Hi! I am new to DNAnexus and have been recently following the webiner "GWAS on the Research Analysis Platform using regenie" along with their code posted on github https://github.com/dnanexus/UKB_RAP/tree/main/GWAS/regenie_workflow
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All went good until partD of this process, where I switched from PLINK to REGNIE in the swiss army knife. CLI gave an error similar to this:
"dx: error: unrecognized arguments: --step 1--lowmem --out pheno_results --bed ukb22418_c1_22_v2_merged --phenoFile pheno_wes_000k.phe --covarFile pheno_wes_000k.phe \ --extract WES_array_snps_qc_pass.snplist --phenoCol pheno --covarCol age --covarCol sex --bsize 1000 --bt --loocv --gz --threads 16"
It seems that the swiss army knife can run PLINK well but does not allow REGENIE to be performed, and I cannot find the cause. Has anyone encountered a similar issue?
Comments
5 comments
I think there might be an error in the code of part D.
For line 42, could you try with
-icmd=${run_regenie_step1}
rather than
-icmd=${run_plink_wes}
Let me know how it goes. If this fix the issue, I will tell my colleague to fix the code.
Another idea, in your command line:
"dx: error: unrecognized arguments: --step 1--lowmem --out pheno_results --bed ukb22418_c1_22_v2_merged --phenoFile pheno_wes_000k.phe --covarFile pheno_wes_000k.phe \ --extract WES_array_snps_qc_pass.snplist --phenoCol pheno --covarCol age --covarCol sex --bsize 1000 --bt --loocv --gz --threads 16"
It seems that there is no space character between "--step 1" and "--lowmem".
Thanks for replying!
However, I fixed the code as suggested, the same error remains.
Thanks! I double-checked that I have the space in my code. I think it was the copying-and-pasting that somehow changed the format.
Hi Colleagues,
I'm having the same issue. Anyone able to resolve this issue? thanks
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