No hits in aln.m8?

[BinhongLiu]

Expected Behavior

I'd like to search a similar structure to AF-D2QBA9-F1-model_v3 within the PDB database. However, not results were produced. Why nothing reported in the aln.m8 file? If this is because no structures have been found that meet the similarity threshold, how can these low-similarity comparisons be output?

Steps to Reproduce (for bugs)

foldseek easy-search AF-D2QBA9-F1-model_v3.cif.gz /home/liuhongbin/database/FoldSeek/pdb100/pdb aln.m8 tmpFolder --exhaustive-search 1

Foldssek Output (for bugs)

easy-search AF-D2QBA9-F1-model_v3.cif.gz /home/liuhongbin/database/FoldSeek/pdb100/pdb aln.m8 tmpFolder --exhaustive-search 1

MMseqs Version: 5.53465f0 Seq. id. threshold 0 Coverage threshold 0 Coverage mode 0 Max reject 2147483647 Max accept 2147483647 Add backtrace false TMscore threshold 0 TMalign hit order 0 TMalign fast 1 Preload mode 0 Threads 176 Verbosity 3 LDDT threshold 0 Sort by structure bit score 1 Substitution matrix aa:3di.out,nucl:3di.out Alignment mode 3 Alignment mode 0 E-value threshold 10 Min alignment length 0 Seq. id. mode 0 Alternative alignments 0 Max sequence length 65535 Compositional bias 1 Compositional bias 1 Gap open cost aa:10,nucl:10 Gap extension cost aa:1,nucl:1 Compressed 0 Seed substitution matrix aa:3di.out,nucl:3di.out Sensitivity 9.5 k-mer length 6 k-score seq:2147483647,prof:2147483647 Max results per query 1000 Split database 0 Split mode 2 Split memory limit 0 Diagonal scoring true Exact k-mer matching 0 Mask residues 0 Mask residues probability 0.99995 Mask lower case residues 1 Minimum diagonal score 15 Selected taxa
Spaced k-mers 1 Spaced k-mer pattern
Local temporary path
Exhaustive search mode true Search iterations 1 Alignment type 2 Remove temporary files true MPI runner
Force restart with latest tmp false Chain name mode 0 Mask b-factor threshold 0 Coord store mode 2 Write lookup file 1 Tar Inclusion Regex .* Tar Exclusion Regex ^$ Alignment format 0 Format alignment output query,target,fident,alnlen,mismatch,gapopen,qstart,qend,tstart,tend,evalue,bits Database output false

createdb AF-D2QBA9-F1-model_v3.cif.gz tmpFolder/6144580022869075475/query --chain-name-mode 0 --mask-bfactor-threshold 0 --coord-store-mode 2 --write-lookup 1 --tar-include '.*' --tar-exclude '^$' --threads 176 -v 3

Output file: tmpFolder/6144580022869075475/query [=================================================================] 100.00% 1 eta - Time for merging to query_ss: 0h 0m 0s 928ms Time for merging to query_h: 0h 0m 0s 499ms Time for merging to query_ca: 0h 0m 0s 588ms Time for merging to query: 0h 0m 0s 481ms Ignore 0 out of 1. Too short: 0, incorrect 0. Time for processing: 0h 0m 4s 125ms Create directory tmpFolder/6144580022869075475/search_tmp search tmpFolder/6144580022869075475/query /home/liuhongbin/database/FoldSeek/pdb100/pdb tmpFolder/6144580022869075475/result tmpFolder/6144580022869075475/search_tmp --alignment-mode 3 --comp-bias-corr 1 --gap-open aa:10,nucl:10 --gap-extend aa:1,nucl:1 -s 9.5 -k 6 --mask 0 --mask-prob 0.99995 --exhaustive-search 1 --remove-tmp-files 1

structurealign tmpFolder/6144580022869075475/query /home/liuhongbin/database/FoldSeek/pdb100/pdb tmpFolder/6144580022869075475/search_tmp/13871818306523928435/pref tmpFolder/6144580022869075475/search_tmp/13871818306523928435/aln --tmscore-threshold 0 --lddt-threshold 0 --sort-by-structure-bits 1 --sub-mat 'aa:3di.out,nucl:3di.out' -a 0 --alignment-mode 3 --alignment-output-mode 0 --wrapped-scoring 0 -e 10 --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 0.5 --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:10,nucl:10 --gap-extend aa:1,nucl:1 --zdrop 40 --threads 176 --compressed 0 -v 3

[=================================================================] 100.00% 1 eta - Time for merging to aln: 0h 0m 0s 259ms Time for processing: 0h 0m 23s 867ms mvdb tmpFolder/6144580022869075475/search_tmp/13871818306523928435/aln tmpFolder/6144580022869075475/result -v 3

Time for processing: 0h 0m 0s 225ms Removing temporary files rmdb tmpFolder/6144580022869075475/search_tmp/13871818306523928435/pref -v 3

Time for processing: 0h 0m 0s 3ms aln.m8 exists and will be overwritten convertalis tmpFolder/6144580022869075475/query /home/liuhongbin/database/FoldSeek/pdb100/pdb tmpFolder/6144580022869075475/result aln.m8 --sub-mat 'aa:3di.out,nucl:3di.out' --format-mode 0 --format-output query,target,fident,alnlen,mismatch,gapopen,qstart,qend,tstart,tend,evalue,bits --translation-table 1 --gap-open aa:10,nucl:10 --gap-extend aa:1,nucl:1 --db-output 0 --db-load-mode 0 --search-type 0 --threads 176 --compressed 0 -v 3

[=================================================================] 100.00% 1 eta - Time for merging to aln.m8: 0h 0m 0s 5ms Time for processing: 0h 0m 0s 142ms rmdb tmpFolder/6144580022869075475/result -v 3

Time for processing: 0h 0m 0s 121ms rmdb tmpFolder/6144580022869075475/query -v 3

Time for processing: 0h 0m 0s 4ms rmdb tmpFolder/6144580022869075475/query_h -v 3

Time for processing: 0h 0m 0s 2ms rmdb tmpFolder/6144580022869075475/query_ca -v 3

Time for processing: 0h 0m 0s 3ms rmdb tmpFolder/6144580022869075475/query_ss -v 3

Time for processing: 0h 0m 0s 4ms

[martin-steinegger]

This structure is just a single helix. Please see my answers here https://github.com/steineggerlab/foldseek/issues/105

[BinhongLiu]

Great! Thanks!