Lost samples after DADA2

[Vicky_Rodriguez]

I’ve been trying to analyze some sequences, when I do the part of the paired-end reads I get 139 both reverse and forward, which is the amount of samples present in my metadata. But when I look at the metrics of the.qzv table given after DADA2 only 88 appear, same as in the taxonomic and diversity analysis.
It is important to emphasize that the 88 samples that if appear are data from a MiSeq and the 51 missing ones are from a NextSeq and as for storage they are larger these last.

Do you know what could be happening?

[MARTIN_MIHULA]

Dear Vicky, can you provide us with more information? Can you put here specification of the command you ran?

[Vicky_Rodriguez]

I gladly share the screenshot of my code running. The version of qiime2 I’m using is 2020.8.

thank you

[colinbrislawn (Colin J Brislawn)]

@Vicky_Rodriguez

It is important to emphasize that the 88 samples that if appear are data from a MiSeq and the 51 missing ones are from a NextSeq and as for storage they are larger these last.

It's recommended to run DADA2 one time on each sequencing run so that DADA2 can
"learn the error rates on a run-by-run basis", then merge the tables. More discussion here!

Thank you for posting your code as well.

Have you looked into the log files being saved by these commands?
Perhaps you can post some of the logs here so we can look for more clues!