more bug fixes and mem/time updates

popsim-consortium · Jun 28, 2024 · 720a4c7 · 720a4c7
1 parent bb13f86
commit 720a4c7
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Showing 4 changed files with 49 additions and 45 deletions.
diff --git a/workflows/dfe.snake b/workflows/dfe.snake
@@ -10,8 +10,12 @@ import ts2fs
 import plots
 import masks
 
-configfile: "workflows/config/snakemake/tiny_config.yaml"
+#quick fix for excluding "Constant" with "pop1" and "pop2" from the analysis
+def drop_constant_populations(paths):
+    return [path for path in paths if not ("Constant" in path and ("pop1" in path or "pop2" in path))]
+
 
+configfile: "workflows/config/snakemake/tiny_config.yaml"
 
 np.random.seed(config["seed"])
 
@@ -73,7 +77,6 @@ if "none" in annotation_dict:
     del annotation_dict["none"]
 annotation_list = list(annotation_dict)
 
-
 rule all:
     input: 
         expand(output_dir + "/plots/{demog}/{dfes}/{annots}/dfe.inference.benchmark.pdf",
@@ -163,8 +166,7 @@ rule dadi_infer_dfe:
     threads: 8
     shell:
         """
-        dadi-cli InferDFE --fs {input[0]} --cache1d {input[1]} --demo-popt {input[2]} --output-prefix {params.prefix} --pdf1d {params.dfe} --p0 {params.dfe_p0} --ubounds {params.dfe_ubounds} --lbounds {params.dfe_lbounds} --ratio {params.ratio} --optimizations {params.opts} --cpus {threads} --nomisid --force-convergence 0
-
+        dadi-cli InferDFE --fs {input[0]} --cache1d {input[1]} --demo-popt {input[2]} --output-prefix {params.prefix} --pdf1d {params.dfe} --p0 {params.dfe_p0} --ubounds {params.dfe_ubounds} --lbounds {params.dfe_lbounds} --ratio {params.ratio} --optimizations {params.opts} --cpus {threads} --nomisid --force-convergence 1
         """
 
 rule get_dadi_dfe_bestfits:
@@ -384,34 +386,34 @@ rule get_grapes_bestfits:
 
 rule plot_results:
     input:
-        dadi_res = expand(output_dir + "/inference/{demog}/dadi/{dfes}/{annots}/{seeds}/pop{ids}/pop{ids}.dadi.bestfit", 
+        dadi_res = drop_constant_populations(expand(output_dir + "/inference/{demog}/dadi/{dfes}/{annots}/{seeds}/pop{ids}/pop{ids}.dadi.bestfit", 
             demog=demo_model_id_list,
             seeds=seed_list,
             dfes=dfe_list,
             annots=annotation_list,
             ids=pids,
-        ),
-        polydfe_res = expand(output_dir + "/inference/{demog}/polyDFE/{dfes}/{annots}/{seeds}/pop{ids}/pop{ids}.polyDFE.bestfit",
+        )),
+        polydfe_res = drop_constant_populations(expand(output_dir + "/inference/{demog}/polyDFE/{dfes}/{annots}/{seeds}/pop{ids}/pop{ids}.polyDFE.bestfit",
             demog=demo_model_id_list,
             seeds=seed_list,
             dfes=dfe_list,
             annots=annotation_list,
             ids=pids,
-        ),
-        dfe_alpha_res = expand(output_dir + "/inference/{demog}/DFE-alpha/{dfes}/{annots}/{seeds}/pop{ids}/pop{ids}.DFE-alpha.bestfit",
+        )),
+        dfe_alpha_res = drop_constant_populations(expand(output_dir + "/inference/{demog}/DFE-alpha/{dfes}/{annots}/{seeds}/pop{ids}/pop{ids}.DFE-alpha.bestfit",
             demog=demo_model_id_list,
             seeds=seed_list,
             dfes=dfe_list,
             annots=annotation_list,
             ids=pids,
-        ),
-        grapes_res = expand(output_dir + "/inference/{demog}/grapes/{dfes}/{annots}/{seeds}/pop{ids}/pop{ids}.grapes.bestfit",
+        )),
+        grapes_res = drop_constant_populations(expand(output_dir + "/inference/{demog}/grapes/{dfes}/{annots}/{seeds}/pop{ids}/pop{ids}.grapes.bestfit",
             demog=demo_model_id_list,
             seeds=seed_list,
             dfes=dfe_list,
             annots=annotation_list,
             ids=pids,
-        )
+        ))
     output:
         output_dir + "/plots/{demog}/{dfes}/{annots}/dfe.inference.benchmark.pdf"
     run:

diff --git a/workflows/masks/HapmapII_GRCh38.mask.bed b/workflows/masks/HapmapII_GRCh38.mask.bed
@@ -1,28 +1,28 @@
-chr10	 38861078	 41705569	
-chr1	 121569984	 143276353	
-chr11	 50795892	 54555633	
-chr12	 34700914	 37463389	
-chr13	 1	 18447064	
-chr14	 1	 19198131	
-chr15	 1	 19809716	
-chr16	 36034945	 46428208	
-chr17	 22738887	 26950488	
-chr18	 15409995	 20934306	
-chr19	 24373307	 27244449	
-chr20	 26328611	 30187700	
-chr21	 10646501	 12968298	
-chr21	 1	 10326653	
-chr22	 1	 15287921	
-chr2	 90236658	 91433610	
-chr2	 92117097	 94663732	
-chr3	 90427071	 93808853	
-chr4	 49627542	 51818712	
-chr5	 46363876	 50291681	
-chr6	 58452161	 60342543	
-chr7	 57870656	 61072218	
-chr8	 43936537	 46006821	
-chr9	 38743712	 40906821	
-chr9	 41438036	 62926704	
-chr9	 66183582	 68223187	
-chrX	 1	 2785350	
-chrX	 58456814	 62611346	
+chr1	121569983	143276353
+chr2	90236657	91433610
+chr2	92117096	94663732
+chr3	90427070	93808853
+chr4	49627541	51818712
+chr5	46363875	50291681
+chr6	58452160	60342543
+chr7	57870655	61072218
+chr8	43936536	46006821
+chr9	38743711	40906821
+chr9	41438035	62926704
+chr9	66183581	68223187
+chr10	38861077	41705569
+chr11	50795891	54555633
+chr12	34700913	37463389
+chr13	0	18447064
+chr14	0	19198131
+chr15	0	19809716
+chr16	36034944	46428208
+chr17	22738886	26950488
+chr18	15409994	20934306
+chr19	24373306	27244449
+chr20	26328610	30187700
+chr21	0	10326653
+chr21	10646500	12968298
+chr22	0	15287921
+chrX	0	2785350
+chrX	58456813	62611346
diff --git a/workflows/n_t.snake b/workflows/n_t.snake
@@ -218,10 +218,10 @@ rule run_stairwayplot:
             chrms=chrm_list)
     output:
         output_dir + "/inference/{demog}/stairwayplot/{dfes}/{annots}/{seeds}/{pops}/stairwayplot_estimated_Ne.txt"
-
     threads: 20
     resources:
-        mem_mb=120000,
+        time = 1_000,
+        mem_mb=120_000,
     run:
         inputs = expand(
             output_dir
@@ -347,7 +347,9 @@ rule run_msmc:
         output_dir + "/inference/{demog}/msmc/{dfes}/{annots}/{seeds}/{pops}/{samps}.trees.multihep.txt.final.txt"
     threads: 8
     resources:
-        mem_mb = lambda wildcards, attempt: attempt * 64000
+        time = lambda wildcards, attempt: attempt * 1_000,
+        mem_mb = lambda wildcards, attempt: attempt * 200_000
+
     run:
         inputs = expand(output_dir + "/inference/{demog}/msmc/{dfes}/{annots}/{seeds}/{pops}/{chrms}.trees.multihep.txt",
                     demog=wildcards.demog,

diff --git a/workflows/simulation.snake b/workflows/simulation.snake
@@ -61,8 +61,8 @@ rule simulation:
     output:
         output_dir + "/simulated_data/{demog}/{dfes}/{annots}/{seeds}/sim_{chrms}.trees"
     resources: 
-        time = lambda wildcards, attempt: attempt * 3000, 
-        mem_mb = lambda wildcards, attempt: attempt * 50000
+        time = lambda wildcards, attempt: attempt * 6000, 
+        mem_mb = lambda wildcards, attempt: attempt * 100000
     run:
         if wildcards.demog == 'Constant': 
             model = stdpopsim.PiecewiseConstantSize(species.population_size)