Problems with Importing Data 10/24

Hi,
I'm having trouble importing my data into qiime2. I have downloaded and updated to the latest version of Conda and qiime (2019.7). I have my data in a folder on my desktop, but terminal keeps saying it can't find the files. Then when I think it is working it says "contains a subdirectory" on the 3rd to last sample. All of the samples are ordered in the same fashion so I don't know what I'm doing wrong. Any help would be greatly appreciated.

2 Likes

Hi Adam,

You will need to do this:

  1. You need a manifest file which will be a file with columns" Sample-id, forward-absolute-path, reverse-absolute-path similar to what’s here: https://docs.qiime2.org/2019.7/tutorials/importing/

  2. The files unfortunately will have to be copied into a folder. You can try this mv command here: https://askubuntu.com/questions/633945/how-can-i-merge-multiple-directories-into-on

  3. Then your command needs to be replaced to: --input-path needs to be /Users/adam/Desktop/Sunflower…/manifest.txt

  4. The absolute file paths will be /Users/Adam/desktop/folder/forward.fastq1.fastq.gz, /Users/Adam/desktop/folder/reverse.fastq1.fastq.gz, etc. (and should be in the same ROW, not column)

  5. You can see someone with this same issue here: importing paired FASTQ file into qiime had errors. any help?

Ben

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Thanks @ben!

One minor correction:

This isn’t strictly necessary, the manifest format is flexible, files can come from many folders.

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Thanks, I moved everything into one folder because it was easier to create a file with similar absolute paths. Ben

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Hi Ben,

Thank you for your help. I moved the files into one folder, which then allowed me to successfully import my data without creating a manifest folder at all. I'm not sure how that worked out, but thank you again for your help!

2 Likes

Great!

Just make sure that these results are as expected. Check the visualization.

Ben

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