run update

UrbsLab · Jun 3, 2024 · 6c3dd8f · 6c3dd8f
1 parent 5f1f122
commit 6c3dd8f
Show file tree

Hide file tree

Showing 2 changed files with 190 additions and 31 deletions.
diff --git a/paper_analysis_codes/hla_hpc_scripts/FIBERS_run _commands.txt b/paper_analysis_codes/hla_hpc_scripts/FIBERS_run _commands.txt
@@ -11,37 +11,82 @@ python run_fibers_hpc.py --d /project/kamoun_shared/data_shared/ryan_new_imp --w
 python run_sum_fibers_hpc.py --d /project/kamoun_shared/data_shared/ryan_new_imp --w /project/kamoun_shared/output_shared/ryanurb/ --o hla_test_new_full --rc LSF --rm 4 --q i2c2_normal --rs 10 --re 10 --loci-list DRB1,DQA1,DQB1
 python run_master_sum_fibers_hpc.py --d /project/kamoun_shared/data_shared/ryan_new_imp --w /project/kamoun_shared/output_shared/ryanurb/ --o Fibers2.0_hla_test_new_full --rs 10 --re 10 --loci-list DRB1,DQA1,DQB1 --rc LSF --rm 16 --q i2c2_normal
 
+
+#BUG Test
+### DRB1, DQA1, DQB1 (NO Ag Covariates adjusted)
+python run_fibers_hpc.py --d /project/kamoun_shared/data_shared/ryan_new_imp --w /project/kamoun_shared/output_shared/ryanurb/ --o bug_test_hla_3locus_noagcov_baseline --i 100 --ps 50 --rc LSF --rm 16 --q i2c2_normal --rs 10 --re 10 --ol graftyrs --c grf_fail --ma 0.5 --dp 5 --f log_rank_residuals --t None --at 10 --cl group_strata --loci-list DRB1,DQA1,DQB1 --cov-list None
+python run_sum_fibers_hpc.py --d /project/kamoun_shared/data_shared/ryan_new_imp --w /project/kamoun_shared/output_shared/ryanurb/ --o bug_test_hla_3locus_noagcov_baseline --rc LSF --rm 4 --q i2c2_normal --rs 10 --re 10 --loci-list DRB1,DQA1,DQB1
+python run_master_sum_fibers_hpc.py --d /project/kamoun_shared/data_shared/ryan_new_imp --w /project/kamoun_shared/output_shared/ryanurb/ --o Fibers2.0_bug_test_hla_3locus_noagcov_baseline --rs 10 --re 10 --loci-list DRB1,DQA1,DQB1 --rc LSF --rm 16 --q i2c2_normal
+
+### DRB1, DQA1, DQB1 - Ag Covariates adjusted
+python run_fibers_hpc.py --d /project/kamoun_shared/data_shared/ryan_new_imp --w /project/kamoun_shared/output_shared/ryanurb/ --o bug_test_hla_3locus_baseline --i 100 --ps 50 --rc LSF --rm 16 --q i2c2_normal --rs 10 --re 10 --ol graftyrs --c grf_fail --ma 0.5 --dp 5 --f log_rank_residuals --t None --at 10 --cl group_strata --loci-list DRB1,DQA1,DQB1 --cov-list A,B,C,DRB1,DQA1,DQB1
+python run_sum_fibers_hpc.py --d /project/kamoun_shared/data_shared/ryan_new_imp --w /project/kamoun_shared/output_shared/ryanurb/ --o bug_test_hla_3locus_baseline --rc LSF --rm 4 --q i2c2_normal --rs 10 --re 10 --loci-list DRB1,DQA1,DQB1
+python run_master_sum_fibers_hpc.py --d /project/kamoun_shared/data_shared/ryan_new_imp --w /project/kamoun_shared/output_shared/ryanurb/ --o Fibers2.0_bug_test_hla_3locus_baseline --rs 10 --re 10 --loci-list DRB1,DQA1,DQB1 --rc LSF --rm 16 --q i2c2_normal
+
+
 # Runs/Analyses
+# Fibers Settings - Iter 500, Pop 200, Div = 5 Thresh = None MaxThresh = 10 Fitness = log_rank_residuals rare_filter = 0.0
+
+### DRB1, DQA1, DQB1 - Ag Covariates adjusted
+python run_fibers_hpc.py --d /project/kamoun_shared/data_shared/ryan_new_imp --w /project/kamoun_shared/output_shared/ryanurb/ --o hla_3locus_baseline --i 500 --ps 200 --rc LSF --rm 16 --q i2c2_normal --rs 10 --re 10 --ol graftyrs --c grf_fail --ma 0.5 --dp 5 --f log_rank_residuals --t None --at 10 --cl group_strata --loci-list DRB1,DQA1,DQB1 --cov-list A,B,C,DRB1,DQA1,DQB1
+python run_sum_fibers_hpc.py --d /project/kamoun_shared/data_shared/ryan_new_imp --w /project/kamoun_shared/output_shared/ryanurb/ --o hla_3locus_baseline --rc LSF --rm 4 --q i2c2_normal --rs 10 --re 10 --loci-list DRB1,DQA1,DQB1
+python run_master_sum_fibers_hpc.py --d /project/kamoun_shared/data_shared/ryan_new_imp --w /project/kamoun_shared/output_shared/ryanurb/ --o Fibers2.0_hla_3locus_baseline --rs 10 --re 10 --loci-list DRB1,DQA1,DQB1 --rc LSF --rm 16 --q i2c2_normal
+
+### DRB1, DQA1, DQB1 + DRB345 - Ag Covariates adjusted
+python run_fibers_hpc.py --d /project/kamoun_shared/data_shared/ryan_new_imp --w /project/kamoun_shared/output_shared/ryanurb/ --o hla_4locus_baseline --i 500 --ps 200 --rc LSF --rm 16 --q i2c2_normal --rs 10 --re 10 --ol graftyrs --c grf_fail --ma 0.5 --dp 5 --f log_rank_residuals --t None --at 10 --cl group_strata --loci-list DRB1,DQA1,DQB1,DRB345 --cov-list A,B,C,DRB1,DQA1,DQB1
+python run_sum_fibers_hpc.py --d /project/kamoun_shared/data_shared/ryan_new_imp --w /project/kamoun_shared/output_shared/ryanurb/ --o hla_4locus_baseline --rc LSF --rm 4 --q i2c2_normal --rs 10 --re 10 --loci-list DRB1,DQA1,DQB1,DRB345 
+python run_master_sum_fibers_hpc.py --d /project/kamoun_shared/data_shared/ryan_new_imp --w /project/kamoun_shared/output_shared/ryanurb/ --o Fibers2.0_hla_4locus_baseline --rs 10 --re 10 --loci-list DRB1,DQA1,DQB1,DRB345 --rc LSF --rm 16 --q i2c2_normal
+
+### DRB1, DQA1, DQB1, DRB345 + A, B, C - Ag Covariates adjusted
+python run_fibers_hpc.py --d /project/kamoun_shared/data_shared/ryan_new_imp --w /project/kamoun_shared/output_shared/ryanurb/ --o hla_7locus_baseline --i 500 --ps 200 --rc LSF --rm 16 --q i2c2_normal --rs 10 --re 10 --ol graftyrs --c grf_fail --ma 0.5 --dp 5 --f log_rank_residuals --t None --at 10 --cl group_strata --loci-list A,B,C,DRB1,DQA1,DQB1,DRB345 --cov-list A,B,C,DRB1,DQA1,DQB1
+python run_sum_fibers_hpc.py --d /project/kamoun_shared/data_shared/ryan_new_imp --w /project/kamoun_shared/output_shared/ryanurb/ --o hla_7locus_baseline --rc LSF --rm 4 --q i2c2_normal --rs 10 --re 10 --loci-list A,B,C,DRB1,DQA1,DQB1,DRB345
+python run_master_sum_fibers_hpc.py --d /project/kamoun_shared/data_shared/ryan_new_imp --w /project/kamoun_shared/output_shared/ryanurb/ --o Fibers2.0_hla_7locus_baseline --rs 10 --re 10 --loci-list A,B,C,DRB1,DQA1,DQB1,DRB345 --rc LSF --rm 16 --q i2c2_normal
+
+### DRB1, DQA1, DQB1 
+python run_fibers_hpc.py --d /project/kamoun_shared/data_shared/ryan_new_imp --w /project/kamoun_shared/output_shared/ryanurb/ --o hla_3locus_noagcov_baseline --i 500 --ps 200 --rc LSF --rm 16 --q i2c2_normal --rs 10 --re 10 --ol graftyrs --c grf_fail --ma 0.5 --dp 5 --f log_rank_residuals --t None --at 10 --cl group_strata --loci-list DRB1,DQA1,DQB1 --cov-list None
+python run_sum_fibers_hpc.py --d /project/kamoun_shared/data_shared/ryan_new_imp --w /project/kamoun_shared/output_shared/ryanurb/ --o hla_3locus_noagcov_baseline --rc LSF --rm 4 --q i2c2_normal --rs 10 --re 10 --loci-list DRB1,DQA1,DQB1
+python run_master_sum_fibers_hpc.py --d /project/kamoun_shared/data_shared/ryan_new_imp --w /project/kamoun_shared/output_shared/ryanurb/ --o Fibers2.0_hla_3locus_noagcov_baseline --rs 10 --re 10 --loci-list DRB1,DQA1,DQB1 --rc LSF --rm 16 --q i2c2_normal
+
+### DRB1, DQA1, DQB1 + DRB345 
+python run_fibers_hpc.py --d /project/kamoun_shared/data_shared/ryan_new_imp --w /project/kamoun_shared/output_shared/ryanurb/ --o hla_4locus_noagcov_baseline --i 500 --ps 200 --rc LSF --rm 16 --q i2c2_normal --rs 10 --re 10 --ol graftyrs --c grf_fail --ma 0.5 --dp 5 --f log_rank_residuals --t None --at 10 --cl group_strata --loci-list DRB1,DQA1,DQB1,DRB345 --cov-list None
+python run_sum_fibers_hpc.py --d /project/kamoun_shared/data_shared/ryan_new_imp --w /project/kamoun_shared/output_shared/ryanurb/ --o hla_4locus_noagcov_baseline --rc LSF --rm 4 --q i2c2_normal --rs 10 --re 10 --loci-list DRB1,DQA1,DQB1,DRB345 
+python run_master_sum_fibers_hpc.py --d /project/kamoun_shared/data_shared/ryan_new_imp --w /project/kamoun_shared/output_shared/ryanurb/ --o Fibers2.0_hla_4locus_noagcov_baseline --rs 10 --re 10 --loci-list DRB1,DQA1,DQB1,DRB345 --rc LSF --rm 16 --q i2c2_normal
+
+### DRB1, DQA1, DQB1, DRB345 + A, B, C 
+python run_fibers_hpc.py --d /project/kamoun_shared/data_shared/ryan_new_imp --w /project/kamoun_shared/output_shared/ryanurb/ --o hla_7locus_noagcov_baseline --i 500 --ps 200 --rc LSF --rm 16 --q i2c2_normal --rs 10 --re 10 --ol graftyrs --c grf_fail --ma 0.5 --dp 5 --f log_rank_residuals --t None --at 10 --cl group_strata --loci-list A,B,C,DRB1,DQA1,DQB1,DRB345 --cov-list None
+python run_sum_fibers_hpc.py --d /project/kamoun_shared/data_shared/ryan_new_imp --w /project/kamoun_shared/output_shared/ryanurb/ --o hla_7locus_noagcov_baseline --rc LSF --rm 4 --q i2c2_normal --rs 10 --re 10 --loci-list A,B,C,DRB1,DQA1,DQB1,DRB345
+python run_master_sum_fibers_hpc.py --d /project/kamoun_shared/data_shared/ryan_new_imp --w /project/kamoun_shared/output_shared/ryanurb/ --o Fibers2.0_hla_7locus_noagcov_baseline --rs 10 --re 10 --loci-list A,B,C,DRB1,DQA1,DQB1,DRB345 --rc LSF --rm 16 --q i2c2_normal
+
+
+# Fibers Settings - Iter 500, Pop 200, Div = 5 Thresh = None MaxThresh = 10 Fitness = log_rank_residuals rare_filter = 0.01
+
+### DRB1, DQA1, DQB1 - Ag Covariates adjusted
+python run_fibers_hpc.py --d /project/kamoun_shared/data_shared/ryan_new_imp --w /project/kamoun_shared/output_shared/ryanurb/ --o hla_filtered_3locus_baseline --ra 0.01 --i 500 --ps 200 --rc LSF --rm 16 --q i2c2_normal --rs 10 --re 10 --ol graftyrs --c grf_fail --ma 0.5 --dp 5 --f log_rank_residuals --t None --at 10 --cl group_strata --loci-list DRB1,DQA1,DQB1 --cov-list A,B,C,DRB1,DQA1,DQB1
+python run_sum_fibers_hpc.py --d /project/kamoun_shared/data_shared/ryan_new_imp --w /project/kamoun_shared/output_shared/ryanurb/ --o hla_filtered_3locus_baseline --rc LSF --rm 4 --q i2c2_normal --rs 10 --re 10 --loci-list DRB1,DQA1,DQB1
+python run_master_sum_fibers_hpc.py --d /project/kamoun_shared/data_shared/ryan_new_imp --w /project/kamoun_shared/output_shared/ryanurb/ --o Fibers2.0_hla_filtered_3locus_baseline --rs 10 --re 10 --loci-list DRB1,DQA1,DQB1 --rc LSF --rm 16 --q i2c2_normal
+
+### DRB1, DQA1, DQB1 + DRB345 - Ag Covariates adjusted
+python run_fibers_hpc.py --d /project/kamoun_shared/data_shared/ryan_new_imp --w /project/kamoun_shared/output_shared/ryanurb/ --o hla_filtered_4locus_baseline --ra 0.01 --i 500 --ps 200 --rc LSF --rm 16 --q i2c2_normal --rs 10 --re 10 --ol graftyrs --c grf_fail --ma 0.5 --dp 5 --f log_rank_residuals --t None --at 10 --cl group_strata --loci-list DRB1,DQA1,DQB1,DRB345 --cov-list A,B,C,DRB1,DQA1,DQB1
+python run_sum_fibers_hpc.py --d /project/kamoun_shared/data_shared/ryan_new_imp --w /project/kamoun_shared/output_shared/ryanurb/ --o hla_filtered_4locus_baseline --rc LSF --rm 4 --q i2c2_normal --rs 10 --re 10 --loci-list DRB1,DQA1,DQB1,DRB345 
+python run_master_sum_fibers_hpc.py --d /project/kamoun_shared/data_shared/ryan_new_imp --w /project/kamoun_shared/output_shared/ryanurb/ --o Fibers2.0_hla_filtered_4locus_baseline --rs 10 --re 10 --loci-list DRB1,DQA1,DQB1,DRB345 --rc LSF --rm 16 --q i2c2_normal
+
+### DRB1, DQA1, DQB1, DRB345 + A, B, C - Ag Covariates adjusted
+python run_fibers_hpc.py --d /project/kamoun_shared/data_shared/ryan_new_imp --w /project/kamoun_shared/output_shared/ryanurb/ --o hla_filtered_7locus_baseline --ra 0.01 --i 500 --ps 200 --rc LSF --rm 16 --q i2c2_normal --rs 10 --re 10 --ol graftyrs --c grf_fail --ma 0.5 --dp 5 --f log_rank_residuals --t None --at 10 --cl group_strata --loci-list A,B,C,DRB1,DQA1,DQB1,DRB345 --cov-list A,B,C,DRB1,DQA1,DQB1
+python run_sum_fibers_hpc.py --d /project/kamoun_shared/data_shared/ryan_new_imp --w /project/kamoun_shared/output_shared/ryanurb/ --o hla_filtered_7locus_baseline --rc LSF --rm 4 --q i2c2_normal --rs 10 --re 10 --loci-list A,B,C,DRB1,DQA1,DQB1,DRB345
+python run_master_sum_fibers_hpc.py --d /project/kamoun_shared/data_shared/ryan_new_imp --w /project/kamoun_shared/output_shared/ryanurb/ --o Fibers2.0_hla_filtered_7locus_baseline --rs 10 --re 10 --loci-list A,B,C,DRB1,DQA1,DQB1,DRB345 --rc LSF --rm 16 --q i2c2_normal
+
+### DRB1, DQA1, DQB1 
+python run_fibers_hpc.py --d /project/kamoun_shared/data_shared/ryan_new_imp --w /project/kamoun_shared/output_shared/ryanurb/ --o hla_filtered_3locus_noagcov_baseline --ra 0.01 --i 500 --ps 200 --rc LSF --rm 16 --q i2c2_normal --rs 10 --re 10 --ol graftyrs --c grf_fail --ma 0.5 --dp 5 --f log_rank_residuals --t None --at 10 --cl group_strata --loci-list DRB1,DQA1,DQB1 --cov-list None
+python run_sum_fibers_hpc.py --d /project/kamoun_shared/data_shared/ryan_new_imp --w /project/kamoun_shared/output_shared/ryanurb/ --o hla_filtered_3locus_noagcov_baseline --rc LSF --rm 4 --q i2c2_normal --rs 10 --re 10 --loci-list DRB1,DQA1,DQB1
+python run_master_sum_fibers_hpc.py --d /project/kamoun_shared/data_shared/ryan_new_imp --w /project/kamoun_shared/output_shared/ryanurb/ --o Fibers2.0_hla_filtered_3locus_noagcov_baseline --rs 10 --re 10 --loci-list DRB1,DQA1,DQB1 --rc LSF --rm 16 --q i2c2_normal
+
+### DRB1, DQA1, DQB1 + DRB345 
+python run_fibers_hpc.py --d /project/kamoun_shared/data_shared/ryan_new_imp --w /project/kamoun_shared/output_shared/ryanurb/ --o hla_filtered_4locus_noagcov_baseline --ra 0.01 --i 500 --ps 200 --rc LSF --rm 16 --q i2c2_normal --rs 10 --re 10 --ol graftyrs --c grf_fail --ma 0.5 --dp 5 --f log_rank_residuals --t None --at 10 --cl group_strata --loci-list DRB1,DQA1,DQB1,DRB345 --cov-list None
+python run_sum_fibers_hpc.py --d /project/kamoun_shared/data_shared/ryan_new_imp --w /project/kamoun_shared/output_shared/ryanurb/ --o hla_filtered_4locus_noagcov_baseline --rc LSF --rm 4 --q i2c2_normal --rs 10 --re 10 --loci-list DRB1,DQA1,DQB1,DRB345 
+python run_master_sum_fibers_hpc.py --d /project/kamoun_shared/data_shared/ryan_new_imp --w /project/kamoun_shared/output_shared/ryanurb/ --o Fibers2.0_hla_filtered_4locus_noagcov_baseline --rs 10 --re 10 --loci-list DRB1,DQA1,DQB1,DRB345 --rc LSF --rm 16 --q i2c2_normal
 
-# Fibers Settings - Iter 500, Pop 200, Div = 5 Thresh = None MaxThresh = 10 Fitness = log_rank_residuals
-
-    ### DRB1, DQA1, DQB1 - Ag Covariates adjusted
-    python run_fibers_hpc.py --d /project/kamoun_shared/data_shared/ryan_new_imp --w /project/kamoun_shared/output_shared/ryanurb/ --o hla_3locus_baseline --i 500 --ps 200 --rc LSF --rm 16 --q i2c2_normal --rs 10 --re 10 --ol graftyrs --c grf_fail --ma 0.5 --dp 5 --f log_rank_residuals --t None --at 10 --cl group_strata --loci-list DRB1,DQA1,DQB1 --cov-list A,B,C,DRB1,DQA1,DQB1
-    python run_sum_fibers_hpc.py --d /project/kamoun_shared/data_shared/ryan_new_imp --w /project/kamoun_shared/output_shared/ryanurb/ --o hla_3locus_baseline --rc LSF --rm 4 --q i2c2_normal --rs 10 --re 10 --loci-list DRB1,DQA1,DQB1
-    python run_master_sum_fibers_hpc.py --d /project/kamoun_shared/data_shared/ryan_new_imp --w /project/kamoun_shared/output_shared/ryanurb/ --o Fibers2.0_hla_3locus_baseline --rs 10 --re 10 --loci-list DRB1,DQA1,DQB1 --rc LSF --rm 16 --q i2c2_normal
-
-    ### DRB1, DQA1, DQB1 + DRB345 - Ag Covariates adjusted
-    python run_fibers_hpc.py --d /project/kamoun_shared/data_shared/ryan_new_imp --w /project/kamoun_shared/output_shared/ryanurb/ --o hla_4locus_baseline --i 500 --ps 200 --rc LSF --rm 16 --q i2c2_normal --rs 10 --re 10 --ol graftyrs --c grf_fail --ma 0.5 --dp 5 --f log_rank_residuals --t None --at 10 --cl group_strata --loci-list DRB1,DQA1,DQB1,DRB345 --cov-list A,B,C,DRB1,DQA1,DQB1
-    python run_sum_fibers_hpc.py --d /project/kamoun_shared/data_shared/ryan_new_imp --w /project/kamoun_shared/output_shared/ryanurb/ --o hla_4locus_baseline --rc LSF --rm 4 --q i2c2_normal --rs 10 --re 10 --loci-list DRB1,DQA1,DQB1,DRB345 
-    python run_master_sum_fibers_hpc.py --d /project/kamoun_shared/data_shared/ryan_new_imp --w /project/kamoun_shared/output_shared/ryanurb/ --o Fibers2.0_hla_4locus_baseline --rs 10 --re 10 --loci-list DRB1,DQA1,DQB1,DRB345 --rc LSF --rm 16 --q i2c2_normal
-
-    ### DRB1, DQA1, DQB1, DRB345 + A, B, C - Ag Covariates adjusted
-    python run_fibers_hpc.py --d /project/kamoun_shared/data_shared/ryan_new_imp --w /project/kamoun_shared/output_shared/ryanurb/ --o hla_7locus_baseline --i 500 --ps 200 --rc LSF --rm 16 --q i2c2_normal --rs 10 --re 10 --ol graftyrs --c grf_fail --ma 0.5 --dp 5 --f log_rank_residuals --t None --at 10 --cl group_strata --loci-list A,B,C,DRB1,DQA1,DQB1,DRB345 --cov-list A,B,C,DRB1,DQA1,DQB1
-    python run_sum_fibers_hpc.py --d /project/kamoun_shared/data_shared/ryan_new_imp --w /project/kamoun_shared/output_shared/ryanurb/ --o hla_7locus_baseline --rc LSF --rm 4 --q i2c2_normal --rs 10 --re 10 --loci-list A,B,C,DRB1,DQA1,DQB1,DRB345
-    python run_master_sum_fibers_hpc.py --d /project/kamoun_shared/data_shared/ryan_new_imp --w /project/kamoun_shared/output_shared/ryanurb/ --o Fibers2.0_hla_7locus_baseline --rs 10 --re 10 --loci-list A,B,C,DRB1,DQA1,DQB1,DRB345 --rc LSF --rm 16 --q i2c2_normal
-
-    ### DRB1, DQA1, DQB1 
-    python run_fibers_hpc.py --d /project/kamoun_shared/data_shared/ryan_new_imp --w /project/kamoun_shared/output_shared/ryanurb/ --o hla_3locus_noagcov_baseline --i 500 --ps 200 --rc LSF --rm 16 --q i2c2_normal --rs 10 --re 10 --ol graftyrs --c grf_fail --ma 0.5 --dp 5 --f log_rank_residuals --t None --at 10 --cl group_strata --loci-list DRB1,DQA1,DQB1 --cov-list None
-    python run_sum_fibers_hpc.py --d /project/kamoun_shared/data_shared/ryan_new_imp --w /project/kamoun_shared/output_shared/ryanurb/ --o hla_3locus_noagcov_baseline --rc LSF --rm 4 --q i2c2_normal --rs 10 --re 10 --loci-list DRB1,DQA1,DQB1
-    python run_master_sum_fibers_hpc.py --d /project/kamoun_shared/data_shared/ryan_new_imp --w /project/kamoun_shared/output_shared/ryanurb/ --o Fibers2.0_hla_3locus_noagcov_baseline --rs 10 --re 10 --loci-list DRB1,DQA1,DQB1 --rc LSF --rm 16 --q i2c2_normal
-
-    ### DRB1, DQA1, DQB1 + DRB345 
-    python run_fibers_hpc.py --d /project/kamoun_shared/data_shared/ryan_new_imp --w /project/kamoun_shared/output_shared/ryanurb/ --o hla_4locus_noagcov_baseline --i 500 --ps 200 --rc LSF --rm 16 --q i2c2_normal --rs 10 --re 10 --ol graftyrs --c grf_fail --ma 0.5 --dp 5 --f log_rank_residuals --t None --at 10 --cl group_strata --loci-list DRB1,DQA1,DQB1,DRB345 --cov-list None
-    python run_sum_fibers_hpc.py --d /project/kamoun_shared/data_shared/ryan_new_imp --w /project/kamoun_shared/output_shared/ryanurb/ --o hla_4locus_noagcov_baseline --rc LSF --rm 4 --q i2c2_normal --rs 10 --re 10 --loci-list DRB1,DQA1,DQB1,DRB345 
-    python run_master_sum_fibers_hpc.py --d /project/kamoun_shared/data_shared/ryan_new_imp --w /project/kamoun_shared/output_shared/ryanurb/ --o Fibers2.0_hla_4locus_noagcov_baseline --rs 10 --re 10 --loci-list DRB1,DQA1,DQB1,DRB345 --rc LSF --rm 16 --q i2c2_normal
-
-    ### DRB1, DQA1, DQB1, DRB345 + A, B, C 
-    python run_fibers_hpc.py --d /project/kamoun_shared/data_shared/ryan_new_imp --w /project/kamoun_shared/output_shared/ryanurb/ --o hla_7locus_noagcov_baseline --i 500 --ps 200 --rc LSF --rm 16 --q i2c2_normal --rs 10 --re 10 --ol graftyrs --c grf_fail --ma 0.5 --dp 5 --f log_rank_residuals --t None --at 10 --cl group_strata --loci-list A,B,C,DRB1,DQA1,DQB1,DRB345 --cov-list None
-    python run_sum_fibers_hpc.py --d /project/kamoun_shared/data_shared/ryan_new_imp --w /project/kamoun_shared/output_shared/ryanurb/ --o hla_7locus_noagcov_baseline --rc LSF --rm 4 --q i2c2_normal --rs 10 --re 10 --loci-list A,B,C,DRB1,DQA1,DQB1,DRB345
-    python run_master_sum_fibers_hpc.py --d /project/kamoun_shared/data_shared/ryan_new_imp --w /project/kamoun_shared/output_shared/ryanurb/ --o Fibers2.0_hla_7locus_noagcov_baseline --rs 10 --re 10 --loci-list A,B,C,DRB1,DQA1,DQB1,DRB345 --rc LSF --rm 16 --q i2c2_normal
+### DRB1, DQA1, DQB1, DRB345 + A, B, C 
+python run_fibers_hpc.py --d /project/kamoun_shared/data_shared/ryan_new_imp --w /project/kamoun_shared/output_shared/ryanurb/ --o hla_filtered_7locus_noagcov_baseline --ra 0.01 --i 500 --ps 200 --rc LSF --rm 16 --q i2c2_normal --rs 10 --re 10 --ol graftyrs --c grf_fail --ma 0.5 --dp 5 --f log_rank_residuals --t None --at 10 --cl group_strata --loci-list A,B,C,DRB1,DQA1,DQB1,DRB345 --cov-list None
+python run_sum_fibers_hpc.py --d /project/kamoun_shared/data_shared/ryan_new_imp --w /project/kamoun_shared/output_shared/ryanurb/ --o hla_filtered_7locus_noagcov_baseline --rc LSF --rm 4 --q i2c2_normal --rs 10 --re 10 --loci-list A,B,C,DRB1,DQA1,DQB1,DRB345
+python run_master_sum_fibers_hpc.py --d /project/kamoun_shared/data_shared/ryan_new_imp --w /project/kamoun_shared/output_shared/ryanurb/ --o Fibers2.0_hla_filtered_7locus_noagcov_baseline --rs 10 --re 10 --loci-list A,B,C,DRB1,DQA1,DQB1,DRB345 --rc LSF --rm 16 --q i2c2_normal