Please help* Invalid file for ‘—input-path’: Path ‘example’ does not exists.

User Support
1

Hello community,

I am fairly new to QIIME2 through the Putty terminal and need a little assistance. I have downloaded paired end fastq files (forward and reverse) and am trying to run it trough QIIME. I have attempted the following code with no success importing the files. They are currently present in my FileZilla server.

mkdir myproject

cd myproject

cd shark

qiime tools import \

--type 'SampleData[PairedEndSequencesWithQuality]' \

--input-path shark \

--output-path paired-end-demux.qza \

--input-format PairedEndFastqManifestPhred33V2

(1/1) Invalid file for ‘—input-path’: Path ‘shark’ does not exists.

I cannot identify any typos that I have conducted, and when checking if the path exists using the ls command – ‘shark’ does come up.

Can you please assist?

2

Hello,

Is it how you are running the command? You do not need to change your working directory to "shark" (cd shark) before importing to Qiime2.

3

Hello @timanix,

I have attempted running the command both ways with no success importing to Qiime2.

when I have used cd shark it comes up with the error message: (1/1) Invalid value for '--input-path': Path 'shark' does not exist.

When I do not use cd shark it comes up with the following error message: There was a problem importing shark: shark is not a file.

4

Hello!
I missed it in the previous post but looks like you are using manifest format:

and at the same time indicate a folder as input:

Please check the importing tutorial to import your data either as manifest format (with a manifest file for raw data locations) or as one directory.

Best,

5

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