Error when using non-human GTF

[ConnorBarnhill]

Hello,

I'm trying to run TALON on PacBio data from a non-human primate (using this gtf file, parent directory here). I'm able to initialize the database, label the reads, and run the talon command with no errors. However, I receive the following error when I try to run the talon_abundance command:

ValueError: Annotation name '<my_label>' not found in this database. Try one of the following:

I'm assuming this has something to do with the GTF file, but the lack of info makes it hard to troubleshoot. I verified that the GTF file has gene annotations, see below. Would appreciate help troubleshooting!

[fairliereese]

I am not certain that this is a problem with your GTF. Can you try running the following python code to see what annotations are in your TALON database?

import sqlite3

database = <your talon database>

conn = sqlite3.connect(database)
cursor = conn.cursor()

cursor.execute("SELECT DISTINCT annot_name FROM gene_annotations")
annotations = [str(x[0]) for x in cursor.fetchall()]
conn.close()

print(annotations)

[fairliereese]

Actually, it looks like it might be your GTF. Despite the results of your awk command, when I download your file, I can't seem to find any gene entries:
cat GCF_012559485.2_MFA1912RKSv2.ncbiRefSeq.gtf | cut -f3 | grep gene | head yields nothing. Check out this wiki entry on adding gene entries to a GTF.