# HG changeset patch
# User geert-vandeweyer
# Date 1406568896 14400
# Node ID f51dd12f22637ec80f49fb519d7b220f35f36448
# Parent  6b9abfbf796a6c0a1958516004027327474c16c5
Uploaded

diff -r 6b9abfbf796a -r f51dd12f2263 run_cf0611.pl
--- a/run_cf0611.pl	Mon Jul 28 13:01:17 2014 -0400
+++ b/run_cf0611.pl	Mon Jul 28 13:34:56 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 $outdir 1 2>&1";
 print STDOUT "$cmd\n";
 system($cmd);
 
@@ -158,7 +158,7 @@
 print STDOUT $na;
 unlink("/tmp/na.stderr.$r");
 
-$cmd="java -Xmx6g -Xms4g -jar $cffile novoout.2.sam $targets $minct2 $dist $outdir 2";
+$cmd="java -Xmx6g -Xms4g -jar $cffile novoout.2.sam $targets $minct2 $dist $outdir 2 2>/dev/null";
 print STDOUT "$cmd\n";
 system($cmd);
 
@@ -192,8 +192,8 @@
 	print STDERR "No breakpoints supported by split reads.\n";
 	exit(1);
     }
-	system("${VELVET}velveth velvet_out 31 -fastq -shortPaired -separate pair1.fq pair2.fq -short single.fq > /dev/null");
-	system("${VELVET}velvetg velvet_out -cov_cutoff 3 -ins_length 300 -exp_cov 100  -ins_length_sd 60 > /dev/null");
+	system("${VELVET}velveth velvet_out 31 -fastq -shortPaired -separate pair1.fq pair2.fq -short single.fq > /dev/null 2>&1");
+	system("${VELVET}velvetg velvet_out -cov_cutoff 3 -ins_length 300 -exp_cov 100  -ins_length_sd 60 > /dev/null 2>&1");
 	# launch blat server at random unused port
 	my $port = 10000 + int(rand(5000));
 	my $status = `${BLAT}gfServer status 127.0.0.1 $port 2>&1` ;