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vg augment crashed #2502
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It's complaining about a node in the GAM not being in the graph. Was x.gam
created by mapping to merged.vg?
…On Thu, Oct 10, 2019 at 2:00 PM Chen Sun ***@***.***> wrote:
I am trying to augment a graph with the .gam file using the following
command line.
vg augment -p -t 12 merged.vg x.gam -C -A x.aug.gam > x.aug.vg
The standard output is:
Reading input graph
vg: src/augment.cpp:327: std::unordered_map<long int, std::set<std::tuple<long int, bool, long unsigned int> > > vg::forwardize_breakpoints(const HandleGraph*, const std::unordered_map<long int, std::set<std::tuple<long int, bool, long unsigned int> > >&): Assertion `graph->has_node(node_id)' failed.
ERROR: Signal 6 occurred. VG has crashed. Run 'vg bugs --new' to report a bug.
Stack trace path: /tmp/vg_crash_PnjvsC/stacktrace.txt
The stacktrace.txt is:
Crash report for vg v1.19.0 "Tramutola"
Stack trace (most recent call last):
#13 Object "/home/cnsun/software/bin/vg", at 0x4d6a79, in _start
#12 Object "/home/cnsun/software/bin/vg", at 0x1ac8318, in __libc_start_main
#11 Object "/home/cnsun/software/bin/vg", at 0x40a7d2, in main
#10 Object "/home/cnsun/software/bin/vg", at 0x9a94e7, in vg::subcommand::Subcommand::operator()(int,
char**) const
#9 Object "/home/cnsun/software/bin/vg", at 0x96dc2b, in main_augment(int, char**)
#8 Object "/home/cnsun/software/bin/vg", at 0xa4538c, in vg::get_input_file(s
td::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, std::function<void (std::istream&)>)
#7 Object "/home/cnsun/software/bin/vg", at 0x96a2f1, in std::_Function_handler<void (std::istream&), main_augment(int, char**)::{lambda(std::istream&)#7}>::_M_invoke(std::_Any_data const&, std::istream&)
#6 Object "/home/cnsun/software/bin/vg", at 0xa7d887, in vg::augment(handlegraph::MutablePathMutableHandleGraph*, std::istream&, std::vector<vg::Translation, std::allocator<vg::Translation> >*, std::ostream*, bool, bool, bool)
#5 Object "/home/cnsun/software/bin/vg", at 0xa7ca2b, in vg::augment_impl(handlegraph::MutablePathMutableHandleGraph*, std::function<void (std::function<void (vg::Alignment&)>, bool)>, std::vector<vg::Translation, std::allocator<vg::Translation> >*, std::ostream*, bool, bool, bool)
#4 Object "/home/cnsun/software/bin/vg", at 0xa78d44, in vg::forwardize_breakpoints(handlegraph::HandleGraph const*, std::unordered_map<long, std::set<std::tuple<long, bool, unsigned long>, std::less<std::tuple<long, bool, unsigned long> >, std::allocator<std::tuple<long, bool, unsigned long> > >, std::hash<long>, std::equal_to<long>, std::allocator<std::pair<long const, std::set<std::tuple<long, bool, unsigned long>, std::less<std::tuple<long, bool, unsigned long> >, std::allocator<std::tuple<long, bool, unsigned long> > > > > > const&)
#3 Object "/home/cnsun/software/bin/vg", at 0x1acc231, in __assert_fail
#2 Object "/home/cnsun/software/bin/vg", at 0x1acc1bb, in __assert_fail_base
#1 Object "/home/cnsun/software/bin/vg", at 0x1ad8be0, in abort
#0 Object "/home/cnsun/software/bin/vg", at 0x10ab3d7, in raise
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To get a more verbose error (if a graph/gam mismatch is indeed the issue) you can run
|
That may be the reason. I generate the |
Perhaps. A few things
|
Thanks for your suggestions. I will try them to see whether they works. |
Merging the input beforehand with |
I am still a little confusing when I using I built the |
Unless your genome is small or your gam is very low coverage, then the answer is probably no, unfortunately. augment will use too much memory. If you have a lot of memory and want to try anyway, I recommend running One work-around, which maybe you were trying to get at to begin with, is to work on chromosomes.
But then you'll run into that assertion error unless your GAM is also split by chromosome (possible but slow). I will patch augment to not fail on these cases so the above by-chromosome workflow would run. Hopefully we'll have whole-genome augmentation running better in the next release. |
I am trying to augment the graph produced using vcf file along with the reference genome (working on a cluster with RAM 700Gb) using following command:
Could you please suggest what is going wrong? I have generated the graph using vg and the gams using vg as well. |
I am trying to augment a graph with the
.gam
file using the following command line.The standard output is:
The
stacktrace.txt
is:The text was updated successfully, but these errors were encountered: