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Error for " vg convert -x" #4099
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I notice that |
That is just an mistake from copying the command to here. |
I was able to run these commands without issue with vg
The resulting files have these sizes
How much RAM do you have? How much free disk? |
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. |
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 usevg 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.
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