Importing data - Manifest errors - absolute-file path not found

[xicesam]

Hello,

I have gone through every forum that have already had similar issues, but nothing has worked. I believe my issue stems from the file path being wrong somewhere. I am using qiime2-2022.11 through Ubuntu on a Windows PC through Linux.

When I run qiime tools import
--type 'SampleData[SequencesWithQuality]'
--input-path FINAL_Manifest_File.txt
--output-path single-end-demux.qza
--input-format SingleEndFastqManifestPhred33V2

I receive these errors:

FINAL_Manifest_File.txt is not a(n) SingleEndFastqManifestPhred33V2 file:
Filepath on line 1 and column "absolute-filepath" could not be found (/Rats/QIIME2/Rats/Fastq/1EurasianBeaver.R1.RUN1.L1.fastq.gz) for sample "1EurasianBeaver.R1.RUN1.L1".

This is my manifest file:

In my file path for Rats/QIMME2/Rats when I run "ls" too see what is in it it shows my manifest file:

Does anyone have any ideas what is going wrong?

[colinvwood (Colin Wood)]

Hello @xicesam,

In your manifest file:

/Rats/QIIME2/Rats/Fastq/1EurasionBeaver.R1.RUN1.L1.fastq.gz

is an absolute file path. But as you can you see from your terminal output it actually lives in:

~/Rats/QIIME2/Rats/...

The ~ means your home directory. You need to insert $HOME before all file paths in the absolute-filepath column:

1EurasionBeaver.R1.RUN1.L1 $HOME/Rats/QIIME2/Rats...`
(...)

Thanks.

[xicesam]

Thank you so much! That worked