3dd09a4b5f9dd8ad5122483b7b040dcec14ac1f4
hiram
  Mon Dec 14 16:40:51 2020 -0800
lastz chainNet per user request hg19 bosTau9 refs #26638

diff --git src/hg/makeDb/doc/hg19.txt src/hg/makeDb/doc/hg19.txt
index 3230572..6770282 100644
--- src/hg/makeDb/doc/hg19.txt
+++ src/hg/makeDb/doc/hg19.txt
@@ -33844,15 +33844,92 @@
 # sys 12m0.858s
 cd ..
 time cat hg19/genomes/*.bed | ./gnomadVcfBedToBigBed stdin stdout | sort -k1,1 -k2,2n > gnomad.v2.1.1.genomes.bed
 # real    199m48.619s
 # user    186m49.769s
 # sys 29m12.841s
 
 # now South Asian variants in the genomes file, change type:
 time bedToBigBed -type=bed9+47 -tab -as=genomes.as gnomad.v2.1.1.genomes.bed /hive/data/genomes/hg19/chrom.sizes genomes.bb
 # pass1 - making usageList (23 chroms): 165336 millis
 # pass2 - checking and writing primary data (253556152 records, 55 fields): 4909106 millis
 #
 # real    89m3.165s
 # user    86m41.554s
 # sys 2m15.722s
+
+#############################################################################
+# LASTZ Cow bosTau9 (DONE - 2020-12-07 - Hiram)
+    mkdir /hive/data/genomes/hg19/bed/lastzBosTau9.2020-12-07
+    cd /hive/data/genomes/hg19/bed/lastzBosTau9.2020-12-07
+
+    printf '# human vs Cow
+BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.03/bin/lastz
+BLASTZ_T=2
+BLASTZ_O=400
+BLASTZ_E=30
+BLASTZ_M=254
+# default BLASTZ_Q score matrix:
+#       A     C     G     T
+# A    91  -114   -31  -123
+# C  -114   100  -125   -31
+# G   -31  -125   100  -114
+# T  -123   -31  -114    91
+
+# TARGET: human hg19
+SEQ1_DIR=/hive/data/genomes/hg19/hg19.2bit
+SEQ1_LEN=/hive/data/genomes/hg19/chrom.sizes
+SEQ1_CHUNK=20000000
+SEQ1_LAP=10000
+
+# QUERY: Cow bosTau9
+SEQ2_DIR=/hive/data/genomes/bosTau9/bosTau9.2bit
+SEQ2_LEN=/hive/data/genomes/bosTau9/chrom.sizes
+SEQ2_CHUNK=20000000
+SEQ2_LIMIT=10
+SEQ2_LAP=0
+
+BASE=/hive/data/genomes/hg19/bed/lastzBosTau9.2020-12-07
+TMPDIR=/dev/shm
+' > DEF
+
+    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
+    #	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
+
+    cat fb.bosTau9.chainRBest.Hg19.txt
+    # 1290810412 bases of 2715853792 (47.529%) in intersection
+
+#############################################################################