Issues with importing data


I have used qiime 2 before with success when importing my data. However, I am working with a new set of data that has been sequenced at another facility that I'm not familiar with. I'm not too sure how to import this set of data.

I received the following files:
Multiple fastq.gz files: one per read (all reads are forward reads). The barcodes have been removed from those reads as per the what the facility informed me. (file names: MI.M03992_0283.001.FLD0145.GM_13-01_R1.fastq.gz, etc..)
There is also one Index File for the forward reads. (file name: M03992_0283_1_i1.fastq.gz)
I also have a metadata file that is generated by the sequencing facility. (file name: metadata_3samples.csv)

Since the files are large, I've shared a link to the files. I have put only 3 files. Link:

Can you please advice me on how to import my data into Qiime2 using which qiime tools import function?

Thank you in advance for helping me with this!

Hi @rnasrah,

Have you had a chance to look through the importing tutorial yet? Looks like you have demultiplexed single end reads so you can use the manifest import method for SingleEndFastqManifestPhred33 types.

Thanks so much @Mehrbod_Estaki.

I tried doing that but I received an error message.

Here is the output that I get:

Here is the link to the file again with the manifest file included:

Can you please guide me as to what I'm doing wrong.

Thanks so much

Hi @rnasrah,

Your error is suggesting that se-33-manifest is not a file in the current directory that your script is being run on. Can you confirm that thet file is indeed in the directory. What is the output ls in the directory you are running this scrip from?
If that’s not the issue we’ll need a bit more info to trouble-shoot. What version of qiim2 are you using, which platform is this run on…Mac, Linux, or windows (via Docker or Virtualmachine?)

Hello again,

When I put 'ls', I do see the file (see pic attached for list of files that pop up)

I'm using qiime2-2018.6. I activate qiime through my terminal window and then use Jupyter notebook to run the commands. I use my Mac computer.

Thank you in advance for your help.

Hey there @rnasrah! It looks like you reset sessions in your latest screenshot - does the import command work now? The important thing to keep in mind here is that you need to keep track of “where” your current working directory is, since all of the commands you craft and submit will need to account for “where” you are. If you are still having troubles, send a screenshot that includes an ls and a qiime tools import... in the same screenshot and notebook session. Thanks!

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Thanks so much! Yes it did work.
Thanks for your help!

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