apcamargo
commented
2 weeks ago This could be because you don't have enough available memory. Can you try setting --splits 8 or even --splits 12? This will make the execution a bit slower, but memory requirements will reduce substantially.
Hello I recently installed genomad v1.8.0. However, when I tried to run the command, it return an error below.
(genomadv1.8.0) dostvip2@DESKTOP-L5H6T8M:/mnt/f/Klebsiella$ genomad end-to-end 09_MOBsuite_OMCS211430/OMCS211430.fasta 11_genomad_OMCS211430 /mnt/f/Klebsiella/genomad_db --threads 6 --restart ╭──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────╮ │ 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: │ │ 11_genomad_OMCS211430/OMCS211430_annotate │ │ ├── OMCS211430_annotate.json (execution parameters) │ │ ├── OMCS211430_genes.tsv (gene annotation data) │ │ ├── OMCS211430_taxonomy.tsv (taxonomic assignment) │ │ ├── OMCS211430_mmseqs2.tsv (MMseqs2 output file) │ │ └── OMCS211430_proteins.faa (protein FASTA file) │ ╰──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────╯ [14:07:13] Executing genomad annotate. [14:07:28] Proteins predicted with pyrodigal-gv were written to OMCS211430_proteins.faa. Traceback (most recent call last): File "/home/dostvip2/miniconda3/envs/genomadv1.8.0/lib/python3.11/site-packages/genomad/mmseqs2.py", line 190, in run_mmseqs2 subprocess.run(command, stdout=fout, stderr=fout, check=True) File "/home/dostvip2/miniconda3/envs/genomadv1.8.0/lib/python3.11/subprocess.py", line 571, in run raise CalledProcessError(retcode, process.args, subprocess.CalledProcessError: Command '['mmseqs', 'prefilter', PosixPath('11_genomad_OMCS211430/OMCS211430_annotate/OMCS211430_mmseqs2/query_db/query_db'), PosixPath('/mnt/f/Klebsiella/genomad_db/genomad_db'), PosixPath('11_genomad_OMCS211430/OMCS211430_annotate/OMCS211430_mmseqs2/search_db/prefilter_db'), '--threads', '6', '-s', '4.2', '--split', '0', '--split-mode', '0', '--max-seqs', '10000000', '--min-ungapped-score', '25', '-k', '5']' returned non-zero exit status 1.
The above exception was the direct cause of the following exception:
Traceback (most recent call last): File "/home/dostvip2/miniconda3/envs/genomadv1.8.0/bin/genomad", line 10, in
sys.exit(cli())
^^^^^
File "/home/dostvip2/miniconda3/envs/genomadv1.8.0/lib/python3.11/site-packages/rich_click/rich_command.py", line 367, in call
return super().call(*args, kwargs)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/dostvip2/miniconda3/envs/genomadv1.8.0/lib/python3.11/site-packages/click/core.py", line 1157, in call
return self.main(args, kwargs)
^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/dostvip2/miniconda3/envs/genomadv1.8.0/lib/python3.11/site-packages/rich_click/rich_command.py", line 152, in main
rv = self.invoke(ctx)
^^^^^^^^^^^^^^^^
File "/home/dostvip2/miniconda3/envs/genomadv1.8.0/lib/python3.11/site-packages/click/core.py", line 1688, in invoke
return _process_result(sub_ctx.command.invoke(sub_ctx))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/dostvip2/miniconda3/envs/genomadv1.8.0/lib/python3.11/site-packages/click/core.py", line 1434, in invoke
return ctx.invoke(self.callback, ctx.params)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/dostvip2/miniconda3/envs/genomadv1.8.0/lib/python3.11/site-packages/click/core.py", line 783, in invoke
return __callback(args, kwargs)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/dostvip2/miniconda3/envs/genomadv1.8.0/lib/python3.11/site-packages/click/decorators.py", line 33, in new_func
return f(get_current_context(), *args, *kwargs)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/dostvip2/miniconda3/envs/genomadv1.8.0/lib/python3.11/site-packages/genomad/cli.py", line 1269, in end_to_end
ctx.invoke(
File "/home/dostvip2/miniconda3/envs/genomadv1.8.0/lib/python3.11/site-packages/click/core.py", line 783, in invoke
return __callback(args, **kwargs)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/dostvip2/miniconda3/envs/genomadv1.8.0/lib/python3.11/site-packages/genomad/cli.py", line 447, in annotate
genomad.annotate.main(
File "/home/dostvip2/miniconda3/envs/genomadv1.8.0/lib/python3.11/site-packages/genomad/modules/annotate.py", line 203, in main
mmseqs2_obj.run_mmseqs2(threads, sensitivity, evalue, splits)
File "/home/dostvip2/miniconda3/envs/genomadv1.8.0/lib/python3.11/site-packages/genomad/mmseqs2.py", line 193, in run_mmseqs2
raise Exception(f"'{command_str}' failed.") from e
Exception: 'mmseqs prefilter 11_genomad_OMCS211430/OMCS211430_annotate/OMCS211430_mmseqs2/query_db/query_db /mnt/f/Klebsiella/genomad_db/genomad_db 11_genomad_OMCS211430/OMCS211430_annotate/OMCS211430_mmseqs2/search_db/prefilter_db --threads 6 -s 4.2 --split 0 --split-mode 0 --max-seqs 10000000 --min-ungapped-score 25 -k 5' failed.