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adding genomad version 1.11.2 #1517

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@erinyoung erinyoung commented Dec 30, 2025

There's a new version of genomad!

According to the release notes there are some small improvements and version updates.

I copied the files from 1.11.1 and updated the version arg.

The full diff:

$ diff build-files/genomad/1.11.{1,2}/Dockerfile
2c2
< ARG GENOMAD_VER="1.11.1"
---
> ARG GENOMAD_VER="1.11.2"
4c4
< ARG MMSEQS2_VER="17-b804f"
---
> ARG MMSEQS2_VER="18-8cc5c"

Pull Request (PR) checklist:

  • Include a description of what is in this pull request in this message.
  • The dockerfile successfully builds to a test target for the user creating the PR. (i.e. docker build --tag samtools:1.15test --target test docker-builds/build-files/samtools/1.15 )
  • Directory structure as name of the tool in lower case with special characters removed with a subdirectory of the version number in build-files (i.e. docker-builds/build-files/spades/3.12.0/Dockerfile)
    • (optional) All test files are located in same directory as the Dockerfile (i.e. build-files/shigatyper/2.0.1/test.sh)
  • Create a simple container-specific README.md in the same directory as the Dockerfile (i.e. docker-builds/build-files/spades/3.12.0/README.md)
    • If this README is longer than 30 lines, there is an explanation as to why more detail was needed
  • Dockerfile includes the recommended LABELS
  • Main README.md has been updated to include the tool and/or version of the dockerfile(s) in this PR
  • Program_Licenses.md contains the tool(s) used in this PR and has been updated for any missing

@erinyoung erinyoung marked this pull request as ready for review December 30, 2025 21:44
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erinyoung commented Dec 30, 2025

Accidentally started as a draft PR, but these files are ready for review.

Sorry!!!

kapsakcj
kapsakcj reviewed Dec 31, 2025
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kapsakcj commented Dec 31, 2025

Here's what was installed by pip:

Successfully installed absl-py-2.3.1 archspec-0.2.5 astunparse-1.6.3 certifi-2025.11.12 charset_normalizer-3.4.4 click-8.3.1 flatbuffers-25.12.19 gast-0.7.0 genomad-1.11.2 google_pasta-0.2.0 grpcio-1.76.0 h5py-3.15.1 idna-3.11 keras-3.12.0 libclang-18.1.1 llvmlite-0.46.0 markdown-3.10 markdown-it-py-4.0.0 markupsafe-3.0.3 mdurl-0.1.2 ml-dtypes-0.5.4 namex-0.1.0 numba-0.63.1 numpy-2.2.6 nvidia-nccl-cu12-2.28.9 opt_einsum-3.4.0 optree-0.18.0 packaging-25.0 pillow-12.0.0 protobuf-6.33.2 pygments-2.19.2 pyrodigal-3.6.3.post1 pyrodigal-gv-0.3.2 python-crfsuite-0.9.12 requests-2.32.5 rich-14.2.0 rich-click-1.9.5 scipy-1.15.3 six-1.17.0 taxopy-0.14.0 tensorboard-2.20.0 tensorboard-data-server-0.7.2 tensorflow-2.20.0 termcolor-3.3.0 typing_extensions-4.15.0 urllib3-2.6.2 werkzeug-3.1.4 wrapt-2.0.1 xgboost-3.1.2

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kapsakcj commented Dec 31, 2025

There was an error regarding CUDA in the test, any idea if this needs to be resolved or not? I doubt this is running on a GPU, but I could be wrong.

#16 257.3 2025-12-30 20:32:44.842529: E external/local_xla/xla/stream_executor/cuda/cuda_platform.cc:51] failed call to cuInit: INTERNAL: CUDA error: Failed call to cuInit: UNKNOWN ERROR (303

Database was downloaded successfully and tests passed (except for the cuda error):

#16 [test 3/3] RUN pip list &&     wget -q https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/025/259/185/GCA_025259185.1_ASM2525918v1/GCA_025259185.1_ASM2525918v1_genomic.fna.gz &&     gunzip GCA_025259185.1_ASM2525918v1_genomic.fna.gz &&     genomad end-to-end GCA_025259185.1_ASM2525918v1_genomic.fna test /genomad_db --splits 16
#16 0.393 Package                 Version
#16 0.393 ----------------------- -----------
#16 0.393 absl-py                 2.3.1
#16 0.393 archspec                0.2.5
#16 0.393 astunparse              1.6.3
#16 0.394 certifi                 2025.11.12
#16 0.394 charset-normalizer      3.4.4
#16 0.394 click                   8.3.1
#16 0.395 flatbuffers             25.12.19
#16 0.395 gast                    0.7.0
#16 0.395 genomad                 1.11.2
#16 0.395 google-pasta            0.2.0
#16 0.396 grpcio                  1.76.0
#16 0.396 h5py                    3.15.1
#16 0.396 idna                    3.11
#16 0.396 keras                   3.12.0
#16 0.396 libclang                18.1.1
#16 0.397 llvmlite                0.46.0
#16 0.397 Markdown                3.10
#16 0.397 markdown-it-py          4.0.0
#16 0.397 MarkupSafe              3.0.3
#16 0.398 mdurl                   0.1.2
#16 0.398 ml_dtypes               0.5.4
#16 0.398 namex                   0.1.0
#16 0.398 numba                   0.63.1
#16 0.399 numpy                   2.2.6
#16 0.399 nvidia-nccl-cu12        2.28.9
#16 0.399 opt_einsum              3.4.0
#16 0.399 optree                  0.18.0
#16 0.400 packaging               25.0
#16 0.400 pillow                  12.0.0
#16 0.400 pip                     22.0.2
#16 0.400 protobuf                6.33.2
#16 0.400 Pygments                2.19.2
#16 0.401 pyrodigal               3.6.3.post1
#16 0.401 pyrodigal_gv            0.3.2
#16 0.401 python-crfsuite         0.9.12
#16 0.401 requests                2.32.5
#16 0.401 rich                    14.2.0
#16 0.402 rich-click              1.9.5
#16 0.402 scipy                   1.15.3
#16 0.402 setuptools              59.6.0
#16 0.402 six                     1.17.0
#16 0.403 taxopy                  0.14.0
#16 0.403 tensorboard             2.20.0
#16 0.403 tensorboard-data-server 0.7.2
#16 0.403 tensorflow              2.20.0
#16 0.403 termcolor               3.3.0
#16 0.404 typing_extensions       4.15.0
#16 0.404 urllib3                 2.6.2
#16 0.404 Werkzeug                3.1.4
#16 0.404 wheel                   0.37.1
#16 0.404 wrapt                   2.0.1
#16 0.405 xgboost                 3.1.2
#16 1.516 ╭──────────────────────────────────────────────────────────────────────────────╮
#16 1.516 │  Executing geNomad annotate (v1.11.2). This will perform gene calling in     │
#16 1.516 │  the input sequences and annotate the predicted proteins with geNomad's      │
#16 1.516 │  markers.                                                                    │
#16 1.516 │  ──────────────────────────────────────────────────────────────────────────  │
#16 1.516 │  Outputs:                                                                    │
#16 1.516 │    test/GCA_025259185.1_ASM2525918v1_genomic_annotate                        │
#16 1.516 │    ├── GCA_025259185.1_ASM2525918v1_genomic_annotate.json (execution         │
#16 1.516 │    │   parameters)                                                           │
#16 1.516 │    ├── GCA_025259185.1_ASM2525918v1_genomic_genes.tsv (gene annotation       │
#16 1.516 │    │   data)                                                                 │
#16 1.516 │    ├── GCA_025259185.1_ASM2525918v1_genomic_taxonomy.tsv (taxonomic          │
#16 1.516 │    │   assignment)                                                           │
#16 1.516 │    ├── GCA_025259185.1_ASM2525918v1_genomic_mmseqs2.tsv (MMseqs2 output      │
#16 1.516 │    │   file)                                                                 │
#16 1.516 │    └── GCA_025259185.1_ASM2525918v1_genomic_proteins.faa (protein FASTA      │
#16 1.516 │        file)                                                                 │
#16 1.516 ╰──────────────────────────────────────────────────────────────────────────────╯
#16 1.539 [20:28:29] Executing genomad annotate.                                          
#16 1.544 [20:28:29] Creating the test/GCA_025259185.1_ASM2525918v1_genomic_annotate      
#16 1.544            directory.                                                           
#16 20.94 [20:28:48] Proteins predicted with pyrodigal-gv were written to                 
#16 20.94            GCA_025259185.1_ASM2525918v1_genomic_proteins.faa.                   
#16 234.9 [20:32:22] Proteins annotated with MMseqs2 and geNomad database (v1.9) were     
#16 234.9            written to GCA_025259185.1_ASM2525918v1_genomic_mmseqs2.tsv.         
#16 235.4 [20:32:22] Gene data was written to                                             
#16 235.4            GCA_025259185.1_ASM2525918v1_genomic_genes.tsv.                      
#16 235.4 [20:32:22] Taxonomic assignment data was written to                             
#16 235.4            GCA_025259185.1_ASM2525918v1_genomic_taxonomy.tsv.                   
#16 235.4 [20:32:22] geNomad annotate finished!                                           
#16 235.4 ╭──────────────────────────────────────────────────────────────────────────────╮
#16 235.4 │  Executing geNomad find-proviruses (v1.11.2). This will find putative        │
#16 235.4 │  proviral regions within the input sequences.                                │
#16 235.4 │  ──────────────────────────────────────────────────────────────────────────  │
#16 235.4 │  Outputs:                                                                    │
#16 235.4 │    test/GCA_025259185.1_ASM2525918v1_genomic_find_proviruses                 │
#16 235.4 │    ├── GCA_025259185.1_ASM2525918v1_genomic_find_proviruses.json (execution  │
#16 235.4 │    │   parameters)                                                           │
#16 235.4 │    ├── GCA_025259185.1_ASM2525918v1_genomic_provirus.tsv (provirus data)     │
#16 235.4 │    ├── GCA_025259185.1_ASM2525918v1_genomic_provirus.fna (provirus           │
#16 235.4 │    │   nucleotide sequences)                                                 │
#16 235.4 │    ├── GCA_025259185.1_ASM2525918v1_genomic_provirus_proteins.faa (provirus  │
#16 235.4 │    │   protein sequences)                                                    │
#16 235.4 │    ├── GCA_025259185.1_ASM2525918v1_genomic_provirus_genes.tsv (provirus     │
#16 235.4 │    │   gene annotation data)                                                 │
#16 235.4 │    ├── GCA_025259185.1_ASM2525918v1_genomic_provirus_taxonomy.tsv (provirus  │
#16 235.4 │    │   taxonomic assignment)                                                 │
#16 235.4 │    ├── GCA_025259185.1_ASM2525918v1_genomic_provirus_mmseqs2.tsv (MMseqs2    │
#16 235.4 │    │   output file)                                                          │
#16 235.4 │    └── GCA_025259185.1_ASM2525918v1_genomic_provirus_aragorn.tsv (Aragorn    │
#16 235.4 │        output file)                                                          │
#16 235.4 ╰──────────────────────────────────────────────────────────────────────────────╯
#16 235.5 [20:32:22] Executing genomad find-proviruses.                                   
#16 235.5 [20:32:22] Creating the                                                         
#16 235.5            test/GCA_025259185.1_ASM2525918v1_genomic_find_proviruses directory. 
#16 237.5 [20:32:24] Integrases identified with MMseqs2 and geNomad database (v1.9) were  
#16 237.5            written to GCA_025259185.1_ASM2525918v1_genomic_provirus_mmseqs2.tsv.
#16 252.4 [20:32:39] tRNAs identified with Aragorn were written to                        
#16 252.4            GCA_025259185.1_ASM2525918v1_genomic_provirus_aragorn.tsv.           
#16 253.0 [20:32:40] Provirus regions identified.                                         
#16 253.0 [20:32:40] Provirus data was written to                                         
#16 253.0            GCA_025259185.1_ASM2525918v1_genomic_provirus.tsv.                   
#16 253.0 [20:32:40] Provirus nucleotide sequences were written to                        
#16 253.0            GCA_025259185.1_ASM2525918v1_genomic_provirus.fna.                   
#16 253.0 [20:32:40] Provirus protein sequences were written to                           
#16 253.0            GCA_025259185.1_ASM2525918v1_genomic_provirus_proteins.faa.          
#16 253.0 [20:32:40] Provirus gene data was written to                                    
#16 253.0            GCA_025259185.1_ASM2525918v1_genomic_provirus_genes.tsv.             
#16 253.1 [20:32:40] Taxonomic assignment data was written to                             
#16 253.1            GCA_025259185.1_ASM2525918v1_genomic_provirus_taxonomy.tsv.          
#16 253.1 [20:32:40] geNomad find-proviruses finished!                                    
#16 253.1 ╭──────────────────────────────────────────────────────────────────────────────╮
#16 253.1 │  Executing geNomad marker-classification (v1.11.2). This will classify the   │
#16 253.1 │  input sequences into chromosome, plasmid, or virus based on the presence    │
#16 253.1 │  of geNomad markers and other gene-related features.                         │
#16 253.1 │  ──────────────────────────────────────────────────────────────────────────  │
#16 253.1 │  Outputs:                                                                    │
#16 253.1 │    test/GCA_025259185.1_ASM2525918v1_genomic_marker_classification           │
#16 253.1 │    ├── GCA_025259185.1_ASM2525918v1_genomic_marker_classification.json       │
#16 253.1 │    │   (execution parameters)                                                │
#16 253.1 │    ├── GCA_025259185.1_ASM2525918v1_genomic_features.tsv (sequence feature   │
#16 253.1 │    │   data: tabular format)                                                 │
#16 253.1 │    ├── GCA_025259185.1_ASM2525918v1_genomic_features.npz (sequence feature   │
#16 253.1 │    │   data: binary format)                                                  │
#16 253.1 │    ├── GCA_025259185.1_ASM2525918v1_genomic_marker_classification.tsv        │
#16 253.1 │    │   (sequence classification: tabular format)                             │
#16 253.1 │    ├── GCA_025259185.1_ASM2525918v1_genomic_marker_classification.npz        │
#16 253.1 │    │   (sequence classification: binary format)                              │
#16 253.1 │    ├── GCA_025259185.1_ASM2525918v1_genomic_provirus_features.tsv (provirus  │
#16 253.1 │    │   feature data: tabular format)                                         │
#16 253.1 │    ├── GCA_025259185.1_ASM2525918v1_genomic_provirus_features.npz (provirus  │
#16 253.1 │    │   feature data: binary format)                                          │
#16 253.1 │    ├── GCA_025259185.1_ASM2525918v1_genomic_provirus_marker_classification.  │
#16 253.1 │    │   tsv (provirus classification: tabular format)                         │
#16 253.1 │    └── GCA_025259185.1_ASM2525918v1_genomic_provirus_marker_classification.  │
#16 253.1 │        npz (provirus classification: binary format)                          │
#16 253.1 ╰──────────────────────────────────────────────────────────────────────────────╯
#16 253.1 [20:32:40] Executing genomad marker-classification.                             
#16 253.1 [20:32:40] Creating the                                                         
#16 253.1            test/GCA_025259185.1_ASM2525918v1_genomic_marker_classification      
#16 253.1            directory.                                                           
#16 253.6 [20:32:41] Sequence features computed.                                          
#16 253.6 [20:32:41] Sequence features in binary format written to                        
#16 253.6            GCA_025259185.1_ASM2525918v1_genomic_features.npz.                   
#16 253.6 [20:32:41] Sequence features in tabular format written to                       
#16 253.6            GCA_025259185.1_ASM2525918v1_genomic_features.tsv.                   
#16 254.1 [20:32:41] Provirus features computed.                                          
#16 254.1 [20:32:41] Provirus features in binary format written to                        
#16 254.1            GCA_025259185.1_ASM2525918v1_genomic_provirus_features.npz.          
#16 254.1 [20:32:41] Provirus features in tabular format written to                       
#16 254.1            GCA_025259185.1_ASM2525918v1_genomic_provirus_features.tsv.          
#16 254.1 [20:32:41] Sequences classified.                                                
#16 254.1 [20:32:41] Sequence classification in binary format written to                  
#16 254.1            GCA_025259185.1_ASM2525918v1_genomic_marker_classification.npz.      
#16 254.1 [20:32:41] Sequence classification in tabular format written to                 
#16 254.1            GCA_025259185.1_ASM2525918v1_genomic_marker_classification.tsv.      
#16 254.1 [20:32:41] Proviruses classified.                                               
#16 254.1 [20:32:41] Provirus classification in binary format written to                  
#16 254.1            GCA_025259185.1_ASM2525918v1_genomic_provirus_marker_classification.n
#16 254.1            pz.                                                                  
#16 254.1 [20:32:41] Provirus classification in tabular format written to                 
#16 254.1            GCA_025259185.1_ASM2525918v1_genomic_provirus_marker_classification.t
#16 254.1            sv.                                                                  
#16 254.1 [20:32:41] geNomad marker-classification finished!                              
#16 255.7 ╭──────────────────────────────────────────────────────────────────────────────╮
#16 255.7 │  Executing geNomad nn-classification (v1.11.2). This will classify the       │
#16 255.7 │  input sequences into chromosome, plasmid, or virus based on the nucleotide  │
#16 255.7 │  sequence.                                                                   │
#16 255.7 │  ──────────────────────────────────────────────────────────────────────────  │
#16 255.7 │  Outputs:                                                                    │
#16 255.7 │    test/GCA_025259185.1_ASM2525918v1_genomic_nn_classification               │
#16 255.7 │    ├── GCA_025259185.1_ASM2525918v1_genomic_nn_classification.json           │
#16 255.7 │    │   (execution parameters)                                                │
#16 255.7 │    ├── GCA_025259185.1_ASM2525918v1_genomic_encoded_sequences (directory     │
#16 255.7 │    │   containing encoded sequence data)                                     │
#16 255.7 │    ├── GCA_025259185.1_ASM2525918v1_genomic_nn_classification.tsv (contig    │
#16 255.7 │    │   classification: tabular format)                                       │
#16 255.7 │    ├── GCA_025259185.1_ASM2525918v1_genomic_nn_classification.npz (contig    │
#16 255.7 │    │   classification: binary format)                                        │
#16 255.7 │    ├── GCA_025259185.1_ASM2525918v1_genomic_encoded_proviruses (directory    │
#16 255.7 │    │   containing encoded sequence data)                                     │
#16 255.7 │    ├── GCA_025259185.1_ASM2525918v1_genomic_provirus_nn_classification.tsv   │
#16 255.7 │    │   (provirus classification: tabular format)                             │
#16 255.7 │    └── GCA_025259185.1_ASM2525918v1_genomic_provirus_nn_classification.npz   │
#16 255.7 │        (provirus classification: binary format)                              │
#16 255.7 ╰──────────────────────────────────────────────────────────────────────────────╯
#16 255.7 [20:32:43] Executing genomad nn-classification.                                 
#16 255.7 [20:32:43] Creating the                                                         
#16 255.7            test/GCA_025259185.1_ASM2525918v1_genomic_nn_classification          
#16 255.7            directory.                                                           
#16 255.7 [20:32:43] Creating the                                                         
#16 255.7            test/GCA_025259185.1_ASM2525918v1_genomic_nn_classification/GCA_02525
#16 255.7            9185.1_ASM2525918v1_genomic_encoded_sequences directory.             
#16 257.3 [20:32:44] Encoded sequence data written to                                     
#16 257.3            GCA_025259185.1_ASM2525918v1_genomic_encoded_sequences.              
#16 257.3 [20:32:44] Creating the                                                         
#16 257.3            test/GCA_025259185.1_ASM2525918v1_genomic_nn_classification/GCA_02525
#16 257.3            9185.1_ASM2525918v1_genomic_encoded_proviruses directory.            
#16 257.3 [20:32:44] Encoded provirus data written to                                     
#16 257.3            GCA_025259185.1_ASM2525918v1_genomic_encoded_proviruses.             
#16 257.3 2025-12-30 20:32:44.842529: E external/local_xla/xla/stream_executor/cuda/cuda_platform.cc:51] failed call to cuInit: INTERNAL: CUDA error: Failed call to cuInit: UNKNOWN ERROR (303)
#16 300.0 
#16 300.0 [20:33:27] Sequences classified.                                                
#16 300.0 [20:33:27] Sequence classification in binary format written to                  
#16 300.0            GCA_025259185.1_ASM2525918v1_genomic_nn_classification.npz.          
#16 300.1 [20:33:27] Sequence classification in tabular format written to                 
#16 300.1            GCA_025259185.1_ASM2525918v1_genomic_nn_classification.tsv.          
#16 302.6 
#16 302.6 [20:33:30] Proviruses classified.                                               
#16 302.6 [20:33:30] Provirus classification in binary format written to                  
#16 302.6            GCA_025259185.1_ASM2525918v1_genomic_provirus_nn_classification.npz. 
#16 302.6 [20:33:30] Provirus classification in tabular format written to                 
#16 302.6            GCA_025259185.1_ASM2525918v1_genomic_provirus_nn_classification.tsv. 
#16 302.6 [20:33:30] geNomad nn-classification finished!                                  
#16 302.6 ╭──────────────────────────────────────────────────────────────────────────────╮
#16 302.6 │  Executing geNomad aggregated-classification (v1.11.2). This will aggregate  │
#16 302.6 │  the results of the marker-classification and nn-classification modules to   │
#16 302.6 │  classify the input sequences into chromosome, plasmid, or virus.            │
#16 302.6 │  ──────────────────────────────────────────────────────────────────────────  │
#16 302.6 │  Outputs:                                                                    │
#16 302.6 │    test/GCA_025259185.1_ASM2525918v1_genomic_aggregated_classification       │
#16 302.6 │    ├── GCA_025259185.1_ASM2525918v1_genomic_aggregated_classification.json   │
#16 302.6 │    │   (execution parameters)                                                │
#16 302.6 │    ├── GCA_025259185.1_ASM2525918v1_genomic_aggregated_classification.tsv    │
#16 302.6 │    │   (sequence classification: tabular format)                             │
#16 302.6 │    ├── GCA_025259185.1_ASM2525918v1_genomic_aggregated_classification.npz    │
#16 302.6 │    │   (sequence classification: binary format)                              │
#16 302.6 │    ├── GCA_025259185.1_ASM2525918v1_genomic_provirus_aggregated_classificat  │
#16 302.6 │    │   ion.tsv (provirus classification: tabular format)                     │
#16 302.6 │    └── GCA_025259185.1_ASM2525918v1_genomic_provirus_aggregated_classificat  │
#16 302.6 │        ion.npz (provirus classification: binary format)                      │
#16 302.6 ╰──────────────────────────────────────────────────────────────────────────────╯
#16 302.7 [20:33:30] Executing genomad aggregated-classification.                         
#16 302.7 [20:33:30] Creating the                                                         
#16 302.7            test/GCA_025259185.1_ASM2525918v1_genomic_aggregated_classification  
#16 302.7            directory.                                                           
#16 302.7 [20:33:30] The total marker frequencies of the input sequences were computed.   
#16 302.7 [20:33:30] Sequences classified.                                                
#16 302.7 [20:33:30] Sequence classification in binary format written to                  
#16 302.7            GCA_025259185.1_ASM2525918v1_genomic_aggregated_classification.npz.  
#16 302.7 [20:33:30] Sequence classification in tabular format written to                 
#16 302.7            GCA_025259185.1_ASM2525918v1_genomic_aggregated_classification.tsv.  
#16 302.7 [20:33:30] Proviruses classified.                                               
#16 302.7 [20:33:30] Provirus classification in binary format written to                  
#16 302.7            GCA_025259185.1_ASM2525918v1_genomic_provirus_aggregated_classificati
#16 302.7            on.npz.                                                              
#16 302.7 [20:33:30] Provirus classification in tabular format written to                 
#16 302.7            GCA_025259185.1_ASM2525918v1_genomic_provirus_aggregated_classificati
#16 302.7            on.tsv.                                                              
#16 302.7 [20:33:30] geNomad aggregated-classification finished!                          
#16 302.7 ╭──────────────────────────────────────────────────────────────────────────────╮
#16 302.7 │  Executing geNomad summary (v1.11.2). This will summarize the results        │
#16 302.7 │  across modules into a classification report.                                │
#16 302.7 │  ──────────────────────────────────────────────────────────────────────────  │
#16 302.7 │  Outputs:                                                                    │
#16 302.7 │    test/GCA_025259185.1_ASM2525918v1_genomic_summary                         │
#16 302.7 │    ├── GCA_025259185.1_ASM2525918v1_genomic_summary.json (execution          │
#16 302.7 │    │   parameters)                                                           │
#16 302.7 │    ├── GCA_025259185.1_ASM2525918v1_genomic_virus_summary.tsv (virus         │
#16 302.7 │    │   classification summary)                                               │
#16 302.7 │    ├── GCA_025259185.1_ASM2525918v1_genomic_plasmid_summary.tsv (plasmid     │
#16 302.7 │    │   classification summary)                                               │
#16 302.7 │    ├── GCA_025259185.1_ASM2525918v1_genomic_virus.fna (virus nucleotide      │
#16 302.7 │    │   FASTA file)                                                           │
#16 302.7 │    ├── GCA_025259185.1_ASM2525918v1_genomic_plasmid.fna (plasmid nucleotide  │
#16 302.7 │    │   FASTA file)                                                           │
#16 302.7 │    ├── GCA_025259185.1_ASM2525918v1_genomic_virus_proteins.faa (virus        │
#16 302.7 │    │   protein FASTA file)                                                   │
#16 302.7 │    ├── GCA_025259185.1_ASM2525918v1_genomic_plasmid_proteins.faa (plasmid    │
#16 302.7 │    │   protein FASTA file)                                                   │
#16 302.7 │    ├── GCA_025259185.1_ASM2525918v1_genomic_virus_genes.tsv (virus gene      │
#16 302.7 │    │   annotation data)                                                      │
#16 302.7 │    └── GCA_025259185.1_ASM2525918v1_genomic_plasmid_genes.tsv (plasmid gene  │
#16 302.7 │        annotation data)                                                      │
#16 302.7 ╰──────────────────────────────────────────────────────────────────────────────╯
#16 302.7 [20:33:30] Executing genomad summary.                                           
#16 302.7 [20:33:30] Creating the test/GCA_025259185.1_ASM2525918v1_genomic_summary       
#16 302.7            directory.                                                           
#16 302.7 [20:33:30] Using scores from aggregated-classification.                         
#16 302.7 [20:33:30] 3 plasmid(s) and 3 virus(es) were identified.                        
#16 302.8 [20:33:30] Nucleotide sequences were written to                                 
#16 302.8            GCA_025259185.1_ASM2525918v1_genomic_plasmid.fna and                 
#16 302.8            GCA_025259185.1_ASM2525918v1_genomic_virus.fna.                      
#16 302.8 [20:33:30] Protein sequences were written to                                    
#16 302.8            GCA_025259185.1_ASM2525918v1_genomic_plasmid_proteins.faa and        
#16 302.8            GCA_025259185.1_ASM2525918v1_genomic_virus_proteins.faa.             
#16 302.8 [20:33:30] Gene annotation data was written to                                  
#16 302.8            GCA_025259185.1_ASM2525918v1_genomic_plasmid_genes.tsv and           
#16 302.8            GCA_025259185.1_ASM2525918v1_genomic_virus_genes.tsv.                
#16 302.8 [20:33:30] Summary files were written to                                        
#16 302.8            GCA_025259185.1_ASM2525918v1_genomic_plasmid_summary.tsv and         
#16 302.8            GCA_025259185.1_ASM2525918v1_genomic_virus_summary.tsv.              
#16 302.8 [20:33:30] geNomad summary finished!                                            
#16 DONE 303.3s

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erinyoung commented Jan 5, 2026

I think this error is from checking to see if CUDA is installed and working and switching it CPU-only if CUDA isn't found. I'm not planning on using CUDA with this image, but I think there is a way to suppress this error message. I'll convert this to draft until I have time to work on it.

@erinyoung erinyoung marked this pull request as draft January 5, 2026 18:11
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