Bowtie2: Single End Reads Reporting 100% or 0% Alignment

Question

[akm126]

I am having trouble using single end reads with Bowtie2. This pipeline has previously been used for paired end reads and works just fine. When I use the following command:

bowtie2 -x HP_bacteria -f -U singleendread.fasta -S singleendread.sam

The files are reported as aligned either 100% or 0%.

1 reads; of these:
  1 (100.00%) were unpaired; of these:
    0 (0.00%) aligned 0 times
    1 (100.00%) aligned exactly 1 time
    0 (0.00%) aligned >1 times
100.00% overall alignment rate

or

1 reads; of these:
  1 (100.00%) were unpaired; of these:
    1 (100.00%) aligned 0 times
    0 (0.00%) aligned exactly 1 time
    0 (0.00%) aligned >1 times
 0.00% overall alignment rate

Based on the previous paired reads, I would expect the files to align between 80 and 90%. Has anyone encountered this problem and know why I am getting this error? Thank you.

[swbarnes2]

The software is reporting that your input file is one read long.

[ATpoint]

Are these two reads the mates of a pair? Please be more clear. What are these two reads and what do they have to do with this 80% alignment?