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Old 04-17-2015, 10:14 AM   #1
TgodoyF
Junior Member
 
Location: Brazil

Join Date: Apr 2015
Posts: 1
Unhappy 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
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Old 04-17-2015, 10:25 AM   #2
Richard Finney
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Location: bethesda

Join Date: Feb 2009
Posts: 700
Default

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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affymetrix, apt-probeset-genotype, cel files, chicken

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