2fdcabb36f9906a0bbb8e6c2c2fbe43e32543946
hiram
  Tue Jun 29 11:14:10 2021 -0700
ncbiRefSeq update refs #27552

diff --git src/hg/makeDb/doc/hg19.txt src/hg/makeDb/doc/hg19.txt
index fcdf044..aa0c1bc 100644
--- src/hg/makeDb/doc/hg19.txt
+++ src/hg/makeDb/doc/hg19.txt
@@ -33830,30 +33830,45 @@
 # update 2020-10-27 (DONE - Hiram - 2020-10-27)
 
   mkdir /hive/data/genomes/hg19/bed/ncbiRefSeq.p13.2020-10-27
   cd /hive/data/genomes/hg19/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_000001405.25_GRCh37.p13 hg19) > do.log 2>&1 &
   # real    6m47.005s
 
   cat fb.ncbiRefSeq.hg19.txt
   # 93720294 bases of 2991710746 (3.133%) in intersection
 
 #############################################################################
+# test update 2021-05-17 (DONE - Hiram - 2021-05-17)
+
+  mkdir /hive/data/genomes/hg19/bed/ncbiRefSeq.p13.2021-05-17
+  cd /hive/data/genomes/hg19/bed/ncbiRefSeq.p13.2021-05-17
+
+  time (~/kent/src/hg/utils/automation/doNcbiRefSeq.pl -buildDir=`pwd` \
+      -bigClusterHub=ku -dbHost=hgwdev \
+      -fileServer=hgwdev -smallClusterHub=hgwdev -workhorse=hgwdev \
+      GCF_000001405.25_GRCh37.p13 hg19) > do.log 2>&1 &
+  # real    7m42.506s
+
+  cat fb.ncbiRefSeq.hg19.txt
+  # 95470885 bases of 2991710746 (3.191%) in intersection
+
+#############################################################################
 # Covid-19 rare mutations, Max, Fri Oct 30 08:40:34 PDT 2020
 # received table from qzhang02@rockefeller.edu, wrote to UCSC.txt
 cd /hive/data/genomes/hg19/bed/covidMuts/
 dos2unix UCSC.txt
 cat UCSC.txt | tawk '{$1="chr"$1; chrom=$1; start=$2; rsId=$3; ref=$4; alt=$5; zygo=$6; gene=$7; genotype=$8; inh=$9; end=$2+length(ref); print chrom, start, end, ref">"alt, "0", ".", start, end, "0,0,0", "1", length(ref), "0", ref, alt, rsId, zygo, gene, genotype, inh;}' | grep -v chrchr > covidMuts.bed
 bedSort covidMuts.bed covidMuts.bed
 bedToBigBed -tab covidMuts.bed ../../chrom.sizes covidMuts.bb -as=../../hg19/bed/covidMuts/covidMuts.as -type=bed12+
 <<<<<<< Updated upstream
 
 #############################################################################
 # gnomAD v2.1.1 update, ChrisL 12-2-2020
 #############################################################################
 # See /hive/data/inside/gnomAD/v2.1.1/run.sh for more information, listed
 # here are the important steps:
 WORKDIR=/hive/data/inside/gnomAD/v2.1.1/
@@ -33938,54 +33953,53 @@
     time (doBlastzChainNet.pl `pwd`/DEF -verbose=2 \
         -chainMinScore=3000 -chainLinearGap=medium \
           -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \
             -syntenicNet) > do.log 2>&1
     # real    239m35.175s
 
     cat fb.hg19.chainBosTau9Link.txt
     # 1407432462 bases of 2991710746 (47.044%) in intersection
 
     cat fb.hg19.chainSynBosTau9Link.txt
     # 1354159575 bases of 2991710746 (45.264%) in intersection
 
     time (doRecipBest.pl -load -workhorse=hgwdev -buildDir=`pwd` hg19 bosTau9) > rbest.log 2>&1 &
     #	real    274m55.811s
 
-    cat fb.hg19.chainRBest.BosTau9.txt
+    sed -e 's/^/    # /;' fb.hg19.chainRBest.BosTau9.txt
     #	1290531802 bases of 2991710746 (43.137%) in intersection
 
     #   running the swap
     mkdir /hive/data/genomes/bosTau9/bed/blastz.hg19.swap
     cd /hive/data/genomes/bosTau9/bed/blastz.hg19.swap
     time (doBlastzChainNet.pl -verbose=2 \
         /hive/data/genomes/hg19/bed/lastzBosTau9.2020-12-07/DEF \
         -swap  -syntenicNet -workhorse=hgwdev \
 	-smallClusterHub=hgwdev -bigClusterHub=ku \
         -chainMinScore=3000 -chainLinearGap=medium) > swap.log 2>&1
     #   real    72m28.826s
 
     cat fb.bosTau9.chainHg19Link.txt
     #   1342159887 bases of 2715853792 (49.419%) in intersection
     cat fb.bosTau9.chainSynHg19Link.txt
     #	1305558878 bases of 2715853792 (48.072%) in intersection
 
     time (doRecipBest.pl -load -workhorse=hgwdev -buildDir=`pwd` bosTau9 hg19) > rbest.log 2>&1 &
-XXX - running - Tue Dec  8 09:13:34 PST 2020
-    # real    272m15.176s
+    # real    297m58.059s
 
-    cat fb.bosTau9.chainRBest.Hg19.txt
-    # 1290810412 bases of 2715853792 (47.529%) in intersection
+    sed -e 's/^/    # /;' fb.bosTau9.chainRBest.Hg19.txt
+    # 1291348753 bases of 2715853792 (47.549%) in intersection
 
 #############################################################################
 # Exome Probesets composite track
 # Tue Jan  5 02:25:06 PST 2021 Made by Ana, Tiana, Pranav, Beagan, reviewed and committed by Max
 # Download data for hg19:
 cd /hive/data/genomes/hg19/bed/exomeProbesets
 We made tracks for the main Exome Kit Vendors: IDT, Twist Biosciences, MGI, Agilent, Roche, and Illumina.
 
 Note: IDT, Agilent and Roche have bed files for the Probes and for the Target Regions. Twist, MGI, and Illumina have bed files for the Target Regions (but not for Probes).
 
 Data downloaded in my windows desktop and copied to hgwdev:
 scp <file.bed> ana@hgwdev.gi.ucsc.edu://hive/data/genomes/hg19/bed/exonArrays/raw/idt
 
 # IDT Datasets: