2e6b6889b0a4f2c0a730c1d2728f56dbdbf91c92
hiram
  Tue May 19 15:41:00 2020 -0700
per user request refs #25581

diff --git src/hg/makeDb/doc/panTro6/lastzRuns.sh src/hg/makeDb/doc/panTro6/lastzRuns.sh
new file mode 100644
index 0000000..ed8fa55
--- /dev/null
+++ src/hg/makeDb/doc/panTro6/lastzRuns.sh
@@ -0,0 +1,84 @@
+##############################################################################
+# Orangutan Lastz run (DONE - 2020-05-19 - Hiram)
+    screen -S panTro6PonAbe3      # use a screen to manage this longish running job
+    mkdir /hive/data/genomes/panTro6/bed/lastzPonAbe3.2020-05-19
+    cd /hive/data/genomes/panTro6/bed/lastzPonAbe3.2020-05-19
+
+    # always set the BLASTZ program so we know what version was used
+    printf "# chimp vs orangutan
+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_L=4500
+BLASTZ_Y=15000
+BLASTZ_Q=/scratch/data/blastz/human_chimp.v2.q
+#    A    C    G    T
+#    90 -330 -236 -356
+#  -330  100 -318 -236
+#  -236 -318  100 -330
+#  -356 -236 -330   90
+
+# TARGET: chimp PanTro6
+SEQ1_DIR=/hive/data/genomes/panTro6/panTro6.2bit
+SEQ1_LEN=/hive/data/genomes/panTro6/chrom.sizes
+SEQ1_CHUNK=20000000
+SEQ1_LIMIT=40
+SEQ1_LAP=10000
+
+# QUERY: Orangutan PonAbe3
+SEQ2_DIR=/hive/data/genomes/ponAbe3/ponAbe3.2bit
+SEQ2_LEN=/hive/data/genomes/ponAbe3/chrom.sizes
+SEQ2_CHUNK=20000000
+SEQ2_LAP=0
+SEQ2_LIMIT=40
+SEQ2_IN_CONTIGS=0
+
+BASE=/hive/data/genomes/panTro6/bed/lastzPonAbe3.2020-05-19
+TMPDIR=/dev/shm
+" > DEF
+
+    time (doBlastzChainNet.pl `pwd`/DEF -verbose=2 \
+        -chainMinScore=5000 -chainLinearGap=medium \
+        -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \
+        -syntenicNet) > do.log 2>&1 &
+    # real    282m16.272s
+
+    cat fb.panTro6.chainPonAbe3Link.txt
+    # 2823472924 bases of 3049335806 (92.593%) in intersection
+    cat fb.panTro6.chainSynPonAbe3Link.txt
+    # 2800840721 bases of 3049335806 (91.851%) in intersection
+
+    # filter with doRecipBest.pl
+    time (doRecipBest.pl -load -workhorse=hgwdev -buildDir=`pwd` \
+        panTro6 ponAbe3) > rbest.log 2>&1 &
+    # real    129m13.848s
+
+    cat fb.panTro6.chainRBestPonAbe3Link.txt
+    # 2640015618 bases of 3049335806 (86.577%) in intersection
+
+    # running the swap
+    mkdir /hive/data/genomes/ponAbe3/bed/blastz.panTro6.swap
+    cd /hive/data/genomes/ponAbe3/bed/blastz.panTro6.swap
+    time (doBlastzChainNet.pl -verbose=2 \
+        -swap /hive/data/genomes/panTro6/bed/lastzPonAbe3.2020-05-19/DEF \
+        -chainMinScore=5000 -chainLinearGap=medium \
+        -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \
+        -syntenicNet) > swap.log 2>&1
+    # real    92m31.689s
+
+    cat fb.ponAbe3.chainPanTro6Link.txt
+    # 2693373164 bases of 3043444524 (88.498%) in intersection
+    cat fb.ponAbe3.chainSynPanTro6Link.txt
+    # 2679121264 bases of 3043444524 (88.029%) in intersection
+
+    time (doRecipBest.pl -load -workhorse=hgwdev -buildDir=`pwd` \
+        ponAbe3 panTro6) > rbest.log 2>&1 &
+    # real    141m23.715s
+
+    cat fb.ponAbe3.chainRBestPanTro6Link.txt
+    # 2641871600 bases of 3043444524 (86.805%) in intersection
+
+#############################################################################