VG crashed when performing construct #2048
Comments
|
There's probably a sequence name in a VCF it can't find in your fasta.
Running with the latest release (1.13.0) should give you a more useful
error message.
…On Tue, Jan 8, 2019 at 12:15 AM tahuh ***@***.***> wrote:
Please describe:
Hi
I'm trying subcommand "construct" using reference sequence
VCF files that I using is COSMIC's coding/non-coding variants from COSMIC
v87 data and dbSNP 150
Also I tried using insertion sequence list from those VCF files.
The command I used is shown below
vg construct -r /Data/reference/hg38.fa -v /Data/reference/CosmicCodingMuts_v87.vcf -v /Data/reference/CosmicNonCodingVariants_v87.vcf -v /Data/reference/dbsnp150.vcf.gz -I /Data/reference/hg38_vg_insersion_cosmic_coding_non_coding_dbsnp150.fa > hg38.vg
The error message vg sent me is written below
vg: src/constructor.cpp:2041: void vg::Constructor::construct_graph(const std::vector<FastaReference*>&, const std::vector<vcflib::VariantCallFile*>&, const std::vector<FastaReference*>&, std::function<void(vg::Graph&)>): Assertion `reference_for.count(fasta_contig)' failed.
ERROR: Signal 6 occurred. VG has crashed. Run 'vg bugs --new' to report a bug.
Stack trace path: /tmp/vg_crash_ktaDns/stacktrace.txt
Error stack is shown below
Crash report for vg v1.12.1-113-g5c08133 "Parolise"
Stack trace (most recent call last):
#10 Object "", at 0xffffffffffffffff, in
#9 Object "/Data/program/vg/bin/vg", at 0x792c18, in _start
#8 Object "/lib/x86_64-linux-gnu/libc-2.23.so", at 0x7ffa46dfe82f, in __libc_start_main
Source "../csu/libc-start.c", line 291, in __libc_start_main [0x7ffa46dfe82f]
#7 Object "/Data/program/vg/bin/vg", at 0x6dc48b, in main
Source "src/main.cpp", line 68, in main [0x6dc48b]
#6 Object "/Data/program/vg/bin/vg", at 0xbb2937, in vg::subcommand::Subcommand::operator()(int, char**) const
| Source "src/subcommand/subcommand.cpp", line 72, in operator()
Source "/usr/include/c++/5/functional", line 2267, in operator() [0xbb2937]
2264: {
2265: if (_M_empty())
2266: __throw_bad_function_call();
>2267: return _M_invoker(_M_functor, std::forward<_ArgTypes>(__args)...);
2268: }
2269:
2270: #if __cpp_rtti
#5 Object "/Data/program/vg/bin/vg", at 0xbec248, in main_construct(int, char**)
Source "src/subcommand/construct_main.cpp", line 342, in main_construct [0xbec248]
#4 Object "/Data/program/vg/bin/vg", at 0xeb7e6c, in vg::Constructor::construct_graph(std::vector<FastaReference*, std::allocator<FastaReference*> > const&, std::vector<vcflib::VariantCallFile*, std::allocator<vcflib::VariantCallFile*> > const&, std::vector<FastaReference*, std::allocator<FastaReference*> > const&, std::function<void (vg::Graph&)>)
Source "src/constructor.cpp", line 2041, in construct_graph [0xeb7e6c]
#3 Object "/lib/x86_64-linux-gnu/libc-2.23.so", at 0x7ffa46e0bc81, in __assert_fail
Source "/build/glibc-Cl5G7W/glibc-2.23/assert/assert.c", line 101, in __assert_fail [0x7ffa46e0bc81]
#2 Object "/lib/x86_64-linux-gnu/libc-2.23.so", at 0x7ffa46e0bbd6, in __assert_fail_base
Source "/build/glibc-Cl5G7W/glibc-2.23/assert/assert.c", line 92, in __assert_fail_base [0x7ffa46e0bbd6]
#1 Object "/lib/x86_64-linux-gnu/libc-2.23.so", at 0x7ffa46e15029, in abort
Source "/build/glibc-Cl5G7W/glibc-2.23/stdlib/abort.c", line 89, in abort [0x7ffa46e15029]
#0 Object "/lib/x86_64-linux-gnu/libc-2.23.so", at 0x7ffa46e13428, in raise
Source "../sysdeps/unix/sysv/linux/raise.c", line 54, in raise [0x7ffa46e13428]
Is there anything that I can try?
—
You are receiving this because you are subscribed to this thread.
Reply to this email directly, view it on GitHub
<#2048>, or mute the thread
<https://github.com/notifications/unsubscribe-auth/AA2_7sZmoDuQ_UcwMvpeyNY5xN2UuXd6ks5vBClngaJpZM4Z0yRk>
.
|
|
@glennhickey The problem was CHROM field of VCF file I have did not have matched FASTA name on reference so I changed VCF's CHROM field as you said and it worked. Thanks for your suggestion. |
|
Hi command line that I typed is same as above Before running construct I have changed chromosome name field of VCF files to our reference FASTA reference name which starts with "chr" but VCF wasn't. Our reference FASTA was downloaded from http://hgdownload.cse.ucsc.edu/goldenPath/hg38/bigZips/ Below is error message Also I observed many warning message like below Is it normal? Our server system equipped with Ubuntu 16.04 LTS and gcc 5.4.0 If you need more information please let me know. Many thanks! |
|
I also omitted dbSNP150 file but keep crashing with Signal 11 error with error stacktrace below It went well without any VCF files specified and any -I option. Is there any reason also? |
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Please describe:
Hi
I'm trying subcommand "construct" using reference sequence
VCF files that I using is COSMIC's coding/non-coding variants from COSMIC v87 data and dbSNP 150
Also I tried using insertion sequence list from those VCF files.
The command I used is shown below
The error message vg sent me is written below
Error stack is shown below
Is there anything that I can try?
The text was updated successfully, but these errors were encountered: