Increase minimum memory for gfa alignments

sgblanch · May 12, 2017 · 0cfea48 · 0cfea48
1 parent 43dc29f
commit 0cfea48
Showing 1 changed file with 5 additions and 5 deletions.
diff --git a/src/pipelines/canu/Configure.pm b/src/pipelines/canu/Configure.pm
@@ -662,23 +662,23 @@ sub configureAssembler () {
 
     if      (getGlobal("genomeSize") < adjustGenomeSize("40m")) {
         setGlobalIfUndef("batMemory",   "2-16");        setGlobalIfUndef("batThreads",   "1-4");
-        setGlobalIfUndef("gfaMemory",   "2-4");         setGlobalIfUndef("gfaThreads",   "1");
+        setGlobalIfUndef("gfaMemory",   "2-8");         setGlobalIfUndef("gfaThreads",   "1-4");
 
     } elsif (getGlobal("genomeSize") < adjustGenomeSize("500m")) {
         setGlobalIfUndef("batMemory",   "16-64");       setGlobalIfUndef("batThreads",   "2-8");
-        setGlobalIfUndef("gfaMemory",   "2-4");         setGlobalIfUndef("gfaThreads",   "2-4");
+        setGlobalIfUndef("gfaMemory",   "4-8");         setGlobalIfUndef("gfaThreads",   "2-8");
 
     } elsif (getGlobal("genomeSize") < adjustGenomeSize("2g")) {
         setGlobalIfUndef("batMemory",   "32-256");      setGlobalIfUndef("batThreads",   "4-16");
-        setGlobalIfUndef("gfaMemory",   "4-8");         setGlobalIfUndef("gfaThreads",   "4-8");
+        setGlobalIfUndef("gfaMemory",   "8-16");         setGlobalIfUndef("gfaThreads",  "4-16");
 
     } elsif (getGlobal("genomeSize") < adjustGenomeSize("5g")) {
         setGlobalIfUndef("batMemory",   "128-512");     setGlobalIfUndef("batThreads",   "8-32");
-        setGlobalIfUndef("gfaMemory",   "8-16");        setGlobalIfUndef("gfaThreads",   "8-16");
+        setGlobalIfUndef("gfaMemory",   "16-32");        setGlobalIfUndef("gfaThreads",  "8-32");
 
     } else {
         setGlobalIfUndef("batMemory",   "256-1024");    setGlobalIfUndef("batThreads",   "16-64");
-        setGlobalIfUndef("gfaMemory",   "16-32");       setGlobalIfUndef("gfaThreads",   "16-64");
+        setGlobalIfUndef("gfaMemory",   "32-64");       setGlobalIfUndef("gfaThreads",   "16-64");
     }
 
     #  Finally, use all that setup to pick actual values for each component.