d5849c76b7b13e3189e1ce67035ba9695a821122
hiram
  Wed Apr 7 16:02:04 2021 -0700
lastz chainNet to assembly hub GCF_002742125.1 refs #27321

diff --git src/hg/makeDb/doc/hg38/lastzRuns.txt src/hg/makeDb/doc/hg38/lastzRuns.txt
index 8f4c106..fa39b7c 100644
--- src/hg/makeDb/doc/hg38/lastzRuns.txt
+++ src/hg/makeDb/doc/hg38/lastzRuns.txt
@@ -13065,21 +13065,120 @@
     time (doBlastzChainNet.pl -verbose=2 \
       /hive/data/genomes/hg38/bed/lastzXenTro10.2021-02-22/DEF \
         -swap -chainMinScore=5000 -chainLinearGap=loose \
           -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
             -syntenicNet) > swap.log 2>&1
     #  real    79m35.244s
 
     sed -e 's/^/    # /;' fb.xenTro10.chainHg38Link.txt
     # 150875559 bases of 1448461978 (10.416%) in intersection
 
     sed -e 's/^/    # /;' fb.xenTro10.chainSynHg38Link.txt
     # 40317510 bases of 1448461978 (2.783%) in intersection
 
   time (doRecipBest.pl -load -workhorse=hgwdev -buildDir=`pwd` xenTro10 hg38) \
        > rbest.log 2>&1
-XXX - running - Tue Mar  2 10:52:22 PST 2021
-    # real    749m24.229s
+    # real    344m19.222s
 
     sed -e 's/^/    # /;' fb.xenTro10.chainRBest.Hg38.txt
+    # 71467857 bases of 1448461978 (4.934%) in intersection
 
-#############################################################################
+##############################################################################
+# LASTZ Rambouillet sheep GCF_002742125.1 (DONE - 2021-04-05 - Hiram)
+    mkdir /hive/data/genomes/mm39/bed/lastzGCF_002742125.1.2021-04-05
+    cd /hive/data/genomes/mm39/bed/lastzGCF_002742125.1.2021-04-05
+
+    printf '# GCF_002742125.1 vs hg38
+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 Hg38
+SEQ1_DIR=/hive/data/genomes/hg38/hg38.2bit
+SEQ1_LEN=/hive/data/genomes/hg38/chrom.sizes
+SEQ1_CHUNK=20000000
+SEQ1_LAP=10000
+
+# QUERY: sheep GCF_002742125.1
+SEQ2_DIR=/hive/data/genomes/asmHubs/GCF/002/742/125/GCF_002742125.1/GCF_002742125.1.2bit
+SEQ2_LEN=/hive/data/genomes/asmHubs/GCF/002/742/125/GCF_002742125.1/GCF_002742125.1.chrom.sizes.txt
+SEQ2_CHUNK=20000000
+SEQ2_LAP=0
+SEQ2_LIMIT=100
+
+BASE=/hive/data/genomes/hg38/bed/lastzGCF_002742125.1.2021-04-05
+TMPDIR=/dev/shm
+' > DEF
+
+export targetDb="hg38"
+export asmId="GCF_002742125.1"
+export gcPath="GCF/002/742/125"
+cd /hive/data/genomes/$targetDb/bed/lastz${asmId}.2021-04-05
+time (doBlastzChainNet.pl -trackHub -noDbNameCheck -verbose=2 `pwd`/DEF \
+   -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \
+     -syntenicNet -chainMinScore=3000 -chainLinearGap=medium) > do.log 2>&1
+cat fb.${targetDb}.chain.${asmId}Link.txt
+cat fb.${targetDb}.chainSyn.${asmId}Link.txt
+
+grep -w real do.log | sed -e 's/^/    # /;'
+    # real    180m56.099s
+
+
+sed -e 's/^/    # /;' fb.$targetDb.chain.${asmId}Link.txt
+    # 1410867422 bases of 3272116950 (43.118%) in intersection
+sed -e 's/^/    # /;' fb.$targetDb.chainSyn.${asmId}Link.txt
+    # 1349986710 bases of 3272116950 (41.257%) in intersection
+
+time (doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \
+-query2Bit="/hive/data/genomes/asmHubs/$gcPath/${asmId}/${asmId}.2bit" \
+-querySizes="/hive/data/genomes/asmHubs/$gcPath/${asmId}/${asmId}.chrom.sizes.txt" \
+$targetDb ${asmId}) >> rbest.log 2>&1
+grep -w real rbest.log | sed -e 's/^/    # /;'
+    # real    353m30.968s
+
+sed -e 's/^/    # /;' fb.$targetDb.chainRBest.$asmId.txt
+    # 1279504252 bases of 3272116950 (39.103%) in intersection
+
+### the swap to the assembly hub
+export target="hg38"
+export Target="Hg38"
+export query="GCF_002742125.1"
+export asmId="GCF_002742125.1_Oar_rambouillet_v1.0"
+export gcPath="GCF/002/742/125"
+
+mkdir -p /hive/data/genomes/asmHubs/refseqBuild/$gcPath/$asmId/trackData/blastz.$target.swap
+cd /hive/data/genomes/asmHubs/refseqBuild/$gcPath/$asmId/trackData/blastz.$target.swap
+
+time (doBlastzChainNet.pl -trackHub -noDbNameCheck -verbose=2 -swapDir=`pwd` \
+    /hive/data/genomes/${target}/bed/lastz.${query}/DEF -syntenicNet \
+  -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \
+    -swap -chainMinScore=3000 -chainLinearGap=medium) >> swap.log 2>&1
+grep -w real swap.log | sed -e 's/^/    # /;'
+    # real      90m38.556s
+
+sed -e 's/^/    # /;' fb.${query}.chain.${Target}Link.txt
+    # 1399154667 bases of 2869914396 (48.752%) in intersection
+sed -e 's/^/    # /;' fb.${query}.chainSyn.${Target}Link.txt
+    # 1341190663 bases of 2869914396 (46.733%) in intersection
+
+time (doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \
+-target2Bit="/hive/data/genomes/asmHubs/$gcPath/${query}/${query}.2bit" \
+-targetSizes="/hive/data/genomes/asmHubs/$gcPath/${query}/${query}.chrom.sizes.txt" \
+$query $target) >> rbest.log 2>&1
+grep -w real rbest.log | sed -e 's/^/    # /;'
+    # real    463m23.874s
+
+sed -e 's/^/    # /;' fb.${query}.chainRBest.${Target}.txt
+    # 1281096559 bases of 2869914396 (44.639%) in intersection
+
+# Complete run time for all the swap operation:
+    # real    554m2.489s
+
+##############################################################################