Created
June 21, 2024 10:17
-
-
Save rmostowy/f08c6389e9e04a380a03ffc03c3bfa85 to your computer and use it in GitHub Desktop.
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| createdb file.fasta mmseqs/DB | |
| MMseqs Version: 15-6f452 | |
| 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 | |
| [405] 0s 31ms | |
| Time for merging to DB_h: 0h 0m 0s 3ms | |
| Time for merging to DB: 0h 0m 0s 11ms | |
| Database type: Nucleotide | |
| Time for processing: 0h 0m 0s 74ms | |
| Create directory mmseqs/tmp | |
| search mmseqs/DB mmseqs/DB mmseqs/resultDB mmseqs/tmp --search-type 3 --threads 8 --sub-mat blastn-scoring.out --seed-sub-mat blastn-scoring.out -s 7.5 --prefilter-mode 2 -e 1e-3 | |
| MMseqs Version: 15-6f452 | |
| Substitution matrix aa:blastn-scoring.out,nucl:blastn-scoring.out | |
| 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 | |
| Coverage threshold 0 | |
| Coverage mode 0 | |
| Max sequence length 10000 | |
| Compositional bias 1 | |
| Compositional bias 1 | |
| Max reject 2147483647 | |
| Max accept 2147483647 | |
| Include identical seq. id. false | |
| Preload mode 0 | |
| Pseudo count a substitution:1.100,context:1.400 | |
| Pseudo count b substitution:4.100,context:5.800 | |
| 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 | |
| Threads 8 | |
| Compressed 0 | |
| Verbosity 3 | |
| Seed substitution matrix aa:blastn-scoring.out,nucl:blastn-scoring.out | |
| Sensitivity 7.5 | |
| k-mer length 15 | |
| Target search mode 0 | |
| k-score seq:2147483647,prof:2147483647 | |
| Alphabet size aa:21,nucl:5 | |
| Max results per query 300 | |
| Split database 0 | |
| Split mode 2 | |
| Split memory limit 0 | |
| Diagonal scoring true | |
| Exact k-mer matching 1 | |
| Mask residues 1 | |
| Mask residues probability 0.9 | |
| Mask lower case residues 0 | |
| Minimum diagonal score 15 | |
| Selected taxa | |
| Spaced k-mers 1 | |
| Spaced k-mer pattern | |
| Local temporary path | |
| Rescore mode 0 | |
| Remove hits by seq. id. and coverage false | |
| Sort results 0 | |
| Mask profile 1 | |
| Profile E-value threshold 0.1 | |
| Global sequence weighting false | |
| Allow deletions false | |
| Filter MSA 1 | |
| Use filter only at N seqs 0 | |
| Maximum seq. id. threshold 0.9 | |
| Minimum seq. id. 0.0 | |
| Minimum score per column -20 | |
| Minimum coverage 0 | |
| Select N most diverse seqs 1000 | |
| Pseudo count mode 0 | |
| Min codons in orf 30 | |
| Max codons in length 32734 | |
| Max orf gaps 2147483647 | |
| Contig start mode 2 | |
| Contig end mode 2 | |
| Orf start mode 1 | |
| Forward frames 1,2,3 | |
| Reverse frames 1,2,3 | |
| Translation table 1 | |
| Translate orf 0 | |
| Use all table starts false | |
| Offset of numeric ids 0 | |
| Create lookup 0 | |
| Add orf stop false | |
| Overlap between sequences 0 | |
| Sequence split mode 1 | |
| Header split mode 0 | |
| Chain overlapping alignments 0 | |
| Merge query 1 | |
| Search type 3 | |
| Search iterations 1 | |
| Start sensitivity 4 | |
| Search steps 1 | |
| Prefilter mode 2 | |
| Exhaustive search mode false | |
| Filter results during exhaustive search 0 | |
| Strand selection 2 | |
| LCA search mode false | |
| Disk space limit 0 | |
| MPI runner | |
| Force restart with latest tmp false | |
| Remove temporary files false | |
| splitsequence mmseqs/DB mmseqs/tmp/6157013917641327162/target_seqs_split --max-seq-len 10000 --sequence-overlap 0 --sequence-split-mode 1 --headers-split-mode 0 --create-lookup 0 --threads 8 --compressed 0 -v 3 | |
| [=================================================================] 100.00% 500 0s 2ms | |
| Time for merging to target_seqs_split_h: 0h 0m 0s 3ms | |
| Time for merging to target_seqs_split: 0h 0m 0s 2ms | |
| Time for processing: 0h 0m 0s 19ms | |
| extractframes mmseqs/DB mmseqs/tmp/6157013917641327162/query_seqs --forward-frames 1 --reverse-frames 1 --create-lookup 0 --threads 8 --compressed 0 -v 3 | |
| [=================================================================] 100.00% 500 0s 15ms | |
| Time for merging to query_seqs_h: 0h 0m 0s 1ms | |
| Time for merging to query_seqs: 0h 0m 0s 25ms | |
| Time for processing: 0h 0m 0s 69ms | |
| splitsequence mmseqs/tmp/6157013917641327162/query_seqs mmseqs/tmp/6157013917641327162/query_seqs_split --max-seq-len 10000 --sequence-overlap 0 --sequence-split-mode 1 --headers-split-mode 0 --create-lookup 0 --threads 8 --compressed 0 -v 3 | |
| [=================================================================] 100.00% 1.00K 0s 1ms | |
| Time for merging to query_seqs_split_h: 0h 0m 0s 2ms | |
| Time for merging to query_seqs_split: 0h 0m 0s 2ms | |
| Time for processing: 0h 0m 0s 11ms | |
| align mmseqs/tmp/6157013917641327162/query_seqs_split mmseqs/tmp/6157013917641327162/target_seqs_split mmseqs/tmp/6157013917641327162/search/pref_0 mmseqs/tmp/6157013917641327162/aln --sub-mat 'aa:blastn-scoring.out,nucl:blastn-scoring.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 --cov-mode 0 --max-seq-len 10000 --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 8 --compressed 0 -v 3 | |
| Compute score, coverage and sequence identity | |
| Query database size: 7214 type: Nucleotide | |
| Target database size: 3607 type: Nucleotide | |
| Calculation of alignments | |
| [=================================================================] 100.00% 7.21K 4m 4s 688ms | |
| Time for merging to aln: 0h 0m 0s 2ms | |
| 26020898 alignments calculated | |
| 5185 sequence pairs passed the thresholds (0.000199 of overall calculated) | |
| 0.718741 hits per query sequence | |
| Time for processing: 0h 4m 4s 909ms | |
| offsetalignment mmseqs/DB mmseqs/tmp/6157013917641327162/query_seqs_split mmseqs/DB mmseqs/tmp/6157013917641327162/target_seqs_split mmseqs/tmp/6157013917641327162/aln mmseqs/resultDB --chain-alignments 0 --merge-query 1 --search-type 3 --threads 8 --compressed 0 --db-load-mode 0 -v 3 | |
| Computing ORF lookup | |
| Computing contig offsets | |
| Computing contig lookup | |
| Time for contig lookup: 0h 0m 0s 0ms | |
| Writing results to: mmseqs/resultDB | |
| [=================================================================] 100.00% 500 0s 2ms | |
| Time for merging to resultDB: 0h 0m 0s 0ms | |
| Time for processing: 0h 0m 0s 7ms | |
| convertalis mmseqs/DB mmseqs/DB mmseqs/resultDB mmseqs/result.m8 | |
| MMseqs Version: 15-6f452 | |
| Substitution matrix aa:blosum62.out,nucl:nucleotide.out | |
| Alignment format 0 | |
| Format alignment output query,target,fident,alnlen,mismatch,gapopen,qstart,qend,tstart,tend,evalue,bits | |
| Translation table 1 | |
| Gap open cost aa:11,nucl:5 | |
| Gap extension cost aa:1,nucl:2 | |
| Database output false | |
| Preload mode 0 | |
| Search type 0 | |
| Threads 12 | |
| Compressed 0 | |
| Verbosity 3 | |
| [=================================================================] 100.00% 500 0s 3ms | |
| Time for merging to result.m8: 0h 0m 0s 3ms | |
| Time for processing: 0h 0m 0s 11ms |
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment