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vgteam / vg

tools for working with genome variation graphs
https://biostars.org/tag/vg/
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Duplicate alignment names with pair-ends reads! #3139

Closed sunnycqcn closed 3 years ago

sunnycqcn commented 3 years ago

Hello developer, I want to use vg to build a fungal pangenome graph. I have total of 148 isolate genome sequences. The first I called the variants using GATK-pipeline. Then I used these variants to run command: vg construct -r L022.fa -v fin.vcf.gz > graph.vg vg index -x graph.xg -k 11 graph.vg vg index -x graph.xg -G graph.gbwt -v fin.vcf.gz graph.vg vg prune -u -g graph.gbwt graph.vg > graph.pruned.vg vg index -g graph.gcsa graph.pruned.vg vg map -t 80 -x graph.xg -g graph.gcsa -f /isilon/saskatoon-rdc/users/fuf/BLgenome/DELLY/seq/L165_R1.fastq -f /isilon/saskatoon-rdc/users/fuf/BLgenome/DELLY/seq/L165_R2.fastq > L165.gam above commands can work well. I did not get any errors. But when I run this command vg index -d L165.gam.index -N L165.gam I got the errors as following: terminate called after throwing an instance of 'std::runtime_error' what(): RocksDB operation failed: IO error: While fdatasync: L165.gam.index/000009.sst: Input/output error ERROR: Signal 6 occurred. VG has crashed. Run 'vg bugs --new' to report a bug. Stack trace path: /tmp/vg_crash_KMtQ1H/stacktrace.txt Please include the stack trace file in your bug report! Then I check the stacktrace.txt: `Crash report for vg v1.29.0 "Sospiro" Stack trace (most recent call last):

15 Object "/home/AAFC-AAC/fuf/miniconda3/envs/gatk/bin/vg", at 0x63c27d, in _start

14 Object "/home/AAFC-AAC/fuf/miniconda3/envs/gatk/bin/vg", at 0x1f4dd3f, in __libc_start_main

13 Object "/home/AAFC-AAC/fuf/miniconda3/envs/gatk/bin/vg", at 0x55db18, in main

12 Object "/home/AAFC-AAC/fuf/miniconda3/envs/gatk/bin/vg", at 0xc0c5cb, in vg::subcommand::Subcommand::operator()(int, char**) const

11 Object "/home/AAFC-AAC/fuf/miniconda3/envs/gatk/bin/vg", at 0xb7b3c1, in main_index(int, char**)

10 Object "/home/AAFC-AAC/fuf/miniconda3/envs/gatk/bin/vg", at 0xdb4a10, in vg::get_input_file(std::__cxx11::basic_string<char, std::char_traits, std::allocator > const&, std::function<void (std::istream&)>)

9 Object "/home/AAFC-AAC/fuf/miniconda3/envs/gatk/bin/vg", at 0xb7d311, in std::_Function_handler<void (std::istream&), main_index(int, char**)::{lambda(std::istream&)#7}>::_M_invoke(std::_Any_data const&, std::istream&)

8 Object "/home/AAFC-AAC/fuf/miniconda3/envs/gatk/bin/vg", at 0xb5e673, in void vg::io::for_each(std::istream&, std::function<void (long, vg::Alignment&)> const&)

7 Object "/home/AAFC-AAC/fuf/miniconda3/envs/gatk/bin/vg", at 0xcc40e9, in vg::Index::cross_alignment(long, vg::Alignment const&)

6 Object "/home/AAFC-AAC/fuf/miniconda3/envs/gatk/bin/vg", at 0x4d65b6, in vg::Index::put_traversal(long, vg::Mapping const&) [clone .cold]

5 Object "/home/AAFC-AAC/fuf/miniconda3/envs/gatk/bin/vg", at 0x1e89b98, in __cxa_throw

4 Object "/home/AAFC-AAC/fuf/miniconda3/envs/gatk/bin/vg", at 0x1e89a36, in std::terminate()

3 Object "/home/AAFC-AAC/fuf/miniconda3/envs/gatk/bin/vg", at 0x1e899cb, in cxxabiv1::terminate(void (*)())

2 Object "/home/AAFC-AAC/fuf/miniconda3/envs/gatk/bin/vg", at 0x55a5e2, in __gnu_cxx::__verbose_terminate_handler() [clone .cold]

1 Object "/home/AAFC-AAC/fuf/miniconda3/envs/gatk/bin/vg", at 0x55d073, in abort

0 Object "/home/AAFC-AAC/fuf/miniconda3/envs/gatk/bin/vg", at 0x12e238b, in raise

` I install VG by conada with version v1.29.0. By the way, did you finish the example as described in wiki (A-pangenomics-example-with-vg-(viruses))? Thanks, Fuyou

glennhickey commented 3 years ago

Please try to answer the questions in the new issue template so that we can better help you, Fuyou.

sunnycqcn commented 3 years ago

Please try to answer the questions in the new issue template so that we can better help you, Fuyou.

Hello Glenn, I have update my issue. Thanks for your suggestions. Fuyou

glennhickey commented 3 years ago

vg index -d is deprecated and is in the process of being removed altogether (#3137). Why are you running it? If there's a wiki or other documentation suggesting it, we need to update it.

sunnycqcn commented 3 years ago

vg index -d is deprecated and is in the process of being removed altogether (#3137). Why are you running it? If there's a wiki or other documentation suggesting it, we need to update it.

I think the wiki instruction is confused and should be updated. It is working well now. Thanks.