`odgi validate` crashing on large graphs

[anshumanmohan]

Running

make clean
make og
turnt --env validate_oracle test/*.og

gives me exit code 134 for the larger files, and, on running in verbose mode, a complaint about the utf-8 encoding.

Seems strange, since it works okay when I run

make clean
make fetch
turnt --env validate_oracle test/*.gfa

That is, letting odgi do an on-the-fly conversion from .gfa to .og works out okay.

[sampsyo]

Here's what turnt -vp --env validate_oracle test/*.og prints for me:

$ odgi build -g DRB1-3123.og -o - | odgi validate -i - 2>&1
Missing value at GFA line: S
                            !b6T?l
                                  P1
warning [libhandlegraph]: Serialized object does not appear to match deserialzation type.
warning [libhandlegraph]: It is either an old version or in the wrong format.
warning [libhandlegraph]: Attempting to load it anyway. Future releases will reject it!
libc++abi: terminating due to uncaught exception of type std::runtime_error: Error rewinding to load non-magic-prefixed SerializableHandleGraph
/bin/sh: line 1: 12560 Done(1)                 odgi build -g DRB1-3123.og -o -
     12561 Abort trap: 6           | odgi validate -i - 2>&1

That is, we're running odgi build -g DRB1-3123.og -o -, which bails out quickly because DRB1-3123.og doesn't look like a GFA file. And indeed; it's not.

It's quite possible I'm missing something, but it seems like the validate_oracle Turnt environment is not set up to accept pre-converted .og files—just actual GFA files. Is there perhaps a different environment that's supposed to take pre-converted odgi files?

[anshumanmohan]

Whoops, you're totally right. It was designed to accept GFAs and I moved to an .og-accepting style for uniformity, but then failed to make the change in my turnt config. Easy fix, coming up first thing tomorrow!

[anshumanmohan]

Also, good to be reminded of the -p flag, especially in combination with -v!