Hello I tried two command
qiime vsearch dereplicate-sequences
–o-dereplicated-sequences rep-seqs-dada2.qza \
qiime dada2 denosise-single
but these commands only generate table-dada2.qza for me, there is no rep-seqs-dada2.qza.
Coould anyone help me, find out what part of my command went wrong?
Thanks for your help
Hi @zhang_sonic! Can you please provide the following info?
- The output from running
- Are you receiving error messages for either of those commands? If so, please post the full error messages. If you’re not receiving error messages, can you confirm that the commands finished running? A screenshot of the commands you’re running and the output they produce may be helpful.
Also note: both of your commands are using the same output file paths to save results (
rep-seqs-dada2.qza). Whichever command you run last will overwrite any existing files with the new results. I recommend using different file paths to save the results from each command to avoid overwriting the files. Also note that the output filenames you’re using with
qiime vsearch dereplicate-sequences are a bit misleading; the vsearch command isn’t using DADA2 denoising, it is only dereplicating the sequences. You might consider using different filenames to better indicate what the results represent, in order to avoid mixing up your data.
Thanks for your help.
Here is where I started
then I ran this command
I ran top command and made sure it was running
Then when it was finished this is what I got
See only the table-dada2-2018.qza was generated, and there is no rep-seqs-dada2-2018.qza.
And I have no idea about where went wrong.
Thanks for the details! Can you try rerunning the DADA2 command directly, this time without using
disown? I wonder if those commands are somehow interfering with the DADA2 command you’re running.
If the command succeeds, you should see output similar to:
Saved FeatureTable[Frequency] to: table-dada2-2018.qza
Saved FeatureData[Sequence] to: rep-seqs-dada2-2018.qza
If that doesn’t work, can you please send a screenshot of the command you ran and any output it produced? Thanks!
I tried this command and let it run without doing anything else just like what you have suggested, and it worked this time. Finally. Thanks for your help.
qiime dada2 denoise-single
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