82a6cccdf25e3e8298cab9f78e24c9e167e3fa96
hiram
  Thu Jan 11 09:44:28 2024 -0800
mm39 to GCF_019923935.1 water buffalo lastz/chain/net complete refs #32804

diff --git src/hg/makeDb/doc/mm39/lastzRuns.txt src/hg/makeDb/doc/mm39/lastzRuns.txt
index fe9199b..5384a0a 100644
--- src/hg/makeDb/doc/mm39/lastzRuns.txt
+++ src/hg/makeDb/doc/mm39/lastzRuns.txt
@@ -3167,15 +3167,95 @@
    -query2bit="/hive/data/genomes/asmHubs/GCF/029/281/585/GCF_029281585.1/GCF_029281585.1.2bit" \
 -querySizes="/hive/data/genomes/asmHubs/GCF/029/281/585/GCF_029281585.1/GCF_029281585.1.chrom.sizes.txt" \
     \
    mm39 GCF_029281585.1) > rbest.log 2>&1
 
     grep -w real rbest.log | sed -e 's/^/    # /;'
     # real	285m21.078s
 
     sed -e 's/^/    # /;' fb.mm39.chainRBest.GCF_029281585.1.txt
     # 895609380 bases of 2728222451 (32.828%) in intersection
 
 real	1606m58.270s
 user	0m4.597s
 sys	0m2.305s
 ##############################################################################
+# LASTZ Mouse Mm39 vs. water buffalo GCF_019923935.1
+#    (DONE - 2024-01-10 - hiram)
+
+    mkdir /hive/data/genomes/mm39/bed/lastzGCF_019923935.1.2024-01-04
+    cd /hive/data/genomes/mm39/bed/lastzGCF_019923935.1.2024-01-04
+
+    printf '# water buffalo GCF_019923935.1 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: water buffalo 2021-09-10 GCF_019923935.1_NDDB_SH_1
+SEQ2_DIR=/hive/data/genomes/asmHubs/GCF/019/923/935/GCF_019923935.1/GCF_019923935.1.2bit
+SEQ2_LEN=/hive/data/genomes/asmHubs/GCF/019/923/935/GCF_019923935.1/GCF_019923935.1.chrom.sizes.txt
+SEQ2_CHUNK=20000000
+SEQ2_LAP=0
+SEQ2_LIMIT=100
+
+BASE=/hive/data/genomes/mm39/bed/lastzGCF_019923935.1.2024-01-04
+TMPDIR=/dev/shm
+
+' > DEF
+
+    time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -verbose=2 `pwd`/DEF -syntenicNet \
+       -qAsmId GCF_019923935.1_NDDB_SH_1 -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \
+        -chainMinScore=3000 -chainLinearGap=medium) > do.log 2>&1
+    grep -w real do.log | sed -e 's/^/    # /;'
+    # real	53m59.287s
+
+    sed -e 's/^/    # /;' fb.mm39.chainGCF_019923935.1Link.txt
+    # 705799341 bases of 2728222451 (25.870%) in intersection
+    sed -e 's/^/    # /;' fb.mm39.chainSynGCF_019923935.1Link.txt
+    # 658049513 bases of 2728222451 (24.120%) in intersection
+
+    time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \
+       \
+      -query2Bit="/hive/data/genomes/asmHubs/GCF/019/923/935/GCF_019923935.1/GCF_019923935.1.2bit" \
+-querySizes="/hive/data/genomes/asmHubs/GCF/019/923/935/GCF_019923935.1/GCF_019923935.1.chrom.sizes.txt" \
+        mm39 GCF_019923935.1) > rbest.log 2>&1
+
+    grep -w real rbest.log | sed -e 's/^/    # /;'
+    # real	2m50.155s
+
+    sed -e 's/^/    # /;' fb.mm39.chainRBest.GCF_019923935.1.txt
+    # 667871734 bases of 2728222451 (24.480%) in intersection
+
+    ### and for the swap
+
+    cd /hive/data/genomes/asmHubs/allBuild/GCF/019/923/935/GCF_019923935.1_NDDB_SH_1/trackData/blastz.mm39.swap
+
+   time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -swap -verbose=2 \
+   -qAsmId GCF_019923935.1_NDDB_SH_1 /hive/data/genomes/mm39/bed/lastzGCF_019923935.1.2024-01-04/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	48m50.148s
+
+    sed -e 's/^/    # /;' fb.GCF_019923935.1.chainMm39Link.txt
+    # 692990771 bases of 2622460639 (26.425%) in intersection
+    sed -e 's/^/    # /;' fb.GCF_019923935.1.chainSynMm39Link.txt
+    # 657252141 bases of 2622460639 (25.062%) in intersection
+\    time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \
+    \
+   -target2bit="/hive/data/genomes/asmHubs/GCF/019/923/935/GCF_019923935.1/GCF_019923935.1.2bit" \
+-targetSizes="/hive/data/genomes/asmHubs/GCF/019/923/935/GCF_019923935.1/GCF_019923935.1.chrom.sizes.txt" \
+   GCF_019923935.1 mm39) > rbest.log 2>&1
+
+    grep -w real rbest.log | sed -e 's/^/    # /;'
+    # real	189m53.630s
+
+    sed -e 's/^/    # /;' fb.GCF_019923935.1.chainRBest.Mm39.txt
+    # 666929206 bases of 2622460639 (25.431%) in intersection
+
+##############################################################################