forwardize_breakpoints error: failure, position X+Y is not inside node X

1. What were you trying to do?

I am trying to call variants using the VG Giraffe pipeline. Specifically I was running vg augment to include the embed new variants inside the graph.

2. What did you want to happen?

To have to output files: aug.gam & aug.vg (according the manual)

3. What actually happened?

It failed with the following error:

Reading input graph
forwardize_breakpoints error: failure, position 25303890+32 is not inside node 25303890
vg: src/augment.cpp:514: std::unordered_map<long long int, std::set<std::tuple<long long int, bool, long unsigned int> > > vg::forwardize_breakpoints(const HandleGraph*, const std::unordered_map<long long int, std::set<std::tuple<long long int, bool, long unsigned int> > >&): Assertion `false' failed.
forwardize_breakpoints error: failure, position 17366035-32 is not inside node 17366035
vg: src/augment.cpp:514: std::unordered_map<long long int, std::set<std::tuple<long long int, bool, long unsigned int> > > vg::forwardize_breakpoints(const HandleGraph*, const std::unordered_map<long long int, std::set<std::tuple<long long int, bool, long unsigned int> > >&): Assertion `false' failed.
ERROR: Signal 6 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug.
Stack trace path: /tmp/vg_crash_b0gUju/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 v1.42.0 "Obolo"
Stack trace (most recent call last) in thread 106186:
#15   Object "", at 0xffffffffffffffff, in 
#14   Object "", at 0x20a6c53, in 
#13   Object "", at 0x20008ca, in 
#12   Object "", at 0x1fa322d, in 
#11   Object "", at 0x1fa5b77, in 
#10   Object "", at 0x1f9d47a, in 
#9    Object "", at 0xcfcea5, in 
#8    Object "", at 0xb73caf, in 
#7    Object "", at 0xe24e7b, in 
#6    Object "", at 0xe24b49, in 
#5    Object "", at 0xe1de96, in 
#4    Object "", at 0x1fcf0d5, in 
#3    Object "", at 0x5d3149, in 
#2    Object "", at 0x5d3221, in 
#1    Object "", at 0x1fd56e5, in 
#0    Object "", at 0x20020ec, in

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

The command that I was running was

vg augment -A .my_sample.giraffe.aug.gam -m 5 -q 20 -p -v my_ref.vg my_sample.giraffe.gam  > my_ref.aug.vg

The data was Illumina resequenced data mapped with vg giraffe with a reference produced with vg construct and vg index on a reference_genome and a VCF file with structural variants made with the combiSV approach using long read sequencing on two genotypes.

6. What does running vg version say?

vg version v1.42.0 "Obolo"
Compiled with g++ (Ubuntu 11.2.0-19ubuntu1) 11.2.0 on Linux
Linked against libstd++ 20220324
Built by ubuntu@ip-172-31-12-246

vgteam / vg

forwardize_breakpoints error: failure, position X+Y is not inside node X #3718