# Run alphagenome locally **URL:** \ **Category:** Help & Support\ **Created:** [February 5, 2026, 8:34am UTC](https://www.alphagenomecommunity.com/t/run-alphagenome-locally/775 "2026-02-05T08:34:44Z")\ **Posts on this page:** 5\ **Page:** 1
**Author:** ![chujie\_sun](https://yyz2.discourse-cdn.com/watermelon/user_avatar/www.alphagenomecommunity.com/chujie_sun/32/904_2.png) [@chujie\_sun](https://www.alphagenomecommunity.com/u/chujie_sun)\ **Post date:** [February 5, 2026, 8:34am UTC](https://www.alphagenomecommunity.com/t/run-alphagenome-locally/775/1 "2026-02-05T08:34:45Z")
Hi, thanks for developing alphagenome. Because the GPU servers in our lab do not have internet access, we are unable to use the API to call AlphaGenome. Therefore, I am trying to run AlphaGenome locally. I have downloaded the model parameter files as well as the reference files, and constructed the `dna_model` using the code below. `from alphagenome_research.model import dna_model` ```auto model = dna_model.create( checkpoint_path='/home/alphagenome_research-main/model/alphagenome-all-folds/', organism_settings={ dna_model.Organism.HOMO_SAPIENS: dna_model.OrganismSettings( fasta_path='/home/alphagenome_research-main/Hs_ref/GRCh38.p13.genome.fa', gtf_feather_path='/home/alphagenome_research-main/Hs_ref/gencode.v46.annotation.gtf.gz.feather', pas_feather_path='/home/alphagenome_research-main/Hs_ref/polyadb_human_v3_exon3_contiguous_gtfv46.feather', splice_site_starts_feather_path='/home/alphagenome_research-main/Hs_ref/gencode.v46.splice_sites_starts.feather', splice_site_ends_feather_path='/home/alphagenome_research-main/Hs_ref/gencode.v46.splice_sites_ends.feather', ) }, device=jax.local_devices()[0], ) ``` Then I run the example codes: ```auto 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], ) ``` However, I encountered the following error: ```auto ValueError Traceback (most recent call last) Cell In[9], line 9 1 interval = genome.Interval(chromosome='chr22', start=35677410, end=36725986) 2 variant = genome.Variant( 3 chromosome='chr22', 4 position=36201698, 5 reference_bases='A', 6 alternate_bases='C', 7 ) ----> 9 outputs = model.predict_variant( 10 interval=interval, 11 variant=variant, 12 ontology_terms=['UBERON:0001157'], 13 requested_outputs=[dna_model.OutputType.RNA_SEQ], 14 ) File ~/softwares/alphagenome_research-main/src/alphagenome_research/model/dna_model.py:625, in AlphaGenomeModel.predict_variant(self, interval, variant, organism, requested_outputs, ontology_terms) 615 alternate_sequence = jax.device_put( 616 np.asarray(self._one_hot_encoder.encode(alternate_sequence))[ 617 np.newaxis 618 ], 619 device, 620 ) 621 organism_indices = jax.device_put( ... 692 f"{fq_name!r} with retrieved shape {param.shape!r} does not match " 693 f"shape={shape!r} dtype={dtype!r}") 695 return param ValueError: 'alphagenome/embed/embeddings' with retrieved shape (2, 1536) does not match shape=[1, 1536] dtype= ``` Could you please advise what might be causing this issue? Thank you very much. ---
**Author:** ![tward](https://yyz2.discourse-cdn.com/watermelon/user_avatar/www.alphagenomecommunity.com/tward/32/17_2.png) [@tward](https://www.alphagenomecommunity.com/u/tward)\ **Post date:** [February 5, 2026, 3:30pm UTC](https://www.alphagenomecommunity.com/t/run-alphagenome-locally/775/2 "2026-02-05T15:30:37Z")
Hi @chujie_sun, welcome to the community! Ah, this is because our model parameters assume that you have 2 organisms, whereas you’re only passing 1 organism into the settings. We’ll look to make this better, but in the meantime, can you try this: ```python from alphagenome_research.model import dna_model model = dna_model.create( checkpoint_path='/path/to/checkpoint', organism_settings={ dna_model.Organism.HOMO_SAPIENS: dna_model.OrganismSettings(), dna_model.Organism.MUS_MUSCULUS: ( dna_model.OrganismSettings() ), # Add empty mouse settings }, ) ``` Specifically, adding an empty `MUS_MUSCULUS` organism setting entry will ensure the model params are loaded correctly. Hopefully this unblocks you! Tom ---
**Author:** ![chujie\_sun](https://yyz2.discourse-cdn.com/watermelon/user_avatar/www.alphagenomecommunity.com/chujie_sun/32/904_2.png) [@chujie\_sun](https://www.alphagenomecommunity.com/u/chujie_sun)\ **Post date:** [February 6, 2026, 1:53am UTC](https://www.alphagenomecommunity.com/t/run-alphagenome-locally/775/3 "2026-02-06T01:53:17Z")
Hi Tom, thanks for your reply. Now it works correctly. Chujie ---
**Author:** ![Ling\_Zheng](https://yyz2.discourse-cdn.com/watermelon/user_avatar/www.alphagenomecommunity.com/ling_zheng/32/870_2.png) [@Ling\_Zheng](https://www.alphagenomecommunity.com/u/Ling_Zheng)\ **Post date:** [February 12, 2026, 8:22am UTC](https://www.alphagenomecommunity.com/t/run-alphagenome-locally/775/6 "2026-02-12T08:22:40Z")
why two organisms？ Could you explain more about it？ thx ---
**Author:** ![tward](https://yyz2.discourse-cdn.com/watermelon/user_avatar/www.alphagenomecommunity.com/tward/32/17_2.png) [@tward](https://www.alphagenomecommunity.com/u/tward)\ **Post date:** [February 12, 2026, 8:50pm UTC](https://www.alphagenomecommunity.com/t/run-alphagenome-locally/775/7 "2026-02-12T20:50:18Z")
Our model was trained on two organisms, so the pre-trained weights include embedding layers for both organisms. You can read mode in the supplementary materials in the [Nature publication](https://www.nature.com/articles/s41586-025-10014-0). The workaround above should no longer be needed as of [commit 1af7e36](https://github.com/google-deepmind/alphagenome_research/commit/1af7e36ca7c85be0e497931aab5f9221fd5037ef), where we default to 2 organisms instead of inferring from the provided metadata. Thanks!