Post Genome Assembly

Question

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I am working on Post Genome Improvement of four strains of Staphylococcus aureus. Here my job is to upgrade the contigs into scaffold of those 4 strain by removing gaps.

The Reads which I got is from Ion Torrent which gives single end. Write now I am using a tool called Enly where it gives the result without any inrement or decreament in the size of the contigs

This is the usage of Emly:

Usage: perl Enly.pl -i [fasta_file_with_contigs, FileName] -b [bases_to_detach, INT] -m [minimum bases to detach, INT] -c [maximum number of cycles, INT] -a [assembler, \"P\" = Phrap \"M\" = Minimo, CASE SENSITIVE OPTION] -r [reference_genome_fasta_file, FileName] -s [% of alignment length, INT], -d [bases to detach at every step] -p [number of cores, INT] -y [scaffold_file, FileName]

And these are the parameters:

COMPULSORY PARAMETERS:
-i    Input File Name [Your contigs file name]
-b    Bases to detach at first cycle [Recommended: a value 100/200 bp greater than the average reads length]
-m    Minimum bases to detach [Recommended: a value 100/200 bp lower than the average reads length]

OPTIONAL PARAMETERS:\n
-c     Maximum number of cycles [default is 10]
-a    Assembler ["P" Phrap or "M" Minimo, default is Phrap, CASE SENSITIVE OPTION!]
-r    Reference genome [Fasta file name]
-s    Alignment % threshold during reads mapping [default is 90]
-d    Bases to detach at every step [default is 50 bp]
-p    Number of cores [default is 4, requires MPI]
-y    Scaffold file

For example:

perl Enly.pl -i TestContigs.fna -b 10 -m 10 -c 50 -a P -r TestReferenceGenome.fna -s 90 -d 20 -p 5 -y TestScaffold

Can anyone tell me where am I going wrong. It will be a great help.

Thank u..:)