40a49b0eb0c44d5a5fd20fb43468405b12d0390c
gperez2
  Tue Jun 29 16:21:53 2021 -0700
lastz chainNet per user request hg19 gorGor6, refs #27757

diff --git src/hg/makeDb/doc/hg19.txt src/hg/makeDb/doc/hg19.txt
index aa0c1bc..2ab3ad1 100644
--- src/hg/makeDb/doc/hg19.txt
+++ src/hg/makeDb/doc/hg19.txt
@@ -34530,15 +34530,94 @@
 ##############################################################################
 # Add Revel track, Max, Thu Apr 15 03:33:49 PDT 2021
 cd /hive/data/genomes/hg19/bed/revel
 aria2c https://rothsj06.u.hpc.mssm.edu/revel_grch38_all_chromosomes.csv.zip
 unzip revel_grch38_all_chromosomes.csv.zip
 # make sure that no weird chroms and no weird multi-nucleotide changes
 cat revel_grch38_all_chromosomes.csv  | tr ',' '\t' | cut -f5 | grep -v alt | awk '{print length($1)}' | uniq > lens.tmp &
 cut -d, revel_grch38_all_chromosomes.csv -f1 | uniq | sort | uniq -c > chroms.tmp &
 pigz revel_grch38_all_chromosomes.csv
 time python revelToWig.py revel_grch38_all_chromosomes.csv.gz hg19
 wigToBigWig t.wig ../../chrom.sizes t.bw &
 wigToBigWig c.wig ../../chrom.sizes c.bw  &
 wigToBigWig a.wig ../../chrom.sizes a.bw &
 wigToBigWig g.wig ../../chrom.sizes g.bw &
 ##############################################################################
+# LASTZ human/hg19 Gorilla/gorGor6 - (DONE - 2021-06-28 - Hiram)
+    mkdir /hive/data/genomes/hg19/bed/lastzGorGor6.2021-06-28/
+    cd /hive/data/genomes/hg19/bed/lastzGorGor6.2021-06-28/
+
+    printf '# human vs gorilla
+BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.03/bin/lastz
+BLASTZ_T=2
+BLASTZ_O=600
+BLASTZ_E=150
+BLASTZ_M=254
+BLASTZ_K=4500
+BLASTZ_Y=15000
+BLASTZ_Q=/hive/data/staging/data/blastz/human_chimp.v2.q
+#       A     C     G     T
+# A    90  -330  -236  -356
+# C  -330   100  -318  -236
+# G  -236  -318   100  -330
+# T  -356  -236  -330    90
+
+# 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
+SEQ1_IN_CONTIGS=0
+
+# QUERY: gorilla gorGor6
+SEQ2_DIR=/hive/data/genomes/gorGor6/gorGor6.2bit
+SEQ2_LEN=/hive/data/genomes/gorGor6/chrom.sizes
+SEQ2_CHUNK=20000000
+SEQ2_LAP=0
+SEQ2_LIMIT=50
+
+BASE=/hive/data/genomes/hg19/bed/lastzGorGor6.2021-06-28
+TMPDIR=/dev/shm
+' > DEF
+
+    time (doBlastzChainNet.pl `pwd`/DEF -verbose=2 \
+        -chainMinScore=3000 -chainLinearGap=medium \
+          -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
+            -syntenicNet) > do.log 2>&1
+    # real    113m7.350s
+
+    cat fb.hg19.chainGorGor6Link.txt
+    # 2874362387 bases of 2991710746 (96.078%) in intersection
+
+    cat fb.hg19.chainSynGorGor6Link.txt
+    # 2854800888 bases of 2991710746 (95.424%) in intersection
+
+    time (doRecipBest.pl -load -workhorse=hgwdev -buildDir=`pwd` hg19 gorGor6) > rbest.log 2>&1 &
+    # real    67m18.231s
+
+    sed -e 's/^/ # /;' fb.hg19.chainRBest.GorGor6.txt
+     # 2691356356 bases of 2991710746 (89.960%) in intersection
+
+    #   running the swap
+    mkdir /hive/data/genomes/gorGor6/bed/blastz.hg19.swap
+    cd /hive/data/genomes/gorGor6/bed/blastz.hg19.swap
+
+    time (doBlastzChainNet.pl -verbose=2 \
+      /hive/data/genomes/hg19/bed/lastzGorGor6.2021-06-28/DEF \
+        -swap -syntenicNet -workhorse=hgwdev  \
+         -smallClusterHub=hgwdev -bigClusterHub=ku \
+            -chainMinScore=3000 -chainLinearGap=medium)  > swap.log 2>&1 &
+    # real 69m32.058s
+
+    cat fb.gorGor6.chainHg19Link.txt
+    2735990533 bases of 2999027915 (91.229%) in intersection
+
+    cat fb.gorGor6.chainSynHg19Link.txt
+    2726237067 bases of 2999027915 (90.904%) in intersection
+
+    time (doRecipBest.pl -load -workhorse=hgwdev -buildDir=`pwd` gorGor6 hg19) > rbest.log 2>&1 &
+    # real    70m15.001s
+
+    sed -e 's/^/    # /;' fb.gorGor6.chainRBest.Hg19.txt
+    # 2694784811 bases of 2999027915 (89.855%) in intersection
+
+##############################################################################