Manifest preparation + Error import

[cortegas (Carmen Ortega-Santos)]

Hi everyone,
I am working with a new sequencing center and I run into the problem that I never worked on a manifest document. I review the documents available on qiime and validate my manifest at keeime.

Carmen:FASTQ CarmenP$ qiime tools import --type 'SampleData[SequencesWithQuality]' --input-path manifest.txt --output-path single-end-demux.qza --input-format PairedEndFastqManifestPhred33

I get the following output
An unexpected error has occurred:

No transformation from <class 'q2_types.per_sample_sequences._format.PairedEndFastqManifestPhred33'> to <class 'q2_types.per_sample_sequences._format.SingleLanePerSampleSingleEndFastqDirFmt'>

See above for debug info.

I have three columns for my manifest: sample-id, fastq.path, and forward/reverse

The company told me that the FASTQ variant format is the default Illumina output: Phred33.

Anyone who has been running into the same problem? Any tips.
I am working from a mac using the terminal qiime2-2022.8 version

Thank you!

[SoilRotifer (Mike Robeson)]

Hi @cortegas,

I noticed that you are passing in:

--output-path single-end-demux.qza \
--type 'SampleData[SequencesWithQuality]'

while using:

--input-format PairedEndFastqManifestPhred33

Based on this, I suspect you should be using the following format instead:

--input-format SingleEndFastqManifestPhred33

if this does not work, try the V2 versions, e.g. SingleEndFastqManifestPhred33V2

For more information check out the Manifest Import documentation.