So it's quite possible that there is not enough free memory to build the index with Bowtie2's default settings. You have only ~2.5x as much memory as the size of the input file, and this is likely a shared machine where other processes may be using memory. You can attempt to reduce Bowtie2's indexing size using parameters like --packed and --offrate 7 or --offrate 8 (these latter ones will make mapping slower). Also, it's worth noting that it looks like the message you posted isn't an error. It's a message that lets you know the default parameters are inadequate, and the wrapper is trying to change the parameters to make the index building succeed on your machine. --bmax and --dcv are other parameters that affect the memory required for indexing, and so it's setting them to more conservative values.

...and why would you align to such a collection?