metaMSBG bugfixes

config.yaml

@@ -25,7 +25,7 @@ illumina:
 pacbio-hifi-assemblers:
  - metaMDBG
  - metaflye
-# - hifiasm-meta
+ - hifiasm-meta
 
 pacbio-clr-assemblers:
 # - metaflye
@@ -36,7 +36,7 @@ ont-assemblers:
 # - miniasm
 
 pacbio-hifi-illumina-hybrid-assemblers:
- - operaMS
+# - operaMS
 
 pacbio-clr-illumina-hybrid-assemblers:
 # - operaMS

rules/assembly.smk

@@ -41,9 +41,9 @@ rule metaMDBG_installation :
 
 rule metaMDBG_assembly :
     conda : "../env/metaMDBG.yaml"
-    threads : 16
+    threads : 48
     resources :
-        cpus_per_task = 16,
+        cpus_per_task = 48,
         mem_mb=50*1000, # 1 giga = 1000 mega
         runtime=3*24*60,
     input : 
@@ -103,7 +103,7 @@ rule operams_assembly :
     threads : 48
     resources :
         cpus_per_task=48,
-        mem_mb=160*1000, # 1 giga = 1000 mega
+        mem_mb=320*1000, # 1 giga = 1000 mega
         runtime=3*24*60,
     shell : 
         "./{input.script} {input.r1} {input.r2} {input.long} {params.output_folder}"

rules/assembly_evaluation.smk

@@ -47,6 +47,8 @@ rule reads_on_contigs_mapping :
 rule assembly_references_free_stats :
     params : 
         threshold = "5000"
+    resources :
+        runtime=2*24*60,
     input : 
         script = "assembly_evaluation/reference_free_report_writer.out",
         assembly = "outputs/{run_name}/{assember_name}/assembly.fasta",
@@ -85,3 +87,4 @@ rule assembly_reference_based_stats :
     output : "outputs/{run_name}/{assember_name}/reference_based_report.txt"
     shell : "python3 {input.script} {input.metaquast_output} {input.coverage_information}  > {output}" 
 
+