Error for " vg convert -x"

[linsindian]

1. What were you trying to do?

I want to use vg surject to convert the GAM file into the BAM file format,so I need to use convert to generate the xg graph.

2. What did you want to happen?

I mapped the long reads of hg002 back to hprc-mc-grch38 using GraphAligner to generate a GAM file and attempted to convert the GAM file to the BAM file format using vg surject. Therefore, I first need to use vg convert to generate an xg file for hprc-mc-grch38 graph. By using the command vg convert -p -t 16 hprc-v1.1-mc-grch38.gfa > hprc-v1.1-mc-grch38.vg, I generated a .vg graph file. However, when I attempted to use vg convert -x -t 16 hprc-v1.1-mc-grch38vg > hprc-v1.1-mc-grch38.xg, I encountered an issue.

3. What actually happened?

vg: /public/home/anovak/build/vg/include/sdsl/int_vector.hpp:1436: sdsl:: int_vector< >::const_reference sdsl::int_vector< >: :operator[](const size_type&) const [with unsigned char t_width = 0; sdsl ::int_vector< >::const_reference = long unsigned int; sdsl::in t_vector< >::size_type = long unsigned int]: Assertion `idx < this->size()' failed. ━━━━━━━━━━━━━━━━━━━━ Crash report for vg v1.51.0 "Quellenhof" Stack trace (most recent call last):

13 Object "/bip7_disk/sindian111/pangenome/vg", at 0x6169f4, in _start

12 Object "/bip7_disk/sindian111/pangenome/vg", at 0x2068296, in __libc_start_main

11 Object "/bip7_disk/sindian111/pangenome/vg", at 0x2066a39, in __libc_start_call_main

10 Object "/bip7_disk/sindian111/pangenome/vg", at 0xdf980b, in vg::subcommand::Subcommand::operator()(int, char**) const

9 Object "/bip7_disk/sindian111/pangenome/vg", at 0xcb33cb, in main_convert(int, char**)

8 Object "/bip7_disk/sindian111/pangenome/vg", at 0xcb09b4, in graph_to_xg_adjusting_paths(handlegraph::PathHandleGraph const, xg::XG, std::unordered_set<std::cxx11::basic_string<char, std::char_traits, std::allocator >, std::hash<std::cxx11::basic_string<char, std::char_traits, std::allocator > >, std::equal_to<std::cxx11::basic_string<char, std::char_traits, std::allocator > >, std::allocator<std::cxx11::basic_string<char, std::char_traits, std::allocator > > > const&, bool)

7 Object "/bip7_disk/sindian111/pangenome/vg", at 0x18950da, in xg::XG::from_enumerators(std::function<void (std::function<void (std::cxx11::basic_string<char, std::char_traits, std::allocator > const&, long long const&)> const&)> const&, std::function<void (std::function<void (long long const&, bool const&, long long const&, bool const&)> const&)> const&, std::function<void (std::function<void (std::cxx11::basic_string<char, std::char_traits, std::allocator > const&, long long const&, bool const&, std::cxx11::basic_string<char, std::char_traits, std::allocator > const&, bool const&, bool const&)> const&)> const&, bool, std::cxx11::basic_string<char, std::char_traits,std::allocator >)

6 Object "/bip7_disk/sindian111/pangenome/vg", at 0x188e047, in xg::XG::index_node_to_path(std::__cxx11::basic_string<char, std::char_traits, std::allocator > const&)

5 Object "/bip7_disk/sindian111/pangenome/vg", at 0x18964fb, in sdsl::int_vector<(unsigned char)0>::operator[](unsigned long const&) const

4 Object "/bip7_disk/sindian111/pangenome/vg", at 0x2078e65, in __assert_fail

3 Object "/bip7_disk/sindian111/pangenome/vg", at 0x5e5673, in __assert_fail_base.cold

2 Object "/bip7_disk/sindian111/pangenome/vg", at 0x5e574b, in abort

1 Object "/bip7_disk/sindian111/pangenome/vg", at 0x207f475, in raise

0 Object "/bip7_disk/sindian111/pangenome/vg", at 0x20abe7c, in __pthread_kill

ERROR: Signal 6 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!

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

The pan-genome graph I'm using is sourced from hprc.

The two step to generate the xg file. vg convert -p -t 16 hprc-v1.1-mc-grch38.gfa > hprc-v1.1-mc-grch38.vg vg convert -x -t 16 hprc-v1.1-mc-grch38vg > hprc-v1.1-mc-grch38.xg

6. What does running vg version say?

vg version v1.51.0 "Quellenhof" Compiled with g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 on Linux Linked against libstd++ 20230528 Built by anovak@courtyard.gi.ucsc.edu

Thank you for reading. Looking forward to your response.

[jeizenga]

I notice that hprc-v1.1-mc-grch38vg is missing the . before the finle extension. Is that also true in original command, or is that an error from copying the commands to this report?

[linsindian]

That is just an mistake from copying the command to here. In the actual command, the file "hprc-v1.1-mc-grch38.vg" is indeed being used correctly.

[glennhickey]

I was able to run these commands without issue with vg 1.51.0. According to /usr/bin/time -v, they took:

convert -p : 6h22m and 123G RAM convert -x : 2h10m and 368G RAM

The resulting files have these sizes

-rw-r--r-- 1 hickey cgl 48118373527 Sep 27 11:30 hprc-v1.1-mc-grch38.gfa
-rw-r--r-- 1 hickey cgl 42775622374 Sep 27 17:54 hprc-v1.1-mc-grch38.vg
-rw-r--r-- 1 hickey cgl 71819679419 Sep 27 20:05 hprc-v1.1-mc-grch38.xg

How much RAM do you have? How much free disk?

[jeizenga]

I'm going to close this issue since we haven't heard any more news on our end. Let me know if this is not correct.