Comments (5)
glennhickey
commented on September 26, 2024
It's probably running out of memory loading all the paths (vg works best on xg/gbz/gbwt at this scale) The simplest work-around is probably
grep -v ^W hprc-v1.0-mc-grch38.gfa > hprc-v1.0-mc-grch38-nohaps.gfa
Then run pack on that. (you dont' have to rerun graphaligner).
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laurentijntilleman
commented on September 26, 2024
I tried this work-around, but I still have the same error.
grep -v ^W hprc-v1.0-mc-grch38.gfa > hprc-v1.0-mc-grch38-nohaps.gfa
vg pack -t 40 -x hprc-v1.0-mc-grch38-nohaps.gfa -i PCR.gam -Q 5 -o PCR.pack
terminate called after throwing an instance of 'std::bad_alloc'
what(): std::bad_alloc
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_fozdcq/stacktrace.txt
Please include the stack trace file in your bug report!
I also tried with the hprc-v1.0-mc-grch38.xg reference:
vg pack -t 40 -x hprc-v1.0-mc-grch38.xg -i PCR.gam -Q 5 -o PCR.pack
terminate called after throwing an instance of 'std::bad_alloc'
what(): std::bad_alloc
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_Xyjddb/stacktrace.txt
Please include the stack trace file in your bug report!
Also here, I got the same error.
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glennhickey
commented on September 26, 2024
Try passing in the .gam to vg pack with -g instead of -i.
-i, --packs-in FILE begin by summing coverage packs from each provided FILE
-g, --gam FILE read alignments from this GAM file (could be '-' for stdin)
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laurentijntilleman
commented on September 26, 2024
The -g option resolved part of the issue. Now I got a new issue when -Q is 0. When -Q is greater than 0, then the pack file looks empty because there are no variants called with vg call
Command used
vg pack -t 40 -x hprc-v1.0-mc-grch38.xg -g PCR.gam -o PCR.pack
Error
vg: /home/anovak/workspace/vg/include/sdsl/int_vector.hpp:1391: sdsl::int_vector<<anonymous> >::reference sdsl::int_vector<<anonymous> >::operator[](const size_type&) [with unsigned char t_width = 0; sdsl::int_vector<<anonymous> >::reference = sdsl::int_vector_reference<sdsl::int_vector<0> >; sdsl::int_vector<<anonymous> >::size_type = long unsigned int]: Assertion `idx < this->size()' failed.
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_YGcHQY/stacktrace.txt
Please include the stack trace file in your bug report!
Crash report
Crash report for vg v1.45.0 "Alpicella"
Stack trace (most recent call last) in thread 121214:
#15 Object "", at 0xffffffffffffffff, in
#14 Object "/tools/vg/vg", at 0x1f3c532, in __clone
#13 Object "/tools/vg/vg", at 0x14498f8, in start_thread
#12 Object "/tools/vg/vg", at 0x1e70d3d, in gomp_thread_start
#11 Object "/tools/vg/vg", at 0xc61502, in void vg::io::for_each_parallel_impl<vg::Alignment>(std::istream&, std::function<void (vg::Alignment&, vg::Alignment&)> const&, std::function<void (vg::Alignment&)> const&, std::function<bool ()> const&, unsigned long) [clone ._omp_fn.0]
#10 Object "/tools/vg/vg", at 0x1e73617, in gomp_team_barrier_wait_end
#9 Object "/tools/vg/vg", at 0x1e6acdb, in gomp_barrier_handle_tasks
#8 Object "/tools/vg/vg", at 0xc60e11, in void vg::io::for_each_parallel_impl<vg::Alignment>(std::istream&, std::function<void (vg::Alignment&, vg::Alignment&)> const&, std::function<void (vg::Alignment&)> const&, std::function<bool ()> const&, unsigned long) [clone ._omp_fn.1]
#7 Object "/tools/vg/vg", at 0xed808a, in vg::Packer::add(vg::Alignment const&, int, int, int)
#6 Object "/tools/vg/vg", at 0xece83b, in vg::Packer::increment_coverage(unsigned long)
#5 Object "/tools/vg/vg", at 0xedc15d, in gcsa::CounterArray::increment(unsigned long)
#4 Object "/tools/vg/vg", at 0xeca81b, in sdsl::int_vector<(unsigned char)0>::operator[](unsigned long const&) [clone .isra.0]
#3 Object "/tools/vg/vg", at 0x1e94295, in __assert_fail
#2 Object "/tools/vg/vg", at 0x5b5e67, in __assert_fail_base.cold
#1 Object "/tools/vg/vg", at 0x5b5f97, in abort
#0 Object "/tools/vg/vg", at 0x144d17b, in raise
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glennhickey
commented on September 26, 2024
The gfa and xg aren't compatible (confusing, I know). So you can't map with the gfa and use that gam with the xg.
If I were you, i'd make a new xg that is compatible with the gfa
grep -v ^W graph.gfa | vg convert - -x > graph.xg
(vg convert -Hx graph.gfa > graph.xg will also work but may use much more memory)
and then run pack on that.
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