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Error looking for reference genome

Open alexreg opened this issue 9 months ago • 0 comments

I get this error when running for the first time. It looks like the program does not correctly handle the case that the reference genome does not exist.

INFO 02:48:33.778722 (0.000 s) - Running Yleaf with command: /opt/homebrew/bin/Yleaf --vcf /Users/alex/Downloads/KGP_sample7.vcf -o output --reference_genome hg38
Traceback (most recent call last):
  File "/opt/homebrew/bin/Yleaf", line 8, in <module>
    sys.exit(main())
             ~~~~^^
  File "/opt/homebrew/Cellar/yleaf/HEAD-f3aae50/libexec/lib/python3.13/site-packages/yleaf/Yleaf.py", line 373, in main
    check_reference(args.reference_genome)
    ~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^
  File "/opt/homebrew/Cellar/yleaf/HEAD-f3aae50/libexec/lib/python3.13/site-packages/yleaf/Yleaf.py", line 663, in check_reference
    if os.path.getsize(reference_file) < 100:
       ~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^
  File "<frozen genericpath>", line 86, in getsize
FileNotFoundError: [Errno 2] No such file or directory: '/opt/homebrew/Cellar/yleaf/HEAD-f3aae50/libexec/lib/python3.13/site-packages/yleaf/data/hg38/full_reference.fa'

alexreg avatar May 07 '25 01:05 alexreg