33c5e452f2df131473468f0206a360a16ba9dcd3
hiram
  Tue Oct 27 13:15:17 2020 -0700
update per alert from Terence for new versions although hg19 needs to wait for the new files refs #26428

diff --git src/hg/makeDb/doc/hg38/ncbiRefSeq.txt src/hg/makeDb/doc/hg38/ncbiRefSeq.txt
index 42f4705..b443fcb 100644
--- src/hg/makeDb/doc/hg38/ncbiRefSeq.txt
+++ src/hg/makeDb/doc/hg38/ncbiRefSeq.txt
@@ -308,15 +308,32 @@
 
     featureBits -enrichment hg38 refGene ncbiRefSeqCurated
  # refGene 3.098%, ncbiRefSeqCurated 3.073%, both 3.067%, cover 98.99%, enrich 32.22x
  # previous:
  # refGene 3.098%, ncbiRefSeqCurated 2.880%, both 2.846%, cover 91.86%, enrich 31.90x
 
 #########################################################################
 # addition of RefSeq Select-restricted subset, Max, Feb 10 2019
 cd /hive/data/genomes/hg38/bed/ncbiRefSeq.p13.2019-12-06/
 zcat download/*_genomic.gff.gz | egrep 'tag=(RefSeq|MANE) Select'  | cut -f9- | tr ';' '\n' | grep Name= | grep -v NP_ | cut -d= -f2 | sort -u > refseqSelectTranscripts.txt
 cat process/hg38.curated.gp | fgrep -f refseqSelectTranscripts.txt - > refseqSelect.curated.gp
 hgLoadGenePred -genePredExt hg38 ncbiRefSeqSelect refseqSelect.curated.gp
 wc -l refseqSelect.curated.gp
 21071 refseqSelect.curated.gp
 #############################################################################
+
+#############################################################################
+# update 2020-10-27 (DONE - Hiram - 2020-10-27)
+
+  mkdir /hive/data/genomes/hg38/bed/ncbiRefSeq.p13.2020-10-27
+  cd /hive/data/genomes/hg38/bed/ncbiRefSeq.p13.2020-10-27
+
+  time (~/kent/src/hg/utils/automation/doNcbiRefSeq.pl -buildDir=`pwd` \
+      -bigClusterHub=ku -dbHost=hgwdev \
+      -fileServer=hgwdev -smallClusterHub=hgwdev -workhorse=hgwdev \
+      GCF_000001405.39_GRCh38.p13 hg38) > do.log 2>&1 &
+  # real    11m46.506s
+
+  cat fb.ncbiRefSeq.hg38.txt
+  # 137385668 bases of 3110768607 (4.416%) in intersection
+
+#############################################################################