CalledProcessError - mmseqs align failed

Hello! Thank you for the wonderful program. I recently tried running geNomad and encountered an error. I would appreciate any suggestions on how to fix it. The error message and the mmseqs2.log file are attached. Please let me know if I’ve missed anything or if you need additional information. Thanks! [mmseqs2.log](https://github.com/user-attachments/files/24037172/mmseqs2.log) ``` genomad end-to-end --min-score 0.6 \ > --cleanup \ > --splits 12 \ > --threads 8 \ > passing_Viralcontigs.fasta \ > "/scratch/gdlab/kailun/Phageome/Phage_analysis_test/geNomad" \ > "/scratch/gdlab/kailun/Phageome/genomad_DBs/v1.9/genomad_db" /ref/sahlab/software/miniforge3/envs/smk_envs_phage_pred/c3c2c6c9a7fdb9755014780de49c5ec0_/lib/python3.11/site-packages/xgboost/core.py:377: FutureWarning: Your system has an old version of glibc (< 2.28). We will stop sup porting Linux distros with glibc older than 2.28 after **May 31, 2025**. Please upgrade to a recent Linux distro (with glibc >= 2.28) to use future versions of XGBoost. Note: You have installed the 'manylinux2014' variant of XGBoost. Certain features such as GPU algorithms or federated learning are not available. To use these features, please upgrade to a recent Linux distro with glibc 2. 28+, and install the 'manylinux_2_28' variant. warnings.warn( ╭────────────────────────────────────────────────────────────────────────────────────────────────────────────╮ │ Executing geNomad annotate (v1.8.0). This will perform gene calling in the input sequences and annotate │ │ the predicted proteins with geNomad's markers. │ │ ──────────────────────────────────────────────────────────────────────────────────────────────────────── │ │ Outputs: │ │ /scratch/gdlab/kailun/Phageome/Phage_analysis_test/geNomad/passing_Viralcontigs_annotate │ │ ├── passing_Viralcontigs_annotate.json (execution parameters) │ │ ├── passing_Viralcontigs_genes.tsv (gene annotation data) │ │ ├── passing_Viralcontigs_taxonomy.tsv (taxonomic assignment) │ │ ├── passing_Viralcontigs_mmseqs2.tsv (MMseqs2 output file) │ │ └── passing_Viralcontigs_proteins.faa (protein FASTA file) │ ╰────────────────────────────────────────────────────────────────────────────────────────────────────────────╯ [11:29:09] Executing genomad annotate. [11:29:09] Creating the /scratch/gdlab/kailun/Phageome/Phage_analysis_test/geNomad/passing_Viralcontigs_annotate directory. [11:29:09] Proteins predicted with pyrodigal-gv were written to passing_Viralcontigs_proteins.faa. Traceback (most recent call last): File "/ref/sahlab/software/miniforge3/envs/smk_envs_phage_pred/c3c2c6c9a7fdb9755014780de49c5ec0_/lib/python3.11/site-packages/genomad/mmseqs2.py", line 190, in run_mmseqs2 subprocess.run(command, stdout=fout, stderr=fout, check=True) File "/ref/sahlab/software/miniforge3/envs/smk_envs_phage_pred/c3c2c6c9a7fdb9755014780de49c5ec0_/lib/python3.11/subprocess.py", line 571, in run raise CalledProcessError(retcode, process.args, subprocess.CalledProcessError: Command '['mmseqs', 'align', PosixPath('/scratch/gdlab/kailun/Phageome/genomad_DBs/v1.9/genomad_db/genomad_db'), PosixPath('/scratch/gdlab/kailun/Phageome/Phage_analysis_test/geNomad/passing_Viralcontigs_annotate/passing_Viralcontigs_mmseqs2/query_db/query_db'), PosixPath('/scratch/gdlab/kailun/Phageome/Phage_analysis_test/geNomad/passing_Viralcontigs_annotate/passing_Viralcontigs_mmseqs2/search_db/align_1_db'), PosixPath('/scratch/gdlab/kailun/Phageome/Phage_analysis_test/geNomad/passing_Viralcontigs_annotate/passing_Viralcontigs_mmseqs2/search_db/align_2_db'), '--threads', '8', '--alignment-mode', '2', '-e', '0.001', '--cov-mode', '2', '-c', '0.2']' returned non-zero exit status 1. The above exception was the direct cause of the following exception: Traceback (most recent call last): File "/ref/sahlab/software/miniforge3/envs/smk_envs_phage_pred/c3c2c6c9a7fdb9755014780de49c5ec0_/bin/genomad", line 10, in <module> sys.exit(cli()) ^^^^^ File "/ref/sahlab/software/miniforge3/envs/smk_envs_phage_pred/c3c2c6c9a7fdb9755014780de49c5ec0_/lib/python3.11/site-packages/rich_click/rich_command.py", line 378, in __call__ return super().__call__(*args, **kwargs) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/ref/sahlab/software/miniforge3/envs/smk_envs_phage_pred/c3c2c6c9a7fdb9755014780de49c5ec0_/lib/python3.11/site-packages/click/core.py", line 1161, in __call__ return self.main(*args, **kwargs) ^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/ref/sahlab/software/miniforge3/envs/smk_envs_phage_pred/c3c2c6c9a7fdb9755014780de49c5ec0_/lib/python3.11/site-packages/rich_click/rich_command.py", line 166, in main rv = self.invoke(ctx) ^^^^^^^^^^^^^^^^ File "/ref/sahlab/software/miniforge3/envs/smk_envs_phage_pred/c3c2c6c9a7fdb9755014780de49c5ec0_/lib/python3.11/site-packages/click/core.py", line 1697, in invoke return _process_result(sub_ctx.command.invoke(sub_ctx)) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/ref/sahlab/software/miniforge3/envs/smk_envs_phage_pred/c3c2c6c9a7fdb9755014780de49c5ec0_/lib/python3.11/site-packages/click/core.py", line 1443, in invoke return ctx.invoke(self.callback, **ctx.params) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/ref/sahlab/software/miniforge3/envs/smk_envs_phage_pred/c3c2c6c9a7fdb9755014780de49c5ec0_/lib/python3.11/site-packages/click/core.py", line 788, in invoke return __callback(*args, **kwargs) ^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/ref/sahlab/software/miniforge3/envs/smk_envs_phage_pred/c3c2c6c9a7fdb9755014780de49c5ec0_/lib/python3.11/site-packages/click/decorators.py", line 33, in new_func return f(get_current_context(), *args, **kwargs) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/ref/sahlab/software/miniforge3/envs/smk_envs_phage_pred/c3c2c6c9a7fdb9755014780de49c5ec0_/lib/python3.11/site-packages/genomad/cli.py", line 1269, in end_to_end ctx.invoke( File "/ref/sahlab/software/miniforge3/envs/smk_envs_phage_pred/c3c2c6c9a7fdb9755014780de49c5ec0_/lib/python3.11/site-packages/click/core.py", line 788, in invoke return __callback(*args, **kwargs) ^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/ref/sahlab/software/miniforge3/envs/smk_envs_phage_pred/c3c2c6c9a7fdb9755014780de49c5ec0_/lib/python3.11/site-packages/genomad/cli.py", line 447, in annotate genomad.annotate.main( File "/ref/sahlab/software/miniforge3/envs/smk_envs_phage_pred/c3c2c6c9a7fdb9755014780de49c5ec0_/lib/python3.11/site-packages/genomad/modules/annotate.py", line 203, in main mmseqs2_obj.run_mmseqs2(threads, sensitivity, evalue, splits) File "/ref/sahlab/software/miniforge3/envs/smk_envs_phage_pred/c3c2c6c9a7fdb9755014780de49c5ec0_/lib/python3.11/site-packages/genomad/mmseqs2.py", line 193, in run_mmseqs2 raise Exception(f"'{command_str}' failed.") from e Exception: 'mmseqs align /scratch/gdlab/kailun/Phageome/genomad_DBs/v1.9/genomad_db/genomad_db /scratch/gdlab/kailun/Phageome/Phage_analysis_test/geNomad/passing_Viralcontigs_annotate/passing_Viralcontigs_mmseqs2/query_db/query_db /scratch/gdlab/kailun/Phageome/Phage_analysis_test/geNomad/passing_Viralcontigs_annotate/passing_Viralcontigs_mmseqs2/search_db/align_1_db /scratch/gdlab/kailun/Phageome/Phage_analysis_test/geNomad/passing_Viralcontigs_annotate/passing_Viralcontigs_mmseqs2/search_db/align_2_db --threads 8 --alignment-mode 2 -e 0.001 --cov-mode 2 -c 0.2' failed. ``` The version I installed is genomad: v1.8.0 mmseqs: 14.7e284