Problems of importing data

[Mengyuan]

Hi,I am new to qiime2 and I want to import my faetq data using a manifest like this,

then I keep getting this error,

but my fastq data is actually in that file,

so I am so confused,and I really hope you can help me about this.
Thank you so much!

[Mehrbod_Estaki]

Hi @Mengyuan,
Not sure if this is the problem, but worth a quick check. If you are using the virtual machine image (which it looks like you are) the files you are looking for are actually just in "/media/sf_Treatment/16S_treatment/Water/Contigs/"
So, you don’t need the /home/qiime2/ bit before your path. At least that’s how it appears in my VM environment.
You can check the validity of your addresses by something simple like
ls "/media/sf_Treatment/16S_treatment/Water/Contigs/"
If you see your folder content then that’s the right path!

[Mengyuan]

@Mehrbod_Estaki ,Thanks for your help! I have checked that the path"/media/sf_Treatment/16S_treatment/Water/Contigs/"
is right ,and in my command ,the input path is also the right one like this

but in the error message, I do not know why it is changed into /home/qiime2/media......
should I change my shared file's path or change the setting of this software?

[thermokarst]

Hi @Mengyuan - I suspect you aren’t using absolute file paths in your manifest — do the entries all begin with a / character? If not, then the shell will automatically prepend your current working directory, which is why the import is adding on /home/qiime2 to the beginning of the path while trying to import. Add those / characters and you should be good to go! If you are still experiencing problems, please provide a sample of your manifest file here so that we can help diagnose the issue. Thanks!

[Mengyuan]

Thank you @thermokarst ! But I think I had added / character at all paths in manifest. Here is my manifest file:manifest.txt (14.8 KB)
Is it right?

[thermokarst]

Hi @Mengyuan - close, but not quite! The $PWD variable inserts your current working directory into the file path, which is why this isn’t working as you would expect. You should be able to update entries that look like this:

$PWD/media/sf_Treatment/16S_treatment/Water/Contigs/1A-W-Win.fastq

to look like this, instead:

/media/sf_Treatment/16S_treatment/Water/Contigs/1A-W-Win.fastq

So, just drop the leading $PWD variable, and make sure the entry starts with a /, which will ensure this is interpreted as an absolute file path. You will need to do this for all of the files (rows) in your manifest file.

Good luck!

[Mengyuan]

Hi @thermokarst ! Thank you so much , it’s work!
And these days are Spring Festival in China,we are all celebrating new year.and also wish you all the best !