<p>After much googling about I realised that I was missing a step! Here are the commands I used to get it running:</p>
<pre><code>mmseqs createdb metagenome1_scaffolds.fasta metagenome1_query_DB
mmseqs taxonomy metagenome1_query_DB /home/mmseqs2/NR/NR metagenome1_mmseqs_taxonomy.txt metagenome1_temp --tax-lineage 1 --orf-filter 1 --threads 24 --split-memory-limit 500G 
mmseqs createtsv metagenome1_DB metagenome1_mmseqs_taxonomy.txt metagenome1_mmseqs_taxonomy_final.txt
</code></pre>
<p>The split-memory-limit flag sped up the process and the final line put all the split files back together</p>

CC BY-SA 4.0
2023-12-04T18:01:01.583Z
Thanks @Rainman
M__
CC BY-SA 4.0
2023-12-04T13:52:55.380Z
2023-12-04T13:52:55.380Z
Rainman
<p>I've been trying to run mmseqs2 on a few metagenomic assemblies and despite my best efforts in reading the wiki and playing with parameters, the process is taking over a day.</p>
<p>In their paper they claim to be 2 - 18x faster than CAT. I ran CAT on the same datasets and they took at most a few hours. So I can only assume that the long run time for mmseqs is down to user error (i.e. me).</p>
<p>I am currently running the commands (general format):</p>
<pre><code>mmseqs createdb metagenome1_scaffolds.fasta metagenome1_query_DB
mmseqs taxonomy metagenome1_query_DB /home/mmseqs2/NR/NR metagenome1_mmseqs_taxonomy.txt metagenome1_temp --tax-lineage 1 --orf-filter 1 --threads 24
</code></pre>
<p>Could someone please let me know where I'm going wrong or what parameters I can tweak to get this running in the expected time frame?</p>

CC BY-SA 4.0
2023-12-02T08:41:19.703Z
Have you contacted the developers about this? Do any of [these issues](https://github.com/soedinglab/MMseqs2/issues?q=is%3Aissue+is%3Aopen+slow) match the problem you're having?
gringer
CC BY-SA 4.0
2023-12-03T22:28:11.163Z
Hi there! I actually got in running in ~4 hours but then the results are split into 24 semi-corrupted files (I used 24 threads). I have since contacted the developers and will post a solution once I get a response and figure it out :)
Rainman
<assembly><metagenome><taxonomy>
MMSeqs taxonomy running for over a day
# MMSeqs taxonomy running for over a day

(Asked by: username_0 on 2023-12-01)

I've been trying to run mmseqs2 on a few metagenomic assemblies and despite my best efforts in reading the wiki and playing with parameters, the process is taking over a day.
In their paper they claim to be 2 - 18x faster than CAT. I ran CAT on the same datasets and they took at most a few hours. So I can only assume that the long run time for mmseqs is down to user error (i.e. me).
I am currently running the commands (general format):
mmseqs createdb metagenome1_scaffolds.fasta metagenome1_query_DB
mmseqs taxonomy metagenome1_query_DB /home/mmseqs2/NR/NR metagenome1_mmseqs_taxonomy.txt metagenome1_temp --tax-lineage 1 --orf-filter 1 --threads 24

Could someone please let me know where I'm going wrong or what parameters I can tweak to get this running in the expected time frame?

**Tags:** assembly, metagenome, taxonomy
> **Comments:**
> **username_1**: Have you contacted the developers about this? Do any of [these issues](https://github.com/soedinglab/MMseqs2/issues?q=is%3Aissue+is%3Aopen+slow) match the problem you're having?  
> **username_0**: Hi there! I actually got in running in ~4 hours but then the results are split into 24 semi-corrupted files (I used 24 threads). I have since contacted the developers and will post a solution once I get a response and figure it out :)  

---

## 1 answers

### Answer by username_0 on 2023-12-04. Score: 1 | Accepted answer

After much googling about I realised that I was missing a step! Here are the commands I used to get it running:
mmseqs createdb metagenome1_scaffolds.fasta metagenome1_query_DB
mmseqs taxonomy metagenome1_query_DB /home/mmseqs2/NR/NR metagenome1_mmseqs_taxonomy.txt metagenome1_temp --tax-lineage 1 --orf-filter 1 --threads 24 --split-memory-limit 500G 
mmseqs createtsv metagenome1_DB metagenome1_mmseqs_taxonomy.txt metagenome1_mmseqs_taxonomy_final.txt

The split-memory-limit flag sped up the process and the final line put all the split files back together

> **Comments:**
> **username_2**: Thanks @Rainman  

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