Virtual Box problem

[Natalia_Bednarska]

Hi, I have problem with running DADA denoise command for my samples (around 100 paired-end sequences). Is this due to memory problems? When I run the command on tutorials data it all run smoothly, any clues?

Thanks!

[thermokarst]

Hi @Natalia_Bednarska!

@Natalia_Bednarska

I have problem with running DADA denoise command for my samples

What kind of problems? Can you share the following info:

• Version of QIIME 2 used
• Command(s) run (copy and paste or screenshot, please!)
• Errors observed (copy and paste or screenshot, please!).

@Natalia_Bednarska

Is this due to memory problems?

Memory errors are one of the most common issues we see, but, we can't say for sure without the information requested above - thanks!

[Natalia_Bednarska]

Hi Mat,
I use version 7 , the most recent one 1564697331.
When I run this command:
qiime dada2 denoise-paired
–i-demultiplexed-seqs demux_seqs.qza
–p-trim-left-f 0
–p-trim-left-r 0
–p-trunc-len-f 0
–p-trunc-len-r 0
–o-table table.qza
–o-representative-sequences rep-seqs.qza
–o-denoising-stats denoising-stats.qza

everything get stuck, computer makes noise and after few hours the terminal closes itself without results.

Regards
Natalia

[thermokarst]

Hi @Natalia_Bednarska - that sounds very strange! I don’t think I have heard any reports like that before. Is the terminal inside the VM closing, or is the entire VM itself closing? Do you know how much memory you have made available to your VM?

[Natalia_Bednarska]

Hi,
I tried this command on Mac and Virtual machine and it basically works in the infinity:) So it doesn’t seem to be related with VB capacity but rather the command needs values.
Another question Matthew: how could I get the OTU list in csv file, or simpler how could I get the files compatible with running this https://www.microbiomeanalyst.ca/MicrobiomeAnalyst/upload/OtuUploadView.xhtml

Thanks

[thermokarst]

@Natalia_Bednarska

So it doesn’t seem to be related with VB capacity but rather the command needs values.

Hmm, do you have a screenshot or log or something to show us what is happening?

One thing worth pointing out is your running this command with no trim/truncation --- this is usually only advisable if the reads have already been quality controlled - have they?

@Natalia_Bednarska

Another question Matthew: how could I get the OTU list in csv file, or simpler how could I get the files compatible with running this MicrobiomeAnalyst

Check out this community tutorial: Exporting and modifying BIOM tables (e.g. adding taxonomy annotations)