evalue filtering via -e flag. Evalue becomes zero when specified e-value threshold is < 1E-45 for easy-search

[chrismacdermaid]

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.

[milot-mirdita]

I think I know what's going on. We read the value as float (instead of double) during command line parameter parsing. I can look into fixing it later. The lowest you should be currently able to specify is about 1e-38.

[milot-mirdita]

Should be fixed now. Statically built binaries with the fix will be available at http://mmseqs.com/latest/ in about an hour. We will also make a new release in the next few weeks.

[chrismacdermaid]

Terrific. Thank you. I'll let you know if things behave accordingly. I suspected it might be single precision float, but the numbers weren't quite lining up. Glad you all were able to pinpoint it and fix it so quickly. Much appreciated.