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From: | Nagle, Michael F |
Subject: | Re: Properly setting $Global::max_file_length to avoid line 12170 error |
Date: | Wed, 5 Oct 2022 05:12:32 +0000 |
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On 10/4/22 22:33, Nagle, Michael F wrote:
The backslashes appear to be coming from parallel. My command has file paths with forward slashes and these are replaced with \_ by parallel, it seems.
To demonstrate, here is one my first command in the a I pass to parallel:
gemma -bfile ./1323_cohort_maf01_geno10.snp.pass -p ./pheno_files/callus_regeneration_PC1-uv_unique_rmoutliers_boxcox_resid.noheader.pheno -k ./1323_cohort_maf01_geno10.cXX.txt -lmm 1 -n 3 -miss 0.1 -o callus_regeneration_PC1-uv_unique_rmoutliers_boxcox_resid-ResidOverPhase
Here is the error for that command:
mkdir output/1/gemma -bfile .\_1323_cohort_maf01_geno10.snp.pass -p .\_pheno_files\_callus_regeneration_PC1-uv_unique_rmoutliers_boxcox_resid.noheader.pheno -k .\_1323_cohort_maf01_geno10.cXX.txt -lmm 1 -n 3 -miss 0.1 -o callus_regeneration_PC1-uv_unique_rmoutliers_boxc: Invalid argument at /home/gmobot/anaconda3/envs/gemma/bin/parallel line 12170.
Are you using backslash continuation lines by any chance?
GEMMA_transformation_a1.jobs
Description: GEMMA_transformation_a1.jobs
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