Mercurial > repos > geert-vandeweyer > clusterfast
changeset 18:6b9abfbf796a draft
Uploaded
author | geert-vandeweyer |
---|---|
date | Mon, 28 Jul 2014 13:01:17 -0400 |
parents | b9711e16f148 |
children | f51dd12f2263 |
files | run_cf0611.pl |
diffstat | 1 files changed, 9 insertions(+), 2 deletions(-) [+] |
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line diff
--- a/run_cf0611.pl Mon Jul 28 12:46:11 2014 -0400 +++ b/run_cf0611.pl Mon Jul 28 13:01:17 2014 -0400 @@ -134,7 +134,7 @@ } ## process. -$cmd="java -Xmx8g -Xms6g -jar $cffile $inbam $targets $minct1 $dist $outdir 1"; +$cmd="java -Xmx8g -Xms6g -jar $cffile $inbam $targets $minct1 $dist $outdir 1 "; print STDOUT "$cmd\n"; system($cmd); @@ -146,10 +146,17 @@ clean_up(); exit(1); } +my $r = int(rand(100)); +while (-e "/tmp/na.stderr.$r") { + $r = int(rand(100)); +} -$cmd="${NOVOALIGN}novoalign -o SAM -i 230 140 -r all -e 999 -c2 -d $novoindex -F STDFQ -f toRemap1.fq toRemap2.fq > novoout.2.sam"; +$cmd="${NOVOALIGN}novoalign -o SAM -i 230 140 -r all -e 999 -c2 -d $novoindex -F STDFQ -f toRemap1.fq toRemap2.fq > novoout.2.sam 2>/tmp/na.stderr.$r"; print STDOUT "$cmd\n"; system($cmd); +my $na = `cat /tmp/na.stderr.$r`; +print STDOUT $na; +unlink("/tmp/na.stderr.$r"); $cmd="java -Xmx6g -Xms4g -jar $cffile novoout.2.sam $targets $minct2 $dist $outdir 2"; print STDOUT "$cmd\n";