update sra download error check and display

LANL-Bioinformatics · Dec 6, 2016 · d5f501b · d5f501b
1 parent 3e799f2
commit d5f501b
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Showing 2 changed files with 6 additions and 6 deletions.
diff --git a/runPipeline b/runPipeline
@@ -727,17 +727,16 @@ sub read_SRAD_Download_dir
     opendir(my $sra_dir_fh,$dir) or die "Cannot read $dir\n";
     my @files = sort grep {/fastq/} readdir($sra_dir_fh);
     closedir $sra_dir_fh;
-    if (!@files && !@pairedReadsFile && !@unpairedReadsFile)
+    if (`grep -i -a "Error" $dir/log.txt`){
+        &lprint("The SRA download failed.\n");
+	exit;
+    }elsif (!@files && !@pairedReadsFile && !@unpairedReadsFile)
     {
         &lprint("No fastq file from the SRA download. try again\n");
 	&Download_SRA();
+	return;
         #die "No input\n";
     }
-    if (`grep -i -a "Error" $dir/log.txt`){
-       `rm -rf $dir/*fastq*`;
-        &lprint("The SRA download failed. try again\n");
-        &Download_SRA();
-    }
     my %pair;
     if (scalar(@files)==1)
     {

diff --git a/scripts/munger/outputMunger_w_temp.pl b/scripts/munger/outputMunger_w_temp.pl
@@ -935,6 +935,7 @@ sub pull_blast {
 sub pull_sra_download {
 	my $err;
 	$err = `grep Failed $out_dir/SRA_Download/log.txt` if (-e "$out_dir/SRA_Download/log.txt");
+	$err .= `grep "ERROR" $out_dir/SRA_Download/log.txt` if (-e "$out_dir/SRA_Download/log.txt");
 	if ($err){
 		$err =~ s/(http\S+)/<a href=\"$1\"  target=\"_blank\">$1<\/a>/;
 		$vars->{SRADERR} = $err;