diff options
Diffstat (limited to 'gn2/wqflask/marker_regression/gemma_mapping.py')
| -rw-r--r-- | gn2/wqflask/marker_regression/gemma_mapping.py | 5 |
1 files changed, 4 insertions, 1 deletions
diff --git a/gn2/wqflask/marker_regression/gemma_mapping.py b/gn2/wqflask/marker_regression/gemma_mapping.py index d8851486..aa059f93 100644 --- a/gn2/wqflask/marker_regression/gemma_mapping.py +++ b/gn2/wqflask/marker_regression/gemma_mapping.py @@ -3,6 +3,7 @@ import math import string import random import json +import logging from gn2.base import webqtlConfig from gn2.base.trait import create_trait @@ -73,6 +74,7 @@ def run_gemma(this_trait, this_dataset, samples, vals, covariates, use_loco, f"{pheno_filepath} -a " f"{snps_filepath} -gk > " f"{k_json_output_filepath}") + logging.debug("generate_k_command: %s", generate_k_command) os.system(generate_k_command) gemma_command = (f"{GEMMA_WRAPPER_COMMAND} --json --loco " @@ -102,7 +104,7 @@ def run_gemma(this_trait, this_dataset, samples, vals, covariates, use_loco, f"{flat_files('genotype/bimbam')}/" f"{genofile_name}_snps.txt -gk > " f"{TEMPDIR}/gn2/{k_output_filename}.json") - + logging.debug("generate_k_command: %s", generate_k_command) os.system(generate_k_command) gemma_command = (f"{GEMMA_WRAPPER_COMMAND} --json --input " @@ -121,6 +123,7 @@ def run_gemma(this_trait, this_dataset, samples, vals, covariates, use_loco, else: gemma_command += f" > {TEMPDIR}/gn2/{gwa_output_filename}.json" + logging.debug("gemma_command: %s", gemma_command) os.system(gemma_command) else: gwa_output_filename = output_files |