VG crashing: invalid, or corrupt input at message #2597
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What commands did you run to get this error?
…On Fri, Jan 10, 2020, 17:32 cademirch ***@***.***> wrote:
*1. What were you trying to do?*
I was trying to make an xg index and annotate a GAM.
*2. What did you want to happen?*
Make an xg index, as well as annotate a GAM
*3. What actually happened?*
vg crashed.
what(): [vg::io::MessageIterator] obsolete, invalid, or corrupt input at
message 12668894457 group 11257826026 ERROR: Signal 6 occurred. VG has
crashed. Run 'vg bugs --new' to report a bug.
*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:*
Crash report for vg v1.21.0 "Fanano"
Stack trace (most recent call last):
#15 Object "/public/home/cmirchan/bin/vg", at 0x4d8e59, in _start
#14 Object "/public/home/cmirchan/bin/vg", at 0x1b00f98, in __libc_start_main
#13 Object "/public/home/cmirchan/bin/vg", at 0x40ae92, in main
#12 Object "/public/home/cmirchan/bin/vg", at 0x9a92b7, in vg::subcommand::Subcommand::operator()(int, char**) const
#11 Object "/public/home/cmirchan/bin/vg", at 0x8effde, in main_annotate(int, char**)
#10 Object "/public/home/cmirchan/bin/vg", at 0xa4470c, in vg::get_input_file(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, std::function<void (std::istream&)>)
#9 Object "/public/home/cmirchan/bin/vg", at 0x8f0afc, in std::_Function_handler<void (std::istream&), main_annotate(int, char**)::{lambda(std::istream&)#3}>::_M_invoke(std::_Any_data const&, std::istream&)
#8 Object "/public/home/cmirchan/bin/vg", at 0x8f43ec, in void vg::io::for_each<vg::Alignment>(std::istream&, std::function<void (long, vg::Alignment&)> const&)
#7 Object "/public/home/cmirchan/bin/vg", at 0xea0308, in vg::io::MessageIterator::operator++()
#6 Object "/public/home/cmirchan/bin/vg", at 0xe9fb9c, in vg::io::MessageIterator::handle(bool, long, long)
#5 Object "/public/home/cmirchan/bin/vg", at 0x1a410c3, in __cxa_throw
#4 Object "/public/home/cmirchan/bin/vg", at 0x1a3fda0, in std::terminate()
#3 Object "/public/home/cmirchan/bin/vg", at 0x1a3fd55, in __cxxabiv1::__terminate(void (*)())
#2 Object "/public/home/cmirchan/bin/vg", at 0x1adb714, in __gnu_cxx::__verbose_terminate_handler()
#1 Object "/public/home/cmirchan/bin/vg", at 0x1b11860, in abort
#0 Object "/public/home/cmirchan/bin/vg", at 0x10d25c7, in raise
*5. What data and command can the vg dev team use to make the problem
happen?*
I can make the data available if need be.
*6. What does running vg version say?*
vg version v1.21.0 "Fanano"
Compiled with g++ (Ubuntu 7.4.0-1ubuntu1~18.04.1) 7.4.0 on Linux
Linked against libstd++ 20181206
Built by ***@***.***
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and
The index command had a similar error, but at a different message and group number: |
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It's not clear where ref.mod.vg is coming from. Can you provide all the
commands in your pipeline?
…On Fri, Jan 10, 2020, 18:54 cademirch ***@***.***> wrote:
vg annotate -n -x ZI284_main.xg -a sim.gam | tail -n+2 | pv -l | sort
>novelty.tsv
and
vg index -x ref.mod.xg ref.mod.vg
The index command had a similar error, but at a different message and
group number:
[E::bgzf_uncompress] Inflate operation failed: 1 terminate called after
throwing an instance of 'std::runtime_error' what():
[vg::io::MessageIterator] obsolete, invalid, or corrupt input at message
3616525884758 group 3616525884754 ERROR: Signal 6 occurred. VG has crashed.
Run 'vg bugs --new' to report a bug. Stack trace path:
/tmp/vg_crash_CQXcOy/stacktrace.txt Please include the stack trace file in
your bug report!
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Yep, sorry about that. |
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What are you trying to do with this snippet? I think it might not be doing
what you expect.
…On Fri, Jan 10, 2020, 19:20 cademirch ***@***.***> wrote:
Yep, sorry about that.
`#!/bin/bash
IFS=$'\n\t'
chroms=("NC_004354.4"
"NT_033779.5"
"NT_033778.4"
"NT_037436.4"
"NT_033777.3"
"NC_004353.4"
"NC_024512.1"
)
for chrom in ${chroms[@]}; do
vg mod -k ${chrom} ZI284.sim.vg >> ref.mod.vg
done`
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I am trying to subset the reference portion of that graph. What I am trying to do is replicate the map-sim script referenced in #1873. I am trying to make the input graphs haps-base, sim-base, and sim-ref. I believe I understand how to create sim-base using |
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You need a phased VCF describing the haplotypes you want to simulate from.
You build the GBWT from that and then extract the haplotype path subgraphs
for each haplotype. The graph that this is built from can be used to obtain
the reference relative coordinates of reads simulated from each of the
graphs.
There is a thread on another issue that describes how it's done. It's time
to script it out entirely.
What input do you have to the simulation?
…On Fri, Jan 10, 2020, 20:07 cademirch ***@***.***> wrote:
I am trying to subset the reference portion of that graph. What I am
trying to do is replicate the map-sim script referenced in #1873
<#1873>. I am trying to make the input
graphs haps-base, sim-base, and sim-ref. I believe I understand how to
create sim-base using vg construct -a, but I am unclear on how to derive
haps-base and sim-ref from sim-base.
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This is what I've attempted so far, and I believe is the way to create these graphs (correct me if I'm wrong) I understand obtaining the reference relative positions using sim_base. However I would also like to know the subset of reads that map exactly to the reference and those which touch non-reference variation. Map-sim refers to using sim-ref which is what I am trying to achieve. Could you point me to that issue? I'm not sure what you mean by input to the simulation, I've got indexed haplotype graphs. Thank you for your help. |
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1. What were you trying to do?
I was trying to make an xg index and annotate a GAM.
2. What did you want to happen?
Make an xg index, as well as annotate a GAM
3. What actually happened?
vg crashed.
what(): [vg::io::MessageIterator] obsolete, invalid, or corrupt input at message 12668894457 group 11257826026 ERROR: Signal 6 occurred. VG has crashed. Run 'vg bugs --new' to report a bug.This crash happened on two separate instances - with two different graphs. The message and group were different for both instances.
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:5. What data and command can the vg dev team use to make the problem happen?
I can make the data available if need be.
6. What does running
vg versionsay?The text was updated successfully, but these errors were encountered: