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  • APT: 'Missing required column: ' source file: 'PriorsReader.cpp:352'

    I've used APT to process the CEL files to generate the cross-marker normalized signal intensity data from Axiom Genome-wide Chicken Array (Affymetrix).

    I've used this following command:

    apt-probeset-genotype -c Axiom_GW_GT_Chicken.r1.cdf -a birdseed --read-models-birdseed Axiom_GW_GT_Chicken.r1.AxiomGT1.models --special-snps Axiom_GW_GT_Chicken.r1.specialSNPs --out-dir apt --cel-files animal.txt

    When I runned this command, the program exited with a fatal error:

    FATAL ERROR:Exception. msg: 'Missing required column: ' source file: 'PriorsReader.cpp:352'

    Could someone help me to fix this problem??

    Thanks

  • #2
    What are the first few lines of your input files?

    Code is here which might give you a clue ...
    TsvPriorsReader::TsvPriorsReader(std::string path, std::set<const char *, Util::ltstr> *probeSetsToLoad)
    {
    affx::TsvFile tsv;
    std::string f_probeset_id;
    int f_copy_number;
    string chip;
    if (tsv.open(path) != affx::TSV_OK) {
    string msg = "Couldn't open file: '" + path + "' to read.";
    throw BroadException(msg.c_str(), __FILE__, __LINE__);
    }

    // check the fields we what are there.
    // we allow "id" as a alias for "probeset_id"
    int probeset_id_cidx = tsv.cname2cidx(0, "probeset_id", "id");
    if (probeset_id_cidx < 0) {
    throw BroadException("Missing required column: ", __FILE__, __LINE__, "probeset_id");
    }
    int copy_number_cidx = tsv.cname2cidx(0, "copy_number");
    if (copy_number_cidx < 0) {
    throw BroadException("Missing required column: ", __FILE__, __LINE__, "copy_number");
    }
    // allow for case in column names.
    int aa_cidx = tsv.cname2cidx(0, "AA", "aa");
    if (aa_cidx < 0) {
    throw BroadException("Missing required column: ", __FILE__, __LINE__, "AA");
    }

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