FAQ: Run time

Run-time resources

• How much RAM does STAR use?
• BAM sorting runs out of memory.

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Q: How much RAM does STAR use?

STAR major memory requirements are:

• Genome + Suffix Array: *~(1+8/genomeSAsparseD)**GenomeLength bytes.
• SAindex: ~6*4^(genomeSAindexNbases) bytes. By default --genomeSAindexNbases 14 and it takes 1.5GB of RAM. If you reduce --genomeSAindexNbases to 12 you can make it <100MB.
• limitIObufferSize*NumberOfThreads for I/O buffers. By default, it's 150MB per thread, but you can probably go as low as 50MB per thread.

Q: BAM sorting runs out of memory.

At the moment, the only safe option for large file and low RAM is to output unsorted BAM with --outSAMtype BAM Unsorted and then sort it with samtools sort -@... -m... Aligned.out bam Aligned.sorted specifying number of threads and max memory per thread.