BWA index error in cygwin

[stellx]

Hi,
I'm using Cygwin (32 bit) on win 7) for analysis.

Bwa index on hg19 gave me this output:

[bwt_gen] Finished constructing BWT in 695 iterations.
[bwa_index] 4644.70 seconds elapse.
[bwa_index] Update BWT... [bwt_bwtupdate_core] Failed to allocate -1157805992 by tes at bwtindex.c line 135: Cannot allocate memory

I know I have to increase memory allocation for cygwin - but can someone help me with a step by step guide as to how to? I tried searching but I couldn't figure out what to do

[GenoMax]

I found this: https://cygwin.com/cygwin-ug-net/setup-maxmem.html

Even if that works you are likely to run into problems since a 32-bit OS is not going to be enough to do bwa alignments with human data.

I suggest that you download the pre-built bwa indexes from iGenomes page (this is a large download so best not done at home): http://support.illumina.com/sequenci...e/igenome.html BWA indexes are part of a package that has bowtie indexes and annotations too.

How much memory do you have on this machine? If you have 8 GB or more it may be better to run a VM/BioLinux instead of cygwin.

[lh3]

bwa does not work with human data on 32-bit machines.

[stellx]

Hi! Thanks for your help.
I just wanted to mention - my Cygwin is 32 bit. (i read there will be packages missing when I use 64 bit cygwin, hence)
OS is 64 bit with a 20GB RAM.

Does this help?

[Brian Bushnell]

According to this thread, you should be able to build bwa on 64-bit cygwin. Though if that does not work, I am always happy to suggest BBMap, which runs in Win7 64-bit, as long as you have Java installed.