Filtering with deblur

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1

qiime feature-table summarize --i-table table.qza --o-visualization table.qzv --m-sample-metadata-file F.metadata4.tsv

error: Plugin error from feature-table:

ids_to_keep must contain at least one ID., I'm certain that the sample IDs are all there in the metadata

I then ran qiime feature-table summarize --i-table table.qza --o-visualization table.qzv
and the number of samples visualised on qiime2view was 0, could be that all the samples were filtered out. the option --p was 240 (screenshot attached) Kindly assist

04%20PM

2

Hi @kedi,

It looks like you’ve got a quality control issue. At 240 bp, none of your sequences are surviving the quality filtering standards. So, my suggestion would be first, to think about trimming your sequences shorter (maybe 100 bp?) to try to keep higher quality reads. However, I’d also suggest contacting your sequencing provider or re-running your data, because these seem like very low quality reads.

Best,
Justine

3

Hi @jwdebelius

Thanks for your prompt response, tried out the 100bp and I still get empty outputs. Kindly assist

4

Hi @kedi,

I think your sequencing quality may just be too low. I encourage you to contact your sequencing provider and ask if they can re-run it for you, or to re-run it yourself.
Did you run Deblur or Dada2? What do the output logs tell you?

Best,
Justine

5

@jwdebelius
Deblur, dada2 is still running.

thanks

6

Hi @kedi,

Duh, that was in the title. I apologise for not reading well. …Have you looked at the summary after the quality filtering step?

Best,
Justine

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