Errors with tumor-only variant calling (-C option) about octopus HOT 5 CLOSED

Hi Nam,

It looks like the octopus Bioconda package was built with debug information. I have come across this assertion violation myself recently, but haven't had time to look into it yet (I wrote this code some time ago!). However, as far as I can tell it does not lead to any adverse behaviour, so I'm quite confident it can be safely ignored. I'll get in touch with the Bioconda maintainer to see if they can rebuild octopus without debug symbols, but in the meantime you can likely get around this by building octopus yourself, or even using the Docker image.

Just to warn you, the tumour only calling in octopus is not well tested at all yet, and runtimes might be very bad. Hopefully I'll address this soon.

from octopus.

Thank you for your quick answer. I got so many problems when building Octopus with CMake, so I will try to use Python3 to build it. Hope it works.

from octopus.

I've made a pull request to Bioconda recipes which should force octopus to be built in release mode and prevent the issue you're having.

from octopus.

Thank you, hope to see it updated soon!

from octopus.

The Bioconda recipe has now been updated so I'll close this issue.

from octopus.