How long for dada2

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

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

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!

ahah no problem, I don't know too however I've a mac .. :wink:

what code?

I used this code for dada2
02

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 :
21

I don't know but I'm blocked

Thanks ! :slight_smile:

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!

2 Likes

Hello,

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 will help in this case.

Cheers,

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 !

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.

@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! :t_rex:

@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

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 :

 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!

Hi @thermokarst

I’m sorry for the response time … It’s good, it worked! But it took a monstrous time! Thank you !

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