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| author | Pjotr Prins | 2024-02-12 17:14:51 +0100 |
|---|---|---|
| committer | Pjotr Prins | 2024-02-12 17:14:51 +0100 |
| commit | e16c108c66213d0dd536f9eee1027d8f6c0b0dcd (patch) | |
| tree | 2d31e3ff3fb94248249cec5fbef5168e6b856bea | |
| parent | 1c46296016ead8a5fa17ff291eeabbd0a0c63e4b (diff) | |
| download | gn-guile-e16c108c66213d0dd536f9eee1027d8f6c0b0dcd.tar.gz | |
Change lmm mode to 9
| -rw-r--r-- | gn/runner/gemma.scm | 2 |
1 files changed, 1 insertions, 1 deletions
diff --git a/gn/runner/gemma.scm b/gn/runner/gemma.scm index 89b6482..131284a 100644 --- a/gn/runner/gemma.scm +++ b/gn/runner/gemma.scm @@ -55,7 +55,7 @@ (let [(err (system (string-append "env GEMMA_COMMAND=gemma /gemma-wrapper/bin/gemma-wrapper --population \"" population "\" --name \"" name "\" --trait \"" trait-name "\" --verbose --loco --json --parallel -- -gk -g BXD.8_geno.txt.gz -p " pheno-fn " -a BXD.8_snps.txt > " k-json-fn )))] (if (not (= err 0)) (exit err))) - (let [(err (system (string-append "env GEMMA_COMMAND=gemma /gemma-wrapper/bin/gemma-wrapper --population \"" population "\" --name \"" name "\" --id \"" ids "\" --trait \"" trait-name "\" --verbose --loco --json --parallel --input " k-json-fn " -- -g BXD.8_geno.txt.gz -p " pheno-fn " -a BXD.8_snps.txt -lmm 2 -maf 0.1 > " gwa-json-fn)))] + (let [(err (system (string-append "env GEMMA_COMMAND=gemma /gemma-wrapper/bin/gemma-wrapper --keep --population \"" population "\" --name \"" name "\" --id \"" ids "\" --trait \"" trait-name "\" --verbose --loco --json --parallel --input " k-json-fn " -- -g BXD.8_geno.txt.gz -p " pheno-fn " -a BXD.8_snps.txt -lmm 9 -maf 0.1 > " gwa-json-fn)))] (if (not (= err 0)) (exit err))) (delete-file pheno-fn) |