e69db257480ddc4aae24ca6ae0130c9450abc362
hiram
  Mon Oct 28 14:07:47 2024 -0700
do not use /dev/shm as a temporary directory refs #34685

diff --git src/hg/utils/automation/doAugustus.pl src/hg/utils/automation/doAugustus.pl
index 38d221e..28debd6 100755
--- src/hg/utils/automation/doAugustus.pl
+++ src/hg/utils/automation/doAugustus.pl
@@ -209,31 +209,31 @@
 #       start==end  for a multiple fasta file
 #     start is 0 relative, will increment by 1 here for augustus
 #     error result will end up in augErr/directory/file.err
 
 set db = "$db"
 set start = \$1
 set end = \$2
 set fasta = \$3
 set chrName = \$fasta:r:t
 
 set resultGz = \$4
 set gtfFile = \$resultGz:t:r
 set errFile = "augErr/\$resultGz:h:t/\$gtfFile:r:t.err"
 mkdir -p \$resultGz:h
 mkdir -p \$errFile:h
-set tmpDir = "/dev/shm/\$db.\$chrName.\$start.\$end"
+set tmpDir = "/tmp/\$db.\$chrName.\$start.\$end"
 
 mkdir -p \$tmpDir
 pushd \$tmpDir
 
 if ( \$start == \$end ) then
 $augustusDir/bin/augustus --species=$species --softmasking=1 --UTR=$utr --protein=off \\
  --AUGUSTUS_CONFIG_PATH=$augustusConfig \\
   --alternatives-from-sampling=true --sample=100 --minexonintronprob=0.2 \\
    --minmeanexonintronprob=0.5 --maxtracks=3 --temperature=2 \\
     \$fasta --outfile=\$gtfFile --errfile=\$errFile:t
 else
  @ start++
 $augustusDir/bin/augustus --species=$species --softmasking=1 --UTR=$utr --protein=off \\
  --AUGUSTUS_CONFIG_PATH=$augustusConfig \\
   --alternatives-from-sampling=true --sample=100 --minexonintronprob=0.2 \\