Bogdan

I had the same error message ("line 8" in that specific .prfl file) - when installing `funannotate` using `mamba` I got version 3.4 of augustus installed. Downgrading to the Dockerfile...

I have worked around the problem by soft-linking a different, functional augustus 3.3.3 binary into the conda environment.

> Can't locate orf.pm in @inc (you may need to install the orf module) @mgarl-10 , did you figure out how to fix this one? I'm now having essentially the...

> When I manually compile v3.4 it seems to work fine so must be something missing in the conda recipe. I've also tried the new/fixed v3.4 first, but it kept...

> `orf.pm` file does not exist anywhere within the environment, `funannotate check` says all Perl dependencies are present. alright, I've mamba-installed funannotate 1.8.11 (the previous available version, 1.8.12 was not...

> May I ask which version 3.3.3 of augustus worked for you? @tjhinet , while my OS-built augustus 3.3.3 did pass `test -t predict`, it failed later during the actual...

@Cantalapiedra, this happened when `eggnog-mapper` was auto-installed by `conda` as a dependency of `funannotate`. (To be more specific it was `mamba` and not `conda`, but that should not have any...

exactly, bioconda channel. installing (previous version) from pypi had the expected "2.1.1" version string.

Thanks a lot for a quick response! I'll try `clip-nanopore`. This dataset is, unfortunately, not public. If I have enough time, I may also test `clip` on this dataset, and...

@Xueliang24 , maybe try adding some more specific `output` to your `predict` rule (because that output folder will also be created by other rules); that specific output you should then...