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glennhickey avatar glennhickey commented on June 25, 2024

Looks like maybe the gam file is nonexistent or corrupted. You can verify by doing something like

vg validate chunk_"$i".pg  -a chunk_"$i".gam

from vg.

mas-agis avatar mas-agis commented on June 25, 2024

It reports similar messages. How to chunk the gam only for chr 17? I chunk the vg and gam together before.

[E::bgzf_read_block] Failed to read BGZF block data at offset 2081999101 expecte                       d 17197 bytes; hread returned 15708
terminate called after throwing an instance of 'std::runtime_error'
  what():  [vg::io::MessageIterator] obsolete, invalid, or corrupt input at mess                       age 136444839394527 group 136439356684927
━━━━━━━━━━━━━━━━━━━━
Crash report for vg v1.52.0 "Bozen"
Stack trace (most recent call last):
#16   Object "/usr/local/bioinfo/src/vg/vg-v1.52.0/vg", at 0x616bb4, in _start
#15   Object "/usr/local/bioinfo/src/vg/vg-v1.52.0/vg", at 0x2065016, in __libc_                       start_main
#14   Object "/usr/local/bioinfo/src/vg/vg-v1.52.0/vg", at 0x20637b9, in __libc_                       start_call_main
#13   Object "/usr/local/bioinfo/src/vg/vg-v1.52.0/vg", at 0xdf9b7b, in vg::subc                       ommand::Subcommand::operator()(int, char**) const
#12   Object "/usr/local/bioinfo/src/vg/vg-v1.52.0/vg", at 0xe642be, in main_val                       idate(int, char**)
#11   Object "/usr/local/bioinfo/src/vg/vg-v1.52.0/vg", at 0x1431727, in vg::get                       _input_file(std::__cxx11::basic_string<char, std::char_traits<char>, std::alloca                       tor<char> > const&, std::function<void (std::istream&)>)
#10   Object "/usr/local/bioinfo/src/vg/vg-v1.52.0/vg", at 0xe651e7, in std::_Fu                       nction_handler<void (std::istream&), main_validate(int, char**)::{lambda(std::is                       tream&)#1}>::_M_invoke(std::_Any_data const&, std::istream&)
#9    Object "/usr/local/bioinfo/src/vg/vg-v1.52.0/vg", at 0xc6198b, in void vg:                       :io::for_each<vg::Alignment>(std::istream&, std::function<void (long, vg::Alignm                       ent&)> const&)
#8    Object "/usr/local/bioinfo/src/vg/vg-v1.52.0/vg", at 0x1d359b8, in vg::io:                       :MessageIterator::operator++()
#7    Object "/usr/local/bioinfo/src/vg/vg-v1.52.0/vg", at 0x5d47ec, in vg::io::                       MessageIterator::handle(bool, long, long) [clone .cold]
#6    Object "/usr/local/bioinfo/src/vg/vg-v1.52.0/vg", at 0x1f9d578, in __cxa_t                       hrow
#5    Object "/usr/local/bioinfo/src/vg/vg-v1.52.0/vg", at 0x1f9d416, in std::te                       rminate()
#4    Object "/usr/local/bioinfo/src/vg/vg-v1.52.0/vg", at 0x1f9d3ab, in __cxxab                       iv1::__terminate(void (*)())
#3    Object "/usr/local/bioinfo/src/vg/vg-v1.52.0/vg", at 0x5e31c3, in __gnu_cx                       x::__verbose_terminate_handler() [clone .cold]
#2    Object "/usr/local/bioinfo/src/vg/vg-v1.52.0/vg", at 0x5e590b, in abort
#1    Object "/usr/local/bioinfo/src/vg/vg-v1.52.0/vg", at 0x207c1f5, in raise
#0    Object "/usr/local/bioinfo/src/vg/vg-v1.52.0/vg", at 0x20a8bfc, in __pthre                       ad_kill
ERROR: Signal 6 occurred. VG has crashed. Visit https://github.com/vgteam/vg/iss                       ues/new/choose to report a bug.
Please include this entire error log in your bug report!

the pg is valid

vg validate chunk_17.pg
graph: valid

from vg.

glennhickey avatar glennhickey commented on June 25, 2024

I think you have to hcunk the vg and gam together (depsite what the options may lead you to believe). You can just do that and only use the gam output.

from vg.

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