error when training prediction model using the example data

[ruoxichen5]

Hi dear PrediXcan group,

I ran into a "invalid option" error when I was trying to custom the prediction model using the example input and script (train_models.py). The recommended version of python and R were already in the default environment.

[rchen7@hii example] python train_models.py qsub -v study=gEUVADIS,expr_RDS=../../data/intermediate/expression_phenotypes/geuvadis.expr.RDS,geno=../../data/intermediate/genotypes/geuvadis.snps.chr1.txt,gene_annot=../../data/intermediate/annotations/gene_annotation/gencode.v12.genes.parsed.RDS,snp_annot=../../data/intermediate/annotations/snp_annotation/geuvadis.annot.chr1.RDS,n_k_folds=10,alpha=0.5,out_dir=../../data/intermediate/model_by_chr/,chrom=1,snpset=HapMap,window=1e6 -N gEUVADIS_model_chr1 -d /hii/work/r/rchen7/project/predixcan/PredictDBPipeline/joblogs/example train_model_by_chr.pbs Unknown option: d Usage: qsub [-a start_time] [-A account] [-e err_path] [-I] [-l resource_list] [-m mail_options] [-M user_list] [-N job_name] [-o out_path] [-p priority] [-q destination] [-v variable_list] [-V] [-W additional_attributes] [-h] [script]

qsub -v study=gEUVADIS,expr_RDS=../../data/intermediate/expression_phenotypes/geuvadis.expr.RDS,geno=../../data/intermediate/genotypes/geuvadis.snps.chr2.txt,gene_annot=../../data/intermediate/annotations/gene_annotation/gencode.v12.genes.parsed.RDS,snp_annot=../../data/intermediate/annotations/snp_annotation/geuvadis.annot.chr2.RDS,n_k_folds=10,alpha=0.5,out_dir=../../data/intermediate/model_by_chr/,chrom=2,snpset=HapMap,window=1e6 -N gEUVADIS_model_chr2 -d /hii/work/r/rchen7/project/predixcan/PredictDBPipeline/joblogs/example train_model_by_chr.pbs Unknown option: d Usage: qsub [-a start_time] [-A account] [-e err_path] [-I] [-l resource_list] [-m mail_options] [-M user_list] [-N job_name] [-o out_path] [-p priority] [-q destination] [-v variable_list] [-V] [-W additional_attributes] [-h] [script]

qsub -v study=gEUVADIS,expr_RDS=../../data/intermediate/expression_phenotypes/geuvadis.expr.RDS,geno=../../data/intermediate/genotypes/geuvadis.snps.chr3.txt,gene_annot=../../data/intermediate/annotations/gene_annotation/gencode.v12.genes.parsed.RDS,snp_annot=../../data/intermediate/annotations/snp_annotation/geuvadis.annot.chr3.RDS,n_k_folds=10,alpha=0.5,out_dir=../../data/intermediate/model_by_chr/,chrom=3,snpset=HapMap,window=1e6 -N gEUVADIS_model_chr3 -d /hii/work/r/rchen7/project/predixcan/PredictDBPipeline/joblogs/example train_model_by_chr.pbs Unknown option: d Usage: qsub [-a start_time] [-A account] [-e err_path] [-I] [-l resource_list] [-m mail_options] [-M user_list] [-N job_name] [-o out_path] [-p priority] [-q destination] [-v variable_list] [-V] [-W additional_attributes] [-h] [script] . . . .

qsub -v study=gEUVADIS,expr_RDS=../../data/intermediate/expression_phenotypes/geuvadis.expr.RDS,geno=../../data/intermediate/genotypes/geuvadis.snps.chr22.txt,gene_annot=../../data/intermediate/annotations/gene_annotation/gencode.v12.genes.parsed.RDS,snp_annot=../../data/intermediate/annotations/snp_annotation/geuvadis.annot.chr22.RDS,n_k_folds=10,alpha=0.5,out_dir=../../data/intermediate/model_by_chr/,chrom=22,snpset=HapMap,window=1e6 -N gEUVADIS_model_chr22 -d /hii/work/r/rchen7/project/predixcan/PredictDBPipeline/joblogs/example train_model_by_chr.pbs Unknown option: d Usage: qsub [-a start_time] [-A account] [-e err_path] [-I] [-l resource_list] [-m mail_options] [-M user_list] [-N job_name] [-o out_path] [-p priority] [-q destination] [-v variable_list] [-V] [-W additional_attributes] [-h] [script]

Any idea why this happened? Really appreciate for your advice.

Thanks

Ruoxi