You were missing a few things. Here's the code as I think it should be: 
#!/usr/bin/perl 

use strict;
use warnings;
use Bio::SeqIO;

my $in  = Bio::SeqIO->new(
          -file   =>  "/root/Desktop/seqIOnew.fasta",
          -format => 'FASTA');
my $out = Bio::SeqIO->new(
          -file   => ">/root/Desktop/new_out.log",
          -format => "EMBL" );                       
while ( my $seq = $in->next_seq() ) {
        print $out->write_seq($seq), "\n";
}

[download]
For the input, I took your sequence and put it in a file called seqIOnew.fasta. I tried to get the accession number, but it returned "unknown". Printing out the $seq, you'll see that there is no accession number, so that's why it came back unknown.

For the output, I used new_out.log on my desktop.

Here's the corrected sequence: 

>gi|1786958|gb|AAC73831.1| membrane spanning protein in TolA-TolQ-TolR
+ complex [Escherichia coli str. K-12 substr. MG1655] MTDMNILDLFLKASLL
+VKLIMLILIGFSIASWAIIIQRTRILNAAAREAEAFEDKFWSGIELSRLYQESQ GKRDNLTGSEQIFY
+SGFKEFVRLHRANSHAPEAVVEGASRAMRISMNRELENLETHIPFLGTVGSISPYI GLFGTVWGIMHA
+FIALGAVKQATLQMVAPGIAEALIATAIGLFAAIPAVMAYNRLNQRVNKLELNYDNFM EEFTAILHRQ
+AFTVSESNKG

[download]
And here's the output: 

ID   unknown; SV 1; linear; ; STD; UNC; 0 BP.
XX
AC   unknown;
XX
DE   membrane spanning protein in TolA-TolQ-TolR complex [Escherichia 
+coli str.
DE   K-12 substr. MG1655]
DE   MTDMNILDLFLKASLLVKLIMLILIGFSIASWAIIIQRTRILNAAAREAEAFEDKFWSGIELSRL
+YQESQ
DE   GKRDNLTGSEQIFYSGFKEFVRLHRANSHAPEAVVEGASRAMRISMNRELENLETHIPFLGTVGS
+ISPYI
DE   GLFGTVWGIMHAFIALGAVKQATLQMVAPGIAEALIATAIGLFAAIPAVMAYNRLNQRVNKLELN
+YDNFM
DE   EEFTAILHRQAFTVSESNKG
XX
FH   Key             Location/Qualifiers
FH
XX
//

[download]

In reply to Re: A strange error message with Bio::SeqIO by Khen1950fx
in thread A strange error message with Bio::SeqIO by genbank

Title:
Use:  <p> text here (a paragraph) </p>
and:  <code> code here </code>
to format your post, it's "PerlMonks-approved HTML":


  • Posts are HTML formatted. Put <p> </p> tags around your paragraphs. Put <code> </code> tags around your code and data!
  • Titles consisting of a single word are discouraged, and in most cases are disallowed outright.
  • Read Where should I post X? if you're not absolutely sure you're posting in the right place.
  • Please read these before you post! —
  • Posts may use any of the Perl Monks Approved HTML tags:
    a, abbr, b, big, blockquote, br, caption, center, col, colgroup, dd, del, details, div, dl, dt, em, font, h1, h2, h3, h4, h5, h6, hr, i, ins, li, ol, p, pre, readmore, small, span, spoiler, strike, strong, sub, summary, sup, table, tbody, td, tfoot, th, thead, tr, tt, u, ul, wbr
  • You may need to use entities for some characters, as follows. (Exception: Within code tags, you can put the characters literally.)
            For:     Use:
    & &amp;
    < &lt;
    > &gt;
    [ &#91;
    ] &#93;
  • Link using PerlMonks shortcuts! What shortcuts can I use for linking?
  • See Writeup Formatting Tips and other pages linked from there for more info.