VG Giraffe crashes during mate alignment

[EddieFerro]

1. What were you trying to do? Align reads to a graph built on a VCF from 8 samples.

2. What did you want to happen? For the alignment to be completed.

3. What actually happened? The program crashes within a couple of minutes of starting it with "ERROR: Signal 11 occurred."

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 v1.45.0 "Alpicella"
Stack trace (most recent call last) in thread 127794:
#11   Object "", at 0xffffffffffffffff, in 
#10   Object "/apps/vg/1.45.0/bin/vg", at 0x1f3c532, in __clone
#9    Object "/apps/vg/1.45.0/bin/vg", at 0x14498f8, in start_thread
#8    Object "/apps/vg/1.45.0/bin/vg", at 0x1e70d3d, in gomp_thread_start
#7    Object "/apps/vg/1.45.0/bin/vg", at 0x10412e5, 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 "/apps/vg/1.45.0/bin/vg", at 0xd371e8, in std::_Function_handler<void (vg::Alignment&, vg::Alignment&), main_giraffe(int, char**)::{lambda()#1}::operator()() const::{lambda(vg::Alignment&, vg::Alignment&)#6}>::_M_invoke(std::_Any_data const&, vg::Alignment&, vg::Alignment&)
#5    Object "/apps/vg/1.45.0/bin/vg", at 0xf9df64, 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> > >&)
#4    Object "/apps/vg/1.45.0/bin/vg", at 0xf98f15, in vg::MinimizerMapper::map_paired(vg::Alignment&, vg::Alignment&)
#3    Object "/apps/vg/1.45.0/bin/vg", at 0xf8cafa, 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)> const&, std::function<void (unsigned long)> const&, std::function<void (unsigned long)> const&) const [clone .constprop.0]
#2    Object "/apps/vg/1.45.0/bin/vg", at 0xf86ada, in std::_Function_handler<bool (unsigned long), vg::MinimizerMapper::map_paired(vg::Alignment&, vg::Alignment&)::{lambda(unsigned long)#20}>::_M_invoke(std::_Any_data const&, unsigned long&&)
#1    Object "/apps/vg/1.45.0/bin/vg", at 0x1b43861, in vg::Alignment::Alignment(vg::Alignment const&)
#0    Object "/apps/vg/1.45.0/bin/vg", at 0x1b4eb81, in void google::protobuf::internal::RepeatedPtrFieldBase::MergeFrom<google::protobuf::RepeatedPtrField<vg::Path>::TypeHandler>(google::protobuf::internal::RepeatedPtrFieldBase const&)

5. What data and command can the vg dev team use to make the problem happen? I used a VCF compiled from 8 samples and the GRCh38 reference file.

6. What does running vg version say?

vg version v1.45.0 "Alpicella"
Compiled with g++ (Ubuntu 9.4.0-1ubuntu1~20.04.1) 9.4.0 on Linux
Linked against libstd++ 20210601

[jeizenga]

Are you able to share the data that led to this crash?

[EddieFerro]

Sure, I can provide the Giraffe index files (.min, .dist, .gbz) or the VCF I used, but they are too large to be attached to this comment. Let me know what data you would need and where I can send it.