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.