fb5a1a487756e0535aef78cf7818c7ea9c5f09e7
hiram
  Wed Sep 1 15:21:45 2021 -0700
using ram=16g on the cluster jobs to help prevent cluster job failures no redmine

diff --git src/hg/utils/automation/doTandemDup.pl src/hg/utils/automation/doTandemDup.pl
index 73a779a..343d6b2 100755
--- src/hg/utils/automation/doTandemDup.pl
+++ src/hg/utils/automation/doTandemDup.pl
@@ -125,30 +125,31 @@
         "stage, or move aside/remove $runDir and run again.\n";
   }
 
   &HgAutomate::mustMkdir($runDir);
 
   my $templateCmd = ('runOne $(path1) {check out exists tmp/$(path1).' .
             "$kmersMinus1" . 'mer.txt.gz}');
   &HgAutomate::makeGsub($runDir, $templateCmd);
   `touch "$runDir/para_hub_$paraHub"`;
 
   my $whatItDoes = "Generate kmers for entire sequence.";
   my $bossScript = newBash HgRemoteScript("$runDir/runKmers.bash",
 		$paraHub, $runDir, $whatItDoes);
 
   my $paraRun = &HgAutomate::paraRun();
+
   $bossScript->add(<<_EOF_
 twoBitInfo $twoBit stdout | cut -f1 > part.list
 printf '#!/bin/bash
 
 set -beEu -o pipefail
 
 export fa=\$1
 export result=\$2
 
 mkdir -p tmp
 
 twoBitToFa ${twoBit}:\$fa stdout \\
   | $Bin/kmerPrint.pl $kmersMinus1 stdin | gzip -c > \$result
 ' > runOne
 chmod +x runOne
@@ -175,31 +176,36 @@
   if ( ! $opt_debug && ( ! -s "$prevRunDir/run.time" ) ) {
     die "pairedEnds: looks like previous kmers step has not been competed, " .
       "file db/bed/tandemDups/kmers/run.time does not exist. run with: -continue kmers to perform previous step.\n";
   }
 
   &HgAutomate::mustMkdir($runDir);
 
   my $templateCmd = ("runOne $kmersMinus1 $gapSize " . '$(path1) {check out exists tmp/$(path1).bed.gz}');
   &HgAutomate::makeGsub($runDir, $templateCmd);
   `touch "$runDir/para_hub_$paraHub"`;
 
   my $whatItDoes = "Collect kmers into pairs.";
   my $bossScript = newBash HgRemoteScript("$runDir/runPairedEnds.bash",
 		$paraHub, $runDir, $whatItDoes);
 
-  my $paraRun = &HgAutomate::paraRun();
+  # trying 16G ram to see if jobs will not fail
+  my $paraRun = "para make -ram=16g jobList
+para check
+para time > run.time
+cat run.time\n";
+
   $bossScript->add(<<_EOF_
 ln -s $prevRunDir/part.list .
 printf '#!/bin/bash
 
 set -beEu -o pipefail
 
 export kmerSize=\$1
 export gapSize=\$2
 export chrName=\$3
 export result=\$4
 
 mkdir -p tmp
 
 $Bin/kmerPairs.pl \$kmerSize \$gapSize \$chrName \$result
 ' > runOne
@@ -227,31 +233,36 @@
   if ( ! $opt_debug && ( ! -s "$prevRunDir/run.time" ) ) {
     die "pairedEnds: looks like previous pairedEnds step has not been competed, " .
       "file db/bed/tandemDups/pairedEnds/run.time does not exist. run with: -continue pairedEnds to perform previous step.\n";
   }
 
   &HgAutomate::mustMkdir($runDir);
 
   my $templateCmd = ('runOne $(path1) {check out exists tmp/$(path1).bed.gz}');
   &HgAutomate::makeGsub($runDir, $templateCmd);
   `touch "$runDir/para_hub_$paraHub"`;
 
   my $whatItDoes = "Collapse kmers pairs into larger paired ends.";
   my $bossScript = newBash HgRemoteScript("$runDir/runCollapsePairedEnds.bash",
 		$paraHub, $runDir, $whatItDoes);
 
-  my $paraRun = &HgAutomate::paraRun();
+  # trying 16G ram to see if jobs will not fail
+  my $paraRun = "para make -ram=16g jobList
+para check
+para time > run.time
+cat run.time\n";
+
   $bossScript->add(<<_EOF_
 ln -s $prevRunDir/part.list .
 printf '#!/bin/bash
 
 set -beEu -o pipefail
 
 export chrName=\$1
 export result=\$2
 mkdir -p tmp
 
 $Bin/kmerCollapsePairedEnds.pl $kmersMinus1 ../pairedEnds/tmp/\$chrName.bed.gz \\
    | gzip -c > tmp/\$chrName.bed.gz
 ' > runOne
 chmod +x runOne
 gensub2 part.list single gsub jobList