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Old 04-20-2013, 01:55 AM   #1
carolW
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Default memory and cpu requirement for bwa

How much memory and CPU are required for running bwa with hg19 and a fastq file as small as the 1000 genomes ftp://ftp-trace.ncbi.nih.gov/1000gen...filt.fastq.gz?

Thanks,

Carol
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Old 04-20-2013, 04:16 AM   #2
shi
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You can find the memory use and running time for mapping a 1000Genomes dataset by a few popular aligners including bwa - http://www.ncbi.nlm.nih.gov/pubmed/23558742
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Old 04-20-2013, 06:32 AM   #3
lh3
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Bwa-0.5.x uses ~4GB RAM; 0.6.x+ uses ~5.1GB. On ~5-year-old machines, bwa aligns 100bp reads at ~7Gbp per CPU day; bwa-sw at ~3Gbp per day; the new component bwa-mem at ~14Gbp per CPU day (similar to bowtie2). On the latest Intel CPUs, they can be 50-100% faster.
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Old 04-20-2013, 08:52 AM   #4
carolW
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It seems that in the construction of bwa index, the step Construct SA from BWT and Occ... after
[BWTIncConstructFromPacked] 680 iterations done. 6177547390 characters processed.
[bwt_gen] Finished constructing BWT in 687 iterations.
[bwa_index] 2546.24 seconds elapse.
[bwa_index] Update BWT... 17.80 sec
[bwa_index] Pack forward-only FASTA... 32.21 sec

is very lengthy. What would be the acceptable amount of time for this step?

Thanks

Carol
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