NanoASV file format requirements :

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Metadata requirements :

Your metadata.csv file should be a true CSV file, with coma. 

Example : 

    ,ID,Refs,Origin,Sampling_Date,Measure_1,Measure_2
    barcode01,1,Test01,Mock Community,01/01/00,1,1
    barcode02,2,Test02,Mock Community,01/01/00,2,2

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Reference file requirements :

- Correct fasta format with ">" based header, followed by sequence.
- Singleleaved and interleaved fasta files are both handled
- The header must at least contain a unique identifier. NanoASV can output a phyloseq object with no more taxonomy than the unique identifier.
- In order to be properly outputed by NanoASV, taxonomy must contain in correct order :
    * The unique identifier (ex: AP017610.220271.221808)
    * A whitespace between the unique ID and the taxonomic informations
    * Multi-level taxonomy must be separated with semicolons (;)
        NanoASV currently handles up to 25 taxonomic levels which should be enough for most application. If it's not, please open an issue on github.

When using personal reference file, you should use the --no-r-cleaning flag. R cleaning step has been mostly intended to work with SILVA and bacterial sequences.

Both the following are valid examples : 

    > AP017610.220271.221808 Bacteria;Proteobacteria;Gammaproteobacteria;Enterobacterales;Enterobacteriaceae;Escherichia-Shigella;Escherichia coli
    UUGAAGAGUUUGAUCAUGGCUCAGAUUGAACGCUGGCGGCAGGCCUAACACAUGCAAGUCGAACGGUAACAGGAAGCAGCUUGCUGCUUUGCUGACGAGUGGCGGACGGGUGAGUAAUGUCUGGGAAACUGCCUGAUGGAGGGGGAUAACUACUGGAAACGGUAGCUAAUACCGCAUAACGUCGCAAGACCAAAGAGGGGGACCUUCGGGCCUCUUGCCAUCGGAUGUGCCCAGAUGGGAUUAGCUAGUAGGUGGGGUAAAGGCUCACCUAGGCGACGAUCCCUAGCUGGUCUGAGAGGAUGACCAGCCACACUGGAACUGAGACACGGUCCAGACUCCUACGGGAGGCAGCAGUGGGGAAUAUUGCACAAUGGGCGCAAGCCUGAUGCAGCCAUGCCGCGUGUAUGAAGAAGGCCUUCGGGUUGUAAAGUACUUUCAGCGGGGAGGAAGGGAGUAAAGUUAAUACCUUUGCUCAUUGACGUUACCCGCAGAAGAAGCACCGGCUAACUCCGUGCCAGCAGCCGCGGUAAUACGGAGGGUGCAAGCGUUAAUCGGAAUUACUGGGCGUAAAGCGCACGCAGGCGGUUUGUUAAGUCAGAUGUGAAAUCCCCGGGCUCAACCUGGGAACUGCAUCUGAUACUGGCAAGCUUGAGUCUCGUAGAGGGGGGUAGAAUUCCAGGUGUAGCGGUGAAAUGCGUAGAGAUCUGGAGGAAUACCGGUGGCGAAGGCGGCCCCCUGGACGAAGACUGACGCUCAGGUGCGAAAGCGUGGGGAGCAAACAGGAUUAGAUACCCUGGUAGUCCACGCCGUAAACGAUGUCGACUUGGAGGUUGUGCCCUUGAGGCGUGGCUUCCGGAGCUAACGCGUUAAGUCGACCGCCUGGGGAGUACGGCCGCAAGGUUAAAACUCAAAUGAAUUGACGGGGGCCCGCACAAGCGGUGGAGCAUGUGGUUUAAUUCGAUGCAACGCGAAGAACCUUACCUGGUCUUGACAUCCACGGAAGUUUUCAGAGAUGAGAAUGUGCCUUCGGGAACCGUGAGACAGGUGCUGCAUGGCUGUCGUCAGCUCGUGUUGUGAAAUGUUGGGUUAAGUCCCGCAACGAGCGCAACCCUUAUCCUUUGUUGCCAGCGGUCCGGCCGGGAACUCAAAGGAGACUGCCAGUGAUAAACUGGAGGAAGGUGGGGAUGACGUCAAGUCAUCAUGGCCCUUACGACCAGGGCUACACACGUGCUACAAUGGCGCAUACAAAGAGAAGCGACCUCGCGAGAGCAAGCGGACCUCAUAAAGUGCGUCGUAGUCCGGAUUGGAGUCUGCAACUCGACUCCAUGAAGUCGGAAUCGCUAGUAAUCGUGGAUCAGAAUGCCACGGUGAAUACGUUCCCGGGCCUUGUACACACCGCCCGUCACACCAUGGGAGUGGGUUGCAAAAGAAGUAGGUAGCUUAACCUUCGGGAGGGCGCUUACCACUUUGUGAUUCAUGACUGGGGUGAAGUCGUAACAAGGUAACCGUAGGGGAACCUGCGGUUGGAUCACCUCCUU

    >AP017610.220271.221808 Bacteria;Proteobacteria;Gammaproteobacteria;Enterobacterales;Enterobacteriaceae;Escherichia-Shigella;Escherichia coli
    UUGAAGAGUUUGAUCAUGGCUCAGAUUGAACGCUGGCGGCAGGCCUAACACAUGCAAGUCGAACGGUAACAGGAAGCAGC
    UUGCUGCUUUGCUGACGAGUGGCGGACGGGUGAGUAAUGUCUGGGAAACUGCCUGAUGGAGGGGGAUAACUACUGGAAAC
    GGUAGCUAAUACCGCAUAACGUCGCAAGACCAAAGAGGGGGACCUUCGGGCCUCUUGCCAUCGGAUGUGCCCAGAUGGGA
    UUAGCUAGUAGGUGGGGUAAAGGCUCACCUAGGCGACGAUCCCUAGCUGGUCUGAGAGGAUGACCAGCCACACUGGAACU
    GAGACACGGUCCAGACUCCUACGGGAGGCAGCAGUGGGGAAUAUUGCACAAUGGGCGCAAGCCUGAUGCAGCCAUGCCGC
    GUGUAUGAAGAAGGCCUUCGGGUUGUAAAGUACUUUCAGCGGGGAGGAAGGGAGUAAAGUUAAUACCUUUGCUCAUUGAC
    GUUACCCGCAGAAGAAGCACCGGCUAACUCCGUGCCAGCAGCCGCGGUAAUACGGAGGGUGCAAGCGUUAAUCGGAAUUA
    CUGGGCGUAAAGCGCACGCAGGCGGUUUGUUAAGUCAGAUGUGAAAUCCCCGGGCUCAACCUGGGAACUGCAUCUGAUAC
    UGGCAAGCUUGAGUCUCGUAGAGGGGGGUAGAAUUCCAGGUGUAGCGGUGAAAUGCGUAGAGAUCUGGAGGAAUACCGGU
    GGCGAAGGCGGCCCCCUGGACGAAGACUGACGCUCAGGUGCGAAAGCGUGGGGAGCAAACAGGAUUAGAUACCCUGGUAG
    UCCACGCCGUAAACGAUGUCGACUUGGAGGUUGUGCCCUUGAGGCGUGGCUUCCGGAGCUAACGCGUUAAGUCGACCGCC
    UGGGGAGUACGGCCGCAAGGUUAAAACUCAAAUGAAUUGACGGGGGCCCGCACAAGCGGUGGAGCAUGUGGUUUAAUUCG
    AUGCAACGCGAAGAACCUUACCUGGUCUUGACAUCCACGGAAGUUUUCAGAGAUGAGAAUGUGCCUUCGGGAACCGUGAG
    ACAGGUGCUGCAUGGCUGUCGUCAGCUCGUGUUGUGAAAUGUUGGGUUAAGUCCCGCAACGAGCGCAACCCUUAUCCUUU
    GUUGCCAGCGGUCCGGCCGGGAACUCAAAGGAGACUGCCAGUGAUAAACUGGAGGAAGGUGGGGAUGACGUCAAGUCAUC
    AUGGCCCUUACGACCAGGGCUACACACGUGCUACAAUGGCGCAUACAAAGAGAAGCGACCUCGCGAGAGCAAGCGGACCU
    CAUAAAGUGCGUCGUAGUCCGGAUUGGAGUCUGCAACUCGACUCCAUGAAGUCGGAAUCGCUAGUAAUCGUGGAUCAGAA
    UGCCACGGUGAAUACGUUCCCGGGCCUUGUACACACCGCCCGUCACACCAUGGGAGUGGGUUGCAAAAGAAGUAGGUAGC
    UUAACCUUCGGGAGGGCGCUUACCACUUUGUGAUUCAUGACUGGGGUGAAGUCGUAACAAGGUAACCGUAGGGGAACCUG
    CGGUUGGAUCACCUCCUU

ERROR : An error arose with your metadata and or reference sequences input data. Please read carefully the above message before trying again.
