Discrepancy between MMseqs search and MMseqs taxonomy

[pbelmann]

Hi all,

if I run the following mmseqs taxonomy command I get for my protein sequence the Clostridium AM magnum hit.

mmseqs taxonomy queryDB /vol/scratch/databases/mmseqs2/gtdb/out/gtdb_database test.faa.gz tmp  --lca-ranks superkingdom,phylum,class,order,family,genus,species,subspecies -c 0.8 --max-seqs 300 --max-accept 50 --cov-mode 0 -e 0.001 --e-profile 0.01  -s 6 --threads 28  --blacklist ""

mmseqs  createtsv queryDB 14_First_11_21_S2_binned.gtdb.taxresults.database  test.taxonomy.tsv --threads 28

test.taxonomy.tsv output:

14_First_11_21_S2_bin.16_6644_ef2cc1_CJIKHDKB_00326     30313   species Clostridium AM magnum   Bacteria;Bacillota A;Clostridia;Clostridiales;Clostridiaceae;Clostridium AM;Clostridium AM magnum;uc_Clostridium AM magnum

If I repeat the same with mmseqs search I get following hits:

mmseqs search queryDB /vol/scratch/databases/mmseqs2/gtdb/out/gtdb_database test.faa.gz tmp  --max-seqs 300 --max-accept 50 --cov-mode 0 -e 0.001 --e-profile 0.01  -s 6 --threads 28
mmseqs convertalis queryDB /vol/scratch/databases/mmseqs2/gtdb/out/gtdb_database test.faa.gz mmseqs.out.tsv

mmseqs.out.tsv output:

uery                                                target                  pident  alnlen  mismatch  gapopen  qstart  qend  tstart  tend  evalue     bits  qlen  tlen  qcov   tcov
14_First_11_21_S2_bin.16_6644_ef2cc1_CJIKHDKB_00326  NZ_JH601103.1_106       88.200  163     19        0        1       163   1       163   1.803E-90  301   164   164   0.994  0.994
14_First_11_21_S2_bin.16_6644_ef2cc1_CJIKHDKB_00326  NZ_FMWM01000002.1_685   49.700  154     76        0        7       159   5       158   6.046E-36  144   164   170   0.933  0.906
14_First_11_21_S2_bin.16_6644_ef2cc1_CJIKHDKB_00326  NZ_FLQT01000003.1_544   49.200  154     77        0        7       159   5       158   2.131E-35  143   164   167   0.933  0.922
14_First_11_21_S2_bin.16_6644_ef2cc1_CJIKHDKB_00326  NZ_LT707417.1_163       49.100  154     77        0        7       159   5       158   2.921E-35  142   164   167   0.933  0.922
14_First_11_21_S2_bin.16_6644_ef2cc1_CJIKHDKB_00326  JAEXBU010000001.1_1     49.000  154     78        0        7       159   5       158   4.002E-35  142   164   167   0.933  0.922
14_First_11_21_S2_bin.16_6644_ef2cc1_CJIKHDKB_00326  NZ_OPYI01000008.1_105   48.900  154     78        0        7       159   5       158   5.484E-35  141   164   167   0.933  0.922
14_First_11_21_S2_bin.16_6644_ef2cc1_CJIKHDKB_00326  NZ_CAIJCS010000014.1_2  48.600  155     79        0        5       158   6       160   7.514E-35  141   164   171   0.939  0.906
14_First_11_21_S2_bin.16_6644_ef2cc1_CJIKHDKB_00326  CABJAE010000022.1_14    48.700  154     78        0        7       159   5       158   1.030E-34  141   164   167   0.933  0.922
14_First_11_21_S2_bin.16_6644_ef2cc1_CJIKHDKB_00326  CYUK01000003.1_1117     48.100  156     80        0        5       159   3       158   1.411E-34  140   164   174   0.945  0.897

From the mmseqs search output one can see that the top hit (NZ_JH601103.1), has the best target, query coverage and evalue.
The top hit belongs to the organism Dolosigranulum pigrum https://www.ncbi.nlm.nih.gov/nuccore/NZ_JH601103 which has the following taxonomy:

d__Bacteria; p__Bacillota; c__Bacilli; o__Lactobacillales; f__Carnobacteriaceae; g__Dolosigranulum; s__Dolosigranulum pigrum

I wonder how this discrepancy between the taxonomy of the mmseqs search top hit and the taxonomy provided by mmseqs taxonomy can happen?

Steps to Reproduce (for bugs)

The gtdb database I used, can be downloaded here

The test sequence can be found here

Your Environment

Include as many relevant details about the environment you experienced the bug in.

• Git commit used (The string after "MMseqs Version:" when you execute MMseqs without any parameters): 0b27c9d
• Which MMseqs version was used (Statically-compiled, self-compiled, Homebrew, etc.): self-compiled
• For self-compiled and Homebrew: Compiler and Cmake versions used and their invocation: cmake: 3.16.3
• Server specifications (especially CPU support for AVX2/SSE and amount of system memory): 236 GB RAM
• Operating system and version: Ubuntu 20.04.6