bc46f17c49d80193157e45e9916ff3032598a245
hiram
  Tue Dec 12 07:45:44 2023 -0800
lastz chain net hg38 to hs1 refs #31977

diff --git src/hg/makeDb/doc/hg38/lastzRuns.txt src/hg/makeDb/doc/hg38/lastzRuns.txt
index 895a954..74f9b92 100644
--- src/hg/makeDb/doc/hg38/lastzRuns.txt
+++ src/hg/makeDb/doc/hg38/lastzRuns.txt
@@ -13807,16 +13807,103 @@
 \    time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \
     \
    -target2bit="/hive/data/genomes/asmHubs/GCA/011/100/615/GCA_011100615.1/GCA_011100615.1.2bit" \
 -targetSizes="/hive/data/genomes/asmHubs/GCA/011/100/615/GCA_011100615.1/GCA_011100615.1.chrom.sizes.txt" \
    GCA_011100615.1 hg38) > rbest.log 2>&1
 
     grep -w real rbest.log | sed -e 's/^/    # /;'
     # real	140m55.957s
 
     sed -e 's/^/    # /;' fb.GCA_011100615.1.chainRBest.Hg38.txt
     # 2394259873 bases of 2906138557 (82.386%) in intersection
 
 real	512m28.587s
 user	0m0.989s
 sys	0m1.306s
+
+##############################################################################
+# LASTZ Human Hg38 vs. Human Hs1
+#    (DONE - 2022-09-26 - hiram)
+
+    mkdir /hive/data/genomes/hg38/bed/lastzHs1.2022-09-21
+    cd /hive/data/genomes/hg38/bed/lastzHs1.2022-09-21
+
+    printf '# Human Hs1 vs. Human Hg38
+BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.03/bin/lastz
+BLASTZ_T=2
+BLASTZ_O=600
+BLASTZ_E=150
+BLASTZ_M=254
+BLASTZ_K=4500
+BLASTZ_Y=15000
+BLASTZ_Q=/hive/data/staging/data/blastz/human_chimp.v2.q
+#       A     C     G     T
+# A    90  -330  -236  -356
+# C  -330   100  -318  -236
+# G  -236  -318   100  -330
+# T  -356  -236  -330    90
+
+# 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: Human  hs1
+SEQ2_DIR=/hive/data/genomes/hs1/hs1.2bit
+SEQ2_LEN=/hive/data/genomes/hs1/chrom.sizes
+SEQ2_CHUNK=20000000
+SEQ2_LAP=0
+SEQ2_LIMIT=100
+
+BASE=/hive/data/genomes/hg38/bed/lastzHs1.2022-09-21
+TMPDIR=/dev/shm
+
+' > DEF
+
+    time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl  -verbose=2 `pwd`/DEF -syntenicNet \
+        -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \
+        -chainMinScore=5000 -chainLinearGap=medium) > do.log 2>&1
+    grep -w real do.log | sed -e 's/^/    # /;'
+
+    sed -e 's/^/    # /;' fb.hg38.chainHs1Link.txt
+    # 3037208207 bases of 3110768607 (97.635%) in intersection
+    sed -e 's/^/    # /;' fb.hg38.chainSynHs1Link.txt
+    # 3034364239 bases of 3110768607 (97.544%) in intersection
+
+    time (~/kent/src/hg/utils/automation/doRecipBest.pl  -load -workhorse=hgwdev -buildDir=`pwd` \
+       \
+       \
+        hg38 hs1) > rbest.log 2>&1
+
+    grep -w real rbest.log | sed -e 's/^/    # /;'
+
+    sed -e 's/^/    # /;' fb.hg38.chainRBest.Hs1.txt
+
+    ### and for the swap
+
+    cd /hive/data/genomes/hs1/bed/blastz.hg38.swap
+
+    time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -swap -verbose=2 \
+       /hive/data/genomes/hg38/bed/lastzHs1.2022-09-21/DEF -swapDir=`pwd` \
+-syntenicNet -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \
+        -chainMinScore=5000 -chainLinearGap=medium) > swap.log 2>&1
+
+    grep -w real swap.log | sed -e 's/^/    # /;'
+    # real      134m42.390s
+
+    sed -e 's/^/    # /;' fb.hs1.chainHg38Link.txt
+    # 2906145588 bases of 3117292070 (93.227%) in intersection
+    sed -e 's/^/    # /;' fb.hs1.chainSynHg38Link.txt
+    # 2896674405 bases of 3117292070 (92.923%) in intersection
+
+    time (~/kent/src/hg/utils/automation/doRecipBest.pl -load -workhorse=hgwdev -buildDir=`pwd` \
+       hs1 hg38) > rbest.log 2>&1
+
+    grep -w real rbest.log | sed -e 's/^/    # /;'
+    # real      88m35.809s
+
+    sed -e 's/^/    # /;' fb.hs1.chainRBest.Hg38.txt
+    # 2863655887 bases of 3117292070 (91.864%) in intersection
+
 ##############################################################################