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Re: Properly setting $Global::max_file_length to avoid line 12170 error

From: Rob Sargent
Subject: Re: Properly setting $Global::max_file_length to avoid line 12170 error
Date: Tue, 4 Oct 2022 22:44:35 -0600
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On 10/4/22 22:33, Nagle, Michael F wrote:
Rob Sargent
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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?

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