BGI-shenzhen
Time and memory consumption
Is there any descriptions about time and memory cconsumption? It would be helpful when running the program in PBS ( Protable Batch System).
For VCF file . A Memory The memory consumed is about 10M ，and there is almost no need to consider the cost of memory。
B Speed The speed has been adjusted and optimized many times, and the version after 1.40 is very fast. The time is related to the amount of sample and the snp dataset. The more sites there are, the time increases in proportion. The more the sample amount, the more time increases. It takes about 1 day for 1000 samples of 1M sites.
Thanks for your explanation. But I got a new question as shown below
The program is killed. What causes it？
I know the reason.
too many sample : 2852900 , it will need a initialize a two-dimensional matrix (2852900 * 2852900); so this will take a big Memory. 2852900 * 2852900
I suggest using one sample for the same genotype.