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vg find command to get subgraphs of genomic regions failed #2585

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JYLeeBioinfo opened this issue Jan 2, 2020 · 9 comments
Open

vg find command to get subgraphs of genomic regions failed #2585

JYLeeBioinfo opened this issue Jan 2, 2020 · 9 comments

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@JYLeeBioinfo
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JYLeeBioinfo commented Jan 2, 2020 •
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1. What were you trying to do?
I was trying to do extract a subgraph of a certain genome region.

The original graph I want to extract the subgrpahs from is hg38 with alternative paths from SV call VCF files.

vg find -x N_sorted_chr1-1mb.xg -E chr1:998639-998887 > individual_svs/N_sorted_chr1-1mb_chr1-998639-998887__12_1.vg 2> individual_svs/N_sorted_chr1-1mb_chr1-998639-998887__12_1.vg.err

2. What did you want to happen?
I wanted to get a vg file

3. What actually happened?
The following error occurred and empty vg file was generated

terminate called after throwing an instance of 'std::runtime_error'
  what():  Attempted to get handle for node 30 not present in graph
ERROR: Signal 6 occurred. VG has crashed. Run 'vg bugs --new' to report a bug.
Stack trace path: /tmp/vg_crash_JnUw8A/stacktrace.txt

One thing strange is that not all regions I tested failed.
I tested 14 regions and 13 regions failed and 1 region succeeded.

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:

all 13 regions that failed gave me the following error message

#13   Object "", at 0xffffffffffffffff, in
#12   Object "/appl/compiler/gcc/7.4.0/applib1/vg/1.19.0/bin/vg", at 0x785150, in _start
#11   Object "/lib64/libc-2.17.so", at 0x363e821b44, in __libc_start_main
#10   Object "/appl/compiler/gcc/7.4.0/applib1/vg/1.19.0/bin/vg", at 0x6ca530, in main
      Source "src/main.cpp", line 74, in main [0x6ca530]
#9    Object "/appl/compiler/gcc/7.4.0/applib1/vg/1.19.0/bin/vg", at 0xc75817, in vg::subcommand::Subcommand::operator()(int, char**) const
    | Source "src/subcommand/subcommand.cpp", line 72, in operator()
      Source "/appl/compiler/gcc/7.4.0/include/c++/7.4.0/bits/std_function.h", line 706, in operator() [0xc75817]
        703:     {
        704:       if (_M_empty())
        705:    __throw_bad_function_call();
      > 706:       return _M_invoker(_M_functor, std::forward<_ArgTypes>(__args)...);
        707:     }
        708:
        709: #if __cpp_rtti
#8    Object "/appl/compiler/gcc/7.4.0/applib1/vg/1.19.0/bin/vg", at 0xbc7922, in main_find(int, char**)
      Source "src/subcommand/find_main.cpp", line 588, in main_find [0xbc7922]
#7    Object "/appl/compiler/gcc/7.4.0/applib1/vg/1.19.0/bin/vg", at 0x106c785, in vg::algorithms::extract_id_range(handlegraph::HandleGraph const&, long const&, long const&, handlegraph::MutableHandleGraph&)
      Source "src/algorithms/subgraph.cpp", line 267, in extract_id_range [0x106c785]
#6    Object "/appl/compiler/gcc/7.4.0/applib1/vg/1.19.0/bin/vg", at 0x157b82c, in xg::XG::get_handle(long const&, bool) const
      Source "deps/xg/src/xg.cpp", line 1580, in get_handle [0x157b82c]
#5    Object "/appl/compiler/gcc/7.4.0/lib64/libstdc++.so.6.0.24", at 0x7feeddc53802, in __cxa_throw
      Source "../../../../libstdc++-v3/libsupc++/eh_throw.cc", line 93, in __cxa_throw [0x7feeddc53802]
#4    Object "/appl/compiler/gcc/7.4.0/lib64/libstdc++.so.6.0.24", at 0x7feeddc535c0, in std::terminate()
      Source "../../../../libstdc++-v3/libsupc++/eh_terminate.cc", line 57, in terminate [0x7feeddc535c0]
#3    Object "/appl/compiler/gcc/7.4.0/lib64/libstdc++.so.6.0.24", at 0x7feeddc53575, in __cxxabiv1::__terminate(void (*)())
      Source "../../../../libstdc++-v3/libsupc++/eh_terminate.cc", line 47, in __cxa_begin_catch [0x7feeddc53575]
#2    Object "/appl/compiler/gcc/7.4.0/lib64/libstdc++.so.6.0.24", at 0x7feeddc55794, in __gnu_cxx::__verbose_terminate_handler()
      Source "../../../../libstdc++-v3/libsupc++/vterminate.cc", line 95, in __verbose_terminate_handler [0x7feeddc55794]
#1    Object "/lib64/libc-2.17.so", at 0x363e8370e7, in abort
#0    Object "/lib64/libc-2.17.so", at 0x363e8359d9, in raise

5. What data and command can the vg dev team use to make the problem happen?
data : https://drive.google.com/open?id=1x1VbO2zcPhRjOVPIEL2W-UIXbOOIKfyw
This is vg and xg I generated using Momig-tools vcf2xg.sh

command

vg find -x N_sorted_chr1-1mb.xg -E chr1:998639-998887 > N_sorted_chr1-1mb_chr1-998639-998887__12_1.vg

6. What does running vg version say?

vg version v1.19.0 "Tramutola"
Compiled with g++ (GCC) 7.4.0 on Linux
Linked against libstd++ 20181206
Built by root@node10
@ekg
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ekg commented Jan 2, 2020 via email

@JYLeeBioinfo
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Hi, it seems the options have changed when vg moved from version 1.19 to 1.20

I am currently using vg1.19.0 and this is the help message I get

    -p, --path TARGET      find the node(s) in the specified path range(s) TARGET=path[:pos1[-pos2]]
    -E, --path-dag TARGET  like -p, but gets any node in the partial order from pos1 to pos2, assumes id sorted DAG

I have tried for hours to install the vg1.20.0 but no success

It's quite hard for me to update VG since the server OS is CentOS 6.10

@ekg
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ekg commented Jan 2, 2020 via email

@JYLeeBioinfo
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Sadly, it does not work...

Kernel too old error for both 1.19 and 1.20 binaries.

So I'm trying to build 1.20 from source

@ekg
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ekg commented Jan 2, 2020 via email

@JYLeeBioinfo
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I tried docker but "kernel too old" message also arose within the containers made from CentOS 6, 7 and ubuntu18.04 images.

@JYLeeBioinfo
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I succeeded in installing vg1.20 but still got the same error.

It seems the xg and vg I built using Momig-tools are causing the error.

So, I tried building vg file using vg construct with vg1.20, but got the another error 😵

#command

vg construct -r /data/REFERENCE/hg38/Homo_sapiens_assembly38.fasta -v N_sorted_chr1-1mb.vcf  -a  -t 28 --handle-sv --flat-alts -p \
 > N_sorted_chr1-1mb.vcf.vg-construct.vg 2> N_sorted_chr1-1mb.vcf.vg-construct.vg.err

#error

vg: src/Variant.cpp:349: bool vcflib::Variant::canonicalize(FastaReference&, std::vector<FastaReference*>, bool, int): Assertion `canonicalizable()' failed.
ERROR: Signal 6 occurred. VG has crashed. Run 'vg bugs --new' to report a bug.
Stack trace path: /tmp/vg_crash_VkQ0Ok/stacktrace.txt
Please include the stack trace file in your bug report!

#trace

Crash report for vg v1.20.0-138-gf275f10 "Ginestra"
Stack trace (most recent call last):
#11   Object "/data2/hd00ljy/data_processing/PMI_Nanopore_WGS/tools_new/11_graph_genome_docker/vg/bin/vg", at 0x794c80, in _start
#10   Object "/lib64/libc-2.12.so", at 0x7f61a0356d1f, in __libc_start_main
#9    Object "/data2/hd00ljy/data_processing/PMI_Nanopore_WGS/tools_new/11_graph_genome_docker/vg/bin/vg", at 0x6d9c60, in main
      Source "src/main.cpp", line 75, in main [0x6d9c60]
#8    Object "/data2/hd00ljy/data_processing/PMI_Nanopore_WGS/tools_new/11_graph_genome_docker/vg/bin/vg", at 0xc900c7, in vg::subcommand::Subcommand::operator()(
int, char**) const
    | Source "src/subcommand/subcommand.cpp", line 72, in operator()
      Source "/usr/local/include/c++/7.4.0/bits/std_function.h", line 706, in operator() [0xc900c7]
        703:     {
        704:       if (_M_empty())
        705:    __throw_bad_function_call();
      > 706:       return _M_invoker(_M_functor, std::forward<_ArgTypes>(__args)...);
        707:     }
        708:
        709: #if __cpp_rtti
#7    Object "/data2/hd00ljy/data_processing/PMI_Nanopore_WGS/tools_new/11_graph_genome_docker/vg/bin/vg", at 0xbc2ce3, in main_construct(int, char**)
      Source "src/subcommand/construct_main.cpp", line 347, in main_construct [0xbc2ce3]
#6    Object "/data2/hd00ljy/data_processing/PMI_Nanopore_WGS/tools_new/11_graph_genome_docker/vg/bin/vg", at 0xd556d3, in vg::Constructor::construct_graph(std::v
ector<FastaReference*, std::allocator<FastaReference*> > const&, std::vector<vcflib::VariantCallFile*, std::allocator<vcflib::VariantCallFile*> > const&, std::vec
tor<FastaReference*, std::allocator<FastaReference*> > const&, std::function<void (vg::Graph&)>)
      Source "src/constructor.cpp", line 2099, in construct_graph [0xd556d3]
#5    Object "/data2/hd00ljy/data_processing/PMI_Nanopore_WGS/tools_new/11_graph_genome_docker/vg/bin/vg", at 0xd53cce, in vg::Constructor::construct_graph(std::_
_cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, FastaReference&, vg::VcfBuffer&, std::vector<FastaReference*, std::allocator<FastaRefer
ence*> > const&, std::function<void (vg::Graph&)>)
      Source "src/constructor.cpp", line 1794, in construct_graph [0xd53cce]
#4    Object "/data2/hd00ljy/data_processing/PMI_Nanopore_WGS/tools_new/11_graph_genome_docker/vg/bin/vg", at 0x1119167, in vcflib::Variant::canonicalize(FastaRef
erence&, std::vector<FastaReference*, std::allocator<FastaReference*> >, bool, int)
#3    Object "/lib64/libc-2.12.so", at 0x7f61a036372f, in __assert_fail
#2    Object "/lib64/libc-2.12.so", at 0x7f61a036366d, in __assert_fail_base
#1    Object "/lib64/libc-2.12.so", at 0x7f61a036bcd4, in abort
#0    Object "/lib64/libc-2.12.so", at 0x7f61a036a4f5, in raise

@ekg
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ekg commented Jan 3, 2020 via email

@JYLeeBioinfo
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I have long-read based SV calls from sniffles SV caller

INS,DEL,TRA,DUP,INV,INVDUP and etc..

For some variants, alt allele is represented like ,

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@ekg @JYLeeBioinfo