e4eb9b464422dc81af82a711fd6470174ed3fb92
angie
  Fri Aug 26 11:56:30 2022 -0700
Add retry for all the URLs. Update to latest nextclade version.

diff --git src/hg/utils/otto/sarscov2phylo/getCogUk.sh src/hg/utils/otto/sarscov2phylo/getCogUk.sh
index 6cac2c6..9aab143 100755
--- src/hg/utils/otto/sarscov2phylo/getCogUk.sh
+++ src/hg/utils/otto/sarscov2phylo/getCogUk.sh
@@ -1,82 +1,78 @@
 #!/bin/bash
 
 set -beEux -o pipefail
 
 # Download latest COG-UK fasta and metadata; update $ottoDir/cogUk.latest link.
 
 scriptDir=$(dirname "${BASH_SOURCE[0]}")
 source $scriptDir/util.sh
 
 today=$(date +%F)
 
 ottoDir=/hive/data/outside/otto/sarscov2phylo
 cogUrlBase=https://cog-uk.s3.climb.ac.uk/phylogenetics/latest
 
 mkdir -p $ottoDir/cogUk.$today
 cd $ottoDir/cogUk.$today
 
 # Sometimes the curl fails with a DNS error, regardless of whether my previous cron job with
-# curl -I succeeded.  Do multiple retries for the first URL; once it's working, it should
-# continue to work for the other URLs (she said hopefully).
+# curl -I succeeded.  Do multiple retries per URL -- sometimes even after one succeeds, the
+# next can still fail e.g. with "curl: (6) Could not resolve host: cog-uk.s3.climb.ac.uk".
 # On some days, the fetch started but failed partway through, even after 5 tries, so
 # keep the partial result around and try again with '-C -'.
-attempt=0
-maxAttempts=5
-retryDelay=60
+function curlRetry {
+    local url=$*
+    local attempt=0
+    local maxAttempts=5
+    local retryDelay=60
     while [[ $((++attempt)) -le $maxAttempts ]]; do
         echo "curl attempt $attempt"
-    if curl -S -s -C - -O $cogUrlBase/cog_all.fasta.gz; then
+        if curl -S -s -C - -O $url; then
             break
         else
             echo "FAILED; will try again after $retryDelay seconds"
             sleep $retryDelay
         fi
     done
     if [[ $attempt -gt $maxAttempts ]]; then
         echo "curl failed $maxAttempts times; quitting."
         exit 1
     fi
-curl -S -s -C - -O $cogUrlBase/cog_metadata.csv.gz
+}
+
+curlRetry $cogUrlBase/cog_all.fasta.gz
+curlRetry $cogUrlBase/cog_metadata.csv.gz
 gunzip cog_metadata.csv.gz
-curl -S -s -C - -O $cogUrlBase/cog_global_tree.newick
+curlRetry $cogUrlBase/cog_global_tree.newick
 
 zcat cog_all.fasta.gz | xz -T 20 > cog_all.fasta.xz
 rm cog_all.fasta.gz
 
 tail -n +2 cog_metadata.csv \
 | awk -F, '{print $1 "\t" $5;}' | sort > cogUkToDate
 
 # Reuse nextclade assignments for older sequences; compute nextclade assignments for new seqs.
 zcat $ottoDir/cogUk.latest/nextclade.full.tsv.gz > nextclade.full.tsv
 cp $ottoDir/cogUk.latest/nextalign.fa.xz .
 comm -13 <(cut -f 1 nextclade.full.tsv | sort) <(fastaNames cog_all.fasta.xz | sort) \
     > seqsForNextclade
 if [ -s seqsForNextclade ]; then
-    splitDir=splitForNextclade
-    rm -rf $splitDir
-    mkdir $splitDir
-    faSomeRecords <(xzcat cog_all.fasta.xz) seqsForNextclade stdout \
-    | faSplit about stdin 300000000 $splitDir/chunk
     nDataDir=~angie/github/nextclade/data/sars-cov-2
-    outDir=$(mktemp -d)
     outTsv=$(mktemp)
-    for chunkFa in $splitDir/chunk*.fa; do
-        nextclade -j 30 -i $chunkFa \
+    outFa=$(mktemp)
+    faSomeRecords <(xzcat cog_all.fasta.xz) seqsForNextclade stdout \
+    | nextclade run -j 30 \
         --input-dataset $nDataDir \
-            --output-dir $outDir \
-            --output-basename out \
+        --output-fasta $outFa \
         --output-tsv $outTsv >& nextclade.log
     tail -n+2 $outTsv | sed -re 's/"//g;' >> nextclade.full.tsv
-        xz -T 20 < $outDir/out.aligned.fasta >> nextalign.fa.xz
-        rm -f $outTsv $outDir/*
-    done
-    rm -rf $outDir
-    rm -rf $splitDir
+    xz -T 20 < $outFa >> nextalign.fa.xz
+    rm -f $outTsv $outFa
 fi
 pigz -f -p 8 nextclade.full.tsv
 
 rm -f $ottoDir/cogUk.latest
 ln -s cogUk.$today $ottoDir/cogUk.latest
 
 rm -f ~angie/public_html/sarscov2phylo/cogUk.$today
 ln -s $ottoDir/cogUk.$today ~angie/public_html/sarscov2phylo/cogUk.$today