-s testing for empty file; works on local, but not on remote

[Jeri]

Hi, I've checked this, double, checked this, and triple checked this with the EXACT files. My code works completely on my local computer, but does not on my remote computer (both compile). I used several catches to identify the problem and it seems that the -s (found in the sub MuscleHMMERsearch) is not allowing the code on the remote server to proceed through the 'if' statement. The remote computer gives a false, while, my local computer gives a true. Or maybe I just need a little guidance? Please, please, please, I beg you, do not say it's my files. I tried them tried, and tried them, and came back again and tried them. I'm certain the -s in the 'if' statement is causing all my woes.

 #!/usr/bin/perl5.8.8

use strict;
use warnings;

my $familyName; #stores the family name

open (my $OUTFILE,">","FamDATA")  || die $!; #opens outfile that will 
+contain the protein families and all their associated sequences with 
+an e-value <= 0.001
print $OUTFILE "family\ttarget,e-value,bit-score"; #header for the out
+file

tempProteinFamFileCreator(); #creates a temp file with protein family 
+sends it to MUSCLE and HMMER, and  then sends table output to sub Tab
+leParse to extract necessary data (this includes the protein families
+ and all their associated sequences with an e-value <= 0, the actual 
+e-value, and the bit-score)
close ($OUTFILE); #closes the outfile

#creates a temp file with protein family sends it to MUSCLE and HMMER,
+ and  then sends table output to sub TableParse to extract necessary 
+data (this includes the protein families and all their associated seq
+uences with an e-value <= 0, the actual e-value, and the bit-score
sub tempProteinFamFileCreator 
{
my $infile = $ARGV[0]."_ProFam"; #captures the name of the infiles (Pr
+otein Family Files) as determined by the STNDIN
open (my $INFILE,"<", $infile) || die $!; #opens the infile (Protein F
+amily Files)

open (my $TEMP,">",'temp')  || die $!; #opens the temp file which will
+ store a single protein family at a time.

while(<$INFILE>) #entering the infile
{
my $line = $_; #sets the default iterator to a value

        if ($line =~/^##(UniRef90_[\w\d]+) Protein Family/)
        {
        close ($TEMP); #closes temp file
        MuscleHMMERsearch(); #enters subroutine MuscleHMMERsearch
        open ($TEMP,">",'temp'); #opens temp file
        seek ($TEMP, 0 ,0); #used to overwrite the temp file each time
+, by returning to the beginning of the file
        $familyName = $1; #storing the protein family name
        }

        if ($line =~/^>UniRef90_[\w\d]+\.UniRef100_[\w\d]+/ || $line =
+~/^[\w\d]+/)
        {
        chomp $_; #removes any remaining white space from around the d
+efault iterator
        print $TEMP "$_\n"; #prints to temp file
        }

        if ($line =~/^>File/)
        {
        close ($TEMP); #closes temp file
        MuscleHMMERsearch(); #enters subroutine MuscleHMMERsearch
        }

} #end of while loop
close ($INFILE); #closes the $INFILE handle
} #end of subroutine tempProteinFamFileCreator

#temp file (single protein family) is sent to MUSCLE, hmmbuild, hmmsea
+rch and creates a table.
sub MuscleHMMERsearch 
{

open (my $TEMP,"<",'temp')  || die $!; #opens temp file (single protei
+n family)

    if (-s "/home/vcg/Documents/Trial/temp") #checks to see if file is
+ not empty
    {
    # MUSCLE creating a multiple alignment file
    my $Fprot = "temp"; 
    my $MAF = "MuscleAlignmentFile";
    my $cmd = "/home/vcg/Documents/Trial/muscle -in $Fprot -out $MAF";
    print $cmd. "\n";
    system ($cmd);
    if ($?) {die "command $cmd failed\n"};

    # HMMER creating a profile HMM from a multiple alignment file
    my $HMMbf = "HMMbuildfile";
    $cmd = "/home/vcg/Documents/Trial/hmmbuild --informat afa $HMMbf $
+MAF";
    print $cmd. "\n";
    system ($cmd);
    if ($?) {die "command $cmd failed\n"};
    $cmd = "rm /home/vcg/Documents/Trial/$MAF";
    system ($cmd);

    # Searching the sequence database with hmmsearch
    my $results = "HMMsearch_results"; 
    $cmd = "/home/vcg/Documents/Trial/hmmsearch --F1 .002 --F2 .001 --
+F3 .00001 --tblout HMMtable.tbl --cpu 1 -E .001 $HMMbf uniref100.fast
+a  >> $results";
    print $cmd. "\n";
    system ($cmd);
    if ($?) {die "command $cmd failed\n"};
    $cmd = "rm /home/vcg/Documents/Trial/$HMMbf";
    system ($cmd);

    TableParser(); #enters subroutine TableParser
    }
} #end of subroutine MuscleHMMERsearch


#table output created in sub MuscleHMMERsearch, is parsed, and the nec
+essary data is extract and sent/appended to a resulting file. This in
+cludes the protein families and all their associated sequences with a
+n e-value <= 0, the actual e-value, and the bit-score.
sub TableParser
{

open (my $TABLE,"<","HMMtable.tbl") || die $!; #opens table ouput crea
+ted in sub MuscleHMMERsearch
print $OUTFILE "\n$familyName\t"; #prints the protein family name

while(<$TABLE>) #space delimited file\ #enters the table file
{
    if ($_=~/^#/){next;} #bypasses headers
    
    my @data = split(" ", $_); #the table file is space delimited. All
+ the data is divided by a space and stored in an array.

    if ($_=~/^UniRef100/)
    {
    my $TargetName = $data[0]; #stores target name/ sequences with e-v
+alue <= 0.001
    my $E_value = $data[4]; #stores the e-value of that sequence
    my $BitScore = $data[5]; #stores the bit-score of that sequence
    print $OUTFILE "$TargetName,$E_value,$BitScore\t"; #prints all thi
+s data to a resulting file
    }    
}
close ($TABLE); #closes $TABLE filehandle
} # end of subroutine TableParser

Thank you, thank you, thank you