For this code:
my @array = ($command, $arg1, $arg2, $arg3);
system (@array);

[download]

It runs perfectly and returns the output to StandardOUT

Clover: Cis-eLement OVERrepresentation
Compiled on Jul 18 2006

Getting raw scores...
Reading background sequences...
Analyzing background sequences...
Getting motif locations...
Sequence file: D:\advanced_programming\test.fa (3 sequences, 16050 bp,
+ 55.6% C+G)
Motif file: D:\advanced_programming\motif.dat (2 motifs)


*** Over- and Under-represented Motifs:

Motif  Raw score  P-value from randomizing
                  background

*** Motif Instances with Score >= 6:

Motif  Location     Strand  Sequence  Score

Background sequence files:
  D:\advanced_programming\background.fa (2 sequences, 284279 bp, 37.3%
+ C+G)
Randomizations:         1000
P-value threshold:      0.01
Motif score threshold:  6
Randomize nucleotides   OFF
Randomize dinucleotides OFF
Randomize motifs        OFF
Lowercase filtering     OFF
Pseudocount:            0.375
Random seed:            1

[download]

This on the other hand: 

my @array = ($command, "$arg1 $arg2 $arg3");
system (@array);

[download]

Returns: 

Clover: Cis-eLement OVERrepresentation
Compiled on Jul 18 2006

Error: motif and sequence files required

Usage summary: clover [options] mymotifs myseqs.fa [BGfiles]

[download]

In reply to Re^6: System call doesn't recognise '>' by Lauras
in thread System call doesn't recognise '>' by Lauras

Title:
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