6997c15d6e5bba74c31803ae79cd1be779688f7a
gperez2
  Sun Aug 13 14:28:50 2023 -0700
crab-eating macaque (GCA_011100615.1) vs. macFas5, lastz/chain/net run for user, refs #31769

diff --git src/hg/makeDb/doc/macFas5/lastzRuns.txt src/hg/makeDb/doc/macFas5/lastzRuns.txt
index 64dcc24..ec63cb0 100644
--- src/hg/makeDb/doc/macFas5/lastzRuns.txt
+++ src/hg/makeDb/doc/macFas5/lastzRuns.txt
@@ -238,15 +238,110 @@
     sed -e 's/^/    # /;' fb.rheMac2.chainSynMacFas5Link.txt
     # 2595637716 bases of 2646704109 (98.071%) in intersection
 \    time (~/kent/src/hg/utils/automation/doRecipBest.pl  -load -workhorse=hgwdev -buildDir=`pwd` \
     \
     \
    rheMac2 macFas5) > rbest.log 2>&1
 
     grep -w real rbest.log | sed -e 's/^/    # /;'
     # real	54m32.803s
 
     sed -e 's/^/    # /;' fb.rheMac2.chainRBest.MacFas5.txt
     # 2596730835 bases of 2646704109 (98.112%) in intersection
 
 
 ##############################################################################
+# LASTZ crab-eating macaque GCA_011100615.1 vs. Crab-eating macaque MacFas5
+#    (DONE - 2023-07-19 - Gerardo)
+
+    mkdir /hive/data/genomes/asmHubs/allBuild/GCA/011/100/615/GCA_011100615.1_Macaca_fascicularis_6.0/trackData/lastzMacFas5.2023-07-19
+    cd /hive/data/genomes/asmHubs/allBuild/GCA/011/100/615/GCA_011100615.1_Macaca_fascicularis_6.0/trackData/lastzMacFas5.2023-07-19
+
+    printf '# Crab-eating macaque MacFas5 vs. crab-eating macaque GCA_011100615.1
+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: crab-eating macaque 2020-03-10 GCA_011100615.1_Macaca_fascicularis_6.0
+SEQ1_DIR=/hive/data/genomes/asmHubs/GCA/011/100/615/GCA_011100615.1/GCA_011100615.1.2bit
+SEQ1_LEN=/hive/data/genomes/asmHubs/GCA/011/100/615/GCA_011100615.1/GCA_011100615.1.chrom.sizes.txt
+SEQ1_CHUNK=20000000
+SEQ1_LAP=10000
+SEQ1_LIMIT=40
+
+# QUERY: Crab-eating macaque  macFas5
+SEQ2_DIR=/hive/data/genomes/macFas5/macFas5.2bit
+SEQ2_LEN=/hive/data/genomes/macFas5/chrom.sizes
+SEQ2_CHUNK=20000000
+SEQ2_LAP=0
+SEQ2_LIMIT=100
+
+BASE=/hive/data/genomes/asmHubs/allBuild/GCA/011/100/615/GCA_011100615.1_Macaca_fascicularis_6.0/trackData/lastzMacFas5.2023-07-19
+TMPDIR=/dev/shm
+
+' > DEF
+
+    time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -verbose=2 `pwd`/DEF -syntenicNet \
+      -tAsmId GCA_011100615.1_Macaca_fascicularis_6.0  -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \
+        -chainMinScore=5000 -chainLinearGap=medium) > do.log 2>&1
+    grep -w real do.log | sed -e 's/^/    # /;'
+    # real	115m11.046s
+
+    sed -e 's/^/    # /;' fb.GCA_011100615.1.chainMacFas5Link.txt
+    # 2761984914 bases of 2906138557 (95.040%) in intersection
+    sed -e 's/^/    # /;' fb.GCA_011100615.1.chainSynMacFas5Link.txt
+    # 2731406308 bases of 2906138557 (93.987%) in intersection
+
+    time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \
+      -target2Bit="/hive/data/genomes/asmHubs/GCA/011/100/615/GCA_011100615.1/GCA_011100615.1.2bit" \
+-targetSizes="/hive/data/genomes/asmHubs/GCA/011/100/615/GCA_011100615.1/GCA_011100615.1.chrom.sizes.txt" \
+       \
+        GCA_011100615.1 macFas5) > rbest.log 2>&1
+
+    grep -w real rbest.log | sed -e 's/^/    # /;'
+    # real	75m47.657s
+
+    sed -e 's/^/    # /;' fb.GCA_011100615.1.chainRBest.MacFas5.txt
+    # 2678569575 bases of 2906138557 (92.169%) in intersection
+
+    ### and for the swap
+
+    cd /hive/data/genomes/macFas5/bed/blastz.GCA_011100615.1.swap
+
+   time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -swap -verbose=2 \
+  -tAsmId GCA_011100615.1_Macaca_fascicularis_6.0  /hive/data/genomes/asmHubs/allBuild/GCA/011/100/615/GCA_011100615.1_Macaca_fascicularis_6.0/trackData/lastzMacFas5.2023-07-19/DEF -swapDir=`pwd` \
+  -syntenicNet -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \
+    -chainMinScore=5000 -chainLinearGap=medium) > swap.log 2>&1
+
+    grep -w real swap.log | sed -e 's/^/    # /;'
+    # real	90m44.045s
+
+    sed -e 's/^/    # /;' fb.macFas5.chainGCA_011100615.1Link.txt
+    # 2690649811 bases of 2946843737 (91.306%) in intersection
+    sed -e 's/^/    # /;' fb.macFas5.chainSynGCA_011100615.1Link.txt
+    # 2679307687 bases of 2946843737 (90.921%) in intersection
+\    time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \
+   -query2bit="/hive/data/genomes/asmHubs/GCA/011/100/615/GCA_011100615.1/GCA_011100615.1.2bit" \
+-querySizes="/hive/data/genomes/asmHubs/GCA/011/100/615/GCA_011100615.1/GCA_011100615.1.chrom.sizes.txt" \
+    \
+   macFas5 GCA_011100615.1) > rbest.log 2>&1
+
+    grep -w real rbest.log | sed -e 's/^/    # /;'
+    # real	72m23.439s
+
+    sed -e 's/^/    # /;' fb.macFas5.chainRBest.GCA_011100615.1.txt
+    # 2680072146 bases of 2946843737 (90.947%) in intersection
+
+real	354m14.218s
+user	0m3.158s
+sys	0m3.325s
+##############################################################################