evalue filtering via -e flag. Evalue becomes zero when specified e-value threshold is < 1E-45 for easy-search #379
Description
Maybe I'm going crazy, but this really does seem like a bug. Perhaps there's something obvious here, but I'm not seeing it.
Expected Behavior
Returning hits with e-values less than specified e-value threshold on the command line when using easy-search.
Current Behavior
e-value threshold becomes zero when specified e-value < 1E-45
mmseqs easy-search da7915829ba14fe0a86c3cc539a89f43.constructs.fa /db/mmseqs/uniprotkb_swiss-prot result.m8 /dev/shm/tmp3343 -e 1E-46
MMseqs Version: 12.113e3
Substitution matrix nucl:nucleotide.out,aa:blosum62.out
Add backtrace false
Alignment mode 3
Allow wrapped scoring false
E-value threshold 0
Seq. id. threshold 0
Min alignment length 0
Steps to Reproduce (for bugs)
Run an easy-search. Specift an e-value threshold < 1E-45
MMseqs Output (for bugs)
MMseqs Version: 12.113e3
Substitution matrix nucl:nucleotide.out,aa:blosum62.out
Add backtrace false
Alignment mode 3
Allow wrapped scoring false
E-value threshold 0
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
Realign hits false
Max reject 2147483647
Max accept 2147483647
Include identical seq. id. false
Preload mode 0
Pseudo count a 1
Pseudo count b 1.5
Score bias 0
Gap open cost nucl:5,aa:11
Gap extension cost nucl:2,aa:1
Zdrop 40
Threads 96
Compressed 0
Verbosity 3
Seed substitution matrix nucl:nucleotide.out,aa:VTML80.out
Sensitivity 5.7
k-mer length 0
k-score 2147483647
Alphabet size nucl:5,aa:21
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 lower case residues 0
Minimum diagonal score 15
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 0.001
Global sequence weighting false
Allow deletions false
Filter MSA 1
Maximum seq. id. threshold 0.9
Minimum seq. id. 0
Minimum score per column -20
Minimum coverage 0
Select N most diverse seqs 1000
Omit consensus false
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
Chain overlapping alignments 0
Merge query 1
Search type 0
Search iterations 1
Start sensitivity 4
Search steps 1
Slice search mode false
Strand selection 1
Disk space limit 0
MPI runner
Force restart with latest tmp false
Remove temporary files true
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
Context
Want to identify close homologues in uniprotkb from RCSB. Filtering by e-value seems a reasonable choice.
Your Environment
Installed via a fresh miniconda env last week.