Importing Fastq manifest format error

[E.Kamil (E. KAMILARI)]

Hi,
I am trying to import some demultiplexed paired-end fastq data in qiime2-2020.2. I created a file called Donkey on my desktop, where I placed my raw reads and a manifest file called donkey.csv.

I keep getting this error: There was a problem importing /home/qiime2/Desktop/Donkey/donkey.csv:
/home/qiime2/Desktop/Donkey/donkey.csv is not a(n) PairedEndFastqManifestPhred33 file:
File referenced on line 2 could not be found ($HOME/qiime2/Desktop/Donkey/150/150_S150_L001_R1_001.fastq.gz).

Here’s the command:
(qiime2-2020.2) qiime2@qiime2core2020-2:/$ qiime tools import --type SampleData[PairedEndSequencesWithQuality] --input-path /home/qiime2/Desktop/Donkey/donkey.csv --output-path paired-end-demux.qza --input-format PairedEndFastqManifestPhred33

That’s how my donkey.csv file looks like:
sample-id,absolute-filepath,direction
sample-DonkeyB1,$HOME/qiime2/Desktop/Donkey/150/150_S150_L001_R1_001.fastq.gz,forward
sample-DonkeyB1,$HOME/qiime2/Desktop/Donkey/150/150_S150_L001_R2_001.fastq.gz,reverse
sample-DonkeyB2,$HOME/qiime2/Desktop/Donkey/151/151_S151_L001_R1_001.fastq.gz,forward
sample-DonkeyB2,$HOME/qiime2/Desktop/Donkey/151/151_S151_L001_R2_001.fastq.gz,reverse

I would appreciate if you could help me out!

[thermokarst]

Hi @E.Kamil!

@E.Kamil

I would appreciate if you could help me out!

We can do that - first thing, let's take a closer look at the error message you shared:

@E.Kamil

File referenced on line 2 could not be found ($HOME/qiime2/Desktop/Donkey/150/150_S150_L001_R1_001.fastq.gz).

This is QIIME 2 saying that it can't find a file at that location on your computer. Is there a typo in the filename? Or maybe in the path to the file? Please double-check your spelling and path names. One tip, is to cd into the directory with your files to import, and type pwd - this will print the absolute path to the directory - you can double-check that it is the same location as what you have written in your manifest file.