vg-arm v1.70.0 crash

[StanelyFu1205]

1. What were you trying to do?
when I ran the following command:

    vg giraffe -p -t ${thread_num} \
           --read-group 'SM:${SAMPLE_ID}' \
           -Z $(pwd)/VG_SVcalling/gui_graph/guiyu.gbz \
           -d $(pwd)/VG_SVcalling/gui_graph/guiyu.dist \
           -m $(pwd)/VG_SVcalling/gui_graph/guiyu.min \
           -N ${SAMPLE_ID}  \
           -f ${data_dir}/${SAMPLE_ID}.clean.R1.fq.gz \
           -f ${data_dir}/${SAMPLE_ID}.clean.R2.fq.gz \
           > ${gam_dir}/${SAMPLE_ID}.gam

I used vg-arm on ubuntu 20.04.

2. What did you want to happen?
ran successfully

3. What actually happened?
got following Crach report

4. If you got a line like Stack trace path: /somewhere/on/your/computer/stacktrace.txt, please copy-paste the contents of that file here:

Crash report for vg v1.70.0 "Zebedassi"
Caught signal 11 raised at address 0x1017744; tracing with backward-cpp
Stack trace (most recent call last):
#17   Object "/vol8/home/cssc_fx/appsoftware/vg/vg", at 0x4551ef, in _start
#16   Object "/vol8/home/cssc_fx/appsoftware/vg/vg", at 0x1e913a3, in __libc_start_main
#15   Object "/vol8/home/cssc_fx/appsoftware/vg/vg", at 0x1e91023, in __libc_start_call_main
#14   Object "/vol8/home/cssc_fx/appsoftware/vg/vg", at 0x455d13, in vg_main(int, char**)
#13   Object "/vol8/home/cssc_fx/appsoftware/vg/vg", at 0xca65c3, in vg::subcommand::Subcommand::operator()(int, char**) const
#12   Object "/vol8/home/cssc_fx/appsoftware/vg/vg", at 0xbd71fb, in main_giraffe(int, char**)
#11   Object "/vol8/home/cssc_fx/appsoftware/vg/vg", at 0xc57bfb, in std::_Function_handler<void (std::function<void ()> const&), vg::subcommand::TickChainLink::get_iterator()::{lambda(std::function<void ()> const&)#1}>::_M_invoke(std::_Any_data const&, std::function<void ()> const&)
#10   Object "/vol8/home/cssc_fx/appsoftware/vg/vg", at 0xbcaf3b, in main_giraffe(int, char**)::{lambda()#1}::operator()() const
#9    Object "/vol8/home/cssc_fx/appsoftware/vg/vg", at 0xd5af57, in vg::fastq_paired_two_files_for_each_parallel_after_wait(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, std::function<void (vg::Alignment&, vg::Alignment&)>, std::function<bool ()>, bool, unsigned long)
#8    Object "/vol8/home/cssc_fx/appsoftware/vg/vg", at 0x1e6c5b3, in GOMP_parallel
#7    Object "/vol8/home/cssc_fx/appsoftware/vg/vg", at 0xd6a4ff, in unsigned long vg::io::paired_for_each_parallel_after_wait<vg::Alignment>(std::function<bool (vg::Alignment&, vg::Alignment&)>, std::function<void (vg::Alignment&, vg::Alignment&)>, std::function<bool ()>, unsigned long) [clone ._omp_fn.0]
#6    Object "/vol8/home/cssc_fx/appsoftware/vg/vg", at 0x1e7083b, in GOMP_task
#5    Object "/vol8/home/cssc_fx/appsoftware/vg/vg", at 0xd6a887, in unsigned long vg::io::paired_for_each_parallel_after_wait<vg::Alignment>(std::function<bool (vg::Alignment&, vg::Alignment&)>, std::function<void (vg::Alignment&, vg::Alignment&)>, std::function<bool ()>, unsigned long) [clone ._omp_fn.1]
#4    Object "/vol8/home/cssc_fx/appsoftware/vg/vg", at 0xbcba8b, in std::_Function_handler<void (vg::Alignment&, vg::Alignment&), main_giraffe(int, char**)::{lambda()#1}::operator()() const::{lambda(vg::Alignment&, vg::Alignment&)#9}>::_M_invoke(std::_Any_data const&, vg::Alignment&, vg::Alignment&)
#3    Object "/vol8/home/cssc_fx/appsoftware/vg/vg", at 0x102a023, in vg::MinimizerMapper::map_paired(vg::Alignment&, vg::Alignment&, std::vector<std::pair<vg::Alignment, vg::Alignment>, std::allocator<std::pair<vg::Alignment, vg::Alignment> > >&)
#2    Object "/vol8/home/cssc_fx/appsoftware/vg/vg", at 0x1026283, in vg::MinimizerMapper::map_paired(vg::Alignment&, vg::Alignment&)
#1    Object "/vol8/home/cssc_fx/appsoftware/vg/vg", at 0x101d61b, in void vg::MinimizerMapper::process_until_threshold_c<double>(unsigned long, std::function<double (unsigned long)> const&, std::function<bool (unsigned long, unsigned long)> const&, double, unsigned long, unsigned long, vg::LazyRNG&, std::function<bool (unsigned long, unsigned long)> const&, std::function<void (unsigned long)> const&, std::function<void (unsigned long)> const&) const [clone .constprop.0]
#0    Object "/vol8/home/cssc_fx/appsoftware/vg/vg", at 0x1017744, in std::_Function_handler<void (unsigned long), vg::MinimizerMapper::map_paired(vg::Alignment&, vg::Alignment&)::{lambda(unsigned long)#21}>::_M_invoke(std::_Any_data const&, unsigned long&&)

Library locations:
ERROR: Signal 11 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug.
━━━━━━━━━━━━━━━━━━━━
Context dump:
	Thread 0: E150022577L1C004R00601644799/1, E150022577L1C004R00601644799/2
Found 1 threads with context.

5. What data and command can the vg dev team use to make the problem happen?

6. What does running vg version say?

vg version v1.70.0 "Zebedassi"
Compiled with g++ (Ubuntu 11.4.0-1ubuntu1~22.04.2) 11.4.0 on Linux
Linked against libstd++ 20230528
Using HTSlib headers 101990, library 1.19.1
Built by root@buildkitsandbox

[adamnovak]

I'm not sure this is necessarily an ARM-Linux-only problem. (Hopefully it isn't, because we don't have any ARM Linux hosts large enough for full-genome read mapping, which will make debugging challenging.)

There's nothing in the stack trace that really illuminates why we get a segfault here; I think to debug this we will have to try and replicate the issue ourselves under the debugger.

Are you able to share your input graph files (guiyu.gbz/.dist/.min) and the FASTQ records for read pair E150022577L1C004R00601644799/1 and /2?