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Old 10-01-2014, 05:17 AM   #1
mrb
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Location: iran

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Cool How come that the Trinity assembler seems to work on a computer with low memory

Hi Dear All

I have a dataset (about 60m reads paired or 120m together~ 14.5Gb each file). at the first I run trinity (latest version) on my dataset with below code on my pc with 16G Ram, 8 Core CPU :

Trinity --seqType fq --JM 10G --left reads_1.fq --right reads_2.fq --CPU 8

the run failed (because RAM deficiency).

after search I found that i have to set CPU with butterfly dependency RAM (bflyHeapSpaceMax) then i change my code as follow and the all of process were OK and trinity.fasta file was created. All of results and statistics is OK (for example mapped back reads to trinity.fasta)

Trinity --seqType fq --bflyHeapSpaceMax 4G --JM 10G --left reads_1.fq --right reads_2.fq --CPU 4

and now i am really confused. because I thought that i should to run my dataset on a server with 100G RAm and ...


I am sure. during running I had't have any error. I insert trinity.timing below:

Statistics:
===========
Trinity Version: trinityrnaseq_r20140717
Compiler: GCC
Trinity Parameters: --bflyHeapSpaceMax 4G --seqType fq --JM 10G --left /home/mrb/NGS/A-Project/Dr.Hosseinpour/Trimmed-data/forward.fq --right /home/mrb/NGS/A-Project/Dr.Hosseinpour/Trimmed-data/reverse.fq --CPU 4
Paired mode
Input data
Left.fasta 8308 MByte
Right.fasta 8302 MByte
Number of unique KMERs: 204827561
Number of reads: 0 Output data
Trinity.fasta 65 MByte

Runtime
=======
Start: Mon Sep 29 12:45:10 IRST 2014
End: Mon Sep 29 23:09:51 IRST 2014
Trinity 37481 seconds
Inchworm 1230 seconds
Chrysalis 22880 seconds
Butterfly 12326 seconds
Rest 1045 seconds

I know that CPU*bflyHeapSpaceMax must be equal your RAM or lesser.

But I dont know with decreasing bflyHeapSpaceMax, quality of my assembly is changed or not.

Now i am really confused. how it is possible with my 16G Ram PC!!!! OR really trinity is improved.

Has decreasing bflyHeapSpaceMax (10G to 4G) any effect on assembly quality or not?


so please help me about this situation. is it my results ok?????

Please guide me.

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Old 10-01-2014, 08:12 AM   #2
westerman
Rick Westerman
 
Location: Purdue University, Indiana, USA

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Quote:
Originally Posted by mrb View Post
Has decreasing bflyHeapSpaceMax (10G to 4G) any effect on assembly quality or not?
No it has no effect. Butterfly will run the same no matter how much or little memory you give it. The only difference is that, as you found out, Butterfly will crash and not complete if it does not have enough memory.
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Old 10-01-2014, 08:25 AM   #3
mrb
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Thanks for your reply.
then my results is OK?
is Trinity improved so we can run it on a PC like mine?

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Old 10-01-2014, 08:58 AM   #4
westerman
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Results ok.

As for running Trinity on a PC, it depends on what you mean by "PC" -- yours is 8-core, 16 GB RAM -- which several years ago would have qualified as 'server-class'. It also depends on the size of your data. At 60M paired reads your data is on the small side.

That said, yes Trinity has improved a lot. The old rule of thumb of 1 GB memory per 1 M reads hasn't been true in a while.
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Old 10-01-2014, 09:12 AM   #5
mrb
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Thanks again.
I thought 1 GB memory per 1 M reads yet and it confused me.

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