A traceback when running locally

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1

Hi, when I ran the script below:

organism_settings = {
    dna_model.Organism.HOMO_SAPIENS: OrganismSettings(
        fasta_path=f'{hg38_meta_dir}/GRCh38.p13.genome.fa',
        gtf_feather_path=f'{hg38_meta_dir}/gencode.v46.annotation.gtf.gz.feather',
        pas_feather_path=f'{hg38_meta_dir}/polyadb_human_v3_exon3_contiguous_gtfv46.feather',
        splice_site_starts_feather_path=f'{hg38_meta_dir}/gencode.v46.splice_sites_starts.feather',
        splice_site_ends_feather_path=f'{hg38_meta_dir}/gencode.v46.splice_sites_ends.feather'
    ),
    dna_model.Organism.MUS_MUSCULUS: (
        dna_model.OrganismSettings()
    ),
}

model = dna_model.create(
    checkpoint_path='/data/projects/xuy/test_alphagenome/weights/alphagenome-jax-all_folds-v1',
    organism_settings=organism_settings,
    device=jax.devices()[0] # default 'GPU', use 'CPU' here
)


from alphagenome.data import genome

interval = genome.Interval(chromosome='chr22', start=35677410, end=36725986)
variant = genome.Variant(
    chromosome='chr22',
    position=36201698,
    reference_bases='A',
    alternate_bases='C',
)

outputs = model.predict_variant(
    interval=interval,
    variant=variant,
    ontology_terms=['UBERON:0001157'],
    requested_outputs=[dna_model.OutputType.RNA_SEQ],
)

Then, I got the Traceback as follows:

Traceback (most recent call last):
File “”, line 1, in
File “/data/projects/xuy/test_alphagenome/alphagenome_research/src/alphagenome_research/model/dna_model.py”, line 625, in predict_variant
reference_predictions, alt_predictions = self._predict_variant(
^^^^^^^^^^^^^^^^^^^^^^
File “/data/projects/xuy/test_alphagenome/alphagenome_research/src/alphagenome_research/model/dna_model.py”, line 219, in _predict_variant
reference_predictions[‘splice_sites_junction’] = junctions_apply_fn(
^^^^^^^^^^^^^^^^^^^
File “/data/projects/xuy/test_alphagenome/alphagenome_research/src/alphagenome_research/model/dna_model.py”, line 1166, in _junctions_apply_fn
(predictions, _), _ = _forward_junctions.apply(
^^^^^^^^^^^^^^^^
ValueError: too many values to unpack (expected 2)

For simplicity, JAX has removed its internal frames from the traceback of the following exception. Set JAX_TRACEBACK_FILTERING=off to include these.

How can I solve this bug? I would be grateful for any advice you may have.

2

Apologies, this was inadvertently broken in commit 1af7e36 which somehow missed our pre-flight checks. This has now been fixed with commit 583895c.

Thanks for the bug report!

3

Thanks for your reply and fixing the bug.