Seqanswers Leaderboard Ad

Collapse

Announcement

Collapse
No announcement yet.
X
 
  • Filter
  • Time
  • Show
Clear All
new posts

  • 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.

  • #2
    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

    Comment


    • #3
      Did you get any lead on this? I've similar query at this page.
      Bioinformaticscally calm

      Comment


      • #4
        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

        Comment


        • #5
          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

          Comment

          Latest Articles

          Collapse

          • seqadmin
            Best Practices for Single-Cell Sequencing Analysis
            by seqadmin



            While isolating and preparing single cells for sequencing was historically the bottleneck, recent technological advancements have shifted the challenge to data analysis. This highlights the rapidly evolving nature of single-cell sequencing. The inherent complexity of single-cell analysis has intensified with the surge in data volume and the incorporation of diverse and more complex datasets. This article explores the challenges in analysis, examines common pitfalls, offers...
            06-06-2024, 07:15 AM
          • seqadmin
            Latest Developments in Precision Medicine
            by seqadmin



            Technological advances have led to drastic improvements in the field of precision medicine, enabling more personalized approaches to treatment. This article explores four leading groups that are overcoming many of the challenges of genomic profiling and precision medicine through their innovative platforms and technologies.

            Somatic Genomics
            “We have such a tremendous amount of genetic diversity that exists within each of us, and not just between us as individuals,”...
            05-24-2024, 01:16 PM

          ad_right_rmr

          Collapse

          News

          Collapse

          Topics Statistics Last Post
          Started by seqadmin, Today, 07:24 AM
          0 responses
          9 views
          0 likes
          Last Post seqadmin  
          Started by seqadmin, Yesterday, 08:58 AM
          0 responses
          11 views
          0 likes
          Last Post seqadmin  
          Started by seqadmin, 06-12-2024, 02:20 PM
          0 responses
          15 views
          0 likes
          Last Post seqadmin  
          Started by seqadmin, 06-07-2024, 06:58 AM
          0 responses
          182 views
          0 likes
          Last Post seqadmin  
          Working...
          X