# How long for dada2
**URL:** https://forum.qiime2.org/t/how-long-for-dada2/2953
**Category:** User Support
**Tags:** dada2, deblur
**Created:** [February 9, 2018, 8:28am UTC](https://forum.qiime2.org/t/how-long-for-dada2/2953 "2018-02-09T08:28:13Z")
**Posts on this page:** 15
**Page:** 1
### Author:  [@chacha](https://forum.qiime2.org/u/chacha)
#### Post date: [February 9, 2018, 8:28am UTC](https://forum.qiime2.org/t/how-long-for-dada2/2953/1 "2018-02-09T08:28:13Z")
Hi,
It's my first analysis!
I launched my dada2 on 2 samples (in paired end) 3 days ago but nothing is happening, is it normal ?
(qiime2-2017.12) AirdeCharlotte:qiime2\_1:2 cha$ qiime dada2 denoise-paired \
> --i-demultiplexed-seqs demux.qza
> --o-table table
> --o-representative-sequences rep-seqs
> --p-trim-left-f 6
> --p-trim-left-r 6
> --p-trunc-len-f 250
> --p-trunc-len-r 230
---
### Author:  [@Micro\_Biologist](https://forum.qiime2.org/u/Micro_Biologist)
#### Post date: [February 9, 2018, 8:53am UTC](https://forum.qiime2.org/t/how-long-for-dada2/2953/2 "2018-02-09T08:53:20Z")
How are you running QIIME2? Linux? Mac? Virtual box?
Check to see if the CPU is being utilized.
If its the linux or VB then opening a new terminal and typing 'top' will show cpu usage.
Also running dada2 with more threads will speed things up.
How many reads do you have in total?
---
### Author:  [@chacha](https://forum.qiime2.org/u/chacha)
#### Post date: [February 9, 2018, 9:14am UTC](https://forum.qiime2.org/t/how-long-for-dada2/2953/3 "2018-02-09T09:14:47Z")
> [@Micro\_Biologist](#):
>
> How are you running QIIME2? Linux? Mac? Virtual box?
>
> Check to see if the CPU is being utilized.
>
> If its the linux or VB then opening a new terminal and typing ‘top’ will show cpu usage.
>
> Also running dada2 with more threads will speed things up.
>
> How many reads do you have in total?
I use a terminal of mac !
It's my screen of the CPU, I don't know how to see just running programs
That, it's my samples
---
### Author:  [@Micro\_Biologist](https://forum.qiime2.org/u/Micro_Biologist)
#### Post date: [February 9, 2018, 9:47am UTC](https://forum.qiime2.org/t/how-long-for-dada2/2953/4 "2018-02-09T09:47:48Z")
Okay, to be brutally honest I have no idea if your cpu is doing work or not! (Not a macOS guy!)
Hopefully, someone else will come along who does know soon!
Can you copy the code you ran in the terminal exactly please. If you put 4 spaces in front it will format it nicely!
---
### Author:  [@chacha](https://forum.qiime2.org/u/chacha)
#### Post date: [February 9, 2018, 10:08am UTC](https://forum.qiime2.org/t/how-long-for-dada2/2953/5 "2018-02-09T10:08:18Z")
ahah no problem, I don't know too however I've a mac .. 😉
what code?
I used this code for dada2
For CPU, I opened a new terminal et ran "top"
I think, it's a problem with my samples (or with me) because when I used deblur, I have this error :
I don't know but I'm blocked
Thanks ! 🙂
---
### Author:  [@Micro\_Biologist](https://forum.qiime2.org/u/Micro_Biologist)
#### Post date: [February 9, 2018, 10:55am UTC](https://forum.qiime2.org/t/how-long-for-dada2/2953/6 "2018-02-09T10:55:07Z")
Okay well I imagine those samples would run in a day if everything is set up correctly.
Try running:
```
qiime dada2 denoise-paired \
--i-demultiplexed-seqs demux.qza \
--p-trunc-len-f 250 \
--p-trunc-len-r 230 \
--p-trim-left-f 6 \
--p-trim-left-r 6 \
--p-n-threads 0 \
--o-table table.qza \
--o-representative-sequences repseqs.qza \
--verbose
```
That will run the program using all available threads, so should run faster due to the --p-n-threads, it will also output more information to the terminal due to --verbose.
Hopefully your mac should start making some noise because all the cores should be going flat out!
EDIT: if no errors are spat out and the cpu is working then its a waiting game!
---
### Author:  [@antgonza](https://forum.qiime2.org/u/antgonza)
#### Post date: [February 9, 2018, 5:04pm UTC](https://forum.qiime2.org/t/how-long-for-dada2/2953/8 "2018-02-09T17:04:06Z")
Hello,
> [@chacha](#):
>
> I think, it’s a problem with my samples (or with me) because when I used deblur, I have this error :
>
> I don’t know but I’m blocked
Just for completeness, that error means that you have duplicated sample IDs and you need to make sure that they are unique. Perhaps [this thread](https://forum.qiime2.org/t/deblur-problem-duplicate-sample-ids-error/1213/11) will help in this case.
Cheers,
---
### Author:  [@chacha](https://forum.qiime2.org/u/chacha)
#### Post date: [February 15, 2018, 9:46am UTC](https://forum.qiime2.org/t/how-long-for-dada2/2953/12 "2018-02-15T09:46:31Z")
Hi
I haven't forgot you, I launched dada2 with verbose 6 days ago .. It's so long ..
Do you think if it's okay ? @Micro_Biologist
@antgonza No I Havent' duplicated sample Ids, It's strange, I checked !
I don't know why there is this error !
---
### Author:  [@Micro\_Biologist](https://forum.qiime2.org/u/Micro_Biologist)
#### Post date: [February 15, 2018, 10:52am UTC](https://forum.qiime2.org/t/how-long-for-dada2/2953/13 "2018-02-15T10:52:03Z")
Its certainly a long time but I wold just keep it running.
Removing chimeras is the last step!
Also I just realized I misread how many reads you have, that length of time seems reasonable assuming you're running it on slightly better than average consumer hardware.
---
### Author:  [@thermokarst](https://forum.qiime2.org/u/thermokarst)
#### Post date: [February 15, 2018, 12:52pm UTC](https://forum.qiime2.org/t/how-long-for-dada2/2953/14 "2018-02-15T12:52:20Z")
@chacha, would you be able to share a `demux summarize` visualization of your demultiplexed seqs here? This would give us something to look at while your dada2 process is churning away. Thanks! 🦖
---
### Author:  [@chacha](https://forum.qiime2.org/u/chacha)
#### Post date: [February 15, 2018, 1:44pm UTC](https://forum.qiime2.org/t/how-long-for-dada2/2953/15 "2018-02-15T13:44:37Z")
@Micro_Biologist, @thermokarst
Yes I have a lot of sequences ..
Sample name
Moorea16\_014 1307810
Moorea16\_011 1139251
Moorea16\_020 1010859
Moorea16\_017 943940
Moorea16\_004 919488
Moorea16\_003 903490
Moorea16\_015 896683
Moorea16\_022 889943
Moorea16\_002 877999
Moorea16\_023 874661
Moorea16\_005 859326
Moorea16\_016 824884
Moorea16\_009 813756
Moorea16\_001 775834
Moorea16\_007 759708
Moorea16\_010 734264
Moorea16\_021 675993
Moorea16\_013 667898
Moorea16\_006 645418
Moorea16\_012 574527
Moorea16\_008 573040
Moorea16\_018 436695
---
### Author:  [@thermokarst](https://forum.qiime2.org/u/thermokarst)
#### Post date: [February 16, 2018, 12:56pm UTC](https://forum.qiime2.org/t/how-long-for-dada2/2953/17 "2018-02-16T12:56:39Z")
Hi @chacha --- it is a bit hard using the screenshot for this, so my estimates might be a bit off, but looking at your data, I would personally consider the following :
```bash
qiime dada2 denoise-paired \
--i-demultiplexed-seqs demux.qza \
--p-trunc-len-f 230 \
--p-trunc-len-r 215 \
--p-trim-left-f 6 \
--p-trim-left-r 6 \
--p-n-threads 0 \
--o-table table.qza \
--o-representative-sequences repseqs.qza
```
I wouldn't cancel your existing denoise command, but maybe consider experimenting with slightly more stringent truncation values, I think you will see a noteworthy decrease in time. Keep us posted!
---
### Author:  [@chacha](https://forum.qiime2.org/u/chacha)
#### Post date: [March 12, 2018, 1:34pm UTC](https://forum.qiime2.org/t/how-long-for-dada2/2953/19 "2018-03-12T13:34:46Z")
Hi @thermokarst
I'm sorry for the response time ... It's good, it worked! But it took a monstrous time! Thank you !
---
### Author:  [@ebolyen](https://forum.qiime2.org/u/ebolyen)
#### Post date: [March 29, 2018, 3:19pm UTC](https://forum.qiime2.org/t/how-long-for-dada2/2953/20 "2018-03-29T15:19:52Z")
An off-topic reply has been split into a new topic: [Deblur host parameters](https://forum.qiime2.org/t/deblur-host-parameters/3596)
Please keep replies on-topic in the future.
---
### Author:  [@system](https://forum.qiime2.org/u/system)
#### Post date: [April 29, 2018, 9:19pm UTC](https://forum.qiime2.org/t/how-long-for-dada2/2953/21 "2018-04-29T21:19:55Z")
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