vg rna crash #4813
Description
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1. What were you trying to do?
run vg rna to create a pangenome graph with splicing information. Trying to follow the long-read rna-seq process on the wiki page using drosophila pangenome and assoc files.
2. What did you want to happen?
see above
3. What actually happened?
vg crashed - see below
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:
[vg rna] Parsing graph file ...
[vg rna] Converting graph format ...
[vg rna] Graph and GBWT index parsed in 17.5919 seconds, 1.23344 GB
[vg rna] Adding transcript splice-junctions and exon boundaries to graph ...
vg: src/transcriptome.cpp:826: void vg::Transcriptome::add_exon(vg::Transcript*, const std::pair<int, int>&) const: Assertion `exon_pos.second < transcript->chrom_length' failed.
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Crash report for vg v1.70.0 "Zebedassi"
Caught signal 6 raised at address 0x23d333c; tracing with backward-cpp
Stack trace (most recent call last):
#14 Object "/apps/vg/1.70.0/bin/vg", at 0x6824b4, in _start
#13 Object "/apps/vg/1.70.0/bin/vg", at 0x238f606, in __libc_start_main
#12 Object "/apps/vg/1.70.0/bin/vg", at 0x238dd69, in __libc_start_call_main
#11 Object "/apps/vg/1.70.0/bin/vg", at 0x6830cb, in vg_main(int, char**)
#10 Object "/apps/vg/1.70.0/bin/vg", at 0xfb4ddb, in vg::subcommand::Subcommand::operator()(int, char**) const
#9 Object "/apps/vg/1.70.0/bin/vg", at 0xf7a802, in main_rna(int, char**)
#8 Object "/apps/vg/1.70.0/bin/vg", at 0x164115b, in vg::Transcriptome::add_reference_transcripts(std::vector<std::istream*, std::allocator<std::istream*> >, std::unique_ptr<gbwt::GBWT, std::default_delete<gbwt::GBWT> >&, bool, bool)
#7 Object "/apps/vg/1.70.0/bin/vg", at 0x16405c0, in vg::Transcriptome::parse_transcripts(std::vector<vg::Transcript, std::allocator<vg::Transcript> >*, unsigned int*, std::istream*, bdsg::PositionOverlay const&, gbwt::GBWT const&, bool) const [clone .constprop.0]
#6 Object "/apps/vg/1.70.0/bin/vg", at 0x163cf0e, in vg::Transcriptome::add_exon(vg::Transcript*, std::pair<int, int> const&, bdsg::PositionOverlay const&) const [clone .constprop.0]
#5 Object "/apps/vg/1.70.0/bin/vg", at 0x161a5f5, in vg::Transcriptome::add_exon(vg::Transcript*, std::pair<int, int> const&) const
#4 Object "/apps/vg/1.70.0/bin/vg", at 0x23a01d5, in __assert_fail
#3 Object "/apps/vg/1.70.0/bin/vg", at 0x63f657, in __assert_fail_base.cold
#2 Object "/apps/vg/1.70.0/bin/vg", at 0x63f72f, in abort
#1 Object "/apps/vg/1.70.0/bin/vg", at 0x23a67e5, in raise
#0 Object "/apps/vg/1.70.0/bin/vg", at 0x23d333c, in __pthread_kill
Library locations:
ERROR: Signal 6 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug.
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Context dump:
Thread 0: Starting 'rna' subcommand
Found 1 threads with context.
5. What data and command can the vg dev team use to make the problem happen?
following gave the error:
vg rna -p \
--threads 16 \
--proj-embed-paths \
--gbz-format $REF/16-fruitfly-mc-2022-05-26-full.gbz \
--transcripts $REF/dmel650_protein_coding_ref_withMods.gtf \
--gbwt-bidirectional \
--write-gbwt $PROJ/transcripts.gbwt \
> $PROJ/dmel_spliced_pangenome.pg
6. What does running vg version say?
vg/1.70.0