`agat_sp_statistics` can hang

[TomHarrop]

Hi @gemygk

In the current container the AGAT agat_sp_statistics step can run forever with output from Tiberius. So far I've left it up to 3 days on the HPC and it doesn't return.

2026-07-01 16:45:35 | INFO     | Running command: agat_sp_statistics.pl -g /home/tharrop/Projects/compare-annotation-tools/debug/input_genome.fasta --gff bembpic.agat_standardised.gff --yaml --output bembpic.agat_sp_statistics > bembpic.agat_sp_statistics.log 2>&1  && mv bembpic.agat_sp_statistics bembpic.agat_sp_statistics.txt

I've run the exact same command with AGAT 1.7.0 and it completes... still very slow but at least it finished.

apptainer exec docker://quay.io/biocontainers/agat:1.7.0--pl5321hdfd78af_0 agat_sp_statistics.pl -g /home/tharrop/Projects/compare-annotation-tools/debug/input_genome.fasta --gff bembpic.agat_standardised.gff --yaml --output bembpic.agat_sp_statistics

...

-------------------------- Job done in 27811 seconds ---------------------------
command : /usr/local/bin/agat_sp_statistics.pl -g /home/tharrop/Projects/compare-annotation-tools/debug/input_genome.fasta --gff bembpic.agat_standardised.gff --yaml --output bembpic.agat_sp_statistics
date : 07/01/2026 at 16h36m34s
Job done! Bye Bye!

PS Just reporting this - we can run the steps directly so no worries if you're not maintaining this tool.

Cheers,
Tom

[gemygk]

Hi @TomHarrop

Thank you for reporting this.

Which version of AGAT agat_sp_statistics were you running when it hung for 3 days? The version included in our AnnoOddities v0.2.0 Docker image was AGAT v1.5.1, so I suspect that may be the cause.

I’ve now updated the AnnoOddities v0.2.1 Docker image to include the latest AGAT v1.7.0. Please let me know if that resolves the issue for you.

And thanks for the note at the end! We do actively maintain AnnoOddities, so if you run into any other issues or have suggestions for improvements, please don’t hesitate to get in touch. Bug reports like this are really helpful.

Thanks,
Gemy

[TomHarrop]

I was using the Docker image v0.2.0 you linked above. I will try again with v0.2.1 and let you know. Thanks for the quick update!

[swarbred]

Hi @TomHarrop have you run the agat_sp_statistics directly on the GFF that is the input to AnnoOddities, did that also run for a similarly long time? Just wondering if its just an issue with agat_sp_statistics and the specific input GFF rather than AnnoOddities.

[gemygk]

@TomHarrop

I tested both versions of AnnoOddities - v0.2.0 (using AGAT v1.5.1) and v0.2.1 (using AGAT v1.7.0) - on a set of Tiberius (v2.0.4) outputs generated from its evidence-based Nextflow pipeline for both Arabidopsis and Wheat. All runs completed successfully.

The Arabidopsis (~24k genes) runs completed in ~8 minutes (using <1 GB RAM), while the Wheat (~150k genes) runs completed in ~50 minutes (using ~6 GB RAM), for both the tiberius.gff3 and tiberius_train.gff3 output files.

Which version of Tiberius were you using, and which output file did you run agat_sp_statistics on? Also, were there any other jobs running on the same node that might have caused resource contention or unusually long runtimes?

[TomHarrop]

I think this might have coincided with switching from Tiberius 2.0.4 to 2.0.6. I’ll check next week and let you know.