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-rw-r--r--gn/runner/gemma.scm2
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)