Trouble importing paired ended data using a manifest

Hello, i need some help, although i have raised a related query before and got a solution from this forum, I am encountering an error when i try to import my paired end reads.

Here is my code

qiime tools import\
 --type 'SampleData[PairedEndSequencesWithQuality]'\
 --input-path FINAL_Oral_manifest3.txt\
 --output-path Oral_demux.qza\
 --source-format PairedEndFastqManifestPhred33

This is the error

There was a problem importing FINAL_Oral_manifest3.csv: FINAL_Oral_manifest3.csv is not a(n) PairedEnd…

I am can send you the manifest if and when needed


Hi @Adrian_Muwonge,
What version of QIIME 2 are you running? Yes, please share your manifest file.

Hello Nicholas, I am using QIIME2

Here is the manifestFINAL_Oral_manifest3.csv (11.9 KB)

Thank you in advance


Hi @Adrian_Muwonge,

The problem seems to be a Byte Order Mark present in your file:

§ hexdump -C Downloads/FINAL_Oral_manifest3.csv  | head
00000000  ef bb bf 73 61 6d 70 6c  65 2d 69 64 2c 61 62 73  |...sample-id,abs|
00000010  6f 6c 75 74 65 2d 66 69  6c 65 70 61 74 68 2c 64  |olute-filepath,d|
00000020  69 72 65 63 74 69 6f 6e  0d 0a 44 43 30 30 32 42  |irection..DC002B|

The three bytes: ef bb bf are tripping up QIIME 2. Unfortunately these bytes are invisible so they are tricky to remove. I've gone ahead and stripped them out for you, let me know if this file works better :slight_smile:

FINAL_Oral_manifest3.csv (11.9 KB)

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Evan,that works many thanks, but how do i avoid this going forward ?


Hi @Adrian_Muwonge,

To be honest I'm not sure, the BOM in this case is just a convention that indicates the bytes following it are UTF-8. This isn't typically used, and usually only happens if software is converting between encodings and "feels like" adding that.

I do know that if you use Excel and export as a UTF-16 text file you will get a similar issue, but it's not actually the same BOM sequence as what you have. So I can't really say how it got in there in the first place. Generally you want to be saving files in the "plainest" text you are able to (UTF-8 is good, and so is ASCII, anything else is likely to have hiccups like this).

Not an awesome answer, but the real solution here is for us to change QIIME 2 to stop worrying about those byte sequences. They don't mean anything and can be ignored, we just need to tell the computer that's what we want to do.

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