7d0bd2b7d089f94c9a8260c417246d4dbfce2523
mspeir
  Sat Mar 29 18:51:22 2025 -0700
adding make docs for several lastz runs from the last 6 months or so

diff --git src/hg/makeDb/doc/hg19.txt src/hg/makeDb/doc/hg19.txt
index bf225a3e6a3..7fc6c75f99a 100644
--- src/hg/makeDb/doc/hg19.txt
+++ src/hg/makeDb/doc/hg19.txt
@@ -35669,30 +35669,86 @@
 cd tmp
 
 chainSwap ../../liftOver/hg19ToHg38.over.chain.gz hg19ToHg38.over.swap.chain
 
 awk '/chain/ {print $3, $4}' hg19ToHg38.over.swap.chain | sort | uniq > hg19ToHg38.over.swap.sizes
 chainToBigChain hg19ToHg38.over.swap.chain bigChainOut bigLinkOut
 bedToBigBed -type=bed6+6 -as=$HOME/kent/src/hg/lib/bigChain.as -tab bigChainOut hg19ToHg38.over.swap.sizes hg19ToHg38.bb
 bedToBigBed -type=bed4+1 -as=$HOME/kent/src/hg/lib/bigLink.as -tab bigLinkOut  hg19ToHg38.over.swap.sizes hg19ToHg38.link.bb
 
 ln -s `pwd`/hg19ToHg38.bb /gbdb/hg19/quickLift/hg38.bb
 ln -s `pwd`/hg19ToHg38.link.bb /gbdb/hg19/quickLift/hg38.link.bb
 hgsql hgcentraltest -Ne 'insert into quickLiftChain values (0, "hg19", "hg38", "/gbdb/hg19/quickLift/hg38.bb")'
 
 ###
 
+##############################################################################
+# LASTZ Human Hg19 vs. Norway rat GCF_036323735.1
+#    (DONE - 2025-02-26 - mspeir)
+
+    mkdir /hive/data/genomes/hg19/bed/lastzGCF_036323735.1.2025-02-26
+    cd /hive/data/genomes/hg19/bed/lastzGCF_036323735.1.2025-02-26
+
+    printf '# Norway rat GCF_036323735.1 vs. Human Hg19
+BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.03/bin/lastz
+
+# TARGET: Human  hg19
+SEQ1_DIR=/hive/data/genomes/hg19/hg19.2bit
+SEQ1_LEN=/hive/data/genomes/hg19/chrom.sizes
+SEQ1_CHUNK=20000000
+SEQ1_LAP=10000
+SEQ1_LIMIT=40
+
+# QUERY: Norway rat 2024-01-31 GCF_036323735.1_GRCr8
+SEQ2_DIR=/hive/data/genomes/asmHubs/GCF/036/323/735/GCF_036323735.1/GCF_036323735.1.2bit
+SEQ2_LEN=/hive/data/genomes/asmHubs/GCF/036/323/735/GCF_036323735.1/GCF_036323735.1.chrom.sizes.txt
+SEQ2_CHUNK=20000000
+SEQ2_LAP=0
+SEQ2_LIMIT=100
+
+BASE=/hive/data/genomes/hg19/bed/lastzGCF_036323735.1.2025-02-26
+TMPDIR=/dev/shm
+
+' > DEF
+
+    time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -verbose=2 `pwd`/DEF -syntenicNet \
+       -qAsmId GCF_036323735.1_GRCr8 -workhorse=hgwdev -smallClusterHub=hgwdev -fileServer=hgwdev -bigClusterHub=hgwdev \
+        -chainMinScore=3000 -chainLinearGap=medium) > do.log 2>&1
+    grep -w real do.log | sed -e 's/^/    # /;'
+    # real	1575m43.169s
+
+    sed -e 's/^/    # /;' fb.hg19.chainGCF_036323735.1Link.txt
+    # 959321585 bases of 3234851260 (29.656%) in intersection
+    sed -e 's/^/    # /;' fb.hg19.chainSynGCF_036323735.1Link.txt
+    # 911355050 bases of 3234851260 (28.173%) in intersection
+
+    time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \
+       \
+      -query2Bit="/hive/data/genomes/asmHubs/GCF/036/323/735/GCF_036323735.1/GCF_036323735.1.2bit" \
+-querySizes="/hive/data/genomes/asmHubs/GCF/036/323/735/GCF_036323735.1/GCF_036323735.1.chrom.sizes.txt" \
+        hg19 GCF_036323735.1) > rbest.log 2>&1
+
+    grep -w real rbest.log | sed -e 's/^/    # /;'
+    # real	178m3.528s
+
+    sed -e 's/^/    # /;' fb.hg19.chainRBest.GCF_036323735.1.txt
+    # 884610372 bases of 3234851260 (27.346%) in intersection
+
+real	2120m31.673s
+user	0m2.938s
+sys	0m1.827s
+
 #########################################################################
 # denovo-db v.1.6.1 (03-13-2025) Megna Chalamala
 
 wget http://denovo-db.gs.washington.edu/denovo-db.non-ssc-samples.variants.tsv.gz
 wget http://denovo-db.gs.washington.edu/denovo-db.ssc-samples.variants.tsv.gz
 wget https://genome.ucsc.edu/goldenPath/help/hg19.chrom.sizes
 
 zcat /cluster/home/mchalama/public_html/tracks/denovo/hg19/denovo-db.ssc-samples.variants.tsv | \
 awk 'BEGIN {OFS="\t"} NR > 1 {
     print $9, $10, $10, $12, "0", ".", $10, $10, "0", $1, $2, $3, $4, $5, $6, $7, $8, $11, $13, $14, $15, $16, $17, $18, $19, $20, $21, $22, $23, $24, $25, $26, $27, $28, $29, "0"
 }' > output_fixed.bed
 nano bedExample2.as
 tail -n +2 output_fixed.bed > output_no_header.bed
 awk '{if($1 !~ /^chr/) $1 = "chr"$1; print}' OFS="\t" output_no_header.bed > output_standard.bed
 awk '{if ($2 != "chromStart") $2 = $2 - 1; print}' OFS="\t" output_no_header.bed > output_adjusted.bed