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-rw-r--r--gn/runner/gemma.scm4
1 files changed, 2 insertions, 2 deletions
diff --git a/gn/runner/gemma.scm b/gn/runner/gemma.scm
index ec2a4d6..69991dd 100644
--- a/gn/runner/gemma.scm
+++ b/gn/runner/gemma.scm
@@ -47,10 +47,10 @@
(k-json-fn (string-append tmpdir "/K.json"))
(gwa-json-fn (string-append tmpdir "/GWA.json"))]
;; --- First we compute K - control output goes to K.json
- (let [(err (system (string-append "gemma-wrapper --verbose --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 )))]
+ (let [(err (system (string-append "/gemma-wrapper/bin/gemma-wrapper --verbose --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 "gemma-wrapper --population \"" population "\" --name \"" name "\" --id \"" trait-name "\" --trait \"" trait-name "\" --verbose --loco --json --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)))]
+ (let [(err (system (string-append "/gemma-wrapper/bin/gemma-wrapper --population \"" population "\" --name \"" name "\" --id \"" trait-name "\" --trait \"" trait-name "\" --verbose --loco --json --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)