Answers.Body: <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>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2023-12-04T18:01:01.583Z
Answers.Text: Thanks @Rainman
Answers.UserDisplayName: M__
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2023-12-04T13:52:55.380Z
Answers.LastActivityDate: 2023-12-04T13:52:55.380Z
Answers.UserDisplayName: Rainman
Body: <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>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2023-12-02T08:41:19.703Z
Comments.Text: 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?
Comments.UserDisplayName: gringer
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2023-12-03T22:28:11.163Z
Comments.Text: 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 :)
Comments.UserDisplayName: Rainman
Tags: <assembly><metagenome><taxonomy>
Title: MMSeqs taxonomy running for over a day
ThreadText: # 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 @username_0  
  
  ---
  
  