QiaoYJYJ commented 2 months ago

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)

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

, in

", 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 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

0xffffffffffffffff, in , in Object "", at 0, in

0 Object "0, in

", at 0, in

0

0 Object "", at 0, in

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

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

0 Object "", at , in

0 Object "", at 0, in

0 0, in

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

0 Object "", at 0, in

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

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

0 Object "", at 0

0 Object ", in

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

0 Object "", at 0, in

", at 0, in

0 Object "", at 0, in

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

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

0 Object "", at 0, in

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

0 Object "", at 0, in

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

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

0 Object "", at 0

0 Object "", at 0, in

0 Object "", at , in

0 Object "", at 0, in

0, in

0 Object "", at 0, in

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

0 ", at 0, in

0 Object " Object "", at 0, in

0 Object "", at 0, in

", at 0, in

0 Object "", at 0, in

0x10 Object "", at #, in 0xffffffffffffffff, in

0x10

0 Object "", at 0, in

Object "", at 0xffffffffffffffff#, 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 cloneclone

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

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 ###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

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

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#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

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

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 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#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]

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#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#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

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

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#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

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_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

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

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

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

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_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 #0x8 Object "/home/hmj/miniconda3/bin/vgabort

", 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

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

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

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

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

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

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

/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

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

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

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)

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 commented 2 months ago

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 commented 2 months ago

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 commented 2 months ago

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

vgteam / vg

vg pack error #4278

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)

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)

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

12 Object "", at 12 Object "", at 00Stack trace (most recent call last)

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

16 Object "", at 0xffffffffffffffff, in

16 Object "", at :

", at 0xffffffffffffffff, in in thread v1.48.0 "Gallipoli" in thread 3858663:

0x10 Object "", at 0xffffffffffffffff, in

0x10 Object "", at 0xffffffffffffffff, in

16 Object "", at

36Stack trace (most recent call last) in thread 3858666:

16 Object "", at :

Stack trace (most recent call last):

0x25 Object "

16 Object "", at 0xffffffffffffffff, in

160x10 Object "", at

0 Object "", at 0, in

0 0xffffffffffffffff, in

Object "16 Object "", at

0x25 Object "", at 00, in 0xffffffffffffffff, in

0x10 Object "", at 0xffffffffffffffff, in

0x10 Object "", at 0xffffffffffffffff, in

, in 0Crash report for vg v1.48.0 "Gallipoli"v1.48.0 "Gallipoli"#0

0x10 Object "", at 0xffffffffffffffff, in

", 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 Object "", at 0, in :

in thread 0x3ae0de

0 Object "", at 0, in

0 Object "", at 0, in

0 Object "", at 00x10 Object "", at 0xffffffffffffffff, in

, in

0 Object "", at 0:

, in 0x10 Object "", at 0xffffffffffffffff, in Object "", at Object "", at ", at 0xffffffffffffffff0

0 Object "0, in

", at 0, in

0 Object "", at 0, in

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

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

0 Object "", at , in

0 Object "", at 0, in

0 0, in

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

0 Object "", at 0, in

0

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

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

0 Object "", at 0

0 Object ", in

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

0 Object "", at 0, in

0 Object "", at 0, in

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

0 Object "", at 0, in

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

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

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

0 Object "", at 0

0 Object "", at 0, in

0 Object "", at 0, in

0 Object "", at , in

0 Object "", at 0, in

0 Object "", at 0, in