1d41751e7047c66060c07042479d29cb82dd9c0b
gperez2
  Sun Sep 15 23:27:57 2024 -0700
Rabbit (GCF_009806435.1) to hg38/mm39 lastz/chain/net run for user, refs #34037

diff --git src/hg/makeDb/doc/mm39/lastzRuns.txt src/hg/makeDb/doc/mm39/lastzRuns.txt
index 0219aea..00923da 100644
--- src/hg/makeDb/doc/mm39/lastzRuns.txt
+++ src/hg/makeDb/doc/mm39/lastzRuns.txt
@@ -3893,15 +3893,98 @@
    -target2bit="/hive/data/genomes/asmHubs/GCA/921/999/865/GCA_921999865.2/GCA_921999865.2.2bit" \
 -targetSizes="/hive/data/genomes/asmHubs/GCA/921/999/865/GCA_921999865.2/GCA_921999865.2.chrom.sizes.txt" \
    GCA_921999865.2 mm39) > rbest.log 2>&1
 
     grep -w real rbest.log | sed -e 's/^/    # /;'
     # real	67m13.662s
 
     sed -e 's/^/    # /;' fb.GCA_921999865.2.chainRBest.Mm39.txt
     # 2497498017 bases of 2514593528 (99.320%) in intersection
 
 real	1318m52.288s
 user	0m2.240s
 sys	0m2.560s
 
 ##############################################################################
+# LASTZ Mouse Mm39 vs. rabbit GCF_009806435.1
+#    (DONE - 2024-06-28 - Gerardo)
+
+    mkdir /hive/data/genomes/mm39/bed/lastzGCF_009806435.1.2024-06-28
+    cd /hive/data/genomes/mm39/bed/lastzGCF_009806435.1.2024-06-28
+
+    printf '# rabbit GCF_009806435.1 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: rabbit 2021-02-04 GCF_009806435.1_UM_NZW_1.0
+SEQ2_DIR=/hive/data/genomes/asmHubs/GCF/009/806/435/GCF_009806435.1/GCF_009806435.1.2bit
+SEQ2_LEN=/hive/data/genomes/asmHubs/GCF/009/806/435/GCF_009806435.1/GCF_009806435.1.chrom.sizes.txt
+SEQ2_CHUNK=20000000
+SEQ2_LAP=0
+SEQ2_LIMIT=100
+
+BASE=/hive/data/genomes/mm39/bed/lastzGCF_009806435.1.2024-06-28
+TMPDIR=/dev/shm
+
+' > DEF
+
+    time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -verbose=2 `pwd`/DEF -syntenicNet \
+       -qAsmId GCF_009806435.1_UM_NZW_1.0 -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \
+        -chainMinScore=3000 -chainLinearGap=medium) > do.log 2>&1
+    grep -w real do.log | sed -e 's/^/    # /;'
+    # real	354m26.805s
+
+    sed -e 's/^/    # /;' fb.mm39.chainGCF_009806435.1Link.txt
+    # 668346839 bases of 2728222451 (24.498%) in intersection
+    sed -e 's/^/    # /;' fb.mm39.chainSynGCF_009806435.1Link.txt
+    # 614245411 bases of 2728222451 (22.514%) in intersection
+
+    time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \
+       \
+      -query2Bit="/hive/data/genomes/asmHubs/GCF/009/806/435/GCF_009806435.1/GCF_009806435.1.2bit" \
+-querySizes="/hive/data/genomes/asmHubs/GCF/009/806/435/GCF_009806435.1/GCF_009806435.1.chrom.sizes.txt" \
+        mm39 GCF_009806435.1) > rbest.log 2>&1
+
+    grep -w real rbest.log | sed -e 's/^/    # /;'
+    # real	270m13.288s
+
+    sed -e 's/^/    # /;' fb.mm39.chainRBest.GCF_009806435.1.txt
+    # 632080850 bases of 2728222451 (23.168%) in intersection
+
+    ### and for the swap
+
+    cd /hive/data/genomes/asmHubs/allBuild/GCF/009/806/435/GCF_009806435.1_UM_NZW_1.0/trackData/blastz.mm39.swap
+
+   time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -swap -verbose=2 \
+   -qAsmId GCF_009806435.1_UM_NZW_1.0 /hive/data/genomes/mm39/bed/lastzGCF_009806435.1.2024-06-28/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	44m16.282s
+
+    sed -e 's/^/    # /;' fb.GCF_009806435.1.chainMm39Link.txt
+    # 700149744 bases of 2841507030 (24.640%) in intersection
+    sed -e 's/^/    # /;' fb.GCF_009806435.1.chainSynMm39Link.txt
+    # 622621309 bases of 2841507030 (21.912%) in intersection
+\    time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \
+    \
+   -target2bit="/hive/data/genomes/asmHubs/GCF/009/806/435/GCF_009806435.1/GCF_009806435.1.2bit" \
+-targetSizes="/hive/data/genomes/asmHubs/GCF/009/806/435/GCF_009806435.1/GCF_009806435.1.chrom.sizes.txt" \
+   GCF_009806435.1 mm39) > rbest.log 2>&1
+
+    grep -w real rbest.log | sed -e 's/^/    # /;'
+    # real	288m41.391s
+
+    sed -e 's/^/    # /;' fb.GCF_009806435.1.chainRBest.Mm39.txt
+    # 632186963 bases of 2841507030 (22.248%) in intersection
+
+real	957m44.686s
+user	0m3.153s
+sys	0m3.273s
+##############################################################################