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soedinglab / MMseqs2

MMseqs2: ultra fast and sensitive search and clustering suite
https://mmseqs.com
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High inter-cluster identity #766

Open EvanKomp opened 11 months ago

EvanKomp commented 11 months ago

Expected Behavior

When min-seq-id is eg 50%, I would expect identity across clusters to be upper bounded by 50%

Current Behavior

Running blastp of sequences from a cluster against sequences from all other cluster yields high percent id and low e value hits.

Here is a table of some results I have tried (tsv). No matter what i do, inter cluster identity remains high:

--cluster-mode  --cluster-steps --cluster-reassign  --cov-mode  -c  -e  -s  --min-seq-id    --threads   --max-seqs  --max-iterations    --alignment-mode    --similarity-type   num_aligned mean_percid mean_e  max_percid  min_e
0.0 3.0 0.0 0.0 0.8 0.001   4.0 0.9 40.0    20.0    1000.0  3.0 2.0 20.0    0.2946001520957981  7.271040887500001e-25   0.4017857142857143  4.56243e-152
0.0 3.0 0.0 0.0 0.8 0.001   4.0 0.4 40.0    20.0    1000.0  3.0 2.0 19.0    0.2699960748418551  6.464939793952533e-09   0.3841336116910229  6.08884e-63
0.0 3.0 1.0 0.0 0.8 0.001   4.0 0.4 40.0    20.0    1000.0  3.0 2.0 19.0    0.2805825389935189  6.463308203666264e-09   0.379746835443038   4.30425e-156
0.0 3.0 1.0 0.0 0.8 0.001   4.0 0.4 40.0    200.0   1000.0  3.0 2.0 19.0    0.2684551720607656  6.4674134954082795e-09  0.365038560411311   1.55836e-137
1.0 3.0 1.0 0.0 0.8 0.001   4.0 0.4 40.0    200.0   1000.0  3.0 2.0 18.0    0.2448913043192062  6.821603006346129e-09   0.365038560411311   5.02351e-59
3.0 3.0 1.0 0.0 0.8 0.001   4.0 0.4 40.0    200.0   1000.0  3.0 2.0 20.0    0.275898345457947   2.438759428532657e-07   0.4268774703557312  4.97171e-133
2.0 3.0 1.0 0.0 0.8 0.001   4.0 0.4 40.0    200.0   1000.0  3.0 2.0 20.0    0.275898345457947   2.438759428532657e-07   0.4268774703557312  4.97171e-133
1.0 3.0 1.0 0.0 0.8 0.001   7.0 0.4 40.0    200.0   1000.0  3.0 2.0 18.0    0.2541259924867629  6.820936331055556e-09   0.3755458515283842  7.644030000000001e-61
1.0 3.0 1.0 0.0 0.8 0.001   7.0 0.4 40.0    200.0   1000.0  3.0 2.0 18.0    0.2541259924867629  6.820936331055556e-09   0.3755458515283842  7.644030000000001e-61
1.0 3.0 1.0 0.0 0.8 0.001   7.0 0.4 40.0    200.0   1000.0  3.0 2.0 18.0    0.25412599248676293 6.820936331055556e-09   0.37554585152838427 7.64403e-61

Steps to Reproduce (for bugs)

My scripts

import os
import shutil
import subprocess
import pandas as pd
from Bio.Blast.Applications import NcbiblastpCommandline
from Bio import SeqIO
from Bio.Blast.NCBIXML import parse

# MMseqs clustering function
def run_mmseqs_clustering(db_path, output_dir, params):
    if not os.path.exists(output_dir):
        os.makedirs(output_dir)
    else:
        shutil.rmtree(output_dir)
        os.makedirs(output_dir)

    cluster_out = os.path.join(output_dir, "mmseq_clu")
    tmp_dir = os.path.join(output_dir, "tmp")
    os.makedirs(tmp_dir, exist_ok=True)
    cmd = ["mmseqs", "cluster", db_path, cluster_out, tmp_dir] + params
    subprocess.run(cmd, check=True)

    # Convert to TSV
    tsv_out = os.path.join(output_dir, "mmseq_clu.tsv")
    subprocess.run(["mmseqs", "createtsv", db_path, db_path, cluster_out, tsv_out], check=True)

    return cluster_out, tsv_out

def params_to_cmd_args(params):
    args = []
    for key, value in params.items():
        args.append(str(key))
        args.append(str(value))
    return args

def local_blastp_query(input_fasta, db, output_path, exclusion_list):
    cmd = [
        'blastp', '-db', db, '-query', input_fasta,
        '-evalue', '1.0', '-outfmt', '5', '-out', output_path,
        '-num_threads', '32', '-word_size', '3',
        '-matrix', 'BLOSUM62', '-qcov_hsp_perc', '80', '-negative_seqidlist', exclusion_list
    ]
    subprocess.run(cmd, check=True)

def main():
    DB_PATH = './mms_smallDB'
    OUTPUT_DIR = './mmseqs_output'

    if os.path.exists(OUTPUT_DIR):
        shutil.rmtree(OUTPUT_DIR)

    # Input parameters for MMseqs
    MMSEQS_PARAMS = {
        '--cluster-mode': 1,
        '--cluster-steps': 3,
        '--cluster-reassign': 1,
        '--cov-mode': 0,
        '-c': 0.8,
        '-e': 0.001,
        '-s': 7,
        '--min-seq-id': 0.4,
        '--threads': 40,
        '--max-seqs': 200,
        '--max-iterations': 1000,
        '--alignment-mode': 3,
        '--similarity-type': 2
    }
    params = params_to_cmd_args(MMSEQS_PARAMS)

    # Cluster using MMseqs
    cluster_out, tsv_out = run_mmseqs_clustering(DB_PATH, OUTPUT_DIR, params)

    # Map sequences to their respective clusters
    cluster_mapping = {}
    with open(tsv_out, 'r') as f:
        for line in f:
            cluster, sequence = line.strip().split('\t')
            cluster_mapping[sequence] = cluster

    # Sample a sequence from 20 distinct clusters
    sampled_sequences = {}
    for sequence, cluster in cluster_mapping.items():
        if cluster not in sampled_sequences and len(sampled_sequences) < 20:
            sampled_sequences[cluster] = sequence

    # Create exclusion list
    exclusion_list = os.path.join(OUTPUT_DIR, "exclusion_list.txt")
    with open(exclusion_list, 'w') as f:
        for sequence, cluster in cluster_mapping.items():
            if cluster in sampled_sequences:
                f.write(f"{sequence}\n")

    # write query sequences to a file
    # we need to go get the sequences from the original database
    index = SeqIO.index('./mmseqs_input.fasta', "fasta")
    query_sequences = os.path.join(OUTPUT_DIR, "blast_query_sequences.fasta")
    with open (query_sequences, 'w') as f:
        for _, sequence in sampled_sequences.items():
            f.write(f">{sequence}\n{index[sequence].seq}\n")

    # Blast the sampled sequences against the MMseqs clustered database
    blast_output = os.path.join(OUTPUT_DIR, "blast_output.xml")
    local_blastp_query(query_sequences, './blast_smallDB', blast_output, exclusion_list)

    # Parse and return alignments
    es = []
    perc_identities = []
    records_iter = parse(open(blast_output, 'r'))

    for record in records_iter:
        # get only the best alignment and hsp for each query
        # (there should only be one)
        try:
            alignment = record.alignments[0]
        except IndexError:
            es.append(None)
            perc_identities.append(None)
            continue
        hsp = alignment.hsps[0]
        e = hsp.expect

        # check if both strands are covered
        # calculate average coverege
        coverage = (hsp.query_end - hsp.query_start + 1 + hsp.sbjct_end - hsp.sbjct_start + 1) / (alignment.length + record.query_length)
        if coverage < 0.9:
            es.append(None)
            perc_identities.append(None)

        # check that the first hsp of the first align is indeed the best
        for align in record.alignments:
            for hsp in align.hsps:
                if hsp.expect < e:
                    raise ValueError('Not the best hsp')

        es.append(e)
        perc_identities.append(hsp.identities / ((alignment.length + record.query_length)/2))

    num_aligned = len([e for e in es if e is not None])
    # remove nans
    es = [e for e in es if e is not None]
    perc_identities = [p for p in perc_identities if p is not None]
    mean_percid = sum(perc_identities)/len(perc_identities)
    mean_e = sum(es)/len(es)
    max_percid = max(perc_identities)
    min_e = min(es)

    result_dict = MMSEQS_PARAMS
    result_dict['num_aligned'] = num_aligned
    result_dict['mean_percid'] = mean_percid
    result_dict['mean_e'] = mean_e
    result_dict['max_percid'] = max_percid
    result_dict['min_e'] = min_e

    # load the current results (tsv) and append the new results
    results_path = os.path.join('./', "results.tsv")
    if os.path.exists(results_path):
        results = pd.read_csv(results_path, sep='\t')
        results = results.append(result_dict, ignore_index=True)
    else:
        results = pd.DataFrame([result_dict])

    results.to_csv(results_path, sep='\t', index=False)

if __name__ == "__main__":
    main()

MMseqs Output (for bugs)

Here is one output example, though I have run the above script varying the parameters for a number of params.

cluster ./mms_smallDB ./mmseqs_output/mmseq_clu ./mmseqs_output/tmp --cluster-mode 1 --cluster-steps 3 --cluster-reassign 1 --cov-mode 0 -c 0.8 -e 0.001 -s 7 --min-seq-id 0.4 --threads 40 --max-seqs 200 --max-iterations 1000 --alignment-mode 3 --similarity-type 2 

MMseqs Version:                         14.7e284
Substitution matrix                     aa:blosum62.out,nucl:nucleotide.out
Seed substitution matrix                aa:VTML80.out,nucl:nucleotide.out
Sensitivity                             7
k-mer length                            0
k-score                                 seq:2147483647,prof:2147483647
Alphabet size                           aa:21,nucl:5
Max sequence length                     65535
Max results per query                   200
Split database                          0
Split mode                              2
Split memory limit                      0
Coverage threshold                      0.8
Coverage mode                           0
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                                 40
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                      0.4
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                            1
Max connected component depth           1000
Similarity type                         2
Single step clustering                  false
Cascaded clustering steps               3
Cluster reassign                        true
Remove temporary files                  false
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

Connected component clustering produces less clusters in a single step clustering.
Please use --single-step-clusterlinclust ./mms_smallDB ./mmseqs_output/tmp/5351426679731834765/clu_redundancy ./mmseqs_output/tmp/5351426679731834765/linclust --cluster-mode 1 --max-iterations 1000 --similarity-type 2 --threads 40 --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 0.4 --min-aln-len 0 --seq-id-mode 0 --alt-ali 0 -c 0.8 --cov-mode 0 --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 0 --force-reuse 0 

kmermatcher ./mms_smallDB ./mmseqs_output/tmp/5351426679731834765/linclust/262265298633898384/pref --sub-mat 'aa:blosum62.out,nucl:nucleotide.out' --alph-size aa:13,nucl:5 --min-seq-id 0.4 --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 0 -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 40 --compressed 0 -v 3 

kmermatcher ./mms_smallDB ./mmseqs_output/tmp/5351426679731834765/linclust/262265298633898384/pref --sub-mat 'aa:blosum62.out,nucl:nucleotide.out' --alph-size aa:13,nucl:5 --min-seq-id 0.4 --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 0 -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 40 --compressed 0 -v 3 

Database size: 100000 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
[=================================================================] 100.00K 0s 853ms
Sort kmer 0h 0m 0s 789ms
Sort by rep. sequence 0h 0m 0s 951ms
Time for fill: 0h 0m 0s 155ms
Time for merging to pref: 0h 0m 0s 0ms
Time for processing: 0h 0m 3s 166ms
rescorediagonal ./mms_smallDB ./mms_smallDB ./mmseqs_output/tmp/5351426679731834765/linclust/262265298633898384/pref ./mmseqs_output/tmp/5351426679731834765/linclust/262265298633898384/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 0 --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 40 --compressed 0 -v 3 

[=================================================================] 100.00K 0s 206ms
Time for merging to pref_rescore1: 0h 0m 0s 757ms
Time for processing: 0h 0m 1s 988ms
clust ./mms_smallDB ./mmseqs_output/tmp/5351426679731834765/linclust/262265298633898384/pref_rescore1 ./mmseqs_output/tmp/5351426679731834765/linclust/262265298633898384/pre_clust --cluster-mode 1 --max-iterations 1000 --similarity-type 2 --threads 40 --compressed 0 -v 3 

Clustering mode: Connected Component
[=================================================================] 100.00K 0s 367ms
Sort entries
Find missing connections
Found 245160 new connections.
Reconstruct initial order
[=================================================================] 100.00K 0s 304ms
Add missing connections
[=================================================================] 100.00K 0s 8ms

Time for read in: 0h 0m 1s 971ms
connected component mode
Total time: 0h 0m 3s 258ms

Size of the sequence database: 100000
Size of the alignment database: 100000
Number of clusters: 31321

Writing results 0h 0m 0s 6ms
Time for merging to pre_clust: 0h 0m 0s 0ms
Time for processing: 0h 0m 3s 597ms
createsubdb ./mmseqs_output/tmp/5351426679731834765/linclust/262265298633898384/order_redundancy ./mms_smallDB ./mmseqs_output/tmp/5351426679731834765/linclust/262265298633898384/input_step_redundancy -v 3 --subdb-mode 1 

Time for merging to input_step_redundancy: 0h 0m 0s 0ms
Time for processing: 0h 0m 0s 14ms
createsubdb ./mmseqs_output/tmp/5351426679731834765/linclust/262265298633898384/order_redundancy ./mmseqs_output/tmp/5351426679731834765/linclust/262265298633898384/pref ./mmseqs_output/tmp/5351426679731834765/linclust/262265298633898384/pref_filter1 -v 3 --subdb-mode 1 

Time for merging to pref_filter1: 0h 0m 0s 0ms
Time for processing: 0h 0m 0s 422ms
filterdb ./mmseqs_output/tmp/5351426679731834765/linclust/262265298633898384/pref_filter1 ./mmseqs_output/tmp/5351426679731834765/linclust/262265298633898384/pref_filter2 --filter-file ./mmseqs_output/tmp/5351426679731834765/linclust/262265298633898384/order_redundancy --threads 40 --compressed 0 -v 3 

Filtering using file(s)
[=================================================================] 31.32K 0s 100ms
Time for merging to pref_filter2: 0h 0m 0s 137ms
Time for processing: 0h 0m 0s 847ms
rescorediagonal ./mmseqs_output/tmp/5351426679731834765/linclust/262265298633898384/input_step_redundancy ./mmseqs_output/tmp/5351426679731834765/linclust/262265298633898384/input_step_redundancy ./mmseqs_output/tmp/5351426679731834765/linclust/262265298633898384/pref_filter2 ./mmseqs_output/tmp/5351426679731834765/linclust/262265298633898384/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 0 --min-seq-id 0.4 --min-aln-len 0 --seq-id-mode 0 --add-self-matches 0 --sort-results 0 --db-load-mode 0 --threads 40 --compressed 0 -v 3 

[=================================================================] 31.32K 0s 42ms
Time for merging to pref_rescore2: 0h 0m 0s 90ms
Time for processing: 0h 0m 0s 772ms
align ./mmseqs_output/tmp/5351426679731834765/linclust/262265298633898384/input_step_redundancy ./mmseqs_output/tmp/5351426679731834765/linclust/262265298633898384/input_step_redundancy ./mmseqs_output/tmp/5351426679731834765/linclust/262265298633898384/pref_rescore2 ./mmseqs_output/tmp/5351426679731834765/linclust/262265298633898384/aln --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 0.4 --min-aln-len 0 --seq-id-mode 0 --alt-ali 0 -c 0.8 --cov-mode 0 --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 --threads 40 --compressed 0 -v 3 

Compute score, coverage and sequence identity
Query database size: 31321 type: Aminoacid
Target database size: 31321 type: Aminoacid
Calculation of alignments
[=================================================================] 31.32K 3s 713ms
Time for merging to aln: 0h 0m 0s 107ms
53166 alignments calculated
45707 sequence pairs passed the thresholds (0.859704 of overall calculated)
1.459308 hits per query sequence
Time for processing: 0h 0m 4s 203ms
clust ./mmseqs_output/tmp/5351426679731834765/linclust/262265298633898384/input_step_redundancy ./mmseqs_output/tmp/5351426679731834765/linclust/262265298633898384/aln ./mmseqs_output/tmp/5351426679731834765/linclust/262265298633898384/clust --cluster-mode 1 --max-iterations 1000 --similarity-type 2 --threads 40 --compressed 0 -v 3 

Clustering mode: Connected Component
[=================================================================] 31.32K 0s 215ms
Sort entries
Find missing connections
Found 14386 new connections.
Reconstruct initial order
[=================================================================] 31.32K 0s 218ms
Add missing connections
[=================================================================] 31.32K 0s 1ms

Time for read in: 0h 0m 1s 273ms
connected component mode
Total time: 0h 0m 1s 458ms

Size of the sequence database: 31321
Size of the alignment database: 31321
Number of clusters: 20942

Writing results 0h 0m 0s 96ms
Time for merging to clust: 0h 0m 0s 0ms
Time for processing: 0h 0m 1s 683ms
mergeclusters ./mms_smallDB ./mmseqs_output/tmp/5351426679731834765/clu_redundancy ./mmseqs_output/tmp/5351426679731834765/linclust/262265298633898384/pre_clust ./mmseqs_output/tmp/5351426679731834765/linclust/262265298633898384/clust --threads 40 --compressed 0 -v 3 

Clustering step 1
[=================================================================] 31.32K 0s 36ms
Clustering step 2
[=================================================================] 20.94K 0s 74ms
Write merged clustering
[=================================================================] 100.00K 0s 404ms
Time for merging to clu_redundancy: 0h 0m 0s 145ms
Time for processing: 0h 0m 0s 639ms
createsubdb ./mmseqs_output/tmp/5351426679731834765/clu_redundancy ./mms_smallDB ./mmseqs_output/tmp/5351426679731834765/input_step_redundancy -v 3 --subdb-mode 1 

Time for merging to input_step_redundancy: 0h 0m 0s 0ms
Time for processing: 0h 0m 0s 13ms
prefilter ./mmseqs_output/tmp/5351426679731834765/input_step_redundancy ./mmseqs_output/tmp/5351426679731834765/input_step_redundancy ./mmseqs_output/tmp/5351426679731834765/pref_step0 --sub-mat 'aa:blosum62.out,nucl:nucleotide.out' --seed-sub-mat 'aa:VTML80.out,nucl:nucleotide.out' -s 1 -k 0 --k-score seq:2147483647,prof:2147483647 --alph-size aa:21,nucl:5 --max-seq-len 65535 --max-seqs 200 --split 0 --split-mode 2 --split-memory-limit 0 -c 0.8 --cov-mode 0 --comp-bias-corr 0 --comp-bias-corr-scale 1 --diag-score 0 --exact-kmer-matching 0 --mask 1 --mask-prob 0.9 --mask-lower-case 0 --min-ungapped-score 0 --add-self-matches 0 --spaced-kmer-mode 1 --db-load-mode 0 --pca substitution:1.100,context:1.400 --pcb substitution:4.100,context:5.800 --threads 40 --compressed 0 -v 3 

Query database size: 20942 type: Aminoacid
Estimated memory consumption: 1G
Target database size: 20942 type: Aminoacid
Index table k-mer threshold: 154 at k-mer size 6 
Index table: counting k-mers
[=================================================================] 20.94K 0s 601ms
Index table: Masked residues: 6638
Index table: fill
[=================================================================] 20.94K 0s 645ms
Index statistics
Entries:          1435009
DB size:          496 MB
Avg k-mer size:   0.022422
Top 10 k-mers
    GPGGTL      342
    LDMPDG      185
    LGDYKP      145
    DVLDMP      119
    PFLEAR      69
    PFPEAR      65
    FDDTDS      59
    ADYTFS      55
    LITRGY      55
    GPGGTT      44
Time for index table init: 0h 0m 2s 668ms
Process prefiltering step 1 of 1

k-mer similarity threshold: 154
Starting prefiltering scores calculation (step 1 of 1)
Query db start 1 to 20942
Target db start 1 to 20942
[=================================================================] 20.94K 0s 928ms

1.256278 k-mers per position
118 DB matches per sequence
0 overflows
0 queries produce too many hits (truncated result)
8 sequences passed prefiltering per query sequence
3 median result list length
0 sequences with 0 size result lists
Time for merging to pref_step0: 0h 0m 0s 51ms
Time for processing: 0h 0m 6s 669ms
align ./mmseqs_output/tmp/5351426679731834765/input_step_redundancy ./mmseqs_output/tmp/5351426679731834765/input_step_redundancy ./mmseqs_output/tmp/5351426679731834765/pref_step0 ./mmseqs_output/tmp/5351426679731834765/aln_step0 --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 0.4 --min-aln-len 0 --seq-id-mode 0 --alt-ali 0 -c 0.8 --cov-mode 0 --max-seq-len 65535 --comp-bias-corr 0 --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 --threads 40 --compressed 0 -v 3 

Compute score, coverage and sequence identity
Query database size: 20942 type: Aminoacid
Target database size: 20942 type: Aminoacid
Calculation of alignments
[=================================================================] 20.94K 15s 380ms
Time for merging to aln_step0: 0h 0m 0s 75ms
172065 alignments calculated
67554 sequence pairs passed the thresholds (0.392607 of overall calculated)
3.225766 hits per query sequence
Time for processing: 0h 0m 16s 166ms
clust ./mmseqs_output/tmp/5351426679731834765/input_step_redundancy ./mmseqs_output/tmp/5351426679731834765/aln_step0 ./mmseqs_output/tmp/5351426679731834765/clu_step0 --cluster-mode 1 --max-iterations 1000 --similarity-type 2 --threads 40 --compressed 0 -v 3 

Clustering mode: Connected Component
[=================================================================] 20.94K 0s 211ms
Sort entries
Find missing connections
Found 98 new connections.
Reconstruct initial order
[=================================================================] 20.94K 0s 218ms
Add missing connections
[=================================================================] 20.94K 0s 1ms

Time for read in: 0h 0m 1s 264ms
connected component mode
Total time: 0h 0m 1s 477ms

Size of the sequence database: 20942
Size of the alignment database: 20942
Number of clusters: 10966

Writing results 0h 0m 0s 66ms
Time for merging to clu_step0: 0h 0m 0s 4ms
Time for processing: 0h 0m 1s 628ms
createsubdb ./mmseqs_output/tmp/5351426679731834765/clu_step0 ./mmseqs_output/tmp/5351426679731834765/input_step_redundancy ./mmseqs_output/tmp/5351426679731834765/input_step1 -v 3 --subdb-mode 1 

Time for merging to input_step1: 0h 0m 0s 0ms
Time for processing: 0h 0m 0s 7ms
prefilter ./mmseqs_output/tmp/5351426679731834765/input_step1 ./mmseqs_output/tmp/5351426679731834765/input_step1 ./mmseqs_output/tmp/5351426679731834765/pref_step1 --sub-mat 'aa:blosum62.out,nucl:nucleotide.out' --seed-sub-mat 'aa:VTML80.out,nucl:nucleotide.out' -s 4 -k 0 --k-score seq:2147483647,prof:2147483647 --alph-size aa:21,nucl:5 --max-seq-len 65535 --max-seqs 200 --split 0 --split-mode 2 --split-memory-limit 0 -c 0.8 --cov-mode 0 --comp-bias-corr 1 --comp-bias-corr-scale 1 --diag-score 1 --exact-kmer-matching 0 --mask 1 --mask-prob 0.9 --mask-lower-case 0 --min-ungapped-score 15 --add-self-matches 0 --spaced-kmer-mode 1 --db-load-mode 0 --pca substitution:1.100,context:1.400 --pcb substitution:4.100,context:5.800 --threads 40 --compressed 0 -v 3 

Query database size: 10966 type: Aminoacid
Estimated memory consumption: 1010M
Target database size: 10966 type: Aminoacid
Index table k-mer threshold: 127 at k-mer size 6 
Index table: counting k-mers
[=================================================================] 10.97K 0s 560ms
Index table: Masked residues: 4144
Index table: fill
[=================================================================] 10.97K 0s 667ms
Index statistics
Entries:          1798942
DB size:          498 MB
Avg k-mer size:   0.028108
Top 10 k-mers
    IGAALA      68
    GPGGTL      58
    GIVAPG      43
    ALTAGI      42
    ALGNGK      34
    GLGNGK      32
    ELPGVN      31
    DLLDLP      29
    GQQVAR      24
    GEQVAR      23
Time for index table init: 0h 0m 2s 664ms
Process prefiltering step 1 of 1

k-mer similarity threshold: 127
Starting prefiltering scores calculation (step 1 of 1)
Query db start 1 to 10966
Target db start 1 to 10966
[=================================================================] 10.97K 3s 91ms

46.510777 k-mers per position
438 DB matches per sequence
0 overflows
0 queries produce too many hits (truncated result)
13 sequences passed prefiltering per query sequence
7 median result list length
0 sequences with 0 size result lists
Time for merging to pref_step1: 0h 0m 0s 41ms
Time for processing: 0h 0m 8s 706ms
align ./mmseqs_output/tmp/5351426679731834765/input_step1 ./mmseqs_output/tmp/5351426679731834765/input_step1 ./mmseqs_output/tmp/5351426679731834765/pref_step1 ./mmseqs_output/tmp/5351426679731834765/aln_step1 --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 0.4 --min-aln-len 0 --seq-id-mode 0 --alt-ali 0 -c 0.8 --cov-mode 0 --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 --threads 40 --compressed 0 -v 3 

Compute score, coverage and sequence identity
Query database size: 10966 type: Aminoacid
Target database size: 10966 type: Aminoacid
Calculation of alignments
[=================================================================] 10.97K 9s 362ms
Time for merging to aln_step1: 0h 0m 0s 91ms
128470 alignments calculated
17027 sequence pairs passed the thresholds (0.132537 of overall calculated)
1.552708 hits per query sequence
Time for processing: 0h 0m 9s 872ms
clust ./mmseqs_output/tmp/5351426679731834765/input_step1 ./mmseqs_output/tmp/5351426679731834765/aln_step1 ./mmseqs_output/tmp/5351426679731834765/clu_step1 --cluster-mode 1 --max-iterations 1000 --similarity-type 2 --threads 40 --compressed 0 -v 3 

Clustering mode: Connected Component
[=================================================================] 10.97K 0s 3ms
Sort entries
Find missing connections
Found 475 new connections.
Reconstruct initial order
[=================================================================] 10.97K 0s 5ms
Add missing connections
[=================================================================] 10.97K 0s 0ms

Time for read in: 0h 0m 0s 613ms
connected component mode
Total time: 0h 0m 0s 705ms

Size of the sequence database: 10966
Size of the alignment database: 10966
Number of clusters: 8338

Writing results 0h 0m 0s 47ms
Time for merging to clu_step1: 0h 0m 0s 4ms
Time for processing: 0h 0m 0s 815ms
createsubdb ./mmseqs_output/tmp/5351426679731834765/clu_step1 ./mmseqs_output/tmp/5351426679731834765/input_step1 ./mmseqs_output/tmp/5351426679731834765/input_step2 -v 3 --subdb-mode 1 

Time for merging to input_step2: 0h 0m 0s 0ms
Time for processing: 0h 0m 0s 8ms
prefilter ./mmseqs_output/tmp/5351426679731834765/input_step2 ./mmseqs_output/tmp/5351426679731834765/input_step2 ./mmseqs_output/tmp/5351426679731834765/pref_step2 --sub-mat 'aa:blosum62.out,nucl:nucleotide.out' --seed-sub-mat 'aa:VTML80.out,nucl:nucleotide.out' -s 7 -k 0 --k-score seq:2147483647,prof:2147483647 --alph-size aa:21,nucl:5 --max-seq-len 65535 --max-seqs 200 --split 0 --split-mode 2 --split-memory-limit 0 -c 0.8 --cov-mode 0 --comp-bias-corr 1 --comp-bias-corr-scale 1 --diag-score 1 --exact-kmer-matching 0 --mask 1 --mask-prob 0.9 --mask-lower-case 0 --min-ungapped-score 15 --add-self-matches 0 --spaced-kmer-mode 1 --db-load-mode 0 --pca substitution:1.100,context:1.400 --pcb substitution:4.100,context:5.800 --threads 40 --compressed 0 -v 3 

Query database size: 8338 type: Aminoacid
Estimated memory consumption: 1003M
Target database size: 8338 type: Aminoacid
Index table k-mer threshold: 100 at k-mer size 6 
Index table: counting k-mers
[=================================================================] 8.34K 0s 514ms
Index table: Masked residues: 3074
Index table: fill
[=================================================================] 8.34K 0s 572ms
Index statistics
Entries:          1408015
DB size:          496 MB
Avg k-mer size:   0.022000
Top 10 k-mers
    GPGGTL      37
    GLGNGK      26
    ALGNGK      23
    DLLDLP      21
    FDDTDS      20
    NGGSLK      17
    DLLDMP      17
    DVLDMP      17
    GEQVAR      16
    FDDTDT      16
Time for index table init: 0h 0m 2s 591ms
Process prefiltering step 1 of 1

k-mer similarity threshold: 100
Starting prefiltering scores calculation (step 1 of 1)
Query db start 1 to 8338
Target db start 1 to 8338
[=================================================================] 8.34K 26s 907ms

903.365687 k-mers per position
4641 DB matches per sequence
0 overflows
0 queries produce too many hits (truncated result)
88 sequences passed prefiltering per query sequence
76 median result list length
0 sequences with 0 size result lists
Time for merging to pref_step2: 0h 0m 0s 36ms
Time for processing: 0h 0m 32s 520ms
align ./mmseqs_output/tmp/5351426679731834765/input_step2 ./mmseqs_output/tmp/5351426679731834765/input_step2 ./mmseqs_output/tmp/5351426679731834765/pref_step2 ./mmseqs_output/tmp/5351426679731834765/aln_step2 --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 0.4 --min-aln-len 0 --seq-id-mode 0 --alt-ali 0 -c 0.8 --cov-mode 0 --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 --threads 40 --compressed 0 -v 3 

Compute score, coverage and sequence identity
Query database size: 8338 type: Aminoacid
Target database size: 8338 type: Aminoacid
Calculation of alignments
[=================================================================] 8.34K 17s 958ms
Time for merging to aln_step2: 0h 0m 0s 88ms
489475 alignments calculated
8622 sequence pairs passed the thresholds (0.017615 of overall calculated)
1.034061 hits per query sequence
Time for processing: 0h 0m 18s 545ms
clust ./mmseqs_output/tmp/5351426679731834765/input_step2 ./mmseqs_output/tmp/5351426679731834765/aln_step2 ./mmseqs_output/tmp/5351426679731834765/clu_step2 --cluster-mode 1 --max-iterations 1000 --similarity-type 2 --threads 40 --compressed 0 -v 3 

Clustering mode: Connected Component
[=================================================================] 8.34K 0s 2ms
Sort entries
Find missing connections
Found 28 new connections.
Reconstruct initial order
[=================================================================] 8.34K 0s 2ms
Add missing connections
[=================================================================] 8.34K 0s 0ms

Time for read in: 0h 0m 0s 408ms
connected component mode
Total time: 0h 0m 0s 491ms

Size of the sequence database: 8338
Size of the alignment database: 8338
Number of clusters: 8185

Writing results 0h 0m 0s 23ms
Time for merging to clu_step2: 0h 0m 0s 4ms
Time for processing: 0h 0m 0s 572ms
mergeclusters ./mms_smallDB ./mmseqs_output/tmp/5351426679731834765/clu ./mmseqs_output/tmp/5351426679731834765/clu_redundancy ./mmseqs_output/tmp/5351426679731834765/clu_step0 ./mmseqs_output/tmp/5351426679731834765/clu_step1 ./mmseqs_output/tmp/5351426679731834765/clu_step2 

Clustering step 1
[=================================================================] 20.94K 0s 219ms
Clustering step 2
[=================================================================] 10.97K 0s 427ms
Clustering step 3
[=================================================================] 8.34K 0s 657ms
Clustering step 4
[=================================================================] 8.19K 0s 758ms
Write merged clustering
[=================================================================] 100.00K 0s 956ms
Time for merging to clu: 0h 0m 0s 164ms
Time for processing: 0h 0m 1s 268ms
align ./mms_smallDB ./mms_smallDB ./mmseqs_output/tmp/5351426679731834765/clu ./mmseqs_output/tmp/5351426679731834765/aln --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 0.4 --min-aln-len 0 --seq-id-mode 0 --alt-ali 0 -c 0.8 --cov-mode 0 --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 --threads 40 --compressed 0 -v 3 

Compute score, coverage and sequence identity
Query database size: 100000 type: Aminoacid
Target database size: 100000 type: Aminoacid
Calculation of alignments
[=================================================================] 8.19K 8s 160ms
Time for merging to aln: 0h 0m 0s 15ms
99829 alignments calculated
73771 sequence pairs passed the thresholds (0.738974 of overall calculated)
9.012951 hits per query sequence
Time for processing: 0h 0m 8s 437ms
subtractdbs ./mmseqs_output/tmp/5351426679731834765/clu ./mmseqs_output/tmp/5351426679731834765/aln ./mmseqs_output/tmp/5351426679731834765/clu_not_accepted --e-profile 100000000 -e 100000000 --threads 40 --compressed 0 -v 3 

subtractdbs ./mmseqs_output/tmp/5351426679731834765/clu ./mmseqs_output/tmp/5351426679731834765/aln ./mmseqs_output/tmp/5351426679731834765/clu_not_accepted --e-profile 100000000 -e 100000000 --threads 40 --compressed 0 -v 3 

Remove ./mmseqs_output/tmp/5351426679731834765/aln ids from ./mmseqs_output/tmp/5351426679731834765/clu
[=================================================================] 8.19K 0s 263ms
Time for merging to clu_not_accepted: 0h 0m 0s 69ms
Time for processing: 0h 0m 0s 514ms
swapdb ./mmseqs_output/tmp/5351426679731834765/clu_not_accepted ./mmseqs_output/tmp/5351426679731834765/clu_not_accepted_swap --threads 40 --compressed 0 -v 3 

[=================================================================] 8.19K 0s 2ms
Computing offsets.
[=================================================================] 8.19K 0s 1ms

Reading results.
[=================================================================] 8.19K 0s 1ms

Output database: ./mmseqs_output/tmp/5351426679731834765/clu_not_accepted_swap
[=================================================================] 100.00K 0s 116ms

Time for merging to clu_not_accepted_swap: 0h 0m 0s 143ms
Time for processing: 0h 0m 0s 577ms
subtractdbs ./mmseqs_output/tmp/5351426679731834765/clu ./mmseqs_output/tmp/5351426679731834765/clu_not_accepted ./mmseqs_output/tmp/5351426679731834765/clu_accepted --e-profile 100000000 -e 100000000 --threads 40 --compressed 0 -v 3 

subtractdbs ./mmseqs_output/tmp/5351426679731834765/clu ./mmseqs_output/tmp/5351426679731834765/clu_not_accepted ./mmseqs_output/tmp/5351426679731834765/clu_accepted --e-profile 100000000 -e 100000000 --threads 40 --compressed 0 -v 3 

Remove ./mmseqs_output/tmp/5351426679731834765/clu_not_accepted ids from ./mmseqs_output/tmp/5351426679731834765/clu
[=================================================================] 8.19K 0s 41ms
Time for merging to clu_accepted: 0h 0m 0s 137ms
Time for processing: 0h 0m 0s 277ms
createsubdb ./mmseqs_output/tmp/5351426679731834765/clu_not_accepted_swap ./mms_smallDB ./mmseqs_output/tmp/5351426679731834765/seq_wrong_assigned -v 3 

Time for merging to seq_wrong_assigned: 0h 0m 0s 0ms
Time for processing: 0h 0m 0s 28ms
createsubdb ./mmseqs_output/tmp/5351426679731834765/clu ./mms_smallDB ./mmseqs_output/tmp/5351426679731834765/seq_seeds -v 3 

Time for merging to seq_seeds: 0h 0m 0s 0ms
Time for processing: 0h 0m 0s 16ms
prefilter ./mmseqs_output/tmp/5351426679731834765/seq_wrong_assigned ./mmseqs_output/tmp/5351426679731834765/seq_seeds.merged ./mmseqs_output/tmp/5351426679731834765/seq_wrong_assigned_pref --sub-mat 'aa:blosum62.out,nucl:nucleotide.out' --seed-sub-mat 'aa:VTML80.out,nucl:nucleotide.out' -s 7 -k 0 --k-score seq:2147483647,prof:2147483647 --alph-size aa:21,nucl:5 --max-seq-len 65535 --max-seqs 200 --split 0 --split-mode 2 --split-memory-limit 0 -c 0.8 --cov-mode 0 --comp-bias-corr 1 --comp-bias-corr-scale 1 --diag-score 1 --exact-kmer-matching 0 --mask 1 --mask-prob 0.9 --mask-lower-case 0 --min-ungapped-score 15 --add-self-matches 0 --spaced-kmer-mode 1 --db-load-mode 0 --pca substitution:1.100,context:1.400 --pcb substitution:4.100,context:5.800 --threads 40 --compressed 0 -v 3 

Query database size: 26229 type: Aminoacid
Estimated memory consumption: 1G
Target database size: 34414 type: Aminoacid
Index table k-mer threshold: 100 at k-mer size 6 
Index table: counting k-mers
[=================================================================] 34.41K 1s 394ms
Index table: Masked residues: 8741
Index table: fill
[=================================================================] 34.41K 1s 378ms
Index statistics
Entries:          6295744
DB size:          524 MB
Avg k-mer size:   0.098371
Top 10 k-mers
    DVLDMP      2320
    PDVMRM      1368
    DRQVAY      1181
    PFPEAR      738
    MPLGAT      728
    MPMGAT      703
    GQQVAR      620
    ADYTFS      597
    LTFLYV      568
    VLLALS      518
Time for index table init: 0h 0m 4s 142ms
Process prefiltering step 1 of 1

k-mer similarity threshold: 100
Starting prefiltering scores calculation (step 1 of 1)
Query db start 1 to 26229
Target db start 1 to 34414
[=================================================================] 26.23K 1m 58s 7ms

775.834912 k-mers per position
60277 DB matches per sequence
0 overflows
0 queries produce too many hits (truncated result)
193 sequences passed prefiltering per query sequence
200 median result list length
0 sequences with 0 size result lists
Time for merging to seq_wrong_assigned_pref: 0h 0m 0s 56ms
Time for processing: 0h 2m 5s 612ms
swapdb ./mmseqs_output/tmp/5351426679731834765/seq_wrong_assigned_pref ./mmseqs_output/tmp/5351426679731834765/seq_wrong_assigned_pref_swaped --threads 40 --compressed 0 -v 3 

[=================================================================] 26.23K 0s 396ms
Computing offsets.
[=================================================================] 26.23K 0s 384ms

Reading results.
[=================================================================] 26.23K 0s 441ms

Output database: ./mmseqs_output/tmp/5351426679731834765/seq_wrong_assigned_pref_swaped
[=================================================================] 100.00K 0s 144ms

Time for merging to seq_wrong_assigned_pref_swaped: 0h 0m 0s 19ms
Time for processing: 0h 0m 2s 119ms
align ./mmseqs_output/tmp/5351426679731834765/seq_seeds.merged ./mmseqs_output/tmp/5351426679731834765/seq_wrong_assigned ./mmseqs_output/tmp/5351426679731834765/seq_wrong_assigned_pref_swaped ./mmseqs_output/tmp/5351426679731834765/seq_wrong_assigned_pref_swaped_aln --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 0.4 --min-aln-len 0 --seq-id-mode 0 --alt-ali 0 -c 0.8 --cov-mode 0 --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 --threads 40 --compressed 0 -v 3 

Compute score, coverage and sequence identity
Query database size: 34414 type: Aminoacid
Target database size: 26229 type: Aminoacid
Calculation of alignments
[=================================================================] 34.29K 6m 32s 543ms
Time for merging to seq_wrong_assigned_pref_swaped_aln: 0h 0m 0s 85ms
4335308 alignments calculated
2294027 sequence pairs passed the thresholds (0.529150 of overall calculated)
66.900757 hits per query sequence
Time for processing: 0h 6m 33s 544ms
filterdb ./mmseqs_output/tmp/5351426679731834765/seq_wrong_assigned_pref_swaped_aln ./mmseqs_output/tmp/5351426679731834765/seq_wrong_assigned_pref_swaped_aln_ocol --trim-to-one-column --threads 40 --compressed 0 -v 3 

Filtering using regular expression
[=================================================================] 34.29K 1s 15ms
Time for merging to seq_wrong_assigned_pref_swaped_aln_ocol: 0h 0m 0s 70ms
Time for processing: 0h 0m 1s 765ms
mergedbs ./mmseqs_output/tmp/5351426679731834765/seq_seeds.merged ./mmseqs_output/tmp/5351426679731834765/clu_accepted_plus_wrong ./mmseqs_output/tmp/5351426679731834765/clu_accepted ./mmseqs_output/tmp/5351426679731834765/seq_wrong_assigned_pref_swaped_aln_ocol --merge-stop-empty 0 --compressed 0 -v 3 

Merging the results to ./mmseqs_output/tmp/5351426679731834765/clu_accepted_plus_wrong
[=================================================================] 34.41K 0s 26ms
Time for merging to clu_accepted_plus_wrong: 0h 0m 0s 5ms
Time for processing: 0h 0m 0s 53ms
tsv2db ./mmseqs_output/tmp/5351426679731834765/missing.single.seqs ./mmseqs_output/tmp/5351426679731834765/missing.single.seqs.db --output-dbtype 6 --compressed 0 -v 3 

Output database type: Clustering
Time for merging to missing.single.seqs.db: 0h 0m 0s 12ms
Time for processing: 0h 0m 0s 34ms
mergedbs ./mms_smallDB ./mmseqs_output/tmp/5351426679731834765/clu_accepted_plus_wrong_plus_single ./mmseqs_output/tmp/5351426679731834765/clu_accepted_plus_wrong ./mmseqs_output/tmp/5351426679731834765/missing.single.seqs.db --merge-stop-empty 0 --compressed 0 -v 3 

Merging the results to ./mmseqs_output/tmp/5351426679731834765/clu_accepted_plus_wrong_plus_single
[=================================================================] 100.00K 0s 35ms
Time for merging to clu_accepted_plus_wrong_plus_single: 0h 0m 0s 12ms
Time for processing: 0h 0m 0s 66ms
clust ./mms_smallDB ./mmseqs_output/tmp/5351426679731834765/clu_accepted_plus_wrong_plus_single ./mmseqs_output/mmseq_clu --cluster-mode 1 --max-iterations 1000 --similarity-type 2 --threads 40 --compressed 0 -v 3 

Clustering mode: Connected Component
[=================================================================] 100.00K 0s 609ms
Sort entries
Find missing connections
Found 596106 new connections.
Reconstruct initial order
[=================================================================] 100.00K 0s 572ms
Add missing connections
[=================================================================] 100.00K 0s 324ms

Time for read in: 0h 0m 2s 881ms
connected component mode
Total time: 0h 0m 4s 86ms

Size of the sequence database: 100000
Size of the alignment database: 100000
Number of clusters: 8463

Writing results 0h 0m 0s 21ms
Time for merging to mmseq_clu: 0h 0m 0s 0ms
Time for processing: 0h 0m 4s 446ms
createtsv ./mms_smallDB ./mms_smallDB ./mmseqs_output/mmseq_clu ./mmseqs_output/mmseq_clu.tsv 

MMseqs Version:                         14.7e284
First sequence as representative        false
Target column                           1
Add full header                         false
Sequence source                         0
Database output                         false
Threads                                 40
Compressed                              0
Verbosity                               3

Time for merging to mmseq_clu.tsv: 0h 0m 0s 64ms
Time for processing: 0h 0m 0s 533ms

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daron-m-standley commented 11 months ago

Perhaps I am reading your example wrong, but Isn't your maximum sequence identity in the tsv table 0.4268774703557312? if so, it would seem that your intercluster sequence identity is below 50%.