9d4bef0d3eb7ba60d763868e2db43256281e38ab
hiram
  Fri Oct 22 13:31:37 2021 -0700
lastz runs to golden hamster refs #28333

diff --git src/hg/makeDb/doc/asmHubs/lastzRuns.txt src/hg/makeDb/doc/asmHubs/lastzRuns.txt
index 85106ac..e37d669 100644
--- src/hg/makeDb/doc/asmHubs/lastzRuns.txt
+++ src/hg/makeDb/doc/asmHubs/lastzRuns.txt
@@ -333,15 +333,520 @@
     # 386385047 bases of 556480649 (69.434%) in intersection
 \    time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \
    -query2bit="/hive/data/genomes/asmHubs/GCF/009/389/715/GCF_009389715.1/GCF_009389715.1.2bit" \
 -querySizes="/hive/data/genomes/asmHubs/GCF/009/389/715/GCF_009389715.1/GCF_009389715.1.chrom.sizes.txt" \
    -target2bit="/hive/data/genomes/asmHubs/GCF/000/413/155/GCF_000413155.1/GCF_000413155.1.2bit" \
 -targetSizes="/hive/data/genomes/asmHubs/GCF/000/413/155/GCF_000413155.1/GCF_000413155.1.chrom.sizes.txt" \
    GCF_000413155.1 GCF_009389715.1) > rbest.log 2>&1
 
     grep -w real rbest.log | sed -e 's/^/    # /;'
     # real	33m7.581s
 
     sed -e 's/^/    # /;' fb.GCF_000413155.1.chainRBest.GCF_009389715.1.txt
     # 430390896 bases of 556480649 (77.342%) in intersection
 
 ##############################################################################
+ time (~/kent/src/hg/utils/automation/pairLastz.sh \
+	hg38 GCF_000349665.1_MesAur1.0 primate mammal) >> goldenHamster.lastz.log 2>&1 &
+
+# real	1326m29.271s
+# user	0m1.945s
+# sys	0m2.347s
+
+##############################################################################
+# LASTZ Human Hg38 vs. golden hamster GCF_000349665.1
+#    (DONE - 2021-10-19 - hiram)
+
+    mkdir /hive/data/genomes/hg38/bed/lastzGCF_000349665.1.2021-10-19
+    cd /hive/data/genomes/hg38/bed/lastzGCF_000349665.1.2021-10-19
+
+    printf '# golden hamster GCF_000349665.1 vs. Human Hg38
+BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.03/bin/lastz
+
+# 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
+SEQ1_LIMIT=40
+
+# QUERY: golden hamster GCF_000349665.1
+SEQ2_DIR=/hive/data/genomes/asmHubs/GCF/000/349/665/GCF_000349665.1/GCF_000349665.1.2bit
+SEQ2_LEN=/hive/data/genomes/asmHubs/GCF/000/349/665/GCF_000349665.1/GCF_000349665.1.chrom.sizes.txt
+SEQ2_CHUNK=20000000
+SEQ2_LAP=0
+SEQ2_LIMIT=100
+
+BASE=/hive/data/genomes/hg38/bed/lastzGCF_000349665.1.2021-10-19
+TMPDIR=/dev/shm
+
+' > DEF
+
+    time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -verbose=2 `pwd`/DEF -syntenicNet \
+       -qAsmId GCF_000349665.1_MesAur1.0 -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \
+        -chainMinScore=3000 -chainLinearGap=medium) > do.log 2>&1
+    grep -w real do.log | sed -e 's/^/    # /;'
+    # real	816m1.961s
+
+    sed -e 's/^/    # /;' fb.hg38.chainGCF_000349665.1Link.txt
+    # 927958037 bases of 3272116950 (28.360%) in intersection
+    sed -e 's/^/    # /;' fb.hg38.chainSynGCF_000349665.1Link.txt
+    # 849347972 bases of 3272116950 (25.957%) in intersection
+
+    time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \
+       \
+      -query2Bit="/hive/data/genomes/asmHubs/GCF/000/349/665/GCF_000349665.1/GCF_000349665.1.2bit" \
+-querySizes="/hive/data/genomes/asmHubs/GCF/000/349/665/GCF_000349665.1/GCF_000349665.1.chrom.sizes.txt" \
+        hg38 GCF_000349665.1) > rbest.log 2>&1
+
+    grep -w real rbest.log | sed -e 's/^/    # /;'
+    # real	227m0.804s
+
+    sed -e 's/^/    # /;' fb.hg38.chainRBest.GCF_000349665.1.txt
+    # 840160627 bases of 3272116950 (25.676%) in intersection
+
+    ### and for the swap
+
+    cd /hive/data/genomes/asmHubs/allBuild/GCF/000/349/665/GCF_000349665.1_MesAur1.0/trackData/blastz.hg38.swap
+
+   time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -swap -verbose=2 \
+   -qAsmId GCF_000349665.1_MesAur1.0 /hive/data/genomes/hg38/bed/lastzGCF_000349665.1.2021-10-19/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	66m26.977s
+
+    sed -e 's/^/    # /;' fb.GCF_000349665.1.chainHg38Link.txt
+    # 864739427 bases of 2504925039 (34.522%) in intersection
+    sed -e 's/^/    # /;' fb.GCF_000349665.1.chainSynHg38Link.txt
+    # 812701606 bases of 2504925039 (32.444%) in intersection
+\    time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \
+    \
+   -target2bit="/hive/data/genomes/asmHubs/GCF/000/349/665/GCF_000349665.1/GCF_000349665.1.2bit" \
+-targetSizes="/hive/data/genomes/asmHubs/GCF/000/349/665/GCF_000349665.1/GCF_000349665.1.chrom.sizes.txt" \
+   GCF_000349665.1 hg38) > rbest.log 2>&1
+
+    grep -w real rbest.log | sed -e 's/^/    # /;'
+    # real	216m58.998s
+
+    sed -e 's/^/    # /;' fb.GCF_000349665.1.chainRBest.Hg38.txt
+    # 841788407 bases of 2504925039 (33.605%) in intersection
+
+##############################################################################
+# LASTZ Mouse Mm10 vs. golden hamster GCF_000349665.1
+#    (DONE - 2021-10-19 - hiram)
+
+    mkdir /hive/data/genomes/mm10/bed/lastzGCF_000349665.1.2021-10-19
+    cd /hive/data/genomes/mm10/bed/lastzGCF_000349665.1.2021-10-19
+
+    printf '# golden hamster GCF_000349665.1 vs. Mouse Mm10
+BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.03/bin/lastz
+
+# TARGET: Mouse Mm10
+SEQ1_DIR=/hive/data/genomes/mm10/mm10.2bit
+SEQ1_LEN=/hive/data/genomes/mm10/chrom.sizes
+SEQ1_CHUNK=20000000
+SEQ1_LAP=10000
+SEQ1_LIMIT=40
+
+# QUERY: golden hamster GCF_000349665.1
+SEQ2_DIR=/hive/data/genomes/asmHubs/GCF/000/349/665/GCF_000349665.1/GCF_000349665.1.2bit
+SEQ2_LEN=/hive/data/genomes/asmHubs/GCF/000/349/665/GCF_000349665.1/GCF_000349665.1.chrom.sizes.txt
+SEQ2_CHUNK=20000000
+SEQ2_LAP=0
+SEQ2_LIMIT=100
+
+BASE=/hive/data/genomes/mm10/bed/lastzGCF_000349665.1.2021-10-19
+TMPDIR=/dev/shm
+
+' > DEF
+
+    time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -verbose=2 `pwd`/DEF -syntenicNet \
+       -qAsmId GCF_000349665.1_MesAur1.0 -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \
+        -chainMinScore=3000 -chainLinearGap=medium) > do.log 2>&1
+    grep -w real do.log | sed -e 's/^/    # /;'
+    # real	822m9.572s
+
+    sed -e 's/^/    # /;' fb.mm10.chainGCF_000349665.1Link.txt
+    # 1517320069 bases of 2818974548 (53.825%) in intersection
+    sed -e 's/^/    # /;' fb.mm10.chainSynGCF_000349665.1Link.txt
+    # 1368250969 bases of 2818974548 (48.537%) in intersection
+
+    time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \
+       \
+      -query2Bit="/hive/data/genomes/asmHubs/GCF/000/349/665/GCF_000349665.1/GCF_000349665.1.2bit" \
+-querySizes="/hive/data/genomes/asmHubs/GCF/000/349/665/GCF_000349665.1/GCF_000349665.1.chrom.sizes.txt" \
+        mm10 GCF_000349665.1) > rbest.log 2>&1
+
+    grep -w real rbest.log | sed -e 's/^/    # /;'
+    # real	457m57.111s
+
+    sed -e 's/^/    # /;' fb.mm10.chainRBest.GCF_000349665.1.txt
+    # 1350867428 bases of 2818974548 (47.921%) in intersection
+
+    ### and for the swap
+# swap into: /hive/data/genomes/asmHubs/allBuild/GCF/000/349/665/GCF_000349665.1_MesAur1.0/trackData/blastz.mm10.swap
+# running /hive/data/genomes/asmHubs/allBuild/GCF/000/349/665/GCF_000349665.1_MesAur1.0/trackData/blastz.mm10.swap/runSwap.sh
+##############################################################################
+# LASTZ Mouse Mm10 vs. golden hamster GCF_000349665.1
+#    (DONE - 2021-10-19 - hiram)
+
+    mkdir /hive/data/genomes/mm10/bed/lastzGCF_000349665.1.2021-10-19
+    cd /hive/data/genomes/mm10/bed/lastzGCF_000349665.1.2021-10-19
+
+    printf '# golden hamster GCF_000349665.1 vs. Mouse Mm10
+BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.03/bin/lastz
+
+# TARGET: Mouse Mm10
+SEQ1_DIR=/hive/data/genomes/mm10/mm10.2bit
+SEQ1_LEN=/hive/data/genomes/mm10/chrom.sizes
+SEQ1_CHUNK=20000000
+SEQ1_LAP=10000
+SEQ1_LIMIT=40
+
+# QUERY: golden hamster GCF_000349665.1
+SEQ2_DIR=/hive/data/genomes/asmHubs/GCF/000/349/665/GCF_000349665.1/GCF_000349665.1.2bit
+SEQ2_LEN=/hive/data/genomes/asmHubs/GCF/000/349/665/GCF_000349665.1/GCF_000349665.1.chrom.sizes.txt
+SEQ2_CHUNK=20000000
+SEQ2_LAP=0
+SEQ2_LIMIT=100
+
+BASE=/hive/data/genomes/mm10/bed/lastzGCF_000349665.1.2021-10-19
+TMPDIR=/dev/shm
+
+' > DEF
+
+    time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -verbose=2 `pwd`/DEF -syntenicNet \
+       -qAsmId GCF_000349665.1_MesAur1.0 -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \
+        -chainMinScore=3000 -chainLinearGap=medium) > do.log 2>&1
+    grep -w real do.log | sed -e 's/^/    # /;'
+    # real	822m9.572s
+
+    sed -e 's/^/    # /;' fb.mm10.chainGCF_000349665.1Link.txt
+    # 1517320069 bases of 2818974548 (53.825%) in intersection
+    sed -e 's/^/    # /;' fb.mm10.chainSynGCF_000349665.1Link.txt
+    # 1368250969 bases of 2818974548 (48.537%) in intersection
+
+    time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \
+       \
+      -query2Bit="/hive/data/genomes/asmHubs/GCF/000/349/665/GCF_000349665.1/GCF_000349665.1.2bit" \
+-querySizes="/hive/data/genomes/asmHubs/GCF/000/349/665/GCF_000349665.1/GCF_000349665.1.chrom.sizes.txt" \
+        mm10 GCF_000349665.1) > rbest.log 2>&1
+
+    grep -w real rbest.log | sed -e 's/^/    # /;'
+    # real	457m57.111s
+
+    sed -e 's/^/    # /;' fb.mm10.chainRBest.GCF_000349665.1.txt
+    # 1350867428 bases of 2818974548 (47.921%) in intersection
+
+    ### and for the swap
+
+    cd /hive/data/genomes/asmHubs/allBuild/GCF/000/349/665/GCF_000349665.1_MesAur1.0/trackData/blastz.mm10.swap
+
+   time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -swap -verbose=2 \
+   -qAsmId GCF_000349665.1_MesAur1.0 /hive/data/genomes/mm10/bed/lastzGCF_000349665.1.2021-10-19/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	101m40.814s
+
+    sed -e 's/^/    # /;' fb.GCF_000349665.1.chainMm10Link.txt
+    # 1420756145 bases of 2504925039 (56.719%) in intersection
+    sed -e 's/^/    # /;' fb.GCF_000349665.1.chainSynMm10Link.txt
+    # 1317050872 bases of 2504925039 (52.578%) in intersection
+\    time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \
+    \
+   -target2bit="/hive/data/genomes/asmHubs/GCF/000/349/665/GCF_000349665.1/GCF_000349665.1.2bit" \
+-targetSizes="/hive/data/genomes/asmHubs/GCF/000/349/665/GCF_000349665.1/GCF_000349665.1.chrom.sizes.txt" \
+   GCF_000349665.1 mm10) > rbest.log 2>&1
+
+    grep -w real rbest.log | sed -e 's/^/    # /;'
+    # real	429m34.320s
+
+    sed -e 's/^/    # /;' fb.GCF_000349665.1.chainRBest.Mm10.txt
+    # 1352697681 bases of 2504925039 (54.002%) in intersection
+
+
+real	1811m22.412s
+user	0m2.184s
+sys	0m3.047s
+##############################################################################
+# LASTZ Mouse Mm39 vs. golden hamster GCF_000349665.1
+#    (DONE - 2021-10-19 - hiram)
+
+    mkdir /hive/data/genomes/mm39/bed/lastzGCF_000349665.1.2021-10-19
+    cd /hive/data/genomes/mm39/bed/lastzGCF_000349665.1.2021-10-19
+
+    printf '# golden hamster GCF_000349665.1 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: golden hamster GCF_000349665.1
+SEQ2_DIR=/hive/data/genomes/asmHubs/GCF/000/349/665/GCF_000349665.1/GCF_000349665.1.2bit
+SEQ2_LEN=/hive/data/genomes/asmHubs/GCF/000/349/665/GCF_000349665.1/GCF_000349665.1.chrom.sizes.txt
+SEQ2_CHUNK=20000000
+SEQ2_LAP=0
+SEQ2_LIMIT=100
+
+BASE=/hive/data/genomes/mm39/bed/lastzGCF_000349665.1.2021-10-19
+TMPDIR=/dev/shm
+
+' > DEF
+
+    time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -verbose=2 `pwd`/DEF -syntenicNet \
+       -qAsmId GCF_000349665.1_MesAur1.0 -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \
+        -chainMinScore=3000 -chainLinearGap=medium) > do.log 2>&1
+    grep -w real do.log | sed -e 's/^/    # /;'
+    # real	827m23.676s
+
+    sed -e 's/^/    # /;' fb.mm39.chainGCF_000349665.1Link.txt
+    # 1471502725 bases of 2728222451 (53.936%) in intersection
+    sed -e 's/^/    # /;' fb.mm39.chainSynGCF_000349665.1Link.txt
+    # 1328672778 bases of 2728222451 (48.701%) in intersection
+
+    time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \
+       \
+      -query2Bit="/hive/data/genomes/asmHubs/GCF/000/349/665/GCF_000349665.1/GCF_000349665.1.2bit" \
+-querySizes="/hive/data/genomes/asmHubs/GCF/000/349/665/GCF_000349665.1/GCF_000349665.1.chrom.sizes.txt" \
+        mm39 GCF_000349665.1) > rbest.log 2>&1
+
+    grep -w real rbest.log | sed -e 's/^/    # /;'
+    # real	477m51.437s
+
+    sed -e 's/^/    # /;' fb.mm39.chainRBest.GCF_000349665.1.txt
+    # 1352204504 bases of 2728222451 (49.564%) in intersection
+
+    ### and for the swap
+# swap into: /hive/data/genomes/asmHubs/allBuild/GCF/000/349/665/GCF_000349665.1_MesAur1.0/trackData/blastz.mm39.swap
+# running /hive/data/genomes/asmHubs/allBuild/GCF/000/349/665/GCF_000349665.1_MesAur1.0/trackData/blastz.mm39.swap/runSwap.sh
+##############################################################################
+# LASTZ Mouse Mm39 vs. golden hamster GCF_000349665.1
+#    (DONE - 2021-10-19 - hiram)
+
+    mkdir /hive/data/genomes/mm39/bed/lastzGCF_000349665.1.2021-10-19
+    cd /hive/data/genomes/mm39/bed/lastzGCF_000349665.1.2021-10-19
+
+    printf '# golden hamster GCF_000349665.1 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: golden hamster GCF_000349665.1
+SEQ2_DIR=/hive/data/genomes/asmHubs/GCF/000/349/665/GCF_000349665.1/GCF_000349665.1.2bit
+SEQ2_LEN=/hive/data/genomes/asmHubs/GCF/000/349/665/GCF_000349665.1/GCF_000349665.1.chrom.sizes.txt
+SEQ2_CHUNK=20000000
+SEQ2_LAP=0
+SEQ2_LIMIT=100
+
+BASE=/hive/data/genomes/mm39/bed/lastzGCF_000349665.1.2021-10-19
+TMPDIR=/dev/shm
+
+' > DEF
+
+    time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -verbose=2 `pwd`/DEF -syntenicNet \
+       -qAsmId GCF_000349665.1_MesAur1.0 -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \
+        -chainMinScore=3000 -chainLinearGap=medium) > do.log 2>&1
+    grep -w real do.log | sed -e 's/^/    # /;'
+    # real	827m23.676s
+
+    sed -e 's/^/    # /;' fb.mm39.chainGCF_000349665.1Link.txt
+    # 1471502725 bases of 2728222451 (53.936%) in intersection
+    sed -e 's/^/    # /;' fb.mm39.chainSynGCF_000349665.1Link.txt
+    # 1328672778 bases of 2728222451 (48.701%) in intersection
+
+    time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \
+       \
+      -query2Bit="/hive/data/genomes/asmHubs/GCF/000/349/665/GCF_000349665.1/GCF_000349665.1.2bit" \
+-querySizes="/hive/data/genomes/asmHubs/GCF/000/349/665/GCF_000349665.1/GCF_000349665.1.chrom.sizes.txt" \
+        mm39 GCF_000349665.1) > rbest.log 2>&1
+
+    grep -w real rbest.log | sed -e 's/^/    # /;'
+    # real	477m51.437s
+
+    sed -e 's/^/    # /;' fb.mm39.chainRBest.GCF_000349665.1.txt
+    # 1352204504 bases of 2728222451 (49.564%) in intersection
+
+    ### and for the swap
+
+    cd /hive/data/genomes/asmHubs/allBuild/GCF/000/349/665/GCF_000349665.1_MesAur1.0/trackData/blastz.mm39.swap
+
+   time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -swap -verbose=2 \
+   -qAsmId GCF_000349665.1_MesAur1.0 /hive/data/genomes/mm39/bed/lastzGCF_000349665.1.2021-10-19/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	101m49.459s
+
+    sed -e 's/^/    # /;' fb.GCF_000349665.1.chainMm39Link.txt
+    # 1419668050 bases of 2504925039 (56.675%) in intersection
+    sed -e 's/^/    # /;' fb.GCF_000349665.1.chainSynMm39Link.txt
+    # 1318426965 bases of 2504925039 (52.633%) in intersection
+\    time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \
+    \
+   -target2bit="/hive/data/genomes/asmHubs/GCF/000/349/665/GCF_000349665.1/GCF_000349665.1.2bit" \
+-targetSizes="/hive/data/genomes/asmHubs/GCF/000/349/665/GCF_000349665.1/GCF_000349665.1.chrom.sizes.txt" \
+   GCF_000349665.1 mm39) > rbest.log 2>&1
+
+    grep -w real rbest.log | sed -e 's/^/    # /;'
+    # real	449m50.789s
+
+    sed -e 's/^/    # /;' fb.GCF_000349665.1.chainRBest.Mm39.txt
+    # 1354030653 bases of 2504925039 (54.055%) in intersection
+
+
+real	1856m55.873s
+user	0m2.166s
+sys	0m3.097s
+##############################################################################
+# LASTZ Rat Rn6 vs. golden hamster GCF_000349665.1
+#    (DONE - 2021-10-19 - hiram)
+
+    mkdir /hive/data/genomes/rn6/bed/lastzGCF_000349665.1.2021-10-19
+    cd /hive/data/genomes/rn6/bed/lastzGCF_000349665.1.2021-10-19
+
+    printf '# golden hamster GCF_000349665.1 vs. Rat Rn6
+BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.03/bin/lastz
+
+# TARGET: Rat Rn6
+SEQ1_DIR=/hive/data/genomes/rn6/rn6.2bit
+SEQ1_LEN=/hive/data/genomes/rn6/chrom.sizes
+SEQ1_CHUNK=20000000
+SEQ1_LAP=10000
+SEQ1_LIMIT=40
+
+# QUERY: golden hamster GCF_000349665.1
+SEQ2_DIR=/hive/data/genomes/asmHubs/GCF/000/349/665/GCF_000349665.1/GCF_000349665.1.2bit
+SEQ2_LEN=/hive/data/genomes/asmHubs/GCF/000/349/665/GCF_000349665.1/GCF_000349665.1.chrom.sizes.txt
+SEQ2_CHUNK=20000000
+SEQ2_LAP=0
+SEQ2_LIMIT=100
+
+BASE=/hive/data/genomes/rn6/bed/lastzGCF_000349665.1.2021-10-19
+TMPDIR=/dev/shm
+
+' > DEF
+
+    time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -verbose=2 `pwd`/DEF -syntenicNet \
+       -qAsmId GCF_000349665.1_MesAur1.0 -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \
+        -chainMinScore=3000 -chainLinearGap=medium) > do.log 2>&1
+    grep -w real do.log | sed -e 's/^/    # /;'
+    # real	825m37.498s
+
+    sed -e 's/^/    # /;' fb.rn6.chainGCF_000349665.1Link.txt
+    # 1514418886 bases of 2870182909 (52.764%) in intersection
+    sed -e 's/^/    # /;' fb.rn6.chainSynGCF_000349665.1Link.txt
+    # 1362599174 bases of 2870182909 (47.474%) in intersection
+
+    time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \
+       \
+      -query2Bit="/hive/data/genomes/asmHubs/GCF/000/349/665/GCF_000349665.1/GCF_000349665.1.2bit" \
+-querySizes="/hive/data/genomes/asmHubs/GCF/000/349/665/GCF_000349665.1/GCF_000349665.1.chrom.sizes.txt" \
+        rn6 GCF_000349665.1) > rbest.log 2>&1
+
+    grep -w real rbest.log | sed -e 's/^/    # /;'
+    # real	573m22.505s
+
+    sed -e 's/^/    # /;' fb.rn6.chainRBest.GCF_000349665.1.txt
+    # 1350327568 bases of 2870182909 (47.047%) in intersection
+
+    ### and for the swap
+# swap into: /hive/data/genomes/asmHubs/allBuild/GCF/000/349/665/GCF_000349665.1_MesAur1.0/trackData/blastz.rn6.swap
+# running /hive/data/genomes/asmHubs/allBuild/GCF/000/349/665/GCF_000349665.1_MesAur1.0/trackData/blastz.rn6.swap/runSwap.sh
+##############################################################################
+# LASTZ Rat Rn6 vs. golden hamster GCF_000349665.1
+#    (DONE - 2021-10-19 - hiram)
+
+    mkdir /hive/data/genomes/rn6/bed/lastzGCF_000349665.1.2021-10-19
+    cd /hive/data/genomes/rn6/bed/lastzGCF_000349665.1.2021-10-19
+
+    printf '# golden hamster GCF_000349665.1 vs. Rat Rn6
+BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.03/bin/lastz
+
+# TARGET: Rat Rn6
+SEQ1_DIR=/hive/data/genomes/rn6/rn6.2bit
+SEQ1_LEN=/hive/data/genomes/rn6/chrom.sizes
+SEQ1_CHUNK=20000000
+SEQ1_LAP=10000
+SEQ1_LIMIT=40
+
+# QUERY: golden hamster GCF_000349665.1
+SEQ2_DIR=/hive/data/genomes/asmHubs/GCF/000/349/665/GCF_000349665.1/GCF_000349665.1.2bit
+SEQ2_LEN=/hive/data/genomes/asmHubs/GCF/000/349/665/GCF_000349665.1/GCF_000349665.1.chrom.sizes.txt
+SEQ2_CHUNK=20000000
+SEQ2_LAP=0
+SEQ2_LIMIT=100
+
+BASE=/hive/data/genomes/rn6/bed/lastzGCF_000349665.1.2021-10-19
+TMPDIR=/dev/shm
+
+' > DEF
+
+    time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -verbose=2 `pwd`/DEF -syntenicNet \
+       -qAsmId GCF_000349665.1_MesAur1.0 -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \
+        -chainMinScore=3000 -chainLinearGap=medium) > do.log 2>&1
+    grep -w real do.log | sed -e 's/^/    # /;'
+    # real	825m37.498s
+
+    sed -e 's/^/    # /;' fb.rn6.chainGCF_000349665.1Link.txt
+    # 1514418886 bases of 2870182909 (52.764%) in intersection
+    sed -e 's/^/    # /;' fb.rn6.chainSynGCF_000349665.1Link.txt
+    # 1362599174 bases of 2870182909 (47.474%) in intersection
+
+    time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \
+       \
+      -query2Bit="/hive/data/genomes/asmHubs/GCF/000/349/665/GCF_000349665.1/GCF_000349665.1.2bit" \
+-querySizes="/hive/data/genomes/asmHubs/GCF/000/349/665/GCF_000349665.1/GCF_000349665.1.chrom.sizes.txt" \
+        rn6 GCF_000349665.1) > rbest.log 2>&1
+
+    grep -w real rbest.log | sed -e 's/^/    # /;'
+    # real	573m22.505s
+
+    sed -e 's/^/    # /;' fb.rn6.chainRBest.GCF_000349665.1.txt
+    # 1350327568 bases of 2870182909 (47.047%) in intersection
+
+    ### and for the swap
+
+    cd /hive/data/genomes/asmHubs/allBuild/GCF/000/349/665/GCF_000349665.1_MesAur1.0/trackData/blastz.rn6.swap
+
+   time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -swap -verbose=2 \
+   -qAsmId GCF_000349665.1_MesAur1.0 /hive/data/genomes/rn6/bed/lastzGCF_000349665.1.2021-10-19/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	101m35.604s
+
+    sed -e 's/^/    # /;' fb.GCF_000349665.1.chainRn6Link.txt
+    # 1413849889 bases of 2504925039 (56.443%) in intersection
+    sed -e 's/^/    # /;' fb.GCF_000349665.1.chainSynRn6Link.txt
+    # 1311578944 bases of 2504925039 (52.360%) in intersection
+\    time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \
+    \
+   -target2bit="/hive/data/genomes/asmHubs/GCF/000/349/665/GCF_000349665.1/GCF_000349665.1.2bit" \
+-targetSizes="/hive/data/genomes/asmHubs/GCF/000/349/665/GCF_000349665.1/GCF_000349665.1.chrom.sizes.txt" \
+   GCF_000349665.1 rn6) > rbest.log 2>&1
+
+    grep -w real rbest.log | sed -e 's/^/    # /;'
+    # real	488m35.716s
+
+    sed -e 's/^/    # /;' fb.GCF_000349665.1.chainRBest.Rn6.txt
+    # 1350825251 bases of 2504925039 (53.927%) in intersection
+
+
+real	1989m11.755s
+user	0m1.959s
+sys	0m2.860s
+##############################################################################