# no error but it closes on .pl run

I need to troubleshoot the pl script below.

It takes the data entry fine until the last input, but it just close after then like below.  No error are showing.  It just closes it by itself.  What would be the cause?

thx much

To enter number N of species
5
Enter the distance (2,1)
3
Enter the distance (3,1)
2
Enter the distance (3,2)
3
Enter the distance (4,1)
4
Enter the distance (4,2)
5
Enter the distance (4,3)
3
Enter the distance (5,1)
4
Enter the distance (5,2)
5
Enter the distance (5,3)
3
Enter the distance (5,4)
3

******************************** pl script *********************************
#!/usr/bin/perl -w

# D. G. M

sub inputfile

# Dated come from a file  (\$matrixfilename)

{
my(\$matfilename)=\$_[0];
my (\$i,\$j);

# Determination of the number of species

\$LINE=<MAT>;
chomp \$LINE;
@element=split / /,\$LINE;
\$n=\$#element+1;

if (\$n<3){
die "To build a phylogenetic tree, minimum 3 species are needed!\n"
}

# Initialization of the matrix of the distances

for (\$i=0;\$i<=\$n;\$i++)
{
for (\$j=0;\$j<=\$n;\$j++)
{
\$dist[\$i][\$j]=1000;
}
}

# Entry of the data

for (\$i=2;\$i<=\$n;\$i++){
\$dist[\$i][1]=\$element[\$i-1];
}

for (\$j=2;\$j<=\$n;\$j++){
\$LINE=<MAT>;
@element=split / /,\$LINE;
for (\$i=\$j+1;\$i<=\$n;\$i++){
\$dist[\$i][\$j]=\$element[\$i-1];
}
}
return @dist;
}

# ---------------------------------------------------------

sub inputmatrix

# Data entered manually

{
my (\$i,\$j);

print "To enter number N of species\n";
\$n=<STDIN>;
chop \$n;

if (\$n<3){
die "To build a phylogenetic tree, minimum 3 species are needed!\n"
}

#  Initialization of the matrix of the distances

for (\$i=0;\$i<=\$n;\$i++)
{
for (\$j=0;\$j<=\$n;\$j++)
{
\$dist[\$i][\$j]=1000;
}
}

# Entry of the data

for (\$i=2;\$i<=\$n;\$i++)
{
for (\$j=1;\$j<=\$i-1;\$j++)
{
print "Enter the distance (\$i,\$j)\n";
\$dist[\$i][\$j]=<STDIN>;
chop \$dist[\$i][\$j];
}
}

# Rem: lines \$i=0 et \$j=0 are without utility ("neutralisee")

return @dist;
}

# ---------------------------------------------------------

sub newmatrix
{
my (\$i,\$j);
mini(@dist);

print "The species are grouped \$q and \$p ";

for (\$i=2;\$i<=\$n;\$i++)
{
for (\$j=1;\$j<=\$i-1;\$j++)
{
if (\$i==\$p || \$j==\$p)
{
\$dist[\$i][\$j]=1000;
}
elsif (\$i!=\$q && \$i!=\$p && \$j!=\$q && \$j!=\$p)
{
\$dist[\$i][\$j]=\$dist[\$i][\$j];
}
elsif (\$i==\$q && \$j<\$q)
{
\$dist[\$i][\$j]=((\$clu[\$q])*\$dist[\$q][\$j]+(\$clu[\$p])*\$dist[\$p][\$j])/(\$clu[\$q]+\$clu[\$p]);
}
elsif (\$j==\$q && \$i>\$q && \$i<\$p)
{
\$dist[\$i][\$j]=((\$clu[\$q])*\$dist[\$i][\$q]+(\$clu[\$p])*\$dist[\$p][\$i])/(\$clu[\$q]+\$clu[\$p]);
}
elsif (\$j==\$q && \$i>\$p)
{
\$dist[\$i][\$j]=((\$clu[\$q])*\$dist[\$i][\$q]+(\$clu[\$p])*\$dist[\$i][\$p])/(\$clu[\$q]+\$clu[\$p]);
}
else
{
print "Bug!i=\$i,j=\$j,p=\$p,q=\$q\n";
}
}
}

\$clu[\$q]=\$clu[\$q]+\$clu[\$p];

\$clustr[\$q]=join(",","(\$clustr[\$q]","\$clustr[\$p])");
print "\nNew Tree => \$clustr[\$q]  => distance=\$min\n\n";

return @dist;
}

#---------------------------------------------------------

sub mini
{

# Determination of the distance minimum

\$min=1000;
for (\$i=2;\$i<=\$n;\$i++)
{
for (\$j=1;\$j<=\$i-1;\$j++)
{
if(\$min>\$dist[\$i][\$j])
{
\$min=\$dist[\$i][\$j];
\$p=\$i;
\$q=\$j;
}
}
}
print "The distance min is \$min  => ";
}

#----------------------------------------------------------

sub showmatrix

# Posting of the matrices

{
my (\$i,\$j,\$l);
print "\n";

for(\$l=1;\$l<=\$n;\$l++){
\$cond[\$l]=0;
\$cond[\$l]=0;
}

\$k=\$k+1;

if (\$k>1){

\$kk=\$k-1;
\$pp[\$kk]=\$p;

for(\$l=1;\$l<=\$kk;\$l++){
for (\$j=1;\$j<=\$n;\$j++){
if (\$j==\$pp[\$l]){
\$cond[\$j]=1;
}
}
}

for(\$l=1;\$l<=\$kk;\$l++){
for (\$i=1;\$i<=\$n;\$i++){
if (\$i==\$pp[\$l]){
\$cond[\$i]=1;
}
}
}
}

for (\$j=1;\$j<=\$n;\$j++){
if (\$cond[\$j]==0){
for (\$i=1;\$i<=\$n;\$i++){
if (\$cond[\$i]==0){
if (\$dist[\$i][\$j]!=1000){
printf "%10.2f",\$dist[\$i][\$j];}
else{
print "         -";
}
}
}
print "\n";
}
}

print "\n";
}

#----------------------------------------------------------

# main

my (\$i);

if (scalar @ARGV==1){
(\$matrixfilename) = \$ARGV[0];
inputfile(\$matrixfilename);
}
else{
if (scalar @ARGV==0){
inputmatrix();
}
else{
die "A number of invalid arguments!\n"
}
}

print "Matrix of distances in using method UPGMA.\n\n";

print "There is \$n species\n\n...";

\$k=0;

# Posting of the initial matrix

print "\n--------------------------------------------\n";
print "Initial matrix:";
print "\n--------------------------------------------\n";
\$p=1001;
showmatrix (@dist);

# Initialization of the clusters & the cluster_string

for (\$i=1;\$i<=\$n;\$i++)
{
\$clu[\$i]=1;
\$clustr[\$i]=\$i;
}

# Calculation and posting of the new matrices

for (\$i=1;\$i<=\$n-1;\$i++)
{
newmatrix(@dist);
print "\n--------------------------------------------\n";
print "New matrix No \$i:";
print "\n--------------------------------------------\n";
showmatrix (@dist);
}
###### Who is Participating?

Commented:
When I run it, I get

To enter number N of species
5
Enter the distance (2,1)
3
Enter the distance (3,1)
2
Enter the distance (3,2)
3
Enter the distance (4,1)
4
Enter the distance (4,2)
5
Enter the distance (4,3)
3
Enter the distance (5,1)
4
Enter the distance (5,2)
5
Enter the distance (5,3)
3
Enter the distance (5,4)
3
Matrix of distances in using method UPGMA.

There is 5 species

...
--------------------------------------------
Initial matrix:
--------------------------------------------

-      3.00      2.00      4.00      4.00
-         -      3.00      5.00      5.00
-         -         -      3.00      3.00
-         -         -         -      3.00
-         -         -         -         -

The distance min is 2  => The species are grouped 1 and 3
New Tree => (1,3)  => distance=2

--------------------------------------------
New matrix No 1:
--------------------------------------------

-      3.00      3.50      3.50
-         -      5.00      5.00
-         -         -      3.00
-         -         -         -

The distance min is 3  => The species are grouped 1 and 2
New Tree => ((1,3),2)  => distance=3

--------------------------------------------
New matrix No 2:
--------------------------------------------

-      4.00      4.00
-         -      3.00
-         -         -

The distance min is 3  => The species are grouped 4 and 5
New Tree => (4,5)  => distance=3

--------------------------------------------
New matrix No 3:
--------------------------------------------

-      4.00
-         -

The distance min is 4  => The species are grouped 1 and 4
New Tree => (((1,3),2),(4,5))  => distance=4

--------------------------------------------
New matrix No 4:
--------------------------------------------

-

What did you want to happen when you run it?
0

Commented:
I get the same output as ozo...
0

Author Commented:
that is odd..
I will try it with other inputs... again.
0

Author Commented:
yes, I got it.

thx much
0
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