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)
Take a closer look at your error message:
See those double-quotes? Apparently they enclose each line of your manifest file like so:
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.
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.
I can’t understand, there are no quotes in my manifest file, how do I remove them?
Thanks for your answers.
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?
Certainly. I was viewing my manifest file with microsoft Excel. Thanks for your correction.
You’re welcome @jessidima !
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