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  • yingeddi2008
    replied
    Still trying to figure out how to construct the taxonomy file

    Hi everyone,

    I am still trying to figure out how to construct the taxonomy file. What is the rule for putting the taxonomy ID and name together? Any leads will be appreciated.

    Thanks,

    Eddi

    Leave a comment:


  • danova
    replied
    I found this script useful to retrain SILVA.

    FROGS is a galaxy/CLI workflow designed to produce an OTUs count matrix from high depth sequencing amplicon data. - geraldinepascal/FROGS

    Leave a comment:


  • bio_informatics
    replied
    Did you get any lead on this? I've similar query at this page.

    Leave a comment:


  • yingeddi2008
    replied
    I am trying to use SILVA database to train RDP classifier to species level. I don't even know how the taxonomy file is generated. And in the RDP README file, it didn't say neither...I don't know how this retrain feature is useful

    Leave a comment:


  • greigite
    started a topic RDP classifier training issues

    RDP classifier training issues

    I am unsuccessfully attempting to retrain the RDP classifier, version 2.7 on the UNITE fungal database. I have tried reformatting and generating a custom tax file with entries like this, following the examples in the sample files folder:
    Code:
    0*Root*-1*0*rootrank
    1*Fungi*0*1*domain
    2*Chytridiomycota*1*2*phylum
    3*Neocallimastigomycetes*2*3*class
    4*Neocallimastigales*3*4*order
    5*Neocallimastigaceae*4*5*family
    6*Piromyces*5*6*genus
    7*Piromyces_sp_I_GRL_10*6*7*species
    8*Piromyces_sp_D_GRL_5*6*7*species
    9*Piromyces_sp_AF_CTS_BTP1*6*7*species
    10*Orpinomyces*5*6*genus
    11*Orpinomyces_sp_NIANP60*10*7*species
    12*Orpinomyces_sp_AF_CTS_BTO1*10*7*species
    13*Orpinomyces_sp_AF_CTS_CHO3*10*7*species
    I reformatted the headers in the UNITE file to look like this:
    Code:
    >Phaeoacremonium_pallidum|EU128053|SH114132.06FU|refs|r__Root;d__Fungi;p__Ascomycota;c__Sordariomycetes;o__Diaporthales;f__Togniniaceae;g__Phaeoacremonium;s__Phaeoacremonium_pallidum;
    However, running the following command
    Code:
    java -jar rdp_classifier_2.7/dist/classifier.jar train --seq sh_
    input.fasta -t rdp_tax_file.txt -o ~/rdp_classifier/
    gives the following error:
    Code:
    Exception in thread "main" java.lang.NumberFormatException: For input string: ""
            at java.lang.NumberFormatException.forInputString(NumberFormatException.java:65)
            at java.lang.Integer.parseInt(Integer.java:504)
            at java.lang.Integer.<init>(Integer.java:677)
            at edu.msu.cme.rdp.classifier.train.TreeFactory.addSequencewithTaxid(TreeFactory.java:157)
            at edu.msu.cme.rdp.classifier.train.TreeFactory.addSequence(TreeFactory.java:141)
            at edu.msu.cme.rdp.classifier.train.ClassifierTraineeMaker.<init>(ClassifierTraineeMaker.java:72)
            at edu.msu.cme.rdp.classifier.train.ClassifierTraineeMaker.main(ClassifierTraineeMaker.java:171)
            at edu.msu.cme.rdp.classifier.cli.ClassifierMain.main(ClassifierMain.java:60)
    Can anyone help me figure this out? Pretty sure I am missing something quite obvious, like for example changing the fasta headers to match the numbers in the tax file.

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