592233336c30a579125ef5a52bd60be145c12521
braney
  Mon Jun 1 14:29:48 2020 -0700
re-do mafGene alignments after bug fix

diff --git src/hg/makeDb/doc/dm6/multiz124way.txt src/hg/makeDb/doc/dm6/multiz124way.txt
index e65f63b..42a4724 100644
--- src/hg/makeDb/doc/dm6/multiz124way.txt
+++ src/hg/makeDb/doc/dm6/multiz124way.txt
@@ -3298,57 +3298,57 @@
     ln -s ../../consPhyloP/all/phyloP124way.bw dm6.phyloP124way.bw
 
     md5sum *.mod *.bw > md5sum.txt
 
     # obtain the README.txt from dm6/phyloP20way and update for this
     mkdir /usr/local/apache/htdocs-hgdownload/goldenPath/dm6/phyloP124way/dm6.124way.phyloP
     cd dm6.124way.phyloP
     ln -s `pwd`/* \
 /usr/local/apache/htdocs-hgdownload/goldenPath/dm6/phyloP124way/dm6.124way.phyloP
     cd ..
 
     ln -s `pwd`/*.mod `pwd`/*.bw `pwd`/*.txt \
       /usr/local/apache/htdocs-hgdownload/goldenPath/dm6/phyloP124way
 
 #############################################################################
-# hgPal downloads (DONE - 2018-11-27 - Hiram)
+# hgPal downloads (DONE - 2018-11-27 - Hiram, REDONE 2010-06-01)
 #   FASTA from 124-way for knownGene, refGene and knownCanonical
 
     ssh hgwdev
     screen -S dm6HgPal
     mkdir /hive/data/genomes/dm6/bed/multiz124way/pal
     cd /hive/data/genomes/dm6/bed/multiz124way/pal
     cat ../species.list | tr '[ ]' '[\n]' > order.list
 
     # this for loop can take hours on a high contig count assembly
     # it is just fine on human/dm6, just a few seconds
     export mz=multiz124way
     export gp=ncbiRefSeq
     export db=dm6
     export I=0
     export D=0
     mkdir exonAA exonNuc
     for C in `sort -nk2 ../../../chrom.sizes | cut -f1`
     do
         I=`echo $I | awk '{print $1+1}'`
         D=`echo $D | awk '{print $1+1}'`
         dNum=`echo $D | awk '{printf "%03d", int($1/1240)}'`
         mkdir -p exonNuc/${dNum} > /dev/null
         mkdir -p exonAA/${dNum} > /dev/null
 	echo "mafGene -chrom=$C -exons -noTrans $db $mz $gp order.list stdout | gzip -c > exonNuc/${dNum}/$C.exonNuc.fa.gz &"
 	echo "mafGene -chrom=$C -exons $db $mz $gp order.list stdout | gzip -c > exonAA/${dNum}/$C.exonAA.fa.gz &"
-        if [ $I -gt 16 ]; then
+        if [ $I -gt 32 ]; then
             echo "date"
             echo "wait"
             I=0
         fi
     done > $gp.jobs
     echo "date" >> $gp.jobs
     echo "wait" >> $gp.jobs
 
     time (sh -x ./$gp.jobs) > $gp.jobs.log 2>&1
     # real    32m22.288s
 
 
     export mz=multiz124way
     export gp=ncbiRefSeq
     time find ./exonAA -type f | grep exonAA.fa.gz | xargs zcat \