Entering edit mode
Dear bioinformaticians
im trying to genotype chip seq data file in CEL format , data type : axiom 1920 Axiom Pyrus 70K SNP arrays
I use affymetrix power tool in linux command line , see https://github.com/freeseek/gtc2vcf and
but when i run the the first step of genotyping , with the standard library file "GenomeWideSNP_6" i have the returning error " Unexpected Error: uncaught exception"
which doesnt indicate me anything about what's wrong
maybe i have to use different library file that fit well with my kind of data but i can't find it on affymetrix database
if you have any idea about this issue , thank you
/apt-probeset-genotype --feat-effects --read-models-brlmmp GenomeWideSNP_6.generic_prior.txt --probeset-ids GenomeWideSNP_6.random.20K.intersect.txt
--log-file probeset.log --write-models -xml-file GenomeWideSNP_6.apt-probeset-genotype.AxiomGT1.xml --out-dir $output --cel-files $cel --summaries --force
Loading options from file: GenomeWideSNP_6.apt-probeset-genotype.AxiomGT1.xml
set-analysis-name = AxiomGT1
chip-type = GenomeWideSNP_6
analysis = artifact-reduction.ResType=2.Clip=0.4.Close=2.Open=2.Fringe=4.CC=2,quant-norm.target=1000.sketch=50000,pm-only,brlmm-p.CM=1.bins=100.mix=1.bic=2.lambda=1.0.HARD=3.SB=0.75.transform=MVA.copyqc=0.00000.wobble=0.05.MS=0.15.copytype=-1.clustertype=2.ocean=0.00001.CSepPen=0.1.CSepThr=4
qmethod-spec = med-polish.expon=true
cdf-file = GenomeWideSNP_6.cdf
chrX-probes = GenomeWideSNP_6.chrXprobes
chrY-probes = GenomeWideSNP_6.chrYprobes
target-sketch = GenomeWideSNP_6.AxiomGT1.sketch
set-gender-method = cn-probe-chrXY-ratio
em-gender = false
female-thresh = 0.54
male-thresh = 1.0
Unexpected Error: uncaught exception.
