diff options
| -rw-r--r-- | wqflask/wqflask/marker_regression/gemma_mapping.py | 5 |
1 files changed, 1 insertions, 4 deletions
diff --git a/wqflask/wqflask/marker_regression/gemma_mapping.py b/wqflask/wqflask/marker_regression/gemma_mapping.py index 16e639dc..61e4897c 100644 --- a/wqflask/wqflask/marker_regression/gemma_mapping.py +++ b/wqflask/wqflask/marker_regression/gemma_mapping.py @@ -46,7 +46,7 @@ def run_gemma(this_trait, this_dataset, samples, vals, covariates, use_loco, maf genofile_name, TEMPDIR, k_output_filename) - logger.debug("k_command:" + generate_k_command) + os.system(generate_k_command) gemma_command = GEMMA_WRAPPER_COMMAND + ' --json --loco --input %s/gn2/%s.json -- ' % (TEMPDIR, k_output_filename) + GEMMAOPTS + ' -g %s/%s_geno.txt -p %s/gn2/%s.txt' % (flat_files('genotype/bimbam'), @@ -78,7 +78,6 @@ def run_gemma(this_trait, this_dataset, samples, vals, covariates, use_loco, maf TEMPDIR, k_output_filename) - logger.debug("k_command:" + generate_k_command) os.system(generate_k_command) gemma_command = GEMMA_WRAPPER_COMMAND + ' --json --input %s/gn2/%s.json -- ' % (TEMPDIR, k_output_filename) + GEMMAOPTS + ' -a %s/%s_snps.txt -lmm 2 -g %s/%s_geno.txt -p %s/gn2/%s.txt' % (flat_files('genotype/bimbam'), @@ -94,8 +93,6 @@ def run_gemma(this_trait, this_dataset, samples, vals, covariates, use_loco, maf else: gemma_command += ' > %s/gn2/%s.json' % (TEMPDIR, gwa_output_filename) - - logger.debug("gemma_command:" + gemma_command) os.system(gemma_command) else: gwa_output_filename = output_files |