3bff517ce5a5210e0c7eb6f700b82eb0236f97f4
hiram
Tue Nov 26 12:06:36 2019 -0800
chain/net hg38 to gorGor6 done refs #24524
diff --git src/hg/makeDb/doc/hg38/lastzRuns.txt src/hg/makeDb/doc/hg38/lastzRuns.txt
index 72cae22..7af83b0 100644
--- src/hg/makeDb/doc/hg38/lastzRuns.txt
+++ src/hg/makeDb/doc/hg38/lastzRuns.txt
@@ -12231,15 +12231,167 @@
-syntenicNet) > swap.log 2>&1
# real 61m39.505s
cat fb.rheMac10.chainHg38Link.txt
# 2485840115 bases of 2936892733 (84.642%) in intersection
cat fb.rheMac10.chainSynHg38Link.txt
# 2465210442 bases of 2936892733 (83.939%) in intersection
time (doRecipBest.pl -workhorse=hgwdev -load -buildDir=`pwd` rheMac10 hg38) > rbest.log 2>&1
# real 126m29.919s
cat fb.rheMac10.chainRBest.Hg38.txt
# 2424028492 bases of 2936892733 (82.537%) in intersection
#########################################################################
+# LASTZ human/hg38 vs. rat/regenRn1 - (DONE - 2019-09-12 - Hiram)
+ mkdir /hive/data/genomes/hg38/bed/lastzRegenRn1.2019-09-12
+ cd /hive/data/genomes/hg38/bed/lastzRegenRn1.2019-09-12
+
+ printf '# human vs rat
+BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.00/bin/lastz
+
+# TARGET: human hg38
+SEQ1_DIR=/hive/data/genomes/hg38/hg38.2bit
+SEQ1_LEN=/hive/data/genomes/hg38/chrom.sizes
+SEQ1_CTGDIR=/hive/data/genomes/hg38/hg38.contigs.2bit
+SEQ1_CTGLEN=/hive/data/genomes/hg38/hg38.contigs.chrom.sizes
+SEQ1_LIFT=/hive/data/genomes/hg38/jkStuff/hg38.contigs.lift
+SEQ1_CHUNK=40000000
+SEQ1_LIMIT=30
+SEQ1_LAP=10000
+
+# QUERY: rat regenRn1
+SEQ2_DIR=/hive/data/genomes/regenRn1/regenRn1.2bit
+SEQ2_LEN=/hive/data/genomes/regenRn1/chrom.sizes
+SEQ2_CHUNK=20000000
+SEQ2_LIMIT=30
+SEQ2_LAP=0
+
+BASE=/hive/data/genomes/hg38/bed/lastzRegenRn1.2019-09-12
+TMPDIR=/dev/shm
+' > DEF
+
+ time (doBlastzChainNet.pl `pwd`/DEF -verbose=2 \
+ -chainMinScore=3000 -chainLinearGap=medium -noDbNameCheck \
+ -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
+ -syntenicNet) > do.log 2>&1 &
+ # real 162m40.237s
+
+ cat fb.hg38.chainRegenRn1Link.txt
+ # 863041482 bases of 3095998939 (27.876%) in intersection
+ cat fb.hg38.chainSynRegenRn1Link.txt
+ # 809332351 bases of 3095998939 (26.141%) in intersection
+
+ time (doRecipBest.pl -workhorse=hgwdev -load -buildDir=`pwd` hg38 regenRn1) > rbest.log 2>&1 &
+XXX - running - Fri Sep 13 11:41:44 PDT 2019
+ # real 328m4.069s
+
+ cat fb.hg38.chainRBest.RegenRn1.txt
+ # 857127621 bases of 3095998939 (27.685%) in intersection
+
+ # and for the swap:
+ mkdir /hive/data/genomes/regenRn1/bed/blastz.hg38.swap
+ cd /hive/data/genomes/regenRn1/bed/blastz.hg38.swap
+
+ time (doBlastzChainNet.pl -verbose=2 \
+ /hive/data/genomes/hg38/bed/lastzRegenRn1.2019-09-12/DEF \
+ -swap -chainMinScore=3000 -chainLinearGap=medium -noDbNameCheck \
+ -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
+ -syntenicNet) > swap.log 2>&1
+ # real 63m47.773s
+
+ cat fb.regenRn1.chainHg38Link.txt
+ # 827167139 bases of 2282482188 (36.240%) in intersection
+ cat fb.regenRn1.chainSynHg38Link.txt
+ # 788025130 bases of 2282482188 (34.525%) in intersection
+
+ time (doRecipBest.pl -workhorse=hgwdev -load -buildDir=`pwd` regenRn1 hg38) > rbest.log 2>&1
+XXX - running - Fri Sep 13 12:07:31 PDT 2019
+ # real 300m30.411s
+
+ cat fb.regenRn1.chainRBest.Hg38.txt
+ # 858923025 bases of 2534810853 (33.885%) in intersection
+
+#########################################################################
+# LASTZ human/hg38 Gorilla/gorGor6 - (DONE - 2019-11-20 - Hiram)
+ mkdir /hive/data/genomes/hg38/bed/lastzGorGor6.2019-11-20
+ cd /hive/data/genomes/hg38/bed/lastzGorGor6.2019-11-20
+
+ printf '# human vs gorilla
+BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.00/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_IN_CONTIGS=0
+
+# QUERY: gorilla gorGor6
+SEQ2_DIR=/hive/data/genomes/gorGor6/gorGor6.2bit
+SEQ2_LEN=/hive/data/genomes/gorGor6/chrom.sizes
+SEQ2_CHUNK=20000000
+SEQ2_LAP=0
+SEQ2_LIMIT=50
+
+BASE=/hive/data/genomes/hg38/bed/lastzGorGor6.2019-11-20
+TMPDIR=/dev/shm
+' > DEF
+
+ time (doBlastzChainNet.pl `pwd`/DEF -verbose=2 \
+ -chainMinScore=3000 -chainLinearGap=medium \
+ -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
+ -syntenicNet) > do.log 2>&1
+ # broken cluster run due to path name for BLASTZ_Q, continuing:
+ time (doBlastzChainNet.pl `pwd`/DEF -verbose=2 \
+ -chainMinScore=3000 -chainLinearGap=medium \
+ -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
+ -continue=cat -syntenicNet) > cat.log 2>&1
+ # real 77m19.538s
+
+ cat fb.hg38.chainGorGor6Link.txt
+ # 2908900659 bases of 3095998939 (93.957%) in intersection
+ cat fb.hg38.chainSynGorGor6Link.txt
+ # 2885980361 bases of 3095998939 (93.216%) in intersection
+
+ time (doRecipBest.pl -load -workhorse=hgwdev -buildDir=`pwd` hg38 gorGor6) \
+ > rbest.log 2>&1 &
+ # real 65m39.724s
+
+ cat fb.hg38.chainRBest.GorGor6.txt
+ # 2693876207 bases of 3095998939 (87.012%) in intersection
+
+ # and for the swap:
+ mkdir /hive/data/genomes/gorGor6/bed/blastz.hg38.swap
+ cd /hive/data/genomes/gorGor6/bed/blastz.hg38.swap
+
+ time (doBlastzChainNet.pl -verbose=2 \
+ /hive/data/genomes/hg38/bed/lastzGorGor6.2019-11-20/DEF \
+ -swap -chainMinScore=3000 -chainLinearGap=medium \
+ -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \
+ -syntenicNet) > swap.log 2>&1
+ # real 63m46.473s
+
+ cat fb.gorGor6.chainHg38Link.txt
+ # 2738870921 bases of 2999027915 (91.325%) in intersection
+ cat fb.gorGor6.chainSynHg38Link.txt
+ # 2728591501 bases of 2999027915 (90.983%) in intersection
+
+ time (doRecipBest.pl -load -workhorse=hgwdev -buildDir=`pwd` gorGor6 hg38) \
+ > rbest.log 2>&1
+XXX - running - Tue Nov 26 11:55:51 PST 2019
+ # real 125m35.459s
+
+###########################################################################