Question: How come that the Trinity assembler seems to work on a computer with low memory
0
gravatar for Mohammad Reza Bakhtiarizadeh
4.9 years ago by
Tehran university

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 ...

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

Please guide me. 

Best

rna-seq next-gen assembly • 4.3k views
ADD COMMENTlink modified 4.9 years ago by rtliu2.0k • written 4.9 years ago by Mohammad Reza Bakhtiarizadeh290
1

"why didn't the tool fail" is an unusual type of question for this site  :-)

ADD REPLYlink written 4.9 years ago by Istvan Albert ♦♦ 81k

My question is:

Is it usual by a PC (16G RAM and 8 core) we could run trinity on 60M reads to de novo transcriptome assembly? like my situation.  Is my results OK? 

ADD REPLYlink written 4.9 years ago by Mohammad Reza Bakhtiarizadeh290

Are you sure that you got all succeeded and no fails, how much time did it take?

50 million reads took around 3-4 days using 4 cores and 15G memory.

  If All commands of trinity has run successfully (have a look), then I think that you have proper fasta in your output.

low RAM should just delay. 

ADD REPLYlink modified 4.9 years ago • written 4.9 years ago by Manvendra Singh2.1k

Thanks so much for your reply. I am sure. during running I didn't 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 think that new version of trinity is improved!! is it possible. I really confused. I blasted some contig and that is ok !!!!!

is it a problem????

 

Best

ADD REPLYlink written 4.9 years ago by Mohammad Reza Bakhtiarizadeh290
Are you getting something like :
 "Invalid maximum heap size: XXXXX "

if not then it should be okay.

aren't you getting something like
succeeded(10346)   28.7749% completed.
> succeeded(10347)   28.7776% completed.
> succeeded(10348)   28.7804% completed.
> succeeded(10349)   28.7832% completed.
> succeeded(10350)   28.786% completed.

??

ADD REPLYlink written 4.9 years ago by Manvendra Singh2.1k

Thanks again for your reply. for the first time that i ran trinity (with CPU 8) I get this error and trinity didnt converged and trinity.fasta didnt create.

but after I changed my code ( --bflyHeapSpaceMax  4G   --CPU 4) I didnt get any error and in Butterfly step it ran ok (All succeeded(45600) 100% completed in one step). 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.

Thanks

 

ADD REPLYlink written 4.9 years ago by Mohammad Reza Bakhtiarizadeh290

May be its improved, but I would suggest to post on their site. Cann't afford to take chance

its here

http://sourceforge.net/projects/trinityrnaseq/

 

ADD REPLYlink written 4.9 years ago by Manvendra Singh2.1k
3
gravatar for rtliu
4.9 years ago by
rtliu2.0k
New Zealand
rtliu2.0k wrote:

Your result is ok.  Over the past few years, Trinity has made huge progress in reducing the RAM requirement and speeding up the processing time by better utilizing mutiple cores of mutiple CPUs.  You may further check N50 of Trinity.fasta with the following command:

$TRINITY_HOME/util/TrinityStats.pl trinity_out_dir/Trinity.fasta

I will be happy if N50 = 1000bp ~ 2000bp.

 

 

 

ADD COMMENTlink written 4.9 years ago by rtliu2.0k

Really thanks for your reply.

At the first after finishing the analysis I checked it. N50 is ~ 1600 bp and range of contig length is 201 - 7500 bp.

I already said all of things is OK. but i didn't know trinity is improved as we can run it on a PC like mine. That is really interesting.

Up to now I graved my project because I doubt on results. So can I continue with this results?

Best

ADD REPLYlink modified 4.9 years ago • written 4.9 years ago by Mohammad Reza Bakhtiarizadeh290

another question:

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

Thanks so much

ADD REPLYlink written 4.9 years ago by Mohammad Reza Bakhtiarizadeh290

No.  10G was used for very few extremely complex components.

ADD REPLYlink written 4.9 years ago by rtliu2.0k
0
gravatar for Istvan Albert
4.9 years ago by
Istvan Albert ♦♦ 81k
University Park, USA
Istvan Albert ♦♦ 81k wrote:

If that data is consistent you can get very good assemblies in general. I have assembled bacterial genomes on a MacBook Air during a lecture. But then the reads were generated artificially with very even coverage and low errors. 

So in all I would say that if the tool finished running with no errors and the results seem sensible then you should be fine.

ADD COMMENTlink written 4.9 years ago by Istvan Albert ♦♦ 81k
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