574a35c43eb5b7eb71a5499785f8e4671e566f53
gperez2
Sun Jul 30 23:55:00 2023 -0700
GCA_011100615.1 vs. mm39 lastz/chain/net run for user, refs #30834
diff --git src/hg/makeDb/doc/asmHubs/lastzRuns.txt src/hg/makeDb/doc/asmHubs/lastzRuns.txt
index 8f2b517..d246985 100644
--- src/hg/makeDb/doc/asmHubs/lastzRuns.txt
+++ src/hg/makeDb/doc/asmHubs/lastzRuns.txt
@@ -2451,15 +2451,98 @@
-target2bit="/hive/data/genomes/asmHubs/GCF/017/639/785/GCF_017639785.1/GCF_017639785.1.2bit" \
-targetSizes="/hive/data/genomes/asmHubs/GCF/017/639/785/GCF_017639785.1/GCF_017639785.1.chrom.sizes.txt" \
GCF_017639785.1 mm10) > rbest.log 2>&1
grep -w real rbest.log | sed -e 's/^/ # /;'
# real 389m15.292s
sed -e 's/^/ # /;' fb.GCF_017639785.1.chainRBest.Mm10.txt
# 1424688161 bases of 2457078271 (57.983%) in intersection
real 1143m22.133s
user 0m1.217s
sys 0m1.403s
##############################################################################
+# LASTZ crab-eating macaque GCA_011100615.1 vs. Mouse Mm39
+# (DONE - 2023-03-17 - Gerardo)
+
+ mkdir /hive/data/genomes/asmHubs/allBuild/GCA/011/100/615/GCA_011100615.1_Macaca_fascicularis_6.0/trackData/lastzMm39.2023-03-17
+ cd /hive/data/genomes/asmHubs/allBuild/GCA/011/100/615/GCA_011100615.1_Macaca_fascicularis_6.0/trackData/lastzMm39.2023-03-17
+
+ printf '# Mouse Mm39 vs. crab-eating macaque GCA_011100615.1
+BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.03/bin/lastz
+
+# TARGET: crab-eating macaque 2020-03-10 GCA_011100615.1_Macaca_fascicularis_6.0
+SEQ1_DIR=/hive/data/genomes/asmHubs/GCA/011/100/615/GCA_011100615.1/GCA_011100615.1.2bit
+SEQ1_LEN=/hive/data/genomes/asmHubs/GCA/011/100/615/GCA_011100615.1/GCA_011100615.1.chrom.sizes.txt
+SEQ1_CHUNK=20000000
+SEQ1_LAP=10000
+SEQ1_LIMIT=40
+
+# QUERY: Mouse mm39
+SEQ2_DIR=/hive/data/genomes/mm39/mm39.2bit
+SEQ2_LEN=/hive/data/genomes/mm39/chrom.sizes
+SEQ2_CHUNK=20000000
+SEQ2_LAP=0
+SEQ2_LIMIT=100
+
+BASE=/hive/data/genomes/asmHubs/allBuild/GCA/011/100/615/GCA_011100615.1_Macaca_fascicularis_6.0/trackData/lastzMm39.2023-03-17
+TMPDIR=/dev/shm
+
+' > DEF
+
+ time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -verbose=2 `pwd`/DEF -syntenicNet \
+ -tAsmId GCA_011100615.1_Macaca_fascicularis_6.0 -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \
+ -chainMinScore=3000 -chainLinearGap=medium) > do.log 2>&1
+ grep -w real do.log | sed -e 's/^/ # /;'
+ # real 218m54.585s
+
+ sed -e 's/^/ # /;' fb.GCA_011100615.1.chainMm39Link.txt
+ # 912976314 bases of 2906138557 (31.415%) in intersection
+ sed -e 's/^/ # /;' fb.GCA_011100615.1.chainSynMm39Link.txt
+ # 869628418 bases of 2906138557 (29.924%) in intersection
+
+ 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 mm39) > rbest.log 2>&1
+
+ grep -w real rbest.log | sed -e 's/^/ # /;'
+ # real 252m48.711s
+
+ sed -e 's/^/ # /;' fb.GCA_011100615.1.chainRBest.Mm39.txt
+ # 867863039 bases of 2906138557 (29.863%) in intersection
+
+ ### and for the swap
+
+ cd /hive/data/genomes/mm39/bed/blastz.GCA_011100615.1.swap
+
+ time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -swap -verbose=2 \
+ -tAsmId GCA_011100615.1_Macaca_fascicularis_6.0 /hive/data/genomes/asmHubs/allBuild/GCA/011/100/615/GCA_011100615.1_Macaca_fascicularis_6.0/trackData/lastzMm39.2023-03-17/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 62m11.211s
+
+ sed -e 's/^/ # /;' fb.mm39.chainGCA_011100615.1Link.txt
+ # 913319506 bases of 2728222451 (33.477%) in intersection
+ sed -e 's/^/ # /;' fb.mm39.chainSynGCA_011100615.1Link.txt
+ # 866991862 bases of 2728222451 (31.779%) in intersection
+\ time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \
+ -query2bit="/hive/data/genomes/asmHubs/GCA/011/100/615/GCA_011100615.1/GCA_011100615.1.2bit" \
+-querySizes="/hive/data/genomes/asmHubs/GCA/011/100/615/GCA_011100615.1/GCA_011100615.1.chrom.sizes.txt" \
+ \
+ mm39 GCA_011100615.1) > rbest.log 2>&1
+
+ grep -w real rbest.log | sed -e 's/^/ # /;'
+ # real 398m10.453s
+
+ sed -e 's/^/ # /;' fb.mm39.chainRBest.GCA_011100615.1.txt
+ # 869048496 bases of 2728222451 (31.854%) in intersection
+
+real 932m5.702s
+user 0m0.997s
+sys 0m1.331s
+##############################################################################