Trying to create submit script to SGE - bash

Question

I'm trying to edit my working bash script to an SGE script in order to submit it as a job to the cluster.
Currently I have:
#!/bin/bash
# Perform fastqc on files in a specified directory.
for ((j=1; j <=17; j++))
do
directory=/data4/una/batch"$j"/
files=$""$directory"/*.fastq.gz"
batch=$"batch_"$j""
outfile=$""$batch"_submit_script.sh"
echo "#!/bin/bash">>$outfile;
echo "# Your job name">>$outfile;
echo "# -N $batch">>$outfile;
echo "# The job should be placed into the queue 'all.q'">>$outfile;
echo "#$ -q all.q">>$outfile;
echo "# Running in the current working directory">>$outfile;
echo "#$ -cwd">>$outfile;
echo "">>$outfile;
echo "# Export some necessary environment variables">>$outfile;
echo "#$ -S /bin/bash">>$outfile;
echo "#$ -v PATH">>$outfile;
echo "#$ -v LD_LIBRARY_PATH">>$outfile;
echo "#$ -v PYTHONPATH">>$outfile;
echo "# Finally, put your command here">>$outfile;
echo "">>$outfile;
echo "#$ for i in $files;">>$outfile;
echo "#$ do;">>$outfile;
echo "#$ fastqc -f fastq -o /data4/una/test/fastq/$i;">>$outfile;
echo "#$done">>$outfile;
echo "">>$outfile;
qsub $outfile;
done
But I'm getting an error:
Unable to read script file because of error: ERROR! invalid option argument "-f"
But
fastqc -f fastq -o /data4/una/test/fastq/$i
is a totally valid line in my bash script.
Thoughts?
Thanks!

Answer 1

It actually was poor formatting for my loop that was causing this error. I didn't need to start those lines with #$ at all, so those lines become:
echo "for i in $files;">>$outfile;
echo "do">>$outfile;
echo " fastqc -f fastq -o /data4/una/test/fastqc $i">>$outfile;
echo "done">>$outfile;
echo "">>$outfile;
qsub $outfile;