[BUG] Error 'The 'gene_name' tag was not found in the input GTF file.' even though gene_name is in GTF file

[joelnitta]

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 am trying to run sqanti3_qc.py with --isoAnnotLite. I have a custom annotated GTF file, including the gene_name tag. This command worked for me in a previous version of SQANTI3 (v5.0).

Code sample and error

(base) root@e4c7381075e1:/wd# sqanti3_qc.py --polyA_motif_list mouse_and_human_poly_a_motif.txt --polyA_peak atlas.clusters.2.0.GRCh38.96.fixed.bed -d /tmp/analysis -o d_magna --report pdf --isoAnnotLite --isoforms d_magna.collapsed.filtered.gff --refGTF daphnia_genome.gtf --refFasta daphnia_genome.fasta

    =====================
      ░██████╗░░█████╗░
      ██╔═══██╗██╔══██╗
      ██║██╗██║██║░░╚═╝
      ╚██████╔╝██║░░██╗
      ░╚═██╔═╝░╚█████╔╝
      ░░░╚═╝░░░░╚════╝░
    =====================
    
[WARNING:2025-08-02 23:38:59,141] Output directory /tmp/analysis already exists. Overwriting!
[ERROR:2025-08-02 23:38:59,228] The 'gene_name' tag was not found in the input GTF file. SQANTI3 requires this tag to function properly.
[ERROR:2025-08-02 23:38:59,229] Please include the 'gene_name' tag in the GTF, or omit the --isoAnnotLite option.

It is probably hard to diagnose without the input files, so please let me know and I can send them by email.

Thank you very much!

[pabloati]

Hi,
Yes, it would help a lot if you could send me the input gtf to pablo.atienza@csic.es currently run the pipeline with --isoAnnotLite and had no problem, so might be a formatting issue that it is not processing correctly :)

[mpizzagalli777]

Hi I am having a similar issue. Was it a problem with the formatting? The reference genome I am using is the full Gencode annotation that has the gene_name in the attributes column. The novel transcriptome that I provided also has the gene_name in the attributes column. Could this be causing the issue?

Also, in issue #461 and the documentation, you reference generating the updated gff3s. Is it a significant issue to use the older version that is currently provided?

[GLagunas-Robles]

I am also running into this issue. Any updates on this?

example of my gtf
Chr1 AUGUSTUS gene 50267 50784 . + . gene_id "g8977"; ID "g8977"; gene_name "g8977";
Chr1 AUGUSTUS transcript 50267 50784 0.55 + . gene_id "g8977"; transcript_id "g8977.t1"; ID "g8977.t1"; Parent "g8977"; gene_name "g8977";