Hi all, thanks for this MMseqs2 that seems very efficient.

Unfortunately it seems to not be willing to run on my machine :

mmseqs easy-cluster /Users/s/Documents/Albatros/protein//short_name-Group/true_plus300_proteins-13-strains_shortname-group.fa /Users/s/Documents/short_name-Group/clusterRes /Volumes/s/tmp --min-seq-id 0.5 -c 0.8 --cov-mode 1
Create directory /Volumes/s/tmp
easy-cluster /Users/s/Documents/Albatros/short_name-Group/true_plus300_proteins-13-strains_shortname-group.fa /Users/s/Documents/Albatros/protein/short_name-Group/clusterRes /Volumes/s/tmp --min-seq-id 0.5 -c 0.8 --cov-mode 1

MMseqs Version: 14-7e284
Substitution matrix aa:blosum62.out,nucl:nucleotide.out
Seed substitution matrix aa:VTML80.out,nucl:nucleotide.out
Sensitivity 4
k-mer length 0
k-score seq:2147483647,prof:2147483647
Alphabet size aa:21,nucl:5
Max sequence length 65535
Max results per query 20
Split database 0
Split mode 2
Split memory limit 0
Coverage threshold 0.8
Coverage mode 1
Compositional bias 1
Compositional bias 1
Diagonal scoring true
Exact k-mer matching 0
Mask residues 1
Mask residues probability 0.9
Mask lower case residues 0
Minimum diagonal score 15
Selected taxa
Include identical seq. id. false
Spaced k-mers 1
Preload mode 0
Pseudo count a substitution:1.100,context:1.400
Pseudo count b substitution:4.100,context:5.800
Spaced k-mer pattern
Local temporary path
Threads 16
Compressed 0
Verbosity 3
Add backtrace false
Alignment mode 3
Alignment mode 0
Allow wrapped scoring false
E-value threshold 0.001
Seq. id. threshold 0.5
Min alignment length 0
Seq. id. mode 0
Alternative alignments 0
Max reject 2147483647
Max accept 2147483647
Score bias 0
Realign hits false
Realign score bias -0.2
Realign max seqs 2147483647
Correlation score weight 0
Gap open cost aa:11,nucl:5
Gap extension cost aa:1,nucl:2
Zdrop 40
Rescore mode 0
Remove hits by seq. id. and coverage false
Sort results 0
Cluster mode 0
Max connected component depth 1000
Similarity type 2
Single step clustering false
Cascaded clustering steps 3
Cluster reassign false
Remove temporary files true
Force restart with latest tmp false
MPI runner
k-mers per sequence 21
Scale k-mers per sequence aa:0.000,nucl:0.200
Adjust k-mer length false
Shift hash 67
Include only extendable false
Skip repeating k-mers false
Database type 0
Shuffle input database true
Createdb mode 1
Write lookup file 0
Offset of numeric ids 0

createdb /Users/s/Documents/protein/true_plus300_proteins-13-strains_shortname-group.fa /Volumes/s/tmp/3581369344000996149/input --dbtype 0 --shuffle 1 --createdb-mode 1 --write-lookup 0 --id-offset 0 --compressed 0 -v 3

Shuffle database cannot be combined with --createdb-mode 0
We recompute with --shuffle 0
Converting sequences
[1718] 0s 24ms
Time for merging to input_h: 0h 0m 0s 10ms
Time for merging to input: 0h 0m 0s 10ms
Database type: Aminoacid
Time for processing: 0h 0m 0s 81ms
Create directory /Volumes/s/tmp/3581369344000996149/clu_tmp
cluster /Volumes/s/tmp/3581369344000996149/input /Volumes/s/tmp/3581369344000996149/clu /Volumes/s/tmp/3581369344000996149/clu_tmp --max-seqs 20 -c 0.8 --cov-mode 1 --spaced-kmer-mode 1 --alignment-mode 3 -e 0.001 --min-seq-id 0.5 --remove-tmp-files 1

Set cluster sensitivity to -s 3.000000
Set cluster mode GREEDY MEM
Set cluster iterations to 3
linclust /Volumes/s/tmp/3581369344000996149/input /Volumes/s/tmp/3581369344000996149/clu_tmp/10544097544295592317/clu_redundancy /Volumes/s/tmp/3581369344000996149/clu_tmp/10544097544295592317/linclust --cluster-mode 3 --max-iterations 1000 --similarity-type 2 --threads 16 --compressed 0 -v 3 --sub-mat 'aa:blosum62.out,nucl:nucleotide.out' -a 0 --alignment-mode 3 --alignment-output-mode 0 --wrapped-scoring 0 -e 0.001 --min-seq-id 0.5 --min-aln-len 0 --seq-id-mode 0 --alt-ali 0 -c 0.8 --cov-mode 1 --max-seq-len 65535 --comp-bias-corr 1 --comp-bias-corr-scale 1 --max-rejected 2147483647 --max-accept 2147483647 --add-self-matches 0 --db-load-mode 0 --pca substitution:1.100,context:1.400 --pcb substitution:4.100,context:5.800 --score-bias 0 --realign 0 --realign-score-bias -0.2 --realign-max-seqs 2147483647 --corr-score-weight 0 --gap-open aa:11,nucl:5 --gap-extend aa:1,nucl:2 --zdrop 40 --alph-size aa:13,nucl:5 --kmer-per-seq 21 --spaced-kmer-mode 1 --kmer-per-seq-scale aa:0.000,nucl:0.200 --adjust-kmer-len 0 --mask 0 --mask-prob 0.9 --mask-lower-case 0 -k 0 --hash-shift 67 --split-memory-limit 0 --include-only-extendable 0 --ignore-multi-kmer 0 --rescore-mode 0 --filter-hits 0 --sort-results 0 --remove-tmp-files 1 --force-reuse 0

kmermatcher /Volumes/s/tmp/3581369344000996149/input /Volumes/s/tmp/3581369344000996149/clu_tmp/10544097544295592317/linclust/18419612973359567408/pref --sub-mat 'aa:blosum62.out,nucl:nucleotide.out' --alph-size aa:13,nucl:5 --min-seq-id 0.5 --kmer-per-seq 21 --spaced-kmer-mode 1 --kmer-per-seq-scale aa:0.000,nucl:0.200 --adjust-kmer-len 0 --mask 0 --mask-prob 0.9 --mask-lower-case 0 --cov-mode 1 -k 0 -c 0.8 --max-seq-len 65535 --hash-shift 67 --split-memory-limit 0 --include-only-extendable 0 --ignore-multi-kmer 0 --threads 16 --compressed 0 -v 3

kmermatcher /Volumes/s/tmp/3581369344000996149/input /Volumes/s/tmp/3581369344000996149/clu_tmp/10544097544295592317/linclust/18419612973359567408/pref --sub-mat 'aa:blosum62.out,nucl:nucleotide.out' --alph-size aa:13,nucl:5 --min-seq-id 0.5 --kmer-per-seq 21 --spaced-kmer-mode 1 --kmer-per-seq-scale aa:0.000,nucl:0.200 --adjust-kmer-len 0 --mask 0 --mask-prob 0.9 --mask-lower-case 0 --cov-mode 1 -k 0 -c 0.8 --max-seq-len 65535 --hash-shift 67 --split-memory-limit 0 --include-only-extendable 0 --ignore-multi-kmer 0 --threads 16 --compressed 0 -v 3

Database size: 1807 type: Aminoacid
Reduced amino acid alphabet: (A S T) (C) (D B N) (E Q Z) (F Y) (G) (H) (I V) (K R) (L J M) (P) (W) (X)

Generate k-mers list for 1 split
[=================================================================] 100.00% 1.81K 0s 10ms
Sort kmer 0h 0m 0s 3ms
Sort by rep. sequence 0h 0m 0s 2ms
Time for fill: 0h 0m 0s 1ms
Time for merging to pref: 0h 0m 0s 11ms
Time for processing: 0h 0m 0s 63ms
rescorediagonal /Volumes/s/tmp/3581369344000996149/input /Volumes/s/tmp/3581369344000996149/input /Volumes/s/tmp/3581369344000996149/clu_tmp/10544097544295592317/linclust/18419612973359567408/pref /Volumes/s/tmp/3581369344000996149/clu_tmp/10544097544295592317/linclust/18419612973359567408/pref_rescore1 --sub-mat 'aa:blosum62.out,nucl:nucleotide.out' --rescore-mode 0 --wrapped-scoring 0 --filter-hits 0 -e 0.001 -c 0.8 -a 0 --cov-mode 1 --min-seq-id 0.5 --min-aln-len 0 --seq-id-mode 0 --add-self-matches 0 --sort-results 0 --db-load-mode 0 --threads 16 --compressed 0 -v 3

[=================================================================] 100.00% 1.81K 0s 7ms
Time for merging to pref_rescore1: 0h 0m 0s 64ms
Time for processing: 0h 0m 0s 310ms
clust /Volumes/s/tmp/3581369344000996149/input /Volumes/s/tmp/3581369344000996149/clu_tmp/10544097544295592317/linclust/18419612973359567408/pref_rescore1 /Volumes/s/tmp/3581369344000996149/clu_tmp/10544097544295592317/linclust/18419612973359567408/pre_clust --cluster-mode 3 --max-iterations 1000 --similarity-type 2 --threads 16 --compressed 0 -v 3

Clustering mode: Greedy Low Mem
Total time: 0h 0m 0s 13ms

Size of the sequence database: 1807
Size of the alignment database: 1807
Number of clusters: 757

Writing results 0h 0m 0s 0ms
Time for merging to pre_clust: 0h 0m 0s 11ms
Time for processing: 0h 0m 0s 49ms
createsubdb /Volumes/s/tmp/3581369344000996149/clu_tmp/10544097544295592317/linclust/18419612973359567408/order_redundancy /Volumes/s/tmp/3581369344000996149/input /Volumes/s/tmp/3581369344000996149/clu_tmp/10544097544295592317/linclust/18419612973359567408/input_step_redundancy -v 3 --subdb-mode 1

Time for merging to input_step_redundancy: 0h 0m 0s 10ms
Time for processing: 0h 0m 0s 70ms
createsubdb /Volumes/s/tmp/3581369344000996149/clu_tmp/10544097544295592317/linclust/18419612973359567408/order_redundancy /Volumes/s/tmp/3581369344000996149/clu_tmp/10544097544295592317/linclust/18419612973359567408/pref /Volumes/s/tmp/3581369344000996149/clu_tmp/10544097544295592317/linclust/18419612973359567408/pref_filter1 -v 3 --subdb-mode 1

Time for merging to pref_filter1: 0h 0m 0s 10ms
Time for processing: 0h 0m 0s 41ms
filterdb /Volumes/s/tmp/3581369344000996149/clu_tmp/10544097544295592317/linclust/18419612973359567408/pref_filter1 /Volumes/s/tmp/3581369344000996149/clu_tmp/10544097544295592317/linclust/18419612973359567408/pref_filter2 --filter-file /Volumes/s/tmp/3581369344000996149/clu_tmp/10544097544295592317/linclust/18419612973359567408/order_redundancy --threads 16 --compressed 0 -v 3

Filtering using file(s)
[=================================================================] 100.00% 757 0s 4ms
Time for merging to pref_filter2: 0h 0m 0s 62ms
Time for processing: 0h 0m 0s 270ms
rescorediagonal /Volumes/s/tmp/3581369344000996149/clu_tmp/10544097544295592317/linclust/18419612973359567408/input_step_redundancy /Volumes/s/tmp/3581369344000996149/clu_tmp/10544097544295592317/linclust/18419612973359567408/input_step_redundancy /Volumes/s/tmp/3581369344000996149/clu_tmp/10544097544295592317/linclust/18419612973359567408/pref_filter2 /Volumes/s/tmp/3581369344000996149/clu_tmp/10544097544295592317/linclust/18419612973359567408/pref_rescore2 --sub-mat 'aa:blosum62.out,nucl:nucleotide.out' --rescore-mode 1 --wrapped-scoring 0 --filter-hits 1 -e 0.001 -c 0.8 -a 0 --cov-mode 1 --min-seq-id 0.5 --min-aln-len 0 --seq-id-mode 0 --add-self-matches 0 --sort-results 0 --db-load-mode 0 --threads 16 --compressed 0 -v 3

/Volumes/s/tmp/3581369344000996149/clu_tmp/10544097544295592317/linclust/18419612973359567408/linclust.sh: line 68: 88046 Segmentation fault: 11 $RUNNER "$MMSEQS" rescorediagonal "$INPUT" "$INPUT" "$RESULTDB" "${TMP_PATH}/pref_rescore2" ${UNGAPPED_ALN_PAR}
Error: Ungapped alignment step died
Error: linclust died
Error: Search died

Running on Mac intel i9 and mmseqs2 14-7e284

Thank you all for your help.