createdb h1_protein.fa h1_protein_search_v2/mmseqs/DBs/query_seq_db 

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
[
Time for merging to query_seq_db_h: 0h 0m 0s 3ms
Time for merging to query_seq_db: 0h 0m 0s 2ms
Database type: Aminoacid
Time for processing: 0h 0m 0s 16ms
Create directory h1_protein_search_v2/mmseqs/tmp
search h1_protein_search_v2/mmseqs/DBs/query_seq_db ilund4u_run_db2/mmseqs_db/all_proteins h1_protein_search_v2/mmseqs/DBs/search_res_db h1_protein_search_v2/mmseqs/tmp -e 1e-05 -s 6 

MMseqs Version:                        	f6c98807d589091c625db68da258d587795acbab
Substitution matrix                    	aa:blosum62.out,nucl:nucleotide.out
Add backtrace                          	false
Alignment mode                         	2
Alignment mode                         	0
Allow wrapped scoring                  	false
E-value threshold                      	1e-05
Seq. id. threshold                     	0
Min alignment length                   	0
Seq. id. mode                          	0
Alternative alignments                 	0
Coverage threshold                     	0
Coverage mode                          	0
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                            	6
k-mer length                           	0
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                   	0
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                            	0
Search iterations                      	1
Start sensitivity                      	4
Search steps                           	1
Prefilter mode                         	0
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                 	false

prefilter h1_protein_search_v2/mmseqs/DBs/query_seq_db ilund4u_run_db2/mmseqs_db/all_proteins h1_protein_search_v2/mmseqs/tmp/6698431742576889962/pref_0 --sub-mat 'aa:blosum62.out,nucl:nucleotide.out' --seed-sub-mat 'aa:VTML80.out,nucl:nucleotide.out' -k 0 --target-search-mode 0 --k-score seq:2147483647,prof:2147483647 --alph-size aa:21,nucl:5 --max-seq-len 65535 --max-seqs 300 --split 0 --split-mode 2 --split-memory-limit 0 -c 0 --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 8 --compressed 0 -v 3 -s 6.0 

Query database size: 1 type: Aminoacid
Estimated memory consumption: 1G
Target database size: 121092 type: Aminoacid
Index table k-mer threshold: 109 at k-mer size 6 
Index table: counting k-mers
[=================================================================] 121.09K 0s 708ms
Index table: Masked residues: 172555
Index table: fill
[=================================================================] 121.09K 0s 578ms
Index statistics
Entries:          22588392
DB size:          617 MB
Avg k-mer size:   0.352944
Top 10 k-mers
    SRIASK	912
    EMRDLR	856
    YLEELY	821
    SETSQL	816
    LTGKFN	816
    LETRIT	816
    TGGNVV	755
    KVSVVY	740
    LKYDGY	727
    PDLTEV	692
Time for index table init: 0h 0m 1s 719ms
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 121092
[=================================================================] 1 0s 1ms

367.142857 k-mers per position
28087 DB matches per sequence
0 overflows
300 sequences passed prefiltering per query sequence
300 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 0m 2s 161ms
align h1_protein_search_v2/mmseqs/DBs/query_seq_db ilund4u_run_db2/mmseqs_db/all_proteins h1_protein_search_v2/mmseqs/tmp/6698431742576889962/pref_0 h1_protein_search_v2/mmseqs/DBs/search_res_db --sub-mat 'aa:blosum62.out,nucl:nucleotide.out' -a 0 --alignment-mode 2 --alignment-output-mode 0 --wrapped-scoring 0 -e 1e-05 --min-seq-id 0 --min-aln-len 0 --seq-id-mode 0 --alt-ali 0 -c 0 --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 8 --compressed 0 -v 3 

Compute score and coverage
Query database size: 1 type: Aminoacid
Target database size: 121092 type: Aminoacid
Calculation of alignments
[=================================================================] 1 0s 0ms
Time for merging to search_res_db: 0h 0m 0s 0ms
300 alignments calculated
169 sequence pairs passed the thresholds (0.563333 of overall calculated)
169.000000 hits per query sequence
Time for processing: 0h 0m 0s 14ms
convertalis h1_protein_search_v2/mmseqs/DBs/query_seq_db ilund4u_run_db2/mmseqs_db/all_proteins h1_protein_search_v2/mmseqs/DBs/search_res_db h1_protein_search_v2/mmseqs/mmseqs_search_results.tsv --format-output query,target,raw,bits,qlen,tlen,alnlen,fident,qstart,qend,tstart,tend,evalue --format-mode 4 

MMseqs Version:        	f6c98807d589091c625db68da258d587795acbab
Substitution matrix    	aa:blosum62.out,nucl:nucleotide.out
Alignment format       	4
Format alignment output	query,target,raw,bits,qlen,tlen,alnlen,fident,qstart,qend,tstart,tend,evalue
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                	8
Compressed             	0
Verbosity              	3

[=================================================================] 1 0s 0ms
Time for merging to mmseqs_search_results.tsv: 0h 0m 0s 0ms
Time for processing: 0h 0m 0s 17ms
