Using https://mmseqs.com/latest/mmseqs-linux-avx2.tar.gz version
if created the Fasta file with spaces and low case letters
the command I used:
cmd = [
"mmseqs", "easy-cluster",
FILTERED_FASTA,
CLUSTER_PREFIX,
TMP_DIR,
"--min-seq-id", "0.7",
"-c", "0.8",
"--cov-mode", "1",
"--threads", f"{threads}",
"--split-memory-limit", "200G",
"-v", "3",
"--cluster-mode", "2",
"--kmer-per-seq", "100",
"--gpu", "1" # GPU Acceleration Enabled
]
running log:
- Sequences extracted for clustering: 10
--- Step 1: Running MMseqs2 GPU Test ---
easy-cluster /home/users/moria1239/mg_no_tmp/mgy_filtered_test.fasta /home/users/moria1239/mg_no_tmp/mgnify_c70_test /tmp/tmp_mmseqs_mgnify_19479 --min-seq-id 0.7 -c 0.8 --cov-mode 1 --threads 32 --split-memory-limit 200G -v 3 --cluster-mode 2 --kmer-per-seq 100 --gpu 1
MMseqs Version: 18cc749
Substitution matrix aa:blosum62.out,nucl:nucleotide.out
Seed substitution matrix aa:VTML80.out,nucl:nucleotide.out
Sensitivity 4
k-mer length 0
Target search mode 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 200G
Coverage threshold 0.8
Coverage mode 1
Compositional bias 1
Compositional bias scale 1
Diagonal scoring true
Exact k-mer matching 0
Mask residues 1
Mask residues probability 0.9
Mask lower case residues 0
Mask lower letter repeating N times 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 32
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 0.7
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 2
Max connected component depth 1000
Similarity type 2
Weight file name
Cluster Weight threshold 0.9
Set mode false
Single step clustering false
Cascaded clustering steps 3
Cluster reassign false
Remove temporary files true
Force restart with latest tmp false
MPI runner
Cluster version 1
k-mers per sequence 100
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
Include count table true
Number of count table based center swapping 2
Include adjacency based center swapping true
Number of adjacency based center swapping 3
Use parallelism false
Linclust version 2
Filter cluDB file
Filter seqDB file
Cluster hash false
Database type 0
Shuffle input database true
Createdb mode 1
Write lookup file 0
Offset of numeric ids 0
Use GPU 1
createdb /home/users/moria1239/mg_no_tmp/mgy_filtered_test.fasta /tmp/tmp_mmseqs_mgnify_19479/4897503383074789744/input --createdb-mode 1 --write-lookup 0 --threads 32 --gpu 1 -v 3
Converting sequences
[
Sort single files in 0h 0m 0s 3ms
Merge all files 0h 0m 0s 17ms
Database type: Aminoacid
Time for processing: 0h 0m 0s 46ms
Create directory /tmp/tmp_mmseqs_mgnify_19479/4897503383074789744/clu_tmp
cluster /tmp/tmp_mmseqs_mgnify_19479/4897503383074789744/input /tmp/tmp_mmseqs_mgnify_19479/4897503383074789744/clu /tmp/tmp_mmseqs_mgnify_19479/4897503383074789744/clu_tmp --max-seqs 20 --split-memory-limit 200G -c 0.8 --cov-mode 1 --spaced-kmer-mode 1 --threads 32 -v 3 --alignment-mode 3 -e 0.001 --min-seq-id 0.7 --cluster-mode 2 --remove-tmp-files 1 --kmer-per-seq 100
Set cluster sensitivity to -s 1.000000
Set cluster iterations to 1
linclust /tmp/tmp_mmseqs_mgnify_19479/4897503383074789744/input /tmp/tmp_mmseqs_mgnify_19479/4897503383074789744/clu_tmp/14454371353291572119/clu_redundancy /tmp/tmp_mmseqs_mgnify_19479/4897503383074789744/clu_tmp/14454371353291572119/linclust --cluster-mode 2 --max-iterations 1000 --similarity-type 2 --threads 32 --compressed 0 -v 3 --cluster-weight-threshold 0.9 --set-mode 0 --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 0.7 --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 100 --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 --mask-n-repeat 0 -k 0 --hash-shift 67 --split-memory-limit 200G --include-only-extendable 0 --ignore-multi-kmer 0 --include-count-table 0 --num-count-table 2 --include-adjacency 1 --num-adjacency 3 --use-parallelism 0 --need-write-buffer 0 --linclust-version 2 --rescore-mode 0 --filter-hits 0 --sort-results 0 --clust-hash 0 --remove-tmp-files 1 --force-reuse 0
kmermatcher /tmp/tmp_mmseqs_mgnify_19479/4897503383074789744/input /tmp/tmp_mmseqs_mgnify_19479/4897503383074789744/clu_tmp/14454371353291572119/linclust/13274294363082975222/pref --sub-mat 'aa:blosum62.out,nucl:nucleotide.out' --alph-size aa:13,nucl:5 --min-seq-id 0.7 --kmer-per-seq 100 --spaced-kmer-mode 0 --kmer-per-seq-scale aa:0.000,nucl:0.200 --adjust-kmer-len 0 --mask 0 --mask-prob 0.9 --mask-lower-case 0 --mask-n-repeat 0 --cov-mode 1 -k 0 -c 0.8 --max-seq-len 65535 --hash-shift 67 --split-memory-limit 200G --include-only-extendable 0 --ignore-multi-kmer 0 --threads 32 --compressed 0 -v 3 --cluster-weight-threshold 0.9 --include-count-table 0 --num-count-table 2 --include-adjacency 1 --num-adjacency 3 --use-parallelism 0 --need-write-buffer 0 --linclust-version 2
kmermatcher /tmp/tmp_mmseqs_mgnify_19479/4897503383074789744/input /tmp/tmp_mmseqs_mgnify_19479/4897503383074789744/clu_tmp/14454371353291572119/linclust/13274294363082975222/pref --sub-mat 'aa:blosum62.out,nucl:nucleotide.out' --alph-size aa:13,nucl:5 --min-seq-id 0.7 --kmer-per-seq 100 --spaced-kmer-mode 0 --kmer-per-seq-scale aa:0.000,nucl:0.200 --adjust-kmer-len 0 --mask 0 --mask-prob 0.9 --mask-lower-case 0 --mask-n-repeat 0 --cov-mode 1 -k 0 -c 0.8 --max-seq-len 65535 --hash-shift 67 --split-memory-limit 200G --include-only-extendable 0 --ignore-multi-kmer 0 --threads 32 --compressed 0 -v 3 --cluster-weight-threshold 0.9 --include-count-table 0 --num-count-table 2 --include-adjacency 1 --num-adjacency 3 --use-parallelism 0 --need-write-buffer 0 --linclust-version 2
Database size: 10 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
[=================================================================] 10 0s 161ms
Sort kmer 0h 0m 0s 0ms
Assign group Mode: Longest center: Time for assign: 0h 0m 0s 0ms
Sort by rep. sequence 0h 0m 0s 0ms
Time for write: 0h 0m 0s 0ms
Assign group Mode: Adjacent sequence: Time for assign: 0h 0m 0s 0ms
Sort by rep. sequence 0h 0m 0s 0ms
Time for write: 0h 0m 0s 0ms
Assign group Mode: Adjacent sequence: Time for assign: 0h 0m 0s 0ms
Sort by rep. sequence 0h 0m 0s 0ms
Time for write: 0h 0m 0s 0ms
Assign group Mode: Adjacent sequence: Time for assign: 0h 0m 0s 0ms
Sort by rep. sequence 0h 0m 0s 0ms
Time for write: 0h 0m 0s 0ms
Merge splits ... Time for fill: 0h 0m 0s 0ms
Time for merging to pref: 0h 0m 0s 0ms
Time for processing: 0h 0m 0s 202ms
align2clust /tmp/tmp_mmseqs_mgnify_19479/4897503383074789744/input /tmp/tmp_mmseqs_mgnify_19479/4897503383074789744/clu_tmp/14454371353291572119/linclust/13274294363082975222/pref /tmp/tmp_mmseqs_mgnify_19479/4897503383074789744/clu_tmp/14454371353291572119/linclust/13274294363082975222/clu --sub-mat 'aa:blosum62.out,nucl:nucleotide.out' -a 0 --alignment-mode 3 --min-seq-id 0.7 --min-aln-len 0 --seq-id-mode 0 --filter-hits 0 -e 0.001 -c 0.8 --cov-mode 1 --add-self-matches 0 --sort-results 0 --db-load-mode 0 --threads 32 --compressed 0 -v 3 --cluster-mode 2
Score per column threshold for filtering: 1.000000
Using GREEDY clustering mode
[======================] 10 0s 49ms
===========================================Size of the alignment database: 10
Number of clusters: 10
Time for run Align2Clust: 0h 0m 0s 153ms sec
Time for merging to clu: 0h 0m 0s 0ms
Time for processing: 0h 0m 0s 156ms
createsubdb /tmp/tmp_mmseqs_mgnify_19479/4897503383074789744/clu_tmp/14454371353291572119/linclust/13274294363082975222/clu /tmp/tmp_mmseqs_mgnify_19479/4897503383074789744/input /tmp/tmp_mmseqs_mgnify_19479/4897503383074789744/clu_tmp/14454371353291572119/linclust/13274294363082975222/input_rep -v 3 --subdb-mode 1
Time for merging to input_rep: 0h 0m 0s 0ms
Time for processing: 0h 0m 0s 2ms
kmermatcher /tmp/tmp_mmseqs_mgnify_19479/4897503383074789744/clu_tmp/14454371353291572119/linclust/13274294363082975222/input_rep /tmp/tmp_mmseqs_mgnify_19479/4897503383074789744/clu_tmp/14454371353291572119/linclust/13274294363082975222/pref_rep --sub-mat 'aa:blosum62.out,nucl:nucleotide.out' --alph-size aa:13,nucl:5 --min-seq-id 0.7 --kmer-per-seq 100 --spaced-kmer-mode 1 --kmer-per-seq-scale aa:0.100,nucl:0.100 --adjust-kmer-len 0 --mask 0 --mask-prob 0.9 --mask-lower-case 0 --mask-n-repeat 0 --cov-mode 1 -k 0 -c 0.8 --max-seq-len 65535 --hash-shift 67 --split-memory-limit 200G --include-only-extendable 0 --ignore-multi-kmer 0 --threads 32 --compressed 0 -v 3 --cluster-weight-threshold 0.9 --include-count-table 0 --num-count-table 2 --include-adjacency 1 --num-adjacency 3 --use-parallelism 0 --need-write-buffer 0 --linclust-version 2
kmermatcher /tmp/tmp_mmseqs_mgnify_19479/4897503383074789744/clu_tmp/14454371353291572119/linclust/13274294363082975222/input_rep /tmp/tmp_mmseqs_mgnify_19479/4897503383074789744/clu_tmp/14454371353291572119/linclust/13274294363082975222/pref_rep --sub-mat 'aa:blosum62.out,nucl:nucleotide.out' --alph-size aa:13,nucl:5 --min-seq-id 0.7 --kmer-per-seq 100 --spaced-kmer-mode 1 --kmer-per-seq-scale aa:0.100,nucl:0.100 --adjust-kmer-len 0 --mask 0 --mask-prob 0.9 --mask-lower-case 0 --mask-n-repeat 0 --cov-mode 1 -k 0 -c 0.8 --max-seq-len 65535 --hash-shift 67 --split-memory-limit 200G --include-only-extendable 0 --ignore-multi-kmer 0 --threads 32 --compressed 0 -v 3 --cluster-weight-threshold 0.9 --include-count-table 0 --num-count-table 2 --include-adjacency 1 --num-adjacency 3 --use-parallelism 0 --need-write-buffer 0 --linclust-version 2
Database size: 10 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
[=================================================================] 10 0s 170ms
Sort kmer 0h 0m 0s 0ms
Assign group Mode: Longest center: Time for assign: 0h 0m 0s 0ms
Sort by rep. sequence 0h 0m 0s 0ms
Time for write: 0h 0m 0s 0ms
Assign group Mode: Adjacent sequence: Time for assign: 0h 0m 0s 0ms
Sort by rep. sequence 0h 0m 0s 0ms
Time for write: 0h 0m 0s 0ms
Assign group Mode: Adjacent sequence: Time for assign: 0h 0m 0s 0ms
Sort by rep. sequence 0h 0m 0s 0ms
Time for write: 0h 0m 0s 0ms
Assign group Mode: Adjacent sequence: Time for assign: 0h 0m 0s 0ms
Sort by rep. sequence 0h 0m 0s 0ms
Time for write: 0h 0m 0s 0ms
Merge splits ... Time for fill: 0h 0m 0s 0ms
Time for merging to pref_rep: 0h 0m 0s 0ms
Time for processing: 0h 0m 0s 209ms
align2clust /tmp/tmp_mmseqs_mgnify_19479/4897503383074789744/clu_tmp/14454371353291572119/linclust/13274294363082975222/input_rep /tmp/tmp_mmseqs_mgnify_19479/4897503383074789744/clu_tmp/14454371353291572119/linclust/13274294363082975222/pref_rep /tmp/tmp_mmseqs_mgnify_19479/4897503383074789744/clu_tmp/14454371353291572119/linclust/13274294363082975222/clu_rep --sub-mat 'aa:blosum62.out,nucl:nucleotide.out' -a 0 --alignment-mode 3 --min-seq-id 0.7 --min-aln-len 0 --seq-id-mode 0 --filter-hits 0 -e 0.001 -c 0.8 --cov-mode 1 --add-self-matches 0 --sort-results 0 --db-load-mode 0 --threads 32 --compressed 0 -v 3 --cluster-mode 2 --filter-cludb-file /tmp/tmp_mmseqs_mgnify_19479/4897503383074789744/clu_tmp/14454371353291572119/linclust/13274294363082975222/clu --filter-seqdb-file /tmp/tmp_mmseqs_mgnify_19479/4897503383074789744/input
Score per column threshold for filtering: 1.000000
Using GREEDY clustering mode
[======================] 10 0s 42ms
===========================================Size of the alignment database: 10
Number of clusters: 10
Time for run Align2Clust: 0h 0m 0s 142ms sec
Time for merging to clu_rep: 0h 0m 0s 0ms
Time for processing: 0h 0m 0s 143ms
mergeclusters /tmp/tmp_mmseqs_mgnify_19479/4897503383074789744/input /tmp/tmp_mmseqs_mgnify_19479/4897503383074789744/clu_tmp/14454371353291572119/clu_redundancy /tmp/tmp_mmseqs_mgnify_19479/4897503383074789744/clu_tmp/14454371353291572119/linclust/13274294363082975222/clu /tmp/tmp_mmseqs_mgnify_19479/4897503383074789744/clu_tmp/14454371353291572119/linclust/13274294363082975222/clu_rep --threads 32 --compressed 0 -v 3
Clustering step 1
[=================================================================] 10 0s 149ms
Clustering step 2
[=================================================================] 10 0s 274ms
Write merged clustering
[=================================================================] 10 0s 450ms
Time for merging to clu_redundancy: 0h 0m 0s 0ms
Time for processing: 0h 0m 0s 458ms
rmdb /tmp/tmp_mmseqs_mgnify_19479/4897503383074789744/clu_tmp/14454371353291572119/linclust/13274294363082975222/pref -v 3
Time for processing: 0h 0m 0s 1ms
createsubdb /tmp/tmp_mmseqs_mgnify_19479/4897503383074789744/clu_tmp/14454371353291572119/clu_redundancy /tmp/tmp_mmseqs_mgnify_19479/4897503383074789744/input /tmp/tmp_mmseqs_mgnify_19479/4897503383074789744/clu_tmp/14454371353291572119/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 1ms
prefilter /tmp/tmp_mmseqs_mgnify_19479/4897503383074789744/clu_tmp/14454371353291572119/input_step_redundancy /tmp/tmp_mmseqs_mgnify_19479/4897503383074789744/clu_tmp/14454371353291572119/input_step_redundancy /tmp/tmp_mmseqs_mgnify_19479/4897503383074789744/clu_tmp/14454371353291572119/pref_step0 --sub-mat 'aa:blosum62.out,nucl:nucleotide.out' --seed-sub-mat 'aa:VTML80.out,nucl:nucleotide.out' -s 1 -k 0 --target-search-mode 0 --k-score seq:2147483647,prof:2147483647 --alph-size aa:21,nucl:5 --max-seq-len 65535 --max-seqs 20 --split 0 --split-mode 2 --split-memory-limit 200G -c 0.8 --cov-mode 1 --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 --mask-n-repeat 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 32 --compressed 0 -v 3
Query database size: 10 type: Aminoacid
Estimated memory consumption: 977M
Target database size: 10 type: Aminoacid
Index table k-mer threshold: 154 at k-mer size 6
Index table: counting k-mers
[=================================================================] 10 0s 163ms
Index table: Masked residues: 0
Index table: fill
[=================================================================] 10 0s 139ms
Index statistics
Entries: 889
DB size: 488 MB
Avg k-mer size: 0.000014
Top 10 k-mers
SWIDAA 1
RSWDAA 1
KPVSCA 1
RYDVDA 1
DNDGEA 1
MAMREA 1
ECGTEA 1
PMRTEA 1
KHYYEA 1
DNIDFA 1
Time for index table init: 0h 0m 0s 734ms
Process prefiltering step 1 of 1
k-mer similarity threshold: 154
Starting prefiltering scores calculation (step 1 of 1)
Query db start 1 to 10
Target db start 1 to 10
[==========================================================] 10 0s 122ms
1.939122 k-mers per position
88 DB matches per sequence
0 overflows
1 sequences passed prefiltering per query sequence
1 median result list length
0 sequences with 0 size result lists
Time for merging to pref_step0: 0h 0m 0s 0ms
Time for processing: 0h 0m 1s 20ms
align /tmp/tmp_mmseqs_mgnify_19479/4897503383074789744/clu_tmp/14454371353291572119/input_step_redundancy /tmp/tmp_mmseqs_mgnify_19479/4897503383074789744/clu_tmp/14454371353291572119/input_step_redundancy /tmp/tmp_mmseqs_mgnify_19479/4897503383074789744/clu_tmp/14454371353291572119/pref_step0 /tmp/tmp_mmseqs_mgnify_19479/4897503383074789744/clu_tmp/14454371353291572119/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 0.7 --min-aln-len 0 --seq-id-mode 0 --alt-ali 0 -c 0.8 --cov-mode 1 --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 32 --compressed 0 -v 3
Compute score, coverage and sequence identity
Query database size: 10 type: Aminoacid
Target database size: 10 type: Aminoacid
Calculation of alignments
[=================================================================] 10 0s 123ms
Time for merging to aln_step0: 0h 0m 0s 0ms
10 alignments calculated
10 sequence pairs passed the thresholds (1.000000 of overall calculated)
1.000000 hits per query sequence
Time for processing: 0h 0m 0s 128ms
clust /tmp/tmp_mmseqs_mgnify_19479/4897503383074789744/clu_tmp/14454371353291572119/input_step_redundancy /tmp/tmp_mmseqs_mgnify_19479/4897503383074789744/clu_tmp/14454371353291572119/aln_step0 /tmp/tmp_mmseqs_mgnify_19479/4897503383074789744/clu_tmp/14454371353291572119/clu_step0 --cluster-mode 2 --max-iterations 1000 --similarity-type 2 --threads 32 --compressed 0 -v 3 --cluster-weight-threshold 0.9 --set-mode 0
Clustering mode: Greedy
Total time: 0h 0m 0s 2ms
Size of the sequence database: 10
Size of the alignment database: 10
Number of clusters: 10
Writing results 0h 0m 0s 0ms
Time for merging to clu_step0: 0h 0m 0s 0ms
Time for processing: 0h 0m 0s 5ms
mergeclusters /tmp/tmp_mmseqs_mgnify_19479/4897503383074789744/input /tmp/tmp_mmseqs_mgnify_19479/4897503383074789744/clu /tmp/tmp_mmseqs_mgnify_19479/4897503383074789744/clu_tmp/14454371353291572119/clu_redundancy /tmp/tmp_mmseqs_mgnify_19479/4897503383074789744/clu_tmp/14454371353291572119/clu_step0 --threads 32 --compressed 0 -v 3
Clustering step 1
[=================================================================] 10 0s 116ms
Clustering step 2
[=================================================================] 10 0s 267ms
Write merged clustering
[=================================================================] 10 0s 405ms
Time for merging to clu: 0h 0m 0s 0ms
Time for processing: 0h 0m 0s 413ms
rmdb /tmp/tmp_mmseqs_mgnify_19479/4897503383074789744/clu_tmp/14454371353291572119/clu_redundancy -v 3
Time for processing: 0h 0m 0s 1ms
rmdb /tmp/tmp_mmseqs_mgnify_19479/4897503383074789744/clu_tmp/14454371353291572119/input_step_redundancy -v 3
Time for processing: 0h 0m 0s 1ms
rmdb /tmp/tmp_mmseqs_mgnify_19479/4897503383074789744/clu_tmp/14454371353291572119/input_step_redundancy_h -v 3
Time for processing: 0h 0m 0s 2ms
rmdb /tmp/tmp_mmseqs_mgnify_19479/4897503383074789744/clu_tmp/14454371353291572119/pref_step0 -v 3
Time for processing: 0h 0m 0s 1ms
rmdb /tmp/tmp_mmseqs_mgnify_19479/4897503383074789744/clu_tmp/14454371353291572119/aln_step0 -v 3
Time for processing: 0h 0m 0s 1ms
rmdb /tmp/tmp_mmseqs_mgnify_19479/4897503383074789744/clu_tmp/14454371353291572119/clu_step0 -v 3
Time for processing: 0h 0m 0s 2ms
createtsv /tmp/tmp_mmseqs_mgnify_19479/4897503383074789744/input /tmp/tmp_mmseqs_mgnify_19479/4897503383074789744/input /tmp/tmp_mmseqs_mgnify_19479/4897503383074789744/clu /tmp/tmp_mmseqs_mgnify_19479/4897503383074789744/cluster.tsv --threads 32 -v 3
Time for merging to cluster.tsv: 0h 0m 0s 0ms
Time for processing: 0h 0m 0s 30ms
result2repseq /tmp/tmp_mmseqs_mgnify_19479/4897503383074789744/input /tmp/tmp_mmseqs_mgnify_19479/4897503383074789744/clu /tmp/tmp_mmseqs_mgnify_19479/4897503383074789744/clu_rep --db-load-mode 0 --compressed 0 --threads 32 -v 3
[=================================================================] 10 0s 141ms
Time for merging to clu_rep: 0h 0m 0s 0ms
Time for processing: 0h 0m 0s 168ms
result2flat /tmp/tmp_mmseqs_mgnify_19479/4897503383074789744/input /tmp/tmp_mmseqs_mgnify_19479/4897503383074789744/input /tmp/tmp_mmseqs_mgnify_19479/4897503383074789744/clu_rep /tmp/tmp_mmseqs_mgnify_19479/4897503383074789744/rep_seq.fasta --use-fasta-header -v 3
Time for processing: 0h 0m 0s 2ms
createseqfiledb /tmp/tmp_mmseqs_mgnify_19479/4897503383074789744/input /tmp/tmp_mmseqs_mgnify_19479/4897503383074789744/clu /tmp/tmp_mmseqs_mgnify_19479/4897503383074789744/clu_seqs --threads 32 -v 3
[=================================================================] 10 0s 136ms
Time for merging to clu_seqs: 0h 0m 0s 0ms
Time for processing: 0h 0m 0s 163ms
result2flat /tmp/tmp_mmseqs_mgnify_19479/4897503383074789744/input /tmp/tmp_mmseqs_mgnify_19479/4897503383074789744/input /tmp/tmp_mmseqs_mgnify_19479/4897503383074789744/clu_seqs /tmp/tmp_mmseqs_mgnify_19479/4897503383074789744/all_seqs.fasta -v 3
Time for processing: 0h 0m 0s 1ms
rmdb /tmp/tmp_mmseqs_mgnify_19479/4897503383074789744/input -v 3
Time for processing: 0h 0m 0s 1ms
rmdb /tmp/tmp_mmseqs_mgnify_19479/4897503383074789744/input_h -v 3
Time for processing: 0h 0m 0s 2ms
rmdb /tmp/tmp_mmseqs_mgnify_19479/4897503383074789744/clu_seqs -v 3
Time for processing: 0h 0m 0s 2ms
rmdb /tmp/tmp_mmseqs_mgnify_19479/4897503383074789744/clu_rep -v 3
Time for processing: 0h 0m 0s 2ms
rmdb /tmp/tmp_mmseqs_mgnify_19479/4897503383074789744/clu -v 3
Time for processing: 0h 0m 0s 1ms
============================================================
✅ Test Complete!
📄 Output FASTA file path: /home/users/moria1239/mg_no_tmp/mgnify_c70_test_rep_seq.fasta
--- FASTA FILE CONTENTS ---
MGYP001826121148
mnmtmemeyhsurr urmrnnhnnmmsmnhmtyesshenyomusesnshyme
MGYP000951978405
ss semgosmmmrhroemmm et tsoseoom tuhmomehermme ooomeshmmeu eurmrhehtushrruot mshm yyty
MGYP003125700799
smoee hs mrmegerryossumsmsm uoeemrourytosuhetmertryoee hm uhseteeymmhm ytrsunoruu ehhmnsmyeunyemyyeesuhooe oooes
MGYP001602832073
shyremeryhogymunehuynehyteugor gmohhunyo utystmenhyeyysoymremtoneenrymohntttysusuyuthergyyeeoryesheyymoesmygnnersyuyeomg
MGYP001548917672
ytmggysesee myneo nsrommonymumugyuhueey e meerrnysmmumyms reounueoe muommsmuyometmeoumhnouymoouoeoonrouhsuetygmoooneoumoemoomom
MGYP002352835322
sme yemsyunmmyyyoeuomumtyttsuyomu omeyy nmgmesrmnygm shmeuoehhymteouotoemymyoso emrreytmmoomyomnoronrumorrrouehumhunhsomsumymnonomos tysmrmhmn o stme muooeorseormmhysmsy
MGYP001791625403
shenmsynonnssnsohnrosneoomhmmumotoosotsrmrnttue mmy yoeo mmnommhyhmmoesmehonhnsmymeetyuhtmteeutrhmrtym ymnnmmmnthsyommsoneoshehmthmmsosnnyemyrsesnrunenummonsnynmomssgrntremhysrsnenyyer
MGYP004689541021
seetsshyesg emssn ymgnemeymtusugytynyssnguosu ooo tyem nssmsemtehosuhtsmtheuh nteehhmmooeooehhstsnnuoseooymhneuroreushnmh nrtesurmyhmysyuomtehutm teem nto uymmouynrresstnyushheregsenuuoterosgemsmoroege osoy mgsmtymee ysryunseurruhtoneeoysnuegtomhe hsmgsetshtsouhegruoueeoeuhermmnuyne emyurhonnymtmutenmehoohouutoymyyo
MGYP000840126895
sttmseysonnoheennhmnmyotoeotsntroyhe hyososn suymgmnoeryyo mhmnsh ssteyoonhssnotutmhryoomytyett rtu rt mtgsst ghomssym nnhrsnrmoy esugsmyohnounemhttmhnthyn h mhtehsgstuohmmrtrthoommrnttmsyseouhumthyo nmtgsnetnmygmmumsgttotgmnosemosnuuheeruyuryouynytmtnoouyysgongynorgurumgmhermmhsgoeehemeooeteheenhoosh oyhmhormtmushhemmnesormnsrymyure heuoemmeruutermnmn
MGYP003337799140
syomeuyyemooooumymuymyumrmeyrheeomoommsyrmeooeyommmoyytmhmyoruntyom mem y mm mmyommommmoyommhemyoohoonnroohmmu reymerseeyryhoouyryyuhmhnmmyoemyoog motenyruemrusreuoomoohumoommsmegmmmymmtoe rygeosymoneerygmhoumrmuoooytrm mtgyyuyyyouenmmoooysyomhgoesgmenyogymoemnmogyorenrymymmmryuhmmmmmmesrgyoruemghtrmmumrrmrtmmoh mtmmgomemy o memguommme mmtyhmouyumme hu gyogonymyyymyyo guehmmmemsemmyteeg
Using https://mmseqs.com/latest/mmseqs-linux-avx2.tar.gz version
if created the Fasta file with spaces and low case letters
the command I used:
cmd = [
"mmseqs", "easy-cluster",
FILTERED_FASTA,
CLUSTER_PREFIX,
TMP_DIR,
"--min-seq-id", "0.7",
"-c", "0.8",
"--cov-mode", "1",
"--threads", f"{threads}",
"--split-memory-limit", "200G",
"-v", "3",
"--cluster-mode", "2",
"--kmer-per-seq", "100",
"--gpu", "1" # GPU Acceleration Enabled
]
running log:
--- Step 1: Running MMseqs2 GPU Test ---
easy-cluster /home/users/moria1239/mg_no_tmp/mgy_filtered_test.fasta /home/users/moria1239/mg_no_tmp/mgnify_c70_test /tmp/tmp_mmseqs_mgnify_19479 --min-seq-id 0.7 -c 0.8 --cov-mode 1 --threads 32 --split-memory-limit 200G -v 3 --cluster-mode 2 --kmer-per-seq 100 --gpu 1
MMseqs Version: 18cc749
Substitution matrix aa:blosum62.out,nucl:nucleotide.out
Seed substitution matrix aa:VTML80.out,nucl:nucleotide.out
Sensitivity 4
k-mer length 0
Target search mode 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 200G
Coverage threshold 0.8
Coverage mode 1
Compositional bias 1
Compositional bias scale 1
Diagonal scoring true
Exact k-mer matching 0
Mask residues 1
Mask residues probability 0.9
Mask lower case residues 0
Mask lower letter repeating N times 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 32
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 0.7
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 2
Max connected component depth 1000
Similarity type 2
Weight file name
Cluster Weight threshold 0.9
Set mode false
Single step clustering false
Cascaded clustering steps 3
Cluster reassign false
Remove temporary files true
Force restart with latest tmp false
MPI runner
Cluster version 1
k-mers per sequence 100
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
Include count table true
Number of count table based center swapping 2
Include adjacency based center swapping true
Number of adjacency based center swapping 3
Use parallelism false
Linclust version 2
Filter cluDB file
Filter seqDB file
Cluster hash false
Database type 0
Shuffle input database true
Createdb mode 1
Write lookup file 0
Offset of numeric ids 0
Use GPU 1
createdb /home/users/moria1239/mg_no_tmp/mgy_filtered_test.fasta /tmp/tmp_mmseqs_mgnify_19479/4897503383074789744/input --createdb-mode 1 --write-lookup 0 --threads 32 --gpu 1 -v 3
Converting sequences
[
Sort single files in 0h 0m 0s 3ms
Merge all files 0h 0m 0s 17ms
Database type: Aminoacid
Time for processing: 0h 0m 0s 46ms
Create directory /tmp/tmp_mmseqs_mgnify_19479/4897503383074789744/clu_tmp
cluster /tmp/tmp_mmseqs_mgnify_19479/4897503383074789744/input /tmp/tmp_mmseqs_mgnify_19479/4897503383074789744/clu /tmp/tmp_mmseqs_mgnify_19479/4897503383074789744/clu_tmp --max-seqs 20 --split-memory-limit 200G -c 0.8 --cov-mode 1 --spaced-kmer-mode 1 --threads 32 -v 3 --alignment-mode 3 -e 0.001 --min-seq-id 0.7 --cluster-mode 2 --remove-tmp-files 1 --kmer-per-seq 100
Set cluster sensitivity to -s 1.000000
Set cluster iterations to 1
linclust /tmp/tmp_mmseqs_mgnify_19479/4897503383074789744/input /tmp/tmp_mmseqs_mgnify_19479/4897503383074789744/clu_tmp/14454371353291572119/clu_redundancy /tmp/tmp_mmseqs_mgnify_19479/4897503383074789744/clu_tmp/14454371353291572119/linclust --cluster-mode 2 --max-iterations 1000 --similarity-type 2 --threads 32 --compressed 0 -v 3 --cluster-weight-threshold 0.9 --set-mode 0 --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 0.7 --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 100 --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 --mask-n-repeat 0 -k 0 --hash-shift 67 --split-memory-limit 200G --include-only-extendable 0 --ignore-multi-kmer 0 --include-count-table 0 --num-count-table 2 --include-adjacency 1 --num-adjacency 3 --use-parallelism 0 --need-write-buffer 0 --linclust-version 2 --rescore-mode 0 --filter-hits 0 --sort-results 0 --clust-hash 0 --remove-tmp-files 1 --force-reuse 0
kmermatcher /tmp/tmp_mmseqs_mgnify_19479/4897503383074789744/input /tmp/tmp_mmseqs_mgnify_19479/4897503383074789744/clu_tmp/14454371353291572119/linclust/13274294363082975222/pref --sub-mat 'aa:blosum62.out,nucl:nucleotide.out' --alph-size aa:13,nucl:5 --min-seq-id 0.7 --kmer-per-seq 100 --spaced-kmer-mode 0 --kmer-per-seq-scale aa:0.000,nucl:0.200 --adjust-kmer-len 0 --mask 0 --mask-prob 0.9 --mask-lower-case 0 --mask-n-repeat 0 --cov-mode 1 -k 0 -c 0.8 --max-seq-len 65535 --hash-shift 67 --split-memory-limit 200G --include-only-extendable 0 --ignore-multi-kmer 0 --threads 32 --compressed 0 -v 3 --cluster-weight-threshold 0.9 --include-count-table 0 --num-count-table 2 --include-adjacency 1 --num-adjacency 3 --use-parallelism 0 --need-write-buffer 0 --linclust-version 2
kmermatcher /tmp/tmp_mmseqs_mgnify_19479/4897503383074789744/input /tmp/tmp_mmseqs_mgnify_19479/4897503383074789744/clu_tmp/14454371353291572119/linclust/13274294363082975222/pref --sub-mat 'aa:blosum62.out,nucl:nucleotide.out' --alph-size aa:13,nucl:5 --min-seq-id 0.7 --kmer-per-seq 100 --spaced-kmer-mode 0 --kmer-per-seq-scale aa:0.000,nucl:0.200 --adjust-kmer-len 0 --mask 0 --mask-prob 0.9 --mask-lower-case 0 --mask-n-repeat 0 --cov-mode 1 -k 0 -c 0.8 --max-seq-len 65535 --hash-shift 67 --split-memory-limit 200G --include-only-extendable 0 --ignore-multi-kmer 0 --threads 32 --compressed 0 -v 3 --cluster-weight-threshold 0.9 --include-count-table 0 --num-count-table 2 --include-adjacency 1 --num-adjacency 3 --use-parallelism 0 --need-write-buffer 0 --linclust-version 2
Database size: 10 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
[=================================================================] 10 0s 161ms
Sort kmer 0h 0m 0s 0ms
Assign group Mode: Longest center: Time for assign: 0h 0m 0s 0ms
Sort by rep. sequence 0h 0m 0s 0ms
Time for write: 0h 0m 0s 0ms
Assign group Mode: Adjacent sequence: Time for assign: 0h 0m 0s 0ms
Sort by rep. sequence 0h 0m 0s 0ms
Time for write: 0h 0m 0s 0ms
Assign group Mode: Adjacent sequence: Time for assign: 0h 0m 0s 0ms
Sort by rep. sequence 0h 0m 0s 0ms
Time for write: 0h 0m 0s 0ms
Assign group Mode: Adjacent sequence: Time for assign: 0h 0m 0s 0ms
Sort by rep. sequence 0h 0m 0s 0ms
Time for write: 0h 0m 0s 0ms
Merge splits ... Time for fill: 0h 0m 0s 0ms
Time for merging to pref: 0h 0m 0s 0ms
Time for processing: 0h 0m 0s 202ms
align2clust /tmp/tmp_mmseqs_mgnify_19479/4897503383074789744/input /tmp/tmp_mmseqs_mgnify_19479/4897503383074789744/clu_tmp/14454371353291572119/linclust/13274294363082975222/pref /tmp/tmp_mmseqs_mgnify_19479/4897503383074789744/clu_tmp/14454371353291572119/linclust/13274294363082975222/clu --sub-mat 'aa:blosum62.out,nucl:nucleotide.out' -a 0 --alignment-mode 3 --min-seq-id 0.7 --min-aln-len 0 --seq-id-mode 0 --filter-hits 0 -e 0.001 -c 0.8 --cov-mode 1 --add-self-matches 0 --sort-results 0 --db-load-mode 0 --threads 32 --compressed 0 -v 3 --cluster-mode 2
Score per column threshold for filtering: 1.000000
Using GREEDY clustering mode
[======================] 10 0s 49ms
===========================================Size of the alignment database: 10
Number of clusters: 10
Time for run Align2Clust: 0h 0m 0s 153ms sec
Time for merging to clu: 0h 0m 0s 0ms
Time for processing: 0h 0m 0s 156ms
createsubdb /tmp/tmp_mmseqs_mgnify_19479/4897503383074789744/clu_tmp/14454371353291572119/linclust/13274294363082975222/clu /tmp/tmp_mmseqs_mgnify_19479/4897503383074789744/input /tmp/tmp_mmseqs_mgnify_19479/4897503383074789744/clu_tmp/14454371353291572119/linclust/13274294363082975222/input_rep -v 3 --subdb-mode 1
Time for merging to input_rep: 0h 0m 0s 0ms
Time for processing: 0h 0m 0s 2ms
kmermatcher /tmp/tmp_mmseqs_mgnify_19479/4897503383074789744/clu_tmp/14454371353291572119/linclust/13274294363082975222/input_rep /tmp/tmp_mmseqs_mgnify_19479/4897503383074789744/clu_tmp/14454371353291572119/linclust/13274294363082975222/pref_rep --sub-mat 'aa:blosum62.out,nucl:nucleotide.out' --alph-size aa:13,nucl:5 --min-seq-id 0.7 --kmer-per-seq 100 --spaced-kmer-mode 1 --kmer-per-seq-scale aa:0.100,nucl:0.100 --adjust-kmer-len 0 --mask 0 --mask-prob 0.9 --mask-lower-case 0 --mask-n-repeat 0 --cov-mode 1 -k 0 -c 0.8 --max-seq-len 65535 --hash-shift 67 --split-memory-limit 200G --include-only-extendable 0 --ignore-multi-kmer 0 --threads 32 --compressed 0 -v 3 --cluster-weight-threshold 0.9 --include-count-table 0 --num-count-table 2 --include-adjacency 1 --num-adjacency 3 --use-parallelism 0 --need-write-buffer 0 --linclust-version 2
kmermatcher /tmp/tmp_mmseqs_mgnify_19479/4897503383074789744/clu_tmp/14454371353291572119/linclust/13274294363082975222/input_rep /tmp/tmp_mmseqs_mgnify_19479/4897503383074789744/clu_tmp/14454371353291572119/linclust/13274294363082975222/pref_rep --sub-mat 'aa:blosum62.out,nucl:nucleotide.out' --alph-size aa:13,nucl:5 --min-seq-id 0.7 --kmer-per-seq 100 --spaced-kmer-mode 1 --kmer-per-seq-scale aa:0.100,nucl:0.100 --adjust-kmer-len 0 --mask 0 --mask-prob 0.9 --mask-lower-case 0 --mask-n-repeat 0 --cov-mode 1 -k 0 -c 0.8 --max-seq-len 65535 --hash-shift 67 --split-memory-limit 200G --include-only-extendable 0 --ignore-multi-kmer 0 --threads 32 --compressed 0 -v 3 --cluster-weight-threshold 0.9 --include-count-table 0 --num-count-table 2 --include-adjacency 1 --num-adjacency 3 --use-parallelism 0 --need-write-buffer 0 --linclust-version 2
Database size: 10 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
[=================================================================] 10 0s 170ms
Sort kmer 0h 0m 0s 0ms
Assign group Mode: Longest center: Time for assign: 0h 0m 0s 0ms
Sort by rep. sequence 0h 0m 0s 0ms
Time for write: 0h 0m 0s 0ms
Assign group Mode: Adjacent sequence: Time for assign: 0h 0m 0s 0ms
Sort by rep. sequence 0h 0m 0s 0ms
Time for write: 0h 0m 0s 0ms
Assign group Mode: Adjacent sequence: Time for assign: 0h 0m 0s 0ms
Sort by rep. sequence 0h 0m 0s 0ms
Time for write: 0h 0m 0s 0ms
Assign group Mode: Adjacent sequence: Time for assign: 0h 0m 0s 0ms
Sort by rep. sequence 0h 0m 0s 0ms
Time for write: 0h 0m 0s 0ms
Merge splits ... Time for fill: 0h 0m 0s 0ms
Time for merging to pref_rep: 0h 0m 0s 0ms
Time for processing: 0h 0m 0s 209ms
align2clust /tmp/tmp_mmseqs_mgnify_19479/4897503383074789744/clu_tmp/14454371353291572119/linclust/13274294363082975222/input_rep /tmp/tmp_mmseqs_mgnify_19479/4897503383074789744/clu_tmp/14454371353291572119/linclust/13274294363082975222/pref_rep /tmp/tmp_mmseqs_mgnify_19479/4897503383074789744/clu_tmp/14454371353291572119/linclust/13274294363082975222/clu_rep --sub-mat 'aa:blosum62.out,nucl:nucleotide.out' -a 0 --alignment-mode 3 --min-seq-id 0.7 --min-aln-len 0 --seq-id-mode 0 --filter-hits 0 -e 0.001 -c 0.8 --cov-mode 1 --add-self-matches 0 --sort-results 0 --db-load-mode 0 --threads 32 --compressed 0 -v 3 --cluster-mode 2 --filter-cludb-file /tmp/tmp_mmseqs_mgnify_19479/4897503383074789744/clu_tmp/14454371353291572119/linclust/13274294363082975222/clu --filter-seqdb-file /tmp/tmp_mmseqs_mgnify_19479/4897503383074789744/input
Score per column threshold for filtering: 1.000000
Using GREEDY clustering mode
[======================] 10 0s 42ms
===========================================Size of the alignment database: 10
Number of clusters: 10
Time for run Align2Clust: 0h 0m 0s 142ms sec
Time for merging to clu_rep: 0h 0m 0s 0ms
Time for processing: 0h 0m 0s 143ms
mergeclusters /tmp/tmp_mmseqs_mgnify_19479/4897503383074789744/input /tmp/tmp_mmseqs_mgnify_19479/4897503383074789744/clu_tmp/14454371353291572119/clu_redundancy /tmp/tmp_mmseqs_mgnify_19479/4897503383074789744/clu_tmp/14454371353291572119/linclust/13274294363082975222/clu /tmp/tmp_mmseqs_mgnify_19479/4897503383074789744/clu_tmp/14454371353291572119/linclust/13274294363082975222/clu_rep --threads 32 --compressed 0 -v 3
Clustering step 1
[=================================================================] 10 0s 149ms
Clustering step 2
[=================================================================] 10 0s 274ms
Write merged clustering
[=================================================================] 10 0s 450ms
Time for merging to clu_redundancy: 0h 0m 0s 0ms
Time for processing: 0h 0m 0s 458ms
rmdb /tmp/tmp_mmseqs_mgnify_19479/4897503383074789744/clu_tmp/14454371353291572119/linclust/13274294363082975222/pref -v 3
Time for processing: 0h 0m 0s 1ms
createsubdb /tmp/tmp_mmseqs_mgnify_19479/4897503383074789744/clu_tmp/14454371353291572119/clu_redundancy /tmp/tmp_mmseqs_mgnify_19479/4897503383074789744/input /tmp/tmp_mmseqs_mgnify_19479/4897503383074789744/clu_tmp/14454371353291572119/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 1ms
prefilter /tmp/tmp_mmseqs_mgnify_19479/4897503383074789744/clu_tmp/14454371353291572119/input_step_redundancy /tmp/tmp_mmseqs_mgnify_19479/4897503383074789744/clu_tmp/14454371353291572119/input_step_redundancy /tmp/tmp_mmseqs_mgnify_19479/4897503383074789744/clu_tmp/14454371353291572119/pref_step0 --sub-mat 'aa:blosum62.out,nucl:nucleotide.out' --seed-sub-mat 'aa:VTML80.out,nucl:nucleotide.out' -s 1 -k 0 --target-search-mode 0 --k-score seq:2147483647,prof:2147483647 --alph-size aa:21,nucl:5 --max-seq-len 65535 --max-seqs 20 --split 0 --split-mode 2 --split-memory-limit 200G -c 0.8 --cov-mode 1 --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 --mask-n-repeat 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 32 --compressed 0 -v 3
Query database size: 10 type: Aminoacid
Estimated memory consumption: 977M
Target database size: 10 type: Aminoacid
Index table k-mer threshold: 154 at k-mer size 6
Index table: counting k-mers
[=================================================================] 10 0s 163ms
Index table: Masked residues: 0
Index table: fill
[=================================================================] 10 0s 139ms
Index statistics
Entries: 889
DB size: 488 MB
Avg k-mer size: 0.000014
Top 10 k-mers
SWIDAA 1
RSWDAA 1
KPVSCA 1
RYDVDA 1
DNDGEA 1
MAMREA 1
ECGTEA 1
PMRTEA 1
KHYYEA 1
DNIDFA 1
Time for index table init: 0h 0m 0s 734ms
Process prefiltering step 1 of 1
k-mer similarity threshold: 154
Starting prefiltering scores calculation (step 1 of 1)
Query db start 1 to 10
Target db start 1 to 10
[==========================================================] 10 0s 122ms
1.939122 k-mers per position
88 DB matches per sequence
0 overflows
1 sequences passed prefiltering per query sequence
1 median result list length
0 sequences with 0 size result lists
Time for merging to pref_step0: 0h 0m 0s 0ms
Time for processing: 0h 0m 1s 20ms
align /tmp/tmp_mmseqs_mgnify_19479/4897503383074789744/clu_tmp/14454371353291572119/input_step_redundancy /tmp/tmp_mmseqs_mgnify_19479/4897503383074789744/clu_tmp/14454371353291572119/input_step_redundancy /tmp/tmp_mmseqs_mgnify_19479/4897503383074789744/clu_tmp/14454371353291572119/pref_step0 /tmp/tmp_mmseqs_mgnify_19479/4897503383074789744/clu_tmp/14454371353291572119/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 0.7 --min-aln-len 0 --seq-id-mode 0 --alt-ali 0 -c 0.8 --cov-mode 1 --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 32 --compressed 0 -v 3
Compute score, coverage and sequence identity
Query database size: 10 type: Aminoacid
Target database size: 10 type: Aminoacid
Calculation of alignments
[=================================================================] 10 0s 123ms
Time for merging to aln_step0: 0h 0m 0s 0ms
10 alignments calculated
10 sequence pairs passed the thresholds (1.000000 of overall calculated)
1.000000 hits per query sequence
Time for processing: 0h 0m 0s 128ms
clust /tmp/tmp_mmseqs_mgnify_19479/4897503383074789744/clu_tmp/14454371353291572119/input_step_redundancy /tmp/tmp_mmseqs_mgnify_19479/4897503383074789744/clu_tmp/14454371353291572119/aln_step0 /tmp/tmp_mmseqs_mgnify_19479/4897503383074789744/clu_tmp/14454371353291572119/clu_step0 --cluster-mode 2 --max-iterations 1000 --similarity-type 2 --threads 32 --compressed 0 -v 3 --cluster-weight-threshold 0.9 --set-mode 0
Clustering mode: Greedy
Total time: 0h 0m 0s 2ms
Size of the sequence database: 10
Size of the alignment database: 10
Number of clusters: 10
Writing results 0h 0m 0s 0ms
Time for merging to clu_step0: 0h 0m 0s 0ms
Time for processing: 0h 0m 0s 5ms
mergeclusters /tmp/tmp_mmseqs_mgnify_19479/4897503383074789744/input /tmp/tmp_mmseqs_mgnify_19479/4897503383074789744/clu /tmp/tmp_mmseqs_mgnify_19479/4897503383074789744/clu_tmp/14454371353291572119/clu_redundancy /tmp/tmp_mmseqs_mgnify_19479/4897503383074789744/clu_tmp/14454371353291572119/clu_step0 --threads 32 --compressed 0 -v 3
Clustering step 1
[=================================================================] 10 0s 116ms
Clustering step 2
[=================================================================] 10 0s 267ms
Write merged clustering
[=================================================================] 10 0s 405ms
Time for merging to clu: 0h 0m 0s 0ms
Time for processing: 0h 0m 0s 413ms
rmdb /tmp/tmp_mmseqs_mgnify_19479/4897503383074789744/clu_tmp/14454371353291572119/clu_redundancy -v 3
Time for processing: 0h 0m 0s 1ms
rmdb /tmp/tmp_mmseqs_mgnify_19479/4897503383074789744/clu_tmp/14454371353291572119/input_step_redundancy -v 3
Time for processing: 0h 0m 0s 1ms
rmdb /tmp/tmp_mmseqs_mgnify_19479/4897503383074789744/clu_tmp/14454371353291572119/input_step_redundancy_h -v 3
Time for processing: 0h 0m 0s 2ms
rmdb /tmp/tmp_mmseqs_mgnify_19479/4897503383074789744/clu_tmp/14454371353291572119/pref_step0 -v 3
Time for processing: 0h 0m 0s 1ms
rmdb /tmp/tmp_mmseqs_mgnify_19479/4897503383074789744/clu_tmp/14454371353291572119/aln_step0 -v 3
Time for processing: 0h 0m 0s 1ms
rmdb /tmp/tmp_mmseqs_mgnify_19479/4897503383074789744/clu_tmp/14454371353291572119/clu_step0 -v 3
Time for processing: 0h 0m 0s 2ms
createtsv /tmp/tmp_mmseqs_mgnify_19479/4897503383074789744/input /tmp/tmp_mmseqs_mgnify_19479/4897503383074789744/input /tmp/tmp_mmseqs_mgnify_19479/4897503383074789744/clu /tmp/tmp_mmseqs_mgnify_19479/4897503383074789744/cluster.tsv --threads 32 -v 3
Time for merging to cluster.tsv: 0h 0m 0s 0ms
Time for processing: 0h 0m 0s 30ms
result2repseq /tmp/tmp_mmseqs_mgnify_19479/4897503383074789744/input /tmp/tmp_mmseqs_mgnify_19479/4897503383074789744/clu /tmp/tmp_mmseqs_mgnify_19479/4897503383074789744/clu_rep --db-load-mode 0 --compressed 0 --threads 32 -v 3
[=================================================================] 10 0s 141ms
Time for merging to clu_rep: 0h 0m 0s 0ms
Time for processing: 0h 0m 0s 168ms
result2flat /tmp/tmp_mmseqs_mgnify_19479/4897503383074789744/input /tmp/tmp_mmseqs_mgnify_19479/4897503383074789744/input /tmp/tmp_mmseqs_mgnify_19479/4897503383074789744/clu_rep /tmp/tmp_mmseqs_mgnify_19479/4897503383074789744/rep_seq.fasta --use-fasta-header -v 3
Time for processing: 0h 0m 0s 2ms
createseqfiledb /tmp/tmp_mmseqs_mgnify_19479/4897503383074789744/input /tmp/tmp_mmseqs_mgnify_19479/4897503383074789744/clu /tmp/tmp_mmseqs_mgnify_19479/4897503383074789744/clu_seqs --threads 32 -v 3
[=================================================================] 10 0s 136ms
Time for merging to clu_seqs: 0h 0m 0s 0ms
Time for processing: 0h 0m 0s 163ms
result2flat /tmp/tmp_mmseqs_mgnify_19479/4897503383074789744/input /tmp/tmp_mmseqs_mgnify_19479/4897503383074789744/input /tmp/tmp_mmseqs_mgnify_19479/4897503383074789744/clu_seqs /tmp/tmp_mmseqs_mgnify_19479/4897503383074789744/all_seqs.fasta -v 3
Time for processing: 0h 0m 0s 1ms
rmdb /tmp/tmp_mmseqs_mgnify_19479/4897503383074789744/input -v 3
Time for processing: 0h 0m 0s 1ms
rmdb /tmp/tmp_mmseqs_mgnify_19479/4897503383074789744/input_h -v 3
Time for processing: 0h 0m 0s 2ms
rmdb /tmp/tmp_mmseqs_mgnify_19479/4897503383074789744/clu_seqs -v 3
Time for processing: 0h 0m 0s 2ms
rmdb /tmp/tmp_mmseqs_mgnify_19479/4897503383074789744/clu_rep -v 3
Time for processing: 0h 0m 0s 2ms
rmdb /tmp/tmp_mmseqs_mgnify_19479/4897503383074789744/clu -v 3
Time for processing: 0h 0m 0s 1ms
============================================================
✅ Test Complete!
📄 Output FASTA file path: /home/users/moria1239/mg_no_tmp/mgnify_c70_test_rep_seq.fasta
--- FASTA FILE CONTENTS ---