Download both reads of Mycoplasma genitalium from http://www.ebi.ac.uk/ena Merge Read 1 and Read 2 using shuffleSequences_fastq.pl

perl shuffleSequences_fastq.pl ERR486827_1.fastq ERR486827_2.fastq ERR486827Merge.fastq

When trying to run SSAKE assembler the error shows up,

./SSAKE -f datafastq/sg/Myco/ERR486827Merge.fastq -p 1 -w 1 -m 20 -o 2 -r 0.7 -t 0 -c 0 -b results/sg/ssake/Myco

=>Reading sequences initiated Tue Dec  6 09:29:36 PKT 2016
Sequence reads loaded:
Input error at line #2: The sequence "CAATGATCCTGCAACATTAGTTGCCATTGTAGTTTTTAATACGCCGCCTTTATTATTTACAAAAGAAATGATCATATATTTAAATGATTATAATATTTCTTTAATACTAAAAAAATACTAAGTTATTATTTAGTTAATACTTTTAACAAT" is not in the right format for paired-end reads  -- Fatal
Make sure your input is in the form (input sequences can be of variable lengths):

>test
GCTACGACTATGACATACAGT:GTAGATTGATCGCATGCACGCT

Where : separates paired reads.  Spaces, <<.>> or any characters other than A,C,G or T in your input file might have caused this error, including reads with Ns.