[BUG] sqanti3_qc.py does not run with --genename enabled, but runs with the same gtf provided in --refGTF

[GLagunas-Robles]

Is there an existing issue for this?

• I have searched the existing issues

Have you loaded the SQANTI3.env conda environment?

• I have loaded the SQANTI3.env conda environment

Are you running SQANTI3 on its latest release?

• I have SQANTI3 updated to the latest release

Problem description

I want to assign isoforms to gene bodies. The genes are being recognized in the QC report without --genename since all genes are counted in the report. I tried a couple of renaming schemes but it didn't seem to do anything.

This is probably not helpful without my gtf which I can provide over email.

Code sample

mamba activate sqanti3

SQANTI3_ENV_LIB_DIR=/user/miniforge3/share/mamba/envs/sqanti3/lib
export LD_LIBRARY_PATH="${SQANTI3_ENV_LIB_DIR}${LD_LIBRARY_PATH:+:${LD_LIBRARY_PATH}}"

python3 sqanti3_qc.py --isoforms default_filtered.filtered.gtf --refGTF braker.gtf
--genename --refFasta $genome --novel_gene_prefix isoseq --report both -t ${T}

Error

nohup: ignoring input

=====================
  ░██████╗░░█████╗░
  ██╔═══██╗██╔══██╗
  ██║██╗██║██║░░╚═╝
  ╚██████╔╝██║░░██╗
  ░╚═██╔═╝░╚█████╔╝
  ░░░╚═╝░░░░╚════╝░
=====================

[ERROR:2026-02-25 12:04:04,411] The 'gene_name' tag was not found in the input GTF file. SQANTI3 requires this tag to function properly.
[ERROR:2026-02-25 12:04:04,414] Please include the 'gene_name' tag in the GTF, or omit the --genename option.

Anything else?

No response

[pabloati]

Hi, could you send your gtf to pablo.atienza@csic.es ? That way I can take a closer look at the formatting of your GTF, which migth be the issue :)