vg pack error

[QiaoYJYJ]

1. What were you trying to do?

I got an error when using vg pack. I run vg pack after the giraffe mapping was completed

2. What did you want to happen?

I have got the gam file by giraffe and I further want to get pack file to calculate per base-pair coverage

3. What actually happened?

vg: src/packer.cpp:883: size_t vg::Packer::average_node_quality(size_t) const: Assertion `total_node_quality(i) == 0' failed.
Crash report for vg
v1.48.0 "Gallipoli"
Crash report for vg v1.48.0 "Gallipoli"
v1.48.0 "Gallipoli"
v1.48.0 "Gallipoli"
Crash report for vg v1.48.0 "Gallipoli"
Stack trace (most recent call last) in thread 3858670:
0x6 Object "/home/hmj/miniconda3/bin/vg", at 0x149621f, in
#0x8 Object "/home/hmj/miniconda3/bin/vg", at 0x5c0007, in abort
#0x7 Object "/home/hmj/miniconda3/bin/vg", at 0x149611b, in raise
#0x5 Object "/home/hmj/miniconda3/bin/vg", at 0x13293e9#0x5 Object "/home/hmj/miniconda3/bin/vg", at 0x13293e9, in vg::emit_stacktrace(int, siginfo_t*, void*)
, in vg::emit_stacktrace(int, siginfo_t*, void*)
#0x5 Object "/home/hmj/miniconda3/bin/vg", at 0x13293e9#0x5 Object "/home/hmj/miniconda3/bin/vg", at 0x13293e9, in vg::emit_stacktrace(int, siginfo_t*, void*)
, in vg::emit_stacktrace(int, siginfo_t*, void*)
#0x5 Object "/home/hmj/miniconda3/bin/vg", at 0x13293e9, in vg::emit_stacktrace(int, siginfo_t*, void*)
#0x5 Object "/home/hmj/miniconda3/bin/vg", at 0x13293e9, in vg::emit_stacktrace(int, siginfo_t*, void*)
#0x5 Object "/home/hmj/miniconda3/bin/vg", at 0x13293e9, in vg::emit_stacktrace(int, siginfo_t*, void*)
#0x5 Object "/home/hmj/miniconda3/bin/vg", at 0x13293e9, in vg::emit_stacktrace(int, siginfo_t*, void*)
#0x5 Object "/home/hmj/miniconda3/bin/vg", at 0x13293e9, in vg::emit_stacktrace(int, siginfo_t*, void*)
#0x5 Object "/home/hmj/miniconda3/bin/vg", at 0x13293e9, in vg::emit_stacktrace(int, siginfo_t*, void*)
#0x5 Object "/home/hmj/miniconda3/bin/vg", at 0x13293e9, in vg::emit_stacktrace(int, siginfo_t*, void*)
#0x5 Object "/home/hmj/miniconda3/bin/vg", at 0x13293e9, in vg::emit_stacktrace(int, siginfo_t*, void*)
#0x5 Object "/home/hmj/miniconda3/bin/vg", at 0x13293e9, in vg::emit_stacktrace(int, siginfo_t*, void*)
#0x5 Object "/home/hmj/miniconda3/bin/vg", at 0x13293e9, in vg::emit_stacktrace(int, siginfo_t*, void*)
#0x5 Object "/home/hmj/miniconda3/bin/vg", at 0x13293e9, in vg::emit_stacktrace(int, siginfo_t*, void*)
#0x5 Object "/home/hmj/miniconda3/bin/vg", at 0x13293e9, in vg::emit_stacktrace(int, siginfo_t*, void*)
#0x7 Object "/home/hmj/miniconda3/bin/vg", at 0x149611b, in raise
#0 Object "/home/hmj/miniconda3/bin/vg", at 0x1a748ff, in dwfl_report_module
ERROR: Signal 0x6 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!

Segmentation fault (core dumped)

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:

Stack trace (most recent call last) in thread 3858670:
Stack trace (most recent call last) in thread 3858670:
Stack trace (most recent call last) in thread 3858670:
Stack trace (most recent call last) in thread 3858670:
Stack trace (most recent call last) in thread 3858670:
Stack trace (most recent call last) in thread 3858670:
Stack trace (most recent call last) in thread Stack trace (most recent call last)Stack trace (most recent call last)3858670:
in thread Stack trace (most recent call last)Stack trace (most recent call last) in thread in thread Stack trace (most recent call last)Stack trace (most recent call last)Stack trace (most recent call last)Stack trace (most recent call last)3858670:
in thread Stack trace (most recent call last)Stack trace (most recent call last)Stack trace (most recent call last)Stack trace (most recent call last)Stack trace (most recent call last) in thread Stack trace (most recent call last) in thread 3858670Stack trace (most recent call last) in thread 3858670:
Stack trace (most recent call last) in thread 3858670:
in thread Stack trace (most recent call last) in thread 3858670Stack trace (most recent call last) in thread 3858670:
Stack trace (most recent call last) in thread 3858670:
in thread 3858670:
3858670Stack trace (most recent call last)Stack trace (most recent call last) in thread 3858670:
3858670:
:
Stack trace (most recent call last) in thread 3858670:
in thread 3858670:
in thread :
in thread 3858670:
:
in thread 3858670:
in thread 3858670:
3858670:
in thread 3858670:
3858670:
Stack trace (most recent call last) in thread 3858670:
3858670Stack trace (most recent call last)Stack trace (most recent call last) in thread 38586703858670:
in thread 3858670 in thread :
:
3858670:
:

Crash report for vg #v1.48.0 "Gallipoli"

#12 Object "", at 12 Object "", at 00Stack trace (most recent call last)
Crash report for vg v1.48.0 "Gallipoli"
, in
, in Stack trace (most recent call last) in thread 3858657:
Crash report for vg v1.48.0 "Gallipoli" in thread

Crash report for vg

Crash report for vg
Crash report for vg v1.48.0 "Gallipoli"v1.48.0 "Gallipoli"v1.48.0 "Gallipoli"

Crash report for vg Crash report for vg v1.48.0 "Gallipoli"
16 Object "
Crash report for vg 3858677v1.48.0 "Gallipoli"
Stack trace (most recent call last) in thread Stack trace (most recent call last) in thread 3858652v1.48.0 "Gallipoli"
Stack trace (most recent call last) in thread Stack trace (most recent call last)38586683858674:

", at Stack trace (most recent call last) in thread
Crash report for vg v1.48.0 "Gallipoli"
Crash report for vg

:
#Stack trace (most recent call last) in thread #160xffffffffffffffff, in

Crash report for vg v1.48.0 "Gallipoli"

:
#16 Object "", at 0xffffffffffffffff, in
Object "

Crash report for vg v1.48.0 "Gallipoli"Stack trace (most recent call last)Crash report for vg Stack trace (most recent call last) in thread 3858663:
#16 Object "", at :
#", at 0xffffffffffffffff, in in thread v1.48.0 "Gallipoli" in thread 3858663:

Crash report for vg
v1.48.0 "Gallipoli"
Stack trace (most recent call last) in thread 3858675:
3858664:

Crash report for vg
Crash report for vg v1.48.0 "Gallipoli"
#0x10 Object "", at 0xffffffffffffffff, in
16 Object "", at 0xffffffffffffffff, in

Crash report for vg 3858649:
#0x10 Object "", at 0xffffffffffffffff, in

Crash report for vg 0x10v1.48.0 "Gallipoli"v1.48.0 "Gallipoli"

Crash report for vg
Crash report for vg v1.48.0 "Gallipoli"v1.48.0 "Gallipoli"
v1.48.0 "Gallipoli"0xffffffffffffffff, in #3858670
Crash report for vg
Stack trace (most recent call last) in thread 3858651

Crash report for vg Stack trace (most recent call last):
#16 Object "", at
37v1.48.0 "Gallipoli"

16 Object "", at v1.48.0 "Gallipoli"
Stack trace (most recent call last) in thread 3858678:
Stack trace (most recent call last) in thread 3858653
Crash report for vg
Object "", at 0, in
#36Stack trace (most recent call last) in thread 3858666:
Stack trace (most recent call last) in thread 3858659:
#16 Object "", at :
#Stack trace (most recent call last):
0xffffffffffffffff Object " Object "Stack trace (most recent call last) in thread #
Stack trace (most recent call last)#0x10v1.48.0 "Gallipoli"
:
#0x25 Object "#
, in
Stack trace (most recent call last) in thread 0x3ae0e6:
0xffffffffffffffff, in
3858659:
#16 Object "", at 0xffffffffffffffff, in
Crash report for vg Stack trace (most recent call last) in thread #0xffffffffffffffff0x3ae0ea16 Object "", at 0xffffffffffffffff, in
v1.48.0 "Gallipoli"

Crash report for vg Stack trace (most recent call last) in thread 3858655:
#160x10 Object "", at
, in v1.48.0 "Gallipoli"
Stack trace (most recent call last)", at ", at 0x10", at 0, in
#0 Object "", at 0, in
#0 0xffffffffffffffff, in
in thread 0x3ae0e4:
:
in thread 0x3ae0e9:

Object "16 Object "", at

#0x25 Object "", at 00, in 0xffffffffffffffff, in
0x10 Object "", at 0xffffffffffffffff Object "", at 0xffffffffffffffff, in
:
#0x10 Object "", at 0xffffffffffffffff, in

Crash report for vg , in v1.48.0 "Gallipoli"
Crash report for vg
Object "", at 0xffffffffffffffff, in
#0x10 Object "", at 0xffffffffffffffff, in

#, in 0Crash report for vg v1.48.0 "Gallipoli"v1.48.0 "Gallipoli"#0
Crash report for vg Stack trace (most recent call last)v1.48.0 "Gallipoli"
0 ", at 0xffffffffffffffff
Stack trace (most recent call last) in thread v1.48.0 "Gallipoli"
in thread
Stack trace (most recent call last) in thread 0x3ae0ed:

Object "", at Object "00x3ae0da:
#0x10 Object "", at 0xffffffffffffffff, in
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#", at 0xffffffffffffffff, in Object ", in , in Stack trace (most recent call last)Stack trace (most recent call last)0 Object "", at Stack trace (most recent call last) in thread 0x3ae0ef#0x3ae0f0
0, in
#0 Object "", at 0, in :
in thread 0x3ae0e5:

in thread 0x3ae0de

:

#0 Object "", at 0, in
#0 Object "", at 0, in
#0 Object "", at 00x10 Object "", at 0xffffffffffffffff, in
0x10 Object "", at 0xffffffffffffffff, in
#, in
#0 Object "", at 0:
0x10#0x10
#, in 0x10 Object "", at 0xffffffffffffffff, in Object "", at Object "", at ", at 0xffffffffffffffff0
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#0 Object "0, in
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#0 Object "", at #0 Object "", at 0, in
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#0 Object "", at 0, in
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#0 Object "", at 0, in Object "0, in
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#0 Object "", at 0, in Object "", at 0, in
#0 ", at 0, in Object "", at 0, in

#0 Object "", at 0
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#", at #0 Object "", at 0, in
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#0 #0 Object "", at Object "", at 0, in

#0 Object "", at 0#0, in 0 Object "", at 0, in
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#0 Object "", at , in
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#0 Object "", at 0, in
#0 Object "#0 Object "", at 0, in
#0 ", at 0, in
#0 Object " Object "", at 0, in
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#0x10 Object "", at #, in 0xffffffffffffffff, in
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#0 Object "", at 0, in
Object "", at 0xffffffffffffffff#, in
0 Object "", at 0, in
#0 Object "", at 0, in
#0 Object "", at 0, in
#0 Object "", at 0, in
#0x10 Object "", at 0xffffffffffffffff, in
#0xf Object "/home/hmj/miniconda3/bin/vg", at 0x1f8f7f2, in __clone#0xf#0xf#0xf Object "/home/hmj/miniconda3/bin/vg", at 0x1f8f7f2, in __clone
Object "/home/hmj/miniconda3/bin/vg", at 0xd15bc8, in
Object "/home/hmj/miniconda3/bin/vg", at 0x1f8f7f2, in __clonemain_pack(int, char**)

#0xb Object "/home/hmj/miniconda3/bin/vg", at 0xf0fa46, in vg::Packer::average_node_quality(unsigned long) const
##0xf####0xf###0xf Object "/home/hmj/miniconda3/bin/vg", at 0x1f8f7f2, in __clone#0xf Object "/home/hmj/miniconda3/bin/vg", at 0x1f8f7f2, in __clone
0xf Object "/home/hmj/miniconda3/bin/vg", at 0x1f8f7f2, in #0xf Object "##0xf Object "/home/hmj/miniconda3/bin/vg", at 0x1f8f7f2, in __clone
#0xf Object "/home/hmj/miniconda3/bin/vg", at 0x1f8f7f2, in __clone
#0xf Object "/home/hmj/miniconda3/bin/vg", at 0x1f8f7f2#
0xf Object "/home/hmj/miniconda3/bin/vg", at 0x1f8f7f2, in #0xf Object "/home/hmj/miniconda3/bin/vg Object "/home/hmj/miniconda3/bin/vg0xf Object "/home/hmj/miniconda3/bin/vg", at 0x1f8f7f2, in __clone#0xf#0xb Object "/home/hmj/miniconda3/bin/vg", at 0xf0fa46, in vg::Packer::average_node_quality(unsigned long) const
0xf Object "/home/hmj/miniconda3/bin/vg", at 0x1f8f7f2, in __clone
__clone__clone
##0xf Object "#0xf Object "/home/hmj/miniconda3/bin/vg", at 0x1f8f7f2, in __clone

", at 0x1f8f7f2, in __clone
0xf Object "/home/hmj/miniconda3/bin/vg", at 0x1f8f7f2, in #0xf Object "/home/hmj/miniconda3/bin/vg", at 0x1f8f7f2, in #0xf Object "/home/hmj/miniconda3/bin/vg", at 0x1f8f7f2
__clone
#0xf Object "#0xf Object "/home/hmj/miniconda3/bin/vg", at 0x1f8f7f2, in __clone
0xf Object "/home/hmj/miniconda3/bin/vg", at /home/hmj/miniconda3/bin/vg0xf0xf Object "/home/hmj/miniconda3/bin/vg", at 0x1f8f7f2, in __clone
/home/hmj/miniconda3/bin/vg", at 0x1f8f7f2, in 0xf Object "", at Object "/home/hmj/miniconda3/bin/vg", at 0x1f8f7f2, in __clone
", at __clone, in __clone
/home/hmj/miniconda3/bin/vg", at 0x1f8f7f2, in __clone
, in __clone0x1f8f7f2, in Object " Object "/home/hmj/miniconda3/bin/vg", at 0x1f8f7f2, in __clone

0x1f8f7f2, in __clone
0x1f8f7f2, in __clone

__clone
__clone
/home/hmj/miniconda3/bin/vg", at 0x1f8f7f2, in __clone
/home/hmj/miniconda3/bin/vg", at 0x1f8f7f2, in __clone
#0xf Object "/home/hmj/miniconda3/bin/vg", at 0x1f8f7f2, in __clone
#0xa Object "/home/hmj/miniconda3/bin/vg", at 0x1ee7555, in __assert_fail
#0xa Object "/home/hmj/miniconda3/bin/vg", at 0x1ee7555, in __assert_fail
####0xe Object "#0xe#0xe#0xe Object "/home/hmj/miniconda3/bin/vg", at 0x1492898, in start_thread
Object "/home/hmj/miniconda3/bin/vg", at 0x1492898, in start_thread
#0xe Object "/home/hmj/miniconda3/bin/vg0xe Object "/home/hmj/miniconda3/bin/vg", at 0x1492898, in start_thread0xe Object "/home/hmj/miniconda3/bin/vg#0xe Object "/home/hmj/miniconda3/bin/vg", at 0x1492898, in start_thread

#0xe Object "/home/hmj/miniconda3/bin/vg", at 0x1492898, in start_thread
Object "/home/hmj/miniconda3/bin/vg", at 0x1492898, in start_thread
/home/hmj/miniconda3/bin/vg", at 0x1492898, in start_thread
", at 0x1492898, in start_thread0xe Object "/home/hmj/miniconda3/bin/vg", at 0x1492898, in ", at
start_thread
0x1492898, in start_thread
##0xe Object "/home/hmj/miniconda3/bin/vg", at 0x1492898, in start_thread
#0xe Object "/home/hmj/miniconda3/bin/vg", at 0x1492898, in start_thread
0xe Object "/home/hmj/miniconda3/bin/vg", at ###0xe Object "#0xe Object "/home/hmj/miniconda3/bin/vg", at 0x1492898, in start_thread
#0xe Object "/home/hmj/miniconda3/bin/vg", at 0x14928980xe Object "#0xe##0xe Object "/home/hmj/miniconda3/bin/vg", at 0x1492898#0xe Object "/home/hmj/miniconda3/bin/vg#0xe Object "/home/hmj/miniconda3/bin/vg", at 0x1492898#0xe Object "/home/hmj/miniconda3/bin/vg", at 0x1492898, in /home/hmj/miniconda3/bin/vg", at #0xe Object "/home/hmj/miniconda3/bin/vg0x1492898, in start_thread
", at 0x1492898, in start_thread Object "/home/hmj/miniconda3/bin/vg", at 0x1492898, in , in start_thread0xe Object "
", at 0x1492898, in start_thread
#0xe Object "start_thread
0x1492898, in , in start_thread

/home/hmj/miniconda3/bin/vg/home/hmj/miniconda3/bin/vg", at /home/hmj/miniconda3/bin/vg", at 0x1492898, in start_threadstart_thread, in ", at start_thread

start_thread
0xe Object "/home/hmj/miniconda3/bin/vg", at 0x14928980x1492898
0x1492898, in , in start_thread
start_thread
, in start_thread
#0xe Object "/home/hmj/miniconda3/bin/vg", at 0x1492898, in start_thread
#0xe Object "/home/hmj/miniconda3/bin/vg", at 0x1492898, in start_thread
#0x9 Object "/home/hmj/miniconda3/bin/vg", at 0x5bfed7, in __assert_fail_base.cold
#0xe Object "/home/hmj/miniconda3/bin/vg", at 0x1492898, in start_thread
#0xe Object "/home/hmj/miniconda3/bin/vg", at 0x1492898, in start_thread
#0x9 Object "/home/hmj/miniconda3/bin/vg", at 0x5bfed7, in __assert_fail_base.cold
#0x8 Object "/home/hmj/miniconda3/bin/vg", at 0x5c0007, in abort
#0xd Object "/home/hmj/miniconda3/bin/vg", at 0x1ec3ffd, in gomp_thread_start
#0xd Object "/home/hmj/miniconda3/bin/vg", at 0x1ec3ffd, in gomp_thread_start
#0xd Object "/home/hmj/miniconda3/bin/vg", at 0x1ec3ffd, in gomp_thread_start
#0xd Object "/home/hmj/miniconda3/bin/vg", at 0x1ec3ffd, in gomp_thread_start
###0xd Object "/home/hmj/miniconda3/bin/vg", at 0x1ec3ffd, in gomp_thread_start
0xd#0xd Object "/home/hmj/miniconda3/bin/vg", at 0x1ec3ffd, in gomp_thread_start
0xd Object "/home/hmj/miniconda3/bin/vg", at 0x1ec3ffd, in gomp_thread_start
#0xd Object "/home/hmj/miniconda3/bin/vg", at Object "#0xd Object "/home/hmj/miniconda3/bin/vg", at 0x1ec3ffd, in gomp_thread_start
/home/hmj/miniconda3/bin/vg", at 0x1ec3ffd, in #0xd Object "/home/hmj/miniconda3/bin/vg", at gomp_thread_start0x1ec3ffd, in
0x1ec3ffd, in gomp_thread_start
gomp_thread_start
#0xd Object "/home/hmj/miniconda3/bin/vg", at 0x1ec3ffd, in gomp_thread_start
#0xd Object "/home/hmj/miniconda3/bin/vg", at 0x1ec3ffd, in gomp_thread_start
#0xd Object "/home/hmj/miniconda3/bin/vg", at 0x1ec3ffd, in gomp_thread_start
#0xd Object "/home/hmj/miniconda3/bin/vg", at 0x1ec3ffd, in gomp_thread_start
#0xd Object "/home/hmj/miniconda3/bin/vg", at 0x1ec3ffd, in gomp_thread_start
#0xd Object "/home/hmj/miniconda3/bin/vg", at 0x1ec3ffd, in gomp_thread_start
#0xd Object "/home/hmj/miniconda3/bin/vg", at 0x1ec3ffd, in gomp_thread_start
#0xd Object "/home/hmj/miniconda3/bin/vg", at 0x1ec3ffd, in gomp_thread_start
#0xd Object "/home/hmj/miniconda3/bin/vg", at 0x1ec3ffd, in gomp_thread_start
#0xd Object "/home/hmj/miniconda3/bin/vg", at 0x1ec3ffd, in gomp_thread_start
#0xd Object "/home/hmj/miniconda3/bin/vg", at 0x1ec3ffd, in gomp_thread_start
#0x8 Object "/home/hmj/miniconda3/bin/vg", at 0x5c0007, in abort
#0xd Object "/home/hmj/miniconda3/bin/vg", at 0x1ec3ffd, in gomp_thread_start#0xd Object "/home/hmj/miniconda3/bin/vg", at
0x1ec3ffd, in gomp_thread_start
#0xd Object "/home/hmj/miniconda3/bin/vg", at 0x1ec3ffd, in gomp_thread_start
#0x7 Object "/home/hmj/miniconda3/bin/vg", at 0x149611b, in raise
#0xd Object "/home/hmj/miniconda3/bin/vg", at 0x1ec3ffd, in gomp_thread_start
#0xd Object "/home/hmj/miniconda3/bin/vg", at 0x1ec3ffd, in gomp_thread_start
#0xd Object "/home/hmj/miniconda3/bin/vg", at 0x1ec3ffd, in gomp_thread_start
#0xd Object "/home/hmj/miniconda3/bin/vg", at 0x1ec3ffd, in gomp_thread_start
#0xc Object "/home/hmj/miniconda3/bin/vg", at 0xf0fea0, in vg::Packer::make_compact() [clone ._omp_fn.6]
#0x7 Object "/home/hmj/miniconda3/bin/vg", at #0xc Object "/home/hmj/miniconda3/bin/vg0x149611b, in raise
", at 0xf0fea0, in vg::Packer::make_compact() [clone ._omp_fn.6]
#0xc Object "/home/hmj/miniconda3/bin/vg", at 0xf0fea0, in vg::Packer::make_compact() [clone ._omp_fn.6]
#0xd Object "/home/hmj/miniconda3/bin/vg", at 0x1ec3ffd, in gomp_thread_start
#0xc Object "/home/hmj/miniconda3/bin/vg", at 0xf0fea0, in vg::Packer::make_compact() [clone ._omp_fn.6]
##0xc Object "/home/hmj/miniconda3/bin/vg", at 0xf0fea0, in vg::Packer::make_compact() [clone ._omp_fn.6]
#0xc Object "/home/hmj/miniconda3/bin/vg", at 0xf0fea0, in vg::Packer::make_compact() [clone ._omp_fn.6]
#0xc Object "/home/hmj/miniconda3/bin/vg", at 0xf0fea00xc Object "/home/hmj/miniconda3/bin/vg", at 0xf0fea0, in vg::Packer::make_compact() [clone ._omp_fn.6]
, in vg::Packer::make_compact() [clone ._omp_fn.6]
###0xc Object "/home/hmj/miniconda3/bin/vg0xc", at 0xf0fea0, in vg::Packer::make_compact() [clone ._omp_fn.6]0xc Object "/home/hmj/miniconda3/bin/vg", at Object "/home/hmj/miniconda3/bin/vg
#0xc Object "/home/hmj/miniconda3/bin/vg", at 0xf0fea0", at , in 0xf0fea00xf0fea0, in vg::Packer::make_compact() [clone ._omp_fn.6]
vg::Packer::make_compact() [clone ._omp_fn.6]
, in vg::Packer::make_compact() [clone ._omp_fn.6]
#0xc Object "/home/hmj/miniconda3/bin/vg", at 0xf0fea0, in vg::Packer::make_compact() [clone ._omp_fn.6]
#0xc Object "/home/hmj/miniconda3/bin/vg", at 0xf0fea0, in vg::Packer::make_compact() [clone ._omp_fn.6]
#0xc Object "/home/hmj/miniconda3/bin/vg", at 0xf0fea0, in vg::Packer::make_compact() [clone ._omp_fn.6]
#0xc Object "/home/hmj/miniconda3/bin/vg", at 0xf0fea0#0xc Object "/home/hmj/miniconda3/bin/vg", at 0xf0fea0, in vg::Packer::make_compact() [clone ._omp_fn.6], in vg::Packer::make_compact() [clone ._omp_fn.6]

#0xc Object "/home/hmj/miniconda3/bin/vg", at 0xf0fea0#0xc Object "/home/hmj/miniconda3/bin/vg", at 0xf0fea0, in vg::Packer::make_compact() [clone ._omp_fn.6], in vg::Packer::make_compact() [clone ._omp_fn.6]

#0xc Object "/home/hmj/miniconda3/bin/vg", at 0xf0fea0, in vg::Packer::make_compact() [clone ._omp_fn.6]
#0xc Object "/home/hmj/miniconda3/bin/vg", at 0xf0fea0, in vg::Packer::make_compact() [clone ._omp_fn.6]
#0xc Object "/home/hmj/miniconda3/bin/vg", at 0xf0fea0, in vg::Packer::make_compact() [clone ._omp_fn.6]
#0xc Object "/home/hmj/miniconda3/bin/vg", at 0xf0fea0, in vg::Packer::make_compact() [clone ._omp_fn.6]
#0xc Object "/home/hmj/miniconda3/bin/vg", at 0xf0fea0, in vg::Packer::make_compact() [clone ._omp_fn.6]
#0xc Object "/home/hmj/miniconda3/bin/vg", at 0xf0fea0, in vg::Packer::make_compact() [clone ._omp_fn.6]
#0x6 Object "/home/hmj/miniconda3/bin/vg", at 0x149621f, in
#0xb Object "/home/hmj/miniconda3/bin/vg", at 0xf0fa46, in vg::Packer::average_node_quality(unsigned long) const
#0xb Object "/home/hmj/miniconda3/bin/vg", at 0xf0fa46, in vg::Packer::average_node_quality(unsigned long) const
#0xb Object "/home/hmj/miniconda3/bin/vg", at 0xf0fa46, in vg::Packer::average_node_quality(unsigned long) const
#0xb Object "/home/hmj/miniconda3/bin/vg", at 0xf0fa46, in vg::Packer::average_node_quality(unsigned long) const
#0xb Object "/home/hmj/miniconda3/bin/vg", at 0xf0fa46, in vg::Packer::average_node_quality(unsigned long) const
#0xb Object "/home/hmj/miniconda3/bin/vg", at 0xf0fa46, in vg::Packer::average_node_quality(unsigned long) const
#0xb#0xb Object "/home/hmj/miniconda3/bin/vg", at 0xf0fa46, in vg::Packer::average_node_quality(unsigned long) const
Object "/home/hmj/miniconda3/bin/vg", at 0xf0fa46, in vg::Packer::average_node_quality(unsigned long) const
#0xb Object "/home/hmj/miniconda3/bin/vg", at 0xf0fa46, in vg::Packer::average_node_quality(unsigned long) const
#0xb Object "/home/hmj/miniconda3/bin/vg", at #0xb0xf0fa46#0xb Object ", in vg::Packer::average_node_quality(unsigned long) const
/home/hmj/miniconda3/bin/vg", at 0xf0fa46, in vg::Packer::average_node_quality(unsigned long) const
Object "/home/hmj/miniconda3/bin/vg", at 0xf0fa46, in vg::Packer::average_node_quality(unsigned long) const
#0xb Object "/home/hmj/miniconda3/bin/vg", at 0xf0fa46, in vg::Packer::average_node_quality(unsigned long) const
#0xc Object "/home/hmj/miniconda3/bin/vg", at 0xf0fea0, in vg::Packer::make_compact() [clone ._omp_fn.6]
#0xb Object "/home/hmj/miniconda3/bin/vg", at 0xf0fa46, in vg::Packer::average_node_quality(unsigned long) const
#0xb Object "/home/hmj/miniconda3/bin/vg", at 0xf0fa46, in vg::Packer::average_node_quality(unsigned long) const
#0xb Object "/home/hmj/miniconda3/bin/vg", at 0xf0fa46, in vg::Packer::average_node_quality(unsigned long) const
#0xb Object "/home/hmj/miniconda3/bin/vg", at 0xf0fa46, in vg::Packer::average_node_quality(unsigned long) const
#0xb Object "/home/hmj/miniconda3/bin/vg#0xb Object "/home/hmj/miniconda3/bin/vg", at 0xf0fa46, in vg::Packer::average_node_quality(unsigned long) const
", at 0xf0fa46, in vg::Packer::average_node_quality(unsigned long) const
#0xc Object "/home/hmj/miniconda3/bin/vg", at 0xf0fea0, in vg::Packer::make_compact() [clone ._omp_fn.6]
#0xb Object "/home/hmj/miniconda3/bin/vg", at 0xf0fa46, in vg::Packer::average_node_quality(unsigned long) const#0xc Object "/home/hmj/miniconda3/bin/vg", at 0xf0fea0, in vg::Packer::make_compact() [clone ._omp_fn.6]

#0xb Object "/home/hmj/miniconda3/bin/vg", at 0xf0fa46, in vg::Packer::average_node_quality(unsigned long) const
#0xc Object "/home/hmj/miniconda3/bin/vg", at 0xf0fea0, in vg::Packer::make_compact() [clone ._omp_fn.6]
#0xb Object "/home/hmj/miniconda3/bin/vg", at 0xf0fa46, in vg::Packer::average_node_quality(unsigned long) const
#0xb Object "/home/hmj/miniconda3/bin/vg", at 0xf0fa46, in vg::Packer::average_node_quality(unsigned long) const
#0x6 Object "/home/hmj/miniconda3/bin/vg#0x5 Object "/home/hmj/miniconda3/bin/vg", at 0x13293e9, in vg::emit_stacktrace(int, siginfo_t*, void*)
", at 0x149621f, in
#0xa Object "/home/hmj/miniconda3/bin/vg", at 0x1ee7555, in __assert_fail
#0xa Object "/home/hmj/miniconda3/bin/vg", at 0x1ee7555, in __assert_fail
#0xa Object "/home/hmj/miniconda3/bin/vg", at 0x1ee7555, in __assert_fail
#0xb Object "/home/hmj/miniconda3/bin/vg", at 0xf0fa46, in vg::Packer::average_node_quality(unsigned long) const
#0xa Object "/home/hmj/miniconda3/bin/vg", at 0x1ee7555, in __assert_fail
#0xa Object "/home/hmj/miniconda3/bin/vg", at 0x1ee7555, in __assert_fail
#0xa Object "/home/hmj/miniconda3/bin/vg", at 0x1ee7555, in __assert_fail
#0xa Object "/home/hmj/miniconda3/bin/vg", at 0x1ee7555, in __assert_fail#0xa Object "/home/hmj/miniconda3/bin/vg", at 0x1ee7555
, in __assert_fail
#0xa Object "/home/hmj/miniconda3/bin/vg", at 0x1ee7555, in __assert_fail
#0xa Object "/home/hmj/miniconda3/bin/vg", at 0x1ee7555, in __assert_fail
#0xa Object "/home/hmj/miniconda3/bin/vg", at 0x1ee7555#0xa Object "/home/hmj/miniconda3/bin/vg", at , in __assert_fail
0x1ee7555#0xb Object "/home/hmj/miniconda3/bin/vg, in __assert_fail
", at 0xf0fa46, in vg::Packer::average_node_quality(unsigned long) const
#0xa Object "/home/hmj/miniconda3/bin/vg", at 0x1ee7555, in __assert_fail
#0xa Object "/home/hmj/miniconda3/bin/vg", at 0x1ee7555, in __assert_fail
#0xa Object "/home/hmj/miniconda3/bin/vg", at 0x1ee7555, in __assert_fail
#0xa Object "/home/hmj/miniconda3/bin/vg", at 0x1ee7555, in __assert_fail
#0xa Object "/home/hmj/miniconda3/bin/vg", at 0x1ee7555, in __assert_fail
#0xb Object "/home/hmj/miniconda3/bin/vg", at 0xf0fa46, in vg::Packer::average_node_quality(unsigned long) const
#0xa Object "/home/hmj/miniconda3/bin/vg", at 0x1ee7555#0xa Object "/home/hmj/miniconda3/bin/vg", at 0x1ee7555, in , in __assert_fail
#0xc Object "/home/hmj/miniconda3/bin/vg", at 0xf0fea0__assert_fail
, in vg::Packer::make_compact() [clone ._omp_fn.6]
#0xb Object "/home/hmj/miniconda3/bin/vg", at 0xf0fa46, in vg::Packer::average_node_quality(unsigned long) const
#0x4 Object "/home/hmj/miniconda3/bin/vg", at 0x132d544, in void backward::Printer::print_stacktracebackward::StackTrace(backward::StackTrace&, std::ostream&, backward::Colorize&)
#0xb Object "/home/hmj/miniconda3/bin/vg", at 0xf0fa46, in vg::Packer::average_node_quality(unsigned long) const
#0xa Object "/home/hmj/miniconda3/bin/vg", at 0x1ee7555, in __assert_fail

0xa Object "/home/hmj/miniconda3/bin/vg", at 0x1ee7555, in __assert_fail0xb Object "/home/hmj/miniconda3/bin/vg", at 0xf0fa46, in vg::Packer::average_node_quality(unsigned long) const

#0xa Object "/home/hmj/miniconda3/bin/vg", at 0x1ee7555, in __assert_fail
#0xa Object "/home/hmj/miniconda3/bin/vg", at 0x1ee7555, in __assert_fail
#0x5 Object "/home/hmj/miniconda3/bin/vg", at 0x13293e9, in vg::emit_stacktrace(int, siginfo_t*, void*)
#0xa Object "/home/hmj/miniconda3/bin/vg", at 0x1ee7555, in __assert_fail
#0xa Object "/home/hmj/miniconda3/bin/vg", at 0x1ee7555, in __assert_fail
#0xa Object "/home/hmj/miniconda3/bin/vg", at 0x1ee7555, in __assert_fail
#0xb Object "/home/hmj/miniconda3/bin/vg", at 0xf0fa46, in vg::Packer::average_node_quality(unsigned long) const
#0xa Object "/home/hmj/miniconda3/bin/vg", at 0x1ee7555, in __assert_fail
#0x9 Object "/home/hmj/miniconda3/bin/vg", at 0x5bfed7, in __assert_fail_base.cold
#0x9 Object "/home/hmj/miniconda3/bin/vg", at 0x5bfed7, in __assert_fail_base.cold
#0x9 Object "/home/hmj/miniconda3/bin/vg", at 0x5bfed7, in __assert_fail_base.cold
#0x9 Object "/home/hmj/miniconda3/bin/vg", at 0x5bfed7, in __assert_fail_base.cold
#0x9 Object "/home/hmj/miniconda3/bin/vg", at 0x5bfed7, in __assert_fail_base.cold
#0x9 Object "/home/hmj/miniconda3/bin/vg", at 0x5bfed7, in __assert_fail_base.cold
#0x9 Object "/home/hmj/miniconda3/bin/vg", at 0x5bfed7, in __assert_fail_base.cold#0x9 Object "/home/hmj/miniconda3/bin/vg", at 0x5bfed7, in __assert_fail_base.cold

#0x9 Object "/home/hmj/miniconda3/bin/vg", at 0x5bfed7, in __assert_fail_base.cold
#0x9 Object "/home/hmj/miniconda3/bin/vg", at 0x5bfed7, in __assert_fail_base.cold
#0x9 Object "/home/hmj/miniconda3/bin/vg", at 0x5bfed7, in __assert_fail_base.cold
#0x9 Object "/home/hmj/miniconda3/bin/vg", at 0x5bfed7, in __assert_fail_base.cold
#0x9 Object "/home/hmj/miniconda3/bin/vg", at 0x5bfed7, in __assert_fail_base.cold
#0x9 Object "/home/hmj/miniconda3/bin/vg", at 0x5bfed7, in __assert_fail_base.cold
#0x9 Object "/home/hmj/miniconda3/bin/vg", at 0x5bfed7, in __assert_fail_base.cold
#0x9 Object "/home/hmj/miniconda3/bin/vg", at 0x5bfed7, in __assert_fail_base.cold
#0x9 Object "/home/hmj/miniconda3/bin/vg", at 0x5bfed7, in __assert_fail_base.cold
#0x3 Object "/home/hmj/miniconda3/bin/vg", at 0x1a76916, in dwfl_linux_proc_report
#0x9 Object "/home/hmj/miniconda3/bin/vg", at 0x5bfed7, in __assert_fail_base.cold
#0x9 Object "/home/hmj/miniconda3/bin/vg", at 0x5bfed7, in __assert_fail_base.cold
#0xa Object "/home/hmj/miniconda3/bin/vg", at 0x1ee7555, in __assert_fail
#0xa Object "/home/hmj/miniconda3/bin/vg", at 0x1ee7555, in __assert_fail
#0x4 Object "/home/hmj/miniconda3/bin/vg", at 0x132d544, in void backward::Printer::print_stacktracebackward::StackTrace(backward::StackTrace&, std::ostream&, backward::Colorize&)
#0x8 Object "/home/hmj/miniconda3/bin/vg", at 0x5c0007, in abort
#0x8 Object "/home/hmj/miniconda3/bin/vg", at 0x5c0007, in abort
#0x8 Object "/home/hmj/miniconda3/bin/vg", at 0x5c0007, in abort
#0x8 Object "/home/hmj/miniconda3/bin/vg", at 0x5c0007, in abort
#0x8 Object "/home/hmj/miniconda3/bin/vg", at 0x5c0007, in abort
#0x8 Object "/home/hmj/miniconda3/bin/vg", at 0x5c0007, in abort
#0x8 Object "/home/hmj/miniconda3/bin/vg", at 0x5c0007, in #0x8 Object "/home/hmj/miniconda3/bin/vgabort
", at 0x5c0007, in abort
#0x8 Object "/home/hmj/miniconda3/bin/vg", at 0x5c0007, in abort
#0x8 Object "/home/hmj/miniconda3/bin/vg", at 0x5c0007, in abort
#0x8 Object "/home/hmj/miniconda3/bin/vg", at 0x5c0007, in abort
#0x8 Object "/home/hmj/miniconda3/bin/vg", at 0x5c0007, in abort
#0x8 Object "/home/hmj/miniconda3/bin/vg", at 0x5c0007, in abort
#0xa Object "/home/hmj/miniconda3/bin/vg#0x8 Object "/home/hmj/miniconda3/bin/vg", at 0x5c0007, in abort
", at 0x1ee7555, in __assert_fail
#0x8 Object "/home/hmj/miniconda3/bin/vg", at 0x5c0007, in abort
#0x8 Object "/home/hmj/miniconda3/bin/vg", at 0x5c0007, in abort
#0x9 Object "/home/hmj/miniconda3/bin/vg", at 0x5bfed7, in __assert_fail_base.cold
#0x9 Object "/home/hmj/miniconda3/bin/vg", at 0x5bfed7, in __assert_fail_base.cold
##0x9 Object "/home/hmj/miniconda3/bin/vg", at 0x5bfed7, in __assert_fail_base.cold
0x8 Object "/home/hmj/miniconda3/bin/vg", at 0x5c0007, in abort
#0x9 Object "/home/hmj/miniconda3/bin/vg", at 0x5bfed7, in __assert_fail_base.cold
#0x8 Object "/home/hmj/miniconda3/bin/vg", at 0x5c0007, in abort
#0x8 Object "/home/hmj/miniconda3/bin/vg", at 0x5c0007, in abort
#0x9 Object "/home/hmj/miniconda3/bin/vg", at 0x5bfed7, in __assert_fail_base.cold
#0x9 Object "/home/hmj/miniconda3/bin/vg", at 0x5bfed7, in __assert_fail_base.cold
#0x9 Object "/home/hmj/miniconda3/bin/vg", at 0x5bfed7, in #0x3 Object "/home/hmj/miniconda3/bin/vg", at __assert_fail_base.cold
0x1a76916, in dwfl_linux_proc_report
#0x9 Object "/home/hmj/miniconda3/bin/vg", at 0x5bfed7, in __assert_fail_base.cold
#0x7 Object "/home/hmj/miniconda3/bin/vg", at 0x149611b, in raise
#0x7 Object "/home/hmj/miniconda3/bin/vg", at 0x149611b, in raise
#0x7 Object "/home/hmj/miniconda3/bin/vg", at 0x149611b, in raise
#0x7 Object "/home/hmj/miniconda3/bin/vg", at 0x149611b, in raise
#0x7 Object "/home/hmj/miniconda3/bin/vg", at 0x149611b, in raise#0x7 Object "/home/hmj/miniconda3/bin/vg", at 0x149611b, in raise

0x7 Object "/home/hmj/miniconda3/bin/vg", at 0x149611b, in raise

0x7 Object "/home/hmj/miniconda3/bin/vg", at 0x149611b, in raise
#0x7 Object "/home/hmj/miniconda3/bin/vg", at 0x149611b, in raise
#0x7 Object "/home/hmj/miniconda3/bin/vg", at 0x149611b, in raise
#0x7 Object "/home/hmj/miniconda3/bin/vg", at 0x149611b, in raise
#0x7 Object "/home/hmj/miniconda3/bin/vg", at 0x149611b, in raise
#0x7 Object "/home/hmj/miniconda3/bin/vg", at 0x149611b, in raise
#0x7 Object "/home/hmj/miniconda3/bin/vg", at 0x149611b, in raise
#0x7 Object "/home/hmj/miniconda3/bin/vg", at 0x149611b, in raise
#0x2 Object "/home/hmj/miniconda3/bin/vg", at #0x7 Object "/home/hmj/miniconda3/bin/vg", at 0x149611b, in raise0x1a7659d, in proc_maps_report

#0x8 Object "/home/hmj/miniconda3/bin/vg", at 0x5c0007, in abort
#0x7 Object "/home/hmj/miniconda3/bin/vg", at 0x149611b, in raise
#0x8 Object "/home/hmj/miniconda3/bin/vg", at 0x5c0007, in abort
#0x8 Object "/home/hmj/miniconda3/bin/vg", at 0x5c0007, in abort
#0x7 Object "/home/hmj/miniconda3/bin/vg", at 0x149611b, in raise
#0x7 Object "/home/hmj/miniconda3/bin/vg", at 0x149611b, in raise#0x8 Object "/home/hmj/miniconda3/bin/vg", at 0x5c0007, in abort

#0x9 Object "/home/hmj/miniconda3/bin/vg", at 0x5bfed7, in __assert_fail_base.cold
#0x8 Object "/home/hmj/miniconda3/bin/vg", at 0x5c0007, in abort
#0x9 Object "/home/hmj/miniconda3/bin/vg#0x8 Object "/home/hmj/miniconda3/bin/vg", at 0x5c0007", at 0x5bfed7, in __assert_fail_base.cold, in abort

#0x8 Object "/home/hmj/miniconda3/bin/vg", at 0x5c0007, in abort
#0x8 Object "/home/hmj/miniconda3/bin/vg", at 0x5c0007, in abort
#0x9 Object "/home/hmj/miniconda3/bin/vg", at 0x5bfed7, in __assert_fail_base.cold
#0x7 Object "/home/hmj/miniconda3/bin/vg", at #0x8 Object "/home/hmj/miniconda3/bin/vg", at 0x5c0007, in abort
#0x7 Object "/home/hmj/miniconda3/bin/vg", at 0x149611b, in raise
0x149611b, in raise#0x7 Object "/home/hmj/miniconda3/bin/vg", at 0x149611b, in raise

#0x7 Object "/home/hmj/miniconda3/bin/vg", at 0x149611b, in raise
#0x7 Object "/home/hmj/miniconda3/bin/vg", at 0x149611b, in raise
##0x2 Object "/home/hmj/miniconda3/bin/vg", at 0x1a7659d, in proc_maps_report#0x6 Object "
0x6 Object "/home/hmj/miniconda3/bin/vg", at 0x149621f, in
#0x6 Object "/home/hmj/miniconda3/bin/vg", at 0x149621f, in
/home/hmj/miniconda3/bin/vg#0x6 Object "/home/hmj/miniconda3/bin/vg", at 0x149621f", at #0x7 Object "/home/hmj/miniconda3/bin/vg", at 0x149611b, in raise
0x149621f, in
, in
#0x6 Object "/home/hmj/miniconda3/bin/vg", at #0x6 Object "/home/hmj/miniconda3/bin/vg", at 0x149621f, in
0x149621f, in
#0x6 Object "/home/hmj/miniconda3/bin/vg", at 0x149621f, in
#0x6 Object "/home/hmj/miniconda3/bin/vg", at 0x149621f, in
#0x7 Object "/home/hmj/miniconda3/bin/vg", at #0x6 Object "/home/hmj/miniconda3/bin/vg", at 0x149621f, in
0x149611b, in raise
#0x6 Object "/home/hmj/miniconda3/bin/vg", at 0x149621f, in
#0x8 Object "/home/hmj/miniconda3/bin/vg", at 0x5c0007, in abort
#0x6 Object "/home/hmj/miniconda3/bin/vg", at 0x149621f, in
#0x6 Object "/home/hmj/miniconda3/bin/vg", at 0x149621f, in
#0x6 Object "/home/hmj/miniconda3/bin/vg", at 0x149621f, in
#0x7 Object "/home/hmj/miniconda3/bin/vg", at 0x149611b, in raise
#0x6 Object "/home/hmj/miniconda3/bin/vg", at 0x149621f, in
#0x6 Object "/home/hmj/miniconda3/bin/vg", at 0x149621f, in
#0x6 Object "/home/hmj/miniconda3/bin/vg", at 0x149621f, in
#0x1 Object "/home/hmj/miniconda3/bin/vg", at 0x1a763fd, in do_report
#0x6 Object "/home/hmj/miniconda3/bin/vg", at ##0x6 Object "/home/hmj/miniconda3/bin/vg", at 0x149621f, in
0x149621f, in
0x6 Object "/home/hmj/miniconda3/bin/vg", at 0x149621f, in
#0x8 Object "/home/hmj/miniconda3/bin/vg", at 0x5c0007, in abort
#0x7 Object "/home/hmj/miniconda3/bin/vg", at 0x149611b, in raise
#0x5 Object "/home/hmj/miniconda3/bin/vg", at 0x13293e9#0x5 Object "/home/hmj/miniconda3/bin/vg", at 0x13293e9, in vg::emit_stacktrace(int, siginfo_t*, void*)
, in vg::emit_stacktrace(int, siginfo_t*, void*)
#0x5 Object "/home/hmj/miniconda3/bin/vg", at 0x13293e9#0x5 Object "/home/hmj/miniconda3/bin/vg", at 0x13293e9, in vg::emit_stacktrace(int, siginfo_t*, void*)
, in vg::emit_stacktrace(int, siginfo_t*, void*)
#0x5 Object "/home/hmj/miniconda3/bin/vg", at 0x13293e9, in vg::emit_stacktrace(int, siginfo_t*, void*)
#0x5 Object "/home/hmj/miniconda3/bin/vg", at 0x13293e9, in vg::emit_stacktrace(int, siginfo_t*, void*)
#0x5 Object "/home/hmj/miniconda3/bin/vg", at 0x13293e9, in vg::emit_stacktrace(int, siginfo_t*, void*)
#0x5 Object "/home/hmj/miniconda3/bin/vg", at 0x13293e9, in vg::emit_stacktrace(int, siginfo_t*, void*)
#0x5 Object "/home/hmj/miniconda3/bin/vg", at 0x13293e9, in vg::emit_stacktrace(int, siginfo_t*, void*)
#0x5 Object "/home/hmj/miniconda3/bin/vg", at 0x13293e9, in vg::emit_stacktrace(int, siginfo_t*, void*)
#0x5 Object "/home/hmj/miniconda3/bin/vg", at 0x13293e9, in vg::emit_stacktrace(int, siginfo_t*, void*)
#0x5 Object "/home/hmj/miniconda3/bin/vg", at 0x13293e9, in vg::emit_stacktrace(int, siginfo_t*, void*)
#0x5 Object "/home/hmj/miniconda3/bin/vg", at 0x13293e9, in vg::emit_stacktrace(int, siginfo_t*, void*)
#0x5 Object "/home/hmj/miniconda3/bin/vg", at 0x13293e9, in vg::emit_stacktrace(int, siginfo_t*, void*)
#0x5 Object "/home/hmj/miniconda3/bin/vg", at 0x13293e9, in vg::emit_stacktrace(int, siginfo_t*, void*)
#0x5 Object "/home/hmj/miniconda3/bin/vg", at 0x13293e9, in vg::emit_stacktrace(int, siginfo_t*, void*)
#0x7 Object "/home/hmj/miniconda3/bin/vg", at 0x149611b, in raise
#0 Object "/home/hmj/miniconda3/bin/vg", at 0x1a748ff, in dwfl_report_module

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

vg pack -x cactus.xg -g cactus.gam -o cactus.pack -Q 5 -s 5

**6. What does running `vg version` say?**

(vg: variation graph tool, version v1.55.0 "Bernolda")

[glennhickey]

I haven't seen this error before and don't really understand what the problem might be. Would you be able to share cactus.xg and cactus.gam so I can try to reproduce it?

[QiaoYJYJ]

Thanks a lot for your help and time!
There are commands what I used:

vg index -x cactus.xg cactus_pan.gfa

vg autoindex --workflow giraffe --prefix cactus1 --gfa cactus_pan.gfa

vg giraffe -Z cactus.giraffe.gbz -m cactus.min -d cactus.dist -f MAQCA-1.fastq -f MAQCA-2.fastq -o gam -p > MAQCA.gam

vg pack -t 32 -x cactus.xg -g MAQCA.gam -o MAQCA.pack

[glennhickey]

Since cactus.giraffe.gbz may have different node ids than cactus.xg, you should be using the former for pack:

vg pack -t 32 -x cactus.giraffe.gbz -g MAQCA.gam -o MAQCA.pack