Hello,
I am using Linux and I tried to index the human genome built 38 (GRCh38). I have available 62.9 GiB of RAM.
I ran the command:
`bwa index -a bwtsw `
In theory, the process should use up to 5 Gb of RAM (from http://bio-bwa.sourceforge.net/bwa.shtml:
Memory Requirement
With bwtsw algorithm, 5GB memory is required for indexing the complete human genome sequences. )
But I got this error:
... [bwt_gen] Finished constructing BWT in 10271 iterations. [bwa_index] 87812.46 seconds elapse. [bwa_index] Update BWT... [bwt_bwtupdate_core] Failed to allocate 51 074 893 080 bytes at bwtindex.c line 158: Cannot allocate memory
yet I have available 6.7E10 bytes of memory! Since the operative system uses 2 Gb to run, there should be at least 15 Gb of free memory still available for BWA. I am not the only one experiencing this issue.
Is there a an option that I forgot? A way around to reduce the memory consumption? Thank you, Luigi
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