From 1f4a8662d5578ade876bce7a8a00733a5ae606ac Mon Sep 17 00:00:00 2001
From: Georgi Tushev <georgi.tushev@brain.mpg.de>
Date: Tue, 5 Feb 2019 13:08:33 +0100
Subject: [PATCH] reduce default cpus

---
 batchAlignment.pl | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/batchAlignment.pl b/batchAlignment.pl
index ac3cf8b..a35b17f 100644
--- a/batchAlignment.pl
+++ b/batchAlignment.pl
@@ -29,7 +29,7 @@
     my $sbatch_partition = "cuttlefish";
     my $sbatch_time = "100:00:00";
     my $sbatch_ntasks = 1;
-    my $sbatch_cpus = 32;
+    my $sbatch_cpus = 16;
     my $sbatch_name = "braintest";
     
     
@@ -117,7 +117,7 @@ ($$$$$)
 
     # count command
     my $file_count = $batch_job->{"path"}{"count"} . "/" . $batch_job->{"file"}{"count"};
-    $command = "featureCounts -T $cpus -t exon -g gene_id -Q 255 -a " . $file_genome_annotation . " \$(ls " . $batch_job->{"path"}{"bam"} . "/*.bam) > " . $file_count;
+    $command = "featureCounts -T $cpus -t exon -g gene_id -Q 255 -a " . $file_genome_annotation . " -o " . $file_count . " \$(ls " . $batch_job->{"path"}{"bam"} . "/*.bam)";
     print "echo featureCounts\n";
     print $command,"\n";
 }