PASA pipeline updating annotation results in no changes

I'm running these commands leaving the numbers as default in config and cleaned transcripts already.

module load Miniconda3/4.9.2

# create database
$PASAHOME/scripts/create_sqlite_cdnaassembly_db.dbi -c alignAssembly.config -S /home/data/pest_genomics/pasa/opt/pasa-2.4.1/schema/cdna_alignment_sqliteschema

# Upload annotations
$PASAHOME/scripts/Load_Current_Gene_Annotations.dbi -c alignAssembly.config -g Chilo_suppressalis_v2_genome_220620_correct2.fasta -P chilo_transfer2_corrected2.gff3

module load SAMtools/1.12-GCC-10.2.0

$PASAHOME/Launch_PASA_pipeline.pl -c annotCompare.config -A -g Chilo_suppressalis_v2_genome_220620_correct2.fasta -t clean_transcripts.fa --CPU 10

When I do this though no changes are made. I use the same transcripts in maker to update the gene set and lots of UTR are added. I was hoping PASA would do a better job but I'm not getting any differences. I've changed the headers of the transcripts thinking maybe that would have an effect but no luck. Anyone experienced the same? I've posted on PASA google group but no response so far.

pasa

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updated 4.7 years ago by Ram

• written 4.7 years ago by rob234king

Please use the formatting bar (especially the code option) to present your post better. You can use backticks for inline code (`text` becomes text), or select a chunk of text and use the highlighted button to format it as a code block. If your code has long lines with a single command, break those lines into multiple lines with proper escape sequences so they're easier to read and still run when copy-pasted. I've done it for you this time.
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written 4.7 years ago by Ram

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