Cannot upload files (metadata and manifest) to qiime

[Siyu_Song]

Hi everyone! I'm very new to Qiime and having difficulty uploading everything into Qiime.

I'm running Qiime through ComputeCanada, where I have successfully built Qiime2 image through Singularity (more information could be found here QIIME - CC Doc). However, whenever I tried to upload files into Qiime, either metadata file or manifest file, Qiime told me that my files cannot be found.

Here is my code:

singularity exec qiime2-2021.11.sif qiime metadata tabulate
--m-input-file /home/siyu/scratch/miseq_2/metadatatsv.tsv
--o-visualization metadata.qzv

Here is my error:

There was an issue with loading the file /home/siyu/scratch/miseq_2/metadatatsv.tsv as metadata:

Metadata file path doesn't exist, or the path points to something other than a file. Please check that the path exists, has read permissions, and points to a regular file (not a directory): /home/siyu/scratch/miseq_2/metadatatsv.tsv

There may be more errors present in the metadata file. To get a full report, sample/feature metadata files can be validated with Keemei: https://keemei.qiime2.org

Find details on QIIME 2 metadata requirements here: Metadata in QIIME 2 — QIIME 2 2021.11.0 documentation

However, the file does exist by checking using ls command, and the file has been approved by Keemei.
[siy[email protected] miseq_2]$ ls /home/siyu/scratch/miseq_2/metadatatsv.tsv

/home/siyu/scratch/miseq_2/metadatatsv.tsv

Similarly, it also happened when I upload my manifest file.
Here is my code:
singularity exec qiime2-2021.11.sif qiime tools import
--type 'SampleData[PairedEndSequencesWithQuality]'
--input-path ~/scratch/manifest
--input-format PairedEndFastqManifestPhred33V2
--output-path paired-end-demux.qza

Here is the error:
There was a problem with the command:
(1/1) Invalid value for '--input-path': Path '/home/siyu/scratch/manifest'
does not exist.

However, the file does exist by checking with ls command
[[email protected] miseq_2]$ ls /home/siyu/scratch/manifest

/home/siyu/scratch/manifest

And here is my manifest file:
manifest.tsv (18.2 KB)

I'll appreciate any comment or suggestion! Thank you so much!!

[cherman2 (Chloe Herman)]

Hi @Siyu_Song,
I am not sure what is happening with your metadatatsv.tsv. Typically this is because 1) the file isn't exactly where you think it is or 2) there is a small spelling error. So I would make sure that the file is in /home/siyu/scratch/miseq_2/ and that everything is spelled correctly. When I run into this issue I use tab autocomplete to make sure that everything is spelled correctly.

As for your manifest file:

@Siyu_Song

--input-path ~/scratch/manifest

The issue is that the file is called manifest.tsv and not manifest

Hope this helps!