Hi all! I'm executing a samtools command via Perl and it gives me this diagnostic message:

samopen SAM header is present: 66338 sequences.

Now, I need to incorporate the Perl script in Galaxy, but because this diagnostic message gets interpreted as an error by Galaxy, I cannot proceed to the next command. Is there a way that I could trap the diagnostic message given by samtools in my Perl script and redirect it to STDOUT? Below is my script: 

open INP, "< $ARGV[0]"
        or die "Cannot read file: $!";

open OUT, "> $ARGV[1]"
        or die "Cannot open file: $!";

@out = `/home/applications/samtools-0.1.7a/samtools view -bS $ARGV[0]`
+;

print OUT @out;

close INP;
close OUT;

[download]

If there's something wrong with the construct of my Perl code, do please tell me, too. Thanks! Diana

In reply to Trapping diagnostic messages by Eldan Aranye

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