Hello Monks, I have some programs that check wether corresponding sites in different single line text files match or differ with respect to a 0 or N character. The program ultimately creates a single file of the same length where at any position in the text file a 0 denotes all searched files contain a 0 in that spot and an N denotes at least one file contained an N. The initial step involves the cp command and for two of my 6 programs I receive this message from my terminal screen. 


usage: cp [-R [-H | -L | -P]] [-fi | -n] [-apvX] source_file target_fi
+le
       cp [-R [-H | -L | -P]] [-fi | -n] [-apvX] source_file ... targe
+t_directory

mv: rename /Users/logancurtis-whitchurch/Dropbox/thesis_folder/consens
+us_files/files/mask.9_Afr_females_chr.23.output.txt

 to 

/Users/logancurtis-whitchurch/Dropbox/thesis_folder/consensus_files/fi
+les/mask.9_Afr_females.chr.23.txt: No such file or directory
.chr.23.txtmask.NA18505

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I am at a loss because these directories do exist and when executing the cp command in an isolated manner with just terminal it works 


#! /usr/bin/perl -w
use strict;
use warnings;
use Term::ANSIColor;

#---------------------------------------------------------------------
+----------
# What: This program will output the number of reference sites assayed
+ in all
#        individuals in a given file, for chromosome 23.
#
# This is for the subpopulation of 9 Afr females. 
#---------------------------------------------------------------------
+----------

my $usage = "get_ref_sites_9_Afr_females.pl [individual_name_list]\n";
die $usage unless @ARGV == 1; 

#---------------------------------------------------------------------
+----------

open (INDV, "<$ARGV[0]") or die "Cannot open $ARGV[0]:$!\n";
my @individuals = <INDV>;        # Define array
close(INDV);


my $chr = 23; 
my $indv_count = 0;

my ($indv, $individuals, $covered, $buf, $data, $n, $count);

while ($indv_count < 9){  #This needs to be the count of the number of
+ individuals
    
        if ($indv_count == 0) {
        
            chomp($individuals[$indv_count]);
            $indv = $individuals[$indv_count];
            $count = 0;
            
            my $file_name = "mask".".$indv".".chr.23.txt";
            
            system("cp /Users/logancurtis-whitchurch/Dropbox/thesis_fo
+lder/CompleteGenomics/all_individuals_called_sites/$file_name /Users/
+logancurtis-whitchurch/Dropbox/thesis_folder/consensus_files/files/ma
+sk.9_Afr_females_chr.$chr.output.txt");

            $indv_count++;

}
    
        else{

            system("mv /Users/logancurtis-whitchurch/Dropbox/thesis_fo
+lder/consensus_files/files/mask.9_Afr_females_chr.$chr.output.txt /Us
+ers/logancurtis-whitchurch/Dropbox/thesis_folder/consensus_files/file
+s/mask.9_Afr_females.chr.$chr.txt");
            
            chomp($individuals[$indv_count]);
            $indv = $individuals[$indv_count];
            $count = 0;
            
            my $file_name = "mask".".$indv".".chr.23.txt";
            
            open(INPUT, "/Users/logancurtis-whitchurch/Dropbox/thesis_
+folder/CompleteGenomics/all_individuals_called_sites/$file_name") or 
+die "can't open $file_name\n";
            
            open(OUT, ">/Users/logancurtis-whitchurch/Dropbox/thesis_f
+older/consensus_files/files/mask.9_Afr_females.chr.$chr.output.txt");
            
            open(MASK, "/Users/logancurtis-whitchurch/Dropbox/thesis_f
+older/consensus_files/files/mask.9_Afr_females.chr.$chr.txt") or die 
+"can't open masked file for chr $chr:$!\n";
            
            my $mask=<MASK>;
            chomp($mask);
            close(MASK); 

            while (($n = read INPUT, $data, 100000) != 0) {
                 
                my @info =  split(//, $data);
                    
                foreach my $info (@info){
        
if($info =~ "N"){
                         substr($mask,($count),1,'N');
                     }
                    $count++;
                }
                $buf .= $data;
                print "$count for $indv for chr $chr are read\n";
            }
    
            print OUT "$mask\n";
            close(INPUT);
            close(OUT);
            $count = 0;
            $indv_count++;
            $mask = "";
            $data = "";
            $n = "";
            $buf = "";
        }
    }

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In reply to cp Program Error by Anonymous Monk

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