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\
Welcome to the forum!
The error message is due to a missing space between
--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 \
Thanks @lizgehret !
Now I'm getting another error: " Missing one or more files for SingleLanePerSamplePairedEndFastqDirFmt: '.+_.+_L[0-9][0-9][0-9]_R_001\.fastq\.gz'"
Would it be because I don't have a manifest file? If so, how do I make one?
/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.