Dear all, I try to call mutations comparing one contig to the reference sequence using pairwise alignment. Biopython provides a perfect package which is called pairwise2 and format_alignment. When I run my script everything goes fine and it gives an output like this
ACCCCACGCCC |||||.||||| ACCCCCCGCCC Score=46
But when I submit my script to the cluster which uses the PBS system, the output seems kind of incorrect as follows.
ACCCCACGCCC ||||||||||| ACCCCCCGCCC Score=46
There are no error messages at all. And I have no idea why the output changes when I submit it to the cluster. I guess this might be a bug of the function format_alignment. It's really hard for me to find the SNP with my own eyes using a result like this.
Can anyone help me to solve this problem? Many thanks!