Remove extra check and debug flag for gemma run

1 files changed, 2 insertions, 2 deletions

diff --git a/gn/runner/gemma.scm b/gn/runner/gemma.scm
index a31846a..d86abd7 100644
--- a/gn/runner/gemma.scm
+++ b/gn/runner/gemma.scm
@@ -48,10 +48,10 @@
     ;; ---- to start GEMMA precompute inside container
     ;; env TMPDIR=. LD_LIBRARY_PATH=$GUIX_ENVIRONMENT/lib/ guile -L . -s ./scripts/precompute/precompute-hits.scm
     ;; --- First we compute K - control output goes to K.json
-    (let [(err (system (string-append "env GEMMA_COMMAND=gemma /gemma-wrapper/bin/gemma-wrapper --population \"" population "\" --name \"" name "\" --trait \"" trait-name "\" --verbose --loco --json --debug --parallel -- -gk -g BXD.8_geno.txt.gz -p " pheno-fn " -a BXD.8_snps.txt > " k-json-fn  )))]
+    (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 "\" --trait \"" trait-name "\" --verbose --loco --json --debug --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 --population \"" population "\" --name \"" name "\" --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)))]
       (if (not (= err 0))
           (exit err)))
     (delete-file pheno-fn)