Creating Multiple Indexes in Bowtie

[niteesh.prasad]

Hi! I am trying to build indexes for all the 1200 .fna files I have using Bowtie, but it gives the "Argument list is too long" error. Following is the code I am using:

$ for i in {1..1250};
do ./bowtie-build Project/genomes/*.fna ../bowtie-0.12.7/indexes/test$i;
done;

I'd greatly appreciate any help with this! Thank you!