Comments (5)
Hello,
Could you please share a more detailed log file. e.g. what is the format of the your dosage file?
Thanks,
Wei
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from saige.
Hi Min-Lee,
Thank you for letting me know about the error. A bug was found in the savvy library for reading vcf and sav dosages and has now been fixed. You may try the new version 0.29.4 on vcf files and please let me know if you have any other question.
Thanks,
Wei
from saige.
Wei, Thanks!
After re-install 0.29.4, I still got the same error message for step2.
library(SAIGE)
SPAGMMATtest(
- vcfFile= "genotype_10markers.vcf.gz",
- vcfFileIndex="genotype_10markers.vcf.gz.tbi",
- vcfField="GT",
- chrom=1,
- minMAF=0.0001,
- minMAC=5,
- sampleFile="sampleIDindosage.txt",
- GMMATmodelFile="example.rda",
- varianceRatioFile="example.varianceRatio.txt",
- SAIGEOutputFile="example.SAIGE.vcf.dosage.out.txt",
- numLinesOutput=2,
- IsOutputAFinCaseCtrl=TRUE,
- )
1000 samples have been used to fit the glmm null model
obj.glmm.null$LOCO: FALSE
Leave-one-chromosome-out option is not applied
variance Ratio is 1
1000 sample IDs are found in sample file
[1] 1000 4
[1] "IID" "IndexInModel" "IndexDose.x" "IndexDose.y"
1000 samples were used in fitting the NULL glmm model and are found in sample file
minMAC: 5
minMAF: 1e-04
Minimum MAF of markers to be testd is 0.0025
Analysis started at 1537563549 Seconds
terminate called after throwing an instance of 'std::length_error'
what(): basic_string::_M_create
Abort (core dumped)
Could you please check it again?
Thanks!
Min-Lee
from saige.
Dear Wei and Min-Lee,
I was running into similar problems but think I resolved it by putting the chromosome number in quotation marks e.g. chrom="1" rather than chrom=1.
Hopefully this resolves it for you, too.
Best wishes,
Jamie
from saige.
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