odgi flip error

[yuliamostovoy]

I'm getting an error when running "odgi flip" using an .og subgraph file built from an HPRC PGGB-generated graph from here. My commands look like this:

odgi build -O -P -t 16 -g chr1.hprc-v1.0-pggb.gfa -o chr1.hprc-v1.0-pggb.og
odgi extract -i chr1.hprc-v1.0-pggb.og -o subgraph.hprc-v1.0-pggb.og -E -L 10000  -r grch38#chr1:1449689-1534685 -t 16 -P
odgi flip -i subgraph.hprc-v1.0-pggb.og -o subgraph.hprc-v1.0-pggb.flip.og -t 16

odgi: /home/jupyter/odgi/src/odgi.cpp:1649: virtual void odgi::graph_t::serialize_members(std::ostream&) const: Assertion `j == _path_count' failed.
Aborted (core dumped)

I'd appreciate any help, thanks!

[yuliamostovoy]

I got this to work by using odgi view to convert the subgraph to gfa, and then inputting that gfa to odgi flip. It just fails with the og file as input. A little downstream, I had the same thing happen with "odgi inject" - threw an error with the og file, worked fine if I converted the og to gfa first. Not sure if I'm doing something wrong here!

[ekg]

This is definitely a known issue. There is a solution that's easy which I'll implement tomorrow (just copying the graph).

On Mon, Jul 18, 2022, 20:28 Yulia Mostovoy @.***> wrote:

I got this to work by using odgi view to convert the subgraph to gfa, and then inputting that gfa to odgi flip. It just fails with the og file as input. A little downstream, I had the same thing happen with "odgi inject"

• threw an error with the og file, worked fine if I converted the og to gfa first. Not sure if I'm doing something wrong here!

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[AndreaGuarracino]

Fixed in #436.