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use vg rna to construct spliced pangenome and crashed #4150

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zhangming-m opened this issue Nov 8, 2023 · 1 comment
Open

use vg rna to construct spliced pangenome and crashed #4150

zhangming-m opened this issue Nov 8, 2023 · 1 comment

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@zhangming-m
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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
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Are you able to share the data that led to this crash?

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