50c3ab948546ac10a2f0bf151ab51c8b836bafd9
angie
  Mon Oct 4 16:58:39 2021 -0700
Use normal priority for cluster run.

diff --git src/hg/utils/otto/sarscov2phylo/usherClusterRun.sh src/hg/utils/otto/sarscov2phylo/usherClusterRun.sh
index 0d06eb0..2cd634c 100755
--- src/hg/utils/otto/sarscov2phylo/usherClusterRun.sh
+++ src/hg/utils/otto/sarscov2phylo/usherClusterRun.sh
@@ -53,31 +53,31 @@
 #!/bin/bash
 set -beEu
 vcf=\$1
 pbIn=\$2
 pbOut=\$3
 log=\$4
 /cluster/home/angie/github/usher/build/usher -u -T $threadCount -A -e 5 --max-parsimony-per-sample 20 -v \$vcf -i \$pbIn -o \$pbOut >& \$log
 EOF
 chmod a+x runUsher.sh
 
 cp /dev/null jobList
 for ((i=0;  $i < $jobCount;  i++)); do
     echo "./runUsher.sh new.$i.masked.vcf.gz prevRenamed.pb {check out exists preTrim.$i.pb} usher.addNew.$i.log" >> jobList
 done
 
-ssh ku "cd $ottoDir/$today && para -cpu=$threadCount -priority=100 make jobList"
+ssh ku "cd $ottoDir/$today && para -cpu=$threadCount -priority=10 make jobList"
 
 # Make a combined log (updateCombinedTree.sh looks there for sequences with excessively high EPPs)
 cat usher.addNew.*.log > usher.addNew.log
 
 # Merge 16 protobufs into 1
 time $matUtils merge -T 8 --input-mat-1 preTrim.0.pb --input-mat-2 preTrim.1.pb -o merged.0.1.pb &
 $matUtils merge -T 8 --input-mat-1 preTrim.2.pb --input-mat-2 preTrim.3.pb -o merged.2.3.pb &
 $matUtils merge -T 8 --input-mat-1 preTrim.4.pb --input-mat-2 preTrim.5.pb -o merged.4.5.pb &
 $matUtils merge -T 8 --input-mat-1 preTrim.6.pb --input-mat-2 preTrim.7.pb -o merged.6.7.pb &
 $matUtils merge -T 8 --input-mat-1 preTrim.8.pb --input-mat-2 preTrim.9.pb -o merged.8.9.pb &
 $matUtils merge -T 8 --input-mat-1 preTrim.10.pb --input-mat-2 preTrim.11.pb -o merged.10.11.pb &
 $matUtils merge -T 8 --input-mat-1 preTrim.12.pb --input-mat-2 preTrim.13.pb -o merged.12.13.pb &
 $matUtils merge -T 8 --input-mat-1 preTrim.14.pb --input-mat-2 preTrim.15.pb -o merged.14.15.pb &
 wait