9e7949fb6dd9cbb6379327b52e762cdecde5341a
hiram
  Thu Oct 7 09:47:15 2021 -0700
finish off lastz/chain/net procedure no redmine

diff --git src/hg/makeDb/doc/asmHubs/lastzRuns.txt src/hg/makeDb/doc/asmHubs/lastzRuns.txt
index df51f1b..4db359e 100644
--- src/hg/makeDb/doc/asmHubs/lastzRuns.txt
+++ src/hg/makeDb/doc/asmHubs/lastzRuns.txt
@@ -1,34 +1,40 @@
-
 ##############################################################################
-# LASTZ tardigrades GCA_001949185.1 (DONE - 2021-10-06 - Hiram)
+# LASTZ tardigrades GCA_001949185.1 (DONE - 2021-10-06 - Gerardo)
 
 # should be able to run this from anywhere, this time it was run from:
     cd kent/src/hg/utils/automation
   
-  time (/hive/data/genomes/asmHubs/allBuild/GCA/001/949/185/GCA_001949185.1_Rvar_4.0/trackData/lastzGCA_002082055.1.2021-10-06/run.sh) \
-      >> /hive/data/genomes/asmHubs/allBuild/GCA/001/949/185/GCA_001949185.1_Rvar_4.0/trackData/lastzGCA_002082055.1.2021-10-06/do.log 2>&1
+  time (~/kent/src/hg/utils/automation/pairLastz.sh \
+        GCA_001949185.1_Rvar_4.0 GCA_002082055.1_nHd_3.1 other other) \
+	   > liftOverTest.log 2>&1
+  # check the total time
+  grep -w real liftOverTest.log  | tail -1 | sed -e 's/^/    # /;'
+    # real      15m52.438s
 
-    grep -w real do.log | tail -1 | sed -e 's/^/    # /;'
-    # real    10m31.512s
+  # this liftOverTest log file happens to have a copy of the make doc, as well
+  # as the copy of the make doc left in the target assembly directory:
+# /hive/data/genomes/asmHubs/allBuild/GCA/001/949/185/GCA_001949185.1_Rvar_4.0/trackData/lastzGCA_002082055.1.2021-10-06/makeDoc.txt
 
     # this command outputs this makeDoc text:
 
     cat kent/src/hg/utils/automation/liftOverTest.log
 
 ##############################################################################
-# LASTZ tardigrades GCA_001949185.1 vs. tardigrades GCA_002082055.1 (DONE - 2021-10-06 - Hiram)
+# LASTZ tardigrades GCA_001949185.1 vs. tardigrades GCA_002082055.1
+#	(DONE - 2021-10-06 - Gerardo)
+
     mkdir /hive/data/genomes/asmHubs/allBuild/GCA/001/949/185/GCA_001949185.1_Rvar_4.0/trackData/lastzGCA_002082055.1.2021-10-06
     cd /hive/data/genomes/asmHubs/allBuild/GCA/001/949/185/GCA_001949185.1_Rvar_4.0/trackData/lastzGCA_002082055.1.2021-10-06
 
     printf '# tardigrades GCA_002082055.1 vs. tardigrades GCA_001949185.1
 BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.03/bin/lastz
 
 # TARGET: tardigrades GCA_001949185.1
 SEQ1_DIR=/hive/data/genomes/asmHubs/GCA/001/949/185/GCA_001949185.1/GCA_001949185.1.2bit
 SEQ1_LEN=/hive/data/genomes/asmHubs/GCA/001/949/185/GCA_001949185.1/GCA_001949185.1.chrom.sizes.txt
 SEQ1_CHUNK=20000000
 SEQ1_LAP=10000
 SEQ1_LIMIT=40
 
 # QUERY: tardigrades GCA_002082055.1
 SEQ2_DIR=/hive/data/genomes/asmHubs/GCA/002/082/055/GCA_002082055.1/GCA_002082055.1.2bit