Does VG giraffe works with genotype-by-sequencing (GBS) short reads data?

[kaurharpreet-umn]

Hello vgteam

I tested the VG pipeline using a graph.vg generated with 3 whole genome reference quality genomes.
I was able to align the GBS data to this graph and generate .gam files.

But I am unable to run the vg augment step. It is crashing and throwing the following error:

My code is-
./vg augment Zm1Zm4Xin.vg 102_R1_001.fastq.gam -A 102_aug.gam -i -S > Zm1Zm4Xin_102aug.vg

Error message is-

[E::bgzf_read_block] Failed to read BGZF block data at offset 64326109 expected 16384 bytes; hread returned 5649
terminate called after throwing an instance of 'std::runtime_error'
what(): [vg::io::MessageIterator] obsolete, invalid, or corrupt input at message 4213007484874 group 4213007484870
━━━━━━━━━━━━━━━━━━━━
Crash report for vg v1.48.0 "Gallipoli"
Stack trace (most recent call last):
#20 Object "/panfs/jay/groups/27/samac/kaurh/Reference/VGToolkit/VGmummer/vg", at 0x5f0e3d, in _start
#19 Object "/panfs/jay/groups/27/samac/kaurh/Reference/VGToolkit/VGmummer/vg", at 0x1ed71af, in __libc_start_main
#18 Object "/panfs/jay/groups/27/samac/kaurh/Reference/VGToolkit/VGmummer/vg", at 0x5c0ade, in main
#17 Object "/panfs/jay/groups/27/samac/kaurh/Reference/VGToolkit/VGmummer/vg", at 0xd3143b, in vg::subcommand::Subcommand::operator()(int, char**) const
#16 Object "/panfs/jay/groups/27/samac/kaurh/Reference/VGToolkit/VGmummer/vg", at 0xd35c68, in main_augment(int, char**)
#15 Object "/panfs/jay/groups/27/samac/kaurh/Reference/VGToolkit/VGmummer/vg", at 0xc07438, in std::unique_ptr<handlegraph::MutablePathMutableHandleGraph, std::default_deletehandlegraph::MutablePathMutableHandleGraph > vg::io::VPKG::load_onehandlegraph::MutablePathMutableHandleGraph(std::__cxx11::basic_string<char, std::char_traits, std::allocator > const&)
#14 Object "/panfs/jay/groups/27/samac/kaurh/Reference/VGToolkit/VGmummer/vg", at 0xc06aac, in std::_Function_handler<void (std::istream&), vg::io::VPKG::try_load_onehandlegraph::MutablePathMutableHandleGraph(std::istream&, std::__cxx11::basic_string<char, std::char_traits, std::allocator > const&)::{lambda(std::istream&)#1}>::_M_invoke(std::_Any_data const&, std::istream&)
#13 Object "/panfs/jay/groups/27/samac/kaurh/Reference/VGToolkit/VGmummer/vg", at 0xc093ef, in std::_Function_handler<void (std::istream&), vg::io::VPKG::try_load_encapsulatedhandlegraph::MutablePathMutableHandleGraph(std::istream&)::{lambda(std::istream&)#1}>::_M_invoke(std::_Any_data const&, std::istream&)
#12 Object "/panfs/jay/groups/27/samac/kaurh/Reference/VGToolkit/VGmummer/vg", at 0x1448a1e, in std::_Function_handler<void* (std::function<void (std::function<void (std::__cxx11::basic_string<char, std::char_traits, std::allocator > const&)> const&)> const&), vg::io::register_loader_saver_hash_graph()::{lambda(std::function<void (std::function<void (std::__cxx11::basic_string<char, std::char_traits, std::allocator > const&)> const&)> const&)#3}>::_M_invoke(std::_Any_data const&, std::function<void (std::function<void (std::__cxx11::basic_string<char, std::char_traits, std::allocator > const&)> const&)> const&)
#11 Object "/panfs/jay/groups/27/samac/kaurh/Reference/VGToolkit/VGmummer/vg", at 0x1412988, in vg::io::load_proto_to_graph(handlegraph::MutablePathMutableHandleGraph*, std::function<void (std::function<void (std::__cxx11::basic_string<char, std::char_traits, std::allocator > const&)> const&)> const&)
#10 Object "/panfs/jay/groups/27/samac/kaurh/Reference/VGToolkit/VGmummer/vg", at 0x14123ba, in vg::io::load_proto_to_graph(handlegraph::MutablePathMutableHandleGraph*, std::function<void (std::function<void (vg::Graph&)> const&)> const&)
#9 Object "/panfs/jay/groups/27/samac/kaurh/Reference/VGToolkit/VGmummer/vg", at 0x140f561, in std::_Function_handler<void (std::function<void (vg::Graph&)> const&), vg::io::load_proto_to_graph(handlegraph::MutablePathMutableHandleGraph*, std::function<void (std::function<void (std::__cxx11::basic_string<char, std::char_traits, std::allocator > const&)> const&)> const&)::{lambda(std::function<void (vg::Graph&)> const&)#1}>::_M_invoke(std::_Any_data const&, std::function<void (vg::Graph&)> const&)
#8 Object "/panfs/jay/groups/27/samac/kaurh/Reference/VGToolkit/VGmummer/vg", at 0xc06824, in std::_Function_handler<void (std::function<void (std::__cxx11::basic_string<char, std::char_traits, std::allocator > const&)> const&), vg::io::VPKG::try_load_encapsulatedhandlegraph::MutablePathMutableHandleGraph(vg::io::MessageIterator&)::{lambda(std::function<void (std::__cxx11::basic_string<char, std::char_traits, std::allocator > const&)> const&)#1}>::_M_invoke(std::_Any_data const&, std::function<void (std::__cxx11::basic_string<char, std::char_traits, std::allocator > const&)> const&)
#7 Object "/panfs/jay/groups/27/samac/kaurh/Reference/VGToolkit/VGmummer/vg", at 0x1bbe2fe, in vg::io::MessageIterator::operator++()
#6 Object "/panfs/jay/groups/27/samac/kaurh/Reference/VGToolkit/VGmummer/vg", at 0x5ab33f, in vg::io::MessageIterator::handle(bool, long, long) [clone .cold]
#5 Object "/panfs/jay/groups/27/samac/kaurh/Reference/VGToolkit/VGmummer/vg", at 0x1e13228, in __cxa_throw
#4 Object "/panfs/jay/groups/27/samac/kaurh/Reference/VGToolkit/VGmummer/vg", at 0x1e130c6, in std::terminate()
#3 Object "/panfs/jay/groups/27/samac/kaurh/Reference/VGToolkit/VGmummer/vg", at 0x1e1305b, in __cxxabiv1::__terminate(void (*)())
#2 Object "/panfs/jay/groups/27/samac/kaurh/Reference/VGToolkit/VGmummer/vg", at 0x5bd66a, in __gnu_cxx::__verbose_terminate_handler() [clone .cold]
#1 Object "/panfs/jay/groups/27/samac/kaurh/Reference/VGToolkit/VGmummer/vg", at 0x5c0007, in abort
#0 Object "/panfs/jay/groups/27/samac/kaurh/Reference/VGToolkit/VGmummer/vg", at 0x149611b, in raise
ERROR: Signal 6 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug.
Please include this entire error log in your bug report!

Thanks for your help!
Harpreet