Crash using vg ids --join

[sc13-bioinf]

Created chr*.vg files from GRCH38 (ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/000/001/405/GCA_000001405.15_GRCh38/seqs_for_alignment_pipelines.ucsc_ids/GCA_000001405.15_GRCh38_no_alt_plus_hs38d1_analysis_set.fna.gz) and http://ftp.1000genomes.ebi.ac.uk/vol1/ftp/data_collections/1000_genomes_project/release/20190312_biallelic_SNV_and_INDEL/ALL.wgs.shapeit2_integrated_snvindels_v2a.GRCh38.27022019.sites.vcf.gz (with chromosome names prefixed with chr)

Graph files created using:

vg construct --reference ${reference_fasta_file_path} --vcf ${variants_vcf_file_path} --region ${chrom} --threads 1 > graph_ref/${chrom}.vg

Crash caused when running:
vg ids --join chr1.vg chr2.vg chr3.vg ....

terminate called after throwing an instance of 'std::runtime_error'
what(): [vg::io::MessageIterator] obsolete, invalid, or corrupt input at message 21101296091831 group 21101296091827
ERROR: Signal 6 occurred. VG has crashed. Run 'vg bugs --new' to report a bug.
Stack trace path: /tmp/vg_crash_nCOB0l/stacktrace.txt

Contents of stacktrace:

Crash report for vg v1.19.0 "Tramutola"
Stack trace (most recent call last):
#18 Object "", at 0xffffffffffffffff, in
#17 Object "/app/software/vg-v1.19.0/bin/vg", at 0x558f9b9924b9, in _start
#16 Object "/lib/x86_64-linux-gnu/libc-2.27.so", at 0x7f00dda2fb96, in __libc_start_main
#15 Object "/app/software/vg-v1.19.0/bin/vg", at 0x558f9b8c7132, in main
Source "src/main.cpp", line 74, in main [0x558f9b8c7132]
#14 Object "/app/software/vg-v1.19.0/bin/vg", at 0x558f9be65ad7, in vg::subcommand::Subcommand::operator()(int, char**) const
| Source "src/subcommand/subcommand.cpp", line 72, in operator()
Source "/usr/include/c++/7/bits/std_function.h", line 706, in operator() [0x558f9be65ad7]
703: {
704: if (_M_empty())
705: __throw_bad_function_call();
> 706: return _M_invoker(_M_functor, std::forward<_ArgTypes>(__args)...);
707: }
708:
709: #if __cpp_rtti
#13 Object "/app/software/vg-v1.19.0/bin/vg", at 0x558f9be4affc, in main_ids(int, char**)
Source "src/subcommand/ids_main.cpp", line 147, in main_ids [0x558f9be4affc]
#12 Object "/app/software/vg-v1.19.0/bin/vg", at 0x558f9c0110ba, in vg::VGset::merge_id_space()
Source "src/vg_set.cpp", line 73, in merge_id_space [0x558f9c0110ba]
#11 Object "/app/software/vg-v1.19.0/bin/vg", at 0x558f9c0108c3, in vg::VGset::transform(std::function<void (vg::VG*)>)
Source "src/vg_set.cpp", line 17, in transform [0x558f9c0108c3]
#10 Object "/app/software/vg-v1.19.0/bin/vg", at 0x558f9c0e3dc5, in vg::VG::VG(std::istream&, bool, bool)
Source "src/vg.cpp", line 25, in VG [0x558f9c0e3dc5]
#9 Object "/app/software/vg-v1.19.0/bin/vg", at 0x558f9c0e37fd, in vg::VG::from_istream(std::istream&, bool, bool)
| Source "src/vg.cpp", line 76, in for_eachvg::Graph
Source "/app/software/vg-v1.19.0/include/vg/io/stream.hpp", line 117, in from_istream [0x558f9c0e37fd]
114: template
115: void for_each(std::istream& in,
116: const std::function<void(T&)>& lambda) {
> 117: for_each(in, static_cast<const typename std::function<void(int64_t, T&)>&>([&lambda](int64_t virtual_offset, T& item) {
118: lambda(item);
119: }));
120: }
#8 Object "/app/software/vg-v1.19.0/bin/vg", at 0x558f9bba285c, in void vg::io::for_eachvg::Graph(std::istream&, std::function<void (long, vg::Graph&)> const&)
| Source "/app/software/vg-v1.19.0/include/vg/io/stream.hpp", line 108, in operator++
| 106: const std::function<void(int64_t, T&)>& lambda) {
| 107:
| > 108: for(ProtobufIterator it(in); it.has_current(); ++it) {
| 109: // For each message in the file, parse and process it with its group VO (or -1)
| 110: lambda(it.tell_group(), *it);
Source "/app/software/vg-v1.19.0/include/vg/io/protobuf_iterator.hpp", line 139, in for_eachvg::Graph [0x558f9bba285c]
137: template
138: auto ProtobufIterator::operator++() -> const ProtobufIterator& {
> 139: ++message_it;
140: fill_value();
141: return *this;
142: }
#7 Object "/app/software/vg-v1.19.0/bin/vg", at 0x558f9c338668, in vg::io::MessageIterator::operator++()
Source "/app/software/vg-v1.19.0/deps/libvgio/src/message_iterator.cpp", line 307, in operator++ [0x558f9c338668]
304: value.second = make_unique();
305: }
306: if (msgSize) {
> 307: handle(coded_in.ReadString(value.second.get(), msgSize), group_vo, item_vo);
308: }
309:
310: // Fill in the tag from the previous to make sure our value pair actually has it.
#6 Object "/app/software/vg-v1.19.0/bin/vg", at 0x558f9c337efc, in vg::io::MessageIterator::handle(bool, long, long)
Source "/app/software/vg-v1.19.0/deps/libvgio/src/message_iterator.cpp", line 418, in handle [0x558f9c337efc]
415: if (!ok) {
416: if (message_virtual_offset) {
417: throw runtime_error("[vg::io::MessageIterator] obsolete, invalid, or corrupt input at message " +
> 418: to_string(message_virtual_offset) + " group " + to_string(group_virtual_offset));
419: } else {
420: throw runtime_error("[vg::io::MessageIterator] obsolete, invalid, or corrupt input at group " +
421: to_string(group_virtual_offset));
#5 Object "/usr/lib/x86_64-linux-gnu/libstdc++.so.6.0.25", at 0x7f00de2d8d23, in __cxa_throw
#4 Object "/usr/lib/x86_64-linux-gnu/libstdc++.so.6.0.25", at 0x7f00de2d8af0, in std::terminate()
#3 Object "/usr/lib/x86_64-linux-gnu/libstdc++.so.6.0.25", at 0x7f00de2d8ab5, in
#2 Object "/usr/lib/x86_64-linux-gnu/libstdc++.so.6.0.25", at 0x7f00de2d2956, in
#1 Object "/lib/x86_64-linux-gnu/libc-2.27.so", at 0x7f00dda4e800, in abort
#0 Object "/lib/x86_64-linux-gnu/libc-2.27.so", at 0x7f00dda4ce97, in raise