manifest error.

Hello,
I made the manifest for my data. unfortunately it gives me an error that I am attaching here:

There was a problem importing /galileo/home/userexternal/jdimarti/manifest_prova_mari.csv:

/galileo/home/userexternal/jdimarti/manifest_prova_mari.csv is not a(n) PairedEndFastqManifestPhred33 file:

Found header on line 1 with the following labels: [’“sample-id’, ‘absolute-filepath’, 'direction”’], expected: [‘sample-id’, ‘absolute-filepath’, ‘direction’]

I read that the error of my manifest are the quotes after the direction, but unfortunately I can not in any way remove this error from my manifest.
What could it be ?
I am attaching my manifest file:
manifest_prova_mari.csv (4.6 KB)

Hi @jessidima,

Take a closer look at your error message:

See those double-quotes? Apparently they enclose each line of your manifest file like so:

“sample-id,absolute-filepath,direction”
“sample-1,/gpfs/work/ELIX4_castrign/gorrasi/bacteria/Fen-Bac-KKT1.R1.fastq.gz,forward”

Just simply remove the " from the beginning and end of each line.

Finally, if this is for paired-end data, you’ll need to slightly change the format. See the Manifest Importing Tutorial.

-Cheers!

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Hello @SoilRotifer
I do not understand. there are no spaces in my manifest file, how do I remove the start and end of each line?

I did not say anything about spaces. As I said, it is the double-quotes, i.e. ", that you need to remove from the beginning and end of each line.

-Mike

Hello @SoilRotifer
I can’t understand, there are no quotes in my manifest file, how do I remove them?
Thanks for your answers.

Hi @jessidima,

What application are you viewing the manifest file in? If you are viewing this file through applications like Microsoft Word or Excel, then these quotes will likely be hidden. I suggest when editing files for bioinformatics tools, that you always do any final editing / sanity-checking with a raw text editor, like BBEdit, Notepad, Sublime, Atom, etc…

Attached is a screen shot of your manifest file when I view it in BBEdit:

See those quotes? That is what QIIME 2 is detecting. Does this make sense?

-Mike

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Certainly. I was viewing my manifest file with microsoft Excel. Thanks for your correction.
-Jessica.

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You’re welcome @jessidima ! :smiley:

-Mike