I'm fairly new to next gen sequencing data analysis and am having some issues with Bowtie2 alignment. It was working fine up until a little while ago but has been giving the following error recently:
(ERR): bowtie2-align exited with value 1. I get this error if I run my bowtie2 command:
$ bowtie2 -x /path/to/genome -U /path/to/fastq |samtools view -bhS - | samtools sort - aligned_file
(followed by an Abort! )and also when I just run bowtie2 (
$ bowtie2) without any parameters. Because of the latter, I thought this was an installation problem, so I re-installed the program, but it still gives me the same error. Any thoughts on what the problem is and how to fix it?