alnRes.m8 exists and will be overwritten
easy-search --search-type 3 --min-seq-id 0.95 -c 1 --cov-mode 2 --max-seqs 1000000 --min-ungapped-score 200 query.fasta targetDB alnRes.m8 tmp 

MMseqs Version:                        	17.b804f
Substitution matrix                    	aa:blosum62.out,nucl:nucleotide.out
Add backtrace                          	false
Alignment mode                         	3
Alignment mode                         	0
Allow wrapped scoring                  	false
E-value threshold                      	0.001
Seq. id. threshold                     	0.95
Min alignment length                   	0
Seq. id. mode                          	0
Alternative alignments                 	0
Coverage threshold                     	1
Coverage mode                          	2
Max sequence length                    	65535
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:VTML80.out,nucl:nucleotide.out
Sensitivity                            	5.7
k-mer length                           	0
Target search mode                     	0
k-score                                	seq:2147483647,prof:2147483647
Alphabet size                          	aa:21,nucl:5
Max results per query                  	1000000
Split database                         	0
Split mode                             	2
Split memory limit                     	0
Diagonal scoring                       	true
Exact k-mer matching                   	0
Mask residues                          	1
Mask residues probability              	0.9
Mask lower case residues               	0
Mask lower letter repeating N times    	0
Minimum diagonal score                 	200
Selected taxa                          	
Spaced k-mers                          	1
Spaced k-mer pattern                   	
Local temporary path                   	
Use GPU                                	0
Use GPU server                         	0
Wait for GPU server                    	600
Prefilter mode                         	0
Rescore mode                           	0
Remove hits by seq. id. and coverage   	false
Sort results                           	0
Mask profile                           	1
Profile E-value threshold              	0.001
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
Profile output 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
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
Exhaustive search mode                 	false
Filter results during exhaustive search	0
Strand selection                       	1
LCA search mode                        	false
Disk space limit                       	0
MPI runner                             	
Force restart with latest tmp          	false
Remove temporary files                 	true
Translation mode                       	0
Alignment format                       	0
Format alignment output                	query,target,fident,alnlen,mismatch,gapopen,qstart,qend,tstart,tend,evalue,bits
Database output                        	false
Overlap threshold                      	0
Database type                          	0
Shuffle input database                 	true
Createdb mode                          	0
Write lookup file                      	0
Greedy best hits                       	false

createdb query.fasta tmp/17855978298342352080/query --dbtype 0 --shuffle 0 --createdb-mode 0 --write-lookup 0 --id-offset 0 --compressed 0 -v 3 

Converting sequences
[
Time for merging to query_h: 0h 0m 0s 0ms
Time for merging to query: 0h 0m 0s 0ms
Database type: Nucleotide
Time for processing: 0h 0m 0s 0ms
Create directory tmp/17855978298342352080/search_tmp
search tmp/17855978298342352080/query targetDB tmp/17855978298342352080/result tmp/17855978298342352080/search_tmp --alignment-mode 3 --min-seq-id 0.95 -c 1 --cov-mode 2 -s 5.7 --max-seqs 1000000 --min-ungapped-score 200 --search-type 3 --remove-tmp-files 1 

splitsequence targetDB tmp/17855978298342352080/search_tmp/17305500037039267211/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 

[=================================================================] 2.52M 0s 404ms
Time for merging to target_seqs_split_h: 0h 0m 0s 597ms
Time for merging to target_seqs_split: 0h 0m 0s 595ms
Time for processing: 0h 0m 2s 706ms
extractframes tmp/17855978298342352080/query tmp/17855978298342352080/search_tmp/17305500037039267211/query_seqs --forward-frames 1 --reverse-frames 1 --translation-table 1 --translate 0 --create-lookup 0 --threads 8 --compressed 0 -v 3 

[=================================================================] 1 0s 1ms
Time for merging to query_seqs_h: 0h 0m 0s 0ms
Time for merging to query_seqs: 0h 0m 0s 0ms
Time for processing: 0h 0m 0s 4ms
splitsequence tmp/17855978298342352080/search_tmp/17305500037039267211/query_seqs tmp/17855978298342352080/search_tmp/17305500037039267211/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 

Time for processing: 0h 0m 0s 0ms
prefilter tmp/17855978298342352080/search_tmp/17305500037039267211/query_seqs_split tmp/17855978298342352080/search_tmp/17305500037039267211/target_seqs_split tmp/17855978298342352080/search_tmp/17305500037039267211/search/pref_0 --sub-mat 'aa:blosum62.out,nucl:nucleotide.out' --seed-sub-mat 'aa:VTML80.out,nucl:nucleotide.out' -k 15 --target-search-mode 0 --k-score seq:2147483647,prof:2147483647 --alph-size aa:21,nucl:5 --max-seq-len 10000 --max-seqs 1000000 --split 0 --split-mode 2 --split-memory-limit 0 -c 1 --cov-mode 2 --comp-bias-corr 1 --comp-bias-corr-scale 1 --diag-score 1 --exact-kmer-matching 1 --mask 1 --mask-prob 0.9 --mask-lower-case 0 --mask-n-repeat 0 --min-ungapped-score 200 --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 8 --compressed 0 -v 3 -s 5.7 

Query database size: 2 type: Nucleotide
Estimated memory consumption: 17G
Target database size: 2518126 type: Nucleotide
Index table k-mer threshold: 0 at k-mer size 15 
Index table: counting k-mers
[=================================================================] 2.52M 30s 755ms
Index table: Masked residues: 7081790
Index table: fill
[=================================================================] 2.52M 51s 187ms
Index statistics
Entries:          1183100244
DB size:          14961 MB
Avg k-mer size:   1.101848
Top 10 k-mers
    TTTTATAATTTATGT	1129779
    CGATAATATAGTTTG	904748
    CATCTTTATATTTTT	719520
    ATATGGAGATGAATG	627787
    ATATATACTATATGG	589217
    CCTTATAATGGTTGG	505210
    ATTTTCTTACTGCGG	479550
    TTTCCGAAAAAATAG	467381
    ATTCATATATCGACG	459675
    GCCCGATAAGTCCCG	433993
Time for index table init: 0h 1m 37s 320ms
Process prefiltering step 1 of 1

k-mer similarity threshold: 0
Starting prefiltering scores calculation (step 1 of 1)
Query db start 1 to 2
Target db start 1 to 2518126
===============================================[==================] 2 0s 2ms

0.929712 k-mers per position
3341324 DB matches per sequence
1 overflows
275406 sequences passed prefiltering per query sequence
548481 median result list length
0 sequences with 0 size result lists
Time for merging to pref_0: 0h 0m 0s 0ms
Time for processing: 0h 1m 39s 410ms
align tmp/17855978298342352080/search_tmp/17305500037039267211/query_seqs_split tmp/17855978298342352080/search_tmp/17305500037039267211/target_seqs_split tmp/17855978298342352080/search_tmp/17305500037039267211/search/pref_0 tmp/17855978298342352080/search_tmp/17305500037039267211/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 0.95 --min-aln-len 0 --seq-id-mode 0 --alt-ali 0 -c 1 --cov-mode 2 --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: 2 type: Nucleotide
Target database size: 2518126 type: Nucleotide
Calculation of alignments
[=================================================================] 2 0s 258ms
Time for merging to aln: 0h 0m 0s 0ms
509189 alignments calculated
2 sequence pairs passed the thresholds (0.000004 of overall calculated)
1.000000 hits per query sequence
Time for processing: 0h 0m 55s 455ms
rmdb tmp/17855978298342352080/search_tmp/17305500037039267211/search/pref_0 -v 3 

Time for processing: 0h 0m 0s 1ms
rmdb tmp/17855978298342352080/search_tmp/17305500037039267211/search/aln_0 -v 3 

Time for processing: 0h 0m 0s 0ms
rmdb tmp/17855978298342352080/search_tmp/17305500037039267211/search/input_0 -v 3 

Time for processing: 0h 0m 0s 0ms
rmdb tmp/17855978298342352080/search_tmp/17305500037039267211/search/aln_merge -v 3 

Time for processing: 0h 0m 0s 0ms
offsetalignment tmp/17855978298342352080/query tmp/17855978298342352080/search_tmp/17305500037039267211/query_seqs_split targetDB tmp/17855978298342352080/search_tmp/17305500037039267211/target_seqs_split tmp/17855978298342352080/search_tmp/17305500037039267211/aln tmp/17855978298342352080/result --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: tmp/17855978298342352080/result
[=================================================================] 1 0s 0ms

Time for merging to result: 0h 0m 0s 0ms
Time for processing: 0h 0m 0s 189ms
rmdb tmp/17855978298342352080/search_tmp/17305500037039267211/q_orfs -v 3 

Time for processing: 0h 0m 0s 0ms
rmdb tmp/17855978298342352080/search_tmp/17305500037039267211/q_orfs_aa -v 3 

Time for processing: 0h 0m 0s 0ms
rmdb tmp/17855978298342352080/search_tmp/17305500037039267211/t_orfs -v 3 

Time for processing: 0h 0m 0s 0ms
rmdb tmp/17855978298342352080/search_tmp/17305500037039267211/t_orfs_aa -v 3 

Time for processing: 0h 0m 0s 0ms
alnRes.m8 exists and will be overwritten
convertalis tmp/17855978298342352080/query targetDB tmp/17855978298342352080/result alnRes.m8 --sub-mat 'aa:blosum62.out,nucl:nucleotide.out' --format-mode 0 --format-output query,target,fident,alnlen,mismatch,gapopen,qstart,qend,tstart,tend,evalue,bits --translation-table 1 --gap-open aa:11,nucl:5 --gap-extend aa:1,nucl:2 --db-output 0 --db-load-mode 0 --search-type 3 --threads 8 --compressed 0 -v 3 

[=================================================================] 1 0s 0ms
Time for merging to alnRes.m8: 0h 0m 0s 0ms
Time for processing: 0h 0m 0s 208ms
rmdb tmp/17855978298342352080/result -v 3 

Time for processing: 0h 0m 0s 0ms
rmdb tmp/17855978298342352080/query -v 3 

Time for processing: 0h 0m 0s 0ms
rmdb tmp/17855978298342352080/query_h -v 3 

Time for processing: 0h 0m 0s 0ms
