Question: BWA shm index preloading: only for BWA MEM?
gravatar for Maximilian Haeussler
19 months ago by
Maximilian Haeussler1.3k wrote:

bwa shm looks very interesting, especially if you have a smallish cluster for your own use.

But unfortunately there is almost no documentation.

What I know:

  • you can do "bwa shm <indexfile>" and it will load the index into RAM. This means it will create /dev/shm/bwactl and /dev/shm/bwaidx-<indexfile>.
  • bwa shm -d deletes the files in /dev/shm, bwa shm -l lists them
  • all subsequent invocations of "bwa mem" will be almost instant.
  • for this to work, use the full pathname with bwa shm, e.g. bwa shm /my/data/dir/hg19.fa
  • for the subsequent run of bwa mem, use just the basename, e.g. bwa mem hg19.fa
  • I can't get bwa aln to work with this, apparently it doesn't support the pre-loaded index (yet?)
  • bwasw also does not seem to support a pre-loaded index

Is there a way to get aln or samse support?

Does any other operation support the pre-loaded index?

bwa hengli • 658 views
ADD COMMENTlink modified 1 day ago by Biostar ♦♦ 20 • written 19 months ago by Maximilian Haeussler1.3k

Tagging: lh3

ADD REPLYlink written 19 months ago by genomax43k
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