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
Thanks!
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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:
/home/qiime2/red_seaweed/demultiplexed_seqs/CON1_S0_L001_R1_001.fastq.gz/CON1_S0_L001_R1_001.fastq
Keep us posted!
1 Like
Thanks Matthew
Importing was perfectly worked !
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(system)
Closed
November 15, 2021, 12:29pm
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