Error during importing my Fastq files

Dear Experts

I am running qiime2 by virtual box (Ubuntu) machine. I am trying to import my fastq files, however [Errno 21] Is a directory error was indicated.

This is the my command

qiime tools import
--type 'SampleData[PairedEndSequencesWithQuality]'
--input-path manifest.tsv
--output-path paired-end-demux.qza
--input-format PairedEndFastqManifestPhred33V2

I have also changed input and output path

--type 'SampleData[PairedEndSequencesWithQuality]'
--input-path /home/qiime2/red_seaweed/manifest.tsv
--output-path /home/qiime2/red_seaweed/paired-end-demux.qza
--input-format PairedEndFastqManifestPhred33V2

I am newbie of the qiime2 including bioinformatics, most things are difficult to me.

Please, if you find any mistake here, let me know experts.

Hi there @You_y_Choi!

This error is saying that the object at path /home/qiime2/red_seaweed/demultiplexed_seqs/CON1_S0_L001_R1_001.fastq.gz is a folder, not a file. QIIME 2 is erroring on this because it expects that path to represent a file, not a folder.

How about you run the following and let us know what it says (copy and paste, or screenshot, please!):

ls -lah /home/qiime2/red_seaweed/demultiplexed_seqs/CON1_S0_L001_R1_001.fastq.gz


1 Like

Matthew thanks for the answer.
I attached screenshot which you suggested.

Hi @You_y_Choi!

Thanks for the screenshot - that provides a great starting place for you to update your manifest file!

The full filepath to that sample is:


Keep us posted!

1 Like

Thanks Matthew
Importing was perfectly worked !


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