GTF from BRAKER2 is not recognized as gtf format

[shin0727]

Hi, I got some problem while using SQUANTI3.
In order to add "UTR annotation" information from "BRAKER.gtf", I got the isoform.gtf file using "flair program".

And then, I ran the following script.

nohup ${SQANTI_DIR}/sqanti3_qc.py ${ISOFORM_GTF} ${BRAKER_GTF} ${My_GENOME} \
    --force_id_ignore \
    --polyA_motif_list SQANTI3-5.2.2/data/polyA_motifs/mouse_and_human.polyA_motif.txt \
    -t ${THREAD} -o ${SAMPLE} -d ${SAMPLE} --report both --isoAnnotLite

But there were some errors in log file.
#############################

SQANTI3-5.2.2/sqanti3_qc.py:75: DeprecationWarning: Use shutil.which instead of find_executable
if distutils.spawn.find_executable(GTF2GENEPRED_PROG) is None:
SQANTI3-5.2.2/sqanti3_qc.py:78: DeprecationWarning: Use shutil.which instead of find_executable
if distutils.spawn.find_executable(GFFREAD_PROG) is None:
SQANTI3-5.2.2/sqanti3_qc.py:108: DeprecationWarning: Use shutil.which instead of find_executable
RSCRIPTPATH = distutils.spawn.find_executable('Rscript')
Rscript (R) version 4.3.3 (2024-02-29)
/home/jwshin0727/Project/240926_IBS_Bat/09_geneAnnotation/02_BRAKER/1_Rf_h1/braker.gtf doesn't appear to be a GTF file (GFF not supported by this program)
Write arguments to /home/jwshin0727/Project/240926_IBS_Bat/09_geneAnnotation/04_sqanti3/1_Rf_h1/1_Rf_h1.params.txt...
**** Running SQANTI3...
**** Parsing provided files....
Reading genome fasta /home/jwshin0727/Project/240926_IBS_Bat/08_repeat/result/1_Rf_h1/SoftMasking/1_Rf_h1.filtered.fa.masked.masked....
Skipping aligning of sequences because GTF file was provided.

Indels will be not calculated since you ran SQANTI3 without alignment step (SQANTI3 with gtf format as transcriptome input).
**** Predicting ORF sequences...
**** Parsing Reference Transcriptome....
Traceback (most recent call last):
File "SQANTI3-5.2.2/sqanti3_qc.py", line 2577, in
main()
File "SQANTI3-5.2.2/sqanti3_qc.py", line 2560, in main
run(args)
File "SQANTI3-5.2.2/sqanti3_qc.py", line 1860, in run
refs_1exon_by_chr, refs_exons_by_chr, junctions_by_chr, junctions_by_gene, start_ends_by_gene = reference_parser(args, list(genome_dict.keys()))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "SQANTI3-5.2.2/sqanti3_qc.py", line 663, in reference_parser
for r in genePredReader(referenceFiles):
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "SQANTI3-5.2.2/sqanti3_qc.py", line 122, in init
self.f = open(filename)
^^^^^^^^^^^^^^
FileNotFoundError: [Errno 2] No such file or directory: '/home/jwshin0727/Project/240926_IBS_Bat/09_geneAnnotation/04_sqanti3/1_Rf_h1/refAnnotation_1_Rf_h1.genePred'

#################
It seems like my braker.gtf file was not recognized as a gtf file. However, when I input my braker.gtf file into the flair program, it worked without any errors. Also, I didn't fixed anything in the braker.gtf file.

One thing that I'm suspicious of is that in the annotation column of the gene, transcript row of my braker.gtf file, it says 'g1' instead of 'gene_id "g1"'. Do you know if this is the cause of the error?

OR is there another method to solve this problem?

thank you.