No splice donors or acceptors found on chromosomes:

[MustafaElshani]

Hi I generated splice junction from short reads from the same samples using the followinghttps://github.com/mortazavilab/TranscriptClean/wiki/TranscriptClean-Tutorial#noncanonical-splice-junction-correction

    STAR --runThreadN 64 \
         --genomeDir "$genomeDir" \
         --readFilesCommand zcat \
         --readFilesIn "../${sample_prefix}__SR/fastq_SR/${sample}_SR_1.fq.gz" "../${sample_prefix}__SR/fastq_SR/${sample}_SR_2.fq.gz" \
         --sjdbGTFfile "$sjdbGTFfile" \
         --outFilterType BySJout \
         --outFilterMultimapNmax 20 \
         --alignSJoverhangMin 8 \
         --alignSJDBoverhangMin 1 \
         --outFilterMismatchNmax 999 \
         --outFilterMismatchNoverLmax 0.04 \
         --alignIntronMin 20 \
         --alignIntronMax 1000000 \
         --alignMatesGapMax 1000000 \
         --outSAMattributes NH HI NM MD jM jI \
         --outSAMtype SAM \
         --outFileNamePrefix "$output_dir/${sample}_"

However after running TranscriptClean I got a UserWarning

TranscriptClean was run as follows
transcriptclean \
    --sam "$temp_sam_file" \
    -j "$splice_junction_file" \
    --genome "$SCRATCH/gencode/v47/GRCh38.primary_assembly.genome.fa" \
    -t 64 \
    --tmpDir $TMPDIR \
    --deleteTmp \
    --outprefix "$transcriptclean_dir/$1_TC"

TranscriptClean/TranscriptClean/TranscriptClean.py:764: UserWarning: Warning: No splice donors or acceptors found on chromosomes: *. If this is unexpected, check your SJ annotation file. "annotation file." % (", ".join(read_chroms)))) ` What does this mean, have the SJ annotation been ignored?