[BUG] Error using IsoAnnotLite with gencode gff3

[VandaLovejoy]

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

Problem description

Hello,
im getting this error message. Why is this? python3 IsoAnnotLite_SQ3.py ~/projects/sg_nex/sqanti3_results/sqanti3_output_with_ref_corrected.gtf ~/projects/sg_nex/sqanti3_results/sqanti3_output_with_ref_classification.txt ~/projects/sg_nex/sqanti3_results/sqanti3_output_with_ref_junctions.txt -gff3 gencode.v48.annotation.gff3 -o myAnnotation -novel -stdout outdir

Running IsoAnnot Lite 2.7.3 (using all gene information) ...
Reading reference annotation file and creating data variables...
Traceback (most recent call last):
File "/home/vandalovejoy/tools/sqanti3/release_sqanti3/src/utilities/IsoAnnotLite_SQ3.py", line 3222, in
main()
File "/home/vandalovejoy/tools/sqanti3/release_sqanti3/src/utilities/IsoAnnotLite_SQ3.py", line 3062, in main
run(args)
File "/home/vandalovejoy/tools/sqanti3/release_sqanti3/src/utilities/IsoAnnotLite_SQ3.py", line 3116, in run
dc_GFF3, dc_GFF3exonsTrans, dc_GFF3transExons, dc_GFF3coding, dc_GFF3strand, dc_GFF3geneTrans, dc_GFF3transGene, dc_GFF3geneNameTrans, dc_GFF3_raw_annot, dc_gene_description = readGFF(gff3) #dc_GFF3exons is sorted
^^^^^^^^^^^^^
File "/home/vandalovejoy/tools/sqanti3/release_sqanti3/src/utilities/IsoAnnotLite_SQ3.py", line 324, in readGFF
g_name = text[1][5:-1] #delete "NAME=" and final ";" == GENE
~~~~^^^
IndexError: list index out of range

Thank you

Code sample

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Error

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Anything else?

No response

[pabloati]

Hi, that is because the format of the GFF3 file is not the correct one. IsoAnnot Lite expects to find the string NAME= on the 8th column, the one with the attributes. In the wiki page of SQANTI3, in the IsoAnnotLite page, you can find some precomputed GFF3 files. You can either use them or take them as reference to create your own :)

[VandaLovejoy]

The precomputed gff3 are extremely old. I have tried to make a precomputed GFF3 using sqanti3 with no success. Ive spent hours trying and I get no annotations.

[pabloati]

We are currently working on updating the precomputed GFF3. You can check the documentation of IsoAnnot for more information on how to do them yourself if you need.