Mock community quality control

This notebook maps observed mock community sequences, which are technically from unknown organisms, to "trueish" taxonomies, i.e., the most likely taxonomic match given a list of expected sequences derived from the input strains. This serves two purposes:

We can then use trueish taxonomies to calculate per-sequence precision/recall scores
Mismatch profiles give us a quantitative assessment of the overall "quality" of a mock community (or at least the quality control methods used to process it).



In [8]:

    
from tax_credit import mock_quality
from os.path import expandvars, join

Define paths to tax-credit repository directory, mockrobiota repository directory, and reference database directory.



In [9]:

    
data_dir = expandvars('$HOME/Desktop/projects/tax-credit/')
mockrobiota_dir = expandvars('$HOME/Desktop/projects/mockrobiota/')
ref_dir = expandvars("$HOME/Desktop/ref_dbs/")

Identify location of your reference databases.



In [12]:

    
ref_dbs = [('greengenes',
            join(ref_dir, 'gg_13_8_otus', 'rep_set', '99_otus.fasta'),
            join(ref_dir, 'gg_13_8_otus', 'taxonomy', '99_otu_taxonomy.txt')),
           ('unite',
            join(ref_dir, 'sh_qiime_release_20.11.2016', 'developer', 'sh_refs_qiime_ver7_99_20.11.2016_dev.fasta'),
            join(ref_dir, 'sh_qiime_release_20.11.2016', 'developer', 'sh_taxonomy_qiime_ver7_99_20.11.2016_dev.txt'))]

Now generate reference sequence/taxonomy dictionaries.



In [13]:

    
refs, taxs = mock_quality.ref_db_to_dict(ref_dbs)

Establish expected sequences and taxonomies



In [15]:

    
mock_quality.match_expected_seqs_to_taxonomy(data_dir, mockrobiota_dir, refs, taxs)









    



mock-1
mock-10
mock-12
mock-13
mock-14
mock-15
mock-16
mock-18
mock-19
mock-2
mock-20
mock-21
mock-22
mock-23
mock-24
mock-25
mock-26






    



---------------------------------------------------------------------------
RuntimeError                              Traceback (most recent call last)
<ipython-input-15-860b175f25f6> in <module>()
----> 1 mock_quality.match_expected_seqs_to_taxonomy(data_dir, mockrobiota_dir, refs, taxs)

/Users/nbokulich/Desktop/projects/tax-credit/tax_credit/mock_quality.py in match_expected_seqs_to_taxonomy(data_dir, mockrobiota_dir, refs, taxs)
    125             taxonomy_map = taxs['unite']
    126         else:
--> 127             raise RuntimeError('could not find identifiers for ' + community)
    128 
    129         # set the destinations

RuntimeError: could not find identifiers for mock-26-ITS1

Map sequences that match to taxonomies



In [16]:

    
mock_quality.generate_trueish_taxonomies(data_dir)









    



mock-1
Guessed taxonomy for 233471 of 319244 reads (73.1%)






    












    












    



mock-10
Guessed taxonomy for 69364 of 130135 reads (53.3%)






    












    












    



mock-12
Guessed taxonomy for 1493872 of 1496419 reads (99.8%)






    












    












    



mock-13
WARNING: d23fbef2f31d48eda40876cdbc49933a matches
k__Bacteria; p__Firmicutes; c__Bacilli; o__Bacillales; f__Staphylococcaceae; g__Staphylococcus; s__epidermidis and
k__Bacteria; p__Firmicutes; c__Bacilli; o__Bacillales; f__Staphylococcaceae; g__Staphylococcus; s__aureus
with 0 mismatches
Guessed taxonomy for 276692 of 279467 reads (99.0%)






    












    












    



mock-14
WARNING: d23fbef2f31d48eda40876cdbc49933a matches
k__Bacteria; p__Firmicutes; c__Bacilli; o__Bacillales; f__Staphylococcaceae; g__Staphylococcus; s__epidermidis and
k__Bacteria; p__Firmicutes; c__Bacilli; o__Bacillales; f__Staphylococcaceae; g__Staphylococcus; s__aureus
with 0 mismatches
Guessed taxonomy for 276964 of 281575 reads (98.4%)






    












    












    



mock-15
WARNING: d23fbef2f31d48eda40876cdbc49933a matches
k__Bacteria; p__Firmicutes; c__Bacilli; o__Bacillales; f__Staphylococcaceae; g__Staphylococcus; s__epidermidis and
k__Bacteria; p__Firmicutes; c__Bacilli; o__Bacillales; f__Staphylococcaceae; g__Staphylococcus; s__aureus
with 0 mismatches
Guessed taxonomy for 483648 of 488167 reads (99.1%)






    












    












    



mock-16
WARNING: a75469000b685732e36dab747a2cb7be matches
k__Bacteria; p__Aquificae; c__Aquificae; o__Aquificales; f__Hydrogenothermaceae; g__Sulfurihydrogenibium; s__ and
k__Bacteria; p__Aquificae; c__Aquificae; o__Aquificales; f__Hydrogenothermaceae; g__Sulfurihydrogenibium; s__yellowstonense
with 0 mismatches
WARNING: 71377a659973f8108dec7aadcaed7c4e matches
k__Bacteria; p__Actinobacteria; c__Actinobacteria; o__Actinomycetales; f__Micromonosporaceae; g__Salinispora; s__arenicola and
k__Bacteria; p__Proteobacteria; c__Betaproteobacteria; o__Burkholderiales; f__Burkholderiaceae; g__Salinispora; s__tropica
with 0 mismatches
Guessed taxonomy for 544486 of 560707 reads (97.1%)






    












    












    



mock-18
Guessed taxonomy for 151227 of 151546 reads (99.8%)






    












    












    



mock-19
WARNING: no expected taxonomy for Escherichia Coli ATCC-11775 5005 (LC140935)
WARNING: no expected taxonomy for Escherichia Coli ATCC-11775 5001 (LC140931)
WARNING: no expected taxonomy for Escherichia Coli ATCC-11775 5001 (LC140931)
WARNING: no expected taxonomy for Escherichia Coli ATCC-11775 5003 (LC140933)
WARNING: no expected taxonomy for Escherichia Coli ATCC-11775 5501 (LC140936)
WARNING: no expected taxonomy for Escherichia Coli ATCC-11775 5004 (LC140934)
WARNING: no expected taxonomy for Escherichia Coli ATCC-11775 5501 (LC140936)
WARNING: no expected taxonomy for Escherichia Coli ATCC-11775 5501 (LC140936)
WARNING: no expected taxonomy for Escherichia Coli ATCC-11775 6001 (LC140938)
WARNING: no expected taxonomy for Escherichia Coli ATCC-11775 5502 (LC140937)
WARNING: no expected taxonomy for Escherichia Coli ATCC-11775 5002 (LC140932)
WARNING: no expected taxonomy for Escherichia Coli ATCC-11775 5004 (LC140934)
WARNING: no expected taxonomy for Escherichia Coli ATCC-11775 5003 (LC140933)
WARNING: no expected taxonomy for Escherichia Coli ATCC-11775 5002 (LC140932)
WARNING: no expected taxonomy for Escherichia Coli ATCC-11775 6001 (LC140938)
WARNING: no expected taxonomy for Escherichia Coli ATCC-11775 5003 (LC140933)
WARNING: no expected taxonomy for Escherichia Coli ATCC-11775 5005 (LC140935)
Guessed taxonomy for 121782 of 121784 reads (100.0%)






    












    












    



mock-2
Guessed taxonomy for 89024 of 193506 reads (46.0%)






    












    












    



mock-20
WARNING: d23fbef2f31d48eda40876cdbc49933a matches
k__Bacteria; p__Firmicutes; c__Bacilli; o__Bacillales; f__Staphylococcaceae; g__Staphylococcus; s__epidermidis and
k__Bacteria; p__Firmicutes; c__Bacilli; o__Bacillales; f__Staphylococcaceae; g__Staphylococcus; s__aureus
with 0 mismatches
Guessed taxonomy for 118783 of 118875 reads (99.9%)






    












    












    



mock-21
WARNING: d23fbef2f31d48eda40876cdbc49933a matches
k__Bacteria; p__Firmicutes; c__Bacilli; o__Bacillales; f__Staphylococcaceae; g__Staphylococcus; s__epidermidis and
k__Bacteria; p__Firmicutes; c__Bacilli; o__Bacillales; f__Staphylococcaceae; g__Staphylococcus; s__aureus
with 0 mismatches
Guessed taxonomy for 127060 of 127106 reads (100.0%)






    












    












    



mock-22
WARNING: 333a40af36286f867e8e903e420016d4 matches
k__Bacteria; p__Firmicutes; c__Bacilli; o__Bacillales; f__Staphylococcaceae; g__Staphylococcus; s__epidermidis and
k__Bacteria; p__Firmicutes; c__Bacilli; o__Bacillales; f__Staphylococcaceae; g__Staphylococcus; s__aureus
with 0 mismatches
Guessed taxonomy for 300472 of 300869 reads (99.9%)






    












    












    



mock-23
WARNING: 333a40af36286f867e8e903e420016d4 matches
k__Bacteria; p__Firmicutes; c__Bacilli; o__Bacillales; f__Staphylococcaceae; g__Staphylococcus; s__epidermidis and
k__Bacteria; p__Firmicutes; c__Bacilli; o__Bacillales; f__Staphylococcaceae; g__Staphylococcus; s__aureus
with 0 mismatches
WARNING: a7b0c414b25cce98084fb827cf1a301d matches
k__Bacteria; p__Firmicutes; c__Bacilli; o__Bacillales; f__Staphylococcaceae; g__Staphylococcus; s__epidermidis and
k__Bacteria; p__Firmicutes; c__Bacilli; o__Bacillales; f__Staphylococcaceae; g__Staphylococcus; s__aureus
with 0 mismatches
Guessed taxonomy for 285837 of 286569 reads (99.7%)






    












    












    



mock-24
Guessed taxonomy for 342833 of 452198 reads (75.8%)






    












    












    



mock-25
Guessed taxonomy for 32752 of 571197 reads (5.7%)






    












    












    



mock-26
WARNING: no expected taxonomy for JQ912668.1 Melampsora larici-populina 18S ribosomal RNA gene, partial sequence; internal transcribed spacer 1, 5.8S ribosomal RNA gene, and internal transcribed spacer 2, complete sequence; and 28S ribosomal RNA gene, partial sequence
WARNING: no expected taxonomy for JQ912672.1 Mucor hiemalis 18S ribosomal RNA gene, partial sequence; internal transcribed spacer 1, 5.8S ribosomal RNA gene, and internal transcribed spacer 2, complete sequence; and 28S ribosomal RNA gene, partial sequence
WARNING: no expected taxonomy for JQ912668.1 Melampsora larici-populina 18S ribosomal RNA gene, partial sequence; internal transcribed spacer 1, 5.8S ribosomal RNA gene, and internal transcribed spacer 2, complete sequence; and 28S ribosomal RNA gene, partial sequence
WARNING: no expected taxonomy for JQ912668.1 Melampsora larici-populina 18S ribosomal RNA gene, partial sequence; internal transcribed spacer 1, 5.8S ribosomal RNA gene, and internal transcribed spacer 2, complete sequence; and 28S ribosomal RNA gene, partial sequence
Guessed taxonomy for 166594 of 215489 reads (77.3%)






    












    












    



mock-26-ITS1
WARNING: no expected taxonomy for JQ912668.1 Melampsora larici-populina 18S ribosomal RNA gene, partial sequence; internal transcribed spacer 1, 5.8S ribosomal RNA gene, and internal transcribed spacer 2, complete sequence; and 28S ribosomal RNA gene, partial sequence
Guessed taxonomy for 14375 of 14720 reads (97.7%)






    












    












    



mock-26-ITS9
WARNING: no expected taxonomy for JQ912668.1 Melampsora larici-populina 18S ribosomal RNA gene, partial sequence; internal transcribed spacer 1, 5.8S ribosomal RNA gene, and internal transcribed spacer 2, complete sequence; and 28S ribosomal RNA gene, partial sequence
WARNING: no expected taxonomy for JQ912672.1 Mucor hiemalis 18S ribosomal RNA gene, partial sequence; internal transcribed spacer 1, 5.8S ribosomal RNA gene, and internal transcribed spacer 2, complete sequence; and 28S ribosomal RNA gene, partial sequence
WARNING: no expected taxonomy for JQ912668.1 Melampsora larici-populina 18S ribosomal RNA gene, partial sequence; internal transcribed spacer 1, 5.8S ribosomal RNA gene, and internal transcribed spacer 2, complete sequence; and 28S ribosomal RNA gene, partial sequence
Guessed taxonomy for 95300 of 99634 reads (95.7%)






    












    












    



mock-3
WARNING: 47ad35356a9bfec68416d32e4f039021 matches
k__Bacteria; p__Firmicutes; c__Bacilli; o__Bacillales; f__Staphylococcaceae; g__Staphylococcus; s__epidermidis and
k__Bacteria; p__Firmicutes; c__Bacilli; o__Bacillales; f__Staphylococcaceae; g__Staphylococcus; s__aureus
with 0 mismatches
Guessed taxonomy for 47135 of 47138 reads (100.0%)






    












    












    



mock-4
WARNING: 67235d72777dee5f2000c1e478dd6418 matches
k__Bacteria; p__Firmicutes; c__Bacilli; o__Bacillales; f__Staphylococcaceae; g__Staphylococcus; s__epidermidis and
k__Bacteria; p__Firmicutes; c__Bacilli; o__Bacillales; f__Staphylococcaceae; g__Staphylococcus; s__aureus
with 1 mismatches
WARNING: 3df62c132a582a43d98dfebb37cb0aa6 matches
k__Bacteria; p__Firmicutes; c__Bacilli; o__Bacillales; f__Staphylococcaceae; g__Staphylococcus; s__epidermidis and
k__Bacteria; p__Firmicutes; c__Bacilli; o__Bacillales; f__Staphylococcaceae; g__Staphylococcus; s__aureus
with 1 mismatches
WARNING: 3ffcfd0d3dfc80d4bdc4b0683f93c8c8 matches
k__Bacteria; p__Firmicutes; c__Bacilli; o__Bacillales; f__Staphylococcaceae; g__Staphylococcus; s__epidermidis and
k__Bacteria; p__Firmicutes; c__Bacilli; o__Bacillales; f__Staphylococcaceae; g__Staphylococcus; s__aureus
with 1 mismatches
WARNING: 47ad35356a9bfec68416d32e4f039021 matches
k__Bacteria; p__Firmicutes; c__Bacilli; o__Bacillales; f__Staphylococcaceae; g__Staphylococcus; s__epidermidis and
k__Bacteria; p__Firmicutes; c__Bacilli; o__Bacillales; f__Staphylococcaceae; g__Staphylococcus; s__aureus
with 0 mismatches
Guessed taxonomy for 3080266 of 3081208 reads (100.0%)






    












    












    



mock-5
WARNING: ee1b612bdfeeba0d53109b502aebe259 matches
k__Bacteria; p__Firmicutes; c__Bacilli; o__Bacillales; f__Staphylococcaceae; g__Staphylococcus; s__epidermidis and
k__Bacteria; p__Firmicutes; c__Bacilli; o__Bacillales; f__Staphylococcaceae; g__Staphylococcus; s__aureus
with 1 mismatches
WARNING: 57228ea8e79d75f4fe69ef08aeba0162 matches
k__Bacteria; p__Firmicutes; c__Bacilli; o__Bacillales; f__Staphylococcaceae; g__Staphylococcus; s__epidermidis and
k__Bacteria; p__Firmicutes; c__Bacilli; o__Bacillales; f__Staphylococcaceae; g__Staphylococcus; s__aureus
with 1 mismatches
WARNING: 4a93a83d1cfff363ca16a6fe13780c61 matches
k__Bacteria; p__Firmicutes; c__Bacilli; o__Bacillales; f__Staphylococcaceae; g__Staphylococcus; s__epidermidis and
k__Bacteria; p__Firmicutes; c__Bacilli; o__Bacillales; f__Staphylococcaceae; g__Staphylococcus; s__aureus
with 0 mismatches
WARNING: 131b92d6eaea53fa125993149cada791 matches
k__Bacteria; p__Firmicutes; c__Bacilli; o__Bacillales; f__Staphylococcaceae; g__Staphylococcus; s__epidermidis and
k__Bacteria; p__Firmicutes; c__Bacilli; o__Bacillales; f__Staphylococcaceae; g__Staphylococcus; s__aureus
with 1 mismatches
WARNING: 9e414c6586c71306d3f35f4c4b5eb3c3 matches
k__Bacteria; p__Firmicutes; c__Bacilli; o__Bacillales; f__Staphylococcaceae; g__Staphylococcus; s__epidermidis and
k__Bacteria; p__Firmicutes; c__Bacilli; o__Bacillales; f__Staphylococcaceae; g__Staphylococcus; s__aureus
with 1 mismatches
WARNING: 52437216aa4e0e30bbe5f69bac13a845 matches
k__Bacteria; p__Firmicutes; c__Bacilli; o__Bacillales; f__Staphylococcaceae; g__Staphylococcus; s__epidermidis and
k__Bacteria; p__Firmicutes; c__Bacilli; o__Bacillales; f__Staphylococcaceae; g__Staphylococcus; s__aureus
with 1 mismatches
WARNING: f077e8929e3596b83d3530c237ae9a13 matches
k__Bacteria; p__Firmicutes; c__Bacilli; o__Bacillales; f__Staphylococcaceae; g__Staphylococcus; s__epidermidis and
k__Bacteria; p__Firmicutes; c__Bacilli; o__Bacillales; f__Staphylococcaceae; g__Staphylococcus; s__aureus
with 1 mismatches
WARNING: 9d73df644ff01f45832ecde0436f923f matches
k__Bacteria; p__Firmicutes; c__Bacilli; o__Bacillales; f__Staphylococcaceae; g__Staphylococcus; s__epidermidis and
k__Bacteria; p__Firmicutes; c__Bacilli; o__Bacillales; f__Staphylococcaceae; g__Staphylococcus; s__aureus
with 1 mismatches
Guessed taxonomy for 5721973 of 5722274 reads (100.0%)






    












    












    



mock-6
WARNING: 9b8f0d83faa2a954da84393a42117591 matches
k__Bacteria; p__Bacteroidetes; c__Bacteroidia; o__Bacteroidales; f__Bacteroidaceae; g__Bacteroides; s__caccae and
k__Bacteria; p__Bacteroidetes; c__Bacteroidia; o__Bacteroidales; f__Bacteroidaceae; g__Bacteroides; s__eggerthii and
k__Bacteria; p__Bacteroidetes; c__Bacteroidia; o__Bacteroidales; f__Bacteroidaceae; g__Bacteroides; s__ovatus
with 0 mismatches
WARNING: dcbd5871b1651983690b99f16fc67118 matches
k__Bacteria; p__Actinobacteria; c__Actinobacteria; o__Bifidobacteriales; f__Bifidobacteriaceae; g__Bifidobacterium; s__adolescentis and
k__Bacteria; p__Actinobacteria; c__Actinobacteria; o__Bifidobacteriales; f__Bifidobacteriaceae; g__Bifidobacterium; s__breve
with 1 mismatches
WARNING: a212b558e5bc499d44e46aeff1d347ff matches
k__Bacteria; p__Proteobacteria; c__Gammaproteobacteria; o__Enterobacteriales; f__Enterobacteriaceae; g__Providencia; s__stuartii and
k__Bacteria; p__Proteobacteria; c__Gammaproteobacteria; o__Enterobacteriales; f__Enterobacteriaceae; g__Proteus; s__ and
k__Bacteria; p__Proteobacteria; c__Gammaproteobacteria; o__Enterobacteriales; f__Enterobacteriaceae; g__Enterobacter; s__cancerogenus and
k__Bacteria; p__Proteobacteria; c__Gammaproteobacteria; o__Enterobacteriales; f__Enterobacteriaceae; g__Edwardsiella; s__
with 3 mismatches
WARNING: 5370f673232483505b6bd7cc56d92885 matches
k__Bacteria; p__Proteobacteria; c__Gammaproteobacteria; o__Enterobacteriales; f__Enterobacteriaceae; g__Providencia; s__stuartii and
k__Bacteria; p__Proteobacteria; c__Gammaproteobacteria; o__Enterobacteriales; f__Enterobacteriaceae; g__Proteus; s__ and
k__Bacteria; p__Proteobacteria; c__Gammaproteobacteria; o__Enterobacteriales; f__Enterobacteriaceae; g__Enterobacter; s__cancerogenus and
k__Bacteria; p__Proteobacteria; c__Gammaproteobacteria; o__Enterobacteriales; f__Enterobacteriaceae; g__Edwardsiella; s__
with 0 mismatches
WARNING: 6e636eb1f6c483664bc5fd61ca884ba9 matches
k__Bacteria; p__Firmicutes; c__Clostridia; o__Clostridiales; f__Lachnospiraceae; g__Butyrivibrio; s__crossotus and
k__Bacteria; p__Firmicutes; c__Clostridia; o__Clostridiales; f__Lachnospiraceae; g__Blautia; s__ and
k__Bacteria; p__Firmicutes; c__Clostridia; o__Clostridiales; f__Lachnospiraceae; g__Dorea; s__formicigenerans and
k__Bacteria; p__Firmicutes; c__Clostridia; o__Clostridiales; f__Lachnospiraceae; g__Ruminococcus; s__lactaris and
k__Bacteria; p__Firmicutes; c__Clostridia; o__Clostridiales; f__Lachnospiraceae; g__Clostridium; s__hathewayi
with 0 mismatches
WARNING: 514b00ebe859de1ff3ba60b3e28f685b matches
k__Bacteria; p__Bacteroidetes; c__Bacteroidia; o__Bacteroidales; f__Bacteroidaceae; g__Bacteroides; s__caccae and
k__Bacteria; p__Bacteroidetes; c__Bacteroidia; o__Bacteroidales; f__Bacteroidaceae; g__Bacteroides; s__eggerthii and
k__Bacteria; p__Bacteroidetes; c__Bacteroidia; o__Bacteroidales; f__Bacteroidaceae; g__Bacteroides; s__ovatus
with 1 mismatches
WARNING: b76682c0d27fcf2d800d26fbc6e52a92 matches
k__Bacteria; p__Proteobacteria; c__Gammaproteobacteria; o__Enterobacteriales; f__Enterobacteriaceae; g__Providencia; s__stuartii and
k__Bacteria; p__Proteobacteria; c__Gammaproteobacteria; o__Enterobacteriales; f__Enterobacteriaceae; g__Proteus; s__ and
k__Bacteria; p__Proteobacteria; c__Gammaproteobacteria; o__Enterobacteriales; f__Enterobacteriaceae; g__Enterobacter; s__cancerogenus and
k__Bacteria; p__Proteobacteria; c__Gammaproteobacteria; o__Enterobacteriales; f__Enterobacteriaceae; g__Edwardsiella; s__
with 2 mismatches
WARNING: 8245c26edb85fd0bded260a3fd8a4d27 matches
k__Bacteria; p__Firmicutes; c__Clostridia; o__Clostridiales; f__Clostridiaceae; g__Clostridium; s__hiranonis and
k__Bacteria; p__Firmicutes; c__Clostridia; o__Clostridiales; f__Peptostreptococcaceae; g__Clostridium; s__bartlettii
with 0 mismatches
WARNING: 251b588c9358a42ea6e6c83dde425376 matches
k__Bacteria; p__Actinobacteria; c__Coriobacteriia; o__Coriobacteriales; f__Coriobacteriaceae; g__Collinsella; s__ and
k__Bacteria; p__Actinobacteria; c__Coriobacteriia; o__Coriobacteriales; f__Coriobacteriaceae; g__Collinsella; s__stercoris
with 0 mismatches
WARNING: 4a207ca16e01e7b0f9e6c5cda1217063 matches
k__Bacteria; p__Actinobacteria; c__Actinobacteria; o__Bifidobacteriales; f__Bifidobacteriaceae; g__Bifidobacterium; s__adolescentis and
k__Bacteria; p__Actinobacteria; c__Actinobacteria; o__Bifidobacteriales; f__Bifidobacteriaceae; g__Bifidobacterium; s__breve
with 0 mismatches
Guessed taxonomy for 591841 of 608716 reads (97.2%)






    












    












    



mock-7
WARNING: 138e5efefb28c54e724d270954529b47 matches
k__Bacteria; p__Actinobacteria; c__Actinobacteria; o__Bifidobacteriales; f__Bifidobacteriaceae; g__Bifidobacterium; s__adolescentis and
k__Bacteria; p__Actinobacteria; c__Actinobacteria; o__Bifidobacteriales; f__Bifidobacteriaceae; g__Bifidobacterium; s__breve
with 1 mismatches
WARNING: 148744b83b8ca9df502e6ddbb9adc745 matches
k__Bacteria; p__Actinobacteria; c__Actinobacteria; o__Bifidobacteriales; f__Bifidobacteriaceae; g__Bifidobacterium; s__adolescentis and
k__Bacteria; p__Actinobacteria; c__Actinobacteria; o__Bifidobacteriales; f__Bifidobacteriaceae; g__Bifidobacterium; s__breve
with 1 mismatches
WARNING: c110dc917e48de08978e6ca40711768e matches
k__Bacteria; p__Proteobacteria; c__Gammaproteobacteria; o__Enterobacteriales; f__Enterobacteriaceae; g__Providencia; s__stuartii and
k__Bacteria; p__Proteobacteria; c__Gammaproteobacteria; o__Enterobacteriales; f__Enterobacteriaceae; g__Providencia; s__
with 1 mismatches
WARNING: 97e6ccfd8b780926ede87c1dbfffe04e matches
k__Bacteria; p__Actinobacteria; c__Actinobacteria; o__Bifidobacteriales; f__Bifidobacteriaceae; g__Bifidobacterium; s__adolescentis and
k__Bacteria; p__Actinobacteria; c__Actinobacteria; o__Bifidobacteriales; f__Bifidobacteriaceae; g__Bifidobacterium; s__breve
with 0 mismatches
Guessed taxonomy for 205680 of 257206 reads (80.0%)






    












    












    



mock-8
WARNING: bc3c153ca462b642a602abddd8d6b55c matches
k__Bacteria; p__Proteobacteria; c__Gammaproteobacteria; o__Enterobacteriales; f__Enterobacteriaceae; g__Providencia; s__stuartii and
k__Bacteria; p__Proteobacteria; c__Gammaproteobacteria; o__Enterobacteriales; f__Enterobacteriaceae; g__Providencia; s__
with 1 mismatches
WARNING: 8716180dd3f0257f482d16113fc9fb2c matches
k__Bacteria; p__Actinobacteria; c__Actinobacteria; o__Bifidobacteriales; f__Bifidobacteriaceae; g__Bifidobacterium; s__adolescentis and
k__Bacteria; p__Actinobacteria; c__Actinobacteria; o__Bifidobacteriales; f__Bifidobacteriaceae; g__Bifidobacterium; s__breve
with 1 mismatches
WARNING: 98acd48dbdfb0a7fb4d751c57fbd31fd matches
k__Bacteria; p__Actinobacteria; c__Actinobacteria; o__Bifidobacteriales; f__Bifidobacteriaceae; g__Bifidobacterium; s__adolescentis and
k__Bacteria; p__Actinobacteria; c__Actinobacteria; o__Bifidobacteriales; f__Bifidobacteriaceae; g__Bifidobacterium; s__ and
k__Bacteria; p__Actinobacteria; c__Actinobacteria; o__Bifidobacteriales; f__Bifidobacteriaceae; g__Bifidobacterium; s__breve
with 3 mismatches
WARNING: e91217bb6b2afd5826dfe6c9df535bef matches
k__Bacteria; p__Actinobacteria; c__Actinobacteria; o__Bifidobacteriales; f__Bifidobacteriaceae; g__Bifidobacterium; s__adolescentis and
k__Bacteria; p__Actinobacteria; c__Actinobacteria; o__Bifidobacteriales; f__Bifidobacteriaceae; g__Bifidobacterium; s__breve
with 2 mismatches
Guessed taxonomy for 191978 of 259433 reads (74.0%)






    












    












    



mock-9
WARNING: no expected taxonomy for GQ458041.1 Debaryomyces hansenii strain ATCC 60978 18S ribosomal RNA gene, partial sequence; internal transcribed spacer 1, 5.8S ribosomal RNA gene, and internal transcribed spacer 2, complete sequence; and 28S ribosomal RNA gene, partial sequence
WARNING: no expected taxonomy for KY104576.1 Pichia kudriavzevii culture-collection CBS:2457 small subunit ribosomal RNA gene, partial sequence; internal transcribed spacer 1, 5.8S ribosomal RNA gene, and internal transcribed spacer 2, complete sequence; and large subunit ribosomal RNA gene, partial sequence
WARNING: 3b7b9fa2c7520ded4f910be5e93836bb matches
k__Fungi;p__Ascomycota;c__Saccharomycetes;o__Saccharomycetales;f__Pichiaceae;g__Pichia; s__ and
NO-EXPECTED-TAXONOMY
with 0 mismatches
WARNING: no expected taxonomy for AM943655.1 Zygosaccharomyces rouxii 5S rRNA gene, 18S rRNA gene, ITS1, 5.8S rRNA gene, ITS2 and 25S rRNA gene, strain CBS 732
WARNING: no expected taxonomy for KY103054.1 Cyberlindnera jadinii culture-collection CBS:567 small subunit ribosomal RNA gene, partial sequence; internal transcribed spacer 1, 5.8S ribosomal RNA gene, and internal transcribed spacer 2, complete sequence; and large subunit ribosomal RNA gene, partial sequence
WARNING: no expected taxonomy for KY104576.1 Pichia kudriavzevii culture-collection CBS:2457 small subunit ribosomal RNA gene, partial sequence; internal transcribed spacer 1, 5.8S ribosomal RNA gene, and internal transcribed spacer 2, complete sequence; and large subunit ribosomal RNA gene, partial sequence
WARNING: 87911359940e653775ec69e92ce60108 matches
k__Fungi;p__Ascomycota;c__Saccharomycetes;o__Saccharomycetales;f__Pichiaceae;g__Pichia; s__ and
NO-EXPECTED-TAXONOMY
with 1 mismatches
WARNING: no expected taxonomy for KY104576.1 Pichia kudriavzevii culture-collection CBS:2457 small subunit ribosomal RNA gene, partial sequence; internal transcribed spacer 1, 5.8S ribosomal RNA gene, and internal transcribed spacer 2, complete sequence; and large subunit ribosomal RNA gene, partial sequence
WARNING: 65300481deec02196e65f2f7d7e4b9b7 matches
k__Fungi;p__Ascomycota;c__Saccharomycetes;o__Saccharomycetales;f__Pichiaceae;g__Pichia; s__ and
NO-EXPECTED-TAXONOMY
with 1 mismatches
Guessed taxonomy for 42316 of 68711 reads (61.6%)



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