# HG changeset patch
# User geert-vandeweyer
# Date 1406566877 14400
# Node ID 6b9abfbf796a6c0a1958516004027327474c16c5
# Parent  b9711e16f1484bd917b8954ccf96b0d363e28a0d
Uploaded

diff -r b9711e16f148 -r 6b9abfbf796a run_cf0611.pl
--- 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";