createdb Phages_results/all_proteins.fa Phages_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 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sequences processed =================================================================================================== 14 Mio. sequences processed =================================================================================================== 15 Mio. sequences processed =================================================================================================== 16 Mio. sequences processed =================================================================================================== 17 Mio. sequences processed =================================================================================================== 18 Mio. sequences processed =================================================================================================== 19 Mio. sequences processed =================================================================================================== 20 Mio. sequences processed =================================================================================================== 21 Mio. sequences processed =================================================================================================== 22 Mio. sequences processed =================================================================================================== 23 Mio. sequences processed =================================================================================================== 24 Mio. sequences processed =================================================================================================== 25 Mio. sequences processed =================================================================================================== 26 Mio. sequences processed =================================================================================================== 27 Mio. sequences processed =================================================================================================== 28 Mio. sequences processed =================================================================================================== 29 Mio. sequences processed =================================================================================================== 30 Mio. sequences processed =================================================================================================== 31 Mio. sequences processed =================================================================================================== 32 Mio. sequences processed =================================================================================================== 33 Mio. sequences processed =================================================================================================== 34 Mio. sequences processed =================================================================================================== 35 Mio. sequences processed =================================================================================================== 36 Mio. sequences processed =================================================================================================== 37 Mio. sequences processed =================================================================================================== 38 Mio. sequences processed =================================================================================================== 39 Mio. sequences processed =================================================================================================== 40 Mio. sequences processed =================================================================================================== 41 Mio. sequences processed =================================================================================================== 42 Mio. sequences processed =============================== Time for merging to sequencesDB_h: 0h 0m 6s 269ms Time for merging to sequencesDB: 0h 0m 9s 919ms Database type: Aminoacid Time for processing: 0h 2m 6s 893ms Create directory Phages_results/mmseqs/DB/tmp cluster Phages_results/mmseqs/DB/sequencesDB Phages_results/mmseqs/DB/clusterDB Phages_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 Phages_results/mmseqs/DB/sequencesDB Phages_results/mmseqs/DB/tmp/15150394144126936494/clu_redundancy Phages_results/mmseqs/DB/tmp/15150394144126936494/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 Phages_results/mmseqs/DB/sequencesDB Phages_results/mmseqs/DB/tmp/15150394144126936494/linclust/5326339828544264126/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 Phages_results/mmseqs/DB/sequencesDB Phages_results/mmseqs/DB/tmp/15150394144126936494/linclust/5326339828544264126/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: 42312854 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 [=================================================================] 42.31M 51s 588ms Sort kmer 0h 0m 4s 767ms Sort by rep. sequence 0h 0m 2s 257ms Time for fill: 0h 0m 5s 615ms Time for merging to pref: 0h 0m 0s 0ms Time for processing: 0h 1m 15s 190ms rescorediagonal Phages_results/mmseqs/DB/sequencesDB Phages_results/mmseqs/DB/sequencesDB Phages_results/mmseqs/DB/tmp/15150394144126936494/linclust/5326339828544264126/pref Phages_results/mmseqs/DB/tmp/15150394144126936494/linclust/5326339828544264126/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 [=================================================================] 42.31M 1m 25s 160ms Time for merging to pref_rescore1: 0h 0m 15s 441ms Time for processing: 0h 1m 51s 535ms clust Phages_results/mmseqs/DB/sequencesDB Phages_results/mmseqs/DB/tmp/15150394144126936494/linclust/5326339828544264126/pref_rescore1 Phages_results/mmseqs/DB/tmp/15150394144126936494/linclust/5326339828544264126/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 [=================================================================] 42.31M 21s 28ms Sort entries Find missing connections Found 116071767 new connections. Reconstruct initial order [=================================================================] 42.31M 20s 631ms Add missing connections [=================================================================] 42.31M 6s 418ms Time for read in: 0h 0m 53s 961ms Total time: 0h 1m 12s 281ms Size of the sequence database: 42312854 Size of the alignment database: 42312854 Number of clusters: 5266308 Writing results 0h 0m 0s 896ms Time for merging to pre_clust: 0h 0m 0s 0ms Time for processing: 0h 1m 16s 507ms createsubdb Phages_results/mmseqs/DB/tmp/15150394144126936494/linclust/5326339828544264126/order_redundancy Phages_results/mmseqs/DB/sequencesDB Phages_results/mmseqs/DB/tmp/15150394144126936494/linclust/5326339828544264126/input_step_redundancy -v 3 --subdb-mode 1 Time for merging to input_step_redundancy: 0h 0m 0s 0ms Time for processing: 0h 0m 3s 449ms createsubdb Phages_results/mmseqs/DB/tmp/15150394144126936494/linclust/5326339828544264126/order_redundancy Phages_results/mmseqs/DB/tmp/15150394144126936494/linclust/5326339828544264126/pref Phages_results/mmseqs/DB/tmp/15150394144126936494/linclust/5326339828544264126/pref_filter1 -v 3 --subdb-mode 1 Time for merging to pref_filter1: 0h 0m 0s 0ms Time for processing: 0h 0m 7s 505ms filterdb Phages_results/mmseqs/DB/tmp/15150394144126936494/linclust/5326339828544264126/pref_filter1 Phages_results/mmseqs/DB/tmp/15150394144126936494/linclust/5326339828544264126/pref_filter2 --filter-file Phages_results/mmseqs/DB/tmp/15150394144126936494/linclust/5326339828544264126/order_redundancy --threads 48 --compressed 0 -v 3 Filtering using file(s) [=================================================================] 5.27M 1s 741ms Time for merging to pref_filter2: 0h 0m 1s 797ms Time for processing: 0h 0m 4s 561ms rescorediagonal Phages_results/mmseqs/DB/tmp/15150394144126936494/linclust/5326339828544264126/input_step_redundancy Phages_results/mmseqs/DB/tmp/15150394144126936494/linclust/5326339828544264126/input_step_redundancy Phages_results/mmseqs/DB/tmp/15150394144126936494/linclust/5326339828544264126/pref_filter2 Phages_results/mmseqs/DB/tmp/15150394144126936494/linclust/5326339828544264126/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. [=================================================================] 5.27M 6s 884ms Time for merging to pref_rescore2: 0h 0m 1s 960ms Time for processing: 0h 0m 12s 855ms align Phages_results/mmseqs/DB/tmp/15150394144126936494/linclust/5326339828544264126/input_step_redundancy Phages_results/mmseqs/DB/tmp/15150394144126936494/linclust/5326339828544264126/input_step_redundancy Phages_results/mmseqs/DB/tmp/15150394144126936494/linclust/5326339828544264126/pref_rescore2 Phages_results/mmseqs/DB/tmp/15150394144126936494/linclust/5326339828544264126/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: 5266308 type: Aminoacid Target database size: 5266308 type: Aminoacid Calculation of alignments [=================================================================] 5.27M 51s 341ms Time for merging to aln: 0h 0m 2s 15ms 8630999 alignments calculated 6722250 sequence pairs passed the thresholds (0.778850 of overall calculated) 1.276464 hits per query sequence Time for processing: 0h 0m 57s 294ms clust Phages_results/mmseqs/DB/tmp/15150394144126936494/linclust/5326339828544264126/input_step_redundancy Phages_results/mmseqs/DB/tmp/15150394144126936494/linclust/5326339828544264126/aln Phages_results/mmseqs/DB/tmp/15150394144126936494/linclust/5326339828544264126/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 [=================================================================] 5.27M 0s 662ms Sort entries Find missing connections Found 1455942 new connections. Reconstruct initial order [=================================================================] 5.27M 0s 580ms Add missing connections [=================================================================] 5.27M 0s 198ms Time for read in: 0h 0m 1s 984ms Total time: 0h 0m 4s 55ms Size of the sequence database: 5266308 Size of the alignment database: 5266308 Number of clusters: 4431661 Writing results 0h 0m 0s 372ms Time for merging to clust: 0h 0m 0s 0ms Time for processing: 0h 0m 4s 919ms mergeclusters Phages_results/mmseqs/DB/sequencesDB Phages_results/mmseqs/DB/tmp/15150394144126936494/clu_redundancy Phages_results/mmseqs/DB/tmp/15150394144126936494/linclust/5326339828544264126/pre_clust Phages_results/mmseqs/DB/tmp/15150394144126936494/linclust/5326339828544264126/clust --threads 48 --compressed 0 -v 3 Clustering step 1 [=================================================================] 5.27M 4s 848ms Clustering step 2 [=================================================================] 4.43M 5s 762ms Write merged clustering [=================================================================] 42.31M 7s 769ms Time for merging to clu_redundancy: 0h 0m 1s 607ms Time for processing: 0h 0m 12s 947ms createsubdb Phages_results/mmseqs/DB/tmp/15150394144126936494/clu_redundancy Phages_results/mmseqs/DB/sequencesDB Phages_results/mmseqs/DB/tmp/15150394144126936494/input_step_redundancy -v 3 --subdb-mode 1 Time for merging to input_step_redundancy: 0h 0m 0s 0ms Time for processing: 0h 0m 3s 466ms prefilter Phages_results/mmseqs/DB/tmp/15150394144126936494/input_step_redundancy Phages_results/mmseqs/DB/tmp/15150394144126936494/input_step_redundancy Phages_results/mmseqs/DB/tmp/15150394144126936494/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: 4431661 type: Aminoacid Estimated memory consumption: 17G Target database size: 4431661 type: Aminoacid Index table k-mer threshold: 154 at k-mer size 6 Index table: counting k-mers [=================================================================] 4.43M 2s 836ms Index table: Masked residues: 16297543 Index table: fill [=================================================================] 4.43M 2s 817ms Index statistics Entries: 412656330 DB size: 2849 MB Avg k-mer size: 6.447755 Top 10 k-mers ECRQPD 2290 KGNDCR 2130 GNGGSP 1935 CEPDSY 1747 LDFGTT 1607 LTPFRG 1599 IGTHGK 1598 FSYPSR 1591 FIRIIW 1583 IQGEWS 1576 Time for index table init: 0h 0m 6s 518ms Process prefiltering step 1 of 1 k-mer similarity threshold: 154 Starting prefiltering scores calculation (step 1 of 1) Query db start 1 to 4431661 Target db start 1 to 4431661 [=================================================================] 4.43M 11s 624ms 1.985019 k-mers per position 3635 DB matches per sequence 0 overflows 15 sequences passed prefiltering per query sequence 19 median result list length 0 sequences with 0 size result lists Time for merging to pref_step0: 0h 0m 1s 552ms Time for processing: 0h 0m 26s 503ms align Phages_results/mmseqs/DB/tmp/15150394144126936494/input_step_redundancy Phages_results/mmseqs/DB/tmp/15150394144126936494/input_step_redundancy Phages_results/mmseqs/DB/tmp/15150394144126936494/pref_step0 Phages_results/mmseqs/DB/tmp/15150394144126936494/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: 4431661 type: Aminoacid Target database size: 4431661 type: Aminoacid Calculation of alignments [=================================================================] 4.43M 1m 39s 228ms Time for merging to aln_step0: 0h 0m 1s 611ms 25233732 alignments calculated 14453559 sequence pairs passed the thresholds (0.572787 of overall calculated) 3.261431 hits per query sequence Time for processing: 0h 1m 44s 733ms clust Phages_results/mmseqs/DB/tmp/15150394144126936494/input_step_redundancy Phages_results/mmseqs/DB/tmp/15150394144126936494/aln_step0 Phages_results/mmseqs/DB/tmp/15150394144126936494/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 [=================================================================] 4.43M 0s 861ms Sort entries Find missing connections Found 2542144 new connections. Reconstruct initial order [=================================================================] 4.43M 0s 758ms Add missing connections [=================================================================] 4.43M 0s 630ms Time for read in: 0h 0m 2s 790ms Total time: 0h 0m 7s 659ms Size of the sequence database: 4431661 Size of the alignment database: 4431661 Number of clusters: 2959117 Writing results 0h 0m 0s 277ms Time for merging to clu_step0: 0h 0m 0s 0ms Time for processing: 0h 0m 8s 380ms createsubdb Phages_results/mmseqs/DB/tmp/15150394144126936494/clu_step0 Phages_results/mmseqs/DB/tmp/15150394144126936494/input_step_redundancy Phages_results/mmseqs/DB/tmp/15150394144126936494/input_step1 -v 3 --subdb-mode 1 Time for merging to input_step1: 0h 0m 0s 0ms Time for processing: 0h 0m 0s 721ms prefilter Phages_results/mmseqs/DB/tmp/15150394144126936494/input_step1 Phages_results/mmseqs/DB/tmp/15150394144126936494/input_step1 Phages_results/mmseqs/DB/tmp/15150394144126936494/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: 2959117 type: Aminoacid Estimated memory consumption: 11G Target database size: 2959117 type: Aminoacid Index table k-mer threshold: 127 at k-mer size 6 Index table: counting k-mers [=================================================================] 2.96M 2s 228ms Index table: Masked residues: 9190830 Index table: fill [=================================================================] 2.96M 3s 171ms Index statistics Entries: 496964123 DB size: 3331 MB Avg k-mer size: 7.765064 Top 10 k-mers GNGGSP 1158 AAAAGA 902 AAAGAA 878 IGTPKL 876 NLWTEN 806 RLPERL 744 AAGAAG 667 AAAGAG 661 NHDNNN 621 LGDNTT 619 Time for index table init: 0h 0m 6s 273ms Process prefiltering step 1 of 1 k-mer similarity threshold: 127 Starting prefiltering scores calculation (step 1 of 1) Query db start 1 to 2959117 Target db start 1 to 2959117 [=================================================================] 2.96M 2m 29s 827ms 60.170219 k-mers per position 65920 DB matches per sequence 0 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 1s 100ms Time for processing: 0h 2m 38s 236ms align Phages_results/mmseqs/DB/tmp/15150394144126936494/input_step1 Phages_results/mmseqs/DB/tmp/15150394144126936494/input_step1 Phages_results/mmseqs/DB/tmp/15150394144126936494/pref_step1 Phages_results/mmseqs/DB/tmp/15150394144126936494/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: 2959117 type: Aminoacid Target database size: 2959117 type: Aminoacid Calculation of alignments [=================================================================] 2.96M 16s 288ms Time for merging to aln_step1: 0h 0m 1s 198ms 15419975 alignments calculated 4819180 sequence pairs passed the thresholds (0.312528 of overall calculated) 1.628587 hits per query sequence Time for processing: 0h 0m 21s 277ms clust Phages_results/mmseqs/DB/tmp/15150394144126936494/input_step1 Phages_results/mmseqs/DB/tmp/15150394144126936494/aln_step1 Phages_results/mmseqs/DB/tmp/15150394144126936494/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 [=================================================================] 2.96M 0s 322ms Sort entries Find missing connections Found 456933 new connections. Reconstruct initial order [=================================================================] 2.96M 0s 334ms Add missing connections [=================================================================] 2.96M 0s 169ms Time for read in: 0h 0m 1s 142ms Total time: 0h 0m 2s 849ms Size of the sequence database: 2959117 Size of the alignment database: 2959117 Number of clusters: 2408621 Writing results 0h 0m 0s 206ms Time for merging to clu_step1: 0h 0m 0s 0ms Time for processing: 0h 0m 3s 376ms createsubdb Phages_results/mmseqs/DB/tmp/15150394144126936494/clu_step1 Phages_results/mmseqs/DB/tmp/15150394144126936494/input_step1 Phages_results/mmseqs/DB/tmp/15150394144126936494/input_step2 -v 3 --subdb-mode 1 Time for merging to input_step2: 0h 0m 0s 0ms Time for processing: 0h 0m 0s 573ms prefilter Phages_results/mmseqs/DB/tmp/15150394144126936494/input_step2 Phages_results/mmseqs/DB/tmp/15150394144126936494/input_step2 Phages_results/mmseqs/DB/tmp/15150394144126936494/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: 2408621 type: Aminoacid Estimated memory consumption: 9G Target database size: 2408621 type: Aminoacid Index table k-mer threshold: 100 at k-mer size 6 Index table: counting k-mers [=================================================================] 2.41M 1s 835ms Index table: Masked residues: 7897708 Index table: fill [=================================================================] 2.41M 2s 627ms Index statistics Entries: 398076751 DB size: 2766 MB Avg k-mer size: 6.219949 Top 10 k-mers AAAAAA 1788 GNGGSP 1082 AAAAAG 915 TLEALG 899 AAAAAL 816 IGTPKL 816 RISGGI 729 AAAADA 694 AAAAVA 668 AAAAAE 644 Time for index table init: 0h 0m 5s 252ms Process prefiltering step 1 of 1 k-mer similarity threshold: 100 Starting prefiltering scores calculation (step 1 of 1) Query db start 1 to 2408621 Target db start 1 to 2408621 [=================================================================] 2.41M 31m 13s 224ms 1014.152892 k-mers per position 1111058 DB matches per sequence 65680 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 776ms Time for processing: 0h 31m 20s 482ms align Phages_results/mmseqs/DB/tmp/15150394144126936494/input_step2 Phages_results/mmseqs/DB/tmp/15150394144126936494/input_step2 Phages_results/mmseqs/DB/tmp/15150394144126936494/pref_step2 Phages_results/mmseqs/DB/tmp/15150394144126936494/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: 2408621 type: Aminoacid Target database size: 2408621 type: Aminoacid Calculation of alignments [=================================================================] 2.41M 8s 558ms Time for merging to aln_step2: 0h 0m 0s 789ms 11096065 alignments calculated 2736639 sequence pairs passed the thresholds (0.246631 of overall calculated) 1.136185 hits per query sequence Time for processing: 0h 0m 13s 103ms clust Phages_results/mmseqs/DB/tmp/15150394144126936494/input_step2 Phages_results/mmseqs/DB/tmp/15150394144126936494/aln_step2 Phages_results/mmseqs/DB/tmp/15150394144126936494/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 [=================================================================] 2.41M 0s 174ms Sort entries Find missing connections Found 96618 new connections. Reconstruct initial order [=================================================================] 2.41M 0s 173ms Add missing connections [=================================================================] 2.41M 0s 53ms Time for read in: 0h 0m 0s 630ms Total time: 0h 0m 1s 619ms Size of the sequence database: 2408621 Size of the alignment database: 2408621 Number of clusters: 2245470 Writing results 0h 0m 0s 188ms Time for merging to clu_step2: 0h 0m 0s 0ms Time for processing: 0h 0m 2s 87ms mergeclusters Phages_results/mmseqs/DB/sequencesDB Phages_results/mmseqs/DB/clusterDB Phages_results/mmseqs/DB/tmp/15150394144126936494/clu_redundancy Phages_results/mmseqs/DB/tmp/15150394144126936494/clu_step0 Phages_results/mmseqs/DB/tmp/15150394144126936494/clu_step1 Phages_results/mmseqs/DB/tmp/15150394144126936494/clu_step2 --threads 48 --compressed 0 -v 3 Clustering step 1 [=================================================================] 4.43M 4s 782ms Clustering step 2 [=================================================================] 2.96M 5s 567ms Clustering step 3 [=================================================================] 2.41M 6s 149ms Clustering step 4 [=================================================================] 2.25M 6s 625ms Write merged clustering [=================================================================] 42.31M 8s 656ms Time for merging to clusterDB: 0h 0m 0s 744ms Time for processing: 0h 0m 13s 445ms createtsv Phages_results/mmseqs/DB/sequencesDB Phages_results/mmseqs/DB/sequencesDB Phages_results/mmseqs/DB/clusterDB Phages_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 4s 10ms Time for processing: 0h 0m 10s 811ms