98bd6fb357fb3c8922e563693f299dd498d9d27f
hiram
  Sat Jul 26 00:42:45 2025 -0700
forgotten testing "head" in the size determination should not be there, no redmine

diff --git src/hg/utils/automation/doAssemblyHub.pl src/hg/utils/automation/doAssemblyHub.pl
index 7d098502636..81537342107 100755
--- src/hg/utils/automation/doAssemblyHub.pl
+++ src/hg/utils/automation/doAssemblyHub.pl
@@ -720,31 +720,31 @@
     \${asmId}_rm.run \\
     \${asmId}_assembly_structure \\
     \$asmId.2bit
 
   ln -s $assemblySource/\${asmId}_genomic.fna.gz .
   ln -s $assemblySource/\${asmId}_assembly_report.txt .
   if [ -s $assemblySource/\${asmId}_rm.out.gz ]; then
     ln -s $assemblySource/\${asmId}_rm.out.gz .
   fi
   if [ -s $assemblySource/\${asmId}_rm.run ]; then
     ln -s $assemblySource/\${asmId}_rm.run .
   fi
   if [ -d $assemblySource/\${asmId}_assembly_structure ]; then
     ln -s $assemblySource/\${asmId}_assembly_structure .
   fi
-  export asmSize=`grep -v "^#" \${asmId}_assembly_report.txt | head | cut -f9 | ave stdin | grep total | awk '{printf "%d", \$NF}'`
+  export asmSize=`grep -v "^#" \${asmId}_assembly_report.txt | cut -f9 | ave stdin | grep total | awk '{printf "%d", \$NF}'`
   export longArg=""
   if [ "\$asmSize" -gt 4294967295 ]; then
     longArg="-long"
   fi
   faToTwoBit \${longArg} \${asmId}_genomic.fna.gz \$asmId.2bit
   twoBitDup \$asmId.2bit > \$asmId.dups.txt
   if [ -s "\$asmId.dups.txt" ]; then
     printf "WARNING duplicate sequences found in \$asmId.2bit\\n" 1>&2
     cat \$asmId.dups.txt 1>&2
     awk '{print \$1}' \$asmId.dups.txt > \$asmId.remove.dups.list
     mv \${asmId}_genomic.fna.gz \${asmId}_genomic.fna.dups.gz
     faSomeRecords -exclude \${asmId}_genomic.fna.dups.gz \\
       \$asmId.remove.dups.list stdout | gzip -c > \${asmId}_genomic.fna.gz
     rm -f \$asmId.2bit
     faToTwoBit \${longArg} \${asmId}_genomic.fna.gz \$asmId.2bit