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| mmseqs cluster DB cluDB tmp | |
| Program call: | |
| DB cluDB tmp | |
| MMseqs Version: 1c45613a4166130d040b52241dc66f7d687f4e54 | |
| Sub Matrix blosum62.out | |
| Sensitivity 4 | |
| K-mer size 0 | |
| K-score 2147483647 | |
| Alphabet size 21 | |
| Max. sequence length 32000 | |
| Query queryProfile false | |
| Target queryProfile false | |
| Max. results per query 300 | |
| Offset result 0 | |
| Split DB 0 | |
| Split mode 2 | |
| Coverage threshold 0.8 | |
| Compositional bias 1 | |
| Diagonal Scoring 1 | |
| Mask Residues 1 | |
| Minimum Diagonal score 15 | |
| Include identical Seq. Id. false | |
| Spaced Kmer 1 | |
| Threads 1 | |
| Verbosity 3 | |
| Add backtrace false | |
| Alignment mode 2 | |
| E-value threshold 0.001 | |
| Seq. Id Threshold 0 | |
| Target Coverage threshold 0 | |
| Realign hit false | |
| Max Reject 2147483647 | |
| Max Accept 2147483647 | |
| Cluster mode 0 | |
| Max depth connected component 1000 | |
| Similarity type 2 | |
| Cascaded clustering false | |
| Cluster fragments false | |
| Remove Temporary Files false | |
| Sets the MPI runner | |
| Rescore mode 0 | |
| Remove hits by seq.id. and coverage false | |
| In substitution scoring mode, performs global alignment along the diagonal false | |
| Set cluster settings automatic to s=6 cascaded=1 | |
| Program call: | |
| DB tmp/clu_redundancy tmp/linclust --cluster-mode 0 --max-seqs 300 -v 3 --max-iterations 1000 --similarity-type 2 --threads 1 --sub-mat blosum62.out --alignment-mode 2 -e 0.001 --min-seq-id 0 -c 0.8 --target-cov 0 --max-seq-len 32000 --comp-bias-corr 1 --max-rejected 2147483647 --max-accept 2147483647 --rescore-mode 0 | |
| MMseqs Version: 1c45613a4166130d040b52241dc66f7d687f4e54 | |
| Cluster mode 0 | |
| Max. results per query 300 | |
| Verbosity 3 | |
| Max depth connected component 1000 | |
| Similarity type 2 | |
| Threads 1 | |
| Sub Matrix blosum62.out | |
| Add backtrace false | |
| Alignment mode 2 | |
| E-value threshold 0.001 | |
| Seq. Id Threshold 0 | |
| Coverage threshold 0.8 | |
| Target Coverage threshold 0 | |
| Max. sequence length 32000 | |
| Compositional bias 1 | |
| Query queryProfile false | |
| Realign hit false | |
| Max Reject 2147483647 | |
| Max Accept 2147483647 | |
| Include identical Seq. Id. false | |
| Rescore mode 0 | |
| Remove hits by seq.id. and coverage false | |
| In substitution scoring mode, performs global alignment along the diagonal false | |
| Remove Temporary Files false | |
| Sets the MPI runner | |
| Program call: | |
| DB tmp/linclust/pref --sub-mat blosum62.out --alph-size 13 --min-seq-id 0 --kmer-per-seq 20 --target-cov 0 -k 0 -c 0.8 --max-seq-len 32000 --threads 1 -v 3 | |
| MMseqs Version: 1c45613a4166130d040b52241dc66f7d687f4e54 | |
| Sub Matrix blosum62.out | |
| Alphabet size 13 | |
| Seq. Id Threshold 0 | |
| Kmer per sequence 20 | |
| Target Coverage threshold 0 | |
| K-mer size 0 | |
| Coverage threshold 0.8 | |
| Max. sequence length 32000 | |
| Threads 1 | |
| Verbosity 3 | |
| Alphabet size: 13 k-mer size: 10 | |
| Y -> F | |
| V -> I | |
| M -> L | |
| Q -> E | |
| T -> S | |
| R -> K | |
| S -> A | |
| N -> D | |
| Reduced amino acid alphabet: | |
| A C D E F G H I K L P W X | |
| Check requirements | |
| Needed memory (6369264 byte) of total memory (17179869184 byte) | |
| Generate k-mers list ... | |
| .Done. | |
| Sort kmer ... Done. | |
| Sort by rep. sequence ... Done | |
| Time for merging files: 0 h 0 m 0 s | |
| Time for processing: 0 h 0 m 2s | |
| Rescore diagonals. | |
| Program call: | |
| DB DB tmp/linclust/pref tmp/linclust/pref_rescore1 --rescore-mode 0 --sub-mat blosum62.out -c 0.8 --target-cov 0 --min-seq-id 0.5 --threads 1 -v 3 | |
| MMseqs Version: 1c45613a4166130d040b52241dc66f7d687f4e54 | |
| Rescore mode 0 | |
| Sub Matrix blosum62.out | |
| Remove hits by seq.id. and coverage false | |
| In substitution scoring mode, performs global alignment along the diagonal false | |
| Coverage threshold 0.8 | |
| Target Coverage threshold 0 | |
| Seq. Id Threshold 0.5 | |
| Include identical Seq. Id. false | |
| Threads 1 | |
| Verbosity 3 | |
| Query file: DB | |
| Target file: DB | |
| Prefilter database: tmp/linclust/pref | |
| Result database: tmp/linclust/pref_rescore1 | |
| .Done. | |
| Time for merging files: 0 h 0 m 0 s | |
| Time for diagonal calculation: 0 h 0 m 0s | |
| Program call: | |
| DB tmp/linclust/pref_rescore1 tmp/linclust/pre_clust --cluster-mode 0 --max-seqs 300 -v 3 --max-iterations 1000 --similarity-type 2 --threads 1 | |
| MMseqs Version: 1c45613a4166130d040b52241dc66f7d687f4e54 | |
| Cluster mode 0 | |
| Max. results per query 300 | |
| Verbosity 3 | |
| Max depth connected component 1000 | |
| Similarity type 2 | |
| Threads 1 | |
| Init... | |
| Opening sequence database... | |
| Opening alignment database... | |
| done. | |
| Clustering mode: Set Cover | |
| . | |
| Sort entries. | |
| Find missing connections. | |
| Found 11693 new connections. | |
| Reconstruct initial order. | |
| . | |
| Add missing connections. | |
| . | |
| Time for Read in: 0 m 0s | |
| Writing results... | |
| ...done. | |
| Time for clustering: 0 m 0s | |
| Time for merging files: 0 h 0 m 0 s | |
| Total time: 0 m 0s | |
| Size of the sequence database: 20000 | |
| Size of the alignment database: 20000 | |
| Number of clusters: 12074 | |
| Program call: | |
| tmp/linclust/order_redundancy DB tmp/linclust/input_step_redundancy | |
| MMseqs Version: 1c45613a4166130d040b52241dc66f7d687f4e54 | |
| Verbosity 3 | |
| Start writing to file tmp/linclust/input_step_redundancy | |
| Time for merging files: 0 h 0 m 0 s | |
| Program call: | |
| tmp/linclust/order_redundancy tmp/linclust/pref tmp/linclust/pref_filter1 | |
| MMseqs Version: 1c45613a4166130d040b52241dc66f7d687f4e54 | |
| Verbosity 3 | |
| Start writing to file tmp/linclust/pref_filter1 | |
| Time for merging files: 0 h 0 m 0 s | |
| Program call: | |
| tmp/linclust/pref_filter1 tmp/linclust/pref_filter2 --filter-file tmp/linclust/order_redundancy | |
| MMseqs Version: 1c45613a4166130d040b52241dc66f7d687f4e54 | |
| Filter column 1 | |
| Filter regex ^.*$ | |
| Positive filter true | |
| Filter file tmp/linclust/order_redundancy | |
| Mapping file | |
| Threads 1 | |
| Verbosity 3 | |
| trim the results to one column false | |
| Extract n lines 0 | |
| Numerical comparison operator | |
| Numerical comparison value 0 | |
| Sort (increasing:1, decreasing: 2, shuffle: 3) the entries by numerical value 0 | |
| Include identical Seq. Id. false | |
| Filtering with a filter files. | |
| .Time for merging files: 0 h 0 m 0 s | |
| Rescore diagonals. | |
| Program call: | |
| tmp/linclust/input_step_redundancy tmp/linclust/input_step_redundancy tmp/linclust/pref_filter2 tmp/linclust/pref_rescore2 --rescore-mode 1 --sub-mat blosum62.out --filter-hits -c 0.8 --target-cov 0 --min-seq-id 0 --threads 1 -v 3 | |
| MMseqs Version: 1c45613a4166130d040b52241dc66f7d687f4e54 | |
| Rescore mode 1 | |
| Sub Matrix blosum62.out | |
| Remove hits by seq.id. and coverage true | |
| In substitution scoring mode, performs global alignment along the diagonal false | |
| Coverage threshold 0.8 | |
| Target Coverage threshold 0 | |
| Seq. Id Threshold 0 | |
| Include identical Seq. Id. false | |
| Threads 1 | |
| Verbosity 3 | |
| Query file: tmp/linclust/input_step_redundancy | |
| Target file: tmp/linclust/input_step_redundancy | |
| Could not find any score per column for cov=0.8 seq.id=0 | |
| No hit will be filtered. | |
| Prefilter database: tmp/linclust/pref_filter2 | |
| Result database: tmp/linclust/pref_rescore2 | |
| .Done. | |
| Time for merging files: 0 h 0 m 0 s | |
| Time for diagonal calculation: 0 h 0 m 0s | |
| Program call: | |
| tmp/linclust/input_step_redundancy tmp/linclust/input_step_redundancy tmp/linclust/pref_rescore2 tmp/linclust/aln --sub-mat blosum62.out --alignment-mode 2 -e 0.001 --min-seq-id 0 -c 0.8 --target-cov 0 --max-seq-len 32000 --max-seqs 300 --comp-bias-corr 1 --max-rejected 2147483647 --max-accept 2147483647 --threads 1 -v 3 | |
| MMseqs Version: 1c45613a4166130d040b52241dc66f7d687f4e54 | |
| Sub Matrix blosum62.out | |
| Add backtrace false | |
| Alignment mode 2 | |
| E-value threshold 0.001 | |
| Seq. Id Threshold 0 | |
| Coverage threshold 0.8 | |
| Target Coverage threshold 0 | |
| Max. sequence length 32000 | |
| Max. results per query 300 | |
| Compositional bias 1 | |
| Query queryProfile false | |
| Realign hit false | |
| Max Reject 2147483647 | |
| Max Accept 2147483647 | |
| Include identical Seq. Id. false | |
| Threads 1 | |
| Verbosity 3 | |
| Init data structures... | |
| Compute score and coverage. | |
| Calculation of Smith-Waterman alignments. | |
| .Time for merging files: 0 h 0 m 0 s | |
| All sequences processed. | |
| 16087 alignments calculated. | |
| 15656 sequence pairs passed the thresholds (0.973208 of overall calculated). | |
| 1.29667 hits per query sequence. | |
| Time for alignments calculation: 0 h 0 m 18s | |
| Program call: | |
| tmp/linclust/input_step_redundancy tmp/linclust/aln tmp/linclust/clust --cluster-mode 0 --max-seqs 300 -v 3 --max-iterations 1000 --similarity-type 2 --threads 1 | |
| MMseqs Version: 1c45613a4166130d040b52241dc66f7d687f4e54 | |
| Cluster mode 0 | |
| Max. results per query 300 | |
| Verbosity 3 | |
| Max depth connected component 1000 | |
| Similarity type 2 | |
| Threads 1 | |
| Init... | |
| Opening sequence database... | |
| Opening alignment database... | |
| done. | |
| Clustering mode: Set Cover | |
| . | |
| Sort entries. | |
| Find missing connections. | |
| Found 3582 new connections. | |
| Reconstruct initial order. | |
| . | |
| Add missing connections. | |
| . | |
| Time for Read in: 0 m 0s | |
| Writing results... | |
| ...done. | |
| Time for clustering: 0 m 1s | |
| Time for merging files: 0 h 0 m 0 s | |
| Total time: 0 m 1s | |
| Size of the sequence database: 12074 | |
| Size of the alignment database: 12074 | |
| Number of clusters: 9318 | |
| Program call: | |
| DB tmp/linclust/clu tmp/linclust/pre_clust tmp/linclust/clust | |
| MMseqs Version: 1c45613a4166130d040b52241dc66f7d687f4e54 | |
| Verbosity 3 | |
| List amount 20000 | |
| Clustering step 1... | |
| Clustering step 2... | |
| Writing the results... | |
| Time for merging files: 0 h 0 m 0 s | |
| ...done. | |
| Program call: | |
| tmp/order_redundancy DB tmp/input_step_redundancy | |
| MMseqs Version: 1c45613a4166130d040b52241dc66f7d687f4e54 | |
| Verbosity 3 | |
| Start writing to file tmp/input_step_redundancy | |
| Time for merging files: 0 h 0 m 0 s | |
| Program call: | |
| tmp/input_step_redundancy tmp/input_step_redundancy tmp/pref_step0 --sub-mat blosum62.out -s 1 -k 0 --k-score 2147483647 --alph-size 21 --max-seq-len 32000 --max-seqs 20 --offset-result 0 --split 0 --split-mode 2 -c 0.8 --comp-bias-corr 0 --diag-score 0 --mask 1 --min-ungapped-score 0 --spaced-kmer-mode 1 --threads 1 -v 3 | |
| MMseqs Version: 1c45613a4166130d040b52241dc66f7d687f4e54 | |
| Sub Matrix blosum62.out | |
| Sensitivity 1 | |
| K-mer size 0 | |
| K-score 2147483647 | |
| Alphabet size 21 | |
| Max. sequence length 32000 | |
| Query queryProfile false | |
| Target queryProfile false | |
| Max. results per query 20 | |
| Offset result 0 | |
| Split DB 0 | |
| Split mode 2 | |
| Coverage threshold 0.8 | |
| Compositional bias 0 | |
| Diagonal Scoring 0 | |
| Mask Residues 1 | |
| Minimum Diagonal score 0 | |
| Include identical Seq. Id. false | |
| Spaced Kmer 1 | |
| Threads 1 | |
| Verbosity 3 | |
| Initialising data structures... | |
| Cound not find precomputed index. Compute index. | |
| Query database: tmp/input_step_redundancy(size=9318) | |
| Target database: tmp/input_step_redundancy(size=9318) | |
| Use kmer size 6 and split 1 using split mode 0 | |
| Needed memory (1401997934 byte) of total memory (17179869184 byte) | |
| Substitution matrices... | |
| Time for init: 0 h 0 m 6s | |
| Process prefiltering step 0 of 1 | |
| Index table: counting k-mers... | |
| Index table: Masked residues: 151919 | |
| Index table: fill... | |
| Index table: removing duplicate entries... | |
| Index table init done. | |
| DB statistic | |
| Entries: 791058 | |
| DB Size: 690875316 (byte) | |
| Avg Kmer Size: 0.00922343 | |
| Top 10 Kmers | |
| HYCVLG 32 | |
| SRRWPI 21 | |
| PNGSFN 17 | |
| RCKCRW 16 | |
| GGTHAY 16 | |
| GLRGCR 14 | |
| VRRWWV 14 | |
| FFEMPR 13 | |
| VDYFCM 12 | |
| KCQFLM 12 | |
| Min Kmer Size: 0 | |
| Empty list: 85042352 | |
| Time for index table init: 0 h 0 m 2s | |
| Error: Could not allocate memory by memalign. Please report this bug to developers | |
| Program call: | |
| tmp/input_step_redundancy tmp/input_step_redundancy tmp/pref_step0 tmp/aln_step0 --sub-mat blosum62.out --alignment-mode 2 -e 0.001 --min-seq-id 0 -c 0.8 --target-cov 0 --max-seq-len 32000 --max-seqs 20 --comp-bias-corr 0 --max-rejected 2147483647 --max-accept 2147483647 --threads 1 -v 3 | |
| MMseqs Version: 1c45613a4166130d040b52241dc66f7d687f4e54 | |
| Sub Matrix blosum62.out | |
| Add backtrace false | |
| Alignment mode 2 | |
| E-value threshold 0.001 | |
| Seq. Id Threshold 0 | |
| Coverage threshold 0.8 | |
| Target Coverage threshold 0 | |
| Max. sequence length 32000 | |
| Max. results per query 20 | |
| Compositional bias 0 | |
| Query queryProfile false | |
| Realign hit false | |
| Max Reject 2147483647 | |
| Max Accept 2147483647 | |
| Include identical Seq. Id. false | |
| Threads 1 | |
| Verbosity 3 | |
| Init data structures... | |
| Compute score and coverage. | |
| Could not open data file tmp/pref_step0! | |
| Program call: | |
| tmp/input_step_redundancy tmp/aln_step0 tmp/clu_step0 --cluster-mode 0 --max-seqs 20 -v 3 --max-iterations 1000 --similarity-type 2 --threads 1 | |
| MMseqs Version: 1c45613a4166130d040b52241dc66f7d687f4e54 | |
| Cluster mode 0 | |
| Max. results per query 20 | |
| Verbosity 3 | |
| Max depth connected component 1000 | |
| Similarity type 2 | |
| Threads 1 | |
| Init... | |
| Opening sequence database... | |
| Opening alignment database... | |
| Could not open data file tmp/aln_step0! | |
| awk: fatal: cannot open file `tmp/clu_step0.index' for reading (No such file or directory) | |
| Program call: | |
| tmp/order_step0 tmp/input_step_redundancy tmp/input_step1 | |
| MMseqs Version: 1c45613a4166130d040b52241dc66f7d687f4e54 | |
| Verbosity 3 | |
| Start writing to file tmp/input_step1 | |
| Time for merging files: 0 h 0 m 0 s | |
| Program call: | |
| tmp/input_step1 tmp/input_step1 tmp/pref_step1 --sub-mat blosum62.out -s 2 -k 0 --k-score 2147483647 --alph-size 21 --max-seq-len 32000 --max-seqs 100 --offset-result 0 --split 0 --split-mode 2 -c 0.8 --comp-bias-corr 1 --diag-score 1 --mask 1 --min-ungapped-score 15 --spaced-kmer-mode 1 --threads 1 -v 3 | |
| MMseqs Version: 1c45613a4166130d040b52241dc66f7d687f4e54 | |
| Sub Matrix blosum62.out | |
| Sensitivity 2 | |
| K-mer size 0 | |
| K-score 2147483647 | |
| Alphabet size 21 | |
| Max. sequence length 32000 | |
| Query queryProfile false | |
| Target queryProfile false | |
| Max. results per query 100 | |
| Offset result 0 | |
| Split DB 0 | |
| Split mode 2 | |
| Coverage threshold 0.8 | |
| Compositional bias 1 | |
| Diagonal Scoring 1 | |
| Mask Residues 1 | |
| Minimum Diagonal score 15 | |
| Include identical Seq. Id. false | |
| Spaced Kmer 1 | |
| Threads 1 | |
| Verbosity 3 | |
| Initialising data structures... | |
| Failed to mmap memory dataSize=0 File=tmp/input_step1 | |
| Program call: | |
| tmp/input_step1 tmp/input_step1 tmp/pref_step1 tmp/aln_step1 --sub-mat blosum62.out --alignment-mode 2 -e 0.001 --min-seq-id 0 -c 0.8 --target-cov 0 --max-seq-len 32000 --max-seqs 100 --comp-bias-corr 1 --max-rejected 2147483647 --max-accept 2147483647 --threads 1 -v 3 | |
| MMseqs Version: 1c45613a4166130d040b52241dc66f7d687f4e54 | |
| Sub Matrix blosum62.out | |
| Add backtrace false | |
| Alignment mode 2 | |
| E-value threshold 0.001 | |
| Seq. Id Threshold 0 | |
| Coverage threshold 0.8 | |
| Target Coverage threshold 0 | |
| Max. sequence length 32000 | |
| Max. results per query 100 | |
| Compositional bias 1 | |
| Query queryProfile false | |
| Realign hit false | |
| Max Reject 2147483647 | |
| Max Accept 2147483647 | |
| Include identical Seq. Id. false | |
| Threads 1 | |
| Verbosity 3 | |
| Init data structures... | |
| Compute score and coverage. | |
| Failed to mmap memory dataSize=0 File=tmp/input_step1 | |
| Program call: | |
| tmp/input_step1 tmp/aln_step1 tmp/clu_step1 --cluster-mode 0 --max-seqs 100 -v 3 --max-iterations 1000 --similarity-type 2 --threads 1 | |
| MMseqs Version: 1c45613a4166130d040b52241dc66f7d687f4e54 | |
| Cluster mode 0 | |
| Max. results per query 100 | |
| Verbosity 3 | |
| Max depth connected component 1000 | |
| Similarity type 2 | |
| Threads 1 | |
| Init... | |
| Opening sequence database... | |
| Opening alignment database... | |
| Could not open data file tmp/aln_step1! | |
| awk: fatal: cannot open file `tmp/clu_step1.index' for reading (No such file or directory) | |
| Program call: | |
| tmp/order_step1 tmp/input_step1 tmp/input_step2 | |
| MMseqs Version: 1c45613a4166130d040b52241dc66f7d687f4e54 | |
| Verbosity 3 | |
| Failed to mmap memory dataSize=0 File=tmp/input_step1 | |
| Program call: | |
| tmp/input_step2 tmp/input_step2 tmp/pref_step2 --sub-mat blosum62.out -s 4 -k 0 --k-score 2147483647 --alph-size 21 --max-seq-len 32000 --max-seqs 200 --offset-result 0 --split 0 --split-mode 2 -c 0.8 --comp-bias-corr 1 --diag-score 1 --mask 1 --min-ungapped-score 15 --spaced-kmer-mode 1 --threads 1 -v 3 | |
| MMseqs Version: 1c45613a4166130d040b52241dc66f7d687f4e54 | |
| Sub Matrix blosum62.out | |
| Sensitivity 4 | |
| K-mer size 0 | |
| K-score 2147483647 | |
| Alphabet size 21 | |
| Max. sequence length 32000 | |
| Query queryProfile false | |
| Target queryProfile false | |
| Max. results per query 200 | |
| Offset result 0 | |
| Split DB 0 | |
| Split mode 2 | |
| Coverage threshold 0.8 | |
| Compositional bias 1 | |
| Diagonal Scoring 1 | |
| Mask Residues 1 | |
| Minimum Diagonal score 15 | |
| Include identical Seq. Id. false | |
| Spaced Kmer 1 | |
| Threads 1 | |
| Verbosity 3 | |
| Initialising data structures... | |
| Could not open data file tmp/input_step2! | |
| Program call: | |
| tmp/input_step2 tmp/input_step2 tmp/pref_step2 tmp/aln_step2 --sub-mat blosum62.out --alignment-mode 2 -e 0.001 --min-seq-id 0 -c 0.8 --target-cov 0 --max-seq-len 32000 --max-seqs 200 --comp-bias-corr 1 --max-rejected 2147483647 --max-accept 2147483647 --threads 1 -v 3 | |
| MMseqs Version: 1c45613a4166130d040b52241dc66f7d687f4e54 | |
| Sub Matrix blosum62.out | |
| Add backtrace false | |
| Alignment mode 2 | |
| E-value threshold 0.001 | |
| Seq. Id Threshold 0 | |
| Coverage threshold 0.8 | |
| Target Coverage threshold 0 | |
| Max. sequence length 32000 | |
| Max. results per query 200 | |
| Compositional bias 1 | |
| Query queryProfile false | |
| Realign hit false | |
| Max Reject 2147483647 | |
| Max Accept 2147483647 | |
| Include identical Seq. Id. false | |
| Threads 1 | |
| Verbosity 3 | |
| Init data structures... | |
| Compute score and coverage. | |
| Could not open data file tmp/input_step2! | |
| Program call: | |
| tmp/input_step2 tmp/aln_step2 tmp/clu_step2 --cluster-mode 0 --max-seqs 200 -v 3 --max-iterations 1000 --similarity-type 2 --threads 1 | |
| MMseqs Version: 1c45613a4166130d040b52241dc66f7d687f4e54 | |
| Cluster mode 0 | |
| Max. results per query 200 | |
| Verbosity 3 | |
| Max depth connected component 1000 | |
| Similarity type 2 | |
| Threads 1 | |
| Init... | |
| Opening sequence database... | |
| Opening alignment database... | |
| Could not open data file tmp/aln_step2! | |
| awk: fatal: cannot open file `tmp/clu_step2.index' for reading (No such file or directory) | |
| Program call: | |
| tmp/order_step2 tmp/input_step2 tmp/input_step3 | |
| MMseqs Version: 1c45613a4166130d040b52241dc66f7d687f4e54 | |
| Verbosity 3 | |
| Could not open data file tmp/input_step2! | |
| Program call: | |
| tmp/input_step3 tmp/input_step3 tmp/pref_step3 --sub-mat blosum62.out -s 6 -k 0 --k-score 2147483647 --alph-size 21 --max-seq-len 32000 --max-seqs 300 --offset-result 0 --split 0 --split-mode 2 -c 0.8 --comp-bias-corr 1 --diag-score 1 --mask 1 --min-ungapped-score 15 --spaced-kmer-mode 1 --threads 1 -v 3 | |
| MMseqs Version: 1c45613a4166130d040b52241dc66f7d687f4e54 | |
| Sub Matrix blosum62.out | |
| Sensitivity 6 | |
| K-mer size 0 | |
| K-score 2147483647 | |
| Alphabet size 21 | |
| Max. sequence length 32000 | |
| Query queryProfile false | |
| Target queryProfile false | |
| Max. results per query 300 | |
| Offset result 0 | |
| Split DB 0 | |
| Split mode 2 | |
| Coverage threshold 0.8 | |
| Compositional bias 1 | |
| Diagonal Scoring 1 | |
| Mask Residues 1 | |
| Minimum Diagonal score 15 | |
| Include identical Seq. Id. false | |
| Spaced Kmer 1 | |
| Threads 1 | |
| Verbosity 3 | |
| Initialising data structures... | |
| Could not open data file tmp/input_step3! | |
| Program call: | |
| tmp/input_step3 tmp/input_step3 tmp/pref_step3 tmp/aln_step3 --sub-mat blosum62.out --alignment-mode 2 -e 0.001 --min-seq-id 0 -c 0.8 --target-cov 0 --max-seq-len 32000 --max-seqs 300 --comp-bias-corr 1 --max-rejected 2147483647 --max-accept 2147483647 --threads 1 -v 3 | |
| MMseqs Version: 1c45613a4166130d040b52241dc66f7d687f4e54 | |
| Sub Matrix blosum62.out | |
| Add backtrace false | |
| Alignment mode 2 | |
| E-value threshold 0.001 | |
| Seq. Id Threshold 0 | |
| Coverage threshold 0.8 | |
| Target Coverage threshold 0 | |
| Max. sequence length 32000 | |
| Max. results per query 300 | |
| Compositional bias 1 | |
| Query queryProfile false | |
| Realign hit false | |
| Max Reject 2147483647 | |
| Max Accept 2147483647 | |
| Include identical Seq. Id. false | |
| Threads 1 | |
| Verbosity 3 | |
| Init data structures... | |
| Compute score and coverage. | |
| Could not open data file tmp/input_step3! | |
| Program call: | |
| tmp/input_step3 tmp/aln_step3 tmp/clu_step3 --cluster-mode 0 --max-seqs 300 -v 3 --max-iterations 1000 --similarity-type 2 --threads 1 | |
| MMseqs Version: 1c45613a4166130d040b52241dc66f7d687f4e54 | |
| Cluster mode 0 | |
| Max. results per query 300 | |
| Verbosity 3 | |
| Max depth connected component 1000 | |
| Similarity type 2 | |
| Threads 1 | |
| Init... | |
| Opening sequence database... | |
| Opening alignment database... | |
| Could not open data file tmp/aln_step3! | |
| Program call: | |
| DB tmp/clu tmp/clu_redundancy tmp/clu_step0 tmp/clu_step1 tmp/clu_step2 tmp/clu_step3 | |
| MMseqs Version: 1c45613a4166130d040b52241dc66f7d687f4e54 | |
| Verbosity 3 | |
| List amount 20000 | |
| Clustering step 1... | |
| Could not open data file tmp/clu_step0! | |
| mv: rename tmp/clu to cluDB: No such file or directory | |
| mv: rename tmp/clu.index to cluDB.index: No such file or directory | |
| Could not move result to cluDB |
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