994fbb05bd562ec59ff2e8d55218fcb149543dd1
gperez2
  Sat Mar 30 15:21:06 2024 -0700
oviAri3 to GCF_016772045.2 lastz/chain/net run for user, refs #33280

diff --git src/hg/makeDb/doc/asmHubs/lastzRuns.txt src/hg/makeDb/doc/asmHubs/lastzRuns.txt
index b1d018f..d644d42 100644
--- src/hg/makeDb/doc/asmHubs/lastzRuns.txt
+++ src/hg/makeDb/doc/asmHubs/lastzRuns.txt
@@ -2619,15 +2619,98 @@
 -querySizes="/hive/data/genomes/asmHubs/GCF/000/002/945/GCF_000002945.1/GCF_000002945.1.chrom.sizes.txt" \
    -target2bit="/hive/data/genomes/asmHubs/GCF/000/146/045/GCF_000146045.2/GCF_000146045.2.2bit" \
 -targetSizes="/hive/data/genomes/asmHubs/GCF/000/146/045/GCF_000146045.2/GCF_000146045.2.chrom.sizes.txt" \
    GCF_000146045.2 GCF_000002945.1) > rbest.log 2>&1
 
     grep -w real rbest.log | sed -e 's/^/    # /;'
     # real	0m37.702s
 
     sed -e 's/^/    # /;' fb.GCF_000146045.2.chainRBest.GCF_000002945.1.txt
     # 1571707 bases of 12157105 (12.928%) in intersection
 
 real	8m57.345s
 user	0m2.512s
 sys	0m3.487s
 ##############################################################################
+# LASTZ sheep GCF_016772045.2 vs. Sheep OviAri3
+#    (DONE - 2024-03-23 - Gerardo)
+
+    mkdir /hive/data/genomes/asmHubs/allBuild/GCF/016/772/045/GCF_016772045.2_ARS-UI_Ramb_v3.0/trackData/lastzOviAri3.2024-03-23
+    cd /hive/data/genomes/asmHubs/allBuild/GCF/016/772/045/GCF_016772045.2_ARS-UI_Ramb_v3.0/trackData/lastzOviAri3.2024-03-23
+
+    printf '# Sheep OviAri3 vs. sheep GCF_016772045.2
+BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.03/bin/lastz
+
+# TARGET: sheep 2023-07-20 GCF_016772045.2_ARS-UI_Ramb_v3.0
+SEQ1_DIR=/hive/data/genomes/asmHubs/GCF/016/772/045/GCF_016772045.2/GCF_016772045.2.2bit
+SEQ1_LEN=/hive/data/genomes/asmHubs/GCF/016/772/045/GCF_016772045.2/GCF_016772045.2.chrom.sizes.txt
+SEQ1_CHUNK=20000000
+SEQ1_LAP=10000
+SEQ1_LIMIT=40
+
+# QUERY: Sheep  oviAri3
+SEQ2_DIR=/hive/data/genomes/oviAri3/oviAri3.2bit
+SEQ2_LEN=/hive/data/genomes/oviAri3/chrom.sizes
+SEQ2_CHUNK=20000000
+SEQ2_LAP=0
+SEQ2_LIMIT=100
+
+BASE=/hive/data/genomes/asmHubs/allBuild/GCF/016/772/045/GCF_016772045.2_ARS-UI_Ramb_v3.0/trackData/lastzOviAri3.2024-03-23
+TMPDIR=/dev/shm
+
+' > DEF
+
+    time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -verbose=2 `pwd`/DEF -syntenicNet \
+      -tAsmId GCF_016772045.2_ARS-UI_Ramb_v3.0  -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \
+        -chainMinScore=3000 -chainLinearGap=medium) > do.log 2>&1
+    grep -w real do.log | sed -e 's/^/    # /;'
+    # real	429m12.994s
+
+    sed -e 's/^/    # /;' fb.GCF_016772045.2.chainOviAri3Link.txt
+    # 2525078490 bases of 2654063983 (95.140%) in intersection
+    sed -e 's/^/    # /;' fb.GCF_016772045.2.chainSynOviAri3Link.txt
+    # 2482973739 bases of 2654063983 (93.554%) in intersection
+
+    time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \
+      -target2Bit="/hive/data/genomes/asmHubs/GCF/016/772/045/GCF_016772045.2/GCF_016772045.2.2bit" \
+-targetSizes="/hive/data/genomes/asmHubs/GCF/016/772/045/GCF_016772045.2/GCF_016772045.2.chrom.sizes.txt" \
+       \
+        GCF_016772045.2 oviAri3) > rbest.log 2>&1
+
+    grep -w real rbest.log | sed -e 's/^/    # /;'
+    # real	85m16.406s
+
+    sed -e 's/^/    # /;' fb.GCF_016772045.2.chainRBest.OviAri3.txt
+    # 2466724548 bases of 2654063983 (92.941%) in intersection
+
+    ### and for the swap
+
+    cd /hive/data/genomes/oviAri3/bed/blastz.GCF_016772045.2.swap
+
+   time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -swap -verbose=2 \
+  -tAsmId GCF_016772045.2_ARS-UI_Ramb_v3.0  /hive/data/genomes/asmHubs/allBuild/GCF/016/772/045/GCF_016772045.2_ARS-UI_Ramb_v3.0/trackData/lastzOviAri3.2024-03-23/DEF -swapDir=`pwd` \
+  -syntenicNet -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \
+    -chainMinScore=3000 -chainLinearGap=medium) > swap.log 2>&1
+
+    grep -w real swap.log | sed -e 's/^/    # /;'
+    # real	214m0.944s
+
+    sed -e 's/^/    # /;' fb.oviAri3.chainGCF_016772045.2Link.txt
+    # 2499925356 bases of 2619054388 (95.451%) in intersection
+    sed -e 's/^/    # /;' fb.oviAri3.chainSynGCF_016772045.2Link.txt
+    # 2475557584 bases of 2619054388 (94.521%) in intersection
+\    time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \
+   -query2bit="/hive/data/genomes/asmHubs/GCF/016/772/045/GCF_016772045.2/GCF_016772045.2.2bit" \
+-querySizes="/hive/data/genomes/asmHubs/GCF/016/772/045/GCF_016772045.2/GCF_016772045.2.chrom.sizes.txt" \
+    \
+   oviAri3 GCF_016772045.2) > rbest.log 2>&1
+
+    grep -w real rbest.log | sed -e 's/^/    # /;'
+    # real	84m46.671s
+
+    sed -e 's/^/    # /;' fb.oviAri3.chainRBest.GCF_016772045.2.txt
+    # 2470476691 bases of 2619054388 (94.327%) in intersection
+
+real	813m22.700s
+user	0m3.066s
+sys	0m3.274s
+##############################################################################