Mercurial > repos > iuc > extract_metaphlan_database
comparison test-data/SRS014464-Anterior_nares-abundances-samefiledifferentname.tabular @ 13:1fa07868c0f3 draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/metaphlan commit 26cbf16569d13b7ddbbbd99fc49ec15ce312a992
| author | iuc |
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| date | Fri, 14 Nov 2025 13:48:12 +0000 |
| parents | 6a1db3b02ea7 |
| children |
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| 12:db58d5898fea | 13:1fa07868c0f3 |
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| 1 #custom_db | 1 #test-db |
| 2 #mpa_v21_CHOCOPhlAnxxx_2 | 2 #/home/ubuntu/miniconda3/envs/__metaphlan@4.2.4/bin/metaphlan in --input_type fasta --read_min_len 70 --bt2_ps sensitive --min_mapq_val 5 --db_dir /home/ubuntu/Documents/glxy/git/tools-iuc/tools/metaphlan/test-data/test-db --index test-db -t rel_ab --tax_lev a --stat avg_g --stat_q 0.2 --perc_nonzero 0.33 --avoid_disqm --sample_id_key SampleID --sample_id Metaphlan_Analysis -o /tmp/tmpm9x253n7/job_working_directory/000/7/outputs/dataset_98364280-d229-4257-888e-ac290df6e8ca.dat --mapout mapout -s /tmp/tmpm9x253n7/job_working_directory/000/7/outputs/dataset_a8ceac4e-3f7c-47e6-bcc3-084f104ca1d8.dat --nproc 1 --offline |
| 3 #/home/bebatut/miniconda3/envs/mulled-v1-b4915a464cf72db4053ec566c65e3f5f431691323f08f9b6b1c9ecfc4f8b9c88/bin/metaphlan in --input_type fasta --read_min_len 70 --bowtie2db ref_db/ --index custom_db --bt2_ps very-sensitive --min_mapq_val 5 -t rel_ab --tax_lev a --min_cu_len 2000 --add_viruses --stat_q 0.2 --perc_nonzero 0.33 --avoid_disqm --sample_id_key SampleID --sample_id Metaphlan_Analysis -o /tmp/tmptu3575j7/files/000/dataset_19.dat --bowtie2out bowtie2out -s /tmp/tmptu3575j7/files/000/dataset_21.dat --biom /tmp/tmptu3575j7/files/000/dataset_22.dat --nproc 1 | 3 #17695 reads processed |
| 4 #SampleID Metaphlan_Analysis | 4 #SampleID Metaphlan_Analysis |
| 5 #clade_name NCBI_tax_id relative_abundance additional_species | 5 #clade_name NCBI_tax_id relative_abundance additional_species |
| 6 UNCLASSIFIED -1 0.0 | |
| 6 k__Bacteria 2 100.0 | 7 k__Bacteria 2 100.0 |
| 7 k__Bacteria|p__Proteobacteria 2|1224 52.20019 | 8 k__Bacteria|p__Proteobacteria 2|1224 40.77283 |
| 8 k__Bacteria|p__Actinobacteria 2|201174 34.37371 | 9 k__Bacteria|p__Firmicutes 2|1239 33.30552 |
| 9 k__Bacteria|p__Firmicutes 2|1239 13.4261 | 10 k__Bacteria|p__Actinobacteria 2|201174 23.9357 |
| 10 k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria 2|1224|1236 52.20019 | 11 k__Bacteria|p__Bacteroidetes 2|976 1.98596 |
| 11 k__Bacteria|p__Actinobacteria|c__Actinobacteria 2|201174|1760 34.37371 | 12 k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria 2|1224|1236 40.77283 |
| 12 k__Bacteria|p__Firmicutes|c__Bacilli 2|1239|91061 13.4261 | 13 k__Bacteria|p__Firmicutes|c__Bacilli 2|1239|91061 33.30552 |
| 13 k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pseudomonadales 2|1224|1236|72274 52.20019 | 14 k__Bacteria|p__Actinobacteria|c__Actinobacteria 2|201174|1760 23.9357 |
| 14 k__Bacteria|p__Actinobacteria|c__Actinobacteria|o__Corynebacteriales 2|201174|1760|85007 24.7409 | 15 k__Bacteria|p__Bacteroidetes|c__Bacteroidia 2|976|200643 1.98596 |
| 15 k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales 2|1239|91061|186826 13.4261 | 16 k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pseudomonadales 2|1224|1236|72274 40.77283 |
| 16 k__Bacteria|p__Actinobacteria|c__Actinobacteria|o__Propionibacteriales 2|201174|1760|85009 9.63281 | 17 k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales 2|1239|91061|186826 33.30552 |
| 17 k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pseudomonadales|f__Moraxellaceae 2|1224|1236|72274|468 52.20019 | 18 k__Bacteria|p__Actinobacteria|c__Actinobacteria|o__Propionibacteriales 2|201174|1760|85009 16.85816 |
| 18 k__Bacteria|p__Actinobacteria|c__Actinobacteria|o__Corynebacteriales|f__Corynebacteriaceae 2|201174|1760|85007|1653 24.7409 | 19 k__Bacteria|p__Actinobacteria|c__Actinobacteria|o__Corynebacteriales 2|201174|1760|85007 7.07754 |
| 19 k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae 2|1239|91061|186826|186828 13.4261 | 20 k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales 2|976|200643|171549 1.98596 |
| 20 k__Bacteria|p__Actinobacteria|c__Actinobacteria|o__Propionibacteriales|f__Propionibacteriaceae 2|201174|1760|85009|31957 9.63281 | 21 k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pseudomonadales|f__Moraxellaceae 2|1224|1236|72274|468 40.77283 |
| 21 k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pseudomonadales|f__Moraxellaceae|g__Moraxella 2|1224|1236|72274|468|475 52.20019 | 22 k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae 2|1239|91061|186826|186828 29.38877 |
| 22 k__Bacteria|p__Actinobacteria|c__Actinobacteria|o__Corynebacteriales|f__Corynebacteriaceae|g__Corynebacterium 2|201174|1760|85007|1653|1716 24.7409 | 23 k__Bacteria|p__Actinobacteria|c__Actinobacteria|o__Propionibacteriales|f__Propionibacteriaceae 2|201174|1760|85009|31957 16.85816 |
| 23 k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Dolosigranulum 2|1239|91061|186826|186828|29393 13.4261 | 24 k__Bacteria|p__Actinobacteria|c__Actinobacteria|o__Corynebacteriales|f__Corynebacteriaceae 2|201174|1760|85007|1653 7.07754 |
| 24 k__Bacteria|p__Actinobacteria|c__Actinobacteria|o__Propionibacteriales|f__Propionibacteriaceae|g__Cutibacterium 2|201174|1760|85009|31957|1912216 9.63281 | 25 k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Aerococcaceae 2|1239|91061|186826|186827 3.91675 |
| 25 k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pseudomonadales|f__Moraxellaceae|g__Moraxella|s__Moraxella_lacunata 2|1224|1236|72274|468|475|477 22.57968 | 26 k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae 2|976|200643|171549|171552 1.98596 |
| 26 k__Bacteria|p__Actinobacteria|c__Actinobacteria|o__Corynebacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium_pseudodiphtheriticum 2|201174|1760|85007|1653|1716|37637 18.75365 | 27 k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pseudomonadales|f__Moraxellaceae|g__Moraxella 2|1224|1236|72274|468|475 40.77283 |
| 27 k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pseudomonadales|f__Moraxellaceae|g__Moraxella|s__Moraxella_nonliquefaciens 2|1224|1236|72274|468|475|478 15.88652 | 28 k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Dolosigranulum 2|1239|91061|186826|186828|29393 29.38877 |
| 28 k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pseudomonadales|f__Moraxellaceae|g__Moraxella|s__Moraxella_equi 2|1224|1236|72274|468|475|60442 13.73399 | 29 k__Bacteria|p__Actinobacteria|c__Actinobacteria|o__Propionibacteriales|f__Propionibacteriaceae|g__Cutibacterium 2|201174|1760|85009|31957|1912216 16.85816 |
| 29 k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Dolosigranulum|s__Dolosigranulum_pigrum 2|1239|91061|186826|186828|29393|29394 13.4261 | 30 k__Bacteria|p__Actinobacteria|c__Actinobacteria|o__Corynebacteriales|f__Corynebacteriaceae|g__Corynebacterium 2|201174|1760|85007|1653|1716 7.07754 |
| 30 k__Bacteria|p__Actinobacteria|c__Actinobacteria|o__Propionibacteriales|f__Propionibacteriaceae|g__Cutibacterium|s__Cutibacterium_acnes 2|201174|1760|85009|31957|1912216|1747 9.63281 | 31 k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Globicatella 2|1239|91061|186826|186827|13075 3.91675 |
| 31 k__Bacteria|p__Actinobacteria|c__Actinobacteria|o__Corynebacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium_accolens 2|201174|1760|85007|1653|1716|38284 5.98726 | 32 k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella 2|976|200643|171549|171552|838 1.98596 |
| 33 k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Dolosigranulum|s__Dolosigranulum_pigrum 2|1239|91061|186826|186828|29393|29394 29.38877 | |
| 34 k__Bacteria|p__Actinobacteria|c__Actinobacteria|o__Propionibacteriales|f__Propionibacteriaceae|g__Cutibacterium|s__Cutibacterium_acnes 2|201174|1760|85009|31957|1912216|1747 16.85816 | |
| 35 k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pseudomonadales|f__Moraxellaceae|g__Moraxella|s__Moraxella_nonliquefaciens 2|1224|1236|72274|468|475|478 11.04599 | |
| 36 k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pseudomonadales|f__Moraxellaceae|g__Moraxella|s__Moraxella_equi 2|1224|1236|72274|468|475|60442 9.86276 | |
| 37 k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pseudomonadales|f__Moraxellaceae|g__Moraxella|s__Moraxella_caprae 2|1224|1236|72274|468|475|90240 7.62178 | |
| 38 k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pseudomonadales|f__Moraxellaceae|g__Moraxella|s__Moraxella_lacunata 2|1224|1236|72274|468|475|477 4.28841 | |
| 39 k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Globicatella|s__Globicatella_sanguinis 2|1239|91061|186826|186827|13075|13076 3.91675 | |
| 40 k__Bacteria|p__Actinobacteria|c__Actinobacteria|o__Corynebacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium_pseudodiphtheriticum 2|201174|1760|85007|1653|1716|37637 3.25437 | |
| 41 k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pseudomonadales|f__Moraxellaceae|g__Moraxella|s__Moraxella_pluranimalium 2|1224|1236|72274|468|475|470453 2.85431 | |
| 42 k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pseudomonadales|f__Moraxellaceae|g__Moraxella|s__Moraxella_ovis 2|1224|1236|72274|468|475|29433 2.5544 | |
| 43 k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pseudomonadales|f__Moraxellaceae|g__Moraxella|s__Moraxella_catarrhalis 2|1224|1236|72274|468|475|480 2.54518 | |
| 44 k__Bacteria|p__Actinobacteria|c__Actinobacteria|o__Corynebacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium_accolens 2|201174|1760|85007|1653|1716|38284 2.44888 | |
| 45 k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella_timonensis 2|976|200643|171549|171552|838|386414 1.98596 | |
| 46 k__Bacteria|p__Actinobacteria|c__Actinobacteria|o__Corynebacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium_pseudogenitalium 2|201174|1760|85007|1653|1716|38303 1.3743 | |
| 47 k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pseudomonadales|f__Moraxellaceae|g__Moraxella|s__Moraxella_equi|t__GCA_002027555 2|1224|1236|72274|468|475|60442| 8.13478 | |
| 48 k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pseudomonadales|f__Moraxellaceae|g__Moraxella|s__Moraxella_caprae|t__GCA_900453285 2|1224|1236|72274|468|475|90240| 7.62178 | |
| 49 k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Dolosigranulum|s__Dolosigranulum_pigrum|t__GCA_000245815 2|1239|91061|186826|186828|29393|29394| 5.70862 | |
| 50 k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pseudomonadales|f__Moraxellaceae|g__Moraxella|s__Moraxella_nonliquefaciens|t__GCA_001679155 2|1224|1236|72274|468|475|478| 4.79602 | |
| 51 k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pseudomonadales|f__Moraxellaceae|g__Moraxella|s__Moraxella_lacunata|t__GCA_001679225 2|1224|1236|72274|468|475|477| 4.28841 | |
| 52 k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Globicatella|s__Globicatella_sanguinis|t__GCA_002847845 2|1239|91061|186826|186827|13075|13076| 3.91675 | |
| 53 k__Bacteria|p__Actinobacteria|c__Actinobacteria|o__Propionibacteriales|f__Propionibacteriaceae|g__Cutibacterium|s__Cutibacterium_acnes|t__GCA_002572775 2|201174|1760|85009|31957|1912216|1747| 3.84553 | |
| 54 k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pseudomonadales|f__Moraxellaceae|g__Moraxella|s__Moraxella_nonliquefaciens|t__GCA_001679125 2|1224|1236|72274|468|475|478| 3.69469 | |
| 55 k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Dolosigranulum|s__Dolosigranulum_pigrum|t__GCA_003264045 2|1239|91061|186826|186828|29393|29394| 3.39602 | |
| 56 k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Dolosigranulum|s__Dolosigranulum_pigrum|t__GCA_003264065 2|1239|91061|186826|186828|29393|29394| 3.28678 | |
| 57 k__Bacteria|p__Actinobacteria|c__Actinobacteria|o__Corynebacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium_pseudodiphtheriticum|t__GCA_000466825 2|201174|1760|85007|1653|1716|37637| 3.25437 | |
| 58 k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Dolosigranulum|s__Dolosigranulum_pigrum|t__GCA_003263975 2|1239|91061|186826|186828|29393|29394| 3.23401 | |
| 59 k__Bacteria|p__Actinobacteria|c__Actinobacteria|o__Propionibacteriales|f__Propionibacteriaceae|g__Cutibacterium|s__Cutibacterium_acnes|t__GCA_003384345 2|201174|1760|85009|31957|1912216|1747| 3.00006 | |
| 60 k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pseudomonadales|f__Moraxellaceae|g__Moraxella|s__Moraxella_pluranimalium|t__GCA_002014825 2|1224|1236|72274|468|475|470453| 2.85431 | |
| 61 k__Bacteria|p__Actinobacteria|c__Actinobacteria|o__Propionibacteriales|f__Propionibacteriaceae|g__Cutibacterium|s__Cutibacterium_acnes|t__GCA_001660855 2|201174|1760|85009|31957|1912216|1747| 2.57775 | |
| 62 k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pseudomonadales|f__Moraxellaceae|g__Moraxella|s__Moraxella_nonliquefaciens|t__GCA_001679005 2|1224|1236|72274|468|475|478| 2.55528 | |
| 63 k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pseudomonadales|f__Moraxellaceae|g__Moraxella|s__Moraxella_ovis|t__GCA_900453155 2|1224|1236|72274|468|475|29433| 2.5544 | |
| 64 k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Dolosigranulum|s__Dolosigranulum_pigrum|t__GCA_003264145 2|1239|91061|186826|186828|29393|29394| 2.55209 | |
| 65 k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pseudomonadales|f__Moraxellaceae|g__Moraxella|s__Moraxella_catarrhalis|t__GCA_000193085 2|1224|1236|72274|468|475|480| 2.54518 | |
| 66 k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Dolosigranulum|s__Dolosigranulum_pigrum|t__GCA_003263915 2|1239|91061|186826|186828|29393|29394| 2.44642 | |
| 67 k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Dolosigranulum|s__Dolosigranulum_pigrum|t__GCA_003264015 2|1239|91061|186826|186828|29393|29394| 2.42412 | |
| 68 k__Bacteria|p__Actinobacteria|c__Actinobacteria|o__Propionibacteriales|f__Propionibacteriaceae|g__Cutibacterium|s__Cutibacterium_acnes|t__GCA_000144045 2|201174|1760|85009|31957|1912216|1747| 2.16928 | |
| 69 k__Bacteria|p__Actinobacteria|c__Actinobacteria|o__Propionibacteriales|f__Propionibacteriaceae|g__Cutibacterium|s__Cutibacterium_acnes|t__GCA_000302515 2|201174|1760|85009|31957|1912216|1747| 2.09203 | |
| 70 k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Dolosigranulum|s__Dolosigranulum_pigrum|t__GCA_003264135 2|1239|91061|186826|186828|29393|29394| 2.07154 | |
| 71 k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella_timonensis|t__GCA_000177055 2|976|200643|171549|171552|838|386414| 1.98596 | |
| 72 k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Dolosigranulum|s__Dolosigranulum_pigrum|t__GCA_003263965 2|1239|91061|186826|186828|29393|29394| 1.82646 | |
| 73 k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pseudomonadales|f__Moraxellaceae|g__Moraxella|s__Moraxella_equi|t__GCA_900453335 2|1224|1236|72274|468|475|60442| 1.72798 | |
| 74 k__Bacteria|p__Actinobacteria|c__Actinobacteria|o__Propionibacteriales|f__Propionibacteriaceae|g__Cutibacterium|s__Cutibacterium_acnes|t__GCA_003384285 2|201174|1760|85009|31957|1912216|1747| 1.43296 | |
| 75 k__Bacteria|p__Actinobacteria|c__Actinobacteria|o__Corynebacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium_accolens|t__GCA_000146485 2|201174|1760|85007|1653|1716|38284| 1.41285 | |
| 76 k__Bacteria|p__Actinobacteria|c__Actinobacteria|o__Corynebacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium_pseudogenitalium|t__GCA_000156615 2|201174|1760|85007|1653|1716|38303| 1.3743 | |
| 77 k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Dolosigranulum|s__Dolosigranulum_pigrum|t__GCA_003264005 2|1239|91061|186826|186828|29393|29394| 1.30558 | |
| 78 k__Bacteria|p__Actinobacteria|c__Actinobacteria|o__Propionibacteriales|f__Propionibacteriaceae|g__Cutibacterium|s__Cutibacterium_acnes|t__GCA_000144005 2|201174|1760|85009|31957|1912216|1747| 1.18889 | |
| 79 k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Dolosigranulum|s__Dolosigranulum_pigrum|t__GCA_003264085 2|1239|91061|186826|186828|29393|29394| 1.13712 | |
| 80 k__Bacteria|p__Actinobacteria|c__Actinobacteria|o__Corynebacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium_accolens|t__GCA_000159115 2|201174|1760|85007|1653|1716|38284| 1.03602 | |
| 81 k__Bacteria|p__Actinobacteria|c__Actinobacteria|o__Propionibacteriales|f__Propionibacteriaceae|g__Cutibacterium|s__Cutibacterium_acnes|t__GCA_001481615 2|201174|1760|85009|31957|1912216|1747| 0.55165 |