Issue in 'vg pack'

[fangbohao]

1. What were you trying to do? I want to 'vg pack' the gam file derived from 'vg giraffe'. An error message appeared. The command line I used is shown below:

vg pack -t 23 -Q 5 -x $gfa_chr8 -g chr8_mapped_TX_426.gam -o chr8_mapped_TX_426.pack

2. What did you want to happen? I want to get the '.pack' file properly.

3. What actually happened? The error message showed.

vg: src/packer.cpp:883: size_t vg::Packer::average_node_quality(size_t) const: Assertion `total_node_quality(i) == 0' failed.
vg: src/packer.cpp:883: size_t vg::Packer::average_node_quality(size_t) const: Assertion `total_node_quality(i) == 0' failed.
vg: src/packer.cpp:883: size_t vg::Packer::average_node_quality(size_t) const: Assertion `total_node_quality(i) == 0' failed.
vg: src/packer.cpp:883: size_t vg::Packer::average_node_quality(size_t) const: Assertion `total_node_quality(i) == 0' failed.
vg: src/packer.cpp:883: size_t vg::Packer::average_node_quality(size_t) const: Assertion `total_node_quality(i) == 0' failed.
vg: src/packer.cpp:883: size_t vg::Packer::average_node_quality(size_t) const: Assertion `total_node_quality(i) == 0' failed.
vg: src/packer.cpp:883: size_t vg::Packer::average_node_quality(size_t) const: Assertion `total_node_quality(i) == 0' failed.
vg: src/packer.cpp:883: size_t vg::Packer::average_node_quality(size_t) const: Assertion `total_node_quality(i) == 0' failed.
vg: src/packer.cpp:883: size_t vg::Packer::average_node_quality(size_t) const: Assertion `total_node_quality(i) == 0' failed.
vg: src/packer.cpp:883: size_t vg::Packer::average_node_quality(size_t) const: Assertion `total_node_quality(i) == 0' failed.
vg: src/packer.cpp:883: size_t vg::Packer::average_node_quality(size_t) const: Assertion `total_node_quality(i) == 0' failed.
vg: src/packer.cpp:883: size_t vg::Packer::average_node_quality(size_t) const: Assertion `total_node_quality(i) == 0' failed.
vg: src/packer.cpp:883: size_t vg::Packer::average_node_quality(size_t) const: Assertion `total_node_quality(i) == 0' failed.
vg: src/packer.cpp:883: size_t vg::Packer::average_node_quality(size_t) const: Assertion `total_node_quality(i) == 0' failed.
vg: src/packer.cpp:883: size_t vg::Packer::average_node_quality(size_t) const: Assertion `total_node_quality(i) == 0' failed.
vg: src/packer.cpp:883: size_t vg::Packer::average_node_quality(size_t) const: Assertion `total_node_quality(i) == 0' failed.
vg: src/packer.cpp:883: size_t vg::Packer::average_node_quality(size_t) const: Assertion `total_node_quality(i) == 0' failed.
vg: src/packer.cpp:883: size_t vg::Packer::average_node_quality(size_t) const: Assertion `total_node_quality(i) == 0' failed.
vg: src/packer.cpp:883: size_t vg::Packer::average_node_quality(size_t) const: Assertion `total_node_quality(i) == 0' failed.
vg: src/packer.cpp:883: size_t vg::Packer::average_node_quality(size_t) const: Assertion `total_node_quality(i) == 0' failed.
vg: src/packer.cpp:883: size_t vg::Packer::average_node_quality(size_t) const: Assertion `total_node_quality(i) == 0' failed.
vg: src/packer.cpp:883: size_t vg::Packer::average_node_quality(size_t) const: Assertion `total_node_quality(i) == 0' failed.
vg: src/packer.cpp:883: size_t vg::Packer::average_node_quality(size_t) const: Assertion `total_node_quality(i) == 0' failed.
ERROR: Signal ERROR: Signal 6ERROR: 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_OK8tPd/stacktrace.txt
Please include the stack trace file in your bug report!ERROR: Signal ERROR: Signal ERROR: Signal ERROR: Signal 6 occurred. VG has crashed. V
isit https://github.com/vgteam/vg/issues/new/choose to report a bug.ERROR: Signal 6ERROR: Signal 6 occurred. VG has crashed. Visit https://g
ithub.com/vgteam/vg/issues/new/choose to report a bug. occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to rep
ort a bug.
Stack trace path: /tmp/vg_crash_Q4HsJe/stacktrace.txt
Please include the stack trace file in your bug report!
6 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug.
Stack trace path: /tmp/vg_crash_ZxoBpb/stacktrace.txt
Please include the stack trace file in your bug report!
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_TWCgBc/stacktrace.txt
Please include the stack trace file in your bug report!
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_VAnkac/stacktrace.txt
Please include the stack trace file in your bug report!
6 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug.(fasrc)

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 v1.41.0 "Salmour"
Stack trace (most recent call last) in thread 229098:
#9    Object "", at 0xffffffffffffffff, in 
#8    Object "", at 0x1f0a562, in 
#7    Object "", at 0x1459fc8, in 
#6    Object "", at 0x1e3ef1d, in 
#5    Object "", at 0x10cf6c0, in 
#4    Object "", at 0x10cf266, in 
#3    Object "", at 0x1e62475, in 
#2    Object "", at 0x5afcc7, in 
#1    Object "", at 0x5afdf7, in 
#0    Object "", at 0x145d3ab, in 

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

6. What does running vg version say?

v1.41.0