Error mmseqs prefilter

[namnh7]

I got an error while running genomad:

[Traceback (most recent call last): File "/data/Namsp/miniconda3/envs/genomad/lib/python3.11/site-packages/genomad/mmseqs2.py", line 190, in run_mmseqs2 subprocess.run(command, stdout=fout, stderr=fout, check=True) File "/data/Namsp/miniconda3/envs/genomad/lib/python3.11/subprocess.py", line 571, in run raise CalledProcessError(retcode, process.args, subprocess.CalledProcessError: Command '['mmseqs', 'prefilter', PosixPath('2_result/genomad/C1/C1_annotate/C1_mmseqs2/query_db/query_db'), PosixPath('3_reference/genomad_db/genomad_db'), PosixPath('2_result/genomad/C1/C1_annotate/C1_mmseqs2/search_db/prefilter_db'), '--threads', '16', '-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 "/data/Namsp/miniconda3/envs/genomad/bin/genomad", line 10, in sys.exit(cli()) ^^^^^ File "/data/Namsp/miniconda3/envs/genomad/lib/python3.11/site-packages/rich_click/rich_command.py", line 367, in call return super().call(*args, kwargs) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/data/Namsp/miniconda3/envs/genomad/lib/python3.11/site-packages/click/core.py", line 1157, in call return self.main(args, kwargs) ^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/data/Namsp/miniconda3/envs/genomad/lib/python3.11/site-packages/rich_click/rich_command.py", line 152, in main rv = self.invoke(ctx) ^^^^^^^^^^^^^^^^ File "/data/Namsp/miniconda3/envs/genomad/lib/python3.11/site-packages/click/core.py", line 1688, in invoke return _process_result(sub_ctx.command.invoke(sub_ctx)) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/data/Namsp/miniconda3/envs/genomad/lib/python3.11/site-packages/click/core.py", line 1434, in invoke return ctx.invoke(self.callback, ctx.params) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/data/Namsp/miniconda3/envs/genomad/lib/python3.11/site-packages/click/core.py", line 783, in invoke return __callback(args, kwargs) ^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/data/Namsp/miniconda3/envs/genomad/lib/python3.11/site-packages/click/decorators.py", line 33, in new_func return f(get_current_context(), *args, *kwargs) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/data/Namsp/miniconda3/envs/genomad/lib/python3.11/site-packages/genomad/cli.py", line 1269, in end_to_end ctx.invoke( File "/data/Namsp/miniconda3/envs/genomad/lib/python3.11/site-packages/click/core.py", line 783, in invoke return __callback(args, **kwargs) ^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/data/Namsp/miniconda3/envs/genomad/lib/python3.11/site-packages/genomad/cli.py", line 447, in annotate genomad.annotate.main( File "/data/Namsp/miniconda3/envs/genomad/lib/python3.11/site-packages/genomad/modules/annotate.py", line 203, in main mmseqs2_obj.run_mmseqs2(threads, sensitivity, evalue, splits) File "/data/Namsp/miniconda3/envs/genomad/lib/python3.11/site-packages/genomad/mmseqs2.py", line 193, in run_mmseqs2 raise Exception(f"'{command_str}' failed.") from e Exception: 'mmseqs prefilter 2_result/genomad/C1/C1_annotate/C1_mmseqs2/query_db/query_db 3_reference/genomad_db/genomad_db 2_result/genomad/C1/C1_annotate/C1_mmseqs2/search_db/prefilter_db --threads 16 -s 4.2 --split 0 --split-mode 0 --max-seqs 10000000 --min-ungapped-score 25 -k 5' failed.

I'm using mmseqs version 15.6f452. Please help me!

[apcamargo]

This might be an issue with memory availability. Have you tried to increase the number of splits (e.g. --splits 12).

[namnh7]

I still got the same error : Traceback (most recent call last): File "/data/Namsp/miniconda3/envs/genomad/lib/python3.11/site-packages/genomad/mmseqs2.py", line 190, in run_mmseqs2 subprocess.run(command, stdout=fout, stderr=fout, check=True) File "/data/Namsp/miniconda3/envs/genomad/lib/python3.11/subprocess.py", line 571, in run raise CalledProcessError(retcode, process.args, subprocess.CalledProcessError: Command '['mmseqs', 'prefilter', PosixPath('2_result/genomad/C1/C1_annotate/C1_mmseqs2/query_db/query_db'), PosixPath('3_reference/genomad_db/genomad_db'), PosixPath('2_result/genomad/C1/C1_annotate/C1_mmseqs2/search_db/prefilter_db'), '--threads', '16', '-s', '4.2', '--split', '12', '--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 "/data/Namsp/miniconda3/envs/genomad/bin/genomad", line 10, in sys.exit(cli()) ^^^^^ File "/data/Namsp/miniconda3/envs/genomad/lib/python3.11/site-packages/rich_click/rich_command.py", line 367, in call return super().call(*args, kwargs) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/data/Namsp/miniconda3/envs/genomad/lib/python3.11/site-packages/click/core.py", line 1157, in call return self.main(args, kwargs) ^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/data/Namsp/miniconda3/envs/genomad/lib/python3.11/site-packages/rich_click/rich_command.py", line 152, in main rv = self.invoke(ctx) ^^^^^^^^^^^^^^^^ File "/data/Namsp/miniconda3/envs/genomad/lib/python3.11/site-packages/click/core.py", line 1688, in invoke return _process_result(sub_ctx.command.invoke(sub_ctx)) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/data/Namsp/miniconda3/envs/genomad/lib/python3.11/site-packages/click/core.py", line 1434, in invoke return ctx.invoke(self.callback, ctx.params) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/data/Namsp/miniconda3/envs/genomad/lib/python3.11/site-packages/click/core.py", line 783, in invoke return __callback(args, kwargs) ^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/data/Namsp/miniconda3/envs/genomad/lib/python3.11/site-packages/click/decorators.py", line 33, in new_func return f(get_current_context(), *args, *kwargs) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/data/Namsp/miniconda3/envs/genomad/lib/python3.11/site-packages/genomad/cli.py", line 1269, in end_to_end ctx.invoke( File "/data/Namsp/miniconda3/envs/genomad/lib/python3.11/site-packages/click/core.py", line 783, in invoke return __callback(args, **kwargs) ^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/data/Namsp/miniconda3/envs/genomad/lib/python3.11/site-packages/genomad/cli.py", line 447, in annotate genomad.annotate.main( File "/data/Namsp/miniconda3/envs/genomad/lib/python3.11/site-packages/genomad/modules/annotate.py", line 203, in main mmseqs2_obj.run_mmseqs2(threads, sensitivity, evalue, splits) File "/data/Namsp/miniconda3/envs/genomad/lib/python3.11/site-packages/genomad/mmseqs2.py", line 193, in run_mmseqs2 raise Exception(f"'{command_str}' failed.") from e Exception: 'mmseqs prefilter 2_result/genomad/C1/C1_annotate/C1_mmseqs2/query_db/query_db 3_reference/genomad_db/genomad_db 2_result/genomad/C1/C1_annotate/C1_mmseqs2/search_db/prefilter_db --threads 16 -s 4.2 --split 12 --split-mode 0 --max-seqs 10000000 --min-ungapped-score 25 -k 5' failed.

[namnh7]

I tried running mmseqs prefilter manually using this command: mmseqs prefilter /data/Namsp/2_result/genomad/C1/C1_annotate/C1_mmseqs2/query_db/query_db /data/Namsp/3_reference/genomad_db/genomad_db /data/Namsp/2_result/genomad/C1/C1_annotate/C1_mmseqs2/search_db/ --threads 16 --split 12 --split-mode 0 --max-seqs 10000000 --min-ungapped-score 25 -k 5

and I got this error: Input database "/data/Namsp/3_reference/genomad_db/genomad_db" has the wrong type (Generic) Allowed input:

• Index
• Nucleotide
• Profile
• Aminoacid

I downloaded the db by the command genomad download-database .

[namnh7]

Hi. I download the database again and mmseqs works. The previous database was not downloaded correctly. Thank you!