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April 21, 2022 15:27
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stdout.fail.txt
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| Create directory ./tmp | |
| easy-cluster fail.fasta mmseqs2_fail ./tmp --threads 24 | |
| MMseqs Version: 13.45111 | |
| Substitution matrix nucl:nucleotide.out,aa:blosum62.out | |
| Seed substitution matrix nucl:nucleotide.out,aa:VTML80.out | |
| Sensitivity 4 | |
| k-mer length 0 | |
| k-score 2147483647 | |
| Alphabet size nucl:5,aa:21 | |
| 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 | |
| Diagonal scoring true | |
| Exact k-mer matching 0 | |
| Mask residues 1 | |
| Mask lower case residues 0 | |
| Minimum diagonal score 15 | |
| Include identical seq. id. false | |
| Spaced k-mers 1 | |
| Preload mode 0 | |
| Pseudo count a 1 | |
| Pseudo count b 1.5 | |
| Spaced k-mer pattern | |
| Local temporary path | |
| Threads 24 | |
| 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 | |
| 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 | |
| Gap open cost nucl:5,aa:11 | |
| Gap extension cost nucl:2,aa:1 | |
| Zdrop 40 | |
| Rescore mode 0 | |
| Remove hits by seq. id. and coverage false | |
| Sort results 0 | |
| Cluster mode 0 | |
| Max connected component depth 1000 | |
| Similarity type 2 | |
| Single step clustering false | |
| Cascaded clustering steps 3 | |
| Cluster reassign false | |
| Remove temporary files true | |
| Force restart with latest tmp false | |
| MPI runner | |
| k-mers per sequence 21 | |
| Scale k-mers per sequence nucl:0.200,aa:0.000 | |
| Adjust k-mer length false | |
| Shift hash 67 | |
| Include only extendable false | |
| Skip repeating k-mers false | |
| Database type 0 | |
| Shuffle input database true | |
| Createdb mode 1 | |
| Write lookup file 0 | |
| Offset of numeric ids 0 | |
| createdb fail.fasta ./tmp/5849537320238823277/input --dbtype 0 --shuffle 1 --createdb-mode 1 --write-lookup 0 --id-offset 0 --compressed 0 -v 3 | |
| Shuffle database cannot be combined with --createdb-mode 0 | |
| We recompute with --shuffle 0 | |
| Converting sequences | |
| [ | |
| Time for merging to input_h: 0h 0m 0s 0ms | |
| Time for merging to input: 0h 0m 0s 0ms | |
| Database type: Aminoacid | |
| Time for processing: 0h 0m 0s 0ms | |
| Create directory ./tmp/5849537320238823277/clu_tmp | |
| cluster ./tmp/5849537320238823277/input ./tmp/5849537320238823277/clu ./tmp/5849537320238823277/clu_tmp --max-seqs 20 -c 0.8 --spaced-kmer-mode 1 --threads 24 --alignment-mode 3 -e 0.001 --remove-tmp-files 1 | |
| Set cluster sensitivity to -s 6.000000 | |
| Set cluster mode SET COVER | |
| Set cluster iterations to 3 | |
| linclust ./tmp/5849537320238823277/input ./tmp/5849537320238823277/clu_tmp/8711759104041117811/clu_redundancy ./tmp/5849537320238823277/clu_tmp/8711759104041117811/linclust --cluster-mode 0 --max-iterations 1000 --similarity-type 2 --threads 24 --compressed 0 -v 3 --sub-mat nucl:nucleotide.out,aa:blosum62.out -a 0 --alignment-mode 3 --alignment-output-mode 0 --wrapped-scoring 0 -e 0.001 --min-seq-id 0 --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 --max-rejected 2147483647 --max-accept 2147483647 --add-self-matches 0 --db-load-mode 0 --pca 1 --pcb 1.5 --score-bias 0 --realign 0 --realign-score-bias -0.2 --realign-max-seqs 2147483647 --gap-open nucl:5,aa:11 --gap-extend nucl:2,aa:1 --zdrop 40 --alph-size nucl:5,aa:13 --kmer-per-seq 21 --spaced-kmer-mode 1 --kmer-per-seq-scale nucl:0.200,aa:0.000 --adjust-kmer-len 0 --mask 0 --mask-lower-case 0 -k 0 --hash-shift 67 --split-memory-limit 0 --include-only-extendable 0 --ignore-multi-kmer 0 --rescore-mode 0 --filter-hits 0 --sort-results 0 --remove-tmp-files 1 --force-reuse 0 | |
| kmermatcher ./tmp/5849537320238823277/input ./tmp/5849537320238823277/clu_tmp/8711759104041117811/linclust/4113800845197740940/pref --sub-mat nucl:nucleotide.out,aa:blosum62.out --alph-size nucl:5,aa:13 --min-seq-id 0 --kmer-per-seq 21 --spaced-kmer-mode 1 --kmer-per-seq-scale nucl:0.200,aa:0.000 --adjust-kmer-len 0 --mask 0 --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 24 --compressed 0 -v 3 | |
| kmermatcher ./tmp/5849537320238823277/input ./tmp/5849537320238823277/clu_tmp/8711759104041117811/linclust/4113800845197740940/pref --sub-mat nucl:nucleotide.out,aa:blosum62.out --alph-size nucl:5,aa:13 --min-seq-id 0 --kmer-per-seq 21 --spaced-kmer-mode 1 --kmer-per-seq-scale nucl:0.200,aa:0.000 --adjust-kmer-len 0 --mask 0 --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 24 --compressed 0 -v 3 | |
| Database size: 2 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 | |
| [=================================================================] 2 0s 1ms | |
| Sort kmer 0h 0m 0s 0ms | |
| Sort by rep. sequence 0h 0m 0s 0ms | |
| Time for fill: 0h 0m 0s 0ms | |
| Time for merging to pref: 0h 0m 0s 0ms | |
| Time for processing: 0h 0m 0s 11ms | |
| rescorediagonal ./tmp/5849537320238823277/input ./tmp/5849537320238823277/input ./tmp/5849537320238823277/clu_tmp/8711759104041117811/linclust/4113800845197740940/pref ./tmp/5849537320238823277/clu_tmp/8711759104041117811/linclust/4113800845197740940/pref_rescore1 --sub-mat nucl:nucleotide.out,aa:blosum62.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 24 --compressed 0 -v 3 | |
| [=================================================================] 2 0s 0ms | |
| Time for merging to pref_rescore1: 0h 0m 0s 0ms | |
| Time for processing: 0h 0m 0s 2ms | |
| clust ./tmp/5849537320238823277/input ./tmp/5849537320238823277/clu_tmp/8711759104041117811/linclust/4113800845197740940/pref_rescore1 ./tmp/5849537320238823277/clu_tmp/8711759104041117811/linclust/4113800845197740940/pre_clust --cluster-mode 0 --max-iterations 1000 --similarity-type 2 --threads 24 --compressed 0 -v 3 | |
| Clustering mode: Set Cover | |
| [=================================================================] 2 0s 0ms | |
| Sort entries | |
| Find missing connections | |
| Found 1 new connections. | |
| Reconstruct initial order | |
| [=================================================================] 2 0s 0ms | |
| Add missing connections | |
| [=================================================================] 2 0s 0ms | |
| Time for read in: 0h 0m 0s 0ms | |
| Total time: 0h 0m 0s 5ms | |
| Size of the sequence database: 2 | |
| Size of the alignment database: 2 | |
| Number of clusters: 1 | |
| Writing results 0h 0m 0s 0ms | |
| Time for merging to pre_clust: 0h 0m 0s 0ms | |
| Time for processing: 0h 0m 0s 6ms | |
| createsubdb ./tmp/5849537320238823277/clu_tmp/8711759104041117811/linclust/4113800845197740940/order_redundancy ./tmp/5849537320238823277/input ./tmp/5849537320238823277/clu_tmp/8711759104041117811/linclust/4113800845197740940/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 0ms | |
| createsubdb ./tmp/5849537320238823277/clu_tmp/8711759104041117811/linclust/4113800845197740940/order_redundancy ./tmp/5849537320238823277/clu_tmp/8711759104041117811/linclust/4113800845197740940/pref ./tmp/5849537320238823277/clu_tmp/8711759104041117811/linclust/4113800845197740940/pref_filter1 -v 3 --subdb-mode 1 | |
| Time for merging to pref_filter1: 0h 0m 0s 0ms | |
| Time for processing: 0h 0m 0s 0ms | |
| filterdb ./tmp/5849537320238823277/clu_tmp/8711759104041117811/linclust/4113800845197740940/pref_filter1 ./tmp/5849537320238823277/clu_tmp/8711759104041117811/linclust/4113800845197740940/pref_filter2 --filter-file ./tmp/5849537320238823277/clu_tmp/8711759104041117811/linclust/4113800845197740940/order_redundancy --threads 24 --compressed 0 -v 3 | |
| Filtering using file(s) | |
| [=================================================================] 1 0s 0ms | |
| Time for merging to pref_filter2: 0h 0m 0s 0ms | |
| Time for processing: 0h 0m 0s 3ms | |
| rescorediagonal ./tmp/5849537320238823277/clu_tmp/8711759104041117811/linclust/4113800845197740940/input_step_redundancy ./tmp/5849537320238823277/clu_tmp/8711759104041117811/linclust/4113800845197740940/input_step_redundancy ./tmp/5849537320238823277/clu_tmp/8711759104041117811/linclust/4113800845197740940/pref_filter2 ./tmp/5849537320238823277/clu_tmp/8711759104041117811/linclust/4113800845197740940/pref_rescore2 --sub-mat nucl:nucleotide.out,aa:blosum62.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 --min-aln-len 0 --seq-id-mode 0 --add-self-matches 0 --sort-results 0 --db-load-mode 0 --threads 24 --compressed 0 -v 3 | |
| Can not find any score per column for coverage 0.800000 and sequence identity 0.000000. No hit will be filtered. | |
| [=================================================================] 1 0s 2ms | |
| Time for merging to pref_rescore2: 0h 0m 0s 0ms | |
| Time for processing: 0h 0m 0s 5ms | |
| align ./tmp/5849537320238823277/clu_tmp/8711759104041117811/linclust/4113800845197740940/input_step_redundancy ./tmp/5849537320238823277/clu_tmp/8711759104041117811/linclust/4113800845197740940/input_step_redundancy ./tmp/5849537320238823277/clu_tmp/8711759104041117811/linclust/4113800845197740940/pref_rescore2 ./tmp/5849537320238823277/clu_tmp/8711759104041117811/linclust/4113800845197740940/aln --sub-mat nucl:nucleotide.out,aa:blosum62.out -a 0 --alignment-mode 3 --alignment-output-mode 0 --wrapped-scoring 0 -e 0.001 --min-seq-id 0 --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 --max-rejected 2147483647 --max-accept 2147483647 --add-self-matches 0 --db-load-mode 0 --pca 1 --pcb 1.5 --score-bias 0 --realign 0 --realign-score-bias -0.2 --realign-max-seqs 2147483647 --gap-open nucl:5,aa:11 --gap-extend nucl:2,aa:1 --zdrop 40 --threads 24 --compressed 0 -v 3 | |
| Compute score, coverage and sequence identity | |
| Query database size: 1 type: Aminoacid | |
| Target database size: 1 type: Aminoacid | |
| Calculation of alignments | |
| [=================================================================] 1 0s 0ms | |
| Time for merging to aln: 0h 0m 0s 0ms | |
| 1 alignments calculated | |
| 1 sequence pairs passed the thresholds (1.000000 of overall calculated) | |
| 1.000000 hits per query sequence | |
| Time for processing: 0h 0m 0s 0ms | |
| clust ./tmp/5849537320238823277/clu_tmp/8711759104041117811/linclust/4113800845197740940/input_step_redundancy ./tmp/5849537320238823277/clu_tmp/8711759104041117811/linclust/4113800845197740940/aln ./tmp/5849537320238823277/clu_tmp/8711759104041117811/linclust/4113800845197740940/clust --cluster-mode 0 --max-iterations 1000 --similarity-type 2 --threads 24 --compressed 0 -v 3 | |
| Clustering mode: Set Cover | |
| [=================================================================] 1 0s 0ms | |
| Sort entries | |
| Find missing connections | |
| Found 0 new connections. | |
| Reconstruct initial order | |
| [=================================================================] 1 0s 0ms | |
| Add missing connections | |
| [=================================================================] 1 0s 0ms | |
| Time for read in: 0h 0m 0s 5ms | |
| Total time: 0h 0m 0s 19ms | |
| Size of the sequence database: 1 | |
| Size of the alignment database: 1 | |
| Number of clusters: 1 | |
| Writing results 0h 0m 0s 0ms | |
| Time for merging to clust: 0h 0m 0s 0ms | |
| Time for processing: 0h 0m 0s 20ms | |
| mergeclusters ./tmp/5849537320238823277/input ./tmp/5849537320238823277/clu_tmp/8711759104041117811/clu_redundancy ./tmp/5849537320238823277/clu_tmp/8711759104041117811/linclust/4113800845197740940/pre_clust ./tmp/5849537320238823277/clu_tmp/8711759104041117811/linclust/4113800845197740940/clust --threads 24 --compressed 0 -v 3 | |
| Clustering step 1 | |
| [=================================================================] 1 0s 0ms | |
| Clustering step 2 | |
| [=================================================================] 1 0s 1ms | |
| Write merged clustering | |
| [=================================================================] 2 0s 2ms | |
| Time for merging to clu_redundancy: 0h 0m 0s 0ms | |
| Time for processing: 0h 0m 0s 5ms | |
| rmdb ./tmp/5849537320238823277/clu_tmp/8711759104041117811/linclust/4113800845197740940/pref_filter1 -v 3 | |
| Time for processing: 0h 0m 0s 0ms | |
| rmdb ./tmp/5849537320238823277/clu_tmp/8711759104041117811/linclust/4113800845197740940/pref -v 3 | |
| Time for processing: 0h 0m 0s 0ms | |
| rmdb ./tmp/5849537320238823277/clu_tmp/8711759104041117811/linclust/4113800845197740940/pref_rescore1 -v 3 | |
| Time for processing: 0h 0m 0s 0ms | |
| rmdb ./tmp/5849537320238823277/clu_tmp/8711759104041117811/linclust/4113800845197740940/pre_clust -v 3 | |
| Time for processing: 0h 0m 0s 0ms | |
| rmdb ./tmp/5849537320238823277/clu_tmp/8711759104041117811/linclust/4113800845197740940/input_step_redundancy -v 3 | |
| Time for processing: 0h 0m 0s 0ms | |
| rmdb ./tmp/5849537320238823277/clu_tmp/8711759104041117811/linclust/4113800845197740940/input_step_redundancy_h -v 3 | |
| Time for processing: 0h 0m 0s 0ms | |
| rmdb ./tmp/5849537320238823277/clu_tmp/8711759104041117811/linclust/4113800845197740940/pref_filter2 -v 3 | |
| Time for processing: 0h 0m 0s 0ms | |
| rmdb ./tmp/5849537320238823277/clu_tmp/8711759104041117811/linclust/4113800845197740940/pref_rescore2 -v 3 | |
| Time for processing: 0h 0m 0s 0ms | |
| rmdb ./tmp/5849537320238823277/clu_tmp/8711759104041117811/linclust/4113800845197740940/aln -v 3 | |
| Time for processing: 0h 0m 0s 0ms | |
| rmdb ./tmp/5849537320238823277/clu_tmp/8711759104041117811/linclust/4113800845197740940/clust -v 3 | |
| Time for processing: 0h 0m 0s 0ms | |
| createsubdb ./tmp/5849537320238823277/clu_tmp/8711759104041117811/clu_redundancy ./tmp/5849537320238823277/input ./tmp/5849537320238823277/clu_tmp/8711759104041117811/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 0ms | |
| prefilter ./tmp/5849537320238823277/clu_tmp/8711759104041117811/input_step_redundancy ./tmp/5849537320238823277/clu_tmp/8711759104041117811/input_step_redundancy ./tmp/5849537320238823277/clu_tmp/8711759104041117811/pref_step0 --sub-mat nucl:nucleotide.out,aa:blosum62.out --seed-sub-mat nucl:nucleotide.out,aa:VTML80.out -s 1 -k 0 --k-score 2147483647 --alph-size nucl:5,aa:21 --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 --diag-score 0 --exact-kmer-matching 0 --mask 1 --mask-lower-case 0 --min-ungapped-score 0 --add-self-matches 0 --spaced-kmer-mode 1 --db-load-mode 0 --pca 1 --pcb 1.5 --threads 24 --compressed 0 -v 3 | |
| Query database size: 1 type: Aminoacid | |
| Estimated memory consumption: 977M | |
| Target database size: 1 type: Aminoacid | |
| Index table k-mer threshold: 154 at k-mer size 6 | |
| Index table: counting k-mers | |
| [=================================================================] 1 0s 0ms | |
| Index table: Masked residues: 0 | |
| Index table: fill | |
| [=================================================================] 1 0s 2ms | |
| Index statistics | |
| Entries: 113 | |
| DB size: 488 MB | |
| Avg k-mer size: 0.000002 | |
| Top 10 k-mers | |
| PWFFAA 1 | |
| YTRACA 1 | |
| LHFADA 1 | |
| YDGLDA 1 | |
| LTPMGA 1 | |
| MAGRGA 1 | |
| HIPHHA 1 | |
| PLRHLA 1 | |
| TWLTMA 1 | |
| VGDGPA 1 | |
| Time for index table init: 0h 0m 0s 269ms | |
| Process prefiltering step 1 of 1 | |
| k-mer similarity threshold: 154 | |
| Starting prefiltering scores calculation (step 1 of 1) | |
| Query db start 1 to 1 | |
| Target db start 1 to 1 | |
| [=================================================================] 1 0s 0ms | |
| 2.734982 k-mers per position | |
| 113 DB matches per sequence | |
| 0 overflows | |
| 0 queries produce too many hits (truncated result) | |
| 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 0s 425ms | |
| align ./tmp/5849537320238823277/clu_tmp/8711759104041117811/input_step_redundancy ./tmp/5849537320238823277/clu_tmp/8711759104041117811/input_step_redundancy ./tmp/5849537320238823277/clu_tmp/8711759104041117811/pref_step0 ./tmp/5849537320238823277/clu_tmp/8711759104041117811/aln_step0 --sub-mat nucl:nucleotide.out,aa:blosum62.out -a 0 --alignment-mode 3 --alignment-output-mode 0 --wrapped-scoring 0 -e 0.001 --min-seq-id 0 --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 --max-rejected 2147483647 --max-accept 2147483647 --add-self-matches 0 --db-load-mode 0 --pca 1 --pcb 1.5 --score-bias 0 --realign 0 --realign-score-bias -0.2 --realign-max-seqs 2147483647 --gap-open nucl:5,aa:11 --gap-extend nucl:2,aa:1 --zdrop 40 --threads 24 --compressed 0 -v 3 | |
| Compute score, coverage and sequence identity | |
| Query database size: 1 type: Aminoacid | |
| Target database size: 1 type: Aminoacid | |
| Calculation of alignments | |
| [=================================================================] 1 0s 0ms | |
| Time for merging to aln_step0: 0h 0m 0s 0ms | |
| 1 alignments calculated | |
| 1 sequence pairs passed the thresholds (1.000000 of overall calculated) | |
| 1.000000 hits per query sequence | |
| Time for processing: 0h 0m 0s 0ms | |
| clust ./tmp/5849537320238823277/clu_tmp/8711759104041117811/input_step_redundancy ./tmp/5849537320238823277/clu_tmp/8711759104041117811/aln_step0 ./tmp/5849537320238823277/clu_tmp/8711759104041117811/clu_step0 --cluster-mode 0 --max-iterations 1000 --similarity-type 2 --threads 24 --compressed 0 -v 3 | |
| Clustering mode: Set Cover | |
| [=================================================================] 1 0s 0ms | |
| Sort entries | |
| Find missing connections | |
| Found 0 new connections. | |
| Reconstruct initial order | |
| [=================================================================] 1 0s 0ms | |
| Add missing connections | |
| [=================================================================] 1 0s 0ms | |
| Time for read in: 0h 0m 0s 0ms | |
| Total time: 0h 0m 0s 0ms | |
| Size of the sequence database: 1 | |
| Size of the alignment database: 1 | |
| Number of clusters: 1 | |
| Writing results 0h 0m 0s 0ms | |
| Time for merging to clu_step0: 0h 0m 0s 0ms | |
| Time for processing: 0h 0m 0s 1ms | |
| createsubdb ./tmp/5849537320238823277/clu_tmp/8711759104041117811/clu_step0 ./tmp/5849537320238823277/clu_tmp/8711759104041117811/input_step_redundancy ./tmp/5849537320238823277/clu_tmp/8711759104041117811/input_step1 -v 3 --subdb-mode 1 | |
| Time for merging to input_step1: 0h 0m 0s 0ms | |
| Time for processing: 0h 0m 0s 0ms | |
| prefilter ./tmp/5849537320238823277/clu_tmp/8711759104041117811/input_step1 ./tmp/5849537320238823277/clu_tmp/8711759104041117811/input_step1 ./tmp/5849537320238823277/clu_tmp/8711759104041117811/pref_step1 --sub-mat nucl:nucleotide.out,aa:blosum62.out --seed-sub-mat nucl:nucleotide.out,aa:VTML80.out -s 3.5 -k 0 --k-score 2147483647 --alph-size nucl:5,aa:21 --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 --diag-score 1 --exact-kmer-matching 0 --mask 1 --mask-lower-case 0 --min-ungapped-score 15 --add-self-matches 0 --spaced-kmer-mode 1 --db-load-mode 0 --pca 1 --pcb 1.5 --threads 24 --compressed 0 -v 3 | |
| Query database size: 1 type: Aminoacid | |
| Estimated memory consumption: 977M | |
| Target database size: 1 type: Aminoacid | |
| Index table k-mer threshold: 131 at k-mer size 6 | |
| Index table: counting k-mers | |
| [=================================================================] 1 0s 0ms | |
| Index table: Masked residues: 0 | |
| Index table: fill | |
| [=================================================================] 1 0s 0ms | |
| Index statistics | |
| Entries: 259 | |
| DB size: 488 MB | |
| Avg k-mer size: 0.000004 | |
| Top 10 k-mers | |
| DATAAA 1 | |
| FLGDAA 1 | |
| AGLEAA 1 | |
| PWFFAA 1 | |
| ETLGAA 1 | |
| ALAPAA 1 | |
| RGGSAA 1 | |
| YTRACA 1 | |
| LHFADA 1 | |
| DGRADA 1 | |
| Time for index table init: 0h 0m 0s 278ms | |
| Process prefiltering step 1 of 1 | |
| k-mer similarity threshold: 131 | |
| Starting prefiltering scores calculation (step 1 of 1) | |
| Query db start 1 to 1 | |
| Target db start 1 to 1 | |
| [=================================================================] 1 0s 0ms | |
| 45.636042 k-mers per position | |
| 229 DB matches per sequence | |
| 0 overflows | |
| 0 queries produce too many hits (truncated result) | |
| 1 sequences passed prefiltering per query sequence | |
| 1 median result list length | |
| 0 sequences with 0 size result lists | |
| Time for merging to pref_step1: 0h 0m 0s 0ms | |
| Time for processing: 0h 0m 0s 446ms | |
| align ./tmp/5849537320238823277/clu_tmp/8711759104041117811/input_step1 ./tmp/5849537320238823277/clu_tmp/8711759104041117811/input_step1 ./tmp/5849537320238823277/clu_tmp/8711759104041117811/pref_step1 ./tmp/5849537320238823277/clu_tmp/8711759104041117811/aln_step1 --sub-mat nucl:nucleotide.out,aa:blosum62.out -a 0 --alignment-mode 3 --alignment-output-mode 0 --wrapped-scoring 0 -e 0.001 --min-seq-id 0 --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 --max-rejected 2147483647 --max-accept 2147483647 --add-self-matches 0 --db-load-mode 0 --pca 1 --pcb 1.5 --score-bias 0 --realign 0 --realign-score-bias -0.2 --realign-max-seqs 2147483647 --gap-open nucl:5,aa:11 --gap-extend nucl:2,aa:1 --zdrop 40 --threads 24 --compressed 0 -v 3 | |
| Compute score, coverage and sequence identity | |
| Query database size: 1 type: Aminoacid | |
| Target database size: 1 type: Aminoacid | |
| Calculation of alignments | |
| [=================================================================] 1 0s 0ms | |
| Time for merging to aln_step1: 0h 0m 0s 0ms | |
| 1 alignments calculated | |
| 1 sequence pairs passed the thresholds (1.000000 of overall calculated) | |
| 1.000000 hits per query sequence | |
| Time for processing: 0h 0m 0s 0ms | |
| clust ./tmp/5849537320238823277/clu_tmp/8711759104041117811/input_step1 ./tmp/5849537320238823277/clu_tmp/8711759104041117811/aln_step1 ./tmp/5849537320238823277/clu_tmp/8711759104041117811/clu_step1 --cluster-mode 0 --max-iterations 1000 --similarity-type 2 --threads 24 --compressed 0 -v 3 | |
| Clustering mode: Set Cover | |
| [=================================================================] 1 0s 0ms | |
| Sort entries | |
| Find missing connections | |
| Found 0 new connections. | |
| Reconstruct initial order | |
| [=================================================================] 1 0s 0ms | |
| Add missing connections | |
| [=================================================================] 1 0s 0ms | |
| Time for read in: 0h 0m 0s 0ms | |
| Total time: 0h 0m 0s 0ms | |
| Size of the sequence database: 1 | |
| Size of the alignment database: 1 | |
| Number of clusters: 1 | |
| Writing results 0h 0m 0s 0ms | |
| Time for merging to clu_step1: 0h 0m 0s 0ms | |
| Time for processing: 0h 0m 0s 0ms | |
| createsubdb ./tmp/5849537320238823277/clu_tmp/8711759104041117811/clu_step1 ./tmp/5849537320238823277/clu_tmp/8711759104041117811/input_step1 ./tmp/5849537320238823277/clu_tmp/8711759104041117811/input_step2 -v 3 --subdb-mode 1 | |
| Time for merging to input_step2: 0h 0m 0s 0ms | |
| Time for processing: 0h 0m 0s 0ms | |
| prefilter ./tmp/5849537320238823277/clu_tmp/8711759104041117811/input_step2 ./tmp/5849537320238823277/clu_tmp/8711759104041117811/input_step2 ./tmp/5849537320238823277/clu_tmp/8711759104041117811/pref_step2 --sub-mat nucl:nucleotide.out,aa:blosum62.out --seed-sub-mat nucl:nucleotide.out,aa:VTML80.out -s 6 -k 0 --k-score 2147483647 --alph-size nucl:5,aa:21 --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 --diag-score 1 --exact-kmer-matching 0 --mask 1 --mask-lower-case 0 --min-ungapped-score 15 --add-self-matches 0 --spaced-kmer-mode 1 --db-load-mode 0 --pca 1 --pcb 1.5 --threads 24 --compressed 0 -v 3 | |
| Query database size: 1 type: Aminoacid | |
| Estimated memory consumption: 977M | |
| Target database size: 1 type: Aminoacid | |
| Index table k-mer threshold: 109 at k-mer size 6 | |
| Index table: counting k-mers | |
| [=================================================================] 1 0s 0ms | |
| Index table: Masked residues: 0 | |
| Index table: fill | |
| [=================================================================] 1 0s 1ms | |
| Index statistics | |
| Entries: 274 | |
| DB size: 488 MB | |
| Avg k-mer size: 0.000004 | |
| Top 10 k-mers | |
| AEAAAA 1 | |
| DATAAA 1 | |
| FLGDAA 1 | |
| AGLEAA 1 | |
| PWFFAA 1 | |
| ETLGAA 1 | |
| ALAPAA 1 | |
| RGGSAA 1 | |
| YTRACA 1 | |
| LHFADA 1 | |
| Time for index table init: 0h 0m 0s 271ms | |
| Process prefiltering step 1 of 1 | |
| k-mer similarity threshold: 109 | |
| Starting prefiltering scores calculation (step 1 of 1) | |
| Query db start 1 to 1 | |
| Target db start 1 to 1 | |
| [=================================================================] 1 0s 0ms | |
| 429.399293 k-mers per position | |
| 272 DB matches per sequence | |
| 0 overflows | |
| 0 queries produce too many hits (truncated result) | |
| 1 sequences passed prefiltering per query sequence | |
| 1 median result list length | |
| 0 sequences with 0 size result lists | |
| Time for merging to pref_step2: 0h 0m 0s 0ms | |
| Time for processing: 0h 0m 0s 429ms | |
| align ./tmp/5849537320238823277/clu_tmp/8711759104041117811/input_step2 ./tmp/5849537320238823277/clu_tmp/8711759104041117811/input_step2 ./tmp/5849537320238823277/clu_tmp/8711759104041117811/pref_step2 ./tmp/5849537320238823277/clu_tmp/8711759104041117811/aln_step2 --sub-mat nucl:nucleotide.out,aa:blosum62.out -a 0 --alignment-mode 3 --alignment-output-mode 0 --wrapped-scoring 0 -e 0.001 --min-seq-id 0 --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 --max-rejected 2147483647 --max-accept 2147483647 --add-self-matches 0 --db-load-mode 0 --pca 1 --pcb 1.5 --score-bias 0 --realign 0 --realign-score-bias -0.2 --realign-max-seqs 2147483647 --gap-open nucl:5,aa:11 --gap-extend nucl:2,aa:1 --zdrop 40 --threads 24 --compressed 0 -v 3 | |
| Compute score, coverage and sequence identity | |
| Query database size: 1 type: Aminoacid | |
| Target database size: 1 type: Aminoacid | |
| Calculation of alignments | |
| [=================================================================] 1 0s 0ms | |
| Time for merging to aln_step2: 0h 0m 0s 0ms | |
| 1 alignments calculated | |
| 1 sequence pairs passed the thresholds (1.000000 of overall calculated) | |
| 1.000000 hits per query sequence | |
| Time for processing: 0h 0m 0s 0ms | |
| clust ./tmp/5849537320238823277/clu_tmp/8711759104041117811/input_step2 ./tmp/5849537320238823277/clu_tmp/8711759104041117811/aln_step2 ./tmp/5849537320238823277/clu_tmp/8711759104041117811/clu_step2 --cluster-mode 0 --max-iterations 1000 --similarity-type 2 --threads 24 --compressed 0 -v 3 | |
| Clustering mode: Set Cover | |
| [=================================================================] 1 0s 0ms | |
| Sort entries | |
| Find missing connections | |
| Found 0 new connections. | |
| Reconstruct initial order | |
| [=================================================================] 1 0s 0ms | |
| Add missing connections | |
| [=================================================================] 1 0s 0ms | |
| Time for read in: 0h 0m 0s 0ms | |
| Total time: 0h 0m 0s 0ms | |
| Size of the sequence database: 1 | |
| Size of the alignment database: 1 | |
| Number of clusters: 1 | |
| Writing results 0h 0m 0s 0ms | |
| Time for merging to clu_step2: 0h 0m 0s 0ms | |
| Time for processing: 0h 0m 0s 1ms | |
| mergeclusters ./tmp/5849537320238823277/input ./tmp/5849537320238823277/clu ./tmp/5849537320238823277/clu_tmp/8711759104041117811/clu_redundancy ./tmp/5849537320238823277/clu_tmp/8711759104041117811/clu_step0 ./tmp/5849537320238823277/clu_tmp/8711759104041117811/clu_step1 ./tmp/5849537320238823277/clu_tmp/8711759104041117811/clu_step2 --threads 24 --compressed 0 -v 3 | |
| Clustering step 1 | |
| [=================================================================] 1 0s 0ms | |
| Clustering step 2 | |
| [=================================================================] 1 0s 1ms | |
| Clustering step 3 | |
| [=================================================================] 1 0s 2ms | |
| Clustering step 4 | |
| [=================================================================] 1 0s 3ms | |
| Write merged clustering | |
| [=================================================================] 2 0s 4ms | |
| Time for merging to clu: 0h 0m 0s 0ms | |
| Time for processing: 0h 0m 0s 10ms | |
| rmdb ./tmp/5849537320238823277/clu_tmp/8711759104041117811/clu_redundancy -v 3 | |
| Time for processing: 0h 0m 0s 0ms | |
| rmdb ./tmp/5849537320238823277/clu_tmp/8711759104041117811/input_step_redundancy -v 3 | |
| Time for processing: 0h 0m 0s 0ms | |
| rmdb ./tmp/5849537320238823277/clu_tmp/8711759104041117811/input_step_redundancy_h -v 3 | |
| Time for processing: 0h 0m 0s 0ms | |
| rmdb ./tmp/5849537320238823277/clu_tmp/8711759104041117811/pref_step0 -v 3 | |
| Time for processing: 0h 0m 0s 0ms | |
| rmdb ./tmp/5849537320238823277/clu_tmp/8711759104041117811/aln_step0 -v 3 | |
| Time for processing: 0h 0m 0s 0ms | |
| rmdb ./tmp/5849537320238823277/clu_tmp/8711759104041117811/clu_step0 -v 3 | |
| Time for processing: 0h 0m 0s 0ms | |
| rmdb ./tmp/5849537320238823277/clu_tmp/8711759104041117811/pref_step1 -v 3 | |
| Time for processing: 0h 0m 0s 0ms | |
| rmdb ./tmp/5849537320238823277/clu_tmp/8711759104041117811/aln_step1 -v 3 | |
| Time for processing: 0h 0m 0s 0ms | |
| rmdb ./tmp/5849537320238823277/clu_tmp/8711759104041117811/clu_step1 -v 3 | |
| Time for processing: 0h 0m 0s 0ms | |
| rmdb ./tmp/5849537320238823277/clu_tmp/8711759104041117811/pref_step2 -v 3 | |
| Time for processing: 0h 0m 0s 0ms | |
| rmdb ./tmp/5849537320238823277/clu_tmp/8711759104041117811/aln_step2 -v 3 | |
| Time for processing: 0h 0m 0s 0ms | |
| rmdb ./tmp/5849537320238823277/clu_tmp/8711759104041117811/clu_step2 -v 3 | |
| Time for processing: 0h 0m 0s 0ms | |
| rmdb ./tmp/5849537320238823277/clu_tmp/8711759104041117811/input_step1 -v 3 | |
| Time for processing: 0h 0m 0s 0ms | |
| rmdb ./tmp/5849537320238823277/clu_tmp/8711759104041117811/input_step1_h -v 3 | |
| Time for processing: 0h 0m 0s 0ms | |
| rmdb ./tmp/5849537320238823277/clu_tmp/8711759104041117811/input_step2 -v 3 | |
| Time for processing: 0h 0m 0s 0ms | |
| rmdb ./tmp/5849537320238823277/clu_tmp/8711759104041117811/input_step2_h -v 3 | |
| Time for processing: 0h 0m 0s 0ms | |
| createtsv ./tmp/5849537320238823277/input ./tmp/5849537320238823277/input ./tmp/5849537320238823277/clu ./tmp/5849537320238823277/cluster.tsv --threads 24 -v 3 | |
| Time for merging to cluster.tsv: 0h 0m 0s 0ms | |
| Time for processing: 0h 0m 0s 6ms | |
| result2repseq ./tmp/5849537320238823277/input ./tmp/5849537320238823277/clu ./tmp/5849537320238823277/clu_rep --db-load-mode 0 --compressed 0 --threads 24 -v 3 | |
| [=================================================================] 1 0s 0ms | |
| Time for merging to clu_rep: 0h 0m 0s 0ms | |
| Time for processing: 0h 0m 0s 2ms | |
| result2flat ./tmp/5849537320238823277/input ./tmp/5849537320238823277/input ./tmp/5849537320238823277/clu_rep ./tmp/5849537320238823277/rep_seq.fasta --use-fasta-header -v 3 | |
| Time for processing: 0h 0m 0s 0ms | |
| createseqfiledb ./tmp/5849537320238823277/input ./tmp/5849537320238823277/clu ./tmp/5849537320238823277/clu_seqs --threads 24 -v 3 | |
| [=================================================================] 1 0s 0ms | |
| Time for merging to clu_seqs: 0h 0m 0s 0ms | |
| Time for processing: 0h 0m 0s 1ms | |
| result2flat ./tmp/5849537320238823277/input ./tmp/5849537320238823277/input ./tmp/5849537320238823277/clu_seqs ./tmp/5849537320238823277/all_seqs.fasta -v 3 | |
| Time for processing: 0h 0m 0s 0ms | |
| rmdb ./tmp/5849537320238823277/input -v 3 | |
| Time for processing: 0h 0m 0s 0ms | |
| rmdb ./tmp/5849537320238823277/input_h -v 3 | |
| Time for processing: 0h 0m 0s 0ms | |
| rmdb ./tmp/5849537320238823277/clu_seqs -v 3 | |
| Time for processing: 0h 0m 0s 0ms | |
| rmdb ./tmp/5849537320238823277/clu_rep -v 3 | |
| Time for processing: 0h 0m 0s 0ms | |
| rmdb ./tmp/5849537320238823277/clu -v 3 | |
| Time for processing: 0h 0m 0s 0ms |
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