bool) ()
#8  0x00000000004095ef in main ()
===========================================================

The operating system is CentOS 7. For what it’s worth, I’ve also asked the CNVnator developers. Thanks!

[couet]

@alanorth

I’ve also asked the CNVnator developers.

Yes it seems to be a question for them first. Let see what they will reply.

[alanorth]

In our case it seemed to be an issue with CNVnator, the tool which is using root. For the reference of future travelers, we increased the size of the constant responsible for the maximum number of contigs, recompiled the tool, and now its running fine.

See: https://github.com/abyzovlab/CNVnator/issues/67

Thanks!