Crash during vg mcmc

[JoshuaDanielRubin]

1. What were you trying to do?

I was trying to use vg mcmc to infer haplotypes from a mgam file.

2. What did you want to happen?

I wanted the program to output a vcf.

3. What actually happened?

The program crashed and gave me this message.

ERROR: Signal 11 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug.
Stack trace path: /tmp/vg_crash_Le1Cfk/stacktrace.txt
Please include the stack trace file in your bug 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 v1.33.0 "Moscona"
Stack trace (most recent call last):
#6    Object "/storage/ctools/vg_1.33.0/vg", at 0x5a79ed, in _start
#5    Object "/storage/ctools/vg_1.33.0/vg", at 0x1b9b76f, in __libc_start_main
#4    Object "/storage/ctools/vg_1.33.0/vg", at 0x57d324, in main
#3    Object "/storage/ctools/vg_1.33.0/vg", at 0xba24fb, in vg::subcommand::Subcommand::operator()(int, char**) const
#2    Object "/storage/ctools/vg_1.33.0/vg", at 0xaf800f, in main_mcmc(int, char**)
#1    Object "/storage/ctools/vg_1.33.0/vg", at 0xcebd1b, in vg::MCMCGenotyper::run_genotype(std::vector<vg::multipath_alignment_t, std::allocator<vg::multipath_alignment_t> > const&, double) const
#0    Object "/storage/ctools/vg_1.33.0/vg", at 0xe506a8, in vg::PhasedGenome::optimal_score_on_genome(vg::multipath_alignment_t const&, vg::VG&)

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

I ran the following command

$vg_path mcmc data/toy.mgam data/toy.vg data/toy.snarls -i 10 -v data/test.vcf > /dev/null

toy.vg was constructed from an MSA, and toy.mgam was produced with the command

$vg_path mpmap -x data/toy.xg -g data/toy.gcsa -f data/NA18510.fq > data/toy.mgam

6. What does running vg version say?

vg version v1.33.0 "Moscona"
Compiled with g++ (Ubuntu 9.3.0-17ubuntu1~20.04) 9.3.0 on Linux
Linked against libstd++ 20200808
Built by anovak@octagon

I also reproduced the error on another machine using the most recent vg version (Cibotolla).

[glennhickey]

vg mcmc neither works nor is under active development at the moment, unfortunately.

we should probably make this more clear in vg help and/or vg mcmc -h.