FAQs & Troubleshooting

This page is just meant for general questions that I notice are asked with some frequency. If you feel like something is missing from here and you'd like to see it included, feel free to ask it by raising an issue on GitHub.

qsub and pysam - ModuleNotFoundError

A known issue with using snakemake + pysam + qsub results in the a break in the pipeline. The issue arises because pysam does not activate correctly when using qsub by default. To fix this you just need to add the -V parameter to your qsub command.

Which databases do I download?

It is probably best to just let Aviary handle the downloading of your databases via the --download parameter. But, if you would like to set them up yourself, please read ahead

For the GTDB:

• GTDB Required for taxonomic annotation Download and point the GTDB environment variable to the db/ folder inside of that download.

The optional databases are as follows:

• EggNog. Download this databse and point to the root folder of the databse.

Aviary will ask for the paths to these database files if they don't exist, otherwise you can place these lines into the activate.d/aviary.sh or .bashrc files changing the specific paths:

export GTDBTK_DATA_PATH=/path/to/gtdb/gtdb_release207/db/ # https://gtdb.ecogenomic.org/downloads
export EGGNOG_DATA_DIR=/path/to/eggnog-mapper/2.1.7/ # https://github.com/eggnogdb/eggnog-mapper/wiki/eggNOG-mapper-v2.1.5-to-v2.1.7#setup
export CONDA_ENV_PATH=/path/to/conda/envs/

Why the name "Aviary"? Why the bird names in general?

Put all your birds in one place.

Where did the logo come from?

I made it (among other bird based + CoverM logos) using GIMP and based the idea off of this tutorial. They are very easy to make so just follow that video if you feel like making something similar.

Where's the paper?

You sound like my supervisor.