A large number of "Taxon not in mapping file" appeared when analyzing the gut microbes of mice,

Microbial community profiling HUMAnN
1

10/22/2023 06:40:40 PM - humann.utilities - INFO: Execute command: /data/home/wuzy/miniconda3/envs/mNGS/envs/humann3/bin/metaphlan /data/home/wuzy/mice_fece/temp/humann3/S1-3-4-LFJ12625_L1_humann_temp/tmpgie5tayh/tmp5d6mw0i1 -t rel_ab -o /data/home/wuzy/mice_fece/temp/humann3/S1-3-4-LFJ12625_L1_humann_temp/S1-3-4-LFJ12625_L1_metaphlan_bugs_list.tsv --input_type fastq --bowtie2out /data/home/wuzy/mice_fece/temp/humann3/S1-3-4-LFJ12625_L1_humann_temp/S1-3-4-LFJ12625_L1_metaphlan_bowtie2.txt --nproc 3
10/22/2023 07:57:38 PM - humann.utilities - DEBUG: b’WARNING: The metagenome profile contains clades that represent multiple species merged into a single representant.\nAn additional column listing the merged species is added to the MetaPhlAn output.\n’
10/22/2023 07:57:38 PM - humann.humann - INFO: TIMESTAMP: Completed prescreen : 4618 seconds
10/22/2023 07:57:38 PM - humann.search.prescreen - DEBUG: Taxon not in mapping file: k__Bacteria|p__Bacteria_unclassified|c__CFGB76064|o__OFGB76064|f__FGB76064|g__GGB20145|s__GGB20145_SGB41587|t__SGB41587 2||||||| 9.06899

10/22/2023 07:57:38 PM - humann.search.prescreen - DEBUG: Taxon not in mapping file: k__Bacteria|p__Firmicutes|c__CFGB76704|o__OFGB76704|f__FGB76704|g__GGB54153|s__GGB54153_SGB41631|t__SGB41631 2|1239|||||| 5.71748

10/22/2023 07:57:38 PM - humann.search.prescreen - DEBUG: Taxon not in mapping file: k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__GGB24132|s__GGB24132_SGB35935|t__SGB35935 2|1239|186801|186802|186806||| 4.4718

10/22/2023 07:57:38 PM - humann.search.prescreen - DEBUG: Taxon not in mapping file: k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Rikenellaceae_unclassified|s__Rikenellaceae_bacterium|t__SGB35894 2|976|200643|171549|171550||2049048| 4.17363

10/22/2023 07:57:38 PM - humann.search.prescreen - DEBUG: Taxon not in mapping file: k__Bacteria|p__Firmicutes|c__CFGB72926|o__OFGB72926|f__FGB72926|g__GGB3661|s__GGB3661_SGB41629|t__SGB41629 2|1239|||||| 2.76808

10/22/2023 07:57:38 PM - humann.search.prescreen - DEBUG: Taxon not in mapping file: k__Bacteria|p__Bacteroidetes|c__CFGB76719|o__OFGB76719|f__FGB76719|g__GGB23844|s__GGB23844_SGB35575|t__SGB35575 2|976|||||| 2.55019

10/22/2023 07:57:38 PM - humann.search.prescreen - DEBUG: Taxon not in mapping file: k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__GGB27481|s__GGB27481_SGB39777|t__SGB39777 2|1239|91061|186826|33958||| 2.42113

10/22/2023 07:57:38 PM - humann.search.prescreen - DEBUG: Taxon not in mapping file: k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Eubacteriales_unclassified|g__Eubacteriales_unclassified|s__Clostridiales_bacterium|t__SGB42493 2|1239|186801|186802|||1898207| 2.41936

10/22/2023 07:57:38 PM - humann.search.prescreen - DEBUG: Taxon not in mapping file: k__Bacteria|p__Proteobacteria|c__Deltaproteobacteria|o__Desulfovibrionales|f__Desulfovibrionaceae|g__Desulfovibrio|s__Desulfovibrio_SGB40192|t__SGB40192 2|1224|28221|213115|194924|872|| 2.22053

10/22/2023 07:57:38 PM - humann.search.prescreen - DEBUG: Taxon not in mapping file: k__Bacteria|p__Firmicutes|c__CFGB76310|o__OFGB76310|f__FGB76310|g__GGB3171|s__GGB3171_SGB4185|t__SGB4185 2|1239|||||| 2.2157

10/22/2023 07:57:38 PM - humann.search.prescreen - DEBUG: Taxon not in mapping file: k__Bacteria|p__Firmicutes|c__CFGB25109|o__OFGB25109|f__FGB25109|g__GGB28880|s__GGB28880_SGB41560|t__SGB41560 2|1239|||||| 1.95349

10/22/2023 07:57:38 PM - humann.search.prescreen - DEBUG: Taxon not in mapping file: k__Bacteria|p__Bacteroidetes|c__CFGB75970|o__OFGB75970|f__FGB75970|g__GGB24149|s__GGB24149_SGB35953|t__SGB35953 2|976|||||| 1.68045

10/22/2023 07:57:38 PM - humann.search.prescreen - DEBUG: Taxon not in mapping file: k__Bacteria|p__Firmicutes|c__CFGB6645|o__OFGB6645|f__FGB6645|g__GGB28991|s__GGB28991_SGB94889|t__SGB94889 2|1239|||||| 1.63904

10/22/2023 07:57:38 PM - humann.search.prescreen - DEBUG: Taxon not in mapping file: k__Bacteria|p__Firmicutes|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__GGB27929|s__GGB27929_SGB40368|t__SGB40368 2|1239|91061|1385|90964||| 1.61945

10/22/2023 07:57:38 PM - humann.search.prescreen - DEBUG: Taxon not in mapping file: k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__GGB28836|s__GGB28836_SGB41495|t__SGB41495 2|1239|186801|186802|186803||| 1.46872

10/22/2023 07:57:38 PM - humann.search.prescreen - DEBUG: Taxon not in mapping file: k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Muribaculaceae|g__Muribaculum|s__Muribaculum_gordoncarteri|t__SGB2087 2|976|200643|171549|2005473|1918540|2530390| 1.44898 k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Muribaculaceae|g__Muribaculaceae_unclassified|s__Muribaculaceae_bacterium_Isolate_102_HZI,k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Muribaculaceae|g__Muribaculum|s__Muribaculum_sp_NM65_B17

10/22/2023 07:57:38 PM - humann.search.prescreen - DEBUG: Taxon not in mapping file: k__Bacteria|p__Firmicutes|c__CFGB8152|o__OFGB8152|f__FGB8152|g__GGB28873|s__GGB28873_SGB41553|t__SGB41553 2|1239|||||| 1.42977

10/22/2023 07:57:38 PM - humann.search.prescreen - DEBUG: Taxon not in mapping file: k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__GGB49462|s__GGB49462_SGB43503|t__SGB43503 2|1239|186801|186802|216572||| 1.39912

10/22/2023 07:57:38 PM - humann.search.prescreen - DEBUG: Taxon not in mapping file: k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes_sp|t__SGB35892 2|976|200643|171549|171550|239759|1872444| 1.37902

10/22/2023 07:57:38 PM - humann.search.prescreen - DEBUG: Taxon not in mapping file: k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Muribaculaceae|g__Muribaculaceae_unclassified|s__Muribaculaceae_bacterium_Isolate_110_HZI|t__SGB21445 2|976|200643|171549|2005473||2486473| 1.26476

10/22/2023 07:57:38 PM - humann.search.prescreen - DEBUG: Taxon not in mapping file: k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__GGB30454|s__GGB30454_SGB43514|t__SGB43514 2|1239|186801|186802|216572||| 1.18671

10/22/2023 07:57:38 PM - humann.search.prescreen - DEBUG: Taxon not in mapping file: k__Bacteria|p__Firmicutes|c__CFGB3154|o__OFGB3154|f__FGB3154|g__GGB29549|s__GGB29549_SGB42343|t__SGB42343 2|1239|||||| 1.12329

10/22/2023 07:57:38 PM - humann.search.prescreen - DEBUG: Taxon not in mapping file: k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__GGB30461|s__GGB30461_SGB43530|t__SGB43530 2|1239|186801|186802|216572||| 1.05291

10/22/2023 07:57:38 PM - humann.search.prescreen - DEBUG: Taxon not in mapping file: k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__GGB30460|s__GGB30460_SGB63207|t__SGB63207 2|1239|186801|186802|216572||| 1.02586

10/22/2023 07:57:38 PM - humann.search.prescreen - DEBUG: Taxon not in mapping file: k__Bacteria|p__Bacteria_unclassified|c__Bacteria_unclassified|o__Bacteria_unclassified|f__Bacteria_unclassified|g__Bacteria_unclassified|s__bacterium_1XD8_76|t__SGB29429 2||||||2320115| 0.97779

10/22/2023 07:57:38 PM - humann.search.prescreen - DEBUG: Taxon not in mapping file: k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Muribaculaceae|g__Muribaculaceae_unclassified|s__Muribaculaceae_bacterium|t__SGB21431 2|976|200643|171549|2005473||2498093| 0.95868

10/22/2023 07:57:38 PM - humann.search.prescreen - DEBUG: Taxon not in mapping file: k__Bacteria|p__Proteobacteria|c__CFGB76404|o__OFGB76404|f__FGB76404|g__GGB30667|s__GGB30667_SGB43809|t__SGB43809 2|1224|||||| 0.70046

10/22/2023 07:57:38 PM - humann.search.prescreen - DEBUG: Taxon not in mapping file: k__Bacteria|p__Bacteroidetes|c__CFGB76349|o__OFGB76349|f__FGB76349|g__GGB27861|s__GGB27861_SGB40295|t__SGB40295 2|976|||||| 0.69235

10/22/2023 07:57:38 PM - humann.search.prescreen - DEBUG: Taxon not in mapping file: k__Bacteria|p__Bacteria_unclassified|c__CFGB8157|o__OFGB8157|f__FGB8157|g__GGB28901|s__GGB28901_SGB41592|t__SGB41592 2||||||| 0.68648

10/22/2023 07:57:38 PM - humann.search.prescreen - DEBUG: Taxon not in mapping file: k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__GGB27873|s__GGB27873_SGB40307|t__SGB40307 2|1239|186801|186802|186803||| 0.68347

10/22/2023 07:57:38 PM - humann.search.prescreen - DEBUG: Taxon not in mapping file: k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Muribaculaceae|g__Muribaculaceae_unclassified|s__Muribaculaceae_bacterium_Isolate_013_NCI|t__SGB27767 2|976|200643|171549|2005473||2489218| 0.68296

10/22/2023 07:57:38 PM - humann.search.prescreen - DEBUG: Taxon not in mapping file: k__Bacteria|p__Bacteria_unclassified|c__CFGB76064|o__OFGB76064|f__FGB76064|g__GGB28895|s__GGB28895_SGB41576|t__SGB41576 2||||||| 0.66187
…

2

Is this situation related to the incompatibility of the metaphlan’s mpa_vOct22_CHOCOPhlAnSGB_202212.tar database and humann’s full_chocophlan.v201901_v31.tar.gz, and can the results be used?

3

MetaPhlAn 4 includes many new mouse-associated species (SGBs) that were assembled directly from mouse metagenomes. They have no equivalents in the HUMAnN 3 database to map against in compatibility, which is why you’re seeing this error.

4

Thanks for your answer.
If the specific species is not found in HUMAnN3, will it search for higher-level species? Is it possible that the species annotations may lack accuracy?

5

HUMAnN is focused on species-level profiling. Anything that can’t be assigned to a known species is forwarded to (taxonomy-agnostic) translated search. It is possible to assign some approximate taxonomy to the results of translated search using the infer_taxonomy script (in HUMAnN 2-3).