lower maf thresh and try to rerun happler

analysis/config/config-ukb.yml

@@ -44,7 +44,7 @@ mode: run
 
 # Discard rare variants with a MAF below this number
 # Defaults to 0 if not specified
-min_maf: 0.01
+min_maf: 0.00005
 
 # Whether to include the causal variant in the set of genotypes provided to the
 # finemapping methods. Set this to true if you're interested in seeing how the

analysis/workflow/rules/genotypes.smk

@@ -150,7 +150,7 @@ rule vcf2plink:
         psam=out+"/snps.psam",
         log=temp(out+"/snps.log"),
     resources:
-        runtime=10,
+        runtime=12,
     threads: 2
     log:
         logs + "/vcf2plink",
@@ -160,7 +160,7 @@ rule vcf2plink:
         "../envs/default.yml"
     shell:
         "plink2 --vcf {input.vcf} --maf {params.maf} --geno 0 --make-pgen "
-        "--threads {threads} {params.samps} --out {params.prefix} &>{log}"
+        "--threads {threads}{params.samps} --out {params.prefix} &>{log}"
 
 
 rule subset_str:
@@ -214,7 +214,8 @@ rule subset:
         psam=out+"/subset/{sampsize}.psam",
         log=temp(out+"/subset/{sampsize}.log"),
     resources:
-        runtime=3,
+        runtime=12,
+    threads: 2
     log:
         logs + "/subset/{sampsize}",
     benchmark:

analysis/workflow/rules/happler.smk

@@ -41,11 +41,12 @@ rule run:
         idx=out + "/happler.hap.gz.tbi",
         dot=out + "/happler.dot",
     resources:
-        runtime=10,
+        runtime=120,
         # slurm_partition="hotel",
         # slurm_extra="--qos=hotel",
         # mem_mb=lambda wildcards, threads: threads*4.57,
-    threads: 6
+        mem_mb=lambda wildcards: 5000,
+    threads: 1
     log:
         logs + "/run",
     benchmark: