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-seq…

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?

[image] 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 h…

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 Than…

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-repre…

Hello, [image] 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 t…

Hi I haven't forgot you, I launched dada2 with verbose 6 days ago .. It's so long .. [01] 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 Moorea1…

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