d6045f07a6bd4aa42e2b415b97f043977a425944
gperez2
  Sun Jul 30 23:48:02 2023 -0700
mm39 vs. GCA_001624445.1 lastz/chain/net run for user, refs #31040

diff --git src/hg/makeDb/doc/mm39/lastzRuns.txt src/hg/makeDb/doc/mm39/lastzRuns.txt
index 682cfdf..8c709ba 100644
--- src/hg/makeDb/doc/mm39/lastzRuns.txt
+++ src/hg/makeDb/doc/mm39/lastzRuns.txt
@@ -2585,17 +2585,99 @@
     sed -e 's/^/    # /;' fb.GCA_001624835.1.chainMm39Link.txt
     # 2231272516 bases of 2689657557 (82.957%) in intersection
     sed -e 's/^/    # /;' fb.GCA_001624835.1.chainSynMm39Link.txt
     # 2222181450 bases of 2689657557 (82.619%) in intersection
 \    time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \
     \
    -target2bit="/hive/data/genomes/asmHubs/GCA/001/624/835/GCA_001624835.1/GCA_001624835.1.2bit" \
 -targetSizes="/hive/data/genomes/asmHubs/GCA/001/624/835/GCA_001624835.1/GCA_001624835.1.chrom.sizes.txt" \
    GCA_001624835.1 mm39) > rbest.log 2>&1
 
     grep -w real rbest.log | sed -e 's/^/    # /;'
     # real	62m37.202s
 
     sed -e 's/^/    # /;' fb.GCA_001624835.1.chainRBest.Mm39.txt
     # 2218790179 bases of 2689657557 (82.493%) in intersection
+##############################################################################
+# LASTZ Mouse Mm39 vs. southeastern Asian house mouse GCA_001624445.1
+#    (DONE - 2023-04-07 - Gerardo)
+
+    mkdir /hive/data/genomes/mm39/bed/lastzGCA_001624445.1.2023-04-07
+    cd /hive/data/genomes/mm39/bed/lastzGCA_001624445.1.2023-04-07
+
+    printf '# southeastern Asian house mouse GCA_001624445.1 vs. Mouse Mm39
+BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.03/bin/lastz
+
+# TARGET: Mouse  mm39
+SEQ1_DIR=/hive/data/genomes/mm39/mm39.2bit
+SEQ1_LEN=/hive/data/genomes/mm39/chrom.sizes
+SEQ1_CHUNK=20000000
+SEQ1_LAP=10000
+SEQ1_LIMIT=40
+
+# QUERY: southeastern Asian house mouse 2016-04-26 GCA_001624445.1_CAST_EiJ_v1
+SEQ2_DIR=/hive/data/genomes/asmHubs/GCA/001/624/445/GCA_001624445.1/GCA_001624445.1.2bit
+SEQ2_LEN=/hive/data/genomes/asmHubs/GCA/001/624/445/GCA_001624445.1/GCA_001624445.1.chrom.sizes.txt
+SEQ2_CHUNK=20000000
+SEQ2_LAP=0
+SEQ2_LIMIT=100
+
+BASE=/hive/data/genomes/mm39/bed/lastzGCA_001624445.1.2023-04-07
+TMPDIR=/dev/shm
+
+' > DEF
+
+    time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -verbose=2 `pwd`/DEF -syntenicNet \
+       -qAsmId GCA_001624445.1_CAST_EiJ_v1 -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \
+        -chainMinScore=3000 -chainLinearGap=medium) > do.log 2>&1
+    grep -w real do.log | sed -e 's/^/    # /;'
+    # real	1058m44.662s
 
+    sed -e 's/^/    # /;' fb.mm39.chainGCA_001624445.1Link.txt
+    # 2329782432 bases of 2728222451 (85.396%) in intersection
+    sed -e 's/^/    # /;' fb.mm39.chainSynGCA_001624445.1Link.txt
+    # 2229270653 bases of 2728222451 (81.711%) in intersection
 
+    time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \
+       \
+      -query2Bit="/hive/data/genomes/asmHubs/GCA/001/624/445/GCA_001624445.1/GCA_001624445.1.2bit" \
+-querySizes="/hive/data/genomes/asmHubs/GCA/001/624/445/GCA_001624445.1/GCA_001624445.1.chrom.sizes.txt" \
+        mm39 GCA_001624445.1) > rbest.log 2>&1
+
+    grep -w real rbest.log | sed -e 's/^/    # /;'
+    # real	127m51.046s
+
+    sed -e 's/^/    # /;' fb.mm39.chainRBest.GCA_001624445.1.txt
+    # 2199319876 bases of 2728222451 (80.614%) in intersection
+
+    ### and for the swap
+
+    cd /hive/data/genomes/asmHubs/allBuild/GCA/001/624/445/GCA_001624445.1_CAST_EiJ_v1/trackData/blastz.mm39.swap
+
+   time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -swap -verbose=2 \
+   -qAsmId GCA_001624445.1_CAST_EiJ_v1 /hive/data/genomes/mm39/bed/lastzGCA_001624445.1.2023-04-07/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	106m53.512s
+
+    sed -e 's/^/    # /;' fb.GCA_001624445.1.chainMm39Link.txt
+    # 2223373125 bases of 2653990650 (83.775%) in intersection
+    sed -e 's/^/    # /;' fb.GCA_001624445.1.chainSynMm39Link.txt
+    # 2205392126 bases of 2653990650 (83.097%) in intersection
+\    time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \
+    \
+   -target2bit="/hive/data/genomes/asmHubs/GCA/001/624/445/GCA_001624445.1/GCA_001624445.1.2bit" \
+-targetSizes="/hive/data/genomes/asmHubs/GCA/001/624/445/GCA_001624445.1/GCA_001624445.1.chrom.sizes.txt" \
+   GCA_001624445.1 mm39) > rbest.log 2>&1
+
+    grep -w real rbest.log | sed -e 's/^/    # /;'
+    # real	99m38.174s
+
+    sed -e 's/^/    # /;' fb.GCA_001624445.1.chainRBest.Mm39.txt
+    # 2202774272 bases of 2653990650 (82.999%) in intersection
+
+real	1393m12.216s
+user	0m2.744s
+sys	0m1.859s
+##############################################################################