q2-galaxy file import troubles

Technical Support
1

I'm trying to operate QIIME2 on Galaxy via q2-galaxy. While running 'qiime tools import' using the manifest file option, a message is displayed:

Unexpected error importing data:
/gpfs1/data/galaxy_server/galaxy-dev/database/files/001/442/dataset_1442460.dat is not a(n) PairedEndFastqManifestPhred33V2 file:
Filepath on line 1 and column "forward-absolute-filepath" could not be found.

I have run QIIME2 previously on the command line using the same importing method and faced no issues. It would be good to know about any ideas/solutions regarding this issue.

2

Hello Debjyoti,

Welcome to the forums! :qiime2:

Here's the core of the error:

not a(n) PairedEndFastqManifestPhred33V2 file
Filepath on line 1 and column "forward-absolute-filepath" could not be found.

Looks like there's something wrong with the file. Would you like to post the file here so we could take a look?

1 Like
3

Hello Colin,

I have attached the manifest file for your consideration.

manifest_hs_t1_galaxy.txt (4.8 KB)

4

Thank you for posting that!

You file format looks good! This means the error must be in the file location:

Qiime2 has been told to import the file named 14_1_S53_R1_001.fastq.gz in the directory from which you are running this import command, but it can't find that file in that directory. Maybe this file was not uploaded successfully to Galaxy, or maybe it's in a different folder?

5

This is the same file I uploaded on Galaxy. That's why I'm not able to understand why it failed to import. Is there any specific file/folder location for Galaxy?

1 Like
6

Hey all,

I wanted to mention here that the "manifest" file formats can't really work in Galaxy as asbolute filepaths to the data don't exist in a user-viewable form. Additionally, on many Galaxy deployments, the host running the jobs is not necessarily going to have access to any of the absolute filepaths, even if they were known, as they aren't inputs to the job.

Instead, you'll want to create a Galaxy collection and have the element identifiers in the collection match the pattern of casava-1.8. This will probably happen by default because it looks like your filenames are already in the expected format. So it should be as simple as uploading your fastq as a collection and then importing the entire collection in one step.

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