Format compatibility problems while demultiplexing

Technical Support
1

Hello everyone, I'm a complete beginner to QIIME2, so I feel like I'm missing something obvious.
I'm running the 2019.7.0 QIIME2 version and using conda.

I'm having trouble demultiplexing my files... which are quite old Roche454 pyrosequencing reads.
I have just simple single-end .fastq files as an input, which I previously imported with:

qiime tools import --type 'SampleData[SequencesWithQuality]' --input-path /home/genomica/DATA/metagenomica/Bactrocera/manifest.txt --output-path /home/genomica/DATA/metagenomica/Bactrocera/sequenze/single_end.qza --input-format SingleEndFastqManifestPhred33V2

Then, before performing denoising with dada2, I ran:

qiime demux emp-single --i-seqs /home/genomica/DATA/metagenomica/Bactrocera/sequenze/single_end.qza --m-barcodes-file /home/genomica/DATA/metagenomica/Bactrocera/metadata.tsv --m-barcodes-column barcode-sequence --output-dir /home/genomica/DATA/metagenomica/Bactrocera/sequenze_output/demux.qza

But I get this error:

(1/1) Invalid value for "--i-seqs": Expected an artifact of at least type
** RawSequences | EMPSingleEndSequences | EMPPairedEndSequences. An artifact of**
** type SampleData[SequencesWithQuality] was provided.**

I tried to specify RawSequences or EMPSingleEndSequences types while generating my artifact .qza file, but it was impossible, and I got, in both cases:

An unexpected error has occurred:

** No transformation from <class 'q2_types.per_sample_sequences._format.SingleEndFastqManifestPhred33V2'> to <class 'q2_demux._format.EMPSingleEndDirFmt'>**

See above for debug info.

I feel like I'm missing something obvious here, but the demultiplexing step doesn't seem to be available for my SampleData[SequencesWithQuality] files. Can anyone help me here?
Thanks in advance!

2

Hi @Sparkle,

Are your reads demultiplexed or not?

If they are not, you want to import with --type EMPSingleEndSequences (See the EMP importing tutorial). That’s what your error message says:

(1/1) Invalid value for “–i-seqs”: Expected an artifact of at least type
** RawSequences | EMPSingleEndSequences | EMPPairedEndSequences. An artifact of**
** type SampleData[SequencesWithQuality] was provided.**

It says you have the wrong semantic type.

Best,
Justine

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