9875f6c8af94b0f0fcdc5e496515438e6af478b5
angie
  Mon May 24 09:59:55 2021 -0700
Add back -x since there have been so many cron failures.  Parallelize re-running of pangolin on all sequences (necessary when a new version of pangolin is released).

diff --git src/hg/utils/otto/sarscov2phylo/getNcbi.sh src/hg/utils/otto/sarscov2phylo/getNcbi.sh
index b7186aa..1e755ce 100755
--- src/hg/utils/otto/sarscov2phylo/getNcbi.sh
+++ src/hg/utils/otto/sarscov2phylo/getNcbi.sh
@@ -1,133 +1,152 @@
 #!/bin/bash
 source ~/.bashrc
-set -beEu -o pipefail
+set -beEu -o -x pipefail
 
 # Download SARS-CoV-2 GenBank FASTA and metadata using NCBI Datasets API.
 # Use E-Utils to get SARS-CoV-2 metadata from BioSample.
 # Use BioSample metadata to fill in gaps in GenBank metadata and report conflicting dates.
 # Use enhanced metadata to rewrite FASTA headers for matching up with sequences in other databases.
 
 scriptDir=$(dirname "${BASH_SOURCE[0]}")
 source $scriptDir/util.sh
 
 today=$(date +%F)
 prevDate=$(date -d yesterday +%F)
 
 ottoDir=/hive/data/outside/otto/sarscov2phylo
 
 mkdir -p $ottoDir/ncbi.$today
 cd $ottoDir/ncbi.$today
 
 # This query gives a large zip file that includes extra stuff, and the download really slows
 # down after a point, but it does provide a consistent set of FASTA and metadata:
 time curl -sS -X GET \
     "https://api.ncbi.nlm.nih.gov/datasets/v1alpha/virus/taxon/2697049/genome/download?refseq_only=false&annotated_only=false&released_since=2020-01-01&complete_only=false&include_annotation_type=DEFAULT&filename=ncbi_dataset.$today.zip" \
     -H "Accept: application/zip" \
     > ncbi_dataset.zip
 
 rm -rf ncbi_dataset
 unzip ncbi_dataset.zip
 # Creates ./ncbi_dataset/
 
 # This makes something just like ncbi.datasets.tsv from the /table/ API query:
 jq -c -r '[.accession, .biosample, .isolate.collectionDate, .location.geographicLocation, .host.sciName, .isolate.name, .completeness, (.length|tostring)] | join("\t")' \
     ncbi_dataset/data/data_report.jsonl \
 | sed -e 's/COMPLETE/complete/; s/PARTIAL/partial/;' \
 | sort \
     > ncbi_dataset.tsv
 
 # Use EUtils (esearch) to get all SARS-CoV-2 BioSample GI# IDs:
 $scriptDir/searchAllSarsCov2BioSample.sh
 sort all.biosample.gids.txt > all.biosample.gids.sorted.txt
 
 # Copy yesterday's all.bioSample.txt so we don't have to refetch all the old stuff.
 if [ -e ../ncbi.$prevDate/all.bioSample.txt.xz ]; then
     xzcat ../ncbi.$prevDate/all.bioSample.txt.xz > all.bioSample.txt
     grep ^Accession all.bioSample.txt | sed -re 's/^.*ID: //' | sort -u > ids.loaded
     comm -23 all.biosample.gids.sorted.txt ids.loaded > ids.notLoaded
 else
     cp -p all.biosample.gids.txt ids.notLoaded
 fi
 wc -l ids.notLoaded
 
 # Use EUtils (efetch) to get BioSample records for the GI# IDs that we don't have yet:
 time $scriptDir/bioSampleIdToText.sh < ids.notLoaded >> all.bioSample.txt
 
 grep ^Accession all.bioSample.txt | sed -re 's/^.*ID: //' | sort > ids.loaded
 comm -23 all.biosample.gids.sorted.txt ids.loaded > ids.notLoaded
 if [ -s ids.notLoaded ]; then
     echo Retrying queries for `wc -l < ids.notLoaded` IDs
     $scriptDir/bioSampleIdToText.sh < ids.notLoaded >> all.bioSample.txt
     grep ^Accession all.bioSample.txt | sed -re 's/^.*ID: //' | sort > ids.loaded
     comm -23 all.biosample.gids.sorted.txt ids.loaded > ids.notLoaded
     if [ -s ids.notLoaded ]; then
         echo "Still have only $accCount accession lines after retrying; quitting."
         exit 1
     fi
 fi
 
 # Extract properties of interest into tab-sep text:
 $scriptDir/bioSampleTextToTab.pl < all.bioSample.txt  > all.bioSample.tab
 
 # Extract BioSample tab-sep lines just for BioSample accessions included in the ncbi_dataset data:
 tawk '$2 != "" {print $2;}' ncbi_dataset.tsv \
 | grep -Fwf - all.bioSample.tab \
     > gb.bioSample.tab
 
 # Use BioSample metadata to fill in missing pieces of GenBank metadata and report conflicting
 # sample collection dates:
 $scriptDir/gbMetadataAddBioSample.pl gb.bioSample.tab ncbi_dataset.tsv \
     > ncbi_dataset.plusBioSample.tsv
 
 # Make a file for joining collection date with ID:
 tawk '$3 != "" {print $1, $3;}' ncbi_dataset.plusBioSample.tsv \
 | sort > gbToDate
 
 # Replace FASTA headers with reconstructed names from enhanced metadata.
 time cleanGenbank < ncbi_dataset/data/genomic.fna \
 | $scriptDir/fixNcbiFastaNames.pl ncbi_dataset.plusBioSample.tsv \
 | xz -T 50 \
     > genbank.fa.xz
 
 # Run pangolin and nextclade on sequences that are new since yesterday
 fastaNames genbank.fa.xz | awk '{print $1;}' | sort > gb.names
 splitDir=splitForNextclade
 rm -rf $splitDir
 mkdir $splitDir
 if [ -e ../ncbi.$prevDate/nextclade.tsv ]; then
     cp ../ncbi.$prevDate/nextclade.tsv .
     cut -f 1 ../ncbi.$prevDate/nextclade.tsv | sort > nextclade.$prevDate.names
     comm -23 gb.names nextclade.$prevDate.names > nextclade.names
     faSomeRecords <(xzcat genbank.fa.xz) nextclade.names nextclade.fa
     faSplit about nextclade.fa 30000000 $splitDir/chunk
 else
     cp /dev/null nextclade.tsv
     faSplit about <(xzcat genbank.fa.xz) 30000000 $splitDir/chunk
 fi
 for chunkFa in $splitDir/chunk*.fa; do
     nextclade -j 50 -i $chunkFa -t >(cut -f 1,2 | tail -n+2 >> nextclade.tsv) >& nextclade.log
 done
 wc -l nextclade.tsv
 rm -rf $splitDir nextclade.fa
+
 conda activate pangolin
+runPangolin() {
+    fa=$1
+    out=$fa.pangolin.csv
+    logfile=$(mktemp)
+    pangolin $fa --outfile $out > $logfile 2>&1
+    rm $logfile
+}
+export -f runPangolin
 if [ -e ../ncbi.$prevDate/lineage_report.csv ]; then
     cp ../ncbi.$prevDate/lineage_report.csv linRepYesterday
     tail -n+2 linRepYesterday | sed -re 's/^([A-Z]+[0-9]+\.[0-9]+).*/\1/' | sort \
         > pangolin.$prevDate.names
     comm -23 gb.names pangolin.$prevDate.names > pangolin.names
     faSomeRecords <(xzcat genbank.fa.xz) pangolin.names pangolin.fa
     pangolin pangolin.fa >& pangolin.log
     tail -n+2 lineage_report.csv >> linRepYesterday
     mv linRepYesterday lineage_report.csv
+    rm -f pangolin.fa
 else
-    pangolin <(xzcat genbank.fa.xz) >& pangolin.log
+    splitDir=splitForPangolin
+    rm -rf $splitDir
+    mkdir $splitDir
+    faSplit about <(xzcat genbank.fa.xz) 30000000 $splitDir/chunk
+    find $splitDir -name chunk\*.fa \
+    | parallel -j 10 "runPangolin {}"
+    head -1 $(ls -1 $splitDir/chunk*.csv | head -1) > lineage_report.csv
+    for f in $splitDir/chunk*.csv; do
+        tail -n+2 $f >> lineage_report.csv
+    done
+    rm -rf $splitDir
 fi
 wc -l lineage_report.csv
-rm -f pangolin.fa
 
 rm -f $ottoDir/ncbi.latest
 ln -s ncbi.$today $ottoDir/ncbi.latest
 
 # Clean up
 rm -r ncbi_dataset
 nice xz all.bioSample.* &