046d71e629864ab8a0e62344ad6b447a3f654543
hiram
  Wed May 20 10:37:08 2020 -0700
per user request panTro6 to ponAbe3 refs #25581

diff --git src/hg/makeDb/doc/panTro6/lastzRuns.sh src/hg/makeDb/doc/panTro6/lastzRuns.sh
index ed8fa55..2ecbd04 100644
--- src/hg/makeDb/doc/panTro6/lastzRuns.sh
+++ src/hg/makeDb/doc/panTro6/lastzRuns.sh
@@ -1,84 +1,84 @@
 ##############################################################################
 # Orangutan Lastz run (DONE - 2020-05-19 - Hiram)
     screen -S panTro6PonAbe3      # use a screen to manage this longish running job
     mkdir /hive/data/genomes/panTro6/bed/lastzPonAbe3.2020-05-19
     cd /hive/data/genomes/panTro6/bed/lastzPonAbe3.2020-05-19
 
     # always set the BLASTZ program so we know what version was used
     printf "# chimp vs orangutan
 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_L=4500
 BLASTZ_Y=15000
-BLASTZ_Q=/scratch/data/blastz/human_chimp.v2.q
+BLASTZ_Q=/hive/data/staging/data/blastz/human_chimp.v2.q
 #    A    C    G    T
 #    90 -330 -236 -356
 #  -330  100 -318 -236
 #  -236 -318  100 -330
 #  -356 -236 -330   90
 
 # TARGET: chimp PanTro6
 SEQ1_DIR=/hive/data/genomes/panTro6/panTro6.2bit
 SEQ1_LEN=/hive/data/genomes/panTro6/chrom.sizes
 SEQ1_CHUNK=20000000
 SEQ1_LIMIT=40
 SEQ1_LAP=10000
 
 # QUERY: Orangutan PonAbe3
 SEQ2_DIR=/hive/data/genomes/ponAbe3/ponAbe3.2bit
 SEQ2_LEN=/hive/data/genomes/ponAbe3/chrom.sizes
 SEQ2_CHUNK=20000000
 SEQ2_LAP=0
 SEQ2_LIMIT=40
 SEQ2_IN_CONTIGS=0
 
 BASE=/hive/data/genomes/panTro6/bed/lastzPonAbe3.2020-05-19
 TMPDIR=/dev/shm
 " > DEF
 
     time (doBlastzChainNet.pl `pwd`/DEF -verbose=2 \
         -chainMinScore=5000 -chainLinearGap=medium \
         -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \
         -syntenicNet) > do.log 2>&1 &
-    # real    282m16.272s
+    # real    94m43.451s
 
     cat fb.panTro6.chainPonAbe3Link.txt
-    # 2823472924 bases of 3049335806 (92.593%) in intersection
+    # 2710778689 bases of 3018592990 (89.803%) in intersection
     cat fb.panTro6.chainSynPonAbe3Link.txt
-    # 2800840721 bases of 3049335806 (91.851%) in intersection
+    # 2692073497 bases of 3018592990 (89.183%) in intersection
 
     # filter with doRecipBest.pl
     time (doRecipBest.pl -load -workhorse=hgwdev -buildDir=`pwd` \
         panTro6 ponAbe3) > rbest.log 2>&1 &
-    # real    129m13.848s
+    # real    79m59.335s
 
-    cat fb.panTro6.chainRBestPonAbe3Link.txt
-    # 2640015618 bases of 3049335806 (86.577%) in intersection
+    cat fb.panTro6.chainRBest.PonAbe3.txt
+    # 2631531198 bases of 3018592990 (87.177%) in intersection
 
     # running the swap
     mkdir /hive/data/genomes/ponAbe3/bed/blastz.panTro6.swap
     cd /hive/data/genomes/ponAbe3/bed/blastz.panTro6.swap
     time (doBlastzChainNet.pl -verbose=2 \
         -swap /hive/data/genomes/panTro6/bed/lastzPonAbe3.2020-05-19/DEF \
         -chainMinScore=5000 -chainLinearGap=medium \
         -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \
         -syntenicNet) > swap.log 2>&1
-    # real    92m31.689s
+    # real    64m29.790s
 
     cat fb.ponAbe3.chainPanTro6Link.txt
-    # 2693373164 bases of 3043444524 (88.498%) in intersection
+    # 2685290576 bases of 3043444524 (88.232%) in int rsection
     cat fb.ponAbe3.chainSynPanTro6Link.txt
-    # 2679121264 bases of 3043444524 (88.029%) in intersection
+    # 2669539267 bases of 3043444524 (87.714%) in intersection
 
     time (doRecipBest.pl -load -workhorse=hgwdev -buildDir=`pwd` \
         ponAbe3 panTro6) > rbest.log 2>&1 &
-    # real    141m23.715s
+    # real    84m51.043s
 
-    cat fb.ponAbe3.chainRBestPanTro6Link.txt
-    # 2641871600 bases of 3043444524 (86.805%) in intersection
+    cat fb.ponAbe3.chainRBest.PanTro6.txt
+    # 2631453596 bases of 3043444524 (86.463%) in intersection
 
 #############################################################################