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ERROR: Signal 6 occurred. VG has crashed
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Entering edit mode
7 months ago
philgev2 ▴ 10

Hi

When I run this command

vg pack -t 1 -x sorted_A019_chr1_dbsnp_aug.xg -g sorted_A019_chr1_dbsnp.filtered.gam -Q 5 -o ./alignment/sorted_A019_chr1_dbsnp_aug.pack

am getting below error,

vg: src/packer.cpp:865: size_t vg::Packer::average_node_quality(size_t) const: Assertion `total_node_quality(i) == 0' failed.
ERROR: Signal 6 occurred. VG has crashed. Run 'vg bugs --new' to report a bug.
Stack trace path: /tmp/vg_crash_LuVMJ2/stacktrace.txt
Please include the stack trace file in your bug report!

Stack trace

Crash report for vg v1.29.0 "Sospiro"
Stack trace (most recent call last):
13   Object "/data/sruthi/softwares/vg", at 0x63c27d, in _start
12   Object "/data/sruthi/softwares/vg", at 0x1f4dd3f, in __libc_start_main
11   Object "/data/sruthi/softwares/vg", at 0x55db18, in main
10   Object "/data/sruthi/softwares/vg", at 0xc0c5cb, in vg::subcommand::Subcommand::operator()(int, char**) const
9    Object "/data/sruthi/softwares/vg", at 0xb75a3b, in main_pack(int, char**)
8    Object "/data/sruthi/softwares/vg", at 0xd93f23, in vg::Packer::save_to_file(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)
7    Object "/data/sruthi/softwares/vg", at 0xd93b5c, in vg::Packer::serialize(std::ostream&, sdsl::structure_tree_node*, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >)
6    Object "/data/sruthi/softwares/vg", at 0xd939f3, in vg::Packer::make_compact()
5    Object "/data/sruthi/softwares/vg", at 0x1f31975, in GOMP_parallel
4    Object "/data/sruthi/softwares/vg", at 0xd99841, in vg::Packer::make_compact() [clone ._omp_fn.6]
3    Object "/data/sruthi/softwares/vg", at 0x1f5e015, in __assert_fail
2    Object "/data/sruthi/softwares/vg", at 0x55cf43, in __assert_fail_base.cold
1    Object "/data/sruthi/softwares/vg", at 0x55d073, in abort
0    Object "/data/sruthi/softwares/vg", at 0x12e238b, in raise

Any suggestions to fix the issue?

Thanks
Philge

vg • 286 views
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Entering edit mode

Please use the formatting bar (especially the code option) to present your post better. You can use backticks for inline code (`text` becomes text), or select a chunk of text and use the highlighted button to format it as a code block. I've done it for you this time.
code_formatting

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Sure. Thank you very much.

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