adding genomad version 1.11.2 by erinyoung · Pull Request #1517 · StaPH-B/docker-builds

erinyoung · 2025-12-30T20:25:56Z

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 · 2025-12-30T21:45:53Z

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

Sorry!!!

README.md

kapsakcj · 2025-12-31T18:59:51Z

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

kapsakcj · 2025-12-31T19:02:35Z

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

erinyoung · 2026-01-05T18:11:02Z

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.

adding genomad version 1.11.2

9953a9a

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

kapsakcj reviewed Dec 31, 2025

View reviewed changes

README.md Outdated Show resolved Hide resolved

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

Fix formatting of geNomad entry in README

928e6eb

Provide feedback

Saved searches

Use saved searches to filter your results more quickly

adding genomad version 1.11.2#1517

adding genomad version 1.11.2#1517
erinyoung wants to merge 2 commits intoStaPH-B:masterfrom
erinyoung:erin-genomad

erinyoung commented Dec 30, 2025

Uh oh!

erinyoung commented Dec 30, 2025

Uh oh!

Uh oh!

kapsakcj commented Dec 31, 2025

Uh oh!

kapsakcj commented Dec 31, 2025

Uh oh!

erinyoung commented Jan 5, 2026

Uh oh!

Reviewers

Assignees

Labels

Projects

Milestone

Development

Uh oh!

2 participants

Conversation

erinyoung commented Dec 30, 2025

Uh oh!

erinyoung commented Dec 30, 2025

Uh oh!

Uh oh!

kapsakcj commented Dec 31, 2025

Uh oh!

kapsakcj commented Dec 31, 2025

Uh oh!

erinyoung commented Jan 5, 2026

Uh oh!

Reviewers

Assignees

Labels

Projects

Milestone

Development

Uh oh!

2 participants