Import Error- 1/2) Invalid value for '--input-path': Path 'paired-end-demux.qza' does not exist. (2/2) Missing option '--output-path'.

[ColeARoman (Cole Alexander Roman)]

Hi all! I am running QIIME 2 (amplicon-2024.2) and I am having errors trying to read in my fastq files from my manifest file. I am running into my error when I am trying to import my data. QIIME 2 is installed via miniconda.

I am getting a " 1/2) Invalid value for '--input-path': Path 'paired-end-demux.qza' does not exist. **(2/2) Missing option '--output-path'.*" when I try to import my data as a tab delimited text file (.txt).

Here is the specific command I am running with the correct file directory:

qiime tools import --type 'SampleData[PairedEndSequencesWithQuality]' --input-path </Users/metagenomics/Desktop/Cole1/Cole1Manifest.txt> --output-path paired-end-demux.qza --input-format PairedEndFastqManifestPhred33V2

Screenshot of my manifest file in .txt format:
Cole1Manifest copy.txt (34.2 KB)

Screenshot of my error in terminal (bottom portion).

Thanks!

[jphagen (Johannah Hagen)]

Hi @ColeARoman,

Welcome to the forum!

The error is telling you that it cannot read the file path as it is written. I think what is tripping it up is the "< >" around the file path. Also there should be a space after the file path and --output-path...
But looking at the screenshot it looks like you were figuring those things out on your own

On this attempt:

the file paths work but it appears that your manifest is not ASCII or UTF8 encoded.
By searching the forum for this issue I found many posts about this error.
This post has some helpful info on how to fix this issue, I believe you may need to re-encode your manifest file.
Once you do that, try again. I recommend using absolute file paths for the input and output paths if possible. If this doesn't work post the error here and we can work through it!

--Hannah

[ColeARoman (Cole Alexander Roman)]

Hi, thank you for your guidance. I had a few errors in my manifest file. However, I had a very interesting additional issue. Whenever I was downloading my manifest file in the proper format I was getting the ASCII or UTF8 encoding error. I used ChatGPT to generate a python script (python united.py) to eventually download my manifest file in a different format.

When I opened the manifest file in this alternative format, there were random characters (e, -, +. etc.) inserted at the end of some of my.fastq files that were not visible to me before in the .txt file. I could finally import my manifest file after removing these seemingly random characters at the end of my files only after transforming my file into an alternative format.

Thanks, and all the best!

[jphagen (Johannah Hagen)]

@ColeARoman,
Im glad you were able to get things working and see what was causing the issue!
and thank you so much for sharing what worked for you. This will surely be helpful for users with similar issues in the future! Happy qiime-ing
--Hannah