import file from local computer

I have my files in a folder (named qiime2) on my local computer.
Inside the folder I have my emp file (also a folder) and the metadata file as tsv file.
I have these files in the emp folder (barcodes.fastq.gz, reverse.fastq.gz, and forward.fastq.gz).
I am using the Atacama tutorial for paired end reads.
I am trying to import the data from the shared folder into qiime (into a new directory that I created). I used this import script:

qiime tools import
–type EMPPairedEndSequences
–input-path emp-paired-end-sequences
–output-path emp-paired-end-sequences.qza

My own script based on the above:
qiime tools import --type 16S-emp-paired-end-sequences
–input-path 16S-emp-paired-end-sequences
–output-path emp-paired-end-sequences.qza

Qiime2 Report: 1/1) Invalid value for ‘–input-path’: Path ‘16S-emp-paired-end-sequences’
does not exist.
Note: The file name in the shared folder is “16S-emp-paired-end-sequences”.

Please, what does this mean?
Thank you for your response.

Hello @bettya,
So it looks like QIIME 2 basically can’t find the input-path that you are using.
Are you working in the same directory that has the emp-file folder?
If not an absolute path to that directory may help!
I hope this helps!
Chloe :turtle:

1 Like

Hi Chloe
Thanks for your response. I believe I should locate the folder that contains my result on the shared folder on qiime and then run the import script in order to continue the steps.
I tried to run the above script in the folder that contains the emp-file folder and it says the file is compressed. What does that mean?

(qiime2-2020.11) [email protected]:~/Desktop/shared/qiime2$ qiime tools import \

–type EMPPairedEndSequences
–input-path emp-paired-end-sequences
–output-path emp-paired-end-sequences.qza

Output: There was a problem importing emp-paired-end-sequences:

emp-paired-end-sequences/forward.fastq.gz is not a(n) FastqGzFormat file:

File is uncompressed.

This is the output. Kindly help!


Hello @bettya,
Yes! exactly you just need to show QIIME2 exactly where that directory is!

The error is saying QIIME2 is expecting a compressed file. Basically a compressed file is a file that has been shrunk down so that it doesn’t take up so much storage. So QIIME2 is saying that the files are not compressed and we will have to get them compressed in order to successfully import.

If these are your files (I think they are probably the tutorial files? ) I would suggest taking a look at this. You will have to gzip those files.

If these are from the tutorial, I am not sure what is happening, but I would maybe re-download them? I also know that the person in the link above was able to just gzip the files and was able to find success.

I hope this helps!
Chloe :turtle:

Hi Chloe
Thanks for your response
I checked the links and this is not a tutorial it’s actually my data. Also, am using a virtual box machine on windows. I can access my data on qiime2 through the shared folder.
I encounter this again:
(qiime2-2020.11) [email protected]:~/Desktop/shared$ cd qiime2
(qiime2-2020.11) [email protected]:~/Desktop/shared/qiime2$ ls
emp-paired-end-sequences sample-metadata.tsv
(qiime2-2020.11) [email protected]:~/Desktop/shared/qiime2$ cd emp-paired-end-sequences/
(qiime2-2020.11) [email protected]:~/Desktop/shared/qiime2/emp-paired-end-sequences$ ls
barcodes.fastq.gz forward.fastq.gz reverse.fastq.gz

(qiime2-2020.11) [email protected]:~/Desktop/shared/qiime2/emp-paired-end-sequences$
qiime tools import \

–type EMPPairedEndSequences
–input-path emp-paired-end-sequences
–output-path emp-paired-end-sequences.qza

Error: There was a problem with the command:
(1/1) Invalid value for ‘–input-path’: Path ‘emp-paired-end-sequences’ does
not exist.

As you can see, the file path to the emp-paired file is stated in the above and the forward and reverse files are in gz format.
Kindly help.

Hi again @bettya,
Thank you for attaching your terminal commands. I have figured out the issue ( I think :blush:). You are in the emp-paired-end-sequences directory and then you are telling QIIME2 look for the emp-paired-end-sequences directory but it can’t find it because you are already in it. So what you need to do is step out of the emp-paired-end-sequences directory and run your qiime tools import from your qiime2 directory!
Hope this helps
Chloe :turtle:

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