funannotate

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Restart after crash of the PASA training terminates normally

5

Hello I am trying to run the PASA training step (v. 1.8.11) with the following command but I get the following error funannotate train -i $genome --cpus 1 -o $outdir...

alexvasilikop

Allow runSubprocess to raise error instead of exiting

1

Fix for issue #784 Allow `runSubprocess` to raise an error instead of running `sys.exit(1)` by setting `raise_not_exit=True`. This can prevent the program from hanging if a subprocess has an error...

mglubber

**Are you using the latest release?** on v1.8.11, but I don't think there are any commits that change the relevant code between 1.8.11 and 1.8.13 **Describe the bug** `funannotate annotate`...

mglubber

Gene products labeled as "hypothetical proteins" even though intermediate files have product names

6

Hi there, I am using funannotate v.1.8.11 with conda. I have a set of gene models for a draft fungal genome that I received from BRAKER2 and refined with PASA;...

ceanothus

Could not locate command line parameters file

17

Trying to run predict step. Augustus is well setup but I get an error: augustus: ERROR Could not locate command line parameters file: /data01/mlandi/TME117-assembly/funannotate/new-sept/train/fun/predict_misc/ab_initio_parameters/augustus/parameters/aug_cmdln_parameters.json. that I don't seem to understand....

LandiMi2

**Are you using the latest release?** Yes - am using docker **Describe the bug** I have two errors with re-using a JSON file. I want to re-use a parameters JSON...

lilypeck

other gff file could not be passed to EVM

7

**Are you using the latest release?** funannotate v1.8.13 **Describe the bug** I have set "-other_gff compreh_init_build.gff3:10" It was recognised by funannotate, was set source to other_pred1. But other_pred1 was not...

xizhesun

Orthofiller output incorporation?

1

Hi John, This isn't an issue so much as a question/query. I've got a few genomes from the same genus that I'm predicting and annotating. I've used Orthofiller (https://github.com/mpdunne/orthofiller) to...

Dikaryotic

Failure to import mamba.mamba_api as api

1

Using latest release Importing using mamba, requisite file is not present mamba create -n funannotate funannotate Traceback (most recent call last): File "/home/nfs/ejordan/.conda/envs/trim/bin/mamba", line 7, in from mamba.mamba import main...

erinnjordan

Functional annotation output: mv: target 'out.tbl' is not a directory

4

Hello, I am not sure what this error output means, as I am not sure what/where the out.tbl file is, and am not aware of how to fix this. If...

mmotoc