--type ERROR when trying to import files

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1

Hello,

I am continually getting this error message when I try to upload my demultiplexed forward and reverse .fastq.gz files:

$ qiime tools import \ --type 'SampleData[PairedEndSequencesWithQuality]' \ --input-path red-colobus-sequences \ --source-format CasavaOneEightSingleLanePerSampleDirFmt \ --output-path demux-paired-end.qza 
Usage: qiime tools import [OPTIONS]

Error: Missing option "--type".

I’m not sure if my files are in the correct Casava format but I have tried using the suggested file naming format. Can you offer some advice?

2

Hi @ahickmot, it looks like the slash (\) characters are causing you some issues here. In this context they are used to delimit new lines.

So you need to either include line breaks:

$ qiime tools import \
    --type 'SampleData[PairedEndSequencesWithQuality]' \
    --input-path red-colobus-sequences \
    --source-format CasavaOneEightSingleLanePerSampleDirFmt \
    --output-path demux-paired-end.qza

Or, if you would rather run this as a single line command:

$ qiime tools import --type 'SampleData[PairedEndSequencesWithQuality]' --input-path red-colobus-sequences --source-format CasavaOneEightSingleLanePerSampleDirFmt --output-path demux-paired-end.qza
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