update configs and runtime

resources/auxiliary_workflows/benchmark/resources/local_haplotype_setup/config_distance/config.yaml

@@ -4,10 +4,7 @@ method_list: [lofreq_local_haplo,
               cliquesnv_local_haplo_snv,
               cliquesnv_local_haplo_tf0.01,
               cliquesnv_local_haplo_snv_tf0.01,
-              viloca,
-              viloca_envp,
-              viloca_multi,
-              viloca_envp_multi,
+              viloca_alpha_0.000001,
               shorah_default_amplicon,
               ]
 replicate_count: 5

resources/auxiliary_workflows/benchmark/resources/local_haplotype_setup/config_distance/params.csv

@@ -1,57 +1,41 @@
 seq_tech,seq_mode,seq_mode_param,read_length,genome_size,coverage,haplos
-#
-# Population 1 -- Illumina
-illumina,shotgun,single_amplicon,249,249,100,5@5@20@4@12@geom@0.75
-illumina,shotgun,single_amplicon,249,249,200,5@5@20@4@12@geom@0.75
-illumina,shotgun,single_amplicon,249,249,500,5@5@20@4@12@geom@0.75
-illumina,shotgun,single_amplicon,249,249,800,5@5@20@4@12@geom@0.75
+# Population 1
+illumina,shotgun,single_amplicon,249,249,1000,2@3@30@20@20@geom@0.75
+# Population 2
 illumina,shotgun,single_amplicon,249,249,1000,5@5@20@4@12@geom@0.75
-illumina,shotgun,single_amplicon,249,249,5000,5@5@20@4@12@geom@0.75
-illumina,shotgun,single_amplicon,249,249,10000,5@5@20@4@12@geom@0.75
-#
-# Population 2 -- Illumina
-illumina,shotgun,single_amplicon,249,249,100,5@10@30@10@10@geom@0.75
-illumina,shotgun,single_amplicon,249,249,200,5@10@30@10@10@geom@0.75
-illumina,shotgun,single_amplicon,249,249,500,5@10@30@10@10@geom@0.75
-illumina,shotgun,single_amplicon,249,249,800,5@10@30@10@10@geom@0.75
-illumina,shotgun,single_amplicon,249,249,1000,5@10@30@10@10@geom@0.75
-illumina,shotgun,single_amplicon,249,249,5000,5@10@30@10@10@geom@0.75
-illumina,shotgun,single_amplicon,249,249,10000,5@10@30@10@10@geom@0.75
-#
-# Population 3 -- Illumina
-illumina,shotgun,single_amplicon,249,249,100,5@3@30@20@20@geom@0.75
-illumina,shotgun,single_amplicon,249,249,200,5@3@30@20@20@geom@0.75
-illumina,shotgun,single_amplicon,249,249,500,5@3@30@20@20@geom@0.75
-illumina,shotgun,single_amplicon,249,249,800,5@3@30@20@20@geom@0.75
-illumina,shotgun,single_amplicon,249,249,1000,5@3@30@20@20@geom@0.75
-illumina,shotgun,single_amplicon,249,249,5000,5@3@30@20@20@geom@0.75
-illumina,shotgun,single_amplicon,249,249,10000,5@3@30@20@20@geom@0.75
-#
-# Population 4-- Illumina
-illumina,shotgun,single_amplicon,249,249,100,10@15@30@20@20@geom@0.75
-illumina,shotgun,single_amplicon,249,249,200,10@15@30@20@20@geom@0.75
-illumina,shotgun,single_amplicon,249,249,500,10@15@30@20@20@geom@0.75
-illumina,shotgun,single_amplicon,249,249,800,10@15@30@20@20@geom@0.75
-illumina,shotgun,single_amplicon,249,249,1000,10@15@30@20@20@geom@0.75
-illumina,shotgun,single_amplicon,249,249,5000,10@15@30@20@20@geom@0.75
-illumina,shotgun,single_amplicon,249,249,10000,10@15@30@20@20@geom@0.75
-#
-# long reads -- population 1
-nanopore,shotgun,single_amplicon,5000,5000,1000,2@3@240@40@120@geom@0.75
-pacbio,shotgun,single_amplicon,5000,5000,1000,2@3@240@40@120@geom@0.75
-#
-# long reads -- population 2
-nanopore,shotgun,single_amplicon,5000,5000,1000,5@5@240@40@120@geom@0.75
-pacbio,shotgun,single_amplicon,5000,5000,1000,5@5@240@40@120@geom@0.75
-#
-# long reads -- population 3
-nanopore,shotgun,single_amplicon,5000,5000,1000,5@10@240@40@120@geom@0.75
-pacbio,shotgun,single_amplicon,5000,5000,1000,5@10@240@40@120@geom@0.75
-#
-# long reads -- population 4
-nanopore,shotgun,single_amplicon,5000,5000,1000,5@10@600@200@200@geom@0.75
-pacbio,shotgun,single_amplicon,5000,5000,1000,5@10@600@200@200@geom@0.75
-#
-# long reads -- population 5
-nanopore,shotgun,single_amplicon,5000,5000,1000,15@5@600@200@200@geom@0.75
-pacbio,shotgun,single_amplicon,5000,5000,1000,15@5@600@200@200@geom@0.75
+# Population 3 (vary covverage)
+illumina,shotgun,single_amplicon,249,249,100,5@5@30@10@15@geom@0.75
+illumina,shotgun,single_amplicon,249,249,500,5@5@30@10@15@geom@0.75
+illumina,shotgun,single_amplicon,249,249,800,5@5@30@10@15@geom@0.75
+illumina,shotgun,single_amplicon,249,249,1000,5@5@30@10@15@geom@0.75
+illumina,shotgun,single_amplicon,249,249,5000,5@5@30@10@15@geom@0.75
+illumina,shotgun,single_amplicon,249,249,10000,5@5@30@10@15@geom@0.75
+# Population 4
+illumina,shotgun,single_amplicon,249,249,1000,5@10@30@10@15@geom@0.75
+# Population 5
+illumina,shotgun,single_amplicon,249,249,1000,5@15@30@10@15@geom@0.75
+# Population 6
+nanopore,shotgun,single_amplicon,5000,5000,1000,2@3@600@400@400@geom@0.75
+pacbio,shotgun,single_amplicon,5000,5000,1000,2@3@600@400@400@geom@0.75
+# Population 7
+nanopore,shotgun,single_amplicon,5000,5000,1000,5@5@400@80@240@geom@0.75
+pacbio,shotgun,single_amplicon,5000,5000,1000,5@5@400@80@240@geom@0.75
+# Population 8 (vary coverage)
+nanopore,shotgun,single_amplicon,5000,5000,100,5@5@600@200@300@geom@0.75
+nanopore,shotgun,single_amplicon,5000,5000,200,5@5@600@200@300@geom@0.75
+nanopore,shotgun,single_amplicon,5000,5000,500,5@5@600@200@300@geom@0.75
+nanopore,shotgun,single_amplicon,5000,5000,800,5@5@600@200@300@geom@0.75
+nanopore,shotgun,single_amplicon,5000,5000,1000,5@5@600@200@300@geom@0.75
+nanopore,shotgun,single_amplicon,5000,5000,5000,5@5@600@200@300@geom@0.75
+pacbio,shotgun,single_amplicon,5000,5000,100,5@5@600@200@300@geom@0.75
+pacbio,shotgun,single_amplicon,5000,5000,200,5@5@600@200@300@geom@0.75
+pacbio,shotgun,single_amplicon,5000,5000,500,5@5@600@200@300@geom@0.75
+pacbio,shotgun,single_amplicon,5000,5000,800,5@5@600@200@300@geom@0.75
+pacbio,shotgun,single_amplicon,5000,5000,1000,5@5@600@200@300@geom@0.75
+pacbio,shotgun,single_amplicon,5000,5000,5000,5@5@600@200@300@geom@0.75
+# Population 9
+nanopore,shotgun,single_amplicon,5000,5000,1000,5@10@600@200@300@geom@0.75
+pacbio,shotgun,single_amplicon,5000,5000,1000,5@10@600@200@300@geom@0.75
+# Population 10
+nanopore,shotgun,single_amplicon,5000,5000,1000,15@5@600@300@200@geom@0.75
+pacbio,shotgun,single_amplicon,5000,5000,1000,15@5@600@300@200@geom@0.75

resources/auxiliary_workflows/benchmark/resources/local_haplotype_setup/config_realdata/config.yaml

@@ -4,7 +4,7 @@ method_list: [lofreq_local_haplo,
               cliquesnv_local_haplo_snv,
               cliquesnv_local_haplo_tf0.01,
               cliquesnv_local_haplo_snv_tf0.01,
-              viloca,
+              viloca_alpha_0.000001,
               ]
 replicate_count: 1
 haplotype_generation: null

resources/auxiliary_workflows/benchmark/resources/local_haplotype_setup/config_realdata/params.csv

@@ -2,20 +2,19 @@ seq_tech,seq_mode,seq_mode_param,read_length,genome_size,coverage,haplos
 #
 # HIV-5-Virus-Mix
 illumina,real_data,5-virus-mix,,,1,
-#illumina,real_data,5-virus-mix,,,0.75,
 #
 # PVY-5-Strain-Mix
 nanopore,amplicon,real_data,Five_strain_PVY,,9698,
-# PVY-5-Strain-Mix
+# IAV- 10 strain mix
 pacbio,amplicon,real_data,Ten_strain_IAV,,2300,
 #
 # Two-Strain-SARS-CoV-2
 illumina,amplicon,real_data,Two-strain-SARS-CoV-2,G1_Wild_100_01,1,
 illumina,amplicon,real_data,Two-strain-SARS-CoV-2,H1_Wild_100_02,1,
 illumina,amplicon,real_data,Two-strain-SARS-CoV-2,D1_Wild_50_01,1,
-illumina,amplicon,real_data,Two-strain-SARS-CoV-2,D3_Wild_50_04,1,
+#illumina,amplicon,real_data,Two-strain-SARS-CoV-2,D3_Wild_50_04,1,
 illumina,amplicon,real_data,Two-strain-SARS-CoV-2,E1_Wild_50_02,1,
-illumina,amplicon,real_data,Two-strain-SARS-CoV-2,A3_Wild_10_04,1,
-illumina,amplicon,real_data,Two-strain-SARS-CoV-2,B1_Wild_10_02,1,
+#illumina,amplicon,real_data,Two-strain-SARS-CoV-2,A3_Wild_10_04,1,
+#illumina,amplicon,real_data,Two-strain-SARS-CoV-2,B1_Wild_10_02,1,
 illumina,amplicon,real_data,Two-strain-SARS-CoV-2,C2_Wild_10_03,1,
-illumina,amplicon,real_data,Two-strain-SARS-CoV-2,G2_Wild_100_03,1,
+#illumina,amplicon,real_data,Two-strain-SARS-CoV-2,G2_Wild_100_03,1,

resources/auxiliary_workflows/benchmark/resources/local_haplotype_setup/workflow/Snakefile

@@ -69,7 +69,7 @@ use rule run_method_local from varyvilocaparams as varyvilocaparams_run_method_l
         f"results/varyvilocaparams/method_runs/{varyvilocaparams.paramspace.wildcard_pattern}/{{method,{'|'.join(['markertoavoidemptyregex'] + varyvilocaparams.method_list)}}}/replicates/{{replicate}}/benchmark_.tsv"
     resources:
         mem_mb=20024,
-        runtime=4,
+        runtime=240,
         threads=10,
 
 
@@ -176,8 +176,9 @@ use rule run_method_local from distance as distance_run_method_local_global with
     benchmark:
         f"results/distance/method_runs/{distance.paramspace.wildcard_pattern}/{{method,{'|'.join(['markertoavoidemptyregex'] + distance.method_list)}}}/replicates/{{replicate}}/benchmark_.tsv"
     resources:
-        mem_mb=8024,
-        runtime=8000,
+        mem_mb=20024,
+        runtime=14400,
+        threads=25
 
 
 use rule performance_measures_local from distance as distance_performance_measures_local with:
@@ -260,9 +261,9 @@ use rule run_method_local from realdata as realdata_run_method_local_global with
     benchmark:
         f"results/realdata/method_runs/{realdata.paramspace.wildcard_pattern}/{{method,{'|'.join(['markertoavoidemptyregex'] + realdata.method_list)}}}/replicates/{{replicate}}/benchmark_.tsv"
     resources:
-        mem_mb=18024,
+        mem_mb=60024,
         runtime=16000,
-        threads=120,
+        threads=30,
 
 
 use rule performance_measures_local from realdata as realdata_performance_measures_local with: