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
"why didn't the tool fail" is an unusual type of question for this site :-)
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?
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.
Thanks so much for your reply. I am sure. during running I didn't any error. I insert
trinity.timing
below: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
Are you getting something like
If not, then it should be okay. Aren't you getting something like
??
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
May be its improved, but I would suggest to post on their site. Can't afford to take chance
its here
http://sourceforge.net/projects/trinityrnaseq/