8d6e4bf13ec2765165ac377b74c8f904fd672cb0 gperez2 Tue Jan 18 10:04:37 2022 -0800 dog GCF_014441545.1 vs. Dog CanFam3 lastz/chain/net run for user, refs #28757 diff --git src/hg/makeDb/doc/asmHubs/lastzRuns.txt src/hg/makeDb/doc/asmHubs/lastzRuns.txt index 1a1c5e0..5ca1574 100644 --- src/hg/makeDb/doc/asmHubs/lastzRuns.txt +++ src/hg/makeDb/doc/asmHubs/lastzRuns.txt @@ -1363,16 +1363,121 @@ -query2bit="/hive/data/genomes/asmHubs/GCF/002/742/125/GCF_002742125.1/GCF_002742125.1.2bit" \ -querySizes="/hive/data/genomes/asmHubs/GCF/002/742/125/GCF_002742125.1/GCF_002742125.1.chrom.sizes.txt" \ \ mm39 GCF_002742125.1) > rbest.log 2>&1 grep -w real rbest.log | sed -e 's/^/ # /;' # real 326m52.826s sed -e 's/^/ # /;' fb.mm39.chainRBest.GCF_002742125.1.txt # 660752248 bases of 2728222451 (24.219%) in intersection real 1011m49.661s user 0m1.668s sys 0m1.378s +############################################################################## +# LASTZ dog GCF_014441545.1 vs. Dog CanFam3 (DONE - 2022-01-13 -Gerardo) + +# should be able to run this from anywhere, this time it was run from: + cd kent/src/hg/utils/automation + + time (~/kent/src/hg/utils/automation/pairLastz.sh \ + GCF_014441545.1_ROS_Cfam_1.0 canFam3 mammal mammal) \ + > GCF014441545_canFam3_20220113.log 2>&1 & + # check the total time +grep -w real GCF014441545_canFam3_20220113.log | tail -1 | sed -e 's/^/ # /;' + # real 758m9.174s + + # this GCF014441545_canFam3_20220113.log log file happens to have a copy of the make doc, as well + # as the copy of the make doc left in the dog GCF_014441545.1 assembly directory: +# /hive/data/genomes/asmHubs/allBuild/GCF/014/441/545/GCF_014441545.1_ROS_Cfam_1.0/trackData/lastzCanFam3.2022-01-13/makeDoc.txt + + # this command outputs this makeDoc text: + + cat kent/src/hg/utils/automation/GCF014441545_canFam3_20220113.log + +############################################################################## +# LASTZ dog GCF_014441545.1 vs. Dog CanFam3 +# (DONE - 2022-01-13 - Gerardo) + + mkdir /hive/data/genomes/asmHubs/allBuild/GCF/014/441/545/GCF_014441545.1_ROS_Cfam_1.0/trackData/lastzCanFam3.2022-01-13 + cd /hive/data/genomes/asmHubs/allBuild/GCF/014/441/545/GCF_014441545.1_ROS_Cfam_1.0/trackData/lastzCanFam3.2022-01-13 + + printf '# Dog CanFam3 vs. dog GCF_014441545.1 +BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.03/bin/lastz + +# TARGET: dog GCF_014441545.1 +SEQ1_DIR=/hive/data/genomes/asmHubs/GCF/014/441/545/GCF_014441545.1/GCF_014441545.1.2bit +SEQ1_LEN=/hive/data/genomes/asmHubs/GCF/014/441/545/GCF_014441545.1/GCF_014441545.1.chrom.sizes.txt +SEQ1_CHUNK=20000000 +SEQ1_LAP=10000 +SEQ1_LIMIT=40 + +# QUERY: Dog CanFam3 +SEQ2_DIR=/hive/data/genomes/canFam3/canFam3.2bit +SEQ2_LEN=/hive/data/genomes/canFam3/chrom.sizes +SEQ2_CHUNK=20000000 +SEQ2_LAP=0 +SEQ2_LIMIT=100 + +BASE=/hive/data/genomes/asmHubs/allBuild/GCF/014/441/545/GCF_014441545.1_ROS_Cfam_1.0/trackData/lastzCanFam3.2022-01-13 +TMPDIR=/dev/shm + +' > DEF + + time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -verbose=2 `pwd`/DEF -syntenicNet \ + -tAsmId GCF_014441545.1_ROS_Cfam_1.0 -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \ + -chainMinScore=3000 -chainLinearGap=medium) > do.log 2>&1 + grep -w real do.log | sed -e 's/^/ # /;' + # real 436m5.199s + + sed -e 's/^/ # /;' fb.GCF_014441545.1.chainCanFam3Link.txt + # 2352312522 bases of 2396858295 (98.141%) in intersection + sed -e 's/^/ # /;' fb.GCF_014441545.1.chainSynCanFam3Link.txt + # 2343016231 bases of 2396858295 (97.754%) in intersection + + time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \ + -target2Bit="/hive/data/genomes/asmHubs/GCF/014/441/545/GCF_014441545.1/GCF_014441545.1.2bit" \ +-targetSizes="/hive/data/genomes/asmHubs/GCF/014/441/545/GCF_014441545.1/GCF_014441545.1.chrom.sizes.txt" \ + \ + GCF_014441545.1 canFam3) > rbest.log 2>&1 + + grep -w real rbest.log | sed -e 's/^/ # /;' + # real 70m5.098s + + sed -e 's/^/ # /;' fb.GCF_014441545.1.chainRBest.CanFam3.txt + # 2305842969 bases of 2396858295 (96.203%) in intersection + + ### and for the swap + + cd /hive/data/genomes/canFam3/bed/blastz.GCF_014441545.1.swap + + time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -swap -verbose=2 \ + -tAsmId GCF_014441545.1_ROS_Cfam_1.0 /hive/data/genomes/asmHubs/allBuild/GCF/014/441/545/GCF_014441545.1_ROS_Cfam_1.0/trackData/lastzCanFam3.2022-01-13/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 185m43.935s + + sed -e 's/^/ # /;' fb.canFam3.chainGCF_014441545.1Link.txt + # 2355576959 bases of 2410976875 (97.702%) in intersection + sed -e 's/^/ # /;' fb.canFam3.chainSynGCF_014441545.1Link.txt + # 2335796753 bases of 2410976875 (96.882%) in intersection +\ time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \ + -query2bit="/hive/data/genomes/asmHubs/GCF/014/441/545/GCF_014441545.1/GCF_014441545.1.2bit" \ +-querySizes="/hive/data/genomes/asmHubs/GCF/014/441/545/GCF_014441545.1/GCF_014441545.1.chrom.sizes.txt" \ + \ + canFam3 GCF_014441545.1) > rbest.log 2>&1 + + grep -w real rbest.log | sed -e 's/^/ # /;' + # real 66m14.435s + + sed -e 's/^/ # /;' fb.canFam3.chainRBest.GCF_014441545.1.txt + # 2307013600 bases of 2410976875 (95.688%) in intersection + +############################################################################## +real 758m9.174s +user 0m1.449s +sys 0m1.346s