Error with export demux.qzv from demux-paired-end.qza

[KE_XU]

I want to use this command to export demux.qzv

qiime demux summarize
–i-data demux-paired-end.qza
–o-visualization demux.qzv

However, it shows an error message said: **(1/1) Invalid value for ‘–i-data’: ‘demux-paired-end.qza’ is not a QIIME 2 Artifact (.qza)

But my demux-paired-end.qza is in current path.

Any help with it?

Thanks in advance.

[jwdebelius (Justine Debelius)]

Hi @KE_XU,

I’m glad you checked your path! I’d also use tab complete to check your spelling. (This one happens to me all the time.) If you’re confident you’re in the right place with the right name, try dropping the artifact into view.qiime2.org. That might give you a better sense about the artifact?

Best,
Justine

[KE_XU]

Thanks for replying!

When I dropped this artifact into view.qiime2.org, it shows Error: Corrupted zip or bug: unexpected signature (\x00\x00\x00\x00, expected \x50\x4B\x03\x04).

But I am not sure what happened with my qza file.
The commend lines I used to generate qza file are:
qiime tools import
–type ‘SampleData[PairedEndSequencesWithQuality]’
–input-path DATA_DEMO
–input-format CasavaOneEightSingleLanePerSampleDirFmt
–output-path demux-paired-end.qza

The files in DATA_DAMO are

, so I used the instruction for importaing data: Casava 1.8 paired-end demultiplexed fastq in tutorial.

What should I do to regenerated my qza file in correct way?

Thanks in advance!

[jwdebelius (Justine Debelius)]

Hi @KE_XU,

Okay, so good news and bad news. It probably means that your fastqs are corrupted somewhere. I find it easier to troubleshoot this with a manifest format (I find CASAVA looks easier and then is a lie). You can import your data in batches, comment out lines, and kind of use trial and error to see how things good. It’s inelegant and somewhat slow but hopeefully you can narrow down to one or two potentially bad FASTQ.

Best,
Justine

[KE_XU]

Greetings Justine,

Thanks for your help!
When following the instruction of creating manifest format file, I still encountered an error.
I tried both PairedEndFastqManifestPhred64V2 and PairedEndFastqManifestPhred33V2. But the results are same.

The manifest file I created is

I only included two paired of samples in my demo data.

Thanks,
Ke

[jwdebelius (Justine Debelius)]

Hi @KE_XU,

Try importing the data as type SampleData[PairedEndSequencesWithQuality].

Best,
Justine

[KE_XU]

Hi Justine,

Thanks for helping!

I tried --input-format PairedEndFastqManifestPhred64V2 does not work, but --input-format PairedEndFastqManifestPhred33V2 work.

It can generate demux-paired-end.qza successfully. But when I dropped demux-paired-end.qza on this website https://view.qiime2.org/, It still has the same error as shows previously.

Thanks,
Ke

[jwdebelius (Justine Debelius)]

Hi @KE_XU,

So, then, it looks like there’s an issue with one or more of the underlying files. If that’s the case, it’s best to figure out which (go through the manifest and see if you can isolate specific samples by commenting out those lines.) Then, you will need to get the original data for those samples.

Best,
Justine