Thread: BWA index
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Old 01-23-2010, 07:10 AM   #4
Location: baltimore

Join Date: Oct 2009
Posts: 89

how much time does it normally take to index 49 fasta format chromosomes (including 24 human chrs + other contigs), If I do the following:

$ bwa index Hsapiens37.fasta

I have been running this for last 24 hours and it is till on...

$ bwa index Hsapiens37.fasta
[bwa_index] Pack FASTA... 138.06 sec
[bwa_index] Reverse the packed sequence... 37.73 sec
[bwa_index] Construct BWT for the packed sequence...

according to BWA homepage any genome that is over 4GB is cannot be index by BWA.
the genome size I am trying to index is 5.3GB. This includes all chromosomes and other 'chrN_random' and chr6 haplotypes. All these in one file is over 5 GB. Has any one successfully tried to index these using BWA.

Last edited by adrian; 01-23-2010 at 07:33 AM.
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