Mercurial > repos > geert-vandeweyer > clusterfast

changeset 20:e79b771cf3a9 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded
author geert-vandeweyer
date Mon, 28 Jul 2014 16:40:44 -0400
parents f51dd12f2263
children 8a7011053512
files run_cf0611.pl
diffstat 1 files changed, 1 insertions(+), 1 deletions(-) [+]
line wrap: on
line diff
--- a/run_cf0611.pl	Mon Jul 28 13:34:56 2014 -0400
+++ b/run_cf0611.pl	Mon Jul 28 16:40:44 2014 -0400
@@ -189,7 +189,7 @@
 sub assemble {
     system("${SAMTOOLS}samtools view merged.sorted.final.temp.bam | sort -k 1,1 -k 2,2n -u | tee merged.sorted.final.unique.sam  | perl ${scriptspath}/split_for_velvet.pl pair1.fq pair2.fq single.fq");
     if(!(-s "pair1.fq")) {
-	print STDERR "No breakpoints supported by split reads.\n";
+	print STDOUT "No breakpoints supported by split reads.\n";
 	exit(1);
     }
 	system("${VELVET}velveth velvet_out 31 -fastq -shortPaired -separate pair1.fq pair2.fq -short single.fq > /dev/null 2>&1");