+19
-17
lines changedFilter options
+19
-17
lines changed Original file line number Diff line number Diff line change
@@ -409,12 +409,9 @@
409 409
configureCloud($asm, $rootdir);
410 410
configureDNANexus();
411 411 412 -
# Set jobs sizes based on genomeSize and available hosts;
413 412
# Check that parameters (except error rates) are valid and consistent;
414 -
# Fail if any thing flagged an error condition;
415 413 416 414
checkParameters();
417 -
configureAssembler(); # Set job sizes and etc bases on genomeSize and hosts available.
418 415 419 416
# Make space for us to work in, and move there.
420 417
#
@@ -656,6 +653,10 @@
656 653
caExit("ERROR: HiFi data cannot currently be combined with another read type", undef);
657 654
}
658 655 656 +
# Now we can set memory/thread limits and any other parameters.
657 + 658 +
configureAssembler($numPacBio, $numNanopore, $numHiFi);
659 + 659 660
checkParameters(); # Check all parameters (except error rates) are valid and consistent.
660 661
printHelp(); # And one final last chance to fail.
661 662
@@ -534,7 +534,10 @@ sub getAllowedResources ($$$$$@) {
534 534
# If minMemory or minThreads isn't defined, pick a reasonable pair based on genome size.
535 535
#
536 536 537 -
sub configureAssembler () {
537 +
sub configureAssembler ($$$) {
538 +
my $numPacBio = shift @_;
539 +
my $numNanopore = shift @_;
540 +
my $numHiFi = shift @_;
538 541 539 542
# For overlapper and mhap, allow larger maximums for larger genomes. More memory won't help
540 543
# smaller genomes, and the smaller minimums won't hurt larger genomes (which are probably being
@@ -782,20 +785,18 @@ sub configureAssembler () {
782 785 783 786
# And bogart.
784 787 785 -
if (getGlobal("genomeSize") < adjustGenomeSize("40m")) {
786 -
setGlobalIfUndef("batMemory", "4-16"); setGlobalIfUndef("batThreads", "2-4");
787 - 788 -
} elsif (getGlobal("genomeSize") < adjustGenomeSize("500m")) {
789 -
setGlobalIfUndef("batMemory", "16-64"); setGlobalIfUndef("batThreads", "2-8");
790 - 791 -
} elsif (getGlobal("genomeSize") < adjustGenomeSize("2g")) {
792 -
setGlobalIfUndef("batMemory", "32-256"); setGlobalIfUndef("batThreads", "4-16");
793 - 794 -
} elsif (getGlobal("genomeSize") < adjustGenomeSize("5g")) {
795 -
setGlobalIfUndef("batMemory", "128-512"); setGlobalIfUndef("batThreads", "8-32");
796 - 788 +
if ($numHiFi == 0) {
789 +
if (getGlobal("genomeSize") < adjustGenomeSize("40m")) { setGlobalIfUndef("batMemory", "4-16"); setGlobalIfUndef("batThreads", "2-4"); }
790 +
elsif (getGlobal("genomeSize") < adjustGenomeSize("500m")) { setGlobalIfUndef("batMemory", "16-48"); setGlobalIfUndef("batThreads", "2-8"); }
791 +
elsif (getGlobal("genomeSize") < adjustGenomeSize("2g")) { setGlobalIfUndef("batMemory", "32-128"); setGlobalIfUndef("batThreads", "4-16"); }
792 +
elsif (getGlobal("genomeSize") < adjustGenomeSize("5g")) { setGlobalIfUndef("batMemory", "64-256"); setGlobalIfUndef("batThreads", "8-32"); }
793 +
else { setGlobalIfUndef("batMemory", "64-512"); setGlobalIfUndef("batThreads", "8-64"); }
797 794
} else {
798 -
setGlobalIfUndef("batMemory", "256-1024"); setGlobalIfUndef("batThreads", "16-64");
795 +
if (getGlobal("genomeSize") < adjustGenomeSize("40m")) { setGlobalIfUndef("batMemory", "4-16"); setGlobalIfUndef("batThreads", "2-4"); }
796 +
elsif (getGlobal("genomeSize") < adjustGenomeSize("500m")) { setGlobalIfUndef("batMemory", "8-32"); setGlobalIfUndef("batThreads", "2-8"); }
797 +
elsif (getGlobal("genomeSize") < adjustGenomeSize("2g")) { setGlobalIfUndef("batMemory", "16-64"); setGlobalIfUndef("batThreads", "4-16"); }
798 +
elsif (getGlobal("genomeSize") < adjustGenomeSize("5g")) { setGlobalIfUndef("batMemory", "32-128"); setGlobalIfUndef("batThreads", "8-32"); }
799 +
else { setGlobalIfUndef("batMemory", "32-256"); setGlobalIfUndef("batThreads", "8-64"); }
799 800
}
800 801 801 802
# Log maxMemory setting.
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