Error in getopt(spec = spec, opt = args) : long flag "bedFile" is invalid

[jingydz]

Command

Rscript /T01Data/zhangjj/software/SAIGE/extdata/step2_SPAtests.R
--bedFile=chr10.bed --bimFile=chr10.bim --famFile=chr10.fam
--AlleleOrder=alt-first
--SAIGEOutputFile=./output/plink.out.txt
--chrom=10 --minMAF=0 --minMAC=20
--GMMATmodelFile=./output/binary_includenonAutoforvarRatio.rda
--varianceRatioFile=./output/binary_includenonAutoforvarRatio.varianceRatio.txt
--is_output_moreDetails=TRUE

Error logfile

Loading required package: RhpcBLASctl
Error in parse_args(parser, positional_arguments = 0) :
Error in getopt(spec = spec, opt = args) : long flag "bedFile" is invalid
Execution halted

[liuze955]

Hi,jingydz
Have you solved this problem? I encountered the same problem during the second step

[QSchenKI]

Hi, I also encounter the same error.

[liuze955]

@QSchenKI Perhaps due to mine data itself, I was able to run normally without covariates, and false positives are not severe. Also, pay attention to the capitalization of parameters

[mohasal12]

Input

cd /mnt/work/workbench/mohasal/.conda/envs/saige/lib/R/library/r-saige/
/usr/bin/time -v Rscript step1_fitNULLGLMM.R
--plinkFile= /mnt/genotype/genotyped_PIDXXX437
--phenoFile= /mnt/work/phenotypes/phenotype.txt
--phenoCol=CD
--covarColList= BatchDetailed,PC1,PC2,PC3,PC4,PC5,PC6,PC7,PC8,PC9,PC10,PC11,PC12,PC13,PC14,PC15,PC16,PC17,PC18,PC19,PC20,BirthYear,CD
--sampleIDColinphenoFile=IID
--traitType=binary
--outputPrefix=/mnt/scratch/huntsaigeout/CD
--nThreads=4
--memoryChunk=8
--sexCol=Sex
--FemaleCode= 2
--MaleCode= 1
--LOCO=FALSE
--IsOverwriteVarianceRatioFile

Log

step1_fitNULLGLMM.R: error: Error in getopt(spec = spec, opt = args) :
"/mnt/genotype/genotyped_PIDXXX437" is not a valid option, or does not support an argument