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
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
Similarly, it also happened when I upload my manifest file.
Here is my code:
singularity exec qiime2-2021.11.sif qiime tools import
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
And here is my manifest file:
manifest.tsv (18.2 KB)
I'll appreciate any comment or suggestion! Thank you so much!!