Error: invalid value file does not exist

Dear all,

I am stuck with a (likely basic) technical issue related to the invalid error value about a file location:
“Error: Invalid value for “–i-demultiplexed-seqs”: File “/home/qiime2/Documents/gz-paired-end-demux.gza” does not exist.”

I have created the demux gza file and a gzv for visualization with no problems:

(qiime2-2019.1) [email protected]:~$ qiime tools import --type ‘SampleData[PairedEndSequencesWithQuality]’ --input-path /home/qiime2/Documents/manifest-gz.csv --output-path /home/qiime2/Documents/gz_paired-end-demux.qza --input-format PairedEndFastqManifestPhred33

Imported /home/qiime2/Documents/manifest_gz.csv as PairedEndFastqManifestPhred33 to /home/qiime2/Documents/gz-paired-end-demux.qza

(qiime2-2019.1) [email protected]:~$ qiime demux summarize --i-data /home/qiime2/Documents/gz-paired-end-demux.qza --o-visualization /home/qiime2/Documents/gz-paired-end-demux.gzv
Saved Visualization to: /home/qiime2/Documents/gz-paired-end-demux.gzv.qzv

When I move into the DADA2 step I get this error:
(qiime2-2019.1) [email protected]:~$ qiime dada2 denoise-paired \

–i-demultiplexed-seqs /home/qiime2/Documents/gz-paired-end-demux.gza
–p-trim-left-f 6
–p-trim-left-r 5
–p-trunc-len-f 100
–p-trunc-len-r 100
–o-table /home/qiime2/Documents/table.gza
–o-representative-sequences /home/qiime2/Documents/rep-seqs.qza
–o-denoising-stats /home/qiime2/Documents/denoising-stats.qza
Usage: qiime dada2 denoise-paired [OPTIONS]
Try “qiime dada2 denoise-paired --help” for help.

Error: Invalid value for “–i-demultiplexed-seqs”: File “/home/qiime2/Documents/gz-paired-end-demux.gza” does not exist.

However, the file exists:
(qiime2-2019.1) [email protected]:~ ls Desktop Downloads Pictures Templates examples.desktop Documents Music Public Videos miniconda (qiime2-2019.1) [email protected]:~ cd Documents
(qiime2-2019.1) [email protected]:~/Documents$ ls
gz gz-paired-end-demux.gzv.qzv gz-paired-end-demux.qza manifest_gz.csv

I am specifying the full route but it seems it does not recognize it. The closest issue related to this that I found in the forum was this one: Error while importing files from tutorial, but it was not solved.

Any suggestion is very welcomed.



Hi @Moriarti,
It looks like this may just be a typo:

Note the file extension you wrote is .gza while the file in your directory is .qza:

I hope that helps!

1 Like

:see_no_evil: Thanks!!