#usr/bin/perl -w
use strict;
use warnings;
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print "File split: STARTED\n";
system "/share/apps/RAMMCAP-2009-1106/qsub-scripts/qsub_fasta_split.pl -i $file_in -o read-split_$file_in -n 46";

print "File split: COMPLETED\n";

my $readsplitf = "read-split_$file_in/output.1";

print "rRNA blast: STARTED\n";
system "/share/apps/RAMMCAP-2009-1106/qsub-scripts/qsub_rRNA_hmm_run.pl -i $readsplitf -o rRNA_hmm_$file_in";
		
print "rRNA blast: FINISHED\n";

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