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Problem with talon_initialize_database

Open Kiliankleemann opened this issue 8 months ago • 13 comments

Tried to run talon_initialize_database but got an error:

talon_initialize_database --f  reference/GRCh38_GENCODE_rmsk_TE_reformatted.gtf \
  --g hg38_rmsk_ucsd \
  --a hg38 \
  --o hg38 
chrY
bulk update genes...
bulk update gene_annotations...
Traceback (most recent call last):
  File "/home/kilian/anaconda3/envs/talon/bin/talon_initialize_database", line 8, in <module>
    sys.exit(main())
  File "/home/kilian/anaconda3/envs/talon/lib/python3.7/site-packages/talon/initialize_talon_database.py", line 1073, in main
    populate_db(db_name, annot_name, chrom_genes, chrom_transcripts, exons, genome_build)
  File "/home/kilian/anaconda3/envs/talon/lib/python3.7/site-packages/talon/initialize_talon_database.py", line 634, in populate_db
    add_transcripts(c, transcripts, annot_name, gene_id_map, genome_build)
  File "/home/kilian/anaconda3/envs/talon/lib/python3.7/site-packages/talon/initialize_talon_database.py", line 743, in add_transcripts
    db_gene_id = gene_id_map[native_gene_id]
KeyError: 'AluY'

Kiliankleemann avatar Oct 19 '23 11:10 Kiliankleemann