51e36af6ab42bd9c0f858a4d00cf63bcac0fb4a7
gperez2
  Sun Apr 7 21:45:15 2024 -0700
mm39 to GCA_921997145.2 lastz/chain/net run for user, refs #33296

diff --git src/hg/makeDb/doc/mm39/lastzRuns.txt src/hg/makeDb/doc/mm39/lastzRuns.txt
index 8e69894..0cdab6a 100644
--- src/hg/makeDb/doc/mm39/lastzRuns.txt
+++ src/hg/makeDb/doc/mm39/lastzRuns.txt
@@ -3411,15 +3411,98 @@
     \
    -target2bit="/hive/data/genomes/asmHubs/GCA/921/997/125/GCA_921997125.2/GCA_921997125.2.2bit" \
 -targetSizes="/hive/data/genomes/asmHubs/GCA/921/997/125/GCA_921997125.2/GCA_921997125.2.chrom.sizes.txt" \
    GCA_921997125.2 mm39) > rbest.log 2>&1
 
     grep -w real rbest.log | sed -e 's/^/    # /;'
     # real	59m10.825s
 
     sed -e 's/^/    # /;' fb.GCA_921997125.2.chainRBest.Mm39.txt
     # 2454104373 bases of 2532437445 (96.907%) in intersection
 
 real	3266m26.008s
 user	0m3.015s
 sys	0m3.143s
 ##############################################################################
+# LASTZ Mouse Mm39 vs. house mouse GCA_921997145.2
+#    (DONE - 2024-03-26 - Gerardo)
+
+    mkdir /hive/data/genomes/mm39/bed/lastzGCA_921997145.2.2024-03-26
+    cd /hive/data/genomes/mm39/bed/lastzGCA_921997145.2.2024-03-26
+
+    printf '# house mouse GCA_921997145.2 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: house mouse 2022-07-01 GCA_921997145.2_BALB_cJ_v3
+SEQ2_DIR=/hive/data/genomes/asmHubs/GCA/921/997/145/GCA_921997145.2/GCA_921997145.2.2bit
+SEQ2_LEN=/hive/data/genomes/asmHubs/GCA/921/997/145/GCA_921997145.2/GCA_921997145.2.chrom.sizes.txt
+SEQ2_CHUNK=20000000
+SEQ2_LAP=0
+SEQ2_LIMIT=100
+
+BASE=/hive/data/genomes/mm39/bed/lastzGCA_921997145.2.2024-03-26
+TMPDIR=/dev/shm
+
+' > DEF
+
+    time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -verbose=2 `pwd`/DEF -syntenicNet \
+       -qAsmId GCA_921997145.2_BALB_cJ_v3 -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \
+        -chainMinScore=3000 -chainLinearGap=medium) > do.log 2>&1
+    grep -w real do.log | sed -e 's/^/    # /;'
+    # real	2547m29.086s
+
+    sed -e 's/^/    # /;' fb.mm39.chainGCA_921997145.2Link.txt
+    # 2585656877 bases of 2728222451 (94.774%) in intersection
+    sed -e 's/^/    # /;' fb.mm39.chainSynGCA_921997145.2Link.txt
+    # 2527529181 bases of 2728222451 (92.644%) in intersection
+
+    time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \
+       \
+      -query2Bit="/hive/data/genomes/asmHubs/GCA/921/997/145/GCA_921997145.2/GCA_921997145.2.2bit" \
+-querySizes="/hive/data/genomes/asmHubs/GCA/921/997/145/GCA_921997145.2/GCA_921997145.2.chrom.sizes.txt" \
+        mm39 GCA_921997145.2) > rbest.log 2>&1
+
+    grep -w real rbest.log | sed -e 's/^/    # /;'
+    # real	82m9.988s
+
+    sed -e 's/^/    # /;' fb.mm39.chainRBest.GCA_921997145.2.txt
+    # 2460723628 bases of 2728222451 (90.195%) in intersection
+
+    ### and for the swap
+
+    cd /hive/data/genomes/asmHubs/allBuild/GCA/921/997/145/GCA_921997145.2_BALB_cJ_v3/trackData/blastz.mm39.swap
+
+   time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -swap -verbose=2 \
+   -qAsmId GCA_921997145.2_BALB_cJ_v3 /hive/data/genomes/mm39/bed/lastzGCA_921997145.2.2024-03-26/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	159m4.651s
+
+    sed -e 's/^/    # /;' fb.GCA_921997145.2.chainMm39Link.txt
+    # 2474241874 bases of 2519913072 (98.188%) in intersection
+    sed -e 's/^/    # /;' fb.GCA_921997145.2.chainSynMm39Link.txt
+    # 2467271087 bases of 2519913072 (97.911%) in intersection
+\    time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \
+    \
+   -target2bit="/hive/data/genomes/asmHubs/GCA/921/997/145/GCA_921997145.2/GCA_921997145.2.2bit" \
+-targetSizes="/hive/data/genomes/asmHubs/GCA/921/997/145/GCA_921997145.2/GCA_921997145.2.chrom.sizes.txt" \
+   GCA_921997145.2 mm39) > rbest.log 2>&1
+
+    grep -w real rbest.log | sed -e 's/^/    # /;'
+    # real	63m16.206s
+
+    sed -e 's/^/    # /;' fb.GCA_921997145.2.chainRBest.Mm39.txt
+    # 2461542910 bases of 2519913072 (97.684%) in intersection
+
+real	2852m3.826s
+user	0m2.832s
+sys	0m2.990s
+##############################################################################