1
$\begingroup$

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?

$\endgroup$
2
  • $\begingroup$ Have you contacted the developers about this? Do any of these issues match the problem you're having? $\endgroup$
    – gringer
    Dec 2, 2023 at 8:41
  • 1
    $\begingroup$ 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 :) $\endgroup$
    – Rainman
    Dec 3, 2023 at 22:28

1 Answer 1

1
$\begingroup$

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

$\endgroup$
1
  • 1
    $\begingroup$ Thanks @Rainman $\endgroup$
    – M__
    Dec 4, 2023 at 18:01

Your Answer

By clicking “Post Your Answer”, you agree to our terms of service and acknowledge you have read our privacy policy.

Not the answer you're looking for? Browse other questions tagged or ask your own question.