Loading data and solving No such command 'import--type' "

I'm trying to upload my data into Qiime2 and I keep getting the same error "Error: No such command 'import--type' ".
Here's my code:
% qiime tools import\

--type 'SampleData[PairedEndSequencesWithQuality]'\

--input-path /Users/dataone/knapweed-demux-16s\

--out-path /Users/dataone/knapweed-demux-16s/demux.qza

Thanks!

Hi @GioFranco,

Welcome to the :qiime2: forum!

The error message is due to a missing space between import and --type in your command - I've modified it below, so you can copy/paste this into your terminal and it should work as expected:

qiime tools import \
--type 'SampleData[PairedEndSequencesWithQuality]' \
--input-path /Users/dataone/knapweed-demux-16s \
--output-path /Users/dataone/knapweed-demux-16s/demux.qza

Cheers :lizard:

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Thanks @lizgehret !

Now I'm getting another error: " Missing one or more files for SingleLanePerSamplePairedEndFastqDirFmt: '.+_.+_L[0-9][0-9][0-9]_R[12]_001\.fastq\.gz'"

Would it be because I don't have a manifest file? If so, how do I make one?

Thanks again!

Hi @GioFranco,

Ah, if /Users/dataone/knapweed-demux-16s is a directory containing multiple fastq files then yes - you'll need a manifest file to map each of your sample IDs to their respective fastq files. You can find instructions on creating a manifest file here.

Cheers :lizard:

1 Like