mmseqs2 error

[manaraleslam2018]

Each time I run this code: genomad end-to-end --cleanup --splits 5 pump1.contigs.fa pump1_genomad_output genomad_db

I have this error: Traceback (most recent call last): File "/home/manar/apps/mamba/lib/python3.10/site-packages/genomad/mmseqs2.py", line 190, in run_mmseqs2 subprocess.run(command, stdout=fout, stderr=fout, check=True) File "/home/manar/apps/mamba/lib/python3.10/subprocess.py", line 526, in run raise CalledProcessError(retcode, process.args, subprocess.CalledProcessError: Command '['mmseqs', 'prefilter', PosixPath('pump1_genomad_output/pump1.contigs_annotate/pump1.contigs_mmseqs2/query_db/query_db'), PosixPath('genomad_db/genomad_db'), PosixPath('pump1_genomad_output/pump1.contigs_annotate/pump1.contigs_mmseqs2/search_db/prefilter_db'), '--threads', '8', '-s', '4.2', '--split', '8', '--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/manar/apps/mamba/bin/genomad", line 8, in sys.exit(cli()) File "/home/manar/apps/mamba/lib/python3.10/site-packages/rich_click/rich_command.py", line 367, in call return super().call(*args, kwargs) File "/home/manar/apps/mamba/lib/python3.10/site-packages/click/core.py", line 1157, in call return self.main(args, kwargs) File "/home/manar/apps/mamba/lib/python3.10/site-packages/rich_click/rich_command.py", line 152, in main rv = self.invoke(ctx) File "/home/manar/apps/mamba/lib/python3.10/site-packages/click/core.py", line 1688, in invoke return _process_result(sub_ctx.command.invoke(sub_ctx)) File "/home/manar/apps/mamba/lib/python3.10/site-packages/click/core.py", line 1434, in invoke return ctx.invoke(self.callback, ctx.params) File "/home/manar/apps/mamba/lib/python3.10/site-packages/click/core.py", line 783, in invoke return __callback(args, kwargs) File "/home/manar/apps/mamba/lib/python3.10/site-packages/click/decorators.py", line 33, in new_func return f(get_current_context(), *args, *kwargs) File "/home/manar/apps/mamba/lib/python3.10/site-packages/genomad/cli.py", line 1269, in end_to_end ctx.invoke( File "/home/manar/apps/mamba/lib/python3.10/site-packages/click/core.py", line 783, in invoke return __callback(args, **kwargs) File "/home/manar/apps/mamba/lib/python3.10/site-packages/genomad/cli.py", line 447, in annotate genomad.annotate.main( File "/home/manar/apps/mamba/lib/python3.10/site-packages/genomad/modules/annotate.py", line 203, in main mmseqs2_obj.run_mmseqs2(threads, sensitivity, evalue, splits) File "/home/manar/apps/mamba/lib/python3.10/site-packages/genomad/mmseqs2.py", line 193, in run_mmseqs2 raise Exception(f"'{command_str}' failed.") from e Exception: 'mmseqs prefilter pump1_genomad_output/pump1.contigs_annotate/pump1.contigs_mmseqs2/query_db/query_db genomad_db/genomad_db pump1_genomad_output/pump1.contigs_annotate/pump1.contigs_mmseqs2/search_db/prefilter_db --threads 8 -s 4.2 --split 8 --split-mode 0 --max-seqs 10000000 --min-ungapped-score 25 -k 5' failed.

Also, please find my log file: mmseqs2.log

[apcamargo]

This error is caused because you're using an old version of MMseqs2, which is incompatible with the geNomad database. Can you try updating to version 14?

[manaraleslam2018]

Thanks, I tried it and the problem is solved

[apcamargo]

Good to hear!