Update Genomad to 1.11.2 by cwoodside1278 · Pull Request #1572 · StaPH-B/docker-builds

cwoodside1278 · 2026-02-25T01:12:01Z

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

Description

This PR is for Genomad update to 1.11.2 from 1.11.1

created new directory structure genomad/1.11.2
Updated to noble from jammy
Left all other ARG versions the same:
- ARG ARAGORN_VER="1.2.41"
- ARG MMSEQS2_VER="17-b804f"
Updated the container-specific read me to genomad/1.11.2
Updated the main read me to include the new version 1.11.2

Diff output

diff -r genomad/1.11.2/Dockerfile genomad/1.11.1/Dockerfile
1c1,2
< ARG GENOMAD_VER="1.11.2"
---
> 
> ARG GENOMAD_VER="1.11.1"
5c6
< FROM ubuntu:noble AS builder
---
> FROM ubuntu:jammy AS builder
21c22
< FROM ubuntu:noble AS app
---
> FROM ubuntu:jammy AS app
27c28
< LABEL base.image="ubuntu:noble"
---
> LABEL base.image="ubuntu:jammy"
54c55
<     python3 -m pip install --no-cache-dir --break-system-packages v${GENOMAD_VER}.tar.gz && \
---
>     python3 -m pip install --no-cache-dir v${GENOMAD_VER}.tar.gz && \

Test Build

[+] Building 695.4s (16/16) FINISHED                                                                                                                                  docker:default
 => [internal] load build definition from Dockerfile                                                                                                                            0.0s
 => => transferring dockerfile: 2.68kB                                                                                                                                          0.0s
 => [internal] load metadata for docker.io/library/ubuntu:noble                                                                                                                 0.0s
 => [internal] load .dockerignore                                                                                                                                               0.0s
 => => transferring context: 2B                                                                                                                                                 0.0s
 => [builder 1/3] FROM docker.io/library/ubuntu:noble@sha256:d1e2e92c075e5ca139d51a140fff46f84315c0fdce203eab2807c7e495eff4f9                                                   0.0s
 => => resolve docker.io/library/ubuntu:noble@sha256:d1e2e92c075e5ca139d51a140fff46f84315c0fdce203eab2807c7e495eff4f9                                                           0.0s
 => CACHED [builder 2/3] RUN apt-get update && apt-get install -y --no-install-recommends     ca-certificates     libc6-dev     make     gcc     wget                           0.0s
 => CACHED [builder 3/3] RUN wget -q https://www.trna.se/ARAGORN/Downloads/aragorn1.2.41.c &&     gcc -O3 -ffast-math -finline-functions -o aragorn aragorn1.2.41.c &&     /ar  0.0s
 => CACHED [app 2/7] COPY --from=builder /aragorn /usr/local/bin/                                                                                                               0.0s
 => CACHED [app 3/7] RUN apt-get update && apt-get install -y --no-install-recommends     ca-certificates     procps     python3     python3-pip     wget &&     apt-get autoc  0.0s
 => CACHED [app 4/7] RUN wget -q https://github.com/soedinglab/MMseqs2/releases/download/17-b804f/mmseqs-linux-avx2.tar.gz &&     tar -xvf mmseqs-linux-avx2.tar.gz &&     rm   0.0s
 => [app 5/7] RUN wget -q https://github.com/apcamargo/genomad/archive/refs/tags/v1.11.2.tar.gz &&     python3 -m pip install --no-cache-dir --break-system-packages v1.11.2.  65.8s
 => [app 6/7] RUN genomad download-database .                                                                                                                                  56.0s 
 => [app 7/7] WORKDIR /data                                                                                                                                                     0.0s 
 => [test 1/3] WORKDIR /test                                                                                                                                                    0.0s 
 => [test 2/3] RUN genomad --help &&     genomad --version &&     aragorn -h &&     mmseqs -h                                                                                   2.9s 
 => [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  414.9s 
 => exporting to image                                                                                                                                                        155.6s 
 => => exporting layers                                                                                                                                                       122.7s 
 => => exporting manifest sha256:12012580a3eca0fc7c39888f89593c04e77ef19e0976df81b3e735d13e4e8862                                                                               0.0s 
 => => exporting config sha256:6624f1bd09f422b1f8221e7415fb1e533a4ae97ee207528370be84318bd6725e                                                                                 0.0s 
 => => exporting attestation manifest sha256:43e41948a7515fc64335850a36af1c767de73aa455172f6ec7fb5c26ae6839b0                                                                   0.0s 
 => => exporting manifest list sha256:608a6c0b647b1ad260e9d6452e074af60210485043454afd7f6003cff3aaa3d4                                                                          0.0s 
 => => naming to docker.io/library/genomad:1.11.2                                                                                                                               0.0s
 => => unpacking to docker.io/library/genomad:1.11.2

Added thsi line: python3 -m pip install --no-cache-dir --break-system-packages v${GENOMAD_VER}.tar.gz && \

erinyoung · 2026-02-25T17:42:10Z

This PR supersedes #1517

erinyoung · 2026-02-25T17:44:09Z

The tests worked

#16 1.818 ╭──────────────────────────────────────────────────────────────────────────────╮
#16 1.818 │  Executing geNomad annotate (v1.11.2). This will perform gene calling in     │
#16 1.818 │  the input sequences and annotate the predicted proteins with geNomad's      │
#16 1.818 │  markers.                                                                    │
#16 1.818 │  ──────────────────────────────────────────────────────────────────────────  │
#16 1.818 │  Outputs:                                                                    │
#16 1.818 │    test/GCA_025259185.1_ASM2525918v1_genomic_annotate                        │
#16 1.818 │    ├── GCA_025259185.1_ASM2525918v1_genomic_annotate.json (execution         │
#16 1.818 │    │   parameters)                                                           │
#16 1.818 │    ├── GCA_025259185.1_ASM2525918v1_genomic_genes.tsv (gene annotation       │
#16 1.818 │    │   data)                                                                 │
#16 1.818 │    ├── GCA_025259185.1_ASM2525918v1_genomic_taxonomy.tsv (taxonomic          │
#16 1.818 │    │   assignment)                                                           │
#16 1.818 │    ├── GCA_025259185.1_ASM2525918v1_genomic_mmseqs2.tsv (MMseqs2 output      │
#16 1.818 │    │   file)                                                                 │
#16 1.818 │    └── GCA_025259185.1_ASM2525918v1_genomic_proteins.faa (protein FASTA      │
#16 1.818 │        file)                                                                 │
#16 1.818 ╰──────────────────────────────────────────────────────────────────────────────╯
#16 1.839 [01:14:36] Executing genomad annotate.                                          
#16 1.841 [01:14:36] Creating the test/GCA_025259185.1_ASM2525918v1_genomic_annotate      
#16 281.8 │    ├── GCA_025259185.1_ASM2525918v1_genomic_plasmid_summary.tsv (plasmid     │
#16 281.8 │    │   classification summary)                                               │
#16 281.8 │    ├── GCA_025259185.1_ASM2525918v1_genomic_virus.fna (virus nucleotide      │
#16 281.8 │    │   FASTA file)                                                           │
#16 281.8 │    ├── GCA_025259185.1_ASM2525918v1_genomic_plasmid.fna (plasmid nucleotide  │
#16 281.8 │    │   FASTA file)                                                           │
#16 281.8 │    ├── GCA_025259185.1_ASM2525918v1_genomic_virus_proteins.faa (virus        │
#16 281.8 │    │   protein FASTA file)                                                   │
#16 281.8 │    ├── GCA_025259185.1_ASM2525918v1_genomic_plasmid_proteins.faa (plasmid    │
#16 281.8 │    │   protein FASTA file)                                                   │
#16 281.8 │    ├── GCA_025259185.1_ASM2525918v1_genomic_virus_genes.tsv (virus gene      │
#16 281.8 │    │   annotation data)                                                      │
#16 281.8 │    └── GCA_025259185.1_ASM2525918v1_genomic_plasmid_genes.tsv (plasmid gene  │
#16 281.8 │        annotation data)                                                      │
#16 281.8 ╰──────────────────────────────────────────────────────────────────────────────╯
#16 281.9 [01:19:16] Executing genomad summary.                                           
#16 281.9 [01:19:16] Creating the test/GCA_025259185.1_ASM2525918v1_genomic_summary       
#16 281.9            directory.                                                           
#16 281.9 [01:19:16] Using scores from aggregated-classification.                         
#16 281.9 [01:19:16] 3 plasmid(s) and 3 virus(es) were identified.                        
#16 281.9 [01:19:16] Nucleotide sequences were written to                                 
#16 281.9            GCA_025259185.1_ASM2525918v1_genomic_plasmid.fna and                 
#16 281.9            GCA_025259185.1_ASM2525918v1_genomic_virus.fna.                      
#16 281.9 [01:19:16] Protein sequences were written to                                    
#16 281.9            GCA_025259185.1_ASM2525918v1_genomic_plasmid_proteins.faa and        
#16 281.9            GCA_025259185.1_ASM2525918v1_genomic_virus_proteins.faa.             
#16 281.9 [01:19:16] Gene annotation data was written to                                  
#16 281.9            GCA_025259185.1_ASM2525918v1_genomic_plasmid_genes.tsv and           
#16 281.9            GCA_025259185.1_ASM2525918v1_genomic_virus_genes.tsv.                
#16 281.9 [01:19:16] Summary files were written to                                        
#16 281.9            GCA_025259185.1_ASM2525918v1_genomic_plasmid_summary.tsv and         
#16 281.9            GCA_025259185.1_ASM2525918v1_genomic_virus_summary.tsv.              
#16 281.9 [01:19:16] geNomad summary finished!                                            
#16 DONE 282.4s

erinyoung · 2026-02-25T17:49:01Z

I don't think this is an error, but it may concern users.

#16 246.9            test/GCA_025259185.1_ASM2525918v1_genomic_nn_classification/GCA_02525
#16 246.9            9185.1_ASM2525918v1_genomic_encoded_proviruses directory.            
#16 246.9 [01:18:41] Encoded provirus data written to                                     
#16 246.9            GCA_025259185.1_ASM2525918v1_genomic_encoded_proviruses.             
#16 246.9 2026-02-25 01:18:41.120428: 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)
#16 278.8 
#16 278.8 [01:19:13] Sequences classified.                                                
#16 278.8 [01:19:13] Sequence classification in binary format written to                  
#16 278.8            GCA_025259185.1_ASM2525918v1_genomic_nn_classification.npz.          
#16 278.8 [01:19:13] Sequence classification in tabular format written to                 
#16 278.8            GCA_025259185.1_ASM2525918v1_genomic_nn_classification.tsv.

I think this error is from tensorflow, and might be silence-able by telling it upfront that there's no GPU or CUDA in this image. What happens if you set the environmental variable CUDA_VISIBLE_DEVICES to ""?

It'd be something like

ENV CUDA_VISIBLE_DEVICES=""

ENV PATH="/mmseqs/bin:$PATH" LC_ALL=C CUDA_VISIBLE_DEVICES=""

cwoodside1278 · 2026-02-27T00:10:27Z

Okay I just added the update you suggested to the dockerfile. It appears to be working without using Cuda/GPUs now.

Build Output

[+] Building 34.0s (16/16) FINISHED                                                                                                                                   docker:default
 => [internal] load build definition from Dockerfile                                                                                                                            0.0s
 => => transferring dockerfile: 2.74kB                                                                                                                                          0.0s
 => [internal] load metadata for docker.io/library/ubuntu:noble                                                                                                                 0.0s
 => [internal] load .dockerignore                                                                                                                                               0.0s
 => => transferring context: 2B                                                                                                                                                 0.0s
 => [builder 1/3] FROM docker.io/library/ubuntu:noble@sha256:d1e2e92c075e5ca139d51a140fff46f84315c0fdce203eab2807c7e495eff4f9                                                   0.0s
 => => resolve docker.io/library/ubuntu:noble@sha256:d1e2e92c075e5ca139d51a140fff46f84315c0fdce203eab2807c7e495eff4f9                                                           0.0s
 => CACHED [builder 2/3] RUN apt-get update && apt-get install -y --no-install-recommends     ca-certificates     libc6-dev     make     gcc     wget                           0.0s
 => CACHED [builder 3/3] RUN wget -q https://www.trna.se/ARAGORN/Downloads/aragorn1.2.41.c &&     gcc -O3 -ffast-math -finline-functions -o aragorn aragorn1.2.41.c &&     /ar  0.0s
 => CACHED [app 2/7] COPY --from=builder /aragorn /usr/local/bin/                                                                                                               0.0s
 => CACHED [app 3/7] RUN apt-get update && apt-get install -y --no-install-recommends     ca-certificates     procps     python3     python3-pip     wget &&     apt-get autoc  0.0s
 => CACHED [app 4/7] RUN wget -q https://github.com/soedinglab/MMseqs2/releases/download/17-b804f/mmseqs-linux-avx2.tar.gz &&     tar -xvf mmseqs-linux-avx2.tar.gz &&     rm   0.0s
 => CACHED [app 5/7] RUN wget -q https://github.com/apcamargo/genomad/archive/refs/tags/v1.11.2.tar.gz &&     python3 -m pip install --no-cache-dir --break-system-packages v1  0.0s
 => CACHED [app 6/7] RUN genomad download-database .                                                                                                                            0.0s
 => CACHED [app 7/7] WORKDIR /data                                                                                                                                              0.0s
 => CACHED [test 1/3] WORKDIR /test                                                                                                                                             0.0s
 => CACHED [test 2/3] RUN genomad --help &&     genomad --version &&     aragorn -h &&     mmseqs -h                                                                            0.0s
 => CACHED [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.f  0.0s
 => exporting to image                                                                                                                                                         33.8s
 => => exporting layers                                                                                                                                                         0.0s
 => => exporting manifest sha256:1ec7e04b73984a0377343d6bb9dfb53541e4e9e9978530069d61190eff9e690d                                                                               0.0s
 => => exporting config sha256:15347a29e59e78b088cab2a55c0c5f883c8b6a266406c1b068d8f43ee4651461                                                                                 0.0s
 => => exporting attestation manifest sha256:5e9ca1b408567414faa37a591e13e1e3c0fbe2ac4008d3108be08f35bfe5fa10                                                                   0.0s
 => => exporting manifest list sha256:30cdd3a3a6282e71ae1047a8a0ab90dfebc1dd7ce155ac1bc1cb462bf3a06e29                                                                          0.0s
 => => naming to docker.io/library/genomad:1.11.2                                                                                                                               0.0s
 => => unpacking to docker.io/library/genomad:1.11.2

erinyoung · 2026-02-27T16:57:35Z

It looks like the error is still there

#16 245.4 2026-02-26 23:43:44.995459: 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)

cwoodside1278 · 2026-02-28T16:21:47Z

Hmmm I ran it again with docker build --no-cache -t genomad:1.11.2 . and I still didn't get that error. Could there be a possibility that when you ran it it still wasn't up to date yet? I am not sure what the next best steps to troubleshoot are here.


[+] Building 843.4s (16/16) FINISHED                                                                                                                                                                                                                                                                                              docker:default
 => [internal] load build definition from Dockerfile                                                                                                                                                                                                                                                                                        0.0s
 => => transferring dockerfile: 2.74kB                                                                                                                                                                                                                                                                                                      0.0s
 => [internal] load metadata for docker.io/library/ubuntu:noble                                                                                                                                                                                                                                                                             0.0s
 => [internal] load .dockerignore                                                                                                                                                                                                                                                                                                           0.0s
 => => transferring context: 2B                                                                                                                                                                                                                                                                                                             0.0s
 => CACHED [builder 1/3] FROM docker.io/library/ubuntu:noble@sha256:d1e2e92c075e5ca139d51a140fff46f84315c0fdce203eab2807c7e495eff4f9                                                                                                                                                                                                        0.0s
 => => resolve docker.io/library/ubuntu:noble@sha256:d1e2e92c075e5ca139d51a140fff46f84315c0fdce203eab2807c7e495eff4f9                                                                                                                                                                                                                       0.0s
 => [builder 2/3] RUN apt-get update && apt-get install -y --no-install-recommends     ca-certificates     libc6-dev     make     gcc     wget                                                                                                                                                                                             14.8s
 => [builder 3/3] RUN wget -q https://www.trna.se/ARAGORN/Downloads/aragorn1.2.41.c &&     gcc -O3 -ffast-math -finline-functions -o aragorn aragorn1.2.41.c &&     /aragorn -h                                                                                                                                                            11.5s 
 => [app 2/7] COPY --from=builder /aragorn /usr/local/bin/                                                                                                                                                                                                                                                                                  0.0s 
 => [app 3/7] RUN apt-get update && apt-get install -y --no-install-recommends     ca-certificates     procps     python3     python3-pip     wget &&     apt-get autoclean && rm -rf /var/lib/apt/lists/*                                                                                                                                 15.8s 
 => [app 4/7] RUN wget -q https://github.com/soedinglab/MMseqs2/releases/download/17-b804f/mmseqs-linux-avx2.tar.gz &&     tar -xvf mmseqs-linux-avx2.tar.gz &&     rm mmseqs-linux-avx2.tar.gz                                                                                                                                             1.1s 
 => [app 5/7] RUN wget -q https://github.com/apcamargo/genomad/archive/refs/tags/v1.11.2.tar.gz &&     python3 -m pip install --no-cache-dir --break-system-packages v1.11.2.tar.gz &&     rm -rf v1.11.2.tar.gz &&     mkdir /data                                                                                                        71.4s 
 => [app 6/7] RUN genomad download-database .                                                                                                                                                                                                                                                                                              55.7s 
 => [app 7/7] WORKDIR /data                                                                                                                                                                                                                                                                                                                 0.0s 
 => [test 1/3] WORKDIR /test                                                                                                                                                                                                                                                                                                                0.0s 
 => [test 2/3] RUN genomad --help &&     genomad --version &&     aragorn -h &&     mmseqs -h                                                                                                                                                                                                                                               3.1s 
 => [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    493.1s 
 => exporting to image                                                                                                                                                                                                                                                                                                                    176.2s 
 => => exporting layers                                                                                                                                                                                                                                                                                                                   134.5s 
 => => exporting manifest sha256:c471e12e58a6cc9bc5586789f80027a5704460d49d86843469ef2d4f6710fc5e                                                                                                                                                                                                                                           0.0s 
 => => exporting config sha256:723300fc67ec3808bc2722ec5684345e1e8e16974ef1f43d7113bc1afe306ac9                                                                                                                                                                                                                                             0.0s 
 => => exporting attestation manifest sha256:d5b24bfcf6ddd7a3b33aecd1ba518b8bab09f5e23e9fa8089b138061ad6ab1aa                                                                                                                                                                                                                               0.0s 
 => => exporting manifest list sha256:2fcbec3229437e389d28a10cc78e655e3841a1facf707da325bdfdfe481eca16                                                                                                                                                                                                                                      0.0s 
 => => naming to docker.io/library/genomad:1.11.2                                                                                                                                                                                                                                                                                           0.0s
 => => unpacking to docker.io/library/genomad:1.11.2

erinyoung · 2026-03-02T17:43:07Z

It's on line 2033 in https://github.com/StaPH-B/docker-builds/actions/runs/22465944978/job/65071833823?pr=1572

Kincekara · 2026-03-02T20:31:51Z

@erinyoung I think we missed this error before, and it exists in the previous image. Replacing tensorflow with tensorflow-cpu suppresses this error, but removes gpu support.

@cwoodside1278, Could you try installing tensorflow-cpu via pip without removing tensorflow?

Kincekara · 2026-03-02T20:38:56Z

@erinyoung If it works without problem, I think you can approve as it is 🙈

I updated the code to contain tensorflow-cpu, but I also left the old code just commented out in case we need it or need to replicate the bug

cwoodside1278 · 2026-03-04T00:07:57Z

Okay I made that update to include tensorflow-cpu and my docker build was fine once again. Can you let me know if the issue is still happening? @erinyoung @Kincekara

erinyoung · 2026-03-04T00:12:18Z

It looks like the error message is gone! Huzzah!

#17 [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
#17 0.417 Package                 Version
#17 0.417 ----------------------- ---------
#17 0.417 absl-py                 2.4.0
#17 0.418 archspec                0.2.5
#17 0.418 astunparse              1.6.3
#17 0.418 certifi                 2026.2.25
#17 0.418 charset-normalizer      3.4.4
#17 0.418 click                   8.3.1
#17 0.418 flatbuffers             25.12.19
#17 0.419 gast                    0.7.0
#17 0.419 genomad                 1.11.2
#17 0.419 google-pasta            0.2.0
#17 0.420 grpcio                  1.78.0
#17 0.420 h5py                    3.15.1
#17 0.420 idna                    3.11
#17 0.420 keras                   3.13.2
#17 0.421 libclang                18.1.1
#17 0.421 llvmlite                0.46.0
#17 0.421 Markdown                3.10.2
#17 0.421 markdown-it-py          4.0.0
#17 0.422 MarkupSafe              3.0.3
#17 0.422 mdurl                   0.1.2
#17 0.422 ml_dtypes               0.5.4
#17 0.422 namex                   0.1.0
#17 0.423 numba                   0.64.0
#17 0.423 numpy                   2.4.2
#17 0.423 nvidia-nccl-cu12        2.29.7
#17 0.423 opt_einsum              3.4.0
#17 0.424 optree                  0.19.0
#17 0.424 packaging               26.0
#17 0.424 pillow                  12.1.1
#17 0.424 pip                     24.0
#17 0.425 protobuf                7.34.0
#17 0.425 Pygments                2.19.2
#17 0.425 pyrodigal               3.7.0
#17 0.426 pyrodigal_gv            0.3.2
#17 0.426 python-crfsuite         0.9.12
#17 0.426 requests                2.32.5
#17 0.426 rich                    14.3.3
#17 0.426 rich-click              1.9.7
#17 0.427 scipy                   1.17.1
#17 0.427 setuptools              68.1.2
#17 0.427 six                     1.17.0
#17 0.428 taxopy                  0.14.0
#17 0.428 tensorboard             2.20.0
#17 0.428 tensorboard-data-server 0.7.2
#17 0.428 tensorflow              2.20.0
#17 0.429 tensorflow_cpu          2.20.0
#17 0.429 termcolor               3.3.0
#17 0.429 typing_extensions       4.15.0
#17 0.429 urllib3                 2.6.3
#17 0.429 Werkzeug                3.1.6
#17 0.430 wheel                   0.42.0
#17 0.430 wrapt                   2.1.1
#17 0.430 xgboost                 3.2.0
#17 2.324 ╭──────────────────────────────────────────────────────────────────────────────╮
#17 2.324 │  Executing geNomad annotate (v1.11.2). This will perform gene calling in     │
#17 2.324 │  the input sequences and annotate the predicted proteins with geNomad's      │
#17 2.324 │  markers.                                                                    │
#17 2.324 │  ──────────────────────────────────────────────────────────────────────────  │
#17 2.324 │  Outputs:                                                                    │
#17 2.324 │    test/GCA_025259185.1_ASM2525918v1_genomic_annotate                        │
#17 2.324 │    ├── GCA_025259185.1_ASM2525918v1_genomic_annotate.json (execution         │
#17 2.324 │    │   parameters)                                                           │
#17 2.324 │    ├── GCA_025259185.1_ASM2525918v1_genomic_genes.tsv (gene annotation       │
#17 2.324 │    │   data)                                                                 │
#17 2.324 │    ├── GCA_025259185.1_ASM2525918v1_genomic_taxonomy.tsv (taxonomic          │
#17 2.324 │    │   assignment)                                                           │
#17 2.324 │    ├── GCA_025259185.1_ASM2525918v1_genomic_mmseqs2.tsv (MMseqs2 output      │
#17 2.324 │    │   file)                                                                 │
#17 2.324 │    └── GCA_025259185.1_ASM2525918v1_genomic_proteins.faa (protein FASTA      │
#17 2.324 │        file)                                                                 │
#17 2.324 ╰──────────────────────────────────────────────────────────────────────────────╯
#17 2.346 [23:45:38] Executing genomad annotate.                                          
#17 2.351 [23:45:38] Creating the test/GCA_025259185.1_ASM2525918v1_genomic_annotate      
#17 2.351            directory.                                                           
#17 23.04 [23:45:59] Proteins predicted with pyrodigal-gv were written to                 
#17 23.04            GCA_025259185.1_ASM2525918v1_genomic_proteins.faa.                   
#17 237.9 [23:49:34] Proteins annotated with MMseqs2 and geNomad database (v1.9) were     
#17 237.9            written to GCA_025259185.1_ASM2525918v1_genomic_mmseqs2.tsv.         
#17 238.5 [23:49:34] Gene data was written to                                             
#17 238.5            GCA_025259185.1_ASM2525918v1_genomic_genes.tsv.                      
#17 238.5 [23:49:34] Taxonomic assignment data was written to                             
#17 238.5            GCA_025259185.1_ASM2525918v1_genomic_taxonomy.tsv.                   
#17 238.6 [23:49:34] geNomad annotate finished!                                           
#17 238.6 ╭──────────────────────────────────────────────────────────────────────────────╮
#17 238.6 │  Executing geNomad find-proviruses (v1.11.2). This will find putative        │
#17 238.6 │  proviral regions within the input sequences.                                │
#17 238.6 │  ──────────────────────────────────────────────────────────────────────────  │
#17 238.6 │  Outputs:                                                                    │
#17 238.6 │    test/GCA_025259185.1_ASM2525918v1_genomic_find_proviruses                 │
#17 238.6 │    ├── GCA_025259185.1_ASM2525918v1_genomic_find_proviruses.json (execution  │
#17 238.6 │    │   parameters)                                                           │
#17 238.6 │    ├── GCA_025259185.1_ASM2525918v1_genomic_provirus.tsv (provirus data)     │
#17 238.6 │    ├── GCA_025259185.1_ASM2525918v1_genomic_provirus.fna (provirus           │
#17 238.6 │    │   nucleotide sequences)                                                 │
#17 238.6 │    ├── GCA_025259185.1_ASM2525918v1_genomic_provirus_proteins.faa (provirus  │
#17 238.6 │    │   protein sequences)                                                    │
#17 238.6 │    ├── GCA_025259185.1_ASM2525918v1_genomic_provirus_genes.tsv (provirus     │
#17 238.6 │    │   gene annotation data)                                                 │
#17 238.6 │    ├── GCA_025259185.1_ASM2525918v1_genomic_provirus_taxonomy.tsv (provirus  │
#17 238.6 │    │   taxonomic assignment)                                                 │
#17 238.6 │    ├── GCA_025259185.1_ASM2525918v1_genomic_provirus_mmseqs2.tsv (MMseqs2    │
#17 238.6 │    │   output file)                                                          │
#17 238.6 │    └── GCA_025259185.1_ASM2525918v1_genomic_provirus_aragorn.tsv (Aragorn    │
#17 238.6 │        output file)                                                          │
#17 238.6 ╰──────────────────────────────────────────────────────────────────────────────╯
#17 238.6 [23:49:34] Executing genomad find-proviruses.                                   
#17 238.6 [23:49:34] Creating the                                                         
#17 238.6            test/GCA_025259185.1_ASM2525918v1_genomic_find_proviruses directory. 
#17 240.6 [23:49:36] Integrases identified with MMseqs2 and geNomad database (v1.9) were  
#17 240.6            written to GCA_025259185.1_ASM2525918v1_genomic_provirus_mmseqs2.tsv.
#17 246.9 [23:49:43] tRNAs identified with Aragorn were written to                        
#17 246.9            GCA_025259185.1_ASM2525918v1_genomic_provirus_aragorn.tsv.           
#17 247.5 [23:49:43] Provirus regions identified.                                         
#17 247.5 [23:49:43] Provirus data was written to                                         
#17 247.5            GCA_025259185.1_ASM2525918v1_genomic_provirus.tsv.                   
#17 247.5 [23:49:43] Provirus nucleotide sequences were written to                        
#17 247.5            GCA_025259185.1_ASM2525918v1_genomic_provirus.fna.                   
#17 247.5 [23:49:43] Provirus protein sequences were written to                           
#17 247.5            GCA_025259185.1_ASM2525918v1_genomic_provirus_proteins.faa.          
#17 247.5 [23:49:43] Provirus gene data was written to                                    
#17 247.5            GCA_025259185.1_ASM2525918v1_genomic_provirus_genes.tsv.             
#17 247.6 [23:49:43] Taxonomic assignment data was written to                             
#17 247.6            GCA_025259185.1_ASM2525918v1_genomic_provirus_taxonomy.tsv.          
#17 247.6 [23:49:43] geNomad find-proviruses finished!                                    
#17 247.6 ╭──────────────────────────────────────────────────────────────────────────────╮
#17 247.6 │  Executing geNomad marker-classification (v1.11.2). This will classify the   │
#17 247.6 │  input sequences into chromosome, plasmid, or virus based on the presence    │
#17 247.6 │  of geNomad markers and other gene-related features.                         │
#17 247.6 │  ──────────────────────────────────────────────────────────────────────────  │
#17 247.6 │  Outputs:                                                                    │
#17 247.6 │    test/GCA_025259185.1_ASM2525918v1_genomic_marker_classification           │
#17 247.6 │    ├── GCA_025259185.1_ASM2525918v1_genomic_marker_classification.json       │
#17 247.6 │    │   (execution parameters)                                                │
#17 247.6 │    ├── GCA_025259185.1_ASM2525918v1_genomic_features.tsv (sequence feature   │
#17 247.6 │    │   data: tabular format)                                                 │
#17 247.6 │    ├── GCA_025259185.1_ASM2525918v1_genomic_features.npz (sequence feature   │
#17 247.6 │    │   data: binary format)                                                  │
#17 247.6 │    ├── GCA_025259185.1_ASM2525918v1_genomic_marker_classification.tsv        │
#17 247.6 │    │   (sequence classification: tabular format)                             │
#17 247.6 │    ├── GCA_025259185.1_ASM2525918v1_genomic_marker_classification.npz        │
#17 247.6 │    │   (sequence classification: binary format)                              │
#17 247.6 │    ├── GCA_025259185.1_ASM2525918v1_genomic_provirus_features.tsv (provirus  │
#17 247.6 │    │   feature data: tabular format)                                         │
#17 247.6 │    ├── GCA_025259185.1_ASM2525918v1_genomic_provirus_features.npz (provirus  │
#17 247.6 │    │   feature data: binary format)                                          │
#17 247.6 │    ├── GCA_025259185.1_ASM2525918v1_genomic_provirus_marker_classification.  │
#17 247.6 │    │   tsv (provirus classification: tabular format)                         │
#17 247.6 │    └── GCA_025259185.1_ASM2525918v1_genomic_provirus_marker_classification.  │
#17 247.6 │        npz (provirus classification: binary format)                          │
#17 247.6 ╰──────────────────────────────────────────────────────────────────────────────╯
#17 247.6 [23:49:43] Executing genomad marker-classification.                             
#17 247.6 [23:49:43] Creating the                                                         
#17 247.6            test/GCA_025259185.1_ASM2525918v1_genomic_marker_classification      
#17 247.6            directory.                                                           
#17 248.2 [23:49:44] Sequence features computed.                                          
#17 248.2 [23:49:44] Sequence features in binary format written to                        
#17 248.2            GCA_025259185.1_ASM2525918v1_genomic_features.npz.                   
#17 248.2 [23:49:44] Sequence features in tabular format written to                       
#17 248.2            GCA_025259185.1_ASM2525918v1_genomic_features.tsv.                   
#17 248.7 [23:49:44] Provirus features computed.                                          
#17 248.7 [23:49:44] Provirus features in binary format written to                        
#17 248.7            GCA_025259185.1_ASM2525918v1_genomic_provirus_features.npz.          
#17 248.7 [23:49:44] Provirus features in tabular format written to                       
#17 248.7            GCA_025259185.1_ASM2525918v1_genomic_provirus_features.tsv.          
#17 248.7 [23:49:44] Sequences classified.                                                
#17 248.7 [23:49:44] Sequence classification in binary format written to                  
#17 248.7            GCA_025259185.1_ASM2525918v1_genomic_marker_classification.npz.      
#17 248.7 [23:49:44] Sequence classification in tabular format written to                 
#17 248.7            GCA_025259185.1_ASM2525918v1_genomic_marker_classification.tsv.      
#17 248.8 [23:49:44] Proviruses classified.                                               
#17 248.8 [23:49:44] Provirus classification in binary format written to                  
#17 248.8            GCA_025259185.1_ASM2525918v1_genomic_provirus_marker_classification.n
#17 248.8            pz.                                                                  
#17 248.8 [23:49:44] Provirus classification in tabular format written to                 
#17 248.8            GCA_025259185.1_ASM2525918v1_genomic_provirus_marker_classification.t
#17 248.8            sv.                                                                  
#17 248.8 [23:49:44] geNomad marker-classification finished!                              
#17 250.5 ╭──────────────────────────────────────────────────────────────────────────────╮
#17 250.5 │  Executing geNomad nn-classification (v1.11.2). This will classify the       │
#17 250.5 │  input sequences into chromosome, plasmid, or virus based on the nucleotide  │
#17 250.5 │  sequence.                                                                   │
#17 250.5 │  ──────────────────────────────────────────────────────────────────────────  │
#17 250.5 │  Outputs:                                                                    │
#17 250.5 │    test/GCA_025259185.1_ASM2525918v1_genomic_nn_classification               │
#17 250.5 │    ├── GCA_025259185.1_ASM2525918v1_genomic_nn_classification.json           │
#17 250.5 │    │   (execution parameters)                                                │
#17 250.5 │    ├── GCA_025259185.1_ASM2525918v1_genomic_encoded_sequences (directory     │
#17 250.5 │    │   containing encoded sequence data)                                     │
#17 250.5 │    ├── GCA_025259185.1_ASM2525918v1_genomic_nn_classification.tsv (contig    │
#17 250.5 │    │   classification: tabular format)                                       │
#17 250.5 │    ├── GCA_025259185.1_ASM2525918v1_genomic_nn_classification.npz (contig    │
#17 250.5 │    │   classification: binary format)                                        │
#17 250.5 │    ├── GCA_025259185.1_ASM2525918v1_genomic_encoded_proviruses (directory    │
#17 250.5 │    │   containing encoded sequence data)                                     │
#17 250.5 │    ├── GCA_025259185.1_ASM2525918v1_genomic_provirus_nn_classification.tsv   │
#17 250.5 │    │   (provirus classification: tabular format)                             │
#17 250.5 │    └── GCA_025259185.1_ASM2525918v1_genomic_provirus_nn_classification.npz   │
#17 250.5 │        (provirus classification: binary format)                              │
#17 250.5 ╰──────────────────────────────────────────────────────────────────────────────╯
#17 250.5 [23:49:46] Executing genomad nn-classification.                                 
#17 250.5 [23:49:46] Creating the                                                         
#17 250.5            test/GCA_025259185.1_ASM2525918v1_genomic_nn_classification          
#17 250.5            directory.                                                           
#17 250.5 [23:49:46] Creating the                                                         
#17 250.5            test/GCA_025259185.1_ASM2525918v1_genomic_nn_classification/GCA_02525
#17 250.5            9185.1_ASM2525918v1_genomic_encoded_sequences directory.             
#17 252.0 [23:49:48] Encoded sequence data written to                                     
#17 252.0            GCA_025259185.1_ASM2525918v1_genomic_encoded_sequences.              
#17 252.0 [23:49:48] Creating the                                                         
#17 252.0            test/GCA_025259185.1_ASM2525918v1_genomic_nn_classification/GCA_02525
#17 252.0            9185.1_ASM2525918v1_genomic_encoded_proviruses directory.            
#17 252.0 [23:49:48] Encoded provirus data written to                                     
#17 252.0            GCA_025259185.1_ASM2525918v1_genomic_encoded_proviruses.             
#17 283.0 
#17 283.0 [23:50:19] Sequences classified.                                                
#17 283.0 [23:50:19] Sequence classification in binary format written to                  
#17 283.0            GCA_025259185.1_ASM2525918v1_genomic_nn_classification.npz.          
#17 283.0 [23:50:19] Sequence classification in tabular format written to                 
#17 283.0            GCA_025259185.1_ASM2525918v1_genomic_nn_classification.tsv.          
#17 286.0 
#17 286.0 [23:50:22] Proviruses classified.                                               
#17 286.0 [23:50:22] Provirus classification in binary format written to                  
#17 286.0            GCA_025259185.1_ASM2525918v1_genomic_provirus_nn_classification.npz. 
#17 286.0 [23:50:22] Provirus classification in tabular format written to                 
#17 286.0            GCA_025259185.1_ASM2525918v1_genomic_provirus_nn_classification.tsv. 
#17 286.0 [23:50:22] geNomad nn-classification finished!                                  
#17 286.0 ╭──────────────────────────────────────────────────────────────────────────────╮
#17 286.0 │  Executing geNomad aggregated-classification (v1.11.2). This will aggregate  │
#17 286.0 │  the results of the marker-classification and nn-classification modules to   │
#17 286.0 │  classify the input sequences into chromosome, plasmid, or virus.            │
#17 286.0 │  ──────────────────────────────────────────────────────────────────────────  │
#17 286.0 │  Outputs:                                                                    │
#17 286.0 │    test/GCA_025259185.1_ASM2525918v1_genomic_aggregated_classification       │
#17 286.0 │    ├── GCA_025259185.1_ASM2525918v1_genomic_aggregated_classification.json   │
#17 286.0 │    │   (execution parameters)                                                │
#17 286.0 │    ├── GCA_025259185.1_ASM2525918v1_genomic_aggregated_classification.tsv    │
#17 286.0 │    │   (sequence classification: tabular format)                             │
#17 286.0 │    ├── GCA_025259185.1_ASM2525918v1_genomic_aggregated_classification.npz    │
#17 286.0 │    │   (sequence classification: binary format)                              │
#17 286.0 │    ├── GCA_025259185.1_ASM2525918v1_genomic_provirus_aggregated_classificat  │
#17 286.0 │    │   ion.tsv (provirus classification: tabular format)                     │
#17 286.0 │    └── GCA_025259185.1_ASM2525918v1_genomic_provirus_aggregated_classificat  │
#17 286.0 │        ion.npz (provirus classification: binary format)                      │
#17 286.0 ╰──────────────────────────────────────────────────────────────────────────────╯
#17 286.1 [23:50:22] Executing genomad aggregated-classification.                         
#17 286.1 [23:50:22] Creating the                                                         
#17 286.1            test/GCA_025259185.1_ASM2525918v1_genomic_aggregated_classification  
#17 286.1            directory.                                                           
#17 286.1 [23:50:22] The total marker frequencies of the input sequences were computed.   
#17 286.1 [23:50:22] Sequences classified.                                                
#17 286.1 [23:50:22] Sequence classification in binary format written to                  
#17 286.1            GCA_025259185.1_ASM2525918v1_genomic_aggregated_classification.npz.  
#17 286.1 [23:50:22] Sequence classification in tabular format written to                 
#17 286.1            GCA_025259185.1_ASM2525918v1_genomic_aggregated_classification.tsv.  
#17 286.1 [23:50:22] Proviruses classified.                                               
#17 286.1 [23:50:22] Provirus classification in binary format written to                  
#17 286.1            GCA_025259185.1_ASM2525918v1_genomic_provirus_aggregated_classificati
#17 286.1            on.npz.                                                              
#17 286.1 [23:50:22] Provirus classification in tabular format written to                 
#17 286.1            GCA_025259185.1_ASM2525918v1_genomic_provirus_aggregated_classificati
#17 286.1            on.tsv.                                                              
#17 286.1 [23:50:22] geNomad aggregated-classification finished!                          
#17 286.1 ╭──────────────────────────────────────────────────────────────────────────────╮
#17 286.1 │  Executing geNomad summary (v1.11.2). This will summarize the results        │
#17 286.1 │  across modules into a classification report.                                │
#17 286.1 │  ──────────────────────────────────────────────────────────────────────────  │
#17 286.1 │  Outputs:                                                                    │
#17 286.1 │    test/GCA_025259185.1_ASM2525918v1_genomic_summary                         │
#17 286.1 │    ├── GCA_025259185.1_ASM2525918v1_genomic_summary.json (execution          │
#17 286.1 │    │   parameters)                                                           │
#17 286.1 │    ├── GCA_025259185.1_ASM2525918v1_genomic_virus_summary.tsv (virus         │
#17 286.1 │    │   classification summary)                                               │
#17 286.1 │    ├── GCA_025259185.1_ASM2525918v1_genomic_plasmid_summary.tsv (plasmid     │
#17 286.1 │    │   classification summary)                                               │
#17 286.1 │    ├── GCA_025259185.1_ASM2525918v1_genomic_virus.fna (virus nucleotide      │
#17 286.1 │    │   FASTA file)                                                           │
#17 286.1 │    ├── GCA_025259185.1_ASM2525918v1_genomic_plasmid.fna (plasmid nucleotide  │
#17 286.1 │    │   FASTA file)                                                           │
#17 286.1 │    ├── GCA_025259185.1_ASM2525918v1_genomic_virus_proteins.faa (virus        │
#17 286.1 │    │   protein FASTA file)                                                   │
#17 286.1 │    ├── GCA_025259185.1_ASM2525918v1_genomic_plasmid_proteins.faa (plasmid    │
#17 286.1 │    │   protein FASTA file)                                                   │
#17 286.1 │    ├── GCA_025259185.1_ASM2525918v1_genomic_virus_genes.tsv (virus gene      │
#17 286.1 │    │   annotation data)                                                      │
#17 286.1 │    └── GCA_025259185.1_ASM2525918v1_genomic_plasmid_genes.tsv (plasmid gene  │
#17 286.1 │        annotation data)                                                      │
#17 286.1 ╰──────────────────────────────────────────────────────────────────────────────╯
#17 286.1 [23:50:22] Executing genomad summary.                                           
#17 286.1 [23:50:22] Creating the test/GCA_025259185.1_ASM2525918v1_genomic_summary       
#17 286.1            directory.                                                           
#17 286.1 [23:50:22] Using scores from aggregated-classification.                         
#17 286.2 [23:50:22] 3 plasmid(s) and 3 virus(es) were identified.                        
#17 286.2 [23:50:22] Nucleotide sequences were written to                                 
#17 286.2            GCA_025259185.1_ASM2525918v1_genomic_plasmid.fna and                 
#17 286.2            GCA_025259185.1_ASM2525918v1_genomic_virus.fna.                      
#17 286.2 [23:50:22] Protein sequences were written to                                    
#17 286.2            GCA_025259185.1_ASM2525918v1_genomic_plasmid_proteins.faa and        
#17 286.2            GCA_025259185.1_ASM2525918v1_genomic_virus_proteins.faa.             
#17 286.2 [23:50:22] Gene annotation data was written to                                  
#17 286.2            GCA_025259185.1_ASM2525918v1_genomic_plasmid_genes.tsv and           
#17 286.2            GCA_025259185.1_ASM2525918v1_genomic_virus_genes.tsv.                
#17 286.2 [23:50:22] Summary files were written to                                        
#17 286.2            GCA_025259185.1_ASM2525918v1_genomic_plasmid_summary.tsv and         
#17 286.2            GCA_025259185.1_ASM2525918v1_genomic_virus_summary.tsv.              
#17 286.2 [23:50:22] geNomad summary finished!

erinyoung

I'll get this merged and deployed.

Thank you for putting this together!

erinyoung · 2026-03-04T00:14:03Z

The status of the deploy can be found here : https://github.com/StaPH-B/docker-builds/actions/runs/22648851692

cwoodside1278 added 4 commits February 24, 2026 19:50

Create README.md for genomad

840fbc0

Create Dockerfile for genomad

3bf7cd5

Update README.md to include genomad 1.11.2

8324370

Update Dockerfile to add a fix

2ac4941

Added thsi line: python3 -m pip install --no-cache-dir --break-system-packages v${GENOMAD_VER}.tar.gz && \

Update Dockerfile for the cuda issue

6a6ec61

ENV PATH="/mmseqs/bin:$PATH" LC_ALL=C CUDA_VISIBLE_DEVICES=""

Update Dockerfile to include tensorflow-cpu

f9feb6e

I updated the code to contain tensorflow-cpu, but I also left the old code just commented out in case we need it or need to replicate the bug

erinyoung approved these changes Mar 4, 2026

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erinyoung merged commit 9109d42 into StaPH-B:master Mar 4, 2026
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cwoodside1278 commented Feb 25, 2026

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erinyoung commented Feb 25, 2026 •

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