I have been trying to align approximately 3 million short sequences (17 - 35 nucleotide long) to a multi fasta file of prokaryotic genomes. The size of my reference fasta is about 10 GB in size. I have tried using bowtie to create the index file and the extension for the same is .ebwtl (large index).
Now, when I try to align using the command
bowtie combined -p 12 -l 17 -a -m5 --best ../seq.fastq -v 2 -S test.sam
Where, combined being the name of the index, I get an error "Could not locate a Bowtie index corresponding to basename "combined""
I have run the same using blastn option with task -short and it took me around 5 days to finish the task. I have also tried it with SHRiMP aligner, and even that throws an error.
I have many such query files and its not feasible to wait for around 5 days to obtain the result. Also, I looked into this tool called MALT and it does not have an option to align short queries, here the default evalue is 50.
Any suggestions to get bowtie working for the index I have??
PS: I used cat command to build the multi fasta reference file.