Very new to Bowtie2 but I'm trying to run it to align two bacterial genomes globally. Not sure which command to run, and the documentation makes it seem like this isn't possible.
I have both genomes as FASTA files. I run
bowtie2-build -f $first_fasta on the first one and then I tried running
bowtie2 -p 8 -x $db_name -f $second_fasta -S $result_file. My system has about 9 GB RAM available for the process but seems to quit because of low memory... I only need one alignment for this so I tried adding
-k 1, but that didn't seem to help either (I've also done this with and without the
-a param with the same results).
The error message is:
This application has requested the Runtime to terminate it in an unusual way. Please contact the application's support team for more information. terminate called after throwing an instance of 'std::bad_alloc' what(): std::bad_alloc (ERR): bowtie2-align exited with value 3
Perhaps there is a totally different series of parameters I'm missing? Can Bowtie2 even do these kind of global alignments?
Thanks so much in advance!
EDIT 1: I'm working on a 64-bit Windows system so I cannot use mummer, minimap2, or mugsy (or any mummer-based program for that matter).