createdb Plasmids_results/all_proteins.fa Plasmids_results/mmseqs/DB/sequencesDB MMseqs Version: f6c98807d589091c625db68da258d587795acbab Database type 0 Shuffle input database true Createdb mode 0 Write lookup file 1 Offset of numeric ids 0 Compressed 0 Verbosity 3 Converting sequences [=================================================================================================== 1 Mio. sequences processed =================================================================================================== 2 Mio. sequences processed =================================================================================================== 3 Mio. sequences processed =================================================================================================== 4 Mio. sequences processed =================================================================================================== 5 Mio. sequences processed =================================================================================================== 6 Mio. sequences processed =================================================================================================== 7 Mio. sequences processed =================================================================================================== 8 Mio. sequences processed =================================================================================================== 9 Mio. sequences processed =================================================================================================== 10 Mio. sequences processed =================================================================================================== 11 Mio. sequences processed =================================================================================================== 12 Mio. sequences processed =================================================================================================== 13 Mio. sequences processed ==================================================== Time for merging to sequencesDB_h: 0h 0m 2s 489ms Time for merging to sequencesDB: 0h 0m 3s 573ms Database type: Aminoacid Time for processing: 0h 0m 45s 109ms Create directory Plasmids_results/mmseqs/DB/tmp cluster Plasmids_results/mmseqs/DB/sequencesDB Plasmids_results/mmseqs/DB/clusterDB Plasmids_results/mmseqs/DB/tmp --cluster-mode 0 --cov-mode 0 --min-seq-id 0.25 -c 0.8 -s 7 MMseqs Version: f6c98807d589091c625db68da258d587795acbab Substitution matrix aa:blosum62.out,nucl:nucleotide.out Seed substitution matrix aa:VTML80.out,nucl:nucleotide.out Sensitivity 7 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 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 48 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 0.25 Min alignment length 0 Seq. id. mode 0 Alternative alignments 0 Max reject 2147483647 Max accept 2147483647 Score bias 0 Realign hits false Realign score bias -0.2 Realign max seqs 2147483647 Correlation score weight 0 Gap open cost aa:11,nucl:5 Gap extension cost aa:1,nucl:2 Zdrop 40 Rescore mode 0 Remove hits by seq. id. and coverage false Sort results 0 Cluster mode 0 Max connected component depth 1000 Similarity type 2 Weight file name Cluster Weight threshold 0.9 Single step clustering false Cascaded clustering steps 3 Cluster reassign false 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 Set cluster iterations to 3 linclust Plasmids_results/mmseqs/DB/sequencesDB Plasmids_results/mmseqs/DB/tmp/16099895145645744648/clu_redundancy Plasmids_results/mmseqs/DB/tmp/16099895145645744648/linclust --cluster-mode 0 --max-iterations 1000 --similarity-type 2 --threads 48 --compressed 0 -v 3 --cluster-weight-threshold 0.9 --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 0.25 --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 Plasmids_results/mmseqs/DB/sequencesDB Plasmids_results/mmseqs/DB/tmp/16099895145645744648/linclust/9969431476690910092/pref --sub-mat 'aa:blosum62.out,nucl:nucleotide.out' --alph-size aa:13,nucl:5 --min-seq-id 0.25 --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 48 --compressed 0 -v 3 --cluster-weight-threshold 0.9 kmermatcher Plasmids_results/mmseqs/DB/sequencesDB Plasmids_results/mmseqs/DB/tmp/16099895145645744648/linclust/9969431476690910092/pref --sub-mat 'aa:blosum62.out,nucl:nucleotide.out' --alph-size aa:13,nucl:5 --min-seq-id 0.25 --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 48 --compressed 0 -v 3 --cluster-weight-threshold 0.9 Database size: 13525330 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 [=================================================================] 13.53M 22s 289ms Sort kmer 0h 0m 1s 435ms Sort by rep. sequence 0h 0m 0s 776ms Time for fill: 0h 0m 1s 940ms Time for merging to pref: 0h 0m 0s 0ms Time for processing: 0h 0m 30s 121ms rescorediagonal Plasmids_results/mmseqs/DB/sequencesDB Plasmids_results/mmseqs/DB/sequencesDB Plasmids_results/mmseqs/DB/tmp/16099895145645744648/linclust/9969431476690910092/pref Plasmids_results/mmseqs/DB/tmp/16099895145645744648/linclust/9969431476690910092/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 48 --compressed 0 -v 3 [=================================================================] 13.53M 35s 171ms Time for merging to pref_rescore1: 0h 0m 5s 852ms Time for processing: 0h 0m 45s 549ms clust Plasmids_results/mmseqs/DB/sequencesDB Plasmids_results/mmseqs/DB/tmp/16099895145645744648/linclust/9969431476690910092/pref_rescore1 Plasmids_results/mmseqs/DB/tmp/16099895145645744648/linclust/9969431476690910092/pre_clust --cluster-mode 0 --max-iterations 1000 --similarity-type 2 --threads 48 --compressed 0 -v 3 --cluster-weight-threshold 0.9 Clustering mode: Set Cover [=================================================================] 13.53M 3s 403ms Sort entries Find missing connections Found 31581809 new connections. Reconstruct initial order [=================================================================] 13.53M 3s 398ms Add missing connections [=================================================================] 13.53M 1s 590ms Time for read in: 0h 0m 9s 969ms Total time: 0h 0m 18s 47ms Size of the sequence database: 13525330 Size of the alignment database: 13525330 Number of clusters: 2958344 Writing results 0h 0m 0s 373ms Time for merging to pre_clust: 0h 0m 0s 0ms Time for processing: 0h 0m 19s 506ms createsubdb Plasmids_results/mmseqs/DB/tmp/16099895145645744648/linclust/9969431476690910092/order_redundancy Plasmids_results/mmseqs/DB/sequencesDB Plasmids_results/mmseqs/DB/tmp/16099895145645744648/linclust/9969431476690910092/input_step_redundancy -v 3 --subdb-mode 1 Time for merging to input_step_redundancy: 0h 0m 0s 0ms Time for processing: 0h 0m 1s 247ms createsubdb Plasmids_results/mmseqs/DB/tmp/16099895145645744648/linclust/9969431476690910092/order_redundancy Plasmids_results/mmseqs/DB/tmp/16099895145645744648/linclust/9969431476690910092/pref Plasmids_results/mmseqs/DB/tmp/16099895145645744648/linclust/9969431476690910092/pref_filter1 -v 3 --subdb-mode 1 Time for merging to pref_filter1: 0h 0m 0s 1ms Time for processing: 0h 0m 3s 508ms filterdb Plasmids_results/mmseqs/DB/tmp/16099895145645744648/linclust/9969431476690910092/pref_filter1 Plasmids_results/mmseqs/DB/tmp/16099895145645744648/linclust/9969431476690910092/pref_filter2 --filter-file Plasmids_results/mmseqs/DB/tmp/16099895145645744648/linclust/9969431476690910092/order_redundancy --threads 48 --compressed 0 -v 3 Filtering using file(s) [=================================================================] 2.96M 0s 800ms Time for merging to pref_filter2: 0h 0m 1s 67ms Time for processing: 0h 0m 2s 419ms rescorediagonal Plasmids_results/mmseqs/DB/tmp/16099895145645744648/linclust/9969431476690910092/input_step_redundancy Plasmids_results/mmseqs/DB/tmp/16099895145645744648/linclust/9969431476690910092/input_step_redundancy Plasmids_results/mmseqs/DB/tmp/16099895145645744648/linclust/9969431476690910092/pref_filter2 Plasmids_results/mmseqs/DB/tmp/16099895145645744648/linclust/9969431476690910092/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 0.25 --min-aln-len 0 --seq-id-mode 0 --add-self-matches 0 --sort-results 0 --db-load-mode 0 --threads 48 --compressed 0 -v 3 Can not find any score per column for coverage 0.800000 and sequence identity 0.250000. No hit will be filtered. [=================================================================] 2.96M 3s 983ms Time for merging to pref_rescore2: 0h 0m 1s 223ms Time for processing: 0h 0m 6s 943ms align Plasmids_results/mmseqs/DB/tmp/16099895145645744648/linclust/9969431476690910092/input_step_redundancy Plasmids_results/mmseqs/DB/tmp/16099895145645744648/linclust/9969431476690910092/input_step_redundancy Plasmids_results/mmseqs/DB/tmp/16099895145645744648/linclust/9969431476690910092/pref_rescore2 Plasmids_results/mmseqs/DB/tmp/16099895145645744648/linclust/9969431476690910092/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 0.25 --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 48 --compressed 0 -v 3 Compute score, coverage and sequence identity Query database size: 2958344 type: Aminoacid Target database size: 2958344 type: Aminoacid Calculation of alignments [=================================================================] 2.96M 15s 835ms Time for merging to aln: 0h 0m 1s 15ms 4760469 alignments calculated 3783632 sequence pairs passed the thresholds (0.794802 of overall calculated) 1.278970 hits per query sequence Time for processing: 0h 0m 19s 34ms clust Plasmids_results/mmseqs/DB/tmp/16099895145645744648/linclust/9969431476690910092/input_step_redundancy Plasmids_results/mmseqs/DB/tmp/16099895145645744648/linclust/9969431476690910092/aln Plasmids_results/mmseqs/DB/tmp/16099895145645744648/linclust/9969431476690910092/clust --cluster-mode 0 --max-iterations 1000 --similarity-type 2 --threads 48 --compressed 0 -v 3 --cluster-weight-threshold 0.9 Clustering mode: Set Cover [=================================================================] 2.96M 0s 335ms Sort entries Find missing connections Found 825288 new connections. Reconstruct initial order [=================================================================] 2.96M 0s 357ms Add missing connections [=================================================================] 2.96M 0s 99ms Time for read in: 0h 0m 1s 136ms Total time: 0h 0m 2s 697ms Size of the sequence database: 2958344 Size of the alignment database: 2958344 Number of clusters: 2486404 Writing results 0h 0m 0s 204ms Time for merging to clust: 0h 0m 0s 0ms Time for processing: 0h 0m 3s 218ms mergeclusters Plasmids_results/mmseqs/DB/sequencesDB Plasmids_results/mmseqs/DB/tmp/16099895145645744648/clu_redundancy Plasmids_results/mmseqs/DB/tmp/16099895145645744648/linclust/9969431476690910092/pre_clust Plasmids_results/mmseqs/DB/tmp/16099895145645744648/linclust/9969431476690910092/clust --threads 48 --compressed 0 -v 3 Clustering step 1 [=================================================================] 2.96M 1s 207ms Clustering step 2 [=================================================================] 2.49M 1s 716ms Write merged clustering [=================================================================] 13.53M 2s 332ms Time for merging to clu_redundancy: 0h 0m 0s 811ms Time for processing: 0h 0m 4s 214ms createsubdb Plasmids_results/mmseqs/DB/tmp/16099895145645744648/clu_redundancy Plasmids_results/mmseqs/DB/sequencesDB Plasmids_results/mmseqs/DB/tmp/16099895145645744648/input_step_redundancy -v 3 --subdb-mode 1 Time for merging to input_step_redundancy: 0h 0m 0s 0ms Time for processing: 0h 0m 1s 203ms prefilter Plasmids_results/mmseqs/DB/tmp/16099895145645744648/input_step_redundancy Plasmids_results/mmseqs/DB/tmp/16099895145645744648/input_step_redundancy Plasmids_results/mmseqs/DB/tmp/16099895145645744648/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 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 48 --compressed 0 -v 3 Query database size: 2486404 type: Aminoacid Estimated memory consumption: 10G Target database size: 2486404 type: Aminoacid Index table k-mer threshold: 154 at k-mer size 6 Index table: counting k-mers [=================================================================] 2.49M 1s 742ms Index table: Masked residues: 5834134 Index table: fill [=================================================================] 2.49M 1s 740ms Index statistics Entries: 248985318 DB size: 1912 MB Avg k-mer size: 3.890396 Top 10 k-mers GPGGTL 4430 YATHQG 2409 YTGTPK 2056 EARGGR 1809 NVHTRW 1766 LNLEHR 1280 KIGWLY 1218 GYLYSY 1175 GVVHIY 1006 KVGWLY 970 Time for index table init: 0h 0m 4s 39ms Process prefiltering step 1 of 1 k-mer similarity threshold: 154 Starting prefiltering scores calculation (step 1 of 1) Query db start 1 to 2486404 Target db start 1 to 2486404 [=================================================================] 2.49M 6s 623ms 1.778431 k-mers per position 2797 DB matches per sequence 0 overflows 13 sequences passed prefiltering per query sequence 15 median result list length 0 sequences with 0 size result lists Time for merging to pref_step0: 0h 0m 1s 158ms Time for processing: 0h 0m 15s 332ms align Plasmids_results/mmseqs/DB/tmp/16099895145645744648/input_step_redundancy Plasmids_results/mmseqs/DB/tmp/16099895145645744648/input_step_redundancy Plasmids_results/mmseqs/DB/tmp/16099895145645744648/pref_step0 Plasmids_results/mmseqs/DB/tmp/16099895145645744648/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 0.25 --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 48 --compressed 0 -v 3 Compute score, coverage and sequence identity Query database size: 2486404 type: Aminoacid Target database size: 2486404 type: Aminoacid Calculation of alignments [=================================================================] 2.49M 43s 753ms Time for merging to aln_step0: 0h 0m 0s 866ms 13642420 alignments calculated 8622055 sequence pairs passed the thresholds (0.632003 of overall calculated) 3.467681 hits per query sequence Time for processing: 0h 0m 46s 354ms clust Plasmids_results/mmseqs/DB/tmp/16099895145645744648/input_step_redundancy Plasmids_results/mmseqs/DB/tmp/16099895145645744648/aln_step0 Plasmids_results/mmseqs/DB/tmp/16099895145645744648/clu_step0 --cluster-mode 0 --max-iterations 1000 --similarity-type 2 --threads 48 --compressed 0 -v 3 --cluster-weight-threshold 0.9 Clustering mode: Set Cover [=================================================================] 2.49M 0s 312ms Sort entries Find missing connections Found 1499829 new connections. Reconstruct initial order [=================================================================] 2.49M 0s 331ms Add missing connections [=================================================================] 2.49M 0s 284ms Time for read in: 0h 0m 1s 234ms Total time: 0h 0m 4s 96ms Size of the sequence database: 2486404 Size of the alignment database: 2486404 Number of clusters: 1661374 Writing results 0h 0m 0s 144ms Time for merging to clu_step0: 0h 0m 0s 0ms Time for processing: 0h 0m 4s 518ms createsubdb Plasmids_results/mmseqs/DB/tmp/16099895145645744648/clu_step0 Plasmids_results/mmseqs/DB/tmp/16099895145645744648/input_step_redundancy Plasmids_results/mmseqs/DB/tmp/16099895145645744648/input_step1 -v 3 --subdb-mode 1 Time for merging to input_step1: 0h 0m 0s 0ms Time for processing: 0h 0m 0s 410ms prefilter Plasmids_results/mmseqs/DB/tmp/16099895145645744648/input_step1 Plasmids_results/mmseqs/DB/tmp/16099895145645744648/input_step1 Plasmids_results/mmseqs/DB/tmp/16099895145645744648/pref_step1 --sub-mat 'aa:blosum62.out,nucl:nucleotide.out' --seed-sub-mat 'aa:VTML80.out,nucl:nucleotide.out' -s 4 -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 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 48 --compressed 0 -v 3 Query database size: 1661374 type: Aminoacid Estimated memory consumption: 6G Target database size: 1661374 type: Aminoacid Index table k-mer threshold: 127 at k-mer size 6 Index table: counting k-mers [=================================================================] 1.66M 1s 453ms Index table: Masked residues: 3805230 Index table: fill [=================================================================] 1.66M 1s 947ms Index statistics Entries: 300219854 DB size: 2206 MB Avg k-mer size: 4.690935 Top 10 k-mers AAAAAG 1357 GPGGTL 1233 AAAAGA 1058 AAALAG 992 AAAAAR 975 AALAAG 875 DDGGSL 846 AAAALG 808 GEGGVV 806 AAAAAP 789 Time for index table init: 0h 0m 4s 18ms Process prefiltering step 1 of 1 k-mer similarity threshold: 127 Starting prefiltering scores calculation (step 1 of 1) Query db start 1 to 1661374 Target db start 1 to 1661374 [=================================================================] 1.66M 1m 22s 927ms 53.744219 k-mers per position 43024 DB matches per sequence 10 overflows 19 sequences passed prefiltering per query sequence 20 median result list length 0 sequences with 0 size result lists Time for merging to pref_step1: 0h 0m 0s 636ms Time for processing: 0h 1m 28s 234ms align Plasmids_results/mmseqs/DB/tmp/16099895145645744648/input_step1 Plasmids_results/mmseqs/DB/tmp/16099895145645744648/input_step1 Plasmids_results/mmseqs/DB/tmp/16099895145645744648/pref_step1 Plasmids_results/mmseqs/DB/tmp/16099895145645744648/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 0.25 --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 48 --compressed 0 -v 3 Compute score, coverage and sequence identity Query database size: 1661374 type: Aminoacid Target database size: 1661374 type: Aminoacid Calculation of alignments [=================================================================] 1.66M 9s 292ms Time for merging to aln_step1: 0h 0m 0s 554ms 8410846 alignments calculated 2754449 sequence pairs passed the thresholds (0.327488 of overall calculated) 1.657934 hits per query sequence Time for processing: 0h 0m 11s 610ms clust Plasmids_results/mmseqs/DB/tmp/16099895145645744648/input_step1 Plasmids_results/mmseqs/DB/tmp/16099895145645744648/aln_step1 Plasmids_results/mmseqs/DB/tmp/16099895145645744648/clu_step1 --cluster-mode 0 --max-iterations 1000 --similarity-type 2 --threads 48 --compressed 0 -v 3 --cluster-weight-threshold 0.9 Clustering mode: Set Cover [=================================================================] 1.66M 0s 120ms Sort entries Find missing connections Found 305999 new connections. Reconstruct initial order [=================================================================] 1.66M 0s 114ms Add missing connections [=================================================================] 1.66M 0s 73ms Time for read in: 0h 0m 0s 492ms Total time: 0h 0m 1s 422ms Size of the sequence database: 1661374 Size of the alignment database: 1661374 Number of clusters: 1371892 Writing results 0h 0m 0s 112ms Time for merging to clu_step1: 0h 0m 0s 0ms Time for processing: 0h 0m 1s 779ms createsubdb Plasmids_results/mmseqs/DB/tmp/16099895145645744648/clu_step1 Plasmids_results/mmseqs/DB/tmp/16099895145645744648/input_step1 Plasmids_results/mmseqs/DB/tmp/16099895145645744648/input_step2 -v 3 --subdb-mode 1 Time for merging to input_step2: 0h 0m 0s 0ms Time for processing: 0h 0m 0s 307ms prefilter Plasmids_results/mmseqs/DB/tmp/16099895145645744648/input_step2 Plasmids_results/mmseqs/DB/tmp/16099895145645744648/input_step2 Plasmids_results/mmseqs/DB/tmp/16099895145645744648/pref_step2 --sub-mat 'aa:blosum62.out,nucl:nucleotide.out' --seed-sub-mat 'aa:VTML80.out,nucl:nucleotide.out' -s 7 -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 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 48 --compressed 0 -v 3 Query database size: 1371892 type: Aminoacid Estimated memory consumption: 5G Target database size: 1371892 type: Aminoacid Index table k-mer threshold: 100 at k-mer size 6 Index table: counting k-mers [=================================================================] 1.37M 1s 136ms Index table: Masked residues: 3268690 Index table: fill [=================================================================] 1.37M 1s 545ms Index statistics Entries: 233135766 DB size: 1822 MB Avg k-mer size: 3.642746 Top 10 k-mers AAAAAA 1771 AALAAA 1301 AAAALA 1137 AAAAAL 1005 AAVAAA 861 AALALA 826 AAAAAV 787 AAALAL 768 AALAAL 730 AAAAVA 707 Time for index table init: 0h 0m 3s 211ms Process prefiltering step 1 of 1 k-mer similarity threshold: 100 Starting prefiltering scores calculation (step 1 of 1) Query db start 1 to 1371892 Target db start 1 to 1371892 [=================================================================] 1.37M 16m 12s 279ms 937.032166 k-mers per position 662240 DB matches per sequence 30648 overflows 19 sequences passed prefiltering per query sequence 20 median result list length 0 sequences with 0 size result lists Time for merging to pref_step2: 0h 0m 0s 425ms Time for processing: 0h 16m 16s 584ms align Plasmids_results/mmseqs/DB/tmp/16099895145645744648/input_step2 Plasmids_results/mmseqs/DB/tmp/16099895145645744648/input_step2 Plasmids_results/mmseqs/DB/tmp/16099895145645744648/pref_step2 Plasmids_results/mmseqs/DB/tmp/16099895145645744648/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 0.25 --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 48 --compressed 0 -v 3 Compute score, coverage and sequence identity Query database size: 1371892 type: Aminoacid Target database size: 1371892 type: Aminoacid Calculation of alignments [=================================================================] 1.37M 4s 328ms Time for merging to aln_step2: 0h 0m 0s 622ms 6037879 alignments calculated 1544585 sequence pairs passed the thresholds (0.255816 of overall calculated) 1.125879 hits per query sequence Time for processing: 0h 0m 6s 617ms clust Plasmids_results/mmseqs/DB/tmp/16099895145645744648/input_step2 Plasmids_results/mmseqs/DB/tmp/16099895145645744648/aln_step2 Plasmids_results/mmseqs/DB/tmp/16099895145645744648/clu_step2 --cluster-mode 0 --max-iterations 1000 --similarity-type 2 --threads 48 --compressed 0 -v 3 --cluster-weight-threshold 0.9 Clustering mode: Set Cover [=================================================================] 1.37M 0s 72ms Sort entries Find missing connections Found 58991 new connections. Reconstruct initial order [=================================================================] 1.37M 0s 73ms Add missing connections [=================================================================] 1.37M 0s 33ms Time for read in: 0h 0m 0s 315ms Total time: 0h 0m 0s 859ms Size of the sequence database: 1371892 Size of the alignment database: 1371892 Number of clusters: 1287337 Writing results 0h 0m 0s 100ms Time for merging to clu_step2: 0h 0m 0s 0ms Time for processing: 0h 0m 1s 173ms mergeclusters Plasmids_results/mmseqs/DB/sequencesDB Plasmids_results/mmseqs/DB/clusterDB Plasmids_results/mmseqs/DB/tmp/16099895145645744648/clu_redundancy Plasmids_results/mmseqs/DB/tmp/16099895145645744648/clu_step0 Plasmids_results/mmseqs/DB/tmp/16099895145645744648/clu_step1 Plasmids_results/mmseqs/DB/tmp/16099895145645744648/clu_step2 --threads 48 --compressed 0 -v 3 Clustering step 1 [=================================================================] 2.49M 1s 195ms Clustering step 2 [=================================================================] 1.66M 1s 591ms Clustering step 3 [=================================================================] 1.37M 1s 890ms Clustering step 4 [=================================================================] 1.29M 2s 162ms Write merged clustering [=================================================================] 13.53M 2s 860ms Time for merging to clusterDB: 0h 0m 0s 454ms Time for processing: 0h 0m 4s 934ms createtsv Plasmids_results/mmseqs/DB/sequencesDB Plasmids_results/mmseqs/DB/sequencesDB Plasmids_results/mmseqs/DB/clusterDB Plasmids_results/mmseqs/mmseqs_clustering.tsv MMseqs Version: f6c98807d589091c625db68da258d587795acbab First sequence as representative false Target column 1 Add full header false Sequence source 0 Database output false Threads 48 Compressed 0 Verbosity 3 Time for merging to mmseqs_clustering.tsv: 0h 0m 1s 526ms Time for processing: 0h 0m 3s 476ms