abdea7a81b3d511adaee6300277721a804f5581f
angie
  Tue Mar 30 11:57:47 2021 -0700
Ongoing fixes for odd characters in sequence names and other pipeline tweaks.

diff --git src/hg/utils/otto/sarscov2phylo/updatePublic.sh src/hg/utils/otto/sarscov2phylo/updatePublic.sh
index 0938a1a..dbb1e5c 100755
--- src/hg/utils/otto/sarscov2phylo/updatePublic.sh
+++ src/hg/utils/otto/sarscov2phylo/updatePublic.sh
@@ -1,49 +1,53 @@
 #!/bin/bash
 source ~/.bashrc
 set -beEu -x -o pipefail
 
 #	Do not modify this script, modify the source tree copy:
 #	kent/src/hg/utils/otto/sarscov2phylo/updatePublic.sh
 
 usage() {
     echo "usage: $0 prevDate problematicSitesVcf"
 }
 
 if [ $# != 2 ]; then
   usage
   exit 1
 fi
 
 prevDate=$1
 problematicSitesVcf=$2
 
 ottoDir=/hive/data/outside/otto/sarscov2phylo
 gisaidDir=/hive/users/angie/gisaid
 
 today=$(date +%F)
 scriptDir=$(dirname "${BASH_SOURCE[0]}")
 
 $scriptDir/gisaidFromChunks.sh
 
 cogUkDir=$ottoDir/cogUk.$today
 mkdir -p $cogUkDir
 cd $cogUkDir
-$scriptDir/getCogUk.sh >& getCogUk.log
+time $scriptDir/getCogUk.sh >& getCogUk.log
 
 ncbiDir=$ottoDir/ncbi.$today
 mkdir -p $ncbiDir
 cd $ncbiDir
-$scriptDir/getNcbi.sh >& getNcbi.log
+time $scriptDir/getNcbi.sh >& getNcbi.log
 
-$scriptDir/updateIdMapping.sh $gisaidDir/{metadata_batch_$today.tsv.gz,sequences_batch_$today.fa.xz}
+time $scriptDir/updateIdMapping.sh \
+    $gisaidDir/{metadata_batch_$today.tsv.gz,sequences_batch_$today.fa.xz}
 
 buildDir=$ottoDir/$today
 mkdir -p $buildDir
 cd $buildDir
-$scriptDir/updatePublicTree.sh $prevDate $problematicSitesVcf >& updatePublicTree.log
+time $scriptDir/updatePublicTree.sh $prevDate $problematicSitesVcf >& updatePublicTree.log
 
 cat hgPhyloPlace.description.txt
 
-$scriptDir/updateCombinedTree.sh $prevDate $problematicSitesVcf >& updateCombinedTree.log
+time $scriptDir/updateCombinedTree.sh $prevDate $problematicSitesVcf >& updateCombinedTree.log
 
 cat hgPhyloPlace.plusGisaid.description.txt
+
+# Clean up
+nice xz -f new*fa &