Hi,
I am trying Bfast for the first time and have some trouble with the creation of the index for the whole human genome.
I want to create the 10 indexes as shown in the Bfast paper and experience very long running times (10 to 20 hours) for each one of them. The memory consumption goes up to 33 Gb, which arise difficulties and may cause this long running time , as maybe the system is swapping memory a lot. (I have a 64 Gb memory system, but I am not the only user)
What is the typical running time for index creation on the human genome?
I understand that if memory is the issue, I might try the "-d" parameter to split the index in parts, which leads to my second question :
Does the index splitting has any performance impact on the next step of the algorithm, finding candidate alignment locations, and to what extent ?
( I suppose it has an impact , otherwise index splitting would be done by default, wouldn't it ?)
Thanks !
I am trying Bfast for the first time and have some trouble with the creation of the index for the whole human genome.
I want to create the 10 indexes as shown in the Bfast paper and experience very long running times (10 to 20 hours) for each one of them. The memory consumption goes up to 33 Gb, which arise difficulties and may cause this long running time , as maybe the system is swapping memory a lot. (I have a 64 Gb memory system, but I am not the only user)
What is the typical running time for index creation on the human genome?
I understand that if memory is the issue, I might try the "-d" parameter to split the index in parts, which leads to my second question :
Does the index splitting has any performance impact on the next step of the algorithm, finding candidate alignment locations, and to what extent ?
( I suppose it has an impact , otherwise index splitting would be done by default, wouldn't it ?)
Thanks !
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