Data Import of Demultiplexed Files

[kac765 (Katie C)]

Hi forum!

I am trying to import demultiplexed data which is in the form of a fast.gz. I created a manifest file to import using the PairedEndFastqManifestPhred33V2[¶] QIIME import tool. This is the error message I am getting back from running the code:

There was a problem importing Manifest.tsv:

Manifest.tsv is not a(n) PairedEndFastqManifestPhred33V2 file:

Filepath on line 1 and column “forward-absolute-filepath” could not be found (/bio617_files/UNKNOWN-ca62-xx-CL-USA-xxxx-132-EC_S1_L001_R1_001.fastq.gz) for sample “sample-ca62”.

My Manifest.tsv is in the same folder as the files that I am trying to import. Does anyone have any experience with this?

[thermokarst]

Hey @kac765!

What the error message is saying is that the manifest can't find this file:

@kac765

/bio617_files/UNKNOWN-ca62-xx-CL-USA-xxxx-132-EC_S1_L001_R1_001.fastq.gz

Often that kind of issue turns up when you have a typo in the filepath - what happens when you run:

ls /bio617_files/UNKNOWN-ca62-xx-CL-USA-xxxx-132-EC_S1_L001_R1_001.fastq.gz

The command above would just run a "list" command on the offending file: we can also run

ls /bio617_files/

to get an even broader listing. Keep us posted!

[ChrisKeefe]

@kac765, just wrapping this up for posterity. As we discussed off channel today, the issue here was that /bio617_files/UNKNOWN.... is an absolute file path to a non-existent directory. bio617_files/ is actually located at ~/Desktop/bio617_files/ on the user’s computer.

Manifest imports require absolute filepaths that correctly describe file locations in order to work. See the example in the import tutorial for details.

Best,
Chris

Note: Edited for clarity 7/22/20