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

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?


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.

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.

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.


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