vg rna crashed

[GSgen]

Hello,

I am using vg rna as:

vg convert -g smooth.gfa -p > out.pg
#creating gbwt
vg gbwt -p -G /smooth.gfa \
    -o out.gbwt \
    -g out.gg 

#creating spliced graph
vg rna -p -n out.gtf -l out.gbwt out.pg > out_graph.pg

But it crashes as:

[vg rna] Parsing graph file ...
[vg rna] Parsing haplotype GBWT index file ...
[vg rna] Graph and GBWT index parsed in 0.688464 seconds, 0.599934 GB
[vg rna] Adding novel exon boundaries and splice-junctions to graph ...
[vg rna] 0 introns and 127175 transcripts parsed, and graph augmented in 113.558 seconds, 12.9742 GB
[vg rna] Projecting haplotype-specfic transcripts ...
vg: src/transcriptome.cpp:646: std::__cxx11::list<vg::EditedTranscriptPath> vg::Transcriptome::project_transcript_gbwt(const vg::Transcript&, const gbwt::GBWT&, float) const: Assertion `haplotype_id_index_it->second.second < exon_idx' failed.
ERROR: Signal 6 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug.
Stack trace path: /tmp/vg_crash_uBjrfT/stacktrace.txt
Please include the stack trace file in your bug report!

Could anyone please suggest how to fix this?

Thank you!

[jonassibbesen]

Hi,

I am not sure why this assertion is failing. Would it be possible for you to share the data?

Best,

Jonas

[GSgen]

Hi @jonassibbesen,

Could you share your email, and I can send you the data.

Thank you!

[jonassibbesen]

[email protected]

Thanks!

[GSgen]

@jonassibbesen, Thank you! I have sent the files to you.

[jjuhyunkim]

I encountered the same error. Have you managed to find a solution for this issue?