Hi Chloe Thanks for your response. I used both 'p-rev-comp-barcodes' and 'p-rev-comp-mapping-barcodes' and it worked. The command: qiime demux emp-paired \ --m-barcodes-file sample-metadata.tsv --m-barcodes-column BarcodeSequence --p-rev-comp-barcodes --p-rev-comp-mapping-barcodes --p-no…

Hi Chloe These are my plots and table summaries from the demux.qzv: [image] [image] [image] [image] The region is V4, the primers are 515/806. I have reads that comprises of 12 samples (12 forwards and 12 reverse) and no sample must be lost due to the type of analysis. Samples were run in…

Hello @bettya , Thank you for all the information Unfortunately I am not sure what your error is to be honest. Could you less /tmp/qiime2-q2cli-err-mk4sd79d.log and send me a screenshot of the result so that I can better understand the error? Or you could run the same command with the --verbose…

Hey @bettya , I think your issue is actually lack of memory. If DADA2 throws a -9 error code it means that DADA2 was not able to complete the command with the amount of memory given. So I would run this command on a computer that has more memory. I hope this helps! Chloe :turtle:

Hi Chloe It did work, thanks. Can I ask on what basis do I have to cut part of my sample sequence during diversity analysis? Why do I have to apply the sampling depth to my sequence? I do not understand why. Can you please explain? Regards.

Hello @bettya , I am not sure that I fully understand your question.I think you asking why you need a sampling depth and why it is worth it to throw out some samples and reads to accommodate the sampling depth? So the short and sweet answer is that we can't investigate samples at different sampling…

Thank you Chloe for your assistance. I did get the explanation very well. I used 3 levels of sampling depth and I am considering using the smallest in order to retain all the samples. I believe I will get more clarity if am able to plot the rearefaction curve but meanwhile I was given this error wh…

The error log: (qiime2-2020.11) qiime2@qiime2core2020-11:~/Desktop/shared/qiime2$ qiime diversity alpha-group-significance \ --i-alpha-diversity core-metrics-results/faith_pd_vector.qza --m-metadata-file sample-metadata.tsv --o-visualization core-metrics-results/faith-pd-group-significance.qz…

Hello @bettya , I am very sorry for my late response. So the issue that I see is that the Metadata does not have a categorical data for it to group your samples into and compare with alpha group significance. Alpha group significance compares categorical groups from your metadata and investigates …

Hi Cherman2 Thanks for your reply. I have been battling with the metadata file. First, I mistakingly opened it with the wrong app, I later changed it back to open with notepad. Now, I want to run the associations between categorical metadata columns and alpha diversity data. I ran this command: …

Hi @bettya , In case this issue hasn't been resolved yet, this is the line you want to pay attention to: [image] bettya: Metadata file path doesn’t exist, or the path points to something other than a file. Please check that the path exists, has read permissions, and points to a regular file (n…

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2021: An error was encountered while running DADA2 in R (return code -9)

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