dada2 demux return nothing of demux.qzv file

[1111 (yudahai)]

when I use the dada2 of qiime2 to demux single-end .fastq file, I met an unexpected results of the .qzv file. There was nothing in the windows of interactive quality plot.
The codes were used as below:
(qiime2-2023.7) [XYB@Dulab PRJNA449268] qiime tools import --type 'SampleData[SequencesWithQuality]' --input-path merge_files_PRJNA449268.tsv --output-path single-end-demux.qza --input-format SingleEndFastqManifestPhred33V2 ***Imported merge_files_PRJNA449268.tsv as SingleEndFastqManifestPhred33V2 to single-end-demux.qza*** (qiime2-2023.7) [XYB@Dulab PRJNA449268] qiime demux summarize --i-data single-end-demux.qza --o-visualization single-end-demux.qzv
Saved Visualization to: single-end-demux.qzv

single-end-demux.qzv (289.7 KB)

[colinvwood (Colin Wood)]

Hello @1111,

Do you mean that when you loaded the .qzv in the browser you only saw a blank page? What browser did you use? What happens if you put the same qzv in old-view.qiime2.org?

[1111 (yudahai)]

Thanks for your response！！I am sorry about the vague description. I mean when I load the qzv file to the new the website of qool tools view, I can't see anything in the quality of sequencing base....

[colinvwood (Colin Wood)]

Hello @1111,

But everything works as expected at old-view.qiime2.org?

[colinvwood (Colin Wood)]

Hello @1111,

It looks like this isn't a problem with the visualization, but with your sequences. They seem to not have recognized quality scores. Could you share a screenshot of a couple of the fastq sequences that you imported, and share the command that you used to import them?

[1111 (yudahai)]

Thanks a lot！ There is a screenshot of one fastq file in PRJNA449268. It seems like that
this file does not have sequencing quality information

So, could you mind tell me if I need to tissue this kind of sequencing file, then how could I import them into qiime2?

[colinvwood (Colin Wood)]

Hello @1111,

I don't believe that you posted one of the files that you imported. The ? character is a valid fastq quality character.

[1111 (yudahai)]

It was really the file imported into analysis. why all the fastq files have ? symbol in this project. It was so weird

[colinvwood (Colin Wood)]

Hello @1111,

Im not sure why those records have only ?s as quality scores. Are you sure that this file is one of the ones you imported? Because the ? character is a valid quality character that codes for the quality score 30 in your case.

[1111 (yudahai)]

I am sorry for my disappearance. I checked the downloaded files and I am sure this file is one of the ones I imported~ Since I cannot handle this issue, I finally dropped this dataset for my analysis. Thanks for your kindful help !