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edits related to production pipeline #114

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merged 8 commits into from
Jul 18, 2024
Merged

edits related to production pipeline #114

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f26ae43
edits related to production pipeline
silastittes May 14, 2024
9151c04
patch for n_t masking when all_sites option is used
silastittes May 16, 2024
5d5dec4
minor tweaks to time and memory limits, and a small error handling step
silastittes Jun 5, 2024
bb13f86
further tweaks to push production scale sims through
silastittes Jun 13, 2024
720a4c7
more bug fixes and mem/time updates
silastittes Jun 28, 2024
3148cb7
more time for stairway plot
silastittes Jul 1, 2024
852e516
more time for stairway
silastittes Jul 8, 2024
c237199
minor tweaks in case pipeline isn't ran from root dir
silastittes Jul 17, 2024
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32 changes: 16 additions & 16 deletions workflows/config/snakemake/production_config_HomSap.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -10,32 +10,32 @@
"num_samples_per_population": [100],
},
{"id":"OutOfAfricaArchaicAdmixture_5R19",
"num_samples_per_population": 3*[100],
"num_samples_per_population": [100, 100, 100],
}
]
"genetic_map": "HapMapII_GRCh38"
"chrm_list": "chr1, chr2, chr3, chr4, chr5, chr6, chr7, chr8, chr9, chr10, chr11, chr12, chr13, chr14, chr15, chr16, chr17, chr18, chr19, chr20, chr21, chr22"
"chrm_list": "chr1,chr2,chr3,chr4,chr5,chr6,chr7,chr8,chr9,chr10,chr11,chr12,chr13,chr14,chr15,chr16,chr17,chr18,chr19,chr20,chr21,chr22"
"dfe_list": ["none", "Gamma_K17"]
"annotation_list": ["all_sites", "ensembl_havana_104_exons", "ensembl_havana_104_exons"]
"mask_file": "workflows/masks/HapmapII_GRCh38.mask.bed"
"stairway_annot_mask" : "" # set this or any of the below to 'none' to skip annot masking
"msmc_annot_mask" : ""
"gone_annot_mask" : ""
"smcpp_annot_mask" : ""
"msmc_annot_mask": ""
"gone_annot_mask": ""
"smcpp_annot_mask": ""

# slim settings
"slim_scaling_factor": 1
"slim_burn_in": 10

# n(t) specific configs
"methods" : ["stairwayplot", "gone", "smcpp", "msmc"]
"num_sampled_genomes_msmc" : [6]
"num_msmc_iterations" : 20
"gone_phase" : 1 # 0 for pseudohaploid, 1 for phased, 2 for unknown phase
"gone_max_snps" : 50000 # default=50000
"gone_threads" : 8
"gone_num_gens" : 2000 # default=2000
"gone_num_bins" : 400 # default=400
"methods": ["stairwayplot", "gone", "smcpp", "msmc"]
"num_sampled_genomes_msmc": [6]
"num_msmc_iterations": 20
"gone_phase": 1 # 0 for pseudohaploid, 1 for phased, 2 for unknown phase
"gone_max_snps": 50000 # default=50000
"gone_threads": 8
"gone_num_gens": 2000 # default=2000
"gone_num_bins": 400 # default=400


# exe paths
Expand All @@ -44,6 +44,6 @@
"dfe_alpha_data_path_1": "ext/dfe-alpha-release-2.16/data"
"dfe_alpha_data_path_2": "three-epoch"
"grapes_exec": "ext/grapes/multi_grapes"
"msmc_exec" : "ext/msmc2/build/release/msmc2"
"stairwayplot_code" : "ext/stairwayplot/swarmops.jar"
"gone_code" : "ext/GONE/Linux"
"msmc_exec": "ext/msmc2/build/release/msmc2"
"stairwayplot_code": "ext/stairwayplot/swarmops.jar"
"gone_code": "ext/GONE/Linux"
40 changes: 18 additions & 22 deletions workflows/config/snakemake/production_config_PhoSin.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -6,36 +6,32 @@
# species-specific settings
"species": "PhoSin"
"demo_models": [
{"id":"Constant",
"num_samples_per_population": [100],
},
{"id":"Vaquita2Epoch_1R22",
"num_samples_per_population": 3*[100],
}
{"id": "Constant", "num_samples_per_population": [100]},
{"id": "Vaquita2Epoch_1R22", "num_samples_per_population": [100]}
]
"genetic_map": null
"chrm_list": "1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21"
"chrm_list": "1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21"
"dfe_list": ["none", "Gamma_R22"]
"annotation_list": ["all_sites", "Phocoena_sinus.mPhoSin1.pri.110_exons"]
"mask_file": "workflows/masks/PhoSin_fake.mask.bed"
"stairway_annot_mask" : "" # set this or any of the below to 'none' to skip annot masking
"msmc_annot_mask" : ""
"gone_annot_mask" : ""
"smcpp_annot_mask" : ""
"stairway_annot_mask": "" # set this or any of the below to 'none' to skip annot masking
"msmc_annot_mask": ""
"gone_annot_mask": ""
"smcpp_annot_mask": ""

# slim settings
"slim_scaling_factor": 1
"slim_burn_in": 10

# n(t) specific configs
"methods" : ["stairwayplot", "gone", "smcpp", "msmc"]
"num_sampled_genomes_msmc" : [6]
"num_msmc_iterations" : 20
"gone_phase" : 1 # 0 for pseudohaploid, 1 for phased, 2 for unknown phase
"gone_max_snps" : 50000 # default=50000
"gone_threads" : 8
"gone_num_gens" : 2000 # default=2000
"gone_num_bins" : 400 # default=400
"methods": ["stairwayplot", "gone", "smcpp", "msmc"]
"num_sampled_genomes_msmc": [6]
"num_msmc_iterations": 20
"gone_phase": 1 # 0 for pseudohaploid, 1 for phased, 2 for unknown phase
"gone_max_snps": 50000 # default=50000
"gone_threads": 8
"gone_num_gens": 2000 # default=2000
"gone_num_bins": 400 # default=400


# exe paths
Expand All @@ -44,6 +40,6 @@
"dfe_alpha_data_path_1": "ext/dfe-alpha-release-2.16/data"
"dfe_alpha_data_path_2": "three-epoch"
"grapes_exec": "ext/grapes/multi_grapes"
"msmc_exec" : "ext/msmc2/build/release/msmc2"
"stairwayplot_code" : "ext/stairwayplot/swarmops.jar"
"gone_code" : "ext/GONE/Linux"
"msmc_exec": "ext/msmc2/build/release/msmc2"
"stairwayplot_code": "ext/stairwayplot/swarmops.jar"
"gone_code": "ext/GONE/Linux"
22 changes: 9 additions & 13 deletions workflows/simulation.snake
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Expand Up @@ -64,28 +64,24 @@ rule simulation:
run:
if wildcards.demog == 'Constant':
model = stdpopsim.PiecewiseConstantSize(species.population_size)
mutation_rate = 1.29e-08 # where is this from?
#samples = model.get_samples(*demo_sample_size_dict[wildcards.demog])
mutation_rate = species.genome.mean_mutation_rate
else:
model = species.get_demographic_model(wildcards.demog)
mutation_rate = model.mutation_rate
#samples = model.get_samples(*demo_sample_size_dict[wildcards.demog]) # YRI, CEU, CHB
samples = {f"{model.populations[i].name}": m for i, m in enumerate(demo_sample_size_dict[wildcards.demog])}
genetic_map_id = config["genetic_map"]
contig = species.get_contig(wildcards.chrms, genetic_map=genetic_map_id)
if wildcards.dfes != "none":
# Load dfe only if provided
dfe = species.get_dfe(wildcards.dfes)
if wildcards.annots == "all_sites":
# Adding selection to the whole contig
contig.add_dfe(intervals=np.array([[0, int(contig.length)]]), DFE=dfe)
elif wildcards.annots == "none":
contig = species.get_contig(wildcards.chrms, genetic_map=genetic_map_id)
else:
## Adding annotation only seletion on exon region
annot = species.get_annotations(wildcards.annots)
annot_intervals = annot.get_chromosome_annotations(wildcards.chrms)
contig.add_dfe(intervals=annot_intervals, DFE=dfe)
if wildcards.annots == "all_sites":
# Adding selection to the whole contig
contig.add_dfe(intervals=np.array([[0, int(contig.length)]]), DFE=dfe)
else:
## Adding annotation only seletion on exon region
annot = species.get_annotations(wildcards.annots)
annot_intervals = annot.get_chromosome_annotations(wildcards.chrms)
contig.add_dfe(intervals=annot_intervals, DFE=dfe)
Comment on lines +82 to +89
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Can someone check this? I was getting a dfe is called before it's defined error. This logic resolves that, but I want to make sure it's correct otherwise.

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this looks good to me


contig.mutation_rate = mutation_rate
engine = stdpopsim.get_engine("slim")
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