How to divide the reference sequence into batches or chunks

Question

[ddzhangzz]

I got error message "error: Reference sequence has more than 2^32-1 characters! Please divide the reference into batches or chunks of about 3.6 billion characters or less each and index each independently.":

    $ bowtie2-build -f hg19mm10.fa hg19mm10
Settings:
  Output files: "hg19mm10.*.bt2"
  Line rate: 6 (line is 64 bytes)
  Lines per side: 1 (side is 64 bytes)
  Offset rate: 4 (one in 16)
  FTable chars: 10
  Strings: unpacked
  Max bucket size: default
  Max bucket size, sqrt multiplier: default
  Max bucket size, len divisor: 4
  Difference-cover sample period: 1024
  Endianness: little
  Actual local endianness: little
  Sanity checking: disabled
  Assertions: disabled
  Random seed: 0
  Sizeofs: void*:8, int:4, long:8, size_t:8
Input files DNA, FASTA:
  hg19mm10.fa
Reading reference sizes
Error: Reference sequence has more than 2^32-1 characters!  Please divide the
reference into batches or chunks of about 3.6 billion characters or less each
and index each independently.

I am wondering how to divide the reference into batches or chunks as suggested. Does someone have this experience?

[Devon Ryan]

Use a more recent version of bowtie2, which supports large indexes.

[ddzhangzz]

Thanks, very helpful!

[GouthamAtla]

what is the main goal behind combining hg19 and mm10 ?

[ddzhangzz]

build index for human and mouse combined

[WouterDeCoster]

What about regions which are already rather similar/conserved? I don't know about your downstream application, but this sounds like a tricky approach.

[Devon Ryan]

This is a pretty standard approach for dealing with mixed samples (I assume that's what OP has).

[WouterDeCoster]

Learned something new, but I assume some ambiguity with highly conserved regions.