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vgteam / vg

tools for working with genome variation graphs
https://biostars.org/tag/vg/
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use vg rna to construct spliced pangenome and crashed #4150

Open zhangming-m opened 1 year ago

zhangming-m commented 1 year ago

my code : vg rna -p --threads 20 --transcripts /data/yxzhu/Oaks/Ref_genome/Ref_genome/Quercus_variabilis/Quercus_variabilis_onlychr_rename_converted.gff3 --use-hap-ref --gbz-format --write-gbwt Quercus9-pg_pantranscriptome.gbwt --write-info Quercus9-pg_pantranscriptome.txt /data/yxzhu/Oaks/pangenome/Quercus9pangenome/Quercus9-pg.gbz

output: Crash report for vg v1.49.0 "Peschici" Stack trace (most recent call last):

13 Object "/data/zhangmm/zyx_RNAseq/software/cactus-bin-v2.6.4/bin/vg", at 0x615534, in _start

12 Object "/data/zhangmm/zyx_RNAseq/software/cactus-bin-v2.6.4/bin/vg", at 0x2056606, in __libc_start_main

11 Object "/data/zhangmm/zyx_RNAseq/software/cactus-bin-v2.6.4/bin/vg", at 0x2054da9, in __libc_start_call_main

10 Object "/data/zhangmm/zyx_RNAseq/software/cactus-bin-v2.6.4/bin/vg", at 0xdf08ab, in vg::subcommand::Subcommand::operator()(int, char**) const

9 Object "/data/zhangmm/zyx_RNAseq/software/cactus-bin-v2.6.4/bin/vg", at 0xdc1be2, in main_rna(int, char**)

8 Object "/data/zhangmm/zyx_RNAseq/software/cactus-bin-v2.6.4/bin/vg", at 0xdbf4d2, in std::__cxx11::basic_string<char, std::char_traits, std::allocator >::basic_string(char const*, std::allocator const&) [clone .constprop.0]

7 Object "/data/zhangmm/zyx_RNAseq/software/cactus-bin-v2.6.4/bin/vg", at 0x5e380b, in std::__throw_logic_error(char const*)

6 Object "/data/zhangmm/zyx_RNAseq/software/cactus-bin-v2.6.4/bin/vg", at 0x1f8ea98, in __cxa_throw

5 Object "/data/zhangmm/zyx_RNAseq/software/cactus-bin-v2.6.4/bin/vg", at 0x1f8e936, in std::terminate()

4 Object "/data/zhangmm/zyx_RNAseq/software/cactus-bin-v2.6.4/bin/vg", at 0x1f8e8cb, in cxxabiv1::terminate(void (*)())

3 Object "/data/zhangmm/zyx_RNAseq/software/cactus-bin-v2.6.4/bin/vg", at 0x5e1c83, in __gnu_cxx::__verbose_terminate_handler() [clone .cold]

2 Object "/data/zhangmm/zyx_RNAseq/software/cactus-bin-v2.6.4/bin/vg", at 0x5e43cb, in abort

1 Object "/data/zhangmm/zyx_RNAseq/software/cactus-bin-v2.6.4/bin/vg", at 0x206d7e5, in raise

0 Object "/data/zhangmm/zyx_RNAseq/software/cactus-bin-v2.6.4/bin/vg", at 0x209a1ec, in __pthread_kill

1. What were you trying to do?

2. What did you want to happen?

3. What actually happened?

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:

Place stacktrace here.

5. What data and command can the vg dev team use to make the problem happen?

6. What does running vg version say?


Place vg version output here
jeizenga commented 1 year ago

Are you able to share the data that led to this crash?