21448602a1ff6c887e857f85ba4ee23da3c9ebb9 hiram Tue Oct 8 15:03:39 2019 -0700 catch up with a missing download file papAnu4.mm10.rbest.axt.gz no redmine diff --git src/hg/makeDb/doc/papAnu4/initialBuild.txt src/hg/makeDb/doc/papAnu4/initialBuild.txt index 2123516..2343eef 100644 --- src/hg/makeDb/doc/papAnu4/initialBuild.txt +++ src/hg/makeDb/doc/papAnu4/initialBuild.txt @@ -646,30 +646,42 @@ -chainMinScore=3000 -chainLinearGap=medium) > swap.log 2>&1 # real 80m51.648s cat fb.papAnu4.chainMm10Link.txt # 907806517 bases of 2937004939 (30.909%) in intersection cat fb.papAnu4.chainSynMm10Link.txt # 866781916 bases of 2937004939 (29.512%) in intersection time (doRecipBest.pl -load -workhorse=hgwdev papAnu4 mm10 \ -buildDir=`pwd` -workhorse=hgwdev) > rbest.log 2>&1 & # real 521m7.590s cat fb.papAnu4.chainRBestMm10Link.txt # 874097827 bases of 2937004939 (29.762%) in intersection + # a download file was missing (DONE - 2019-03-29 - Hiram) + cd /hive/data/genomes/papAnu4/bed/lastz.mm10/axtChain + + time netToAxt papAnu4.mm10.rbest.net.gz papAnu4.mm10.rbest.chain.gz \ + /hive/data/genomes/papAnu4/papAnu4.2bit /hive/data/genomes/mm10/mm10.2bit stdout \ + | axtSort stdin stdout \ + | gzip -c > ../axtRBestNet/papAnu4.mm10.rbest.axt.gz + + # real 10m29.580s + # user 9m16.998s + # sys 0m33.232s + ############################################################################## # Create kluster run files (DONE - 2018-01-08 - Hiram) # numerator is papAnu4 gapless bases "real" as reported by: featureBits -noRandom -noHap papAnu4 gap # 9485884 bases of 2728012961 (0.348%) in intersection # ^^^ # denominator is hg19 gapless bases as reported by: # featureBits -noRandom -noHap hg19 gap # 234344806 bases of 2861349177 (8.190%) in intersection # 1024 is threshold used for human -repMatch: calc \( 2728012961 / 2861349177 \) \* 1024 # ( 2728012961 / 2861349177 ) * 1024 = 976.282550